Index: /branches/ccl_branches/ipponly-20191108/magic/Makefile =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/Makefile (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/Makefile (revision 41117) @@ -0,0 +1,91 @@ + +MAGIC_DIR = ~/magic_tarballs + +# necessary support for libQt (only used by magic) +QTDIR = qt-everywhere-opensource-src-4.6.1 +QTSRC = $(MAGIC_DIR)/qt-everywhere-opensource-src-4.6.1.tar.gz +QTDEP := $(shell test -f $(QTSRC) && echo $(QTSRC)) + +PSCFG = ../psconfig/psconfig.csh +PSPREFIX := $(shell csh $(PSCFG) $(PSVERSION) --prefix) + +default: all + +all: ssa-core-cpp magic verify + +install: magic.install verify.install + +clean: + if [ -d magic ]; then (cd magic && make -f Makefile.magic clean); fi + # if [ -d ssa-core-cpp ]; then (cd ssa-core-cpp && make clean); fi + +update: +# get the source code (replace this with SVN interactions) + tar xvzf $(MAGIC_DIR)/magic.tgz + tar xvzf $(MAGIC_DIR)/ssa-core-cpp.tgz + cp Makefile.magic magic/Makefile.magic + cp magic/VerifyStreaks/main.cpp verify/VerifyStreaks.cpp + +# tar xvzf $(QTSRC) + +qt-everywhere: $(QTDIR)/lib/libQtCore.so + +QTOPT = -fast \ + -opensource \ + -nomake tools \ + -nomake examples \ + -nomake demos \ + -nomake docs \ + -nomake translations \ + -no-xmlpatterns \ + -no-multimedia \ + -no-audio-backend \ + -no-phonon \ + -no-phonon-backend \ + -no-svg \ + -no-webkit \ + -no-javascript-jit \ + -no-script \ + -no-scripttools + +# the target (QTDEP) is blank unless QTSRC exists +$(QTDIR)/lib/libQtCore.so: $(QTDEP) + echo $(PSCFG) + echo $(PSPREFIX) + if [ -d $(QTDIR) ]; then (cd $(QTDIR) && echo "yes" | ./configure $(QTOPT) -prefix $(PSPREFIX)); fi + if [ -d $(QTDIR) ]; then (cd $(QTDIR) && make); fi + if [ -d $(QTDIR) ]; then (cd $(QTDIR) && make install); fi + +ssa-core-cpp: ssa-core-cpp/build/libSSA.a + +ssa-core-cpp/build/libSSA.a: + if [ -d ssa-core-cpp ]; then (cd ssa-core-cpp && ./configure --disable-doxygen && make); fi + +magic: magic/DetectStreaks + +magic/DetectStreaks: + if [ -d magic ]; then (cd magic && make -f Makefile.magic); fi + +magic.install: ssa-core-cpp + if [ -d magic ]; then (cd magic && make -f Makefile.magic install); fi + +update.verify: + cp magic/VerifyStreaks/main.cpp verify/VerifyStreaks.cpp + +verify: verify/VerifyStreaks + +verify/VerifyStreaks: + if [ -d magic ]; then (cd verify && make); fi + +verify.install: + if [ -d magic ]; then (cd verify && make install); fi + +# REMOVE = remove/src +# +# remove: FORCE +# @cd $(REMOVE) && make -f Makefile.simple all +# +# remove.install: remove +# @cd $(REMOVE) && make -f Makefile.simple install + +FORCE: Index: /branches/ccl_branches/ipponly-20191108/magic/Makefile.magic =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/Makefile.magic (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/Makefile.magic (revision 41117) @@ -0,0 +1,38 @@ +TARGETS = DetectStreaks + +CXX = c++ +CXXFLAGS = -W -Wall -O3 -DNDEBUG +# CXXFLAGS = -W -Wall -g + +SSA_SRC_DIR = ../ssa-core-cpp/src +INCLUDEDIRS = -I. -I$(SSA_SRC_DIR) +OTHER_SRCS = $(SSA_SRC_DIR)/math/Constants.cpp + +# CFITSIO_DIR = ../cfitsio +CFITSIO_DIR = $(PSCONFDIR)/$(PSCONFIG) + +CFITSIO_INC = -I$(CFITSIO_DIR) +CFITSIO_LIB = -L$(CFITSIO_DIR) -lcfitsio + +all : $(TARGETS) + +RemoveStreaks : $(OTHER_SRCS) + +DetectStats : $(OTHER_SRCS) + +% :: %.cpp + $(CXX) $(CXXFLAGS) $(INCLUDEDIRS) $(CFITSIO_INC) $< $(OTHER_SRCS) $(CFITSIO_LIB) -o $@ + +.PHONY : clean + +.SILENT : clean + +clean : + - rm $(TARGETS) + +DESTDIR=$(PSCONFDIR)/$(PSCONFIG) + +install: $(TARGETS) + cp DetectStreaks $(DESTDIR)/bin + chmod 755 $(DESTDIR)/bin/DetectStreaks + Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/Doxyfile.in =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/Doxyfile.in (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/Doxyfile.in (revision 41117) @@ -0,0 +1,1310 @@ +# Doxyfile 1.5.4 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file that +# follow. The default is UTF-8 which is also the encoding used for all text before +# the first occurrence of this tag. Doxygen uses libiconv (or the iconv built into +# libc) for the transcoding. See http://www.gnu.org/software/libiconv for the list of +# possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = censor + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = ipp-2.7.dev + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./docs + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Finnish, French, German, Greek, Hungarian, +# Italian, Japanese, Japanese-en (Japanese with English messages), Korean, +# Korean-en, Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian, +# Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = NO + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the DETAILS_AT_TOP tag is set to YES then Doxygen +# will output the detailed description near the top, like JavaDoc. +# If set to NO, the detailed description appears after the member +# documentation. + +DETAILS_AT_TOP = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for Java. +# For instance, namespaces will be presented as packages, qualified scopes +# will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to +# include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct (or union) is +# documented as struct with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code where the coding convention is that all structs are +# typedef'ed and only the typedef is referenced never the struct's name. + +TYPEDEF_HIDES_STRUCT = NO + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be extracted +# and appear in the documentation as a namespace called 'anonymous_namespace{file}', +# where file will be replaced with the base name of the file that contains the anonymous +# namespace. By default anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from the +# version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text " + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = ./src + +# This tag can be used to specify the character encoding of the source files that +# doxygen parses. Internally doxygen uses the UTF-8 encoding, which is also the default +# input encoding. Doxygen uses libiconv (or the iconv built into libc) for the transcoding. +# See http://www.gnu.org/software/libiconv for the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = *.h + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the output. +# The symbol name can be a fully qualified name, a word, or if the wildcard * is used, +# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. If you have enabled CALL_GRAPH or CALLER_GRAPH +# then you must also enable this option. If you don't then doxygen will produce +# a warning and turn it on anyway + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES (the default) +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES (the default) +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. Otherwise they will link to the documentstion. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = NO + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be +# generated containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, +# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are +# probably better off using the HTML help feature. + +GENERATE_TREEVIEW = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4wide + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = NO + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = NO + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = YES + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. This is useful +# if you want to understand what is going on. On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to +# produce the chart and insert it in the documentation. The MSCGEN_PATH tag allows you to +# specify the directory where the mscgen tool resides. If left empty the tool is assumed to +# be found in the default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = NO + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH, SOURCE_BROWSER and HAVE_DOT tags are set to YES then doxygen will +# generate a call dependency graph for every global function or class method. +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable call graphs for selected +# functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH, SOURCE_BROWSER and HAVE_DOT tags are set to YES then doxygen will +# generate a caller dependency graph for every global function or class method. +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable caller graphs for selected +# functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + +DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The MAX_DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the number +# of direct children of the root node in a graph is already larger than +# MAX_DOT_GRAPH_NOTES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, which results in a white background. +# Warning: Depending on the platform used, enabling this option may lead to +# badly anti-aliased labels on the edges of a graph (i.e. they become hard to +# read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to the search engine +#--------------------------------------------------------------------------- + +# The SEARCHENGINE tag specifies whether or not a search engine should be +# used. If set to NO the values of all tags below this one will be ignored. + +SEARCHENGINE = NO Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/Makefile.am =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/Makefile.am (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/Makefile.am (revision 41117) @@ -0,0 +1,4 @@ +SUBDIRS = src + +CLEANFILES = *.pyc *~ core core.* + Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/autogen.sh =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/autogen.sh (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/autogen.sh (revision 41117) @@ -0,0 +1,103 @@ +#!/bin/sh +# Run this to generate all the initial makefiles, etc. + +srcdir=`dirname $0` +test -z "$srcdir" && srcdir=. + +ORIGDIR=`pwd` +cd $srcdir + +PROJECT=censor +TEST_TYPE=-f +# change this to be a unique filename in the top level dir +FILE=autogen.sh + +DIE=0 + +LIBTOOLIZE=libtoolize +ACLOCAL="aclocal $ACLOCAL_FLAGS" +AUTOHEADER=autoheader +AUTOMAKE=automake +AUTOCONF=autoconf + +($LIBTOOLIZE --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $LIBTOOLIZE installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/libtool/" + DIE=1 +} + +($ACLOCAL --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $ACLOCAL installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/" + DIE=1 +} + +($AUTOHEADER --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOHEADER installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/" + DIE=1 +} + +($AUTOMAKE --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOMAKE installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/" + DIE=1 +} + +($AUTOCONF --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOCONF installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/" + DIE=1 +} + +if test "$DIE" -eq 1; then + exit 1 +fi + +test $TEST_TYPE $FILE || { + echo "You must run this script in the top-level $PROJECT directory" + exit 1 +} + +if test -z "$*"; then + echo "I am going to run ./configure with no arguments - if you wish " + echo "to pass any to it, please specify them on the $0 command line." +fi + +$LIBTOOLIZE --copy --force || echo "$LIBTOOLIZE failed" +$ACLOCAL || echo "$ACLOCAL failed" +$AUTOHEADER || echo "$AUTOHEADER failed" +$AUTOMAKE --add-missing --force-missing --copy || echo "$AUTOMAKE failed" +$AUTOCONF || echo "$AUTOCONF failed" + +cd $ORIGDIR + +run_configure=true +for arg in $*; do + case $arg in + --no-configure) + run_configure=false + ;; + *) + ;; + esac +done + +if $run_configure; then + $srcdir/configure --enable-maintainer-mode "$@" + echo + echo "Now type 'make' to compile $PROJECT." +else + echo + echo "Now run 'configure' and 'make' to compile $PROJECT." +fi Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/censorObjects.pc.in =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/censorObjects.pc.in (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/censorObjects.pc.in (revision 41117) @@ -0,0 +1,12 @@ +prefix=@prefix@ +exec_prefix=@exec_prefix@ +libdir=@libdir@ +includedir=@includedir@ + +Name: libcensor +Description: Pan-STARRS Photometry Library +Version: @VERSION@ +Requires: pslib psmodules +Libs: -L${libdir} -lcensor +Libs.private: @CENSOR_LIBS@ +Cflags: -I${includedir} @CENSOR_CFLAGS@ Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/configure.ac =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/configure.ac (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/configure.ac (revision 41117) @@ -0,0 +1,49 @@ +dnl Process this file with autoconf to produce a configure script. +AC_PREREQ(2.61) + +AC_INIT([censorObjects], [0.9.0], [ipp-support@ifa.hawaii.edu]) +AC_CONFIG_SRCDIR([src]) + +AM_INIT_AUTOMAKE([1.6 foreign dist-bzip2]) +AM_CONFIG_HEADER([src/config.h]) +AM_MAINTAINER_MODE + +IPP_STDLDFLAGS + +AC_LANG(C) +AC_GNU_SOURCE +AC_PROG_CC_C99 +AC_PROG_INSTALL +AC_PROG_LIBTOOL +AC_SYS_LARGEFILE + +dnl ------------------------------------------------------------ + +AC_PATH_PROG([ERRORCODES], [psParseErrorCodes], [missing]) +if test "$ERRORCODES" = "missing" ; then + AC_MSG_ERROR([psParseErrorCodes is required]) +fi + +dnl ------------- psLib, psModules --------------- +PKG_CHECK_MODULES([PSLIB], [pslib >= 1.0.0]) +PKG_CHECK_MODULES([PSMODULE], [psmodules >= 1.0.0]) + +dnl Set CFLAGS for build +IPP_STDOPTS +IPP_STDCFLAGS + +echo "CENSOR_CFLAGS: $CENSOR_CFLAGS" +echo "CENSOR_LIBS: $CENSOR_LIBS" + +IPP_VERSION + +AC_SUBST([CENSOR_CFLAGS]) +AC_SUBST([CENSOR_LIBS]) + +AC_CONFIG_FILES([ + Makefile + src/Makefile + Doxyfile +]) + +AC_OUTPUT Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/Makefile.am =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/Makefile.am (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/Makefile.am (revision 41117) @@ -0,0 +1,43 @@ + +# Force recompilation of censorVersion.c, since it gets the version information +censorVersion.c: censorVersionDefinitions.h +censorVersionDefinitions.h: censorVersionDefinitions.h.in FORCE + pslib-setsvnversion.pl CENSOR censorVersionDefinitions.h.in censorVersionDefinitions.h +FORCE: ; + +bin_PROGRAMS = censorObjects + +censorObjects_CFLAGS = $(CENSOR_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) +censorObjects_LDFLAGS = $(CENSOR_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS) + +censorObjects_SOURCES = \ + censor.c \ + censorArguments.c \ + censorParseCamera.c \ + censorLoop.c \ + censorReadout.c \ + censorErrorCodes.c \ + censorVersion.c \ + censorCleanup.c + +include_HEADERS = \ + censor.h \ + censorErrorCodes.h + +clean-local: + -rm -f TAGS + +# Tags for emacs +tags: + etags `find . -name \*.[ch] -print` + +### Error codes. +BUILT_SOURCES = censorErrorCodes.h censorErrorCodes.c censorVersionDefinitions.h +CLEANFILES = censorErrorCodes.h censorErrorCodes.c +EXTRA_DIST = censorErrorCodes.dat censorErrorCodes.h.in censorErrorCodes.c.in + +censorErrorCodes.h : censorErrorCodes.dat censorErrorCodes.h.in + $(ERRORCODES) --data=censorErrorCodes.dat --outdir=. censorErrorCodes.h + +censorErrorCodes.c : censorErrorCodes.dat censorErrorCodes.c.in censorErrorCodes.h + $(ERRORCODES) --data=censorErrorCodes.dat --outdir=. censorErrorCodes.c Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censor.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censor.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censor.c (revision 41117) @@ -0,0 +1,73 @@ +/** @file censor.c + * + * @brief + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.28 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-07 02:03:34 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# include "censor.h" + +static void usage(void) { + fprintf(stderr, "USAGE: censorObjects -file (sources) -masklist (masklist) (output)\n"); + fprintf(stderr, " censorObjects -file (sources) -mask (mask.fits) (output)\n"); + fprintf(stderr, " censorObjects -list (sourceslist) -masklist (masklist) (output)\n"); + fprintf(stderr, " censorObjects -list (sourceslist) -mask (mask.fits) (output)\n"); + exit(PS_EXIT_CONFIG_ERROR); +} + +int main (int argc, char **argv) +{ + psTimerStart ("complete"); + + censorErrorRegister(); // register our error codes/messages + + // model inits are needed in pmSourceIO + // models defined in psphot/src/models are not available in censor + pmModelClassInit(); + + // load configuration information + pmConfig *config = censorArguments(argc, argv); + if (!config) { + usage(); + } + + censorVersionPrint(); + + // load identify the data sources + if (!censorParseCamera (config)) { + psErrorStackPrint(stderr, "error setting up the camera\n"); + psFree(config); + exit(PS_EXIT_CONFIG_ERROR); + } + + bool status; + bool checkInputOnly = psMetadataLookupBool(&status, config->arguments, + "CHECK.INPUT.ONLY"); + + if (!checkInputOnly) { + // load the raw detection data (using PSPHOT.SOURCES filerule) + // select subset of stars for astrometry + if (!censorLoop (config)) { + psErrorStackPrint(stderr, "error loading input data\n"); + psFree(config); + exit(PS_EXIT_DATA_ERROR); + } + + psLogMsg("censor", 3, "complete censor run: %f sec\n", psTimerMark ("complete")); + } else { + if (!checkInputLoop (config)) { + psErrorStackPrint(stderr, "error loading input data\n"); + psFree(config); + exit(PS_EXIT_DATA_ERROR); + } + psLogMsg("censor", 3, "complete check input run: %f sec\n", psTimerMark ("complete")); + } + + censorCleanup(config); + exit(PS_EXIT_SUCCESS); +} Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censor.h =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censor.h (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censor.h (revision 41117) @@ -0,0 +1,47 @@ +/** @file censor.h + * + * @brief censorObjects rejects objects from smf files that land on magic masks + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.49 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-09 21:25:34 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# ifndef CENSOR_H +# define CENSOR_H + +# include +# include +# include // for strcasecmp +# include // for unlink +# include +# include +# include +# include "censorErrorCodes.h" + +/// @addtogroup censor +/// @{ + +# define CENSOR_RECIPE "CENSOR" ///< Name of the recipe to use + +pmConfig *censorArguments (int argc, char **argv); +bool censorParseCamera (pmConfig *config); +bool censorLoop (pmConfig *config); +bool checkInputLoop (pmConfig *config); +bool censorReadout (pmReadout *readout, pmConfig *config, const pmFPAview *view, bool badMaskFile); +void censorCleanup (pmConfig *config); +bool censorBadFileByView (bool badFile, pmFPAfile *file, pmConfig *config, pmFPAview *view); + +// Return version strings. +psString censorVersion(void); +psString censorSource(void); +psString censorVersionLong(void); +bool censorVersionHeader(psMetadata *header); +bool censorVersionHeaderFull(psMetadata *header); +void censorVersionPrint(void); + +///@} +# endif /* CENSOR_H */ Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorArguments.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorArguments.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorArguments.c (revision 41117) @@ -0,0 +1,69 @@ +/** @file censorArguments.c + * + * @brief + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.34.2.1 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-19 17:59:50 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# include "censor.h" + +pmConfig *censorArguments (int argc, char **argv) { + + bool status; + int N; + + if (argc == 1) { + psError(CENSOR_ERR_ARGUMENTS, true, "No arguments supplied"); + psErrorStackPrint(stderr, "exit"); + return NULL; + } + + // load config data from default locations + pmConfig *config = pmConfigRead(&argc, argv, CENSOR_RECIPE); + if (config == NULL) { + psError(CENSOR_ERR_CONFIG, false, "Can't read site configuration"); + psErrorStackPrint(stderr, "exit"); + return NULL; + } + + status = pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list"); + if (!status) { + psError(CENSOR_ERR_ARGUMENTS, true, "Missing -file (input) or -list (input)"); + psErrorStackPrint(stderr, "exit"); + return NULL; + } + + if ((N = psArgumentGet (argc, argv, "-checkinputonly"))) { + psArgumentRemove (N, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "CHECK.INPUT.ONLY", PS_META_REPLACE, "do not censor just check input sources", true); + return config; + } + + // define the input mask + status = pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT.MASK", "-mask", "-masklist"); + + // dump the configuration to a file? + if ((N = psArgumentGet (argc, argv, "-dumpconfig"))) { + psArgumentRemove (N, &argc, argv); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "DUMP_CONFIG", PS_META_REPLACE, "", argv[N]); + psArgumentRemove (N, &argc, argv); + } + + + if (argc != 2) { + psError(CENSOR_ERR_ARGUMENTS, true, "Incorrect arguments supplied"); + psErrorStackPrint(stderr, "exit"); + return NULL; + } + + // output positions is fixed + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "", argv[1]); + + psTrace("censor", 1, "Done with censorArguments...\n"); + return (config); +} Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorCleanup.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorCleanup.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorCleanup.c (revision 41117) @@ -0,0 +1,30 @@ +/** @file censorCleanup.c + * + * @brief + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.8.2.1 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-19 17:59:50 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# include "censor.h" + +void censorCleanup (pmConfig *config) { + + psFree (config); + pmVisualClose (); + + psTimerStop (); + psMemCheckCorruption (stderr, true); + pmModelClassCleanup (); + psTimeFinalize (); + pmConceptsDone (); + pmConfigDone (); + fprintf (stderr, "found %d leaks at %s\n", psMemCheckLeaks (0, NULL, stdout, false), "censor"); + // fprintf (stderr, "found %d leaks at %s\n", psMemCheckLeaks (0, NULL, NULL, false), "censor"); + + return; +} Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.c.in =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.c.in (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.c.in (revision 41117) @@ -0,0 +1,37 @@ +/** @file censorErrorCodes.c + * + * @brief + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-07 02:03:34 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +#include "pslib.h" +#include "censorErrorCodes.h" + +/* + * The line + { CENSOR_ERR_$X{ErrorCode}, "$X{ErrorDescription}"}, + * (without the Xs) + * will be replaced by values from errorCodes.dat + */ +void censorErrorRegister(void) +{ + static psErrorDescription errors[] = { + { CENSOR_ERR_BASE, "First value we use; lower values belong to psLib" }, + { CENSOR_ERR_${ErrorCode}, "${ErrorDescription}"}, + }; + static int nerror = CENSOR_ERR_NERROR - CENSOR_ERR_BASE; // number of values in enum + + for (int i = 0; i < nerror; i++) { + psErrorDescription *tmp = psAlloc(sizeof(psErrorDescription)); + *tmp = errors[i]; + psErrorRegister(tmp, 1); + psFree(tmp); /* it's on the internal list */ + } + nerror = 0; // don't register more than once +} Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.dat =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.dat (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.dat (revision 41117) @@ -0,0 +1,12 @@ +# +# This file is used to generate pmErrorClasses.h +# +BASE = 16000 First value we use +UNKNOWN Unknown censorObject error code +NOT_IMPLEMENTED Desired feature is not yet implemented +ARGUMENTS Incorrect arguments +CONFIG Problem in configure files +IO Problem in FITS I/O +WCS Error interpreting FITS WCS information +DATA Problem in data values +REFSTARS Problem in data values Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.h.in =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.h.in (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorErrorCodes.h.in (revision 41117) @@ -0,0 +1,30 @@ +/** @file censorErrorCodes.h + * + * @brief + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.3 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-07 02:03:34 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +#if !defined(CENSOR_ERROR_CODES_H) +#define CENSOR_ERROR_CODES_H +/* + * The line + * CENSOR_ERR_$X{ErrorCode}, + * (without the X) + * + * will be replaced by values from errorCodes.dat + */ +typedef enum { + CENSOR_ERR_BASE = 16000, + CENSOR_ERR_${ErrorCode}, + CENSOR_ERR_NERROR +} censorErrorCode; + +void censorErrorRegister(void); + +#endif Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorLoop.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorLoop.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorLoop.c (revision 41117) @@ -0,0 +1,251 @@ +/** @file censorLoop.c + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.12 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-07 02:03:34 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# include "censor.h" + +# define ESCAPE { \ + psError(PS_ERR_UNKNOWN, false, "Failure in censorLoop"); \ + psFree (view); \ + return false; \ +} + +/** + * \brief this loop loads the data from the input smf file(s) and mask(s). call censorReadout + * to perform the actual rejection. + */ +bool censorLoop (pmConfig *config) { + pmChip *chip; + pmCell *cell; + pmReadout *readout; + + psTimerStart ("censor"); + + + // select the current recipe + psMetadata *recipe = psMetadataLookupPtr (NULL, config->recipes, CENSOR_RECIPE); + if (!recipe) { + psError(CENSOR_ERR_CONFIG, true, "Can't find CENSOR recipe!\n"); + return false; + } + + // select the input data sources + pmFPAfile *input = psMetadataLookupPtr (NULL, config->files, "CENSOR.INPUT"); + if (!input) { + psError(CENSOR_ERR_CONFIG, true, "Can't find input data!\n"); + return false; + } + + // select the input data sources + pmFPAfile *inMask = psMetadataLookupPtr (NULL, config->files, "CENSOR.INPUT.MASK"); + if (!inMask) { + psError(CENSOR_ERR_CONFIG, true, "Can't find input masks!\n"); + return false; + } + + pmFPAview *view = pmFPAviewAlloc (0); + + bool badMaskFile = false; + + // check on the mask file at this level if possible + badMaskFile = censorBadFileByView(badMaskFile, inMask, config, view); + + bool checkInputOnly = psMetadataLookupBool(NULL, config->arguments, "CHECK.INPUT.ONLY"); + + // files associated with the science image + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + + // check PHU header to see if we are using mosaic-level or per-chip astrometry + bool bilevelAstrometry = false; + pmHDU *phu = pmFPAviewThisPHU (view, input->fpa); + if (phu) { + char *ctype = psMetadataLookupStr (NULL, phu->header, "CTYPE1"); + if (ctype) bilevelAstrometry = !strcmp (&ctype[4], "-DIS"); + } + if (bilevelAstrometry) { + pmAstromReadBilevelMosaic (input->fpa, phu->header); + } + + while ((chip = pmFPAviewNextChip (view, input->fpa, 1)) != NULL) { + psTrace ("censor", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); + if (!chip->process || !chip->file_exists) { continue; } + + // check on the mask file at this level if possible + badMaskFile = censorBadFileByView(badMaskFile, inMask, config, view); + + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + + // read WCS data from the corresponding header + + pmHDU *hdu = pmFPAviewThisHDU (view, input->fpa); + + if (bilevelAstrometry) { + if (!pmAstromReadBilevelChip (chip, hdu->header)) { + psWarning("Could not get WCS information from header for chip %d, skipping", view->chip); + continue; + } + } else { + if (!pmAstromReadWCS(input->fpa, chip, hdu->header, 1.0)) { + psWarning( "Unable to read WCS astrometry from chip %d, skipping", view->chip); + continue; + } + } + + while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { + psTrace ("censor", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (!cell->process || !cell->file_exists) { continue; } + + // check on the mask file at this level if possible + badMaskFile = censorBadFileByView(badMaskFile, inMask, config, view); + + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + + // process each of the readouts + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + + // check on the mask file at this level if possible + badMaskFile = censorBadFileByView(badMaskFile, inMask, config, view); + + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + if (!readout->data_exists) { continue; } + + if (!checkInputOnly) { + if (!censorReadout (readout, config, view, badMaskFile)) ESCAPE; + } + + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + } + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + } + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + } + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + + psLogMsg ("censor", 3, "censorLoop done : %f sec\n", psTimerMark ("censor")); + + psFree (view); + return true; +} + +bool censorBadFileByView (bool badFile, pmFPAfile *file, pmConfig *config, pmFPAview *view) { + + // get the current level + pmFPALevel level = pmFPAviewLevel (view); + + // can we try to open this file? (if not, leave the existing badView intact) + if (level != file->fileLevel) return badFile; + + // free, and if needed, realloc badView below + badFile = false; + + char *filename = pmFPAfileName(file, view, config); + if (filename) { + // activate the file + pmFPAfileActivate (config->files, true, file->name); + psFree (filename); + return false; + } + + // de-activate the file + pmFPAfileActivate (config->files, false, file->name); + return true; +} + +/** + * \brief this loop loads the data from the input smf file(s) and mask(s). call censorReadout + * to perform the actual rejection. + */ +bool checkInputLoop (pmConfig *config) { + pmChip *chip; + pmCell *cell; + pmReadout *readout; + + psTimerStart ("checksources"); + + // select the input data sources + pmFPAfile *input = psMetadataLookupPtr (NULL, config->files, "CENSOR.INPUT"); + if (!input) { + psError(CENSOR_ERR_CONFIG, true, "Can't find input data!\n"); + return false; + } + + pmFPAview *view = pmFPAviewAlloc (0); + + // files associated with the science image + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + + // check PHU header to see if we are using mosaic-level or per-chip astrometry + bool bilevelAstrometry = false; + pmHDU *phu = pmFPAviewThisPHU (view, input->fpa); + if (phu) { + char *ctype = psMetadataLookupStr (NULL, phu->header, "CTYPE1"); + if (ctype) bilevelAstrometry = !strcmp (&ctype[4], "-DIS"); + } + if (bilevelAstrometry) { + pmAstromReadBilevelMosaic (input->fpa, phu->header); + } + + while ((chip = pmFPAviewNextChip (view, input->fpa, 1)) != NULL) { + psTrace ("checksources", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); + if (!chip->process || !chip->file_exists) { continue; } + + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + + // read WCS data from the corresponding header + + pmHDU *hdu = pmFPAviewThisHDU (view, input->fpa); + + if (bilevelAstrometry) { + if (!pmAstromReadBilevelChip (chip, hdu->header)) { + psWarning("Could not get WCS information from header for chip %d, skipping", view->chip); + continue; + } + } else { + if (!pmAstromReadWCS(input->fpa, chip, hdu->header, 1.0)) { + psWarning( "Unable to read WCS astrometry from chip %d, skipping", view->chip); + continue; + } + } + + while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { + psTrace ("checksources", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (!cell->process || !cell->file_exists) { continue; } + + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + + // process each of the readouts + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + + if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE; + if (!readout->data_exists) { continue; } + + // select the raw objects for this readout, flag is they fall in a mask + pmDetections *detections = psMetadataLookupPtr (NULL, readout->analysis, "PSPHOT.DETECTIONS"); + if (detections == NULL) { + psError(CENSOR_ERR_CONFIG, true, "Can't find detections for this readout"); + return false; + } + if (!detections->allSources) { + psError(CENSOR_ERR_CONFIG, true, "Can't find sources for this readout"); + return false; + } + + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + } + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + } + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + } + if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE; + + psLogMsg ("checksources", 3, "checkInputLoop done : %f sec\n", psTimerMark ("checksources")); + + psFree (view); + return true; +} Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorParseCamera.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorParseCamera.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorParseCamera.c (revision 41117) @@ -0,0 +1,57 @@ +/** @file censorParseCamera.c + * + * @brief + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.18 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-07 02:03:34 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# include "censor.h" + +bool censorParseCamera (pmConfig *config) { + + bool status = false; + + // the input image(s) are required arguments; they define the camera + pmFPAfile *input = pmFPAfileDefineFromArgs (&status, config, "CENSOR.INPUT", "INPUT"); + if (!status) { + psError(CENSOR_ERR_CONFIG, false, "Failed to build FPA from CENSOR.INPUT"); + return false; + } + + bool checkInputOnly = psMetadataLookupBool(&status, config->arguments, "CHECK.INPUT.ONLY"); + if (checkInputOnly) { + // nothing else to do + return true; + } + + + pmFPAfile *output = pmFPAfileDefineOutput (config, input->fpa, "CENSOR.OUTPUT"); + if (!output) { + psError(CENSOR_ERR_CONFIG, false, "Failed to build output FPA from CENSOR.INPUT"); + return false; + } + output->save = true; + + // look for the file on the argument list + pmFPAfile *inMask = pmFPAfileDefineFromArgs (&status, config, "CENSOR.INPUT.MASK", "INPUT.MASK"); + if (!status) { + psError (PS_ERR_UNKNOWN, false, "failed to load input mask definition"); + return false; + } + if (!inMask) { + psError (PS_ERR_UNKNOWN, false, "failed to load input mask"); + return false; + } + if (inMask->type != PM_FPA_FILE_MASK) { + psError(PS_ERR_IO, true, "CENSOR.INPUT.MASK is not of type MASK"); + return false; + } + + psTrace("censor", 1, "Done with censorParseCamera...\n"); + return true; +} Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorReadout.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorReadout.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorReadout.c (revision 41117) @@ -0,0 +1,92 @@ +/** @file censorReadout.c + * + * @brief reject detections that land within the streak mask regions + * + * @ingroup censor + * + * @author IfA + * @version $Revision: 1.7 $ $Name: not supported by cvs2svn $ + * @date $Date: 2009-02-07 02:03:34 $ + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +# include "censor.h" + +bool censorReadout (pmReadout *readout, pmConfig *config, const pmFPAview *view, bool badMaskFile) { + + bool status; + + // if there is no mask file for this readout drop all sources + if (badMaskFile) { + psMetadataRemoveKey (readout->analysis, "PSPHOT.DETECTIONS"); + return true; + } + + // select the current recipe + psMetadata *recipe = psMetadataLookupPtr (&status, config->recipes, CENSOR_RECIPE); + if (!recipe) { + psError(CENSOR_ERR_CONFIG, true, "Can't find CENSOR recipe"); + return false; + } + + psImageMaskType streakMaskValue = pmConfigMaskGet("STREAK", config); // Mask value for streak pixels + + psLogMsg ("censor", PS_LOG_INFO, "generating a bright-star mask"); + + // select the reference mask fpa :: we use this to determine cell boundaries + pmFPAfile *inMask = psMetadataLookupPtr (NULL, config->files, "CENSOR.INPUT.MASK"); + if (!inMask) { + psError(CENSOR_ERR_CONFIG, true, "Can't find mask files"); + return false; + } + + // XXX why not do this? + pmReadout *readoutMask = pmFPAviewThisReadout (view, inMask->fpa); + if (!readoutMask) { + psError(CENSOR_ERR_CONFIG, true, "Can't find mask for this readout"); + return false; + } + + // select the raw objects for this readout, flag is they fall in a mask + pmDetections *detections = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.DETECTIONS"); + if (detections == NULL) { + psError(CENSOR_ERR_CONFIG, true, "Can't find detections for this readout"); + return false; + } + psArray *inSources = detections->allSources; + psAssert (inSources, "missing sources?"); + + // create a replacement output array: + psArray *outSources = psArrayAllocEmpty(100); + + // only keep sources that do not match the specified mask bit + for (int i = 0; i < inSources->n; i++) { + pmSource *source = inSources->data[i]; + + int xChip = source->peak->x; + int yChip = source->peak->y; + + bool onChip = true; + onChip &= (xChip >= 0); + onChip &= (xChip < readoutMask->mask->numCols); + onChip &= (yChip >= 0); + onChip &= (yChip < readoutMask->mask->numRows); + + if (onChip) { + psImageMaskType value = readoutMask->mask->data.PS_TYPE_IMAGE_MASK_DATA[yChip][xChip]; + if (value & streakMaskValue) { + // skip sources on streak masks + continue; + } + } + psArrayAdd (outSources, 100, source); + } + + psLogMsg ("censor", PS_LOG_INFO, "keeping %ld of %ld sources", outSources->n, inSources->n); + + psFree (detections->allSources); + detections->allSources = outSources; + + return true; +} + Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorVersion.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorVersion.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorVersion.c (revision 41117) @@ -0,0 +1,115 @@ +/** @file censorVersion.c + * + * @brief + * + * @ingroup censor + * + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +#include "censor.h" +#include "censorVersionDefinitions.h" + +#ifndef CENSOR_VERSION +#error "CENSOR_VERSION is not set" +#endif +#ifndef CENSOR_BRANCH +#error "CENSOR_BRANCH is not set" +#endif +#ifndef CENSOR_SOURCE +#error "CENSOR_SOURCE is not set" +#endif + +psString censorVersion(void) +{ + char *value = NULL; + psStringAppend(&value, "%s@%s", CENSOR_BRANCH, CENSOR_VERSION); + return value; +} + +psString censorSource(void) +{ + return psStringCopy(CENSOR_SOURCE); +} + +psString censorVersionLong(void) +{ + psString version = censorVersion(); // Version, to return + psString source = censorSource(); // Source + + psStringPrepend(&version, "censor "); + psStringAppend(&version, " from %s, built %s, %s", source, __DATE__, __TIME__); + psFree(source); + +#ifdef __OPTIMIZE__ + psStringAppend(&version, " optimised"); +#else + psStringAppend(&version, " unoptimised"); +#endif + + return version; +}; + +bool censorVersionHeader(psMetadata *header) +{ + PS_ASSERT_METADATA_NON_NULL(header, false); + + psString version = censorVersion(); // Software version + psString source = censorSource(); // Software source + + psMetadataAddStr(header, PS_LIST_TAIL, "CENSOR_V", 0, NULL, source); + + psStringPrepend(&version, "censor version: "); + psStringPrepend(&source, "censor source: "); + + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, version); + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, source); + + psFree(version); + psFree(source); + + return true; +} + +bool censorVersionHeaderFull(psMetadata *header) +{ + PS_ASSERT_METADATA_NON_NULL(header, false); + + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now + psString timeString = psTimeToISO(time); // The time in an ISO string + psFree(time); + psString history = NULL; // History string + psStringAppend(&history, "censor at %s", timeString); + psFree(timeString); + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, history); + psFree(history); + + psLibVersionHeader(header); + psModulesVersionHeader(header); + censorVersionHeader(header); + + return true; +} + +void censorVersionPrint(void) +{ + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now + psString timeString = psTimeToISO(time); // The time in an ISO string + psFree(time); + psLogMsg("censor", PS_LOG_INFO, "censor at %s", timeString); + psFree(timeString); + + psString pslib = psLibVersionLong();// psLib version + psString psmodules = psModulesVersionLong(); // psModules version + psString censor = censorVersionLong(); // censor version + + psLogMsg("censor", PS_LOG_INFO, "%s", pslib); + psLogMsg("censor", PS_LOG_INFO, "%s", psmodules); + psLogMsg("censor", PS_LOG_INFO, "%s", censor); + + psFree(pslib); + psFree(psmodules); + psFree(censor); + + return; +} Index: /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorVersionDefinitions.h.in =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorVersionDefinitions.h.in (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/censorObjects/src/censorVersionDefinitions.h.in (revision 41117) @@ -0,0 +1,8 @@ +#ifndef CENSOR_VERSION_DEFINITIONS_H +#define CENSOR_VERSION_DEFINITIONS_H + +#define CENSOR_VERSION @CENSOR_VERSION@ // SVN version +#define CENSOR_BRANCH @CENSOR_BRANCH@ // SVN branch +#define CENSOR_SOURCE @CENSOR_SOURCE@ // SVN source + +#endif Index: /branches/ccl_branches/ipponly-20191108/magic/remove/Doxyfile.in =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/Doxyfile.in (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/Doxyfile.in (revision 41117) @@ -0,0 +1,1310 @@ +# Doxyfile 1.5.4 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project +# +# All text after a hash (#) is considered a comment and will be ignored +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" ") + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file that +# follow. The default is UTF-8 which is also the encoding used for all text before +# the first occurrence of this tag. Doxygen uses libiconv (or the iconv built into +# libc) for the transcoding. See http://www.gnu.org/software/libiconv for the list of +# possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded +# by quotes) that should identify the project. + +PROJECT_NAME = streaksremove + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = ipp-2.7.dev + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = ./docs + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Finnish, French, German, Greek, Hungarian, +# Italian, Japanese, Japanese-en (Japanese with English messages), Korean, +# Korean-en, Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian, +# Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = NO + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful is your file systems +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the DETAILS_AT_TOP tag is set to YES then Doxygen +# will output the detailed description near the top, like JavaDoc. +# If set to NO, the detailed description appears after the member +# documentation. + +DETAILS_AT_TOP = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for Java. +# For instance, namespaces will be presented as packages, qualified scopes +# will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want to +# include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). 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By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct (or union) is +# documented as struct with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code where the coding convention is that all structs are +# typedef'ed and only the typedef is referenced never the struct's name. + +TYPEDEF_HIDES_STRUCT = NO + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be extracted +# and appear in the documentation as a namespace called 'anonymous_namespace{file}', +# where file will be replaced with the base name of the file that contains the anonymous +# namespace. By default anonymous namespace are hidden. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if sectionname ... \endif. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or define consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and defines in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# If the sources in your project are distributed over multiple directories +# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy +# in the documentation. The default is NO. + +SHOW_DIRECTORIES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from the +# version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be abled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +WARN_FORMAT = "$file:$line: $text " + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = ./src + +# This tag can be used to specify the character encoding of the source files that +# doxygen parses. Internally doxygen uses the UTF-8 encoding, which is also the default +# input encoding. Doxygen uses libiconv (or the iconv built into libc) for the transcoding. +# See http://www.gnu.org/software/libiconv for the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx +# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 + +FILE_PATTERNS = *.h + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used select whether or not files or +# directories that are symbolic links (a Unix filesystem feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the output. +# The symbol name can be a fully qualified name, a word, or if the wildcard * is used, +# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. If FILTER_PATTERNS is specified, this tag will be +# ignored. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER +# is applied to all files. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. If you have enabled CALL_GRAPH or CALLER_GRAPH +# then you must also enable this option. If you don't then doxygen will produce +# a warning and turn it on anyway + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C and C++ comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES (the default) +# then for each documented function all documented +# functions referencing it will be listed. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES (the default) +# then for each documented function all documented entities +# called/used by that function will be listed. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. Otherwise they will link to the documentstion. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = NO + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If the tag is left blank doxygen +# will generate a default style sheet. Note that doxygen will try to copy +# the style sheet file to the HTML output directory, so don't put your own +# stylesheet in the HTML output directory as well, or it will be erased! + +HTML_STYLESHEET = + +# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, +# files or namespaces will be aligned in HTML using tables. If set to +# NO a bullet list will be used. + +HTML_ALIGN_MEMBERS = YES + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. For this to work a browser that supports +# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox +# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). + +HTML_DYNAMIC_SECTIONS = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index at +# top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. + +DISABLE_INDEX = NO + +# This tag can be used to set the number of enum values (range [1..20]) +# that doxygen will group on one line in the generated HTML documentation. + +ENUM_VALUES_PER_LINE = 4 + +# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be +# generated containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, +# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are +# probably better off using the HTML help feature. + +GENERATE_TREEVIEW = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, a4wide, letter, legal and +# executive. If left blank a4wide will be used. + +PAPER_TYPE = a4wide + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = NO + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = NO + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = YES + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. This is useful +# if you want to understand what is going on. On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +MACRO_EXPANSION = NO + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +EXPAND_ONLY_PREDEF = NO + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# in the INCLUDE_PATH (see below) will be search if a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all function-like macros that are alone +# on a line, have an all uppercase name, and do not end with a semicolon. Such +# function macros are typically used for boiler-plate code, and will confuse +# the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. +# Optionally an initial location of the external documentation +# can be added for each tagfile. The format of a tag file without +# this location is as follows: +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths or +# URLs. If a location is present for each tag, the installdox tool +# does not have to be run to correct the links. +# Note that each tag file must have a unique name +# (where the name does NOT include the path) +# If a tag file is not located in the directory in which doxygen +# is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +PERL_PATH = /usr/bin/perl + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option is superseded by the HAVE_DOT option below. This is only a +# fallback. It is recommended to install and use dot, since it yields more +# powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to +# produce the chart and insert it in the documentation. The MSCGEN_PATH tag allows you to +# specify the directory where the mscgen tool resides. If left empty the tool is assumed to +# be found in the default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +HIDE_UNDOC_RELATIONS = YES + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +HAVE_DOT = NO + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# the CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +UML_LOOK = NO + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +TEMPLATE_RELATIONS = NO + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH, SOURCE_BROWSER and HAVE_DOT tags are set to YES then doxygen will +# generate a call dependency graph for every global function or class method. +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable call graphs for selected +# functions only using the \callgraph command. + +CALL_GRAPH = NO + +# If the CALLER_GRAPH, SOURCE_BROWSER and HAVE_DOT tags are set to YES then doxygen will +# generate a caller dependency graph for every global function or class method. +# Note that enabling this option will significantly increase the time of a run. +# So in most cases it will be better to enable caller graphs for selected +# functions only using the \callergraph command. + +CALLER_GRAPH = NO + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are png, jpg, or gif +# If left blank png will be used. + +DOT_IMAGE_FORMAT = png + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The MAX_DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the number +# of direct children of the root node in a graph is already larger than +# MAX_DOT_GRAPH_NOTES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, which results in a white background. +# Warning: Depending on the platform used, enabling this option may lead to +# badly anti-aliased labels on the edges of a graph (i.e. they become hard to +# read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to the search engine +#--------------------------------------------------------------------------- + +# The SEARCHENGINE tag specifies whether or not a search engine should be +# used. If set to NO the values of all tags below this one will be ignored. + +SEARCHENGINE = NO Index: /branches/ccl_branches/ipponly-20191108/magic/remove/Makefile.am =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/Makefile.am (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/Makefile.am (revision 41117) @@ -0,0 +1,4 @@ +SUBDIRS = src + +CLEANFILES = *.pyc *~ core core.* + Index: /branches/ccl_branches/ipponly-20191108/magic/remove/autogen.sh =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/autogen.sh (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/autogen.sh (revision 41117) @@ -0,0 +1,103 @@ +#!/bin/sh +# Run this to generate all the initial makefiles, etc. + +srcdir=`dirname $0` +test -z "$srcdir" && srcdir=. + +ORIGDIR=`pwd` +cd $srcdir + +PROJECT=streaks +TEST_TYPE=-f +# change this to be a unique filename in the top level dir +FILE=autogen.sh + +DIE=0 + +LIBTOOLIZE=libtoolize +ACLOCAL="aclocal $ACLOCAL_FLAGS" +AUTOHEADER=autoheader +AUTOMAKE=automake +AUTOCONF=autoconf + +($LIBTOOLIZE --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $LIBTOOLIZE installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/libtool/" + DIE=1 +} + +($ACLOCAL --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $ACLOCAL installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/" + DIE=1 +} + +($AUTOHEADER --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOHEADER installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/" + DIE=1 +} + +($AUTOMAKE --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOMAKE installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/automake/" + DIE=1 +} + +($AUTOCONF --version) < /dev/null > /dev/null 2>&1 || { + echo + echo "You must have $AUTOCONF installed to compile $PROJECT." + echo "Download the appropriate package for your distribution," + echo "or get the source tarball at http://ftp.gnu.org/gnu/autoconf/" + DIE=1 +} + +if test "$DIE" -eq 1; then + exit 1 +fi + +test $TEST_TYPE $FILE || { + echo "You must run this script in the top-level $PROJECT directory" + exit 1 +} + +if test -z "$*"; then + echo "I am going to run ./configure with no arguments - if you wish " + echo "to pass any to it, please specify them on the $0 command line." +fi + +$LIBTOOLIZE --copy --force || echo "$LIBTOOLIZE failed" +$ACLOCAL || echo "$ACLOCAL failed" +$AUTOHEADER || echo "$AUTOHEADER failed" +$AUTOMAKE --add-missing --force-missing --copy || echo "$AUTOMAKE failed" +$AUTOCONF || echo "$AUTOCONF failed" + +cd $ORIGDIR + +run_configure=true +for arg in $*; do + case $arg in + --no-configure) + run_configure=false + ;; + *) + ;; + esac +done + +if $run_configure; then + $srcdir/configure --enable-maintainer-mode "$@" + echo + echo "Now type 'make' to compile $PROJECT." +else + echo + echo "Now run 'configure' and 'make' to compile $PROJECT." +fi Index: /branches/ccl_branches/ipponly-20191108/magic/remove/configure.ac =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/configure.ac (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/configure.ac (revision 41117) @@ -0,0 +1,45 @@ +dnl Process this file with autoconf to produce a configure script. +AC_PREREQ(2.61) + +AC_INIT([streaksremove], [0.9.0], [ipp-support@ifa.hawaii.edu]) +AC_CONFIG_SRCDIR([src]) + +AM_INIT_AUTOMAKE([1.6 foreign dist-bzip2]) +AM_CONFIG_HEADER([src/config.h]) +AM_MAINTAINER_MODE + +IPP_STDLDFLAGS + +AC_LANG(C) +AC_GNU_SOURCE +AC_PROG_CC_C99 +AC_PROG_INSTALL +AC_PROG_LIBTOOL +AC_SYS_LARGEFILE + +dnl ------------------------------------------------------------ + +dnl ------------- psLib, psModules --------------- +PKG_CHECK_MODULES([PSLIB], [pslib >= 1.0.0]) +PKG_CHECK_MODULES([PSMODULE], [psmodules >= 1.0.0]) +PKG_CHECK_MODULES([NEBCLIENT], [nebclient >= 0.17]) + +dnl Set CFLAGS for build +IPP_STDOPTS +IPP_STDCFLAGS + +echo "STREAKSREMOVE_CFLAGS: $STREAKSREMOVE_CFLAGS" +echo "STREAKSREMOVE_LIBS: $STREAKSREMOVE_LIBS" + +IPP_VERSION + +AC_SUBST([STREAKSREMOVE_CFLAGS]) +AC_SUBST([STREAKSREMOVE_LIBS]) + +AC_CONFIG_FILES([ + Makefile + src/Makefile + Doxyfile +]) + +AC_OUTPUT Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/Line.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/Line.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/Line.c (revision 41117) @@ -0,0 +1,507 @@ +/* Standard includes */ + +#include + +/* psLib includes */ + +#include "psMemory.h" + +/* streakremove includes */ + +#include "Line.h" + +/** Internal routine to swap double values */ + +void SwapDouble (double* first, double* second) +{ + double temp = *first; + *first = *second; + *second = temp; +} + +/** Internal routine to swap integer values */ + +void SwapInt (int* first, int* second) +{ + int temp = *first; + *first = *second; + *second = temp; +} + +/** Return if a point is inside the current line segment assuming the + point and line are colinear */ + +bool InLineSegment (Line* line, strkPt* tuple) +{ + // If the current line is not vertical, check to see if the point + // is inside the two endpoints independent of direction + + if (line->begin.x != line->end.x) + { + return (tuple->x >= line->begin.x && + tuple->x <= line->end.x) || + (tuple->x >= line->end.x && + tuple->x <= line->begin.x); + } + return (tuple->y >= line->begin.y && + tuple->y <= line->end.y) || + (tuple->y >= line->end.y && + tuple->y <= line->begin.y); +} + +double DistanceSquared (Line* line, double x, double y) +{ + // Define U as the vector from the line segment start to end + // Define V as the vector from the line segment start to the tuple + // Define W as the vector from the line segment end to the tuple + + double ux, uy, vx, vy, b, px, py; + ux = line->end.x - line->begin.x; + uy = line->end.y - line->begin.y; + + vx = x - line->begin.x; + vy = y - line->begin.y; + + double u_u = ux * ux + uy * uy; // (u . u) + double u_v = ux * vx + uy * vy; // (u . v) + + if (u_v <= 0) return vx * vx + vy * vy; // (v . v) + if (u_u <= u_v) + { + double wx = x - line->end.x; + double wy = y - line->end.y; + return wx * wx + wy * wy; // (w . w) + } + + // Compute P(b) is the base of the perpendicular dropped from tuple to + // the line + + b = u_v / u_u; + px = vx - b * ux; + py = vy - b * uy; + return px * px + py * py; // norm (p) +} + +/** Return true if two lines intersect within their limits and in + all cases including coplanar lines, set one or two points of + intersection + + @param[in] first first line to compare for intercept + @param[in] second second line to compare for intercept + @param[out] tuple1 first intercept point if found + @param[out] tuple2 second intercept point if lines are coplanar + @param[in] inFirstSegment true if the line intercept must be within + the bounds of the first line. False if the + first line should be considered as infinite + @param[in] inSecondSegment true if the line intercept must be within + the bounds of the first line. False if the + second line should be considered as infinite + @return the number of intercept points */ + +int LineIntercept (Line* first, Line* second, strkPt* tuple1, strkPt* tuple2, + bool inFirstSegment, bool inSecondSegment) +{ + double len1, len2, w2x, w2y, t0, t1; + double dx1 = first->end.x - first->begin.x; + double dy1 = first->end.y - first->begin.y; + double dx2 = second->end.x - second->begin.x; + double dy2 = second->end.y - second->begin.y; + double wx = first->begin.x - second->begin.x; + double wy = first->begin.y - second->begin.y; + + // Calculate the perpendicular product, dt + + double dt = dx1 * dy2 - dy1 * dx2; + + // Are the lines parallel? + + if (fabs (dt) <= 1e-8) + { + // Check to see if they are overlap + + if (dx1 * wy - dy1 * wx != 0 || dx2 * wy - dy2 * wx != 0) return 0; + + // The line are coplanar, so check to see if they are degenerate + + len1 = dx1 * dx1 + dy1 * dy1; + len2 = dx2 * dx2 + dy2 * dy2; + + // First, check to see if both lines are points and if they are + // distinct tuples + + if (len1 == 0 && len2 == 0) + { + if (first->begin.x != second->begin.x || + first->begin.y != second->begin.y) return 0; + *tuple1 = first->begin; + return 1; + } + + // Check to see if the first line is a point and is inside the + // second line + + if (len1 == 0) + { + if (InLineSegment (second, &first->begin)) + *tuple1 = first->begin; + else + return 0; + } + + // Check to see if the second line is a point and is inside the + // first line + + if (len2 == 0) + { + if (InLineSegment (first, &second->begin)) + *tuple1 = second->begin; + else + return 0; + } + + // Since both lines are coplanar and have length, search for + // overlap tuples + + w2x = first->end.x - second->begin.x; + w2y = first->end.y - second->begin.y; + + t0 = (dx2 != 0) ? wx / dx2 : wy / dy2; + t1 = (dx2 != 0) ? w2x / dx2 : w2y / dy2; + + if (t0 > t1) SwapDouble (&t0, &t1); + if ((inFirstSegment || inSecondSegment) && (t0 > 1 || t1 < 0)) + { + return 0; // No overlap + } + t0 = (t0 < 0) ? 0 : t0; // Clip to min 0 + t1 = (t1 > 1) ? 1 : t1; // Clip to max 1 + + // Set the first tuple of intersection + + tuple1->x = second->begin.x + t0 * dx2; + tuple1->y = second->begin.y + t0 * dy2; + + // Check to see if the intersection is a single tuple + + if (t0 == t1) return 1; + + // Otherwise, set the second tuple of intersection as well + + tuple2->x = second->begin.x + t1 * dx2; + tuple2->y = second->begin.y + t1 * dy2; + return 2; + } + + // The segments are skew and may intersect in a tuple. + // Get the intersect parameter for the first line + + double i1 = (dx2 * wy - dy2 * wx) / dt; + if (inFirstSegment && (i1 < 0 || i1 > 1)) return 0; + + // Get the intersect parameter for the second line + + double i2 = (dx1 * wy - dy1 * wx) / dt; + if (inSecondSegment && (i2 < 0 || i2 > 1)) return 0; + + tuple1->x = first->begin.x + i1 * dx1; + tuple1->y = first->begin.y + i1 * dy1; + return 1; +} + +/** Clip the line between (0,0) and the specified upper bound + + @param[in,out] line line to be clipped within the bounds + @param[in] numCols maximum X (columns) for the line + @param[in] numRows maximum Y (rows) for the line + @return true if line overlaps the clip boundaries */ + +bool LineClip (Line *line, int numCols, int numRows) +{ + unsigned int i, found = 0; + Line boundLine, clipLine; + strkPt tuple1, tuple2, vertices[4]; + vertices[0].x = 0; vertices[0].y = 0; + vertices[1].x = numCols; vertices[1].y = 0; + vertices[2].x = numCols; vertices[2].y = numRows; + vertices[3].x = 0; vertices[3].y = numRows; + + clipLine.begin.x = 0; + clipLine.begin.y = 0; + clipLine.end.x = 0; + clipLine.end.y = 0; + + for (i = 0; i < 4 && found < 2; ++i) + { + boundLine.begin = vertices[i]; + boundLine.end = vertices[(i + 1) % 4]; + if (LineIntercept (line, &boundLine, &tuple1, &tuple2, false, true)) + { + if (found == 0) + { + clipLine.begin = tuple1; + ++found; + } + else if (tuple1.x != clipLine.begin.x || + tuple1.y != clipLine.begin.y) + { + clipLine.end = tuple1; + ++found; + } + } + } + + // If two endpoints are found, clip the line + + if (found > 1) + { + if (clipLine.begin.x <= clipLine.end.x) + { + line->begin = clipLine.begin; + line->end = clipLine.end; + } + else + { + line->begin = clipLine.end; + line->end = clipLine.begin; + } + } + return found > 1; +} + +/** Clip the line between (minX,minY) and (maxX,maxY) + + @param[in,out] line line to be clipped within the bounds + @param[in] minX minimum X (columns) for the line + @param[in] minY minimum Y (rows) for the line + @param[in] maxX maximum X (columns) for the line + @param[in] maxY maximum Y (rows) for the line + @return true if line overlaps the clip boundaries */ + +bool LineClipFull (Line *line, int minX, int minY, int maxX, int maxY) +{ + unsigned int i, found = 0; + Line boundLine, clipLine; + strkPt tuple1, tuple2, vertices[4]; + vertices[0].x = minX; vertices[0].y = minY; + vertices[1].x = maxX; vertices[1].y = minY; + vertices[2].x = maxX; vertices[2].y = maxY; + vertices[3].x = minX; vertices[3].y = maxY; + + clipLine.begin.x = 0; + clipLine.begin.y = 0; + clipLine.end.x = 0; + clipLine.end.y = 0; + + for (i = 0; i < 4 && found < 2; ++i) + { + boundLine.begin = vertices[i]; + boundLine.end = vertices[(i + 1) % 4]; + if (LineIntercept (line, &boundLine, &tuple1, &tuple2, false, true)) + { + if (found == 0) + { + clipLine.begin = tuple1; + ++found; + } + else if (tuple1.x != clipLine.begin.x || + tuple1.y != clipLine.begin.y) + { + clipLine.end = tuple1; + ++found; + } + } + } + + // If two endpoints are found, clip the line + + if (found > 1) + { + if (clipLine.begin.x <= clipLine.end.x) + { + line->begin = clipLine.begin; + line->end = clipLine.end; + } + else + { + line->begin = clipLine.end; + line->end = clipLine.begin; + } + } + return found > 1; +} + +/** Move a line by the specified X and Y offsets + @param[in,out] line Line to move by X and Y offsets + @param[in] xOffset X shift applied to both endpoints + @param[in] yOffset Y shift applied to both endpoints */ + +void LineMove (Line *line, double xOffset, double yOffset) +{ + line->begin.x += xOffset; + line->begin.y += yOffset; + line->end.x += xOffset; + line->end.y += yOffset; +} + +/** Return the maximum bounds between the line endpoints and + current bounds + @param[in] line Line endpoints to compare + @param[in,out] xMin minimum X value to update + @param[in,out] xMax maximum X value to update + @param[in,out] yMin minimum Y value to update + @param[in,out] yMax maximum Y value to update */ + +void MaxBounds (Line *line, int *xMin, int *xMax, int *yMin, int *yMax) +{ + if (line->begin.x < *xMin) *xMin = (int) floor (line->begin.x); + if (line->end.x < *xMin) *xMin = (int) floor (line->end.x); + if (line->begin.y < *yMin) *yMin = (int) floor (line->begin.y); + if (line->end.y < *yMin) *yMin = (int) floor (line->end.y); + + if (line->begin.x > *xMax) *xMax = (int) ceil (line->begin.x); + if (line->end.x > *xMax) *xMax = (int) ceil (line->end.x); + if (line->begin.y > *yMax) *yMax = (int) ceil (line->begin.y); + if (line->end.y > *yMax) *yMax = (int) ceil (line->end.y); +} + +/** Map a line to an image for its specified width and store as + a list of pixel positions + + @param[out] pixels list of PixelPos pointers corresponding + based on the line settings + @param[in] line Line to map to pixels + @param[in] numCols maximum X (columns) for the line + @param[in] numRows maximum Y (rows) for the line */ + +void PixelsFromLine (StreakPixels* pixels, Line *line, int numCols, int numRows) +{ + Line offsetLine; + double slope, xOffset, yOffset, xMid, yMid; + int x, y, xBegin = numCols, yBegin = numRows, xEnd = 0, yEnd = 0; + + // Extract the endpoints + + double x1 = line->begin.x; + double y1 = line->begin.y; + double x2 = line->end.x; + double y2 = line->end.y; + + // Determine the width and height of the line + + double dx = x2 - x1; + double dy = y2 - y1; + double dr = sqrt (dx * dx + dy * dy); + double halfWidth = line->width / 2.0; + if (!dr) return; + + // Compute the intercepts of line width bounds and determine maximum + // bounds in each axis + + xOffset = -halfWidth * dy / dr; + yOffset = halfWidth * dx / dr; + + offsetLine = *line; + LineMove (&offsetLine, xOffset, yOffset); + if (LineClip (&offsetLine, numCols, numRows)) + MaxBounds (&offsetLine, &xBegin, &xEnd, &yBegin, &yEnd); + + offsetLine = *line; + LineMove (&offsetLine, -xOffset, -yOffset); + if (LineClip (&offsetLine, numCols, numRows)) + MaxBounds (&offsetLine, &xBegin, &xEnd, &yBegin, &yEnd); + + // Step point by point based on the dominate axis + + if (fabs (dx) > fabs (dy)) + { + // --------------------- + // horizontal(ish) lines + // --------------------- + // If line is back to front, reorder endpoints and recompute + // the line width and height + + if (x1 > x2) + { + SwapDouble (&x1, &x2); + SwapDouble (&y1, &y2); + dx = x2 - x1; + dy = y2 - y1; + } + + // Compute the slope of the line + + slope = dy / dx; + + // Compute the x and y offsets for the line width extent + + if (xBegin > xEnd) + SwapInt (&xBegin, &xEnd); + else + ++xEnd; + if (xBegin < 0) xBegin = 0; + if (xEnd > numCols) xEnd = numCols; + + yMid = y1 + slope * (xBegin - x1); + yOffset = fabs (halfWidth * dr / dx); + + for (x = xBegin; x != xEnd; ++x) + { + yBegin = (int) floor (yMid - yOffset); + yEnd = (int) ceil (yMid + yOffset) + 1; + for (y = yBegin; y != yEnd; ++y) + { + if (y >= 0 && y < numRows) + { + psImageSet(pixels, x, y, 1); + } + } + yMid += slope; + } + } + else + { + // ------------------- + // vertical(ish) lines + // ------------------- + // If line is back to front, reorder endpoints and recompute + // the line width and height + + if (y1 > y2) + { + SwapDouble (&x1, &x2); + SwapDouble (&y1, &y2); + dx = x2 - x1; + dy = y2 - y1; + } + + // Compute the slope of the line + + slope = dx / dy; + + // Compute the x and y offsets for the line width extent + + if (yBegin > yEnd) + SwapInt (&yBegin, &yEnd); + else + ++yEnd; + if (yBegin < 0) yBegin = 0; + if (yEnd > numRows) yEnd = numRows; + + xMid = x1 + slope * (yBegin - y1); + xOffset = fabs (halfWidth * dr / dy); + + for (y = yBegin; y != yEnd; ++y) + { + xBegin = (int) floor (xMid - xOffset); + xEnd = (int) ceil (xMid + xOffset) + 1; + for (x = xBegin; x != xEnd; ++x) + { + if (x >=0 && x < numCols) + { + psImageSet(pixels, x, y, 1); + } + } + xMid += slope; + } + } // if (fabs (dx) > fabs (dy)) +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/Line.h =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/Line.h (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/Line.h (revision 41117) @@ -0,0 +1,46 @@ +#ifndef STREAK_LINE_H +#define STREAK_LINE_H + +#include "streaksextern.h" + +/** Define a line object converted from streak equatorial object */ + +typedef struct { + strkPt begin; + strkPt end; + double width; +} Line; + +/** Clip the line between (0,0) and the specified upper bound + + @param[in,out] line line to be clipped within the bounds + @param[in] numCols maximum X (columns) for the line + @param[in] numRows maximum Y (rows) for the line + @return true if line overlaps the clip boundaries */ + +extern bool LineClip (Line *line, int numCols, int numRows); + +/** Clip the line between (minX,minY) and (maxX,maxY) + + @param[in,out] line line to be clipped within the bounds + @param[in] minX minimum X (columns) for the line + @param[in] minY minimum Y (rows) for the line + @param[in] maxX maximum X (columns) for the line + @param[in] maxY maximum Y (rows) for the line + @return true if line overlaps the clip boundaries */ + +extern bool LineClipFull (Line *line, int minX, int minY, int maxX, int maxY); + +/** Map a line to an image for its specified width and append as + a list of pixel positions + + @param[out] pixels list of PixelPos pointers corresponding + based on the line settings + @param[in] line Line to map to pixels + @param[in] numCols maximum X (columns) for the line + @param[in] numRows maximum Y (rows) for the line */ + +extern void PixelsFromLine (StreakPixels* pixels, Line *line, + int numCols, int numRows); + +#endif /* STREAK_LINE_H */ Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/Makefile.am =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/Makefile.am (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/Makefile.am (revision 41117) @@ -0,0 +1,81 @@ + +# Force recompilation of streaksVersion.c, since it gets the version information +streaksVersion.c: streaksVersionDefinitions.h +streaksVersionDefinitions.h: streaksVersionDefinitions.h.in FORCE + pslib-setsvnversion.pl STREAKS streaksVersionDefinitions.h.in streaksVersionDefinitions.h +FORCE: ; + +bin_PROGRAMS = streaksremove streaksrelease streaksreplace streakscompare isdestreaked + +STREAKSREMOVE_CFLAGS=-DSTREAKS_COMPRESS_OUTPUT=1 + +STREAKSCFLAGS = $(STREAKSREMOVE_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) ${NEBCLIENT_CFLAGS} +STREAKSLDFLAGS = $(STREAKSREMOVE_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS) ${NEBCLIENT_LIBS} + +streaksremove_CFLAGS = $(STREAKSCFLAGS) +streaksremove_LDFLAGS = $(STREAKSLDFLAGS) +streaksreplace_CFLAGS = $(STREAKSCFLAGS) +streaksreplace_LDFLAGS = $(STREAKSLDFLAGS) +streaksrelease_CFLAGS = $(STREAKSCFLAGS) +streaksrelease_LDFLAGS = $(STREAKSLDFLAGS) +streakscompare_CFLAGS = $(STREAKSCFLAGS) +streakscompare_LDFLAGS = $(STREAKSLDFLAGS) +isdestreaked_CFLAGS = $(STREAKSCFLAGS) +isdestreaked_LDFLAGS = $(STREAKSLDFLAGS) + +COMMON_SOURCES = \ + streaksio.c \ + streaksutil.c \ + streaksastrom.c \ + streaksVersion.c + +streaksremove_SOURCES = \ + streaksremove.c \ + streaksextern.c \ + diffedpixels.c \ + Line.c \ + $(COMMON_SOURCES) + +streaksrelease_SOURCES = \ + streaksrelease.c\ + streaksio.c \ + streaksutil.c \ + streaksastrom.c \ + streaksVersion.c + +streaksreplace_SOURCES = \ + streaksreplace.c\ + streaksio.c \ + streaksutil.c \ + streaksastrom.c \ + streaksVersion.c + +streakscompare_SOURCES = \ + streakscompare.c\ + streaksio.c \ + streaksutil.c \ + streaksastrom.c \ + streaksVersion.c + +isdestreaked_SOURCES = \ + isdestreaked.c\ + streaksio.c \ + streaksutil.c \ + streaksastrom.c \ + streaksVersion.c + +include_HEADERS = \ + streaksremove.h \ + streaksastrom.h \ + streaksextern.h \ + streaksio.h \ + streaksVersionDefinitions.h + +clean-local: + -rm -f TAGS + -rm -f tags + +# Tags for emacs and vi +tags: + etags `find . -name \*.[ch] -print` + ctags `find . -name \*.[ch] -print` Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/Makefile.simple =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/Makefile.simple (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/Makefile.simple (revision 41117) @@ -0,0 +1,87 @@ +# skeleton Makefile for streaksremove +# +# The intent is that these programs may be built against an +# IPP installation outside the IPP build enviornment. + +COMMON_OBJECTS = \ + streaksio.o \ + streaksutil.o \ + streaksastrom.o + +REMOVE_OBJECTS= \ + streaksremove.o \ + streaksextern.o \ + diffedpixels.o \ + Line.o + +REPLACE_OBJECTS= \ + streaksreplace.o + +COMPARE_OBJECTS= \ + streakscompare.o + +RELEASE_OBJECTS= \ + streaksrelease.o + +ISDESTREAKED_OBJECTS= \ + isdestreaked.o + + +HEADERS= Line.h streaksastrom.h streaksextern.h streaksio.h streaksremove.h + +STREAKSFLAGS=-DSTREAKS_COMPRESS_OUTPUT=1 +OPTFLAGS= -g -O2 -Wall -Werror +#OPTFLAGS= -g +CFLAGS=`psmodules-config --cflags` `pslib-config --cflags` -std=gnu99 ${OPTFLAGS} ${STREAKSFLAGS} +#CFLAGS=`psmodules-config --cflags` `pslib-config --cflags` -std=gnu99 ${OPTFLAGS} +LDFLAGS=`psmodules-config --libs` `pslib-config --libs` + +PROGRAMS= streaksremove streaksreplace streakscompare streaksrelease isdestreaked +HEADERS=Line.h streaksastrom.h streaksextern.h streaksio.h streaksremove.h + +all: ${PROGRAMS} + +# programs all depend on the common objects and the common headers +PROGRAM_OBJECTS = \ + ${REMOVE_OBJECTS} \ + ${REPLACE_OBJECTS} \ + ${COMPARE_OBJECTS} \ + ${RELEASE_OBJECTS} \ + ${ISDESTREAKED_OBJECTS} + +${COMMON_OBJECTS}: ${HEADERS} + +${PROGRAM_OBJECTS}: ${HEADERS} ${COMMON_OBJECTS} + +streaksremove: ${REMOVE_OBJECTS} ${COMMON_OBJECTS} + +streaksreplace: ${REPLACE_OBJECTS} ${COMMON_OBJECTS} + +streakscompare: ${COMPARE_OBJECTS} ${COMMON_OBJECTS} + +streaksrelease: ${RELEASE_OBJECTS} ${COMMON_OBJECTS} + +isdestreaked: ${ISDESTREAKED_OBJECTS} ${COMMON_OBJECTS} + + +install: ${PROGRAMS} + install -t $(PSCONFDIR)/$(PSCONFIG)/bin streaksremove + install -t $(PSCONFDIR)/$(PSCONFIG)/bin streaksreplace + install -t $(PSCONFDIR)/$(PSCONFIG)/bin streakscompare + install -t $(PSCONFDIR)/$(PSCONFIG)/bin streaksrelease + install -t $(PSCONFDIR)/$(PSCONFIG)/bin isdestreaked + +clean: + rm -f *.o ${PROGRAMS} + + +clean-local: + -rm -f TAGS + +# Tags for emacs +tags: + etags `find . -name \*.[ch] -print` + +### Error codes. +BUILT_SOURCES = +CLEANFILES = Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/diffedpixels.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/diffedpixels.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/diffedpixels.c (revision 41117) @@ -0,0 +1,277 @@ +#include "streaksremove.h" +#include "pmAstrometryWCS.h" + +#define DEBUG_PRINT 1 + +static void addTouchedPixels(streakFiles *sf, psString fileName); +static void nameCorners(psPlane pt[4]); +static int xLeft(psPlane *pt, int y); +static int xRight(psPlane *pt, int y); + +#define BL 0 +#define BR 1 +#define TL 2 +#define TR 3 + +// Examine the set of diff skycells and compute the pixels that were +// included in difference processing +bool +computeDiffedPixels(streakFiles *sf) +{ + bool status; + pmConfig *config = sf->config; + + psArray *skycells = psMetadataLookupPtr(&status, config->arguments, "SKYCELLS"); + if (skycells == NULL) { + return false; + } + + int n = psArrayLength(skycells); + + psRegion *bounds = pmChipPixels(sf->chip); + + int width = bounds->x1 - bounds->x0; + int height = bounds->y1 - bounds->y0; + + psFree(bounds); + + sf->diffedPixels = psImageAlloc(width, height, PS_TYPE_U8); + psImageInit(sf->diffedPixels, 0); + + for (int i=0; iinAstrom->fpa->toSky->type != PS_PROJ_DIS) { + pmAstromWriteWCS(header, sf->inAstrom->fpa, sf->chip, 0.001); + } + psFits *fits = psFitsOpen("diffedpixels.fits", "w"); + + psFitsWriteImage(fits, header, sf->diffedPixels, 0, NULL); + psFitsClose(fits); + psFree(header); + } + return true; +} + +static void +addTouchedPixels(streakFiles *sf, psString fileName) +{ + // read fits header + psFits *fits = psFitsOpen(fileName, "r"); + if (!fits) { + psError(PS_ERR_IO, false, "failed to open skycell file: %s", fileName); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psMetadata *header = psFitsReadHeader(NULL, fits); + psFitsClose(fits); + if (!header) { + psError(PS_ERR_IO, false, "failed to read fixts header from skycell file: %s", fileName); + streaksExit("", PS_EXIT_DATA_ERROR); + } + // set up astrometry for conversion from skycell image to sky + pmAstromWCS *wcs = pmAstromWCSfromHeader(header); + if (!wcs) { + psError(PS_ERR_IO, false, "failed to read astrometry from skycell file: %s", fileName); + streaksExit("", PS_EXIT_DATA_ERROR); + } + int naxis1 = psMetadataLookupS32(NULL, header, "NAXIS1"); + int naxis2 = psMetadataLookupS32(NULL, header, "NAXIS2"); + + psFree(header); + + /* now set up our wrapper to the chip astrometry to apply to the whole chip */ + sf->astrom = streakSetAstrometry(sf->astrom, sf->stage, sf->inAstrom->fpa, sf->chip, false, NULL, + sf->diffedPixels->numCols, sf->diffedPixels->numRows); + + // convert corners of skycell to chip coordinates + // compute overlap with the chip using astrometry + psPlane pt[4]; + pt[0].x = 0; + pt[0].y = 0; + + pt[1].x = naxis1 - 1; + pt[1].y = 0; + + pt[2].x = naxis1 - 1; + pt[2].y = naxis2 - 1; + + pt[3].x = 0; + pt[3].y = naxis2 - 1; + + for (int i = 0; i < 4 ; i++ ) { + psSphere sky; + + // convert corner of skycell to sky coordinates + if (!pmAstromWCStoSky(&sky, wcs, &pt[i])) { + psErrorStackPrint(stderr, "failed to convert pt %d of %s to sky coords", i, fileName); + streaksExit("", PS_EXIT_DATA_ERROR); + } + strkPt p; + // convert to chip coordinates + if (!skyToCell(&p, sf->astrom, sky.r, sky.d)) { + psErrorStackPrint(stderr, "failed to convert pt %d of %s to sky coords", i, fileName); + streaksExit("", PS_EXIT_DATA_ERROR); + } + pt[i].x = round(p.x); + pt[i].y = round(p.y); + } + + psFree(wcs); + + // Identify the bottom left, bottom right, top left, and top right corners + nameCorners(pt); + +#ifdef DEBUG_PRINT + fprintf(stderr, "\nSKYCELL %s\n", fileName); + fprintf(stderr, "BL %f %f\n", pt[BL].x, pt[BL].y); + fprintf(stderr, "BR %f %f\n", pt[BR].x, pt[BR].y); + fprintf(stderr, "TL %f %f\n", pt[TL].x, pt[TL].y); + fprintf(stderr, "TR %f %f\n", pt[TR].x, pt[TR].y); +#endif + + int xmax = sf->diffedPixels->numCols - 1; + int ymin; + int ymax; + + if (pt[BL].y <= pt[BR].y) { + ymin = fmax(0, pt[BL].y); + } else { + ymin = fmax(0, pt[BR].y); + } + if (pt[TR].y >= pt[TL].y) { + ymax = fmin(pt[TR].y, sf->diffedPixels->numRows - 1); + } else { + ymax = fmin(pt[TL].y, sf->diffedPixels->numRows - 1); + } + +#if (DEBUG_PRINT > 1) + fprintf(stderr, "\nxmin: %d xmax: %d\n", 0, xmax); + fprintf(stderr, "\nymin: %d ymax: %d\n", ymin, ymax); +#endif + + // Now set the touched pixels + for (int y = ymin ; y <= ymax; y++) { + + int xleft = xLeft(pt, y) - 1; + int xright = xRight(pt, y) + 1; + + if (xright < 0) { + continue; + } + if (xleft > xmax) { + continue; + } + if (xleft < 0) { + xleft = 0; + } + if (xright > xmax) { + xright = xmax; + } +#if (DEBUG_PRINT > 1) + fprintf(stderr, " y: %d xleft: %d xright: %d\n", y, xleft, xright); +#endif + + psU8 *rowPixels = sf->diffedPixels->data.U8[y]; + + int n = xright - xleft + 1; + if (n > 0) { + memset(&rowPixels[xleft], 255, n); + } + } +} + +// x as a function of y for the line between two points +// Note: the caller guarentees that the y's of the two points are different +static double xOfY(psPlane *pI, psPlane *pJ, int y) +{ + double m_inv = (double) (pJ->x - pI->x) / (double) (pJ->y - pI->y); + + double x = ((double) y - pI->y) * m_inv + (double) pI->x; + + return x; +} + +static int xLeft(psPlane *pt, int y) +{ + double x_d; + + if ((y <= pt[BL].y ) && ((pt[BL].y >= pt[BR].y))) { + // left boundary is the line from bottom left to bottom right + x_d = xOfY(&pt[BL], &pt[BR], y); + } else if ( y <= pt[TL].y ) { + // left boundary is the line from Bottom left to top left + x_d = xOfY(&pt[BL], &pt[TL], y); + } else { + // left boundary is the line from top left to top right + x_d= xOfY(&pt[TL], &pt[TR], y); + } + + return (int) floor(x_d); +} + +static int xRight(psPlane *pt, int y) +{ + double x_d; + if ((y <= pt[BR].y) && (pt[BR].y > pt[BL].y)) { + // right boundary is the line from Bottom right to Top right + x_d = xOfY(&pt[BL], &pt[BR], y); + } else if ( y<= pt[TR].y) { + // right boundary is the line from Top left to top right + x_d = xOfY(&pt[BR], &pt[TR], y); + } else { + x_d = xOfY(&pt[TL], &pt[TR], y); + } + return (int) ceil(x_d); +} + +static void +nameCorners(psPlane pt[4]) +{ + // sort points top to bottom (in case of ties take favor rightmost) + int i; + int j; + for (i=0; i<4; i++) { + for (j = i + 1; j < 4; j++) { + if ((pt[j].y > pt[i].y) || + ((pt[j].y == pt[i].y) && (pt[j].x > pt[i].x))) { + psPlane tmpPt = pt[j]; + pt[j] = pt[i]; + pt[i] = tmpPt; + } + } + } + psPlane bl, br; + // sort bottom two points in x + if (pt[3].x < pt[2].x) { + bl = pt[3]; + br = pt[2]; + } else { + bl = pt[2]; + br = pt[3]; + } + // sort the top two points in x + psPlane tl, tr; + if (pt[0].x < pt[1].x) { + tl = pt[0]; + tr = pt[1]; + } else { + tl = pt[1]; + tr = pt[0]; + } + pt[BL] = bl; + pt[BR] = br; + pt[TL] = tl; + pt[TR] = tr; +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/isdestreaked.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/isdestreaked.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/isdestreaked.c (revision 41117) @@ -0,0 +1,41 @@ +#include "streaksremove.h" + +char *streaksProgram = "isdestreaked"; + +int +main(int argc, char *argv[]) +{ + pmConfig *config = pmConfigRead(&argc, argv, NULL); + if (!config) { + psErrorStackPrint(stderr, "failed to parse arguments\n"); + exit(PS_EXIT_CONFIG_ERROR); + } + + char *fileName = argv[1]; + if (!fileName) { + fprintf(stderr, "Usage: %s filename\n", argv[0]); + exit(PS_EXIT_DATA_ERROR); + } + + psFits *fits = psFitsOpen(fileName, "r"); + if (!fits) { + psErrorStackPrint(stderr, "failed to open fits file: %s\n", fileName); + exit(PS_EXIT_DATA_ERROR); + } + + psMetadata *header = psFitsReadHeader(NULL, fits); + if (!header) { + psErrorStackPrint(stderr, "failed to read header for: %s", fileName); + exit(PS_EXIT_DATA_ERROR); + } + + bool mdok; + bool isDestreaked = psMetadataLookupBool(&mdok, header, "PSDESTRK"); + if (mdok && isDestreaked) { + printf("%s is a destreaked file\n", fileName); + exit(0); + } else { + printf("%s is not a destreaked file\n", fileName); + exit(42); + } +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksVersion.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksVersion.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksVersion.c (revision 41117) @@ -0,0 +1,115 @@ +/** @file streaksVersion.c + * + * @brief + * + * @ingroup streaks + * + * Copyright 2009 Institute for Astronomy, University of Hawaii + */ + +#include "streaksremove.h" +#include "streaksVersionDefinitions.h" + +#ifndef STREAKS_VERSION +#error "STREAKS_VERSION is not set" +#endif +#ifndef STREAKS_BRANCH +#error "STREAKS_BRANCH is not set" +#endif +#ifndef STREAKS_SOURCE +#error "STREAKS_SOURCE is not set" +#endif + +psString streaksVersion(void) +{ + char *value = NULL; + psStringAppend(&value, "%s@%s", STREAKS_BRANCH, STREAKS_VERSION); + return value; +} + +psString streaksSource(void) +{ + return psStringCopy(STREAKS_SOURCE); +} + +psString streaksVersionLong(void) +{ + psString version = streaksVersion(); // Version, to return + psString source = streaksSource(); // Source + + psStringPrepend(&version, "%s ", streaksProgram); + psStringAppend(&version, " from %s, built %s, %s", source, __DATE__, __TIME__); + psFree(source); + +#ifdef __OPTIMIZE__ + psStringAppend(&version, " optimised"); +#else + psStringAppend(&version, " unoptimised"); +#endif + + return version; +}; + +bool streaksVersionHeader(psMetadata *header) +{ + PS_ASSERT_METADATA_NON_NULL(header, false); + + psString version = streaksVersion(); // Software version + psString source = streaksSource(); // Software source + + psMetadataAddStr(header, PS_LIST_TAIL, "STREAK_V", PS_META_REPLACE, NULL, source); + + psStringPrepend(&version, "%s version: ", streaksProgram); + psStringPrepend(&source, "%s source: ", streaksProgram); + + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, version); + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, source); + + psFree(version); + psFree(source); + + return true; +} + +bool streaksVersionHeaderFull(psMetadata *header) +{ + PS_ASSERT_METADATA_NON_NULL(header, false); + + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now + psString timeString = psTimeToISO(time); // The time in an ISO string + psFree(time); + psString history = NULL; // History string + psStringAppend(&history, "%s at %s", streaksProgram, timeString); + psFree(timeString); + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, history); + psFree(history); + + psLibVersionHeader(header); + psModulesVersionHeader(header); + streaksVersionHeader(header); + + return true; +} + +void streaksVersionPrint(void) +{ + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now + psString timeString = psTimeToISO(time); // The time in an ISO string + psFree(time); + psLogMsg("streaks", PS_LOG_INFO, "%s at %s", streaksProgram, timeString); + psFree(timeString); + + psString pslib = psLibVersionLong();// psLib version + psString psmodules = psModulesVersionLong(); // psModules version + psString streaks = streaksVersionLong(); // streaks version + + psLogMsg("streaks", PS_LOG_INFO, "%s", pslib); + psLogMsg("streaks", PS_LOG_INFO, "%s", psmodules); + psLogMsg("streaks", PS_LOG_INFO, "%s", streaks); + + psFree(pslib); + psFree(psmodules); + psFree(streaks); + + return; +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksVersionDefinitions.h.in =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksVersionDefinitions.h.in (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksVersionDefinitions.h.in (revision 41117) @@ -0,0 +1,8 @@ +#ifndef STREAKS_VERSION_DEFINITIONS_H +#define STREAKS_VERSION_DEFINITIONS_H + +#define STREAKS_VERSION @STREAKS_VERSION@ // SVN version +#define STREAKS_BRANCH @STREAKS_BRANCH@ // SVN branch +#define STREAKS_SOURCE @STREAKS_SOURCE@ // SVN source + +#endif Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksastrom.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksastrom.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksastrom.c (revision 41117) @@ -0,0 +1,436 @@ +#include "streaksremove.h" + +static void freeAstrometry(strkAstrom *astrom) +{ + if (!astrom) { + return; + } + psFree(astrom->pt); +} + +// Initialize the astrometry object for current cell +strkAstrom * +streakSetAstrometry(strkAstrom *astrom, ippStage stage, pmFPA *fpa, pmChip *chip, bool fromCell, psMetadata *md, int numCols, int numRows) +{ + if (!astrom) { + astrom = psAlloc(sizeof(strkAstrom)); + psMemSetDeallocator(astrom, (psFreeFunc) freeAstrometry); + astrom->pt = pmAstromObjAlloc(); + } + astrom->fpa = fpa; + astrom->chip = chip; + + int cell_x0, cell_y0; + int xParityCell, yParityCell; + bool mdok; + + if (fromCell) { + // XXX: I think that this is not needed + // We are only asked to get the concepts from the cell when we're reading from a pmfile (skycell) + // In that case we (x0,y0) = (0,0) and the parirties are positive + // If the x0, y0 are not zero they are probably in the FITS unity based array format + // We should probably assert that these are zero + cell_x0 = psMetadataLookupS32(&mdok, md, "CELL.X0"); + if (!mdok) { + psError(PS_ERR_UNKNOWN, true, "CELL.X0 for cell is not set.\n"); + return NULL; + } + cell_y0 = psMetadataLookupS32(&mdok, md, "CELL.Y0"); + if (!mdok) { + psError(PS_ERR_UNKNOWN, true, "CELL.Y0 for cell is not set.\n"); + return NULL; + } + xParityCell = psMetadataLookupS32(&mdok, md, "CELL.XPARITY"); + if (!mdok || (xParityCell != 1 && xParityCell != -1)) { + psError(PS_ERR_UNKNOWN, true, "CELL.XPARITY for cell is not set.\n"); + return false; + } + yParityCell = psMetadataLookupS32(&mdok, md, "CELL.YPARITY"); + if (!mdok || (yParityCell != 1 && yParityCell != -1)) { + psError(PS_ERR_UNKNOWN, true, "CELL.YPARITY for cell is not set.\n"); + return false; + } + } else if (md && (stage == IPP_STAGE_RAW)) { + // The metadata is the raw header + // Assumes GPC1 + // + // Shouldn't these lookups be F32 ? + cell_x0 = psMetadataLookupS32(&mdok, md, "IMNPIX1"); + if (!mdok) { + psError(PS_ERR_UNKNOWN, true, "IMNPIX1 for cell is not set.\n"); + // return NULL; + } + cell_y0 = psMetadataLookupS32(&mdok, md, "IMNPIX2"); + if (!mdok) { + psError(PS_ERR_UNKNOWN, true, "IMNPIX2 for cell is not set.\n"); + return NULL; + } + + xParityCell = psMetadataLookupS32(&mdok, md, "ATM1_1"); + if (!mdok || (xParityCell != 1 && xParityCell != -1)) { + psError(PS_ERR_UNKNOWN, true, "CELL.XPARITY for cell is not set.\n"); + return false; + } + yParityCell = psMetadataLookupS32(&mdok, md, "ATM2_2"); + if (!mdok || (yParityCell != 1 && yParityCell != -1)) { + psError(PS_ERR_UNKNOWN, true, "CELL.YPARITY for cell is not set.\n"); + return false; + } + } else { + // no metadata regular cell + // used by warpedpixels + cell_x0 = 0; + cell_y0 = 0; + xParityCell = 1; + yParityCell = 1; + } + + astrom->cell_x0 = (double) cell_x0; + astrom->cell_y0 = (double) cell_y0; + // XXX: make sure we're applying cell parity correctly + // the mosaic code uses (xParityCell * xParityChip == xParityTarget) ? -1 : 1 + // (yParityCell * yParityChip == yParityTarget) ? -1 : 1 + // since the transform already accounts for the chip parity we just use the cell parity + astrom->xParity = (double) xParityCell; + astrom->yParity = (double) yParityCell; + + astrom->numCols = numCols; + astrom->numRows = numRows; + + return astrom; +} + + + +void +chipToCell(double *xCell, double *yCell, strkAstrom *astrom, double xChip, double yChip) +{ + // convert from chip to cell + if (astrom->xParity > 0) { + *xCell = xChip - astrom->cell_x0; + } else { + *xCell = astrom->cell_x0 - 1 - xChip; + } + if (astrom->yParity > 0) { + *yCell = yChip - astrom->cell_y0; + } else { + *yCell = astrom->cell_y0 - 1 - yChip; + } +} + +void +cellToChip(double *xChip, double *yChip, strkAstrom *astrom, double xCell, double yCell) +{ + if (astrom->xParity > 0) { + *xChip = xCell + astrom->cell_x0; + } else { + *xChip = astrom->cell_x0 - 1 - xCell; + } + if (astrom->yParity > 0) { + *yChip = yCell + astrom->cell_y0; + } else { + *yChip = astrom->cell_y0 - 1 - yCell; + } +} + +void +cellToChipInt(unsigned int *xChip, unsigned int *yChip, strkAstrom *astrom, int xCell, int yCell) +{ + if (astrom->xParity > 0) { + *xChip = xCell + astrom->cell_x0; + } else { + *xChip = astrom->cell_x0 - 1 - xCell; + } + if (astrom->yParity > 0) { + *yChip = yCell + astrom->cell_y0; + } else { + *yChip = astrom->cell_y0 - 1 - yCell; + } +} + +bool +SkyToLocal(strkPt *outPt, strkAstrom *astrom, double ra, double dec) +{ + // generate a local project using the RA, DEC of the 0,0 pixel of the chip as the + // projection center with the same plate scale as the nominal TP->Sky astrometry. + + pmFPA *fpa = (pmFPA *) astrom->fpa; + + // find the RA,DEC coords of the 0,0 pixel for this chip: + + psPlane ptTP; + psSphere ptSky; + + ptSky.r = ra; + ptSky.d = dec; + ptSky.rErr = 0.0; + ptSky.dErr = 0.0; + + psProject(&ptTP, &ptSky, fpa->toSky); + + outPt->x = ptTP.x; + outPt->y = ptTP.y; + + return true; +} + +bool +LocalToSky(strkPt *outPt, strkAstrom *astrom, strkPt *inPt) +{ + // generate a local project using the RA, DEC of the 0,0 pixel of the chip as the + // projection center with the same plate scale as the nominal TP->Sky astrometry. + + pmFPA *fpa = (pmFPA *) astrom->fpa; + + // find the RA,DEC coords of the 0,0 pixel for this chip: + + psPlane ptTP; + psSphere ptSky; + + ptTP.x = inPt->x; + ptTP.y = inPt->y; + ptTP.xErr = 0.0; + ptTP.yErr = 0.0; + + psDeproject(&ptSky, &ptTP, fpa->toSky); + + outPt->x = ptSky.r; + outPt->y = ptSky.d; + + return true; +} + +bool +componentBounds(int *minX, int *minY, int *maxX, int *maxY, strkAstrom *astrom, int numCols, int numRows) +{ + // find the bounds of the (padded) chip region in tangent-plane coordinates + + pmFPA *fpa = (pmFPA *) astrom->fpa; + pmChip *chip = (pmChip *) astrom->chip; + + psPlane ptCH, ptFP, TPo, TPx, TPy; + + // coordinate of the chip center: + ptCH.x = 0.5*numCols; + ptCH.y = 0.5*numRows; + psPlaneTransformApply(&ptFP, chip->toFPA, &ptCH); + psPlaneTransformApply(&TPo, fpa->toTPA, &ptFP); + + // coordinate of the chip center + dX/2: + ptCH.x = numCols; + ptCH.y = 0.5*numRows; + psPlaneTransformApply(&ptFP, chip->toFPA, &ptCH); + psPlaneTransformApply(&TPx, fpa->toTPA, &ptFP); + + // coordinate of the chip center + dY/2: + ptCH.x = 0.5*numCols; + ptCH.y = numRows; + psPlaneTransformApply(&ptFP, chip->toFPA, &ptCH); + psPlaneTransformApply(&TPy, fpa->toTPA, &ptFP); + + // half-lengths of the two sides in tangent-plane coords: + double xSize = hypot (TPx.x - TPo.x, TPx.y - TPo.y); + double ySize = hypot (TPy.x - TPo.x, TPy.y - TPo.y); + double radius = hypot (xSize, ySize); + + // define the region encompassed by the radius with some padding: + *minX = TPo.x - 1.1*radius; + *minY = TPo.y - 1.1*radius; + *maxX = TPo.x + 1.1*radius; + *maxY = TPo.y + 1.1*radius; + + return true; +} + +bool +skyToCell(strkPt *outPt, strkAstrom *astrom, double ra, double dec) +{ + pmFPA *fpa = (pmFPA *) astrom->fpa; + pmChip *chip = (pmChip *) astrom->chip; + pmAstromObj *pt = (pmAstromObj *) astrom->pt; + + pt->sky->r = ra; + pt->sky->d = dec; + pt->sky->rErr = 0; // Is setting these errors to zero the right thing to do? + pt->sky->dErr = 0; + + // convert from sky to TP to FP + psProject(pt->TP, pt->sky, fpa->toSky); + psPlaneTransformApply(pt->FP, fpa->fromTPA, pt->TP); + // convert from FP to chip + psPlaneTransformApply(pt->chip, chip->fromFPA, pt->FP); + + chipToCell(&outPt->x, &outPt->y, astrom, pt->chip->x, pt->chip->y); + +// printf("cell: %f %f chip: %f %f\n", outPt->x, outPt->y, pt->chip->x, pt->chip->y); + + return true; +} + +bool +cellToSky(strkPt *outPt, strkAstrom *astrom, double x, double y) +{ + pmFPA *fpa = (pmFPA *) astrom->fpa; + pmChip *chip = (pmChip *) astrom->chip; + pmAstromObj *pt = (pmAstromObj *) astrom->pt; + + cellToChip(&pt->chip->x, &pt->chip->y, astrom, x, y); + + pt->chip->xErr = 0; // Is setting these errors to zero the right thing to do? + pt->chip->yErr = 0; + + // chip to FP + psPlaneTransformApply(pt->FP, chip->toFPA, pt->chip); + // FP to TP to sky + psPlaneTransformApply(pt->TP, fpa->toTPA, pt->FP); + psDeproject(pt->sky, pt->TP, fpa->toSky); + + outPt->x = pt->sky->r; + outPt->y = pt->sky->d; + + return true; +} + + +static bool +readAstrometry(streakFiles *sf) +{ + pmHDU *phu = pmFPAviewThisPHU(sf->view, sf->inAstrom->fpa); + if (phu) { + bool status; + char *ctype = psMetadataLookupStr(&status, phu->header, "CTYPE1"); + if (ctype) { + sf->bilevelAstrometry = !strcmp (&ctype[4], "-DIS"); + } + } + + pmHDU *hdu = pmFPAviewThisHDU(sf->view, sf->inAstrom->fpa); + PS_ASSERT_PTR_NON_NULL(hdu, 1) + PS_ASSERT_PTR_NON_NULL(hdu->header, 1) + if (sf->bilevelAstrometry) { + if (!pmAstromReadBilevelMosaic(sf->inAstrom->fpa, phu->header)) { + psError(PS_ERR_UNKNOWN, false, "Unable to read bilevel mosaic astrometry for input FPA."); + return false; + } + if (!pmAstromReadBilevelChip (sf->chip, hdu->header)) { + psError(PS_ERR_UNKNOWN, false, "Unable to read bilevel chip astrometry for input FPA."); + return false; + } + } else { + + // we use a default FPA pixel scale of 1.0 + if (!pmAstromReadWCS (sf->inAstrom->fpa, sf->chip, hdu->header, 1.0)) { + psError(PS_ERR_UNKNOWN, false, "Unable to read WCS astrometry for input FPA."); + return false; + } + } + + return true; +} + +void +setupAstrometry(streakFiles *sf) +{ + bool status; + // load astrometry file + if (USE_SUPPLIED_ASTROM(sf->stage)) { + sf->inAstrom = pmFPAfileDefineFromArgs(&status, sf->config, "PSWARP.ASTROM", "ASTROM"); + } else { + // otherwise get astrometry from pmfile + if (!sf->inImage->pmfile) { + streaksExit("unexpected null pmFPAfile", PS_EXIT_CONFIG_ERROR); + } + sf->inAstrom = sf->inImage->pmfile; + } + sf->view = pmFPAviewAlloc(0); + + if (!pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_BEFORE)) { + psError(PS_ERR_UNKNOWN, false, "Failed to load input."); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + while ((sf->chip = pmFPAviewNextChip(sf->view, sf->inAstrom->fpa, 1))) { + if (sf->inAstrom->fpa->chips->n == 1) { + // There's only one chip in this FPA and we've got it so break + break; + } + bool status; + psString chip_name = psMetadataLookupStr(&status, sf->chip->concepts, "CHIP.NAME"); + if (!strcmp(chip_name, sf->class_id)) { + break; + } + } + if (!sf->chip) { + psError(PS_ERR_UNKNOWN, true, "Failed to find chip with data."); + streaksExit("", PS_EXIT_DATA_ERROR); + } + if (!pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_BEFORE)) { + psError(PS_ERR_UNKNOWN, false, "failed to load chip"); + streaksExit("", PS_EXIT_DATA_ERROR); + } + if (!readAstrometry(sf)) { + psError(PS_ERR_UNKNOWN, false, "failed to read astrometry"); + streaksExit("", PS_EXIT_DATA_ERROR); + } +} + +static void chipToSky(pmAstromObj *pt, pmFPA *fpa, pmChip *chip) +{ + // chip to FP + psPlaneTransformApply(pt->FP, chip->toFPA, pt->chip); + // FP to TP to sky + psPlaneTransformApply(pt->TP, fpa->toTPA, pt->FP); + psDeproject(pt->sky, pt->TP, fpa->toSky); +} + + +bool +linearizeTransforms(strkAstrom *astrom) +{ + pmFPA *inFPA = (pmFPA *) astrom->fpa; + pmChip *inChip = (pmChip *) astrom->chip; + + // compute ra and dec of chip center + pmAstromObj *center = pmAstromObjAlloc(); + center->chip->x = (double) astrom->numCols / 2.; + center->chip->xErr = 0; + center->chip->y = (double) astrom->numRows / 2.; + center->chip->yErr = 0; + + chipToSky(center, inFPA, inChip); + + psRegion bounds = {0, astrom->numCols - 1, 0, astrom->numRows - 1 }; + + // create skeleton containers for the linearized transforms; + pmFPA outFPA; + pmChip outChip; + + memset(&outFPA, 0, sizeof(outFPA)); + memset(&outChip, 0, sizeof(outChip)); + + outFPA.toSky = psProjectionAlloc (center->sky->r, center->sky->d, inFPA->toSky->Xs, inFPA->toSky->Ys, PS_PROJ_TAN); + + psFree(center); + + if (!pmAstromLinearizeToSky(inFPA, inChip, &outFPA, &outChip, &bounds)) { + psError(PS_ERR_UNKNOWN, false, "Failed to linearize astrometry\n"); + return false; + } + + psFree(inFPA->toSky); + inFPA->toSky = outFPA.toSky; + + psFree(inFPA->toTPA); + inFPA->toTPA = outFPA.toTPA; + + psFree(inFPA->fromTPA); + inFPA->fromTPA = outFPA.fromTPA; + + psFree(inChip->toFPA) + inChip->toFPA = outChip.toFPA; + + psFree(inChip->fromFPA); + inChip->fromFPA = outChip.fromFPA; + + return true; +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksastrom.h =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksastrom.h (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksastrom.h (revision 41117) @@ -0,0 +1,38 @@ +#ifndef STREAKSASTROM_H +#define STREAKSASTROM_H + +// Structure that encapsulates Astrometry +// Note: this file should have no dependence on ipp data types +// XXX: we might be able to remove this restrction. Paul S has +// used some of our datatypes in his code +// +typedef struct { + // opaque pointers to psModules types + void *pt; // pmAstromObj * + void *fpa; // pmFPA * + void *chip; // pmChip * + + double cell_x0; + double cell_y0; + double xParity; // 1 or -1 + double yParity; + int numCols; + int numRows; +} strkAstrom; + + +// XXX: Since Paul is including ipp headers perhaps we can replace uses of strkPt with psPlane +typedef struct { + double x; + double y; +} strkPt; + +extern bool skyToCell(strkPt *, strkAstrom *astrom, double ra, double dec); +extern bool cellToSky(strkPt *, strkAstrom *astrom, double x, double y); +extern bool linearizeTransforms(strkAstrom *astrom); + +extern bool SkyToLocal(strkPt *outPt, strkAstrom *astrom, double ra, double dec); +extern bool LocalToSky(strkPt *outPt, strkAstrom *astrom, strkPt *inPt); +extern bool componentBounds(int *minX, int *minY, int *maxX, int *maxY, strkAstrom *astrom, int numCols, int numRows); + +#endif // STREAKS_ASTROM_H Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streakscompare.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streakscompare.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streakscompare.c (revision 41117) @@ -0,0 +1,181 @@ +#include "streaksremove.h" + +char *streaksProgram = "streakscompare"; + +static pmConfig * parseArguments(int, char **); + +int main(int argc, char *argv[]) +{ + bool status; + + psLibInit(NULL); + + pmConfig *config = parseArguments(argc, argv); + if (!config) { + streaksExit("failed to parse arguments", PS_EXIT_CONFIG_ERROR); + } + + ippStage stage = psMetadataLookupS32(&status, config->arguments, "STAGE"); + + sFile *file1 = sFileOpen(config, stage, "INPUT1", NULL, true, false); + sFile *file2 = sFileOpen(config, stage, "INPUT2", NULL, true, false); + + int ncomponents; + if (stage == IPP_STAGE_RAW) { + if (file1->nHDU != file2->nHDU) { + streaksExit("mages do not have same number of components\n", PS_EXIT_DATA_ERROR); + } + if (!(psFitsMoveExtNum(file1->fits, 1, true) && psFitsMoveExtNum(file2->fits, 1, true))) { + streaksExit("failed to skip primary header of raw file\n", PS_EXIT_DATA_ERROR); + } + ncomponents = file1->nHDU - 1; + } else { + ncomponents = 1; + } + + int numErrors = 0; + for (int component = 0; component < ncomponents; component++) { + if (component && !(psFitsMoveExtNum(file1->fits, 1, true) + && psFitsMoveExtNum(file2->fits, 1, true))) { + streaksExit("failed to advance to next extesion\n", PS_EXIT_DATA_ERROR); + } + readImage(file1, 0, stage, false); + readImage(file2, 0, stage, false); + + psImage *image1 = file1->image; + psImage *image2 = file2->image; + + // TODO: do more sanity checking. For example check that extname's (if any) match + // check for matching image cubes + if (image1 && image2) { + if ((image1->numRows != image2->numRows) || (image1->numCols != image2->numCols)) { + streaksExit("image sizes do not match\n", PS_EXIT_DATA_ERROR); + } + int width = image1->numCols; + int height = image1->numRows; + for (int y = 0; y < height; y++) { + for (int x = 0; x < width; x++) { + bool error = false; + + double value1 = psImageGet(image1, x, y); + double value2 = psImageGet(image1, x, y); + + if (!isnan(value1) && !isnan(value2)) { + if (value1 != value2) { + error = true; + } + } else { + // if one's a nan they had both better be + error = ! isnan(value1) && isnan(value2); + } + + if (error) { + numErrors++; + fprintf(stderr, "pixel at %5d %5d do not match %f %f\n", x, y, value1, value2); + } + } + } + } else if (! ((image1 == NULL) && (image2 == NULL))) { + // if one image is null (video extension) both should be + streaksExit("image1 null but not image2!", PS_EXIT_DATA_ERROR); + } + } + + fprintf(stderr, "%d errors\n", numErrors); + + closeImage(file1); + closeImage(file2); + + psFree(config); + psLibFinalize(); + + fprintf(stderr, "Found %d leaks at %s\n", psMemCheckLeaks (0, NULL, NULL, false), "streakscompare"); + + // PAU + return 0; +} +static void usage(void) +{ + fprintf(stderr, "USAGE: streakscompare file1 file2\n"); + + exit(2); +} + +static pmConfig *parseArguments(int argc, char **argv) +{ + int argnum; + + pmConfig *config = pmConfigRead(&argc, argv, NULL); + if (!config) { + return NULL; + } + + ippStage stage = IPP_STAGE_NONE; + if ((argnum = psArgumentGet(argc, argv, "-stage"))) { + psArgumentRemove(argnum, &argc, argv); + stage = parseStage(argv[argnum]); + psMetadataAddS32(config->arguments, PS_LIST_TAIL, "STAGE", 0, + "pipeline stage for streak removal", stage); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-stage is required\n"); + usage(); + } + + // If we are asked to replace inputs with the outputs and input image is in nebulous + // we require mask, weight, and tmproot to all be + bool nebulousImage = false; + if ((argnum = psArgumentGet(argc, argv, "-image1"))) { + // for raw and chip level images we use psFits for I/O and ... + nebulousImage = IN_NEBULOUS(argv[argnum+1]); + if (CHIP_LEVEL_INPUT(stage)) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT1", 0, + "name of input image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + // ... for warped images we use pmFPAfiles + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "INPUT1", "-image1", NULL)) { ; + psError(PS_ERR_UNKNOWN, false, "failed to process -image"); + usage(); + } + } + } else { + psError(PS_ERR_UNKNOWN, true, "-image1 is required\n"); + usage(); + } + if ((argnum = psArgumentGet(argc, argv, "-image2"))) { + // for raw and chip level images we use psFits for I/O and ... + nebulousImage = IN_NEBULOUS(argv[argnum+1]); + if (CHIP_LEVEL_INPUT(stage)) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT2", 0, + "name of input image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + // ... for warped images we use pmFPAfiles + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "INPUT2", "-image2", NULL)) { ; + psError(PS_ERR_UNKNOWN, false, "failed to process -image"); + usage(); + } + } + } else { + psError(PS_ERR_UNKNOWN, true, "-image2 is required\n"); + usage(); + } + + if (nebulousImage) { /* do something? */ } + + if (argc != 1) { + psString unexpectedArguments = NULL; + for (int i=1; i + +/* psLib includes */ + +#include "psMemory.h" + +/* streakremove includes */ + +#include "streaksextern.h" +#include "Line.h" + +/** Create a list of pixel positions from a Streaks pointer list + converting the equatorial coordinates into the pixel coordinates + using strkAstrom and building streak pixels using the specified + width and store in StreakPixels object returned + + @param[in] streaks List of streak pointer objects to convert to + pixel positions output in StreakPixels + @param[in] astrom Astrometry object for converting streak equatorial + coordinates into pixel positions + @param[in] numCols number of columns in the image to map streak equatorial + coordinates into pixel positions + @param[in] numRows number of rows in the image to map streak equatorial + coordinates into pixel positions + @return list of PixelPos pointers for the streaks mapped to the image + pixels +*/ + +StreakPixels *streak_on_component(Streaks *streaks, strkAstrom *astrom, + int numCols, int numRows) +{ + int i; + Line line; + StreakPixels *pixels = psImageAlloc(numCols, numRows, PS_TYPE_U8); + psImageInit(pixels, 0); + int streaksOnComponent = 0; + + int minX, minY, maxX, maxY; + + // find the chip dimensions in the tangent-plane coordinates (length of hypotenuse) + componentBounds (&minX, &minY, &maxX, &maxY, astrom, numCols, numRows); + + for (i = 0; i != streaks->size; ++i) + { + /* Convert streak equatorial coordinates into pixel based line */ + + line.width = streaks->list[i].width; + + /* Use tangent plane coordinates to narrow down the ra,dec range of the line closer to + * the chip boundaries. Use these new ra,dec positions to generate the line on the + * chip using the full non-linear astrometry */ + + // project the ends of the line using a linear projection centered on the chip center: + Line full; + SkyToLocal (&full.begin, astrom, streaks->list[i].ra1, streaks->list[i].dec1); + SkyToLocal (&full.end, astrom, streaks->list[i].ra2, streaks->list[i].dec2); + + // clip the line to a square box with diameter = hypotenuse of the chip image centerd + // on the chip center in tangent-plane coordinates. skip the rest of this streak if + // the line does not intersect this region + if (!LineClipFull (&full, minX, minY, maxX, maxY)) { + continue; + } + + // convert the end points back into ra, dec pairs: + strkPt sky1, sky2; + LocalToSky (&sky1, astrom, &full.begin); + LocalToSky (&sky2, astrom, &full.end); + + if (skyToCell (&line.begin, astrom, sky1.x, sky1.y) && + skyToCell (&line.end, astrom, sky2.x, sky2.y) && + LineClip (&line, numCols, numRows)) + { + PixelsFromLine (pixels, &line, numCols, numRows); + streaksOnComponent++; + } + } + fprintf(stderr, "%d streaks on this component\n", streaksOnComponent); + return pixels; +} + +static void streaksFree(Streaks *streaks); + +/** Read a list of streak equatorial coordinate definitions and width + from a text file. The format is: + + @verbatim + numStreaks + ra1 dec1 ra2 dec2 width + ... + @endverbatim + + @param[in] fileName path to streak text file to read + @return a list of streak objects. If there is an error in reading + the text file, return NULL +*/ + +Streaks *readStreaksFile(char *fileName) +{ + int i; + Streaks *streaks = NULL; + FILE *file = fopen (fileName, "r"); + if (file != NULL) + { + streaks = psAlloc (sizeof(Streaks)); + if (fscanf (file, "%u", &streaks->size) != 1) + { + psFree (streaks); + fclose (file); + return NULL; + } + streaks->list = psAlloc (streaks->size * sizeof(streak)); + psMemSetDeallocator(streaks, (psFreeFunc) streaksFree); + for (i = 0; i != streaks->size; ++i) + { + if (fscanf (file, "%lf %lf %lf %lf %lf", + &streaks->list[i].ra1, &streaks->list[i].dec1, + &streaks->list[i].ra2, &streaks->list[i].dec2, + &streaks->list[i].width) != 5) + { + psFree (streaks->list); + psFree (streaks); + streaks = NULL; + break; + } + } + fclose (file); + } + return streaks; +} + +static void streaksFree(Streaks *streaks) +{ + psFree(streaks->list); +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksextern.h =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksextern.h (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksextern.h (revision 41117) @@ -0,0 +1,75 @@ +#ifndef STREAKSEXTERN_H +#define STREAKSEXTERN_H + +/** psLib includes */ + +#include "psImage.h" + +/** streakremove includes */ + +#include "streaksastrom.h" + +/** Equatorial coordinates of streak endpoints in radians */ + +typedef struct { + double ra1; + double dec1; + double ra2; + double dec2; + double width; /**< Width of streak in pixels */ +} streak; + +/** List of streak objects to map to image pixel positions */ + +typedef struct { + unsigned int size; + streak *list; +} Streaks; + +/** Pixel position within an image */ + +typedef struct { + unsigned int x; /**< X (column) pixel position */ + unsigned int y; /**< Y (row) pixel position */ +} PixelPos; + +/** For now, use psArray to define a list of PixelPos pointers */ + +typedef psImage StreakPixels; + +/** Create a list of pixel positions from a Streaks pointer list + converting the equatorial coordinates into the pixel coordinates + using strkAstrom and building streak pixels using the specified + width and store in StreakPixels object returned + + @param[in] streaks List of streak pointer objects to convert to + pixel positions output in StreakPixels + @param[in] astrom Astrometry object for converting streak equatorial + coordinates into pixel positions + @param[in] numCols number of columns in the image to map streak equatorial + coordinates into pixel positions + @param[in] numRows number of rows in the image to map streak equatorial + coordinates into pixel positions + @return list of PixelPos pointers for the streaks mapped to the image + pixels +*/ + +extern StreakPixels *streak_on_component(Streaks *streaks, strkAstrom *astrom, + int numCols, int numRows); + +/** Read a list of streak equatorial coordinate definitions and width + from a text file. The format is: + + @verbatim + numStreaks + ra1 dec1 ra2 dec2 width + @endverbatim + + @param[in] fileName path to streak text file to read + @return a list of streak objects. If there is an error in reading + the text file, return NULL +*/ + +extern Streaks *readStreaksFile(char *fileName); + +#endif /* STREAKSEXTERN_H */ Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksio.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksio.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksio.c (revision 41117) @@ -0,0 +1,1338 @@ +#include "streaksremove.h" +#include "libgen.h" +#include "unistd.h" + +static void sFileFree(sFile *sfile); +static void streakFilesFree(streakFiles *sf); +static void freeImages(streakFiles *); +static void setExciseValue(sFile *in); + +static nebServer *ourNebServer = NULL; + +// Assumptions about the file structure of non-raw files +// The 'image' for each file (image, mask weight) is contained in the first +// extension. + + +// open the files required for streaks procesing. +// if remove is true the calling program is streaksremove and the recovery files are outputs +// if false the recovery files are inputs +streakFiles *openFiles(pmConfig *config, bool remove, char *program_name) +{ + bool status; + streakFiles *sf = psAlloc(sizeof(streakFiles)); + psMemSetDeallocator(sf, (psFreeFunc) streakFilesFree); + memset(sf, 0, sizeof(*sf)); + + sf->config = config; + sf->program_name = basename(program_name); + + if (remove) { + // remember pointer so that streaksExit can delete temps + setStreakFiles(sf); + } + + + // error checking is done by sFileOpen. If a file can't be opened we just exit + ippStage stage = psMetadataLookupS32(&status, config->arguments, "STAGE"); + + sf->stage = stage; + sf->extnum = 0; + + sf->class_id = psMetadataLookupStr(&status, config->arguments, "CLASS_ID"); + + sf->inImage = sFileOpen(config, stage, "INPUT", NULL, true, false); + sf->nHDU = sf->inImage->nHDU; + + // don't need to free inputBasename see basename(3) + // The names of the temporary and recovery files are taken from the input + char *inputBasename = basename(sf->inImage->name); + sf->outImage = sFileOpen(config, stage, "OUTPUT", inputBasename, true, true); + + if (remove) { + // XXX: the recovery file should be required if stage is raw and the replace flag is set + // that is if the input raw image is to be destroyed + sf->recImage = sFileOpen(config, stage, "RECOVERY", inputBasename, false, false); + } else { + sf->recImage = sFileOpen(config, stage, "RECOVERY.IMAGE", NULL, true, false); + } + + sf->inMask = sFileOpen(config, stage, "INPUT.MASK", NULL, false, false); + if (sf->inMask && (sf->stage != IPP_STAGE_RAW)) { + inputBasename = basename(sf->inMask->name); + sf->outMask = sFileOpen(config, stage, "OUTPUT", inputBasename, true, true); + if (remove) { + sf->recMask = sFileOpen(config, stage, "RECOVERY", inputBasename, false, false); + } else { + sf->recMask = sFileOpen(config, stage, "RECOVERY.MASK", NULL, true, false); + } + } + // If we're in streaksremove and operating on a chip stage image + // if we are passed a mask it is camera stage mask and we also + // need to destreak the chip level mask file as well + // If it doesn't exist, we didn't have a camera mask + if (remove && sf->inMask && (stage == IPP_STAGE_CHIP)) { + sf->inChMask = sFileOpen(config, stage, "INPUT.CHMASK", NULL, false, false); + if (sf->inChMask) { + inputBasename = basename(sf->inChMask->name); + sf->outChMask = sFileOpen(config, stage, "OUTPUT", inputBasename, true, true); + sf->recChMask = sFileOpen(config, stage, "RECOVERY", inputBasename, false, false); + } + } + + sf->inWeight = sFileOpen(config, stage, "INPUT.WEIGHT", NULL, false, false); + if (sf->inWeight) { + inputBasename = basename(sf->inWeight->name); + sf->outWeight = sFileOpen(config, stage, "OUTPUT", inputBasename, true, true); + if (remove) { + sf->recWeight = sFileOpen(config, stage, "RECOVERY", inputBasename, false, false); + } else { + sf->recWeight = sFileOpen(config, stage, "RECOVERY.WEIGHT", NULL, true, false); + } + } + if (remove) { + sf->inSources = sFileOpen(config, stage, "SOURCES", NULL, false, false); + if (sf->inSources) { + inputBasename = basename(sf->inSources->name); + sf->outSources = sFileOpen(config, stage, "OUTPUT", inputBasename, true, true); + } + } + + psElemType tileType; // Type corresponding to "long" + if (sizeof(long) == sizeof(psS64)) { + tileType = PS_TYPE_S64; + } else if (sizeof(long) == sizeof(psS32)) { + tileType = PS_TYPE_S32; + } else { + psAbort("can't map (long) type to a psLib type"); + } + + sf->tiles = psVectorAlloc(3, tileType); // Tile sizes + if (tileType == PS_TYPE_S64) { + sf->tiles->data.S64[0] = 0; + sf->tiles->data.S64[1] = 1; + sf->tiles->data.S64[2] = 1; + } else { + sf->tiles->data.S32[0] = 0; + sf->tiles->data.S32[1] = 1; + sf->tiles->data.S32[2] = 1; + } + + sf->transparentStreaks = psMetadataLookupF64(&status, config->arguments, "TRANSPARENT_STREAKS"); + + return sf; +} + +static void +streakFilesFree(streakFiles *sf) +{ + freeImages(sf); + psFree(sf->stats); + psFree(sf->diffedPixels); + psFree(sf->tiles); + psFree(sf->view); + psFree(sf->astrom); +} + + +// getNebServer() +// +// it gets created the first time a nebulous file is accessed. +// if config is passed in we are to create it and exit if not able. +// if config is null we return NULL indicating that there are no nebulous files in use +// The purpose of this is to avoid passing extra arguments between all of the functions. +// but it is probably a bad idea. +// +static nebServer *getNebServer(pmConfig *config) +{ + if (ourNebServer) { + return ourNebServer; + } + + if (!config) { + return NULL; + } + + psString serverURI = getenv("NEB_SERVER"); + + // XXX: Note: all of the flags to psError should be true, but I don't think nebclient + // uses psError + if (!serverURI) { + bool status; + serverURI = psMetadataLookupStr(&status, config->site, "NEB_SERVER"); + if (!status) { + psError(PM_ERR_CONFIG, true, "failed to lookup config value for NEB_SERVER."); + streaksExit("", PS_EXIT_CONFIG_ERROR); + } + } + + if (!serverURI) { + psError(PM_ERR_CONFIG, true, "Could not determine nebulous server URI."); + + streaksExit("", PS_EXIT_CONFIG_ERROR); + } + + ourNebServer = nebServerAlloc(serverURI); + if (!ourNebServer) { + psError(PM_ERR_SYS, true, "failed to create a nebServer object from %s.", serverURI); + streaksExit("", PS_EXIT_CONFIG_ERROR); + } + + return ourNebServer; +} + +// figure out if a nebulous instance is a non-destreaked file +static bool +nebFileIsDestreaked(sFile *sfile) +{ + if (!sfile->resolved_name) { + psError(PS_ERR_PROGRAMMING, true, "resolved name is null"); + return false; + } + psFits *fits = psFitsOpen(sfile->resolved_name, "r"); + if (!fits) { + psError(PS_ERR_IO, true, "failed open %s", sfile->name); + // can't tell if it is a destreaked file + return false; + } + psMetadata *header = psFitsReadHeader(NULL, fits); + if (!header) { + psError(PS_ERR_IO, true, "failed to read header for: %s", sfile->name); + return false; + } + bool mdok; + bool isDestreaked = psMetadataLookupBool(&mdok, header, "PSDESTRK"); + if (mdok && isDestreaked) { + return true; + } else { + psError(PS_ERR_IO, false, "output file already exists and may not be de-streaked: %s", sfile->name); + return false; + } +} + +static psString +resolveFilename(pmConfig *config, sFile *sfile, bool create, bool checkIfDestreaked) +{ + sfile->inNebulous = IN_NEBULOUS(sfile->name); + + if (sfile->inNebulous) { + // make sure we have our neb server connection + nebServer *server = getNebServer(config); + if (create) { + // delete the existing file, since there may be more than one + // instance. It will get created below in pmConfigConvertFilename + if ((sfile->resolved_name = nebFind(server, sfile->name)) != NULL) { + if (checkIfDestreaked && !nebFileIsDestreaked(sfile)) { + psError(PS_ERR_IO, false, "attempting to delete file that has not been destreaked %s", sfile->name); + return NULL; + } + nebFree(sfile->resolved_name); + sfile->resolved_name = NULL; + nebDelete(server, sfile->name); + } + } + } + + return pmConfigConvertFilename(sfile->name, config, create, create); +} + +sFile *sFileOpen(pmConfig *config, ippStage stage, psString fileSelect, + psString outputFilename, bool required, bool checkIfDestreaked) +{ + bool status; + sFile *sfile = psAlloc(sizeof(sFile)); + memset(sfile, 0, sizeof(sFile)); + + // We use psFits directly to read the image unless the stage is warp + // or diff. In those cases we use the pmFPAfile functions to read the image file + // to make managing the astrometry easy. + // The reason we don't use pmFPAfile in all cases is that I was having trouble getting + // all of the keywords in the raw image files written to the output destreaked files + + if (!outputFilename && !CHIP_LEVEL_INPUT(stage) && !strcmp(fileSelect, "INPUT")) { + // stage is warp or diff AND fileSelect eq "INPUT" + // get data from pmFPAfile. + + // we need to know what the nebulous and real filenames are so we steal + // some code from pmFPAfileDefineFromArgs + // XXX: create a pmFPAfile function that does this and use it there + psArray *infiles = psMetadataLookupPtr(&status, config->arguments, "INPUT"); + if (!status) { + psError(PS_ERR_PROGRAMMING, false, "INPUT not found in config->arguments"); + streaksExit("", PS_EXIT_PROG_ERROR); + } + if (infiles->n != 1) { + psError(PS_ERR_IO, false, "Found n == %ld files in %s in arguments expencted 1\n", + infiles->n, "INPUT"); + streaksExit("", PS_EXIT_DATA_ERROR); + } + // end of file name lookup code adapted from pmFPAfileDefineFromArgs + // + sfile->name = psStringCopy(infiles->data[0]); + sfile->inNebulous = IN_NEBULOUS(sfile->name); + + // XXX: I should probably be using a different file rule for diffs, but I don't + // have an input rule that takes a diff image. + // Since they're skycells, this should be compatible + sfile->pmfile = pmFPAfileDefineFromArgs(&status, config, "PPSUB.INPUT", "INPUT"); + if (!sfile->pmfile) { + psError(PS_ERR_IO, false, "Failed to define file for %s", fileSelect); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + pmFPAview *view = pmFPAviewAlloc(0); + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + psError(PS_ERR_UNKNOWN, false, "Failed to load input."); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(view); + sfile->resolved_name = psStringCopy(sfile->pmfile->filename); + + sfile->nHDU = psFitsGetSize(sfile->pmfile->fits); + + // copy header from fpu + sfile->header = (psMetadata*) psMemIncrRefCounter(sfile->pmfile->fpa->hdu->header); + + return sfile; + } + + // For all other files we use using psFits for i/o + + psString name = psMetadataLookupStr(&status, config->arguments, fileSelect); + if (!status || !name) { + sFileFree(sfile); + if (required) { + psError(PS_ERR_IO, false, "Failed to lookup name for %s", fileSelect); + streaksExit("", 1); + } + return NULL; + } + + // if outputFilename is not null name it contains the "directory" (perhaps with a prefix like SR_) + // and outputFilename is the basename name of the file (or nebulous key) + // and the file is to be opened for writing + if (outputFilename) { + sfile->write = true; + psStringAppend(&sfile->name, "%s%s", name, outputFilename); + sfile->resolved_name = resolveFilename(config, sfile, true, checkIfDestreaked); + if (!sfile->resolved_name) { + psError(PS_ERR_IO, false, "Failed to resolve filename for %s", sfile->name); + sFileFree(sfile); + streaksExit("", 1); + } + sfile->fits = psFitsOpen(sfile->resolved_name, "w"); + if (sfile->fits) { + sfile->fits->options = psFitsOptionsAlloc(); + } + } else { + sfile->name = psStringCopy(name); + sfile->resolved_name = resolveFilename(config, sfile, false, false); + if (!sfile->resolved_name) { + psError(PS_ERR_IO, false, "Failed to resolve name for %s", sfile->name); + sFileFree(sfile); + streaksExit("", 1); + } + sfile->fits = psFitsOpen(sfile->resolved_name, "r"); + if (sfile->fits) { + sfile->nHDU = psFitsGetSize(sfile->fits); + } + } + + if (!sfile->fits) { + psError(PS_ERR_IO, false, "failed to open fits file %s for %s", + sfile->resolved_name, outputFilename ? "writing" : "reading"); + sFileFree(sfile); + streaksExit("", 1); + } + + return sfile; +} + + +static bool +moveExt(sFile *sfile, int extnum) +{ + bool status = psFitsMoveExtNum(sfile->fits, extnum, false); + if (!status) { + psError(PS_ERR_IO, false, + "failed to move to extension %d for %s", extnum, sfile->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + return true; +} + +bool +streakFilesNextExtension(streakFiles *sf) +{ + // unless stage is raw when we get here we're done + if (sf->stage != IPP_STAGE_RAW) { + if (sf->view) { + sf->view->readout = -1; + pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER); + sf->view->cell = -1; + pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER); + sf->view->chip = -1; + pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER); + } + return false; + } + + ++sf->extnum; + if (sf->nHDU == 1) { + // return true the first time through + return (sf->extnum == 1); + } + if (sf->extnum < sf->nHDU) { + moveExt(sf->inImage, sf->extnum); + // No mask and weight images for raw stage + return true; + } else { + // we're all done + return false; + } +} + +void +addDestreakKeyword(psMetadata *header, bool value) +{ + psMetadataAddBool(header, PS_LIST_TAIL, "PSDESTRK", PS_META_REPLACE, + "Have streaks been removed from image?", value); +} + +void +addRecoveryKeyword(psMetadata *header) +{ + psMetadataAddBool(header, PS_LIST_TAIL, "PSRECOVR", PS_META_REPLACE, + "Does this image contain excised streak pixels?", true); +} + +void +copyPHU(streakFiles *sfiles, bool remove, bool destreak) +{ + psAssert(sfiles->stage == IPP_STAGE_RAW, "copyPHU should only be used for raw stage"); + + psMetadata *imageHeader = psFitsReadHeader(NULL, sfiles->inImage->fits); + if (!imageHeader) { + psError(PS_ERR_IO, false, "failed to read primary header from %s\n", + sfiles->inImage->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psMetadata *recHeader = NULL; + if (remove && sfiles->recImage) { + recHeader = psMetadataCopy(NULL, imageHeader); + addRecoveryKeyword(recHeader); + } + + // add keyword indicating that streaks have been removed + addDestreakKeyword(imageHeader, destreak); + + if (!psFitsWriteBlank(sfiles->outImage->fits, imageHeader, NULL)) { + psError(PS_ERR_IO, false, "failed to write primary header to %s", + sfiles->outImage->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + if (recHeader && !psFitsWriteBlank(sfiles->recImage->fits, recHeader, NULL)) { + psError(PS_ERR_IO, false, "failed to write primary header to %s", + sfiles->recImage->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(recHeader); + recHeader = NULL; + psFree(imageHeader); + + sFile *inMask = sfiles->inMask; + if (inMask && sfiles->outMask) { + psMetadata *maskHeader = psFitsReadHeader(NULL, inMask->fits); + if (!maskHeader) { + psError(PS_ERR_IO, false, "failed to read primary header from %s\n", + sfiles->inMask->resolved_name); + streaksExit("", 1); + } + if (remove && sfiles->recMask) { + recHeader = psMetadataCopy(NULL, maskHeader); + // add keyword indicating that this is the recovery image + addRecoveryKeyword(recHeader); + } + // add keyword indicating that streaks have been removed + addDestreakKeyword(maskHeader, destreak); + if (!psFitsWriteBlank(sfiles->outMask->fits, maskHeader, NULL)) { + psError(PS_ERR_IO, false, "failed to write primary header to %s", + sfiles->outMask->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + if (recHeader && !psFitsWriteBlank(sfiles->recMask->fits, recHeader, NULL)) { + psError(PS_ERR_IO, false, "failed to write primary header to %s", + sfiles->recMask->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(recHeader); + recHeader = NULL; + psFree(maskHeader); + } + sFile *inWeight = sfiles->inWeight; + if (inWeight) { + psMetadata *weightHeader = psFitsReadHeader(NULL, inWeight->fits); + if (!weightHeader) { + psError(PS_ERR_IO, false, "failed to read primary header from %s\n", + sfiles->inWeight->resolved_name); + streaksExit("", 1); + } + if (remove && sfiles->recWeight) { + recHeader = psMetadataCopy(NULL, weightHeader); + // add keyword indicating that this is a recovery image + addRecoveryKeyword(recHeader); + } + + // add keyword indicating that streaks have been removed + addDestreakKeyword(weightHeader, destreak); + if (!psFitsWriteBlank(sfiles->outWeight->fits, weightHeader, NULL)) { + psError(PS_ERR_IO, false, "failed to write primary header to %s", + sfiles->outWeight->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + if (recHeader && !psFitsWriteBlank(sfiles->recWeight->fits, recHeader, NULL)) { + psError(PS_ERR_IO, false, "failed to write primary header to %s", + sfiles->recWeight->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(weightHeader); + psFree(recHeader); + } +} + +// Determine whether the current header for this file is an image or not +// Find a cleaner way to do this +static bool +isImage(sFile *in) +{ + bool status; + psString exttype = psMetadataLookupStr(&status, in->header, "EXTTYPE"); + if (exttype && !strcmp(exttype, "IMAGE")) { + return true; + } + // examine current header and determine if it is an image + psString xtension = psMetadataLookupStr(&status, in->header, "XTENSION"); + if (xtension) { + if (!strcmp(xtension, "IMAGE")) { + return true; + } else if (!strcmp(xtension, "BINTABLE")) { + psString ztension = psMetadataLookupStr(&status, in->header, "ZTENSION"); + if (ztension && !strcmp(ztension, "IMAGE")) { + return true; + } + } + } else if (psMetadataLookupBool(&status, in->header, "ZIMAGE")) { + return true; + } else if (in->nHDU == 1) { + // no extensions in the file, can just return true? For now require + // at least one dimension + int naxis = psMetadataLookupS32(&status, in->header, "NAXIS"); + return naxis > 0; + } + return false; +} + +void +readImageFrom_pmFile(streakFiles *sf) +{ + // XXX: This function assumes that it is only used for a single + // chip single cell FPA (i.e. a skycell) + assert(sf->inImage->pmfile->fpa->chips->n == 1); + + pmFPAview *view = sf->view; + if (view) { + // The view was allocated and the chip set by setupAstrometry() + assert(view->chip == 0); + } else { + sf->view = pmFPAviewAlloc(0); + view = sf->view; + sf->chip = pmFPAviewNextChip(view, sf->inImage->pmfile->fpa, 1); + assert(sf->chip != NULL); + } + view->cell = 0; + sf->cell = pmFPAviewThisCell(view, sf->inImage->pmfile->fpa); + + if (!sf->cell) { + streaksExit("no cells found in chip", PS_EXIT_PROG_ERROR); + } + if (sf->cell->readouts->n != 1) { + psError(PS_ERR_PROGRAMMING, true, "unexpected number of readouts found: %ld", sf->cell->readouts->n); + streaksExit("", PS_EXIT_PROG_ERROR); + } + view->readout = 0; + pmReadout *readout = pmFPAviewThisReadout(view, sf->inImage->pmfile->fpa); + if (!readout) { + streaksExit("readout 0 not found", PS_EXIT_PROG_ERROR); + } + + sf->inImage->image = (psImage*) psMemIncrRefCounter(readout->image); + sf->inImage->numCols = readout->image->numCols; + sf->inImage->numRows = readout->image->numRows; + setExciseValue(sf->inImage); +} + +static void +setDataExtent(ippStage stage, sFile *in, bool rawImage) +{ + if (rawImage) { + psString datasec = psMetadataLookupStr(NULL, in->header, "DATASEC"); + if (!datasec) { + psError(PS_ERR_IO, false, "failed to find DATASEC in header"); + streaksExit("", PS_EXIT_DATA_ERROR); + } + int xmin, xmax, ymin, ymax; + sscanf(datasec, "[%d:%d,%d:%d]", &xmin, &xmax, &ymin, &ymax); + + // I've inadvertantly introduced an implicit assumption that cell coordinates + // are the same as image coordinates. This is true for GPC1 + // Test for this condition not being true + if (xmin != 1) { + psError(PS_ERR_IO, true, "can't handle datasec with minimum x != 1: %s", datasec); + streaksExit("", PS_EXIT_PROG_ERROR); + } + if (ymin != 1) { + psError(PS_ERR_IO, true, "can't handle datasec with minimum y != 1: %s", datasec); + streaksExit("", PS_EXIT_PROG_ERROR); + } + + // These values are different than the size of the actual image which includes + // the bias area. + in->numCols = xmax - xmin + 1; + in->numRows = ymax - ymin + 1; + } else { + in->numCols = in->image->numCols; + in->numRows = in->image->numRows; + } +} + +void +readImage(sFile *in, int extnum, ippStage stage, bool isMask) +{ + psRegion region = {0, 0, 0, 0}; + + if (in->header) psFree(in->header); + if (in->image) { + psFree(in->image); + in->image = NULL; + } + if (in->imagecube) { + psFree(in->imagecube); + in->imagecube = NULL; + } + + in->header = psFitsReadHeader(NULL, in->fits); + if (!in->header) { + psError(PS_ERR_IO, false, "failed to read header from %s extnum: %d", + in->resolved_name, extnum); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + bool status; + in->extname = psMetadataLookupStr(&status, in->header, "EXTNAME"); + + if (!isImage(in)) { + psLogMsg("streaksremove", PS_LOG_INFO, "%s contains no image\n", in->name); + return; + } + + in->numZPlanes = psMetadataLookupS32(NULL, in->header, "NAXIS3"); + + if (in->numZPlanes == 0) { + in->image = psFitsReadImage(in->fits, region, 0); + if (!in->image) { + psError(PS_ERR_IO, false, "failed to read image from %s extnum: %d", + in->resolved_name, extnum); + streaksExit("", PS_EXIT_DATA_ERROR); + } + setExciseValue(in); + } else { + if (stage != IPP_STAGE_RAW) { + psError(PS_ERR_PROGRAMMING, true, "unexpected image cube found in non-raw image"); + streaksExit("", PS_EXIT_PROG_ERROR); + } + in->imagecube = psFitsReadImageCube(in->fits, region); + if (!in->imagecube) { + psError(PS_ERR_IO, false, "failed to read image cube from %s extnum: %d", + in->resolved_name, extnum); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + // Ensure input is of the expected type + psElemType expected = isMask ? PS_TYPE_IMAGE_MASK : PS_TYPE_F32; // Expected type for image + for (int i = 0; i < in->imagecube->n; i++) { + psImage *image = in->imagecube->data[i]; // Image of interest + if (image->type.type != expected) { + psImage *temp = psImageCopy(NULL, image, expected); + psFree(image); + in->imagecube->data[i] = temp; + } + } + } + setDataExtent(stage, in, (stage == IPP_STAGE_RAW) && !isMask); +} + +static void +setFitsOptions(sFile *sfile, int bitpix, float bscale, float bzero, psFitsCompressionType compType, + psVector *tiles) +{ + if (!sfile || !sfile->write) { + return; + } + if (sfile->fits->options) { + psFree(sfile->fits->options); + } + sfile->fits->options = psFitsOptionsAlloc(); + sfile->fits->options->scaling = PS_FITS_SCALE_MANUAL; + sfile->fits->options->fuzz = false; + sfile->fits->options->bitpix = bitpix; + sfile->fits->options->bscale = bscale; + sfile->fits->options->bzero = bzero; + + psFitsSetCompression(sfile->fits, compType, tiles, 8, 0, 0); +} + +void +copyFitsOptions(sFile *out, sFile *rec, sFile *in, psVector *tiles) +{ + bool mdok; + psString compTypeStr = psMetadataLookupStr(&mdok, in->header, "ZCMPTYPE"); + psFitsCompressionType compType = psFitsCompressionTypeFromString(compTypeStr); + if (compType == PS_FITS_COMPRESS_NONE) { + return; + } + // Get current BITPIX, BSCALE, BZERO, EXTNAME + // Probably not necessary to look the numerical values up in this + // way, but guards against changes to psLib and cfitsio FITS + // handling. + psMetadataItem *bitpixItem = psMetadataLookup(in->header, "BITPIX"); + psAssert(bitpixItem, "Every FITS image should have BITPIX"); + int bitpix = psMetadataItemParseS32(bitpixItem); + psMetadataItem *bscaleItem = psMetadataLookup(in->header, "BSCALE"); + + float bscale; + if (!bscaleItem) { + psWarning("BSCALE isn't set; defaulting to unity"); + bscale = 1.0; + } else { + bscale = psMetadataItemParseF32(bscaleItem); + } + psMetadataItem *bzeroItem = psMetadataLookup(in->header, "BZERO"); + float bzero; + if (!bzeroItem) { + psWarning("BZERO isn't set; defaulting to zero"); + bzero = 0.0; + } else { + bzero = psMetadataItemParseF32(bzeroItem); + } + +#ifdef STREAKS_COMPRESS_OUTPUT + // printf("%d %f %f\n", bitpix, bscale, bzero); + setFitsOptions(out, bitpix, bscale, bzero, compType, tiles); + setFitsOptions(rec, bitpix, bscale, bzero, compType, tiles); +#endif +} + + +void +copyTable(sFile *out, sFile *in, int extnum) +{ + bool mdok; + psString xtension = psMetadataLookupStr(&mdok, in->header, "XTENSION"); + psString extname = psMetadataLookupStr(&mdok, in->header, "EXTNAME"); + + if (!xtension) { + psWarning("extnum %d has no image and xtension is not defined in %s", + extnum, in->resolved_name); + // XXX abort? + return; + } + if (!extname) { + psWarning("extnum %d has no image and extname not defined in %s", + extnum, in->resolved_name); + // XXX abort? + return; + } + psFitsTable *table = psFitsReadTableNew(in->fits); + if (!table) { + psError(PS_ERR_UNKNOWN, false, "failed to read table in extension %d from in->resolved name", extnum); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + if (!psFitsWriteTableNew(out->fits, out->header, table, extname)) { + psError(PS_ERR_UNKNOWN, false, "failed to copy table in extension %d", extnum); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(table); +} + +static void +createNewImage(sFile *out, sFile *in, int extnum, double initValue) +{ + out->image = psImageRecycle(out->image, in->image->numCols, in->image->numRows, in->image->type.type); + if (!out->image) { + psError(PS_ERR_UNKNOWN, false, "failed to allocate image for extnsion %d", extnum); + streaksExit("", PS_EXIT_UNKNOWN_ERROR); + } + psImageInit(out->image, initValue); +} + +void +setupImageRefs(sFile *out, sFile *recoveryOut, sFile *in, int extnum, bool exciseAll) +{ + if (!in->image) { + // Input file is likely corrupt. XXX: Shouldn't we have caught this earlier? + psError(PS_ERR_UNKNOWN, true, "image is null for extension %d of %s file is likely corrupt", extnum, in->name); + streaksExit("", PS_EXIT_UNKNOWN_ERROR); + } + if (!exciseAll) { + // set output image to be the input image + out->image = (psImage*) psMemIncrRefCounter(in->image); + if (recoveryOut) { + // create a recovery image initialized to NAN + createNewImage(recoveryOut , in, extnum, NAN); + } + } else { + // Excising all pixels in the input + // set the output to an image all NANs + createNewImage(out, in, extnum, NAN); + if (recoveryOut) { + // save the whole input as the recovery image + recoveryOut->image = (psImage*) psMemIncrRefCounter(in->image); + } + } +} + +void +writeImage(sFile *sfile, psString extname, int extnum) +{ + if (!sfile || !sfile->image) { + return; + } + streaksVersionHeaderFull(sfile->header); + + if (!psFitsWriteImage(sfile->fits, sfile->header, sfile->image, 0, extname)) { + psError(PS_ERR_IO, false, "failed to write image to %s extnum: %d", + sfile->resolved_name, extnum); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(sfile->image); + sfile->image = NULL; + psFree(sfile->header); + sfile->header = NULL; +} + +void +writeImageCube(sFile *sfile, psArray *imagecube, psString extname, int extnum) +{ + if (!sfile || !imagecube) { + return; + } + streaksVersionHeaderFull(sfile->header); + if (!psFitsWriteImageCube(sfile->fits, sfile->header, imagecube, extname)) { + psError(PS_ERR_IO, false, "failed to write image to %s extnum: %d", + sfile->resolved_name, extnum); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(sfile->header); + sfile->header = NULL; +} + +void +sFileFree(sFile *sfile) +{ + if (!sfile) { + return; + } + psFree(sfile->name); + psFree(sfile->resolved_name); + psFree(sfile->fits); + psFree(sfile); +} + +void +closeImage(sFile *sfile) +{ + if (!sfile) { + return; + } + if (sfile->fits && !psFitsClose(sfile->fits)) { + psError(PS_ERR_IO, false, "failed to close image to %s", + sfile->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + sfile->fits = NULL; + psFree(sfile->header); + sfile->header = NULL; + psFree(sfile->image); + sfile->image = NULL; + psFree(sfile->imagecube); + sfile->imagecube = NULL; +} + +void +closeImages(streakFiles *sf) +{ + if (sf->stage == IPP_STAGE_RAW) { + if (sf->view) { + sf->view->readout = -1; + pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER); + sf->view->cell = -1; + pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER); + sf->view->chip = -1; + pmFPAfileIOChecks(sf->config, sf->view, PM_FPA_AFTER); + } + } + closeImage(sf->inImage); + closeImage(sf->outImage); + closeImage(sf->recImage); + if (sf->inMask) { + closeImage(sf->inMask); + closeImage(sf->outMask); + closeImage(sf->recMask); + } + if (sf->inChMask) { + closeImage(sf->inChMask); + closeImage(sf->outChMask); + closeImage(sf->recChMask); + } + if (sf->inWeight) { + closeImage(sf->inWeight); + closeImage(sf->outWeight); + closeImage(sf->recWeight); + } +} + +static void +freeImages(streakFiles *sf) +{ + sFileFree(sf->inImage); + sFileFree(sf->outImage); + sFileFree(sf->recImage); + if (sf->inMask) { + sFileFree(sf->inMask); + sFileFree(sf->outMask); + sFileFree(sf->recMask); + } + if (sf->inChMask) { + sFileFree(sf->inChMask); + sFileFree(sf->outChMask); + sFileFree(sf->recChMask); + } + if (sf->inWeight) { + sFileFree(sf->inWeight); + sFileFree(sf->outWeight); + sFileFree(sf->recWeight); + } + if (sf->inSources) { + sFileFree(sf->inSources); + sFileFree(sf->outSources); + } +} + +bool +replicate(sFile *outFile, sFile *inFile) +{ + if (!outFile->inNebulous) { + return true; + } + nebServer *server = getNebServer(NULL); + + char *user_copies = nebGetXattr(server, inFile->name, "user.copies"); + bool free_user_copies = true; + if (user_copies == NULL) { + // input does not have replication requested + return true; + } + if (!nebSetXattr(server, outFile->name, "user.copies", user_copies, NEB_REPLACE)) { + psError(PM_ERR_UNKNOWN, true, "nebSetXattr failed for %s\n%s", outFile->name, nebErr(server)); + return false; + } + if (!nebReplicate(server, outFile->name, NULL, NULL)) { + psError(PM_ERR_UNKNOWN, true, "nebReplicate failed for %s\n%s", outFile->name, nebErr(server)); + return false; + } + if (free_user_copies) { + nebFree(user_copies); + } + return true; +} + +// for any of the outputs that are stored in Nebulous set their extended attributes +// and replicate the files + +bool +replicateOutputs(streakFiles *sfiles) +{ + if (!replicate(sfiles->outImage, sfiles->inImage)) { + psError(PM_ERR_SYS, false, "failed to replicate outImage."); + return false; + } + + if (sfiles->outMask) { + if (!replicate(sfiles->outMask, sfiles->inMask)) { + psError(PM_ERR_SYS, false, "failed to replicate outImage."); + return false; + } + } + if (sfiles->outChMask) { + if (!replicate(sfiles->outChMask, sfiles->inChMask)) { + psError(PM_ERR_SYS, false, "failed to replicate outImage."); + return false; + } + } + if (sfiles->outWeight) { + if (!replicate(sfiles->outWeight, sfiles->inWeight)) { + psError(PM_ERR_SYS, false, "failed to replicate outImage."); + return false; + } + } + + if (sfiles->outSources) { + if (!replicate(sfiles->outSources, sfiles->inSources)) { + psError(PM_ERR_SYS, false, "failed to replicate outSources."); + return false; + } + } + +// XXX: replicate the recovery images (if in nebulous) +// perhaps whether we do that or not should be configurable. +// Sounds like we need a recipe + + return true; +} + +static bool +swapOutputToInput(sFile *in, sFile *out) +{ + + if (in->inNebulous) { + nebServer *server = getNebServer(NULL); + + if (!nebSwap(server, in->name, out->name)) { + psError(PM_ERR_SYS, true, "failed to swap files for %s: %s.", + in->name, nebErr(server)); + return false; + } + } else { + psString command = NULL; + + // regular files. use mv creating a backup + // NOTE: -b is a gnu option and may not always be available + psStringAppend(&command, "mv -b --suffix=.bak %s %s", out->resolved_name, in->resolved_name); + int status = system(command); + if (status != 0) { + psError(PM_ERR_SYS, true, "%s failed with status %d.", + command, status); + psFree(command); + return false; + } + psFree(command); + // XXX: shouldn't I be doing mv in->resolved_name.bak out->resolved_name + // to complete the swap if !remove? + } + + return true; +} + +bool +swapOutputsToInputs(streakFiles *sfiles) +{ + if (sfiles->outMask) { + if (!swapOutputToInput(sfiles->inMask, sfiles->outMask)) { + psError(PM_ERR_SYS, false, "failed to swap instances for Mask."); + return false; + } + } + + if (sfiles->outWeight) { + if (!swapOutputToInput(sfiles->inWeight, sfiles->outWeight)) { + psError(PM_ERR_SYS, false, "failed to swap instances for Weight."); + return false; + } + } + + if (sfiles->outChMask) { + if (!swapOutputToInput(sfiles->inChMask, sfiles->outChMask)) { + psError(PM_ERR_SYS, false, "failed to swap instances for chip mask."); + return false; + } + } + + if (sfiles->outSources) { + if (!swapOutputToInput(sfiles->inSources, sfiles->outSources)) { + psError(PM_ERR_SYS, false, "failed to swap instances for sources."); + return false; + } + } + + if (!swapOutputToInput(sfiles->inImage, sfiles->outImage)) { + psError(PM_ERR_SYS, false, "failed to swap instances for Image."); + return false; + } + + + return true; +} + +static bool +deleteFile(sFile *sfile) +{ + if (sfile->inNebulous) { + nebServer *server = getNebServer(NULL); + if (!nebDelete(server, sfile->name)) { + psError(PM_ERR_SYS, false, "failed to delete %s\n%s.", sfile->name, + nebErr(server)); + return false; + } + } else { + if (unlink(sfile->resolved_name)) { + psError(PM_ERR_SYS, false, "failed to delete %s\n%s.", sfile->resolved_name, + strerror(errno)); + return false; + } + } + return true; +} + +bool +deleteTemps(streakFiles *sfiles) +{ + if (sfiles->outMask) { + deleteFile(sfiles->outMask); + } + + if (sfiles->outChMask) { + deleteFile(sfiles->outChMask); + } + + if (sfiles->outWeight) { + deleteFile(sfiles->outWeight); + } + + if (sfiles->outImage) { + deleteFile(sfiles->outImage); + } + + if (sfiles->outSources) { + deleteFile(sfiles->outSources); + } + + return true; +} + +bool +isExciseValue(double value, double exciseValue) +{ + if (isnan(exciseValue)) { + return isnan(value); + } else { + return value == exciseValue; + } +} + +void +setMaskedToNAN(streakFiles *sfiles, psU32 maskMask, bool printCounts) +{ + long maskedPixels = 0; + long nandPixels = 0; + long nandWeights = 0; + + psImage *image = sfiles->outImage->image; + int imageType = image->type.type; + double exciseValue = sfiles->inImage->exciseValue; + + psImage *mask = sfiles->inMask->image; + psImage *weight = NULL; + int weightType = 0; + double weightExciseValue = NAN; + if (sfiles->outWeight) { + weight = sfiles->outWeight->image; + weightType = weight->type.type; + weightExciseValue = sfiles->inWeight->exciseValue; + } + + if (printCounts) { + psTimerStart("NAN_MASKED"); + } + + for (int y=0; y < sfiles->inImage->numRows; y++) { + for (int x=0; x < sfiles->inImage->numCols; x++) { + // these gets are not necessary, we could just set the pixels to nan + // but I want to get the counts + double imageVal = 0; // avoid compiler warning + if (imageType == PS_TYPE_F32) { + imageVal = image->data.F32[y][x]; + } else if (imageType == PS_TYPE_S16) { + imageVal = image->data.S16[y][x]; + } else if (imageType == PS_TYPE_U16) { + imageVal = image->data.U16[y][x]; + } else { + psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n", + imageType); + streaksExit("", PS_EXIT_PROG_ERROR); + } + psU32 maskVal = 0; + if (sfiles->stage == IPP_STAGE_RAW) { + unsigned int xChip, yChip; + cellToChipInt(&xChip, &yChip, sfiles->astrom, x, y); + maskVal = mask->data.PS_TYPE_IMAGE_MASK_DATA[yChip][xChip]; + } else { + maskVal = mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x]; + } + if (maskVal & maskMask) { + ++maskedPixels; + if (!isExciseValue(imageVal, exciseValue)) { + ++nandPixels; + if (imageType == PS_TYPE_F32) { + image->data.F32[y][x] = exciseValue; + } else if (imageType == PS_TYPE_S16) { + image->data.S16[y][x] = exciseValue; + } else if (imageType == PS_TYPE_U16) { + image->data.U16[y][x] = exciseValue; + } else { + psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n", + imageType); + streaksExit("", PS_EXIT_PROG_ERROR); + } + } + if (weight) { + if (weightType == PS_TYPE_F32) { + double weightVal = weight->data.F32[y][x]; + if (!isnan(weightVal)) { + ++nandWeights; + weight->data.F32[y][x] = NAN; + } + } else if (weightType == PS_TYPE_F64) { + double weightVal = weight->data.F64[y][x]; + if (!isnan(weightVal)) { + ++nandWeights; + weight->data.F64[y][x] = NAN; + } + } else if(weightType == PS_TYPE_S16) { + double weightVal = weight->data.S16[y][x]; + if (!isExciseValue(weightVal, weightExciseValue)) { + ++nandWeights; + image->data.S16[y][x] = weightExciseValue; + } + } else if (weightType == PS_TYPE_U16) { + double weightVal = weight->data.U16[y][x]; + if (!isExciseValue(weightVal, weightExciseValue)) { + ++nandWeights; + image->data.U16[y][x] = weightExciseValue; + } + } else { + psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n", + weightType); + streaksExit("", PS_EXIT_PROG_ERROR); + } + } + } + } + } + if (printCounts) { + psLogMsg(sfiles->program_name, PS_LOG_INFO, "time to NAN mask pixels: %f\n", psTimerClear("NAN_MASKED")); + long totalPixels = image->numRows * image->numCols; + psLogMsg(sfiles->program_name, PS_LOG_INFO, "pixels: %10ld\n", totalPixels); + psLogMsg(sfiles->program_name, PS_LOG_INFO, "masked pixels: %10ld %4.2f%%\n", maskedPixels, 100. * maskedPixels / totalPixels); + psLogMsg(sfiles->program_name, PS_LOG_INFO, "nand pixels: %10ld %4.2f%%\n", nandPixels, 100. * nandPixels / totalPixels); + if (weight) { + psLogMsg(sfiles->program_name, PS_LOG_INFO, "nand weights: %10ld %4.2f%%\n", nandWeights, 100. * nandWeights / totalPixels); + } + } +} + +void +streaksNebulousCleanup(void) +{ + nebServerFree(ourNebServer); + ourNebServer = NULL; +} +static void +setExciseValue(sFile *in) +{ + if (in->image->type.type == PS_TYPE_U16) { + in->exciseValue = 65535; + psMetadataAddU16(in->header, PS_LIST_TAIL, "BLANK", 0, "", 65535); + psMetadataAddU16(in->header, PS_LIST_TAIL, "ZBLANK", 0, "", 65535); + } else if (in->image->type.type == PS_TYPE_S16) { + in->exciseValue = 32767; + psMetadataAddU16(in->header, PS_LIST_TAIL, "BLANK", 0, "", 32767); + psMetadataAddU16(in->header, PS_LIST_TAIL, "ZBLANK", 0, "", 32767); + } else if (in->image->type.type == PS_TYPE_F32) { + in->exciseValue = NAN; + } else if (in->image->type.type == PS_TYPE_F64) { + in->exciseValue = NAN; + } else { + psError(PS_ERR_PROGRAMMING, true, "unexpected image type found: %d\n", in->image->type.type); + streaksExit("", PS_EXIT_PROG_ERROR); + } +} + +// Get the mask values that we need. +// If an input mask file is provided get them from there. +// Otherwise get them from the recipe MASKS +void +strkGetMaskValues(streakFiles *sfiles) +{ + if (sfiles->maskStreak) { + // already done + return; + } + if (!pmCensorGetMasks(sfiles->config, &sfiles->maskMask, &sfiles->maskStreak)) { + streaksExit("failed to find mask values", PS_EXIT_CONFIG_ERROR); + } +} + +static void +doCopyExtraExtensions(streakFiles *sf, sFile *in, sFile *out) +{ + for (int extnum = sf->extnum; extnum < in->nHDU; extnum++) { + moveExt(in, extnum); + readImage(in, extnum, sf->stage, false); + + if (SFILE_IS_IMAGE(in)) { + // Turn off compression (code adapted from pmFPAWrite) + int bitpix = out->fits->options ? out->fits->options->bitpix : 0; // Desired bits per pixel + psFitsCompression *compress = psFitsCompressionGet(out->fits); // Current compression options + if (!psFitsSetCompression(out->fits, PS_FITS_COMPRESS_NONE, NULL, 0, 0, 0)) { + psError(PM_ERR_UNKNOWN, false, "failed to turn off compression for extension %d\n", extnum); + streaksExit("", PS_EXIT_UNKNOWN_ERROR); + } + if (out->fits->options) { + out->fits->options->bitpix = 0; + } + if (!psFitsWriteImage(out->fits, in->header, in->image, 0, in->extname)) { + psError(PM_ERR_UNKNOWN, false, "failed to write image for extension %d\n", extnum); + streaksExit("", PS_EXIT_UNKNOWN_ERROR); + } + if (out->fits->options) { + out->fits->options->bitpix = bitpix; + } + if (!psFitsCompressionApply(out->fits, compress)) { + psError(PM_ERR_UNKNOWN, false, "failed to rest compression image for extension %d\n", extnum); + streaksExit("", PS_EXIT_UNKNOWN_ERROR); + } + psFree(compress); + } else { + copyTable(out, in, extnum); + } + } +} + +void +copyExtraExtensions(streakFiles *sf) +{ + // XXX: Bad assumption, the begining of the mask and weight files have the same structure as the image + // So we are currently at the image portion + sf->extnum = sf->inImage->nHDU; + + if (sf->inWeight && sf->outWeight) { + doCopyExtraExtensions(sf, sf->inWeight, sf->outWeight); + } + if (sf->inMask && sf->outMask) { + doCopyExtraExtensions(sf, sf->inMask, sf->outMask); + } + if (sf->inChMask && sf->outChMask) { + doCopyExtraExtensions(sf, sf->inChMask, sf->outChMask); + } +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksio.h =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksio.h (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksio.h (revision 41117) @@ -0,0 +1,39 @@ +#ifndef STREAKS_IO_H +#define STREAKS_IO_H 1 + +streakFiles *openFiles(pmConfig *config, bool remove, char *program_name); + +sFile *sFileOpen(pmConfig *config, ippStage stage, psString fileSelect, + psString outputFilename, bool required, bool checkIfDestreaked); + +void closeImages(streakFiles *sfiles); + +void closeImage(sFile *sfile); + +void readImage(sFile *sfile, int extnum, ippStage stage, bool isMask); +void copyPHU(streakFiles *sfiles, bool remove, bool destreaked); +void copyTable(sFile *out, sFile *in, int extnum); +void copyFitsOptions(sFile *out, sFile *rec, sFile *in, psVector *tiles); +void setupImageRefs(sFile *out, sFile *recoveryOut, sFile *in, int extnum, bool exciseAll); +void strkGetMaskValues(streakFiles *sfiles); +void copyExtraExtensions(streakFiles *sfiles); + +void writeImage(sFile *sfile, psString extname, int extnum); +void writeImageCube(sFile *sfile, psArray *imagecube, psString extname, int extnum); +bool replicate(sFile *outFile, sFile *inFile); +void readImageFrom_pmFile(streakFiles *sf); + +void addDestreakKeyword(psMetadata *, bool value); +void addRecoveryKeyword(psMetadata *); + +bool streakFilesNextExtension(streakFiles *sf); + +bool isExciseValue(double, double); +void setMaskedToNAN(streakFiles *sfiles, psU32 maskMask, bool printCounts); + +bool replicateOutputs(streakFiles *sf); +bool swapOutputsToInputs(streakFiles *sf); +bool deleteTemps(streakFiles *sf); +void streaksNebulousCleanup(void); + +#endif // STREAKS_IO_H Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksrelease.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksrelease.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksrelease.c (revision 41117) @@ -0,0 +1,316 @@ +#include "streaksremove.h" + +static pmConfig *parseArguments(int argc, char **argv); +static bool readAndCopyToOutput(streakFiles *sf, bool exciseAll); +static void writeImages(streakFiles *sf, bool exciseImageCube); + +char *streaksProgram = "streaksrelease"; + +int +main(int argc, char *argv[]) +{ + psLibInit(NULL); + psTimerStart("STREAKSREMOVE"); + + pmConfig *config = parseArguments(argc, argv); + if (!config) { + psError(PS_ERR_UNKNOWN, false, "failed to parse arguments\n"); + return PS_EXIT_CONFIG_ERROR; + } + + // Does true work here? + streakFiles *sfiles = openFiles(config, true, argv[0]); + + if (sfiles->stage == IPP_STAGE_RAW) { + // copy PHU to output files + copyPHU(sfiles, false, true); + + // advance to the first image extension + if (!streakFilesNextExtension(sfiles)) { + psErrorStackPrint(stderr, "failed to advance to first extension of input images"); + exit (PS_EXIT_PROG_ERROR); + } + } + + // Iterate through each component of the input (there is only one except for raw images) + do { + psTimerStart("PROCESS_COMPONENT"); + + // read the images and copy the data from the inputs to the outputs + // This also sets up the astrometry and initializes the recovery image(s) + + if (!readAndCopyToOutput(sfiles, false)) { + // false return value indicates that this extension is not an image and + // the contents has already been copied to the output file. + // we don't need to process this extesion for streaks. + continue; + } + + // now that we've read the input files, lookup the mask values that we read + strkGetMaskValues(sfiles); + + if (!sfiles->inImage->imagecube) { + setMaskedToNAN(sfiles, sfiles->maskMask, true); + } + + // write out the destreaked temporary images and the recovery images + writeImages(sfiles, false); + + printf("time to process component %d: %f\n", sfiles->extnum, psTimerClear("PROCESS_COMPONENT")); + } while (streakFilesNextExtension(sfiles)); + + // check the weight and mask files for extra extensions that might be in files + // (covariance matrix for example) + copyExtraExtensions(sfiles); + + + + psTimerStart("CLOSE_IMAGES"); + // close all files + closeImages(sfiles); + printf("time to close images: %f\n", psTimerClear("CLOSE_IMAGES")); + + printf("time to run streaksrelease: %f\n", psTimerClear("STREAKSREMOVE")); + + // nebServerFree(ourNebServer); + psFree(config); + pmConceptsDone(); + pmConfigDone(); + psLibFinalize(); + + // PAU + fprintf(stderr, "Found %d leaks at %s\n", psMemCheckLeaks (0, NULL, NULL, false), "streaksrelease"); + + + return 0; +} + +static void usage() +{ + psErrorStackPrint(stderr, "\n"); + fprintf(stderr, "USAGE: streaksrelease -stage raw|chip|warp|diff -image IMAGE.fits -outroot directory\n\n"); + fprintf(stderr, "Other arguments:\n"); + fprintf(stderr, "\t-class_id class_id: class_id (required for raw and chip stages)\n"); + fprintf(stderr, "\t-mask MASK.fits mask file to de-streak\n"); + fprintf(stderr, "\t-weight WEIGHT.fits: weight file to de-streak\n"); + fprintf(stderr, "\t-chip_mask MASK.fits: name of mask for chip stage (camera stage mask is passed tih -mask)\n"); + + exit(2); +} + +static pmConfig *parseArguments(int argc, char **argv) +{ + + pmConfig *config = pmConfigRead(&argc, argv, NULL); + if (!config) { + streaksExit("failed to parse arguments", PS_EXIT_CONFIG_ERROR); + } + + int argnum; + ippStage stage = IPP_STAGE_NONE; + if ((argnum = psArgumentGet(argc, argv, "-stage"))) { + psArgumentRemove(argnum, &argc, argv); + stage = parseStage(argv[argnum]); + psMetadataAddS32(config->arguments, PS_LIST_TAIL, "STAGE", 0, + "pipeline stage for streak removal", stage); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-stage is required\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-class_id"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "CLASS_ID", 0, + "class_id", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else if ((stage == IPP_STAGE_RAW) || (stage == IPP_STAGE_CHIP)) { + psError(PS_ERR_UNKNOWN, true, "-class_id is required\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-image"))) { + // for raw and chip level images we use psFits for I/O and ... + if (CHIP_LEVEL_INPUT(stage)) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT", 0, + "name of input image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + // ... for warped images we use pmFPAfiles + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "INPUT", "-image", NULL)) { ; + psError(PS_ERR_UNKNOWN, false, "failed to process -image"); + usage(); + } + } + } else { + psError(PS_ERR_UNKNOWN, true, "-image is required\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-mask"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.MASK", 0, + "name of input mask image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-chip_mask"))) { + if (stage != IPP_STAGE_CHIP) { + psError(PS_ERR_UNKNOWN, true, "-chip_mask only allowed at chip stage"); + usage(); + } + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.CHMASK", 0, + "name of input chip mask image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-weight"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.WEIGHT", 0, + "name of input weight image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-outroot"))) { + psArgumentRemove(argnum, &argc, argv); + psString dir = pathToDirectory(argv[argnum]); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "directory for output files", + dir); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-outroot is required\n"); + usage(); + } + + if (argc != 1) { + psString unexpectedArguments = NULL; + for (int i=1; iinImage->pmfile) { + // image data from pmFPAfile (diff or warp file) + readImageFrom_pmFile(sf); + } else { + // image data directly from psFits + readImage(sf->inImage, sf->extnum, sf->stage, false); + + // astrom struct is only needed for raw stage, and only the chip to cell parameters are used + sf->astrom = streakSetAstrometry(sf->astrom, sf->stage, NULL, NULL, false, + sf->inImage->header, sf->inImage->numCols, sf->inImage->numRows); + } + sf->outImage->header = (psMetadata*) psMemIncrRefCounter(sf->inImage->header); + + if (!SFILE_IS_IMAGE(sf->inImage)) { + // fprintf(stderr, "skipping extnum: %d not an image\n", sf->extnum); + // XXX: This extension is probably a video table. + copyTable(sf->outImage, sf->inImage, sf->extnum); + return false; + } + + if (sf->inImage->image) { + setupImageRefs(sf->outImage, sf->recImage, sf->inImage, sf->extnum, exciseAll); + } else { + // image cubes are handled specially + } + + // set up the compression parameters + copyFitsOptions(sf->outImage, sf->recImage, sf->inImage, sf->tiles); + + if (sf->inMask) { + readImage(sf->inMask, sf->extnum, sf->stage, true); + if (sf->outMask) { + sf->outMask->header = (psMetadata*) psMemIncrRefCounter(sf->inMask->header); + if (sf->recMask) { + sf->recMask->header = (psMetadata*) psMemIncrRefCounter(sf->inMask->header); + } + setupImageRefs(sf->outMask, sf->recMask, sf->inMask, sf->extnum, exciseAll); + if (sf->outChMask) { + sf->outChMask->header = (psMetadata *) psMemIncrRefCounter(sf->outMask->header); + sf->outChMask->image = (psImage *) psMemIncrRefCounter(sf->outMask->image); + if (sf->recChMask) { + sf->recChMask->header = (psMetadata *) psMemIncrRefCounter(sf->recMask->header); + sf->recChMask->image = (psImage *) psMemIncrRefCounter(sf->recMask->image); + } + } + + copyFitsOptions(sf->outMask, sf->recMask, sf->inMask, sf->tiles); + if (sf->outChMask) { + copyFitsOptions(sf->outChMask, sf->recChMask, sf->inMask, sf->tiles); + } + } + } + + if (sf->inWeight) { + readImage(sf->inWeight, sf->extnum, sf->stage, false); + sf->outWeight->header = (psMetadata*) psMemIncrRefCounter(sf->inWeight->header); + if (sf->recWeight) { + sf->recWeight->header = (psMetadata*) psMemIncrRefCounter(sf->inWeight->header); + } + setupImageRefs(sf->outWeight, sf->recWeight, sf->inWeight, sf->extnum, exciseAll); + + copyFitsOptions(sf->outWeight, sf->recWeight, sf->inWeight, sf->tiles); + } + // and for raw images, create sub images that represent the actual image + // area (no overscan) + + return true; +} + + + +// XXXX: why isn't this in streaksio.c ?? See also streakremove.c +static void +writeImages(streakFiles *sf, bool exciseImageCube) +{ + psString extname = NULL; + if (sf->nHDU > 1) { + bool mdok; + extname = psMetadataLookupStr(&mdok, sf->inImage->header, "EXTNAME"); + } + if (sf->inImage->numZPlanes == 0) { + // note exciseing complete images is handled in readAndCopyToOutput + writeImage(sf->outImage, extname, sf->extnum); + writeImage(sf->recImage, extname, sf->extnum); + } else { + // we have an image cube + // double initValue; + if (exciseImageCube) { + // copy the entire input image to the recovery image + writeImageCube(sf->recImage, sf->inImage->imagecube, extname, sf->extnum); + // initValue = NAN; + } else { + // otherwise write it to the output + writeImageCube(sf->outImage, sf->inImage->imagecube, extname, sf->extnum); + // initValue = 0; + } + + // Assumption: there are no mask and weight images for video cells + return; + } + if (sf->outMask) { + writeImage(sf->outMask, extname, sf->extnum); + writeImage(sf->recMask, extname, sf->extnum); + if (sf->stage == IPP_STAGE_CHIP) { + writeImage(sf->outChMask, extname, sf->extnum); + writeImage(sf->recChMask, extname, sf->extnum); + } + } + if (sf->outWeight) { + writeImage(sf->outWeight, extname, sf->extnum); + writeImage(sf->recWeight, extname, sf->extnum); + } +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksremove.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksremove.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksremove.c (revision 41117) @@ -0,0 +1,1089 @@ +/* + * streaksremove + * + * Convert satellite streak detctions into masks and remove the covered pixels from the + * input images. + * Optionally swap the inputs with the outputs so that subsequent references to the original + * images access the destreaked versions. + */ + +#include "streaksremove.h" + +static pmConfig *parseArguments(int argc, char **argv); +static bool readAndCopyToOutput(streakFiles *sf, bool exciseAll); +static long exciseNonDiffedPixels(streakFiles *sfiles, psImageMaskType newMaskValue); +static bool diffedPixel(streakFiles *sfiles, int x, int y); +static void excisePixel(streakFiles *sfiles, unsigned int x, unsigned int y, bool streak, psImageMaskType newMaskValue); +static void writeImages(streakFiles *sf, bool exciseImageCube); +static void updateAstrometry(streakFiles *sfiles); +static void censorSources(streakFiles *sfiles, psImageMaskType maskStreak); +static long censorPixels(streakFiles *sfiles, psImage * pixels, bool checkNonDiffedPixels, psU16 maskStreak); + +char *streaksProgram = "streaksremove"; + +// Note: For clarity the flow of this program is in main(). +// There is not a lot of error checking is done in main. +// Until the end, where we might be doing Nebulous operations, called functions exit when an error +// is encountered. +int +main(int argc, char *argv[]) +{ + bool status; + + psLibInit(NULL); + psTimerStart("TOTAL_TIME"); + + pmConfig *config = parseArguments(argc, argv); + if (!config) { + psError(PS_ERR_UNKNOWN, false, "failed to parse arguments\n"); + streaksExit("", PS_EXIT_CONFIG_ERROR); + } + + psString streaksFileName = psMetadataLookupStr(NULL, config->arguments, "STREAKS"); + + // call Paul Sydney's code to parse the streaks file that DetectStreaks produced + Streaks *streaks = readStreaksFile(streaksFileName); + if (!streaks) { + psError(PS_ERR_UNKNOWN, false, "failed to read streaks file: %s", streaksFileName); + streaksExit("", PS_EXIT_PROG_ERROR); + } + + // open all of the input and output files, save their descriptions in the streakFiles struct + streakFiles *sfiles = openFiles(config, true, argv[0]); + setupAstrometry(sfiles); + sfiles->stats = psMetadataAlloc(); + + // Optionally we can set pixels that are masked to NAN since they couldn't have been + // examined for streaks. Usually this is done by the distribution system just prior + // to release + bool nanForRelease = psMetadataLookupBool(&status, config->arguments, "NAN_FOR_RELEASE"); + if (nanForRelease && (sfiles->inMask == NULL)) { + psError(PS_ERR_UNKNOWN, true, "mask image must be supplied with -release."); + streaksExit("", PS_EXIT_PROG_ERROR); + } + + bool exciseAll = false; + // --keepnondiffed is a test and debug mode + bool keepNonDiffedPixels = psMetadataLookupBool(&status, config->arguments, "KEEP_NON_DIFFED"); + + // we need to check for non diffed pixels unless we've been asked not to or the stage is diff + // (By definition pixels in diff images were included in the difference images) + bool checkNonDiffedPixels = ! (keepNonDiffedPixels || (sfiles->stage == IPP_STAGE_DIFF) ); + + if (checkNonDiffedPixels ) { + // From magic ICD: + // In the raw and detrended images, the pixels which were not + // included in any of the streak-processed warps must also be masked. + // Note that the warp and difference skycells are only generated if more + // than a small fraction of the pixels are lit by the input image. + // if no skycells are provided sfiles->exciseAll is set to true + + psTimerStart("COMPUTE_DIFFED_PIXELS"); + if (! computeDiffedPixels(sfiles) ) { + // we have no choice to excise all pixels + exciseAll = true; + } + psF64 cdp_t = psTimerClear("COMPUTE_DIFFED_PIXELS"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "COMPUTE_UNDIFFED_PIXELS", PS_META_REPLACE, "time to compute non-diffedpixels", cdp_t); + psLogMsg("streaksremove", PS_LOG_INFO, "time to compute diffed pixels: %f\n", cdp_t); + } + + if (sfiles->stage == IPP_STAGE_RAW) { + // Except for raw stage, all of our (GPC1) files have one image extension. + // Raw files have a phu and multiple extensions, one per chip + // Since this is a raw file, copy it's PHU to output files + copyPHU(sfiles, true, true); + + // advance to the first image extension + if (!streakFilesNextExtension(sfiles)) { + psErrorStackPrint(stderr, "failed to advance to first extension of input images"); + exit (PS_EXIT_PROG_ERROR); + } + } + + long totalPixels = 0; + long totalStreakPixels = 0; + long nonDiffedPixels = 0; + + // accumulators for the various timers + psF64 gsp_t = 0; + psF64 enw_t = 0; + psF64 rms_t = 0; + psF64 cs_t = 0; + psF64 wi_t = 0; + psF64 ua_t = 0; + // Iterate through each component of the input (except for raw images there is only one) + do { + bool exciseImageCube = false; + + psTimerStart("PROCESS_COMPONENT"); + + // read the images and copy the data from the inputs to the outputs + // This also sets up the astrometry and initializes the recovery image(s) + + if (!readAndCopyToOutput(sfiles, exciseAll)) { + // false return value indicates that this extension is not an image and + // the contents has already been copied to the output file. + // we don't need to process this extesion for streaks. + continue; + } + + // now that we've read the input files, lookup the mask values + strkGetMaskValues(sfiles); + + totalPixels += sfiles->inImage->numRows * sfiles->inImage->numCols; + + if (!exciseAll) { + // Identify pixels to mask because of streaks + + psTimerStart("GET_STREAK_PIXELS"); + + // call Paul Sydney's code to compute the set of pixels that are covered by the detected streaks + StreakPixels *pixels = streak_on_component(streaks, sfiles->astrom, sfiles->inImage->numCols, + sfiles->inImage->numRows); + gsp_t += psTimerClear("GET_STREAK_PIXELS"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "GET_STREAK_PIXELS", PS_META_REPLACE, "", gsp_t); + psLogMsg("streaksremove", PS_LOG_INFO, "time to get streak pixels: %f\n", psTimerClear("GET_STREAK_PIXELS")); + + // if this extension contained an image, excise the streaked pixels. + // otherwise it contained an image cube (video cell) which is handled in the if block + if (sfiles->inImage->image) { + if (checkNonDiffedPixels) { + psTimerStart("EXCISE_NON_DIFFED"); + + // set non-diffed pixels and variance to NAN, mask to maskStreak (since the pixel + // is excised as part of the destreaking process) + nonDiffedPixels += exciseNonDiffedPixels(sfiles, sfiles->maskStreak); + + enw_t += psTimerClear("EXCISE_NON_DIFFED"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "EXCISE_NON_DIFFED", PS_META_REPLACE, "", enw_t); + psLogMsg("streaksremove", PS_LOG_INFO, "time to excise non diffed pixels: %f\n", enw_t); + } + + psTimerStart("REMOVE_STREAKS"); + + totalStreakPixels += censorPixels(sfiles, pixels, checkNonDiffedPixels, sfiles->maskStreak); + + rms_t += psTimerClear("REMOVE_STREAKS"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "REMOVE_STREAKS", PS_META_REPLACE, "", enw_t); + psLogMsg("streaksremove", PS_LOG_INFO, "time to remove streak pixels: %f\n", rms_t); + + if (nanForRelease) { + // set any pixels that were masked, to NAN (unless they are already NAN) + setMaskedToNAN(sfiles, sfiles->maskMask, true); + } + + } else { + // this component contains an image cube + // For now excise it completely + exciseImageCube = true; + } + psFree(pixels); + } + + if (sfiles->stage == IPP_STAGE_CHIP) { + // as a convience to the user of the output, replace the bogus WCS transform in the + // chip processed files with the data calcuated by psastro at the camera stage + // (actually we use a linear approximation) + psTimerStart("UPDATE_ASTROMETRY"); + updateAstrometry(sfiles); + ua_t += psTimerClear("UPDATE_ASTROMETRY"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "UPDATE_ASTROMETRY", PS_META_REPLACE, "", ua_t); + psLogMsg("streaksremove", PS_LOG_INFO, "time to update astrometry: %f\n", ua_t); + } + + psTimerStart("CENSOR_SOURCES"); + censorSources(sfiles, sfiles->maskStreak); + cs_t += psTimerClear("CENSOR_SOURCES"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "CENSOR_SOURCES", PS_META_REPLACE, "", cs_t); + + // write the destreaked "temporary" images and the recovery images + psTimerStart("WRITE_IMAGES"); + writeImages(sfiles, exciseImageCube); + wi_t += psTimerClear("WRITE_IMAGES"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "WRITE_IMAGES", PS_META_REPLACE, "", wi_t); + + psLogMsg("streaksremove", PS_LOG_INFO, "time to process component %d: %f\n", sfiles->extnum, psTimerClear("PROCESS_COMPONENT")); + + } while (streakFilesNextExtension(sfiles)); + + + psFree(streaks); + + if (exciseAll) { + totalStreakPixels = totalPixels; + } + + psF64 streakFraction = (double) totalStreakPixels / totalPixels; + psLogMsg("streaksremove", PS_LOG_INFO, " total pixels: %8ld\n", totalPixels); + psLogMsg("streaksremove", PS_LOG_INFO, " streak pixels: %8ld %4.2f%%\n", totalStreakPixels, streakFraction * 100); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "STREAK_FRACTION", PS_META_REPLACE, "", streakFraction); + + psF64 nonDiffedFraction = (double) nonDiffedPixels / totalPixels; + psLogMsg("streaksremove", PS_LOG_INFO, "nondiffed pixels: %8ld %4.2f%%\n", nonDiffedPixels, nonDiffedFraction * 100); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "NONDIFFED_FRACTION", PS_META_REPLACE, "", nonDiffedFraction); + + // check the weight and mask files for extra extensions that might be in files + // (covariance matrix for example) + copyExtraExtensions(sfiles); + + // all done close the files. This is where the files are written so it can take a long time. + + psTimerStart("CLOSE_IMAGES"); + closeImages(sfiles); + psF64 ci_t = psTimerClear("CLOSE_IMAGES"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "CLOSE_IMAGES", PS_META_REPLACE, "", ci_t); + + psLogMsg("streaksremove", PS_LOG_INFO, "time to close images: %f\n", ci_t); + +#ifdef DO_REPLICATE + psTimerStart("REPLICATE_OUTPUTS"); + if (!replicateOutputs(sfiles)) { + psErrorStackPrint(stderr, "failed to replicate output files"); + deleteTemps(sfiles); + exit(PS_EXIT_UNKNOWN_ERROR); + } + psF64 ro_t = psTimerClear("REPLICATE_OUTPUTS"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "REPLICATE_OUTPUTS", PS_META_REPLACE, "", ro_t); +#endif + + // NOTE: from here on we can't just quit if something goes wrong. + // especially if we're working at the raw stage + // turn off automatic deletion of output files by streaksExit + setStreakFiles(NULL); + + if (psMetadataLookupBool(&status, config->arguments, "REPLACE")) { + // swap the instances for the input and output + // Note this is a nebulous database operation. No file I/O is performed + psTimerStart("SWAP_INSTANCES"); + if (!swapOutputsToInputs(sfiles)) { + // It is up to the program that reverts failed destreak runs to insure that + // any original non-destreaked input files that have been swapped are restored and that the de-streaked + // versions are deleted. + + psErrorStackPrint(stderr, "failed to swap files"); + + // XXX: pick a specific error code for this failure + exit(PS_EXIT_UNKNOWN_ERROR); + } + psF64 si_t = psTimerClear("SWAP_INSTANCES"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "SWAP_INSTANCES", PS_META_REPLACE, "", si_t); + } + + psF64 total_time = psTimerClear("TOTAL_TIME"); + psMetadataAddF32(sfiles->stats, PS_LIST_TAIL, "TOTAL_TIME", PS_META_REPLACE, "", total_time); + psLogMsg("streaksremove", PS_LOG_INFO, "time to run streaksremove: %f\n", total_time); + + psString statsFileName= psMetadataLookupStr(&status, config->arguments, "STATS"); + + if (statsFileName) { + psString resolved = pmConfigConvertFilename(statsFileName, config, true, true); // Resolved filename + if (!resolved) { + psError(psErrorCodeLast(), false, "Unable to resolve statistics file name"); + return false; + } + if (!psMetadataConfigWrite(sfiles->stats, resolved, NULL)) { + psError(psErrorCodeLast(), false, "Unable to serialize stats metadata.\n"); + psFree(resolved); + return false; + } + psFree(resolved); + } + + // all done. Clean up and look for memory leaks. + + psFree(sfiles); + psFree(config); + pmConceptsDone(); + pmModelClassCleanup(); + streaksNebulousCleanup(); + pmConfigDone(); + psLibFinalize(); + + int leaks = psMemCheckLeaks (0, NULL, stdout, false); + + fprintf(stderr, "Found %d leaks at %s\n", leaks, "streaksremove"); + + return 0; +} + +static long +censorPixels(streakFiles *sfiles, psImage *pixels, bool checkNonDiffedPixels, psU16 maskStreak) +{ + long streakPixels = 0; + + for (int y=0 ; y < sfiles->inImage->numRows; y++) { + for (int x = 0; x < sfiles->inImage->numCols; x++) { + if (psImageGet(pixels, x, y)) { + if (!checkNonDiffedPixels || diffedPixel(sfiles, x, y)) { + ++streakPixels; + + excisePixel(sfiles, x, y, true, maskStreak); + + } else { + // This pixel was not included in any warp and has thus already excised + // by exciseNonDiffedPixels + } + } + } + } + return streakPixels; +} + +static void usage() +{ + fprintf(stderr, "USAGE: streaksremove -stage raw|chip|warp|diff -image IMAGE.fits -tmproot directory -streaks streaks_file\n\n"); + fprintf(stderr, "Optional arguments:\n"); + fprintf(stderr, "\t-class_id class_id: class_id (required for raw and chip stages)\n"); + fprintf(stderr, "\t-recovery: directory to save excised pixel images\n"); + fprintf(stderr, "\t-mask MASK.fits mask file to de-streak\n"); + fprintf(stderr, "\t-weight WEIGHT.fits: weight file to de-streak\n"); + fprintf(stderr, "\t-replace: replace the input images with the output\n"); + fprintf(stderr, "\t-keepnondiffed: do not exise pixels that were not part of difference processing\n"); + fprintf(stderr, "\t-transparent val: instead of setting excicsed pixel to NAN add val\n"); + fprintf(stderr, "\t-chip_mask MASK.fits: name of mask for chip stage (camera stage mask is passed tih -mask)\n"); + + exit(2); + + +} +static pmConfig *parseArguments(int argc, char **argv) +{ + + pmConfig *config = pmConfigRead(&argc, argv, NULL); + if (!config) { + streaksExit("failed to parse arguments", PS_EXIT_CONFIG_ERROR); + } + + int argnum; + ippStage stage = IPP_STAGE_NONE; + if ((argnum = psArgumentGet(argc, argv, "-stage"))) { + psArgumentRemove(argnum, &argc, argv); + stage = parseStage(argv[argnum]); + psMetadataAddS32(config->arguments, PS_LIST_TAIL, "STAGE", 0, + "pipeline stage for streak removal", stage); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-stage is required\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-class_id"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "CLASS_ID", 0, + "class_id", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else if ((stage == IPP_STAGE_RAW) || (stage == IPP_STAGE_CHIP)) { + psError(PS_ERR_UNKNOWN, true, "-class_id is required\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-streaks"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "STREAKS", 0, + "STREAKS", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-streaks is required\n"); + usage(); + } + + + // If input image is in nebulous we require mask, weight, and tmproot to all be + // nebulous paths + bool nebulousImage = false; + if ((argnum = psArgumentGet(argc, argv, "-image"))) { + // for raw and chip level images we use psFits for I/O and ... + nebulousImage = IN_NEBULOUS(argv[argnum+1]); + if (CHIP_LEVEL_INPUT(stage)) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT", 0, + "name of input image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + // ... for warped images we use pmFPAfiles + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "INPUT", "-image", NULL)) { ; + psError(PS_ERR_UNKNOWN, false, "failed to process -image"); + usage(); + } + } + } else { + psError(PS_ERR_UNKNOWN, true, "-image is required\n"); + usage(); + } + + bool gotReplace = false; + if ((argnum = psArgumentGet(argc, argv, "-replace"))) { + if (!nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "replace is only supported for nebulous files"); + usage(); + } + gotReplace = true; + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "REPLACE", 0, "replace input files", + true); + } + + if ((argnum = psArgumentGet(argc, argv, "-release"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "NAN_FOR_RELEASE", 0, "set masked pixels to NAN", + true); + } + + if ((argnum = psArgumentGet(argc, argv, "-keepnondiffed"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "KEEP_NON_DIFFED", 0, + "skip excising of non diffed pixels", true); + } + + if ((argnum = psArgumentGet(argc, argv, "-transparent"))) { + if (gotReplace) { + psError(PS_ERR_UNKNOWN, true, "cannot make transparent streaks if -replace"); + usage(); + } + psArgumentRemove(argnum, &argc, argv); + double transparentStreaks = atof(argv[argnum]); + psMetadataAddF32(config->arguments, PS_LIST_TAIL, "TRANSPARENT_STREAKS", 0, + "value to adjust excised pixels", transparentStreaks); + psArgumentRemove(argnum, &argc, argv); + } + + // if skycells are not provided then we have to execise all pixels unless -keepnondiffed + pmConfigFileSetsMD(config->arguments, &argc, argv, "SKYCELLS", "-skycell", "-skycelllist"); + + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "ASTROM", "-astrom", NULL)) { ; + if (CHIP_LEVEL_INPUT(stage)) { + psError(PS_ERR_UNKNOWN, true, "-astrom is required for raw and chip stages\n"); + usage(); + } + } + + if ((argnum = psArgumentGet(argc, argv, "-mask"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousMask = IN_NEBULOUS(argv[argnum]); + // This isn't a strict requirement if stage == IPP_STAGE_CHIP + if (nebulousMask != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "mask image must be %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.MASK", 0, + "name of input mask image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-chip_mask"))) { + if (stage != IPP_STAGE_CHIP) { + psError(PS_ERR_UNKNOWN, true, "-chip_mask only allowed at chip stage"); + usage(); + } + psArgumentRemove(argnum, &argc, argv); + bool nebulousMask = IN_NEBULOUS(argv[argnum]); + if (nebulousMask != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "chip mask image must be %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.CHMASK", 0, + "name of input chip mask image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-weight"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousWeight = IN_NEBULOUS(argv[argnum]); + if (nebulousWeight != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "weight image must have %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.WEIGHT", 0, + "name of input weight image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + if ((argnum = psArgumentGet(argc, argv, "-sources"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousSources = IN_NEBULOUS(argv[argnum]); + if (nebulousSources != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "sources file must have %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "SOURCES", 0, + "name of input sources file", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-stats"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "STATS", 0, + "name of input stats file", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-tmproot"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousTmp = IN_NEBULOUS(argv[argnum]); + if (gotReplace && (nebulousTmp != nebulousImage)) { + psError(PS_ERR_UNKNOWN, true, "tmproot must have %snebulous path with %s image path with -replace\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "path for (temporary if replae) output files", + argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-tmproot is required\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-recovery"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "RECOVERY", 0, "path for recovery files", + argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else if ((stage == IPP_STAGE_RAW) && gotReplace) { + psError(PS_ERR_UNKNOWN, true, "-recovery is required for -stage raw with -replace\n"); + usage(); + } + + if (argc != 1) { + psString unexpectedArguments = NULL; + for (int i=1; ibilevelAstrometry) { + if (!linearizeTransforms(sf->astrom)) { + // fit failed, leave the transform in the file unchanged + return; + } + } + if (!pmAstromWriteWCS(sf->outImage->header, sf->inAstrom->fpa, sf->chip, 0.001)) { + psError(PS_ERR_UNKNOWN, false, "failed to update astrometry for extension %d", sf->extnum); + streaksExit("", PS_EXIT_UNKNOWN_ERROR); + } + if (sf->outMask) { + pmAstromWriteWCS(sf->outMask->header, sf->inAstrom->fpa, sf->chip, 0.001); + } + if (sf->outWeight) { + pmAstromWriteWCS(sf->outWeight->header, sf->inAstrom->fpa, sf->chip, 0.001); + } +} + +static void +setStreakBits(psImage *maskImage, psU32 maskStreak) +{ + for (int y=0 ; y < maskImage->numRows; y++) { + for (int x=0 ; x < maskImage->numCols; x++) { + maskImage->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= maskStreak; + } + } +} + +// set the image for the output files to the contents of the corresponding input file. +static bool +readAndCopyToOutput(streakFiles *sf, bool exciseAll) +{ + if (sf->inImage->pmfile) { + // image data from pmFPAfile (diff or warp file) + readImageFrom_pmFile(sf); + sf->astrom = streakSetAstrometry(sf->astrom, sf->stage, sf->inAstrom->fpa, + sf->chip, true, sf->cell->concepts, sf->inImage->numCols, sf->inImage->numRows); + } else { + // image data directly from psFits + readImage(sf->inImage, sf->extnum, sf->stage, false); + if (SFILE_IS_IMAGE(sf->inImage)) { + sf->astrom = streakSetAstrometry(sf->astrom, sf->stage, sf->inAstrom->fpa, sf->chip, false, + sf->inImage->header, sf->inImage->numCols, sf->inImage->numRows); + } + } + if (!sf->astrom) { + psError(PS_ERR_UNKNOWN, false, "failed to set up astrometry for extension %d", sf->extnum); + streaksExit("", PS_EXIT_UNKNOWN_ERROR); + } + sf->outImage->header = psMemIncrRefCounter(sf->inImage->header); + if (sf->recImage) { + sf->recImage->header = psMetadataCopy(NULL, sf->inImage->header); + addRecoveryKeyword(sf->recImage->header); + } + addDestreakKeyword(sf->outImage->header, true); + + if (!SFILE_IS_IMAGE(sf->inImage)) { + // fprintf(stderr, "skipping extnum: %d not an image\n", sf->extnum); + // XXX: This extension is probably a video table. + copyTable(sf->outImage, sf->inImage, sf->extnum); + return false; + } + + if (sf->inImage->image) { + setupImageRefs(sf->outImage, sf->recImage, sf->inImage, sf->extnum, exciseAll); + } else { + // Image cubes are handeled specially + } + + // set up the compression parameters + copyFitsOptions(sf->outImage, sf->recImage, sf->inImage, sf->tiles); + + if (sf->inMask) { + readImage(sf->inMask, sf->extnum, sf->stage, true); + if (sf->outMask) { + sf->outMask->header = (psMetadata*) psMemIncrRefCounter(sf->inMask->header); + if (sf->recMask) { + sf->recMask->header = psMetadataCopy(NULL, sf->outMask->header); + addRecoveryKeyword(sf->recMask->header); + } + addDestreakKeyword(sf->outMask->header, true); + // Note: we don't excise the mask pixels even if exciseAll is true. + setupImageRefs(sf->outMask, sf->recMask, sf->inMask, sf->extnum, false); + if (exciseAll) { + strkGetMaskValues(sf); + + // add the STREAK bit to the mask image pixels + setStreakBits(sf->inMask->image, sf->maskStreak); + } + if (sf->outChMask) { + sf->outChMask->header = (psMetadata *) psMemIncrRefCounter(sf->outMask->header); + sf->outChMask->image = (psImage *) psMemIncrRefCounter(sf->outMask->image); + if (sf->recChMask) { + sf->recChMask->header = (psMetadata *) psMemIncrRefCounter(sf->recMask->header); + sf->recChMask->image = (psImage *) psMemIncrRefCounter(sf->recMask->image); + } + } + + copyFitsOptions(sf->outMask, sf->recMask, sf->inMask, sf->tiles); + if (sf->outChMask) { + copyFitsOptions(sf->outChMask, sf->recChMask, sf->inMask, sf->tiles); + } + } + } + + if (sf->inWeight) { + readImage(sf->inWeight, sf->extnum, sf->stage, false); + sf->outWeight->header = (psMetadata*) psMemIncrRefCounter(sf->inWeight->header); + if (sf->recWeight) { + sf->recWeight->header = psMetadataCopy(NULL, sf->outWeight->header); + addRecoveryKeyword(sf->recWeight->header); + } + addDestreakKeyword(sf->outWeight->header, true); + setupImageRefs(sf->outWeight, sf->recWeight, sf->inWeight, sf->extnum, exciseAll); + + copyFitsOptions(sf->outWeight, sf->recWeight, sf->inWeight, sf->tiles); + } + + return true; +} + +static void +writeImages(streakFiles *sf, bool exciseImageCube) +{ + psString extname = NULL; + if (sf->nHDU > 1) { + bool mdok; + extname = psMetadataLookupStr(&mdok, sf->inImage->header, "EXTNAME"); + } + if (sf->inImage->numZPlanes == 0) { + // note exciseing complete images is handled in readAndCopyToOutput + writeImage(sf->outImage, extname, sf->extnum); + writeImage(sf->recImage, extname, sf->extnum); + } else { + // we have an image cube + if (exciseImageCube) { + // copy the entire input image to the recovery image + writeImageCube(sf->recImage, sf->inImage->imagecube, extname, sf->extnum); + } else { + // otherwise write it to the output + writeImageCube(sf->outImage, sf->inImage->imagecube, extname, sf->extnum); + } + + // Now deal with the other output image + if (exciseImageCube) { + // Set the values in the imagecube images to NAN and write them to the output image + for (int i = 0; i < psArrayLength(sf->inImage->imagecube); i++) { + psImage *image = psArrayGet (sf->inImage->imagecube, i); + // XXX: NAN isn't right. It should be the integer equivalent. Should use exciseValue + // but it isn't set with this code path. Fix that. + psImageInit(image, 65535); + } + writeImageCube(sf->outImage, sf->inImage->imagecube, extname, sf->extnum); + } else { + if (sf->recImage) { + // Set the values in the imagecube images to zero + for (int i = 0; i < psArrayLength(sf->inImage->imagecube); i++) { + psImage *image = psArrayGet (sf->inImage->imagecube, i); + psImageInit(image, 0); + } + // copy the entire zeroed image to the recovery image + writeImageCube(sf->recImage, sf->inImage->imagecube, extname, sf->extnum); + } + } + // XXX: check this + // Assumption: there are no mask and weight images for video cells + return; + } + if (sf->outMask) { + writeImage(sf->outMask, extname, sf->extnum); + writeImage(sf->recMask, extname, sf->extnum); + if (sf->stage == IPP_STAGE_CHIP) { + writeImage(sf->outChMask, extname, sf->extnum); + writeImage(sf->recChMask, extname, sf->extnum); + } + } + if (sf->outWeight) { + writeImage(sf->outWeight, extname, sf->extnum); + writeImage(sf->recWeight, extname, sf->extnum); + } +} + +static void +excisePixel(streakFiles *sfiles, unsigned int x, unsigned int y, bool streak, psImageMaskType newMaskValue) +{ + double exciseValue = sfiles->inImage->exciseValue; + + // we clip so that the streak calculation code doesn't have to + if ((x < 0) || (x >= sfiles->inImage->numCols) || (y < 0) || (y >= sfiles->inImage->numRows)) { + return; + } + + if (sfiles->inImage->image->type.type == PS_TYPE_U16) { + psU16 imageValue = sfiles->inImage->image->data.U16[y][x]; + if (sfiles->recImage && !isExciseValue(imageValue, sfiles->inImage->exciseValue) ) { + sfiles->recImage->image->data.U16[y][x] = imageValue; + } + + if (sfiles->transparentStreaks == 0) { + sfiles->outImage->image->data.U16[y][x] = exciseValue; + } else { + if (streak) { + // as a visualization aid don't mask the pixel, just change the intensity + sfiles->outImage->image->data.U16[y][x] = imageValue + sfiles->transparentStreaks; + } else { + sfiles->outImage->image->data.U16[y][x] = exciseValue; + } + } + } else if (sfiles->inImage->image->type.type == PS_TYPE_F32) { + float imageValue = sfiles->inImage->image->data.F32[y][x]; + if (sfiles->recImage && !isExciseValue(imageValue, sfiles->inImage->exciseValue) ) { + sfiles->recImage->image->data.F32[y][x] = imageValue; + } + + if (sfiles->transparentStreaks == 0) { + sfiles->outImage->image->data.F32[y][x] = exciseValue; + } else { + if (streak) { + // as a visualization aid don't mask the pixel, just change the intensity + sfiles->outImage->image->data.F32[y][x] = imageValue + sfiles->transparentStreaks; + } else { + sfiles->outImage->image->data.F32[y][x] = exciseValue; + } + } + } else { + // We could handle F64 but I don't think we ever get them. + // Should catch this earlier + psError(PS_ERR_IO, true, "unexpected image type %x found", sfiles->inImage->image->type.type ); + streaksExit("", PS_EXIT_PROG_ERROR); + } + + if (sfiles->outWeight) { + // Assume that weight images are always a floating point type + if (sfiles->inWeight->image->type.type == PS_TYPE_F32) { + if (sfiles->recWeight) { + sfiles->recWeight->image->data.F32[y][x] = sfiles->inWeight->image->data.F32[y][x]; + } + sfiles->outWeight->image->data.F32[y][x] = NAN; + } else if (sfiles->inWeight->image->type.type == PS_TYPE_F64) { + if (sfiles->recWeight) { + sfiles->recWeight->image->data.F64[y][x] = sfiles->inWeight->image->data.F64[y][x]; + } + sfiles->outWeight->image->data.F64[y][x] = NAN; + } else { + // Should catch this earlier + psError(PS_ERR_IO, true, "unexpected weight image type %x found", sfiles->inWeight->image->type.type ); + streaksExit("", PS_EXIT_PROG_ERROR); + } + } + if (sfiles->outMask) { + if (sfiles->recMask) { + sfiles->recMask->image->data.PS_TYPE_IMAGE_MASK_DATA[y][x] = + sfiles->inMask->image->data.PS_TYPE_IMAGE_MASK_DATA[y][x]; + } + sfiles->outMask->image->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= newMaskValue; + } +} + +static long +exciseNonDiffedPixels(streakFiles *sfiles, psImageMaskType newMaskValue) +{ + int cell_x0 = sfiles->astrom->cell_x0; + int cell_y0 = sfiles->astrom->cell_y0; + int xParity = sfiles->astrom->xParity; + int yParity = sfiles->astrom->yParity; + int numCols = sfiles->inImage->numCols; // for raw images this was calculated from the width of datasec + int numRows = sfiles->inImage->numRows; // for raw images this was calculated from the height of datasec + + long excisedPixels = 0; + +// printf("%2d x0: %4d y0: %4d xpar: %d ypar: %d\n", sfiles->extnum, cell_x0, cell_y0, xParity, yParity); + + // XXX: in the case of raw images we are making an implicit assumption here + // that the DATASEC begins at (x, y) = (0, 0) in the array for this image + // While this is true for GPC1 it isn't necessarily true + for (int yCell = 0; yCell < numRows; yCell++) { + int yChip; + if (yParity == 1) { + yChip = cell_y0 + yCell; + } else { + yChip = cell_y0 - yCell; + } + + psU8 *pixels = sfiles->diffedPixels->data.U8[yChip]; + + if (xParity == 1) { + pixels += cell_x0; + for (int xCell = 0; xCell < numCols; xCell++, pixels++) { + if (! *pixels ) { + excisePixel(sfiles, xCell, yCell, false, newMaskValue); + excisedPixels++; + } + } + } else { + // negative parity + // point to the right most pixel in chip coordinates (lowest in cell coords) + pixels += cell_x0 - numCols; + for (int xCell = numCols - 1; xCell >= 0 ; xCell--, pixels++) { + if (!*pixels) { + excisePixel(sfiles, xCell, yCell, false, newMaskValue); + excisedPixels++; + } + } + } + } + return excisedPixels; +} + +static bool +diffedPixel(streakFiles *sfiles, int x, int y) +{ + PixelPos chipCoord; + + if (!CHIP_LEVEL_INPUT(sfiles->stage)) { + // if we're here on a skycell image by definition this pixel was diffed + return true; + } + + // we clip so that the streak calculation code doesn't have to + // clipping here insures that we don't touch the overscan regions + if ((x < 0) || (x >= sfiles->inImage->numCols) || + (y < 0) || (y >= sfiles->inImage->numRows)) { + return false; + } + + cellToChipInt(&chipCoord.x, &chipCoord.y, sfiles->astrom, x, y); + + if (chipCoord.x < 0 || chipCoord.x >= sfiles->diffedPixels->numCols) { + return false; + } + if (chipCoord.y < 0 || chipCoord.y >= sfiles->diffedPixels->numRows) { + return false; + } + + return psImageGet(sfiles->diffedPixels, chipCoord.x, chipCoord.y) ? true : false; +} + +// read a sources file (.cmf) and remove any rows whose coordinate is convered by a +// streak mask +static void +censorSources(streakFiles *sfiles, psImageMaskType maskStreak) +{ + if ((!sfiles->inSources) || (!sfiles->outMask)) { + return; + } + psImage *maskImage = sfiles->outMask->image; + if (!maskImage) { + psError(PS_ERR_IO, false, "maskImage is null!"); + streaksExit("", PS_EXIT_PROG_ERROR); + } + + sFile *in = sfiles->inSources; + sFile *out = sfiles->outSources; + + // Primary header, should be "something.hdr" + { + psMetadata *header = psFitsReadHeader(NULL, in->fits); + if (!header) { + psError(PS_ERR_IO, false, "failed to read header from %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + bool status; + psString extname = psMetadataLookupStr(&status, header, "EXTNAME"); + if (!extname) { + psError(PS_ERR_IO, false, "failed to find extname in header of %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + addDestreakKeyword(header, true); + + if (!psFitsWriteBlank(out->fits, header, extname)) { + psError(PS_ERR_IO, false, "failed to write blank in header of %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(header); + } + + // Extension with PSF fits, should be "CLASS_ID.psf" + // This assumes that the sources extension comes first + { + if (!psFitsMoveExtNum(in->fits, 1, true)) { + psErrorStackPrint(stderr, "failed to move to extension 1 in from %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + psMetadata *header = psFitsReadHeader(NULL, in->fits); + if (!header) { + psErrorStackPrint(stderr, "failed to read header from %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psString extname = psMetadataLookupStr(NULL, header, "EXTNAME"); + if (!extname) { + psError(PS_ERR_IO, false, "failed to find extname in header of %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + +#ifdef CHECK_MEM_USE + bool printStats = false; + size_t allocated = 0; + size_t persistent = 0; + size_t allocatedBefore = psMemStats(printStats, &allocated, &persistent); + printf("Before: %12lld %12lld %12lld\n", (long long) allocated, (long long) persistent, (long long) allocatedBefore); +#endif + + psFitsTable *table = psFitsReadTableNew(in->fits); + +#ifdef CHECK_MEM_USE + size_t allocatedAfter = psMemStats(printStats, &allocated, &persistent); + printf("After: %12lld %12lld %12lld\n", (long long) allocated, (long long) persistent, (long long) allocatedAfter); + printf("Change: %12lld\n", (long long) allocatedAfter - allocatedBefore); +#endif + + if (!table) { + psErrorStackPrint(stderr, "failed to read table in %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + int numCensored = 0; + bool *rowCensored = NULL; + if (table->numRows > 0) { + // For speed we get intimate with the table + // avoid 2 * numRows lookups of the column number by looking + // it up ahead of time and verifying that the type is what we + // expect. + int xCol = psFitsTableGetColumnNumber(table, "X_PSF"); + assert(xCol >= 0 && xCol < table->numCols); + assert(table->columns[xCol].type == PS_DATA_F32); + + int yCol = psFitsTableGetColumnNumber(table, "Y_PSF"); + assert(yCol >= 0 && yCol < table->numCols); + assert(table->columns[yCol].type == PS_DATA_F32); + + // We mark censored rows in this array. + rowCensored = psAlloc(table->numRows * sizeof(bool)); + memset(rowCensored, 0, table->numRows * sizeof(bool)); + + for (int i = 0 ; i < table->numRows; i++) { + +#ifndef GO_SLOWER + psF32 x = table->columns[xCol].data.F32[i]; + psF32 y = table->columns[yCol].data.F32[i]; +#else + psF32 x = psFitsTableGetF32(NULL, table, i, "X_PSF"); + psF32 y = psFitsTableGetF32(NULL, table, i, "Y_PSF"); +#endif + psImageMaskType mask; + if ((x >= maskImage->numCols) || (y >= maskImage->numRows) || (x < 0) || (y < 0) || isnan(x) || isnan(y)) { + mask = maskStreak; + } else { + mask = maskImage->data.PS_TYPE_IMAGE_MASK_DATA[(int)y][(int)x]; + } + + // Key the source if the center pixel is not masked with maskStreak + if (mask & maskStreak) { + rowCensored[i] = true; + numCensored++; + } + } + + // remove the censored rows from the table + if (!psFitsTableCensor(table, rowCensored)) { + streaksExit("", PS_EXIT_PROG_ERROR); + } + + addDestreakKeyword(header, true); + } + + if (table->numCols > 0) { + printf("Censored %d sources\n", numCensored); + if (! psFitsWriteTableNew(out->fits, header, table, extname)) { + psErrorStackPrint(stderr, "failed to write table to %s", out->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + } else { + printf("No input sources\n"); + // We'd like to write a blank table, but this is as good as it gets without more work to parse the + // header and create dummy columns. + if (!psFitsWriteBlank(out->fits, header, extname)) { + psErrorStackPrint(stderr, "failed to write empty header to %s", out->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + } + psFree(header); + psFree(table); + psFree(rowCensored); + } + + // Copy any other extensions in the file (deteff for example) to the output + // XXX: This assumes that all we have is binary tables. + for (int i = 2; i< in->nHDU; i++) { + if (!psFitsMoveExtNum(in->fits, 1, true)) { + psErrorStackPrint(stderr, "failed to move to extension number %d in %s", i, in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psMetadata *header = psFitsReadHeader(NULL, in->fits); + if (!header) { + psErrorStackPrint(stderr, "failed to read header from %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psString extname = psMetadataLookupStr(NULL, header, "EXTNAME"); + if (!extname) { + psError(PS_ERR_IO, false, "failed to find extname in header of %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + + psFitsTable *table = psFitsReadTableNew(in->fits); + if (!table) { + psErrorStackPrint(stderr, "failed to read table in %s", in->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + if (! psFitsWriteTableNew(out->fits, header, table, extname)) { + psErrorStackPrint(stderr, "failed to write table to %s", out->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + psFree(header); + psFree(table); + } + + if (!psFitsClose(out->fits)) { + psErrorStackPrint(stderr, "failed to close table %s", out->resolved_name); + streaksExit("", PS_EXIT_DATA_ERROR); + } + out->fits = NULL; // freed by psFitsclose() +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksremove.h =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksremove.h (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksremove.h (revision 41117) @@ -0,0 +1,103 @@ +#ifndef STREAKS_H +#define STREAKS_H + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "string.h" +#include "pslib.h" +#include "psmodules.h" +#include "nebclient.h" + +#include "streaksextern.h" +#include "streaksastrom.h" + +typedef struct { + psString resolved_name; + psString name; + bool inNebulous; + bool write; + psFits *fits; + int nHDU; + psString extname; + psMetadata *header; + int numZPlanes; + psImage *image; + psArray *imagecube; + pmFPAfile *pmfile; + int col0; + int numCols; // number of columns in data section of image (doesn't include bias section) + int xParity; + int row0; + int numRows; // number of rows in data section of image (does not include bias section) + int yParity; + double exciseValue; + psString program; +} sFile; + +// used for error messages +extern char * streaksProgram; + +typedef struct { + pmConfig *config; + ippStage stage; + int extnum; + int nHDU; // number of HDUs in the inputs (all must be equal) + sFile *inImage; + sFile *inMask; + sFile *inWeight; + sFile *outImage; + sFile *outMask; + sFile *outWeight; + sFile *recImage; + sFile *recMask; + sFile *recWeight; + sFile *inChMask; // for chip stage input mask is camera mask and output goes to both chip and cam masks + sFile *outChMask; + sFile *recChMask; + sFile *inSources; + sFile *outSources; + psMetadata *stats; + FILE *statsFile; + psString class_id; + pmFPAfile *inAstrom; + strkAstrom *astrom; + bool bilevelAstrometry; + pmFPAview *view; + pmChip *chip; // current chip + pmCell *cell; // current cell + psImage *diffedPixels; + psVector *tiles; + double transparentStreaks; + psString program_name; + psU32 maskStreak; + psU32 maskMask; +} streakFiles; + +#include "streaksio.h" + +extern void setupAstrometry(streakFiles *); +extern strkAstrom *streakSetAstrometry(strkAstrom *, ippStage stage, pmFPA *, pmChip *, bool fromCell, psMetadata *md, + int numCols, int numRows); +// can't declare this in streaksastrom due to header file ordering +extern void cellToChip(double *xChip, double *yChip, strkAstrom *astrom, double xCell, double yCell); +extern void cellToChipInt(unsigned int *xChip, unsigned int *yChip, strkAstrom *astrom, int xCell, int yCell); + +extern bool computeDiffedPixels(streakFiles *sf); +extern void streaksExit(psString, int); +extern ippStage parseStage(psString); +extern psString pathToDirectory(char *path); +extern void setStreakFiles( streakFiles *); + +extern bool streaksVersionHeaderFull(psMetadata *header); +extern psString streaksVersionLong(void); + +#define CHIP_LEVEL_INPUT(_stage) ((_stage == IPP_STAGE_RAW) || (_stage == IPP_STAGE_CHIP)) +#define USE_SUPPLIED_ASTROM(_stage) CHIP_LEVEL_INPUT(_stage) + +#define SFILE_IS_IMAGE(_sfile) (_sfile->image || _sfile->imagecube) +#define IN_NEBULOUS(_filename) (!strncasecmp(_filename, "neb://", strlen("neb://"))) + + +#endif // STREAKS_H Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksreplace.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksreplace.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksreplace.c (revision 41117) @@ -0,0 +1,388 @@ +#include "streaksremove.h" + +static pmConfig *parseArguments(int, char **); +static bool readAndCopyToOutput(streakFiles *sf, bool restoreImageCube); +static void writeImages(streakFiles *sf, bool exciseImageCube); +static bool readAndCopyToOutput(streakFiles *sf, bool restoreImageCube); + +char *streaksProgram = "streaksreplace"; + +int main(int argc, char *argv[]) +{ + bool status; + + psLibInit(NULL); + + pmConfig *config = parseArguments(argc, argv); + if (!config) { + psError(PS_ERR_UNKNOWN, false, "failed to parse arguments\n"); + return PS_EXIT_CONFIG_ERROR; + } + + psMetadata *masks = psMetadataLookupMetadata(&status, config->recipes, "MASKS"); + if (!status) { + psError(PM_ERR_CONFIG, false, "failed to lookup MASKS in recipes\n"); + return PS_EXIT_CONFIG_ERROR; + } + // TODO: perhaps we should save this in the image header and get it from there? + double maskStreak = (double) psMetadataLookupU8(&status, masks, "STREAK"); + if (!status) { + psError(PM_ERR_CONFIG, false, "failed to lookup mask value for STREAK in recipes\n"); + return PS_EXIT_CONFIG_ERROR; + } + + streakFiles *sfiles = openFiles(config, false, argv[0]); + + if (sfiles->stage == IPP_STAGE_RAW) { + // copy PHU to output files + copyPHU(sfiles, false, false); + + // advance to the first image extension + if (!streakFilesNextExtension(sfiles)) { + psErrorStackPrint(stderr, "failed to advance to first extension of input images"); + exit (PS_EXIT_PROG_ERROR); + } + } + + // Iterate through components of input files + do { + bool restoreImageCube = false; + + // read the images and copy the data from the inputs to the outputs + // This also sets up the astrometry and initializes the recovery image(s) + + if (!readAndCopyToOutput(sfiles, restoreImageCube)) { + // false return value indicates that this extension is not an image and + // the contents has already been copied to the output file. + // we don't need to process this extesion for streaks. + continue; + } + + // If pixel in recovery image is not NAN, then it contains an excised pixel + // that has been stored in the recovery image + for (int y=0; y < sfiles->inImage->numRows; y++) { + for (int x=0; x < sfiles->inImage->numCols; x++) { + double recValue = psImageGet(sfiles->recImage->image, x, y); + if (!isnan(recValue)) { + psImageSet(sfiles->inImage->image, x, y, recValue); + } + if (sfiles->inMask) { + double recMaskValue = psImageGet(sfiles->recMask->image, x, y); + if (recValue != maskStreak) { + psImageSet(sfiles->inMask->image, x, y, recMaskValue); + } + } + if (sfiles->inWeight) { + double recWeightValue = psImageGet(sfiles->recWeight->image, x, y); + if (!isnan(recWeightValue)) { + psImageSet(sfiles->inWeight->image, x, y, recWeightValue); + } + } + } + } + + // write out the re-streaked images + writeImages(sfiles, restoreImageCube); + + } while (streakFilesNextExtension(sfiles)); + + // check the weight and mask files for extra extensions that might be in files + // (covariance matrix for example) + copyExtraExtensions(sfiles); + + // close all files + closeImages(sfiles); + + if (!replicateOutputs(sfiles)) { + psErrorStackPrint(stderr, "failed to replicate output files"); + exit(PS_EXIT_UNKNOWN_ERROR); + } + +// nebServerFree(ourNebServer); + psFree(config); + pmConceptsDone(); + pmConfigDone(); + psLibFinalize(); + + // PAU + fprintf(stderr, "Found %d leaks at %s\n", psMemCheckLeaks (0, NULL, NULL, false), "streaksreplace"); + + return 0; +} +static void usage(void) +{ + fprintf(stderr, "USAGE: streaksreplace -stage raw|chip|warp|diff -image IMAGE.fits -tmproot directory\n\n"); + fprintf(stderr, "Optional arguments:\n"); + fprintf(stderr, "\t-mask MASK.fits mask file to re-streak\n"); + fprintf(stderr, "\t-recmask RECOVERYMASK.fits: recovery mask file (required with -mask)\n"); + fprintf(stderr, "\t-weight WEIGHT.fits: weight file to re-streak\n"); + fprintf(stderr, "\t-recweight RECOVERYWEIGHT.fits: recovery weight file (required with -weight)\n"); + fprintf(stderr, "\t-replace: replace the input images with the output\n"); + fprintf(stderr, "\t-remove: remove the original image after processing (requires -replace)\n"); + + exit(2); +} + +static pmConfig *parseArguments(int argc, char **argv) +{ + pmConfig *config = pmConfigRead(&argc, argv, NULL); + if (!config) { + streaksExit("failed to parse arguments", PS_EXIT_CONFIG_ERROR); + } + + int argnum; + ippStage stage = IPP_STAGE_NONE; + if ((argnum = psArgumentGet(argc, argv, "-stage"))) { + psArgumentRemove(argnum, &argc, argv); + stage = parseStage(argv[argnum]); + psMetadataAddS32(config->arguments, PS_LIST_TAIL, "STAGE", 0, + "pipeline stage for streak removal", stage); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-stage is required\n"); + usage(); + } + + // If we are asked to replace inputs with the outputs and input image is in nebulous + // we require mask, weight, and tmproot to all be + bool nebulousImage = false; + if ((argnum = psArgumentGet(argc, argv, "-image"))) { + // for raw and chip level images we use psFits for I/O and ... + nebulousImage = IN_NEBULOUS(argv[argnum+1]); + if (CHIP_LEVEL_INPUT(stage)) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT", 0, + "name of input image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + // ... for warped images we use pmFPAfiles + if (!pmConfigFileSetsMD(config->arguments, &argc, argv, "INPUT", "-image", NULL)) { ; + psError(PS_ERR_UNKNOWN, false, "failed to process -image"); + usage(); + } + } + } else { + psError(PS_ERR_UNKNOWN, true, "-image is required\n"); + usage(); + } + + bool gotReplace = false; + if ((argnum = psArgumentGet(argc, argv, "-replace"))) { + gotReplace = true; + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "REPLACE", 0, "replace input files", + true); + } + + bool gotMask = false; + if ((argnum = psArgumentGet(argc, argv, "-mask"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousMask = IN_NEBULOUS(argv[argnum]); + if (nebulousMask != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "mask image must be %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + gotMask = true; + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.MASK", 0, + "name of input mask image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + bool gotWeight = false; + if ((argnum = psArgumentGet(argc, argv, "-weight"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousWeight = IN_NEBULOUS(argv[argnum]); + if (nebulousWeight != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "weight image must have %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + gotWeight = true; + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "INPUT.WEIGHT", 0, + "name of input weight image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-tmproot"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousTmp = IN_NEBULOUS(argv[argnum]); + if (gotReplace && (nebulousTmp != nebulousImage)) { + psError(PS_ERR_UNKNOWN, true, "tmproot must have %snebulous path with %s image path with -replace\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psString dir = pathToDirectory(argv[argnum]); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "directory for temporary files", + dir); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-tmproot is required\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-recimage"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "RECOVERY.IMAGE", 0, "recovery image file name", + argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else { + psError(PS_ERR_UNKNOWN, true, "-recimage is required\n"); + usage(); + } + if ((argnum = psArgumentGet(argc, argv, "-recmask"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousMask = IN_NEBULOUS(argv[argnum]); + if (nebulousMask != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "mask image must be %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "RECOVERY.MASK", 0, + "name of input mask image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else if (gotMask) { + psError(PS_ERR_UNKNOWN, true, "-recmask is required with -mask\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-recweight"))) { + psArgumentRemove(argnum, &argc, argv); + bool nebulousWeight = IN_NEBULOUS(argv[argnum]); + if (nebulousWeight != nebulousImage) { + psError(PS_ERR_UNKNOWN, true, "weight image must have %snebulous path with %s image path\n", + nebulousImage ? "" : "non ", nebulousImage ? "nebulous" : "regular"); + usage(); + } + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "RECOVERY.WEIGHT", 0, + "name of input weight image", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } else if (gotWeight) { + psError(PS_ERR_UNKNOWN, true, "-recweight is required with -weight\n"); + usage(); + } + + if ((argnum = psArgumentGet(argc, argv, "-remove"))) { + if (!gotReplace) { + psError(PS_ERR_UNKNOWN, true, "-replace is required with -remove\n"); + usage(); + } + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "REMOVE", 0, "remove original files", + true); + } + + if (argc != 1) { + psString unexpectedArguments = NULL; + for (int i=1; iinImage->pmfile) { + // image data from pmFPAfile (diff or warp file) + readImageFrom_pmFile(sf); + } else { + // image data directly from psFits + readImage(sf->inImage, sf->extnum, sf->stage, false); + } + // read the recovery pixels + readImage(sf->recImage, sf->extnum, sf->stage, false); + + sf->outImage->header = (psMetadata*) psMemIncrRefCounter(sf->inImage->header); + addDestreakKeyword(sf->outImage->header, false); + + if (!SFILE_IS_IMAGE(sf->inImage)) { + // fprintf(stderr, "skipping extnum: %d not an image\n", sf->extnum); + // XXX: This extension is probably a video table. + copyTable(sf->outImage, sf->inImage, sf->extnum); + return false; + } + + if (sf->inImage->image) { + setupImageRefs(sf->outImage, NULL, sf->inImage, sf->extnum, false); + } else { + // Image cubes are handeled specially + } + + // set up the compression parameters + copyFitsOptions(sf->outImage, sf->recImage, sf->inImage, sf->tiles); + + if (sf->inMask) { + readImage(sf->inMask, sf->extnum, sf->stage, true); + readImage(sf->recMask, sf->extnum, sf->stage, true); + sf->outMask->header = (psMetadata*) psMemIncrRefCounter(sf->inMask->header); + + addDestreakKeyword(sf->outMask->header, false); + + setupImageRefs(sf->outMask, NULL, sf->inMask, sf->extnum, false); + + copyFitsOptions(sf->outMask, NULL, sf->inMask, sf->tiles); + } + + if (sf->inWeight) { + readImage(sf->inWeight, sf->extnum, sf->stage, false); + readImage(sf->recWeight, sf->extnum, sf->stage, false); + + sf->outWeight->header = (psMetadata*) psMemIncrRefCounter(sf->inWeight->header); + addDestreakKeyword(sf->outWeight->header, false); + setupImageRefs(sf->outWeight, NULL, sf->inWeight, sf->extnum, false); + + copyFitsOptions(sf->outWeight, NULL, sf->inWeight, sf->tiles); + } + + return true; +} + +static void writeImages(streakFiles *sf, bool exciseImageCube) +{ + psString extname = NULL; + if (sf->nHDU > 1) { + bool mdok; + extname = psMetadataLookupStr(&mdok, sf->inImage->header, "EXTNAME"); + } + if (sf->inImage->numZPlanes == 0) { + // note exciseing complete images is handled in readAndCopyToOutput + writeImage(sf->outImage, extname, sf->extnum); + } else { +#ifdef TODO + // we have an image cube + double initValue; + // otherwise write it to the output + writeImageCube(sf->outImage, sf->recImage->imagecube, extname, sf->extnum); + + // borrow one of the images from the imagecube and set it to init value + psImage *image = psArrayGet (sf->inImage->imagecube, 0); + psMemIncrRefCounter(image); + psImageInit(image, initValue); + if (exciseImageCube) { + sf->outImage->image = image; + writeImage(sf->outImage, extname, sf->extnum); + } else { + // write zero valued image to reccovery + if (sf->recImage) { + sf->recImage->image = image; + writeImage(sf->recImage, extname, sf->extnum); + } + } +#endif + // Assumption: there are no mask and weight images for video cells because they only appear + // at the raw stage. TODO: insure this + return; + } + if (sf->outMask) { + writeImage(sf->outMask, extname, sf->extnum); + } + if (sf->outWeight) { + writeImage(sf->outWeight, extname, sf->extnum); + } +} Index: /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksutil.c =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksutil.c (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/remove/src/streaksutil.c (revision 41117) @@ -0,0 +1,52 @@ +#include "streaksremove.h" + +psString pathToDirectory(char *path) +{ + // insure that path ends in / + int len = strlen(path); + psString dir = NULL; + if (strrchr(path, '/') != (path + len - 1)) { + psStringAppend(&dir, "%s/", path); + } else { + dir = psStringCopy(path); + } + return dir; +} + +ippStage +parseStage(psString stageStr) +{ + if (!strcmp("raw", stageStr)) { + return IPP_STAGE_RAW; + } else if (!strcmp("chip", stageStr)) { + return IPP_STAGE_CHIP; + } else if (!strcmp("warp", stageStr)) { + return IPP_STAGE_WARP; + } else if (!strcmp("diff", stageStr)) { + return IPP_STAGE_DIFF; + } else { + psError(PS_ERR_UNKNOWN, true, "unknown stage string: %s\n", stageStr); + streaksExit("", PS_EXIT_DATA_ERROR); + // notreached + return IPP_STAGE_NONE; + } +} + +streakFiles *ourStreakFiles = NULL; + +void +setStreakFiles(streakFiles *sfiles) +{ + ourStreakFiles = sfiles; +} + +// to enhance clarity in these programs we don't propagate errors up the stack +// we just bail out +void streaksExit(psString str, int exitCode) { + psErrorStackPrint(stderr, "%s", str); + if (ourStreakFiles) { + deleteTemps(ourStreakFiles); + } + exit(exitCode); +} + Index: /branches/ccl_branches/ipponly-20191108/magic/verify/Makefile =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/verify/Makefile (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/verify/Makefile (revision 41117) @@ -0,0 +1,38 @@ +TARGETS = VerifyStreaks + +CXX = c++ +CXXFLAGS = -W -Wall -O3 -DNDEBUG +# CXXFLAGS = -W -Wall -g + +QTLIB_INC = /home/panstarrs/ipp/src/qtlib/include +QTLIB_LIB = /home/panstarrs/ipp/src/qtlib/lib + +SSA_SRC = ../ssa-core-cpp/src +SSA_LIB = ../ssa-core-cpp/build +MAGIC_SRC = ../magic/ + +PSLIB_DIR = $(PSCONFDIR)/$(PSCONFIG)/lib +PSINC_DIR = $(PSCONFDIR)/$(PSCONFIG)/include + +CINC = -I. -I$(QTLIB_INC) -I$(SSA_SRC) -I$(PSINC_DIR) -I$(MAGIC_SRC) +CLIB = -L. -L$(QTLIB_LIB) -L$(SSA_LIB) -I$(PSINC_DIR) -lcfitsio -lSSA -lQtCore -lQtGui + +all : $(TARGETS) + +% :: %.cpp + $(CXX) $(CXXFLAGS) $(CINC) $< $(CLIB) -o $@ + +.PHONY : clean + +.SILENT : clean + +clean : + - rm $(TARGETS) + +DESTDIR=$(PSCONFDIR)/$(PSCONFIG) + +install: $(TARGETS) + cp VerifyStreaks $(DESTDIR)/bin + chmod 755 $(DESTDIR)/bin/VerifyStreaks + cp verifystreaks.sh $(DESTDIR)/bin + chmod 755 $(DESTDIR)/bin/verifystreaks.sh Index: /branches/ccl_branches/ipponly-20191108/magic/verify/verifystreaks.sh =================================================================== --- /branches/ccl_branches/ipponly-20191108/magic/verify/verifystreaks.sh (revision 41117) +++ /branches/ccl_branches/ipponly-20191108/magic/verify/verifystreaks.sh (revision 41117) @@ -0,0 +1,21 @@ +#!/bin/csh -f + +if ($#argv != 4) then + echo "USAGE: verifystreaks.sh (workdir) (exp_id) (magic_id) (outdir)" + exit 1 +endif + +set workdir = $1 +set expID = $2 +set magicID = $3 +set outdir = $4 + +mkdir -p $outdir + +# make clusters file: +ls $workdir/$expID/$expID.mgc.$magicID.*.clusters | sed s/.clusters// > $outdir/clusters.list + +# run VerifyStreaks + +VerifyStreaks --out $outdir --clusters $outdir/clusters.list $workdir/$expID/$expID.mgc.$magicID.root.streakMap +