Index: /branches/eam_branches/eam_branch_20090312/ppImage/Doxyfile.in =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/Doxyfile.in (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/Doxyfile.in (revision 23312) @@ -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 = ppImage + +# 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/eam_branches/eam_branch_20090312/ppImage/Makefile.am =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/Makefile.am (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/Makefile.am (revision 23312) @@ -0,0 +1,3 @@ +SUBDIRS = src + +CLEANFILES = *~ core core.* Index: /branches/eam_branches/eam_branch_20090312/ppImage/autogen.sh =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/autogen.sh (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/autogen.sh (revision 23312) @@ -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=ppImage +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 $PROJECT." +fi Index: /branches/eam_branches/eam_branch_20090312/ppImage/configure.ac =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/configure.ac (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/configure.ac (revision 23312) @@ -0,0 +1,36 @@ +AC_PREREQ(2.61) + +AC_INIT([ppImage], [1.1.0], [ipp-support@ifa.hawaii.edu]) +AC_CONFIG_SRCDIR([src]) + +AM_INIT_AUTOMAKE([1.6 foreign dist-bzip2]) +AM_CONFIG_HEADER([src/config.h]) +AM_MAINTAINER_MODE + +IPP_STDCFLAGS + +AC_LANG(C) +AC_GNU_SOURCE +AC_PROG_CC_C99 +AC_PROG_INSTALL +AC_PROG_LIBTOOL +AC_SYS_LARGEFILE + +PKG_CHECK_MODULES([PSLIB], [pslib >= 1.0.0]) +PKG_CHECK_MODULES([PSMODULE], [psmodules >= 1.0.0]) +PKG_CHECK_MODULES([PSPHOT], [psphot >= 0.8.0]) +PKG_CHECK_MODULES([PSASTRO], [psastro >= 0.8.0]) +PKG_CHECK_MODULES([PPSTATS], [ppStats >= 1.0.0]) + +IPP_STDOPTS +CFLAGS="${CFLAGS=} -Wall -Werror" + +AC_SUBST([PPIMAGE_CFLAGS]) +AC_SUBST([PPIMAGE_LIBS]) + +AC_CONFIG_FILES([ + Makefile + src/Makefile + Doxyfile +]) +AC_OUTPUT Index: /branches/eam_branches/eam_branch_20090312/ppImage/notes.txt =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/notes.txt (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/notes.txt (revision 23312) @@ -0,0 +1,23 @@ + +ppImage pmFPAfiles: + + pmFPAfile *input = pmFPAfileDefineFromArgs (&status, config, "PPIMAGE.INPUT", "INPUT"); + pmFPAfile *inputMask = pmFPAfileBindFromArgs(&status, input, config, "PPIMAGE.INPUT.MASK", "INPUT.MASK"); + pmFPAfile *inputWeight = pmFPAfileBindFromArgs(&status, input, config, "PPIMAGE.INPUT.WEIGHT", "INPUT.WEIGHT"); + pmFPAfile *output = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT"); + pmFPAfile *outMask = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.MASK"); + pmFPAfile *outWeight = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.WEIGHT"); + pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, input->fpa, "PPIMAGE.CHIP"); + pmFPAfile *chipMask = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.MASK"); + pmFPAfile *chipWeight = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.WEIGHT"); + pmFPAfile *byFPA1 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA1"); + pmFPAfile *byFPA2 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA2"); + + pmFPAfile *psphotInput = pmFPAfileDefineFromFPA (config, chipImage->fpa, 1, 1, "PSPHOT.INPUT"); + pmFPAfile *psphotOutput = psMetadataLookupPtr (&status, config->files, "PSPHOT.OUTPUT"); + pmFPAfile *psastroInput = pmFPAfileDefineInput (config, psphotOutput->fpa, "PSASTRO.INPUT"); + + pmFPAfile *bin1 = pmFPAfileDefineFromFPA (config, chipImage->fpa, options->xBin1, options->yBin1, "PPIMAGE.BIN1"); + pmFPAfile *bin2 = pmFPAfileDefineFromFPA (config, chipImage->fpa, options->xBin2, options->yBin2, "PPIMAGE.BIN2"); + pmFPAfile *jpg1 = pmFPAfileDefineOutput (config, byFPA1->fpa, "PPIMAGE.JPEG1"); + pmFPAfile *jpg2 = pmFPAfileDefineOutput (config, byFPA2->fpa, "PPIMAGE.JPEG2"); Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/Makefile.am =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/Makefile.am (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/Makefile.am (revision 23312) @@ -0,0 +1,50 @@ +bin_PROGRAMS = ppImage + +noinst_HEADERS = \ + ppImage.h + +#PPIMAGE_VERSION=`if [ -e ../../VERSION ]; then cat ../../VERSION; else svnversion; fi` +#PPIMAGE_BRANCH=`if [ -e ../../BRANCH ]; then cat ../../BRANCH; else svn info | sed -n -e '/URL:/ h' -e '/Repository Root:/ { x; H; x; s|Repository Root: \(.*\)\nURL: \1\(.*\)|\2| ; s|^/|| ; s|/[a-zA-Z]*/src.*|| ; p }'; fi` +#PPIMAGE_SOURCE=`if [ -e ../../SOURCE ]; then cat ../../SOURCE; else svn info | sed -n -e 's/Repository UUID: // p'; fi` + +# Force recompilation of ppImageVersion.c, since it gets the version information +# ppImageVersion.c: FORCE +# touch ppImageVersion.c +# FORCE: ; + +ppImage_CFLAGS = $(PPIMAGE_CFLAGS) $(PPSTATS_CFLAGS) $(PSASTRO_CFLAGS) $(PSPHOT_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS) -DPPIMAGE_VERSION=$(SVN_VERSION) -DPPIMAGE_BRANCH=$(SVN_BRANCH) -DPPIMAGE_SOURCE=$(SVN_SOURCE) +ppImage_LDFLAGS = $(PPIMAGE_LIBS) $(PSASTRO_LIBS) $(PPSTATS_LIBS) $(PSPHOT_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS) +ppImage_SOURCES = \ + ppImage.c \ + ppImageArguments.c \ + ppImageParseCamera.c \ + ppImageLoop.c \ + ppImageCleanup.c \ + ppImageOptions.c \ + ppImageDetrendReadout.c \ + ppImageDetrendRecord.c \ + ppImageDetrendNonLinear.c \ + ppImageDetrendFringe.c \ + ppImageDetrendFree.c \ + ppImageRebinReadout.c \ + ppImageMosaic.c \ + ppImagePhotom.c \ + ppImageAstrom.c \ + ppImageAddstar.c \ + ppImageStatsOutput.c \ + ppImagePixelStats.c \ + ppImageMetadataStats.c \ + ppImageReplaceBackground.c \ + ppImageDefineFile.c \ + ppImageSetMaskBits.c \ + ppImageFileCheck.c \ + ppImageVersion.c \ + ppImageMemory.c + +CLEANFILES = *~ + +clean-local: + -rm -f TAGS +# Tags for emacs +tags: + etags `find . -name \*.[ch] -print` Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocus.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocus.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocus.c (revision 23312) @@ -0,0 +1,74 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +int main(int argc, char **argv) { + + psLibInit(NULL); + + psTimerStart(TIMER_TOTAL); + + // Parse the configuration and arguments + // Open the input image(s) + // Determine camera, format from header if not already defined + // Construct camera in preparation for reading + pmConfig *config = ppFocusArguments(argc, argv); + if (config == NULL) { + psErrorStackPrint(stderr, " "); + exit(1); + } + + // we search the argument data for the named fileset (argname) + psArray *infiles = psMetadataLookupPtr(NULL, config->arguments, "INPUT"); + if (!infiles) { + psTrace("pmFPAfile", 5, "Failed to find INPUT in argument list"); + exit(1); + } + + // allocate vectors for analysis + psVector *focus = psVectorAllocEmpty(infiles->n, PS_TYPE_F32); + psVector *fwhm = psVectorAllocEmpty(infiles->n, PS_TYPE_F32); + + for (int i = 0; i < infiles->n; i++) { + + // define recipe options + // define the active I/O files + ppImageOptions *options = ppFocusParseCamera(config, i); + if (options == NULL) { + psErrorStackPrint(stderr, " "); + exit(1); + } + + // Image Arithmetic Loop + // XXX ppFocus REQUIRES photom: for it to be true? + // + if (!ppImageLoop(config, options)) { + psErrorStackPrint(stderr, " "); + exit(1); + } + + // determine FWHM at reference location in image + // (also removes PPIMAGE.INPUT from config->files) + ppFocusGetFWHM (config, focus, fwhm); + + ppFocusDropCamera (config); + psFree (options); + } + + ppFocusFitFWHM (config, focus, fwhm); + + psLogMsg ("ppFocus", 3, "complete ppFocus run: %f sec\n", psTimerMark (TIMER_TOTAL)); + + // Cleaning up + psFree (focus); + psFree (fwhm); + ppImageCleanup(config, NULL); + return EXIT_SUCCESS; +} + +// ppFocus is a lot like ppImage, but with a few important differences: +// - the input list is a set of independent images (not multiple files for a single image) +// - each pass to ppImageLoop performs the analysis on a different pmFPAfile +// - after each ppImageLoop, grap the input pmFPAfile and extract the FWHM stats Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusArguments.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusArguments.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusArguments.c (revision 23312) @@ -0,0 +1,72 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +static void usage (void) { + fprintf (stderr, "USAGE: ppFocus [-file focus.*.fits] [-list INPUT.txt] OUTPUT\n"); + exit (2); +} + +pmConfig *ppFocusArguments(int argc, char **argv) { + + int N; + bool status; + + if (argc == 1) usage (); + + // load the site-wide configuration information + pmConfig *config = pmConfigRead(&argc, argv, RECIPE_NAME); + if (config == NULL) { + psErrorStackPrint(stderr, "Can't find site configuration!\n"); + exit(EXIT_FAILURE); + } + + // save the following additional recipe values based on command-line options + // these options override the PPIMAGE recipe values loaded from recipe files + psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); + + // save these recipe options until we have loaded the options + // psMetadata *options = psMetadataAlloc (); + // psMetadataAddPtr (config->arguments, PS_LIST_TAIL, "PPIMAGE.OPTIONS", PS_DATA_METADATA, "", options); + + // the following options override the PPIMAGE recipe options + + // recipe option: -usemask : override MASK setting in phase2.recipe + if ((N = psArgumentGet(argc, argv, "-usemask"))) { + psArgumentRemove (N, &argc, argv); + psMetadataAddBool (options, PS_LIST_TAIL, "MASK", PS_META_REPLACE, "", true); + psArgumentRemove (N, &argc, argv); + } + + // XXX add other PPIMAGE recipe options here + + // the input file is a required argument; if not found, we will exit + status = pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list"); + if (!status) { usage ();} + + // if these command-line options are supplied, load the file name lists into config->arguments + // override any configuration-specified source for these files + pmConfigFileSetsMD (config->arguments, &argc, argv, "BIAS", "-bias", "-biaslist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "DARK", "-dark", "-darklist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "FLAT", "-flat", "-flatlist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "MASK", "-mask", "-masklist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "FRINGE", "-fringe", "-fringelist"); + + // chip selection is used to limit chips to be processed + if ((N = psArgumentGet (argc, argv, "-chip"))) { + psArgumentRemove (N, &argc, argv); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "CHIP_SELECTIONS", PS_DATA_STRING, "", + argv[N]); + psArgumentRemove (N, &argc, argv); + } + + if (argc != 2) usage (); + + // Add the input and output images (which remain on the command-line) to the arguments list + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "Name of the output image", + argv[1]); + + return config; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusFitFWHM.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusFitFWHM.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusFitFWHM.c (revision 23312) @@ -0,0 +1,30 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +bool ppFocusFitFWHM (pmConfig *config, psVector *focus, psVector *fwhm) { + + float minFocus; + + psPolynomial1D *poly = psPolynomial1DAlloc (PS_POLYNOMIAL_ORD, 2); + + if (!psVectorFitPolynomial1D (poly, NULL, 0, fwhm, NULL, focus)) { + psError (PS_ERR_UNKNOWN, false, "failed to fit focus/fwhm trend; invalid image data?"); + return false; + } + + if (poly->coeff[2] <= 0.0) { + psLogMsg ("ppFocus", 3, "poor focus fit: zero or negative curvature\n"); + psLogMsg ("ppFocus", 3, "fit coeffs: %f %f %f\n", + poly->coeff[0], poly->coeff[1], poly->coeff[2]); + } + + minFocus = -0.5 * poly->coeff[1] / poly->coeff[2]; + psLogMsg ("ppFocus", 3, "best fit focus: %f\n", minFocus); + psLogMsg ("ppFocus", 3, "fwhm @ min: %f\n", psPolynomial1DEval (poly, minFocus)); + + psFree (poly); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusGetFWHM.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusGetFWHM.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusGetFWHM.c (revision 23312) @@ -0,0 +1,79 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +bool ppFocusGetFWHM (pmConfig *config, psVector *focus, psVector *fwhm) { + + bool status; + pmChip *chip; + pmCell *cell; + pmReadout *readout; + psMetadata *header; + float FOCUS, FWHM, FWHM_X, FWHM_Y, FWHMsum; + int FWHMnum; + + pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSPHOT.OUTPUT"); + if (!status) { + psErrorStackPrint(stderr, "Can't find input data!\n"); + exit(EXIT_FAILURE); + } + + pmFPAview *view = pmFPAviewAlloc (0); + + // - find readouts with measured PSFs + // - measure the average central FWHM for each PSF + FWHMsum = 0.0; + FWHMnum = 0; + + while ((chip = pmFPAviewNextChip (view, input->fpa, 1)) != NULL) { + psLogMsg ("ppImageLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); + if (!chip->process || !chip->file_exists) { continue; } + + while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { + psLogMsg ("ppImageLoop", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (!cell->process || !cell->file_exists) { continue; } + + // process each of the readouts + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + if (!readout->data_exists) { continue; } + + // get average FWHM + // psphotReadout writes the FWHM values into the PSPHOT.HEADER table + // the source of this value depends on the psphot options. + // - if breakPoint is set to PEAKS, the value will not be defined + // - if breakPoint is set to MOMENTS, the PSFSTAR moments are used + // - in all other cases, the psf model is used + header = psMetadataLookupPtr (&status, readout->analysis, "PSPHOT.HEADER"); + if (header == NULL) { + psError(PS_ERR_IO, false, "Missing header in ppFocus"); + continue; + } + + FWHM_X = psMetadataLookupF32 (&status, header, "FWHM_X"); + FWHM_Y = psMetadataLookupF32 (&status, header, "FWHM_Y"); + + FWHMsum += 0.5*(FWHM_X + FWHM_Y); + FWHMnum ++; + + psLogMsg ("ppFocus", 4, "focus pt: %f,%f, fwhm sum: %f, fwhm num: %d\n", FWHM_X, FWHM_Y, FWHMsum, FWHMnum); + } + } + } + + FWHM = FWHMsum / FWHMnum; + + FOCUS = psMetadataLookupF32 (&status, input->fpa->concepts, "FPA.FOCUS"); + + fwhm->data.F32[fwhm->n] = FWHM; + focus->data.F32[focus->n] = FOCUS; + + psVectorExtend (fwhm, 10, 1); + psVectorExtend (focus, 10, 1); + + psLogMsg ("ppFocus", 4, "focus: %f, fwhm: %f (%d)\n", FOCUS, FWHM, FWHMnum); + + psFree (view); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusParseCamera.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusParseCamera.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppFocusParseCamera.c (revision 23312) @@ -0,0 +1,133 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +// XXX clean up error checks: return NULL, not psAbort +ppImageOptions *ppFocusParseCamera (pmConfig *config, int entry) { + + bool status = false; + + // the first input image defines the camera, and all recipes and options that follow + // select only the first file from the INPUT array + pmFPAfile *input = pmFPAfileDefineSingleFromArgs (&status, config, "PPIMAGE.INPUT", "INPUT", entry); + if (!status) { + psError(PS_ERR_IO, false, "Failed to build FPA from PPIMAGE.INPUT"); + return NULL; + } + + // parse the options from the metadata format to the ppImageOptions structure + ppImageOptions *options = ppImageOptionsParse (config); + + // the following are defined from the argument list, if given, + // otherwise they revert to the config information or detrend database if specified + // not all input or output images are used in a given recipe + if (options->doBias) { + if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.BIAS", "BIAS", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_BIAS)) { + psError (PS_ERR_IO, false, "Can't find a bias image source"); + return NULL; + } + } + if (options->doDark) { + if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.DARK", "DARK", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_DARK)) { + psError (PS_ERR_IO, false, "Can't find a dark image source"); + return NULL; + } + } + if (options->doMask) { + if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.MASK", "MASK", PM_FPA_FILE_MASK, PM_DETREND_TYPE_MASK)) { + psError (PS_ERR_IO, false, "Can't find a mask image source"); + return NULL; + } + } + if (options->doFlat) { + if (!ppImageDefineFile (config, input->fpa, "PPIMAGE.FLAT", "FLAT", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_FLAT)) { + psError (PS_ERR_IO, false, "Can't find a shutter image source"); + return NULL; + } + } + + // the following files are output targets + pmFPAfile *output = pmFPAfileDefineOutput (config, input->fpa, "PPIMAGE.OUTPUT"); + pmFPAfile *byChip = pmFPAfileDefineNewCamera (config, "PPIMAGE.OUTPUT.CHIP"); + pmFPAfile *byFPA1 = pmFPAfileDefineNewCamera (config, "PPIMAGE.OUTPUT.FPA1"); + pmFPAfile *byFPA2 = pmFPAfileDefineNewCamera (config, "PPIMAGE.OUTPUT.FPA2"); + + // save any of these files? + output->save = options->BaseFITS; + byChip->save = options->ChipFITS; + byFPA1->save = options->FPA1FITS; + byFPA2->save = options->FPA2FITS; + + // output is used as a carrier: input to byChip + output->freeLevel = PM_FPA_LEVEL_CHIP; + + // define the binned target files (which may just be carriers for some camera configurations) + pmFPAfile *bin1 = pmFPAfileDefineFromFPA (config, byChip->fpa, options->xBin1, options->yBin1, "PPIMAGE.BIN1"); + pmFPAfile *bin2 = pmFPAfileDefineFromFPA (config, byChip->fpa, options->xBin2, options->yBin2, "PPIMAGE.BIN2"); + + // bin1 and bin2 are used as carriers: input for byFPA1, byFPA2 + bin1->freeLevel = PM_FPA_LEVEL_FPA; + bin2->freeLevel = PM_FPA_LEVEL_FPA; + + pmFPAfile *jpg1 = pmFPAfileDefineOutput (config, byFPA1->fpa, "PPIMAGE.JPEG1"); + pmFPAfile *jpg2 = pmFPAfileDefineOutput (config, byFPA2->fpa, "PPIMAGE.JPEG2"); + + // XXX we could potentially not define these pmFPAfiles if no output is requested... + bin1->save = options->Bin1FITS; + bin2->save = options->Bin2FITS; + jpg1->save = options->Bin1JPEG; + jpg2->save = options->Bin2JPEG; + + // Chip selection: turn on only the chips specified (pass status to suppress missing-key log msg) + char *chipLine = psMetadataLookupStr(&status, config->arguments, "CHIP_SELECTIONS"); + psArray *chips = psStringSplitArray (chipLine, ",", false); + if (chips->n > 0) { + pmFPASelectChip (input->fpa, -1, true); // deselect all chips + for (int i = 0; i < chips->n; i++) { + int chipNum = atoi(chips->data[i]); + if (! pmFPASelectChip(input->fpa, chipNum, false)) { + psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum); + return false; + } + } + } + psFree (chips); + + return (options); +} + +// remove from config all pmFPAfiles which could have been added (ignore missing entries) +void ppFocusDropCamera (pmConfig *config) { + + psMetadataRemoveKey (config->files, "PPIMAGE.INPUT"); + + psMetadataRemoveKey (config->files, "PPIMAGE.BIAS"); + psMetadataRemoveKey (config->files, "PPIMAGE.DARK"); + psMetadataRemoveKey (config->files, "PPIMAGE.MASK"); + psMetadataRemoveKey (config->files, "PPIMAGE.FLAT"); + + psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT"); + psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT.CHIP"); + psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT.FPA1"); + psMetadataRemoveKey (config->files, "PPIMAGE.OUTPUT.FPA2"); + + psMetadataRemoveKey (config->files, "PPIMAGE.BIN1"); + psMetadataRemoveKey (config->files, "PPIMAGE.BIN2"); + + psMetadataRemoveKey (config->files, "PPIMAGE.JPEG1"); + psMetadataRemoveKey (config->files, "PPIMAGE.JPEG2"); + + psMetadataRemoveKey (config->files, "PSPHOT.INPUT"); + psMetadataRemoveKey (config->files, "PSPHOT.OUTPUT"); + psMetadataRemoveKey (config->files, "PSPHOT.RESID"); + psMetadataRemoveKey (config->files, "PSPHOT.BACKMDL"); + psMetadataRemoveKey (config->files, "PSPHOT.BACKGND"); + psMetadataRemoveKey (config->files, "PSPHOT.BACKSUB"); + psMetadataRemoveKey (config->files, "PSPHOT.PSF.LOAD"); + psMetadataRemoveKey (config->files, "PSPHOT.PSF.SAVE"); + + return; +} + Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImage.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImage.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImage.c (revision 23312) @@ -0,0 +1,48 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +int main(int argc, char **argv) { + + psLibInit(NULL); + + psTimerStart(TIMER_TOTAL); + + // Parse the configuration and arguments + // Open the input image(s) + // Determine camera, format from header if not already defined + // Construct camera in preparation for reading + pmConfig *config = ppImageArguments(argc, argv); + if (config == NULL) { + psErrorStackPrint(stderr, "Unable to parse command-line arguments."); + ppImageCleanup(config, NULL); + exit(PS_EXIT_CONFIG_ERROR); + } + + ppImageVersionPrint(); + + // define recipe options + // define the active I/O files + ppImageOptions *options = ppImageParseCamera(config); + if (options == NULL) { + psErrorStackPrint(stderr, "Unable to parse camera."); + ppImageCleanup(config, options); + exit(PS_EXIT_CONFIG_ERROR); + } + + // Image Arithmetic Loop + if (!ppImageLoop(config, options)) { + psErrorStackPrint(stderr, "Unable to loop over input"); + ppImageCleanup(config, options); + exit(PS_EXIT_SYS_ERROR); + } + + psLogMsg("ppImage", PS_LOG_INFO, "Complete ppImage run: %f sec\n", psTimerMark(TIMER_TOTAL)); + + // Cleaning up + ppImageCleanup(config, options); + + return PS_EXIT_SUCCESS; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImage.h =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImage.h (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImage.h (revision 23312) @@ -0,0 +1,244 @@ +#ifndef PP_IMAGE_H +#define PP_IMAGE_H + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include +#include // for strcasecmp +#include // for unlink +#include "pslib.h" +#include "psmodules.h" +#include "psphot.h" +#include "psastro.h" +#include "ppStats.h" + +#define RECIPE_NAME "PPIMAGE" // Name of the recipe to use +#define TIMER_TOTAL "PPIMAGE.TOTAL" // Name of timer for total time +#define TIMER_DETREND "PPIMAGE.DETREND" // Name of timer for detrend time +#define TIMER_PHOT "PPIMAGE.PHOT" // Name of timer for photometry time + +// Options for ppImage processing +typedef struct { + // actions which ppImage should perform + bool doMaskBuild; // Build internal mask + bool doVarianceBuild; // Build internal variance map + bool doMask; // Mask bad pixels + bool doNonLin; // Non-linearity correction + bool doOverscan; // Overscan subtraction + bool doBias; // Bias subtraction + bool doDark; // Dark subtraction + bool doRemnance; // Remnance masking + bool doShutter; // Shutter correction + bool doFlat; // Flat-field normalisation + bool doFringe; // Fringe subtraction + bool doPhotom; // Source identification and photometry + bool doBG; // Background subtraction + bool doAstromChip; // per-chip Astrometry + bool doAstromMosaic; // full-mosaic Astrometry + bool doStats; // call ppStats on the image + + // output files requested + bool BaseFITS; + bool BaseMaskFITS; + bool BaseVarianceFITS; + + bool ChipFITS; + bool ChipMaskFITS; + bool ChipVarianceFITS; + + bool FPA1FITS; + bool FPA2FITS; + bool Bin1FITS; + bool Bin1JPEG; + bool Bin2FITS; + bool Bin2JPEG; + + // make values for abstract concepts of masking + psImageMaskType maskValue; // apply this bit-mask to choose masked bits + psImageMaskType markValue; // apply this bit-mask to choose masked bits + psImageMaskType satMask; // Mask value to give saturated pixels + psImageMaskType badMask; // Mask value to give bad pixels + psImageMaskType flatMask; // Mask value to give bad flat pixels + psImageMaskType blankMask; // Mask value to give blank pixels + + // non-linear correction parameters + psDataType nonLinearType; + psMetadataItem *nonLinearData; + void *nonLinearSource; + + // options for the analysis + pmOverscanOptions *overscan; // Overscan options + + // binning parameters + int xBin1; // x-binning, scale 1 + int yBin1; // y-binning, scale 1 + int xBin2; // x-binning, scale 2 + int yBin2; // y-binning, scale 2 + + // parameters used by the fringe analysis + float fringeRej; // Fringe rejection limit + int fringeIter; // Fringe iterations + float fringeKeep; // Fringe keep fraction + + int remnanceSize; // Size for remnance detection + float remnanceThresh; // Threshold for remnance detection + + char *normClass; // class to use for per-class normalization +} ppImageOptions; + +// Cells to be used in the detrend +typedef struct { + pmCell *input; // The input cell, to be operated upon + pmCell *mask; // The bad pixel mask + pmCell *bias; // The bias correction + pmCell *dark; // The dark correction + pmCell *flat; // The flat-field correction +} ppImageDetrend; + +ppImageOptions *ppImageOptionsAlloc(void); + +// Determine the processing options +ppImageOptions *ppImageOptionsParse(pmConfig *config); + +// Get the configuration +pmConfig *ppImageArguments(int argc, char **argv); + +// Determine what type of camera, and initialise +ppImageOptions *ppImageParseCamera(pmConfig *config); +bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options); + +// Loop over the input +bool ppImageLoop(pmConfig *config, ppImageOptions *options); + +// free memory, check for leaks +void ppImageCleanup (pmConfig *config, ppImageOptions *options); + +// perform the detrend analysis on the current readout +bool ppImageDetrendReadout (pmConfig *config, ppImageOptions *options, pmFPAview *view); + +bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options); + +bool ppImageDetrendNonLinear(pmReadout *input, ppImageOptions *options); +bool ppImageDetrendNonLinearLookup(pmReadout *input, psMetadataItem *dataItem); +bool ppImageDetrendNonLinearPolynomial(pmReadout *input, psMetadataItem *dataItem); + +bool ppImageDetrendCell(ppImageDetrend *detrend, ppImageOptions *options, pmConfig *config); +bool ppImageDetrendBias(pmReadout *inputReadout, pmReadout *bias, pmReadout *dark, ppImageOptions *options); +pmReadout* ppImageDetrendSelectFirst(pmCell *cell, char *name, bool doThis); + +bool ppImageDetrendFree(pmConfig *config, pmFPAview *view); +bool ppImageFringeFree(pmConfig *config, pmFPAview *view); + +// Record which detrend file was used for the detrending +bool ppImageDetrendRecord( + pmCell *cell, // Cell of interest + const pmConfig *config, // Configuration + const ppImageOptions *options, // Processing options + const pmFPAview *view // View to cell + ); + +bool ppImageRebinChip (pmConfig *config, pmFPAview *view, ppImageOptions *options, char *outName); + +bool ppImagePhotom (pmConfig *config, pmFPAview *view); +bool ppImageAstrom (pmConfig *config); +bool ppImageAddstar (pmConfig *config); + +// Subtract background from the chip-mosaicked image +bool ppImageSubtractBackground( + pmConfig *config, // Configuration + const pmFPAview *view, // View to chip of interest + const ppImageOptions *options // Processing options + ); + +bool ppImageMosaicChip (pmConfig *config, const ppImageOptions *options, const pmFPAview *view, + const char *outFile, const char *inFile); +bool ppImageMosaicFPA (pmConfig *config, const ppImageOptions *options, + const char *outFile, const char *inFile); + +bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options); + +void ppImageFileCheck (pmConfig *config); + +// functions used by ppFocus +pmConfig *ppFocusArguments(int argc, char **argv); +ppImageOptions *ppFocusParseCamera (pmConfig *config, int entry); +bool ppFocusGetFWHM (pmConfig *config, psVector *focus, psVector *fwhm); +bool ppFocusFitFWHM (pmConfig *config, psVector *focus, psVector *fwhm); + +void ppFocusDropCamera (pmConfig *config); + +bool ppImageDefineFile (pmConfig *config, pmFPA *input, char *filerule, char *argname, pmFPAfileType fileType, pmDetrendType detrendType); + +// write stats to output file +bool ppImageStatsOutput(pmConfig *config, // Configuration + psMetadata *stats, // Statistics output + const ppImageOptions *options // Options + ); + + +// Measure fringes +bool ppImageDetrendFringeMeasure(pmReadout *readout, // Readout to measure + pmCell *fringe, // Fringe cell (each readout is a different component) + const bool isResidual, + const ppImageOptions *options // Options + ); + +// Solve the fringe system +bool ppImageDetrendFringeSolve(pmChip *scienceChip, // Chip with science + const pmChip *refChip, // Chip with reference fringes + const bool isResidual, + const ppImageOptions *options // Options + ); + +// Generate fringe frame +bool ppImageDetrendFringeGenerate(pmCell *science, // Science cell + pmCell *fringes, // Fringe cell, one readout per fringe component + const ppImageOptions *options // Options + ); + + +bool ppImageDetrendFringeApply (pmConfig *config, // config + pmChip *chip, // science chip + const pmFPAview *inputView, // current view + const ppImageOptions *options // options + ); + +/// Return short version information +psString ppImageVersion(void); + +/// Return software source +psString ppImageSource(void); + +/// Return long version information +psString ppImageVersionLong(void); + +/// Populate the header with version information for all dependencies +bool ppImageVersionHeader(psMetadata *metadata ///< Header to populate + ); + +/// Print version information +void ppImageVersionPrint(void); + + +// calculate stats, including MD5 +bool ppImagePixelStats(pmConfig *config,// Configuration + psMetadata *stats, // Statistics output + const ppImageOptions *options, // Options + const pmFPAview *inputView // View to data + ); + +// calculate stats from headers and concepts +bool ppImageMetadataStats(pmConfig *config, // Configuration + psMetadata *stats, // Statistics output + const ppImageOptions *options // Options + ); + +void ppImageFileCheck(pmConfig *config); + +/// Dump memory summary to text file +void ppImageMemoryDump(const char *description); + +#endif Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageAddstar.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageAddstar.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageAddstar.c (revision 23312) @@ -0,0 +1,120 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +bool setFilename (pmFPAfile *file, pmFPAview *view); +bool addstarFile (char *addstarCommand, char *filename); + +bool ppImageAddstar (pmConfig *config) { + + bool status; + pmChip *chip; + pmCell *cell; + pmReadout *readout; + + // select recipe options supplied on command line + psMetadata *recipe = psMetadataLookupPtr (&status, config->recipes, RECIPE_NAME); + + // find a pmFPAfile PSASTRO.OUTPUT + pmFPAfile *file = psMetadataLookupPtr (&status, config->files, "PSASTRO.OUTPUT"); + if (!status) { + psError (PS_ERR_IO, true, "no PSASTRO.OUTPUT file defined"); + return false; + } + + // find the addstar command: %s is replaced with name of output file + char *addstarCommand = psMetadataLookupStr (&status, recipe, "ADDSTAR.COMMAND"); + + pmFPAview *view = pmFPAviewAlloc (0); + if (file->fileLevel == PM_FPA_LEVEL_CHIP) { + // call addstar on this file + setFilename (file, view); + addstarFile (addstarCommand, file->filename); + return true; + } + + while ((chip = pmFPAviewNextChip (view, file->fpa, 1)) != NULL) { + psLogMsg ("ppImageAddstar", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); + if (!chip->process || !chip->file_exists) { continue; } + + if (file->fileLevel == PM_FPA_LEVEL_CHIP) { + // call addstar on this file + setFilename (file, view); + addstarFile (addstarCommand, file->filename); + continue; + } + + while ((cell = pmFPAviewNextCell (view, file->fpa, 1)) != NULL) { + psLogMsg ("ppImageAddstar", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (! cell->process || ! cell->file_exists) { continue; } + + if (file->fileLevel == PM_FPA_LEVEL_CELL) { + // call addstar on this file + setFilename (file, view); + addstarFile (addstarCommand, file->filename); + continue; + } + + // process each of the readouts + while ((readout = pmFPAviewNextReadout (view, file->fpa, 1)) != NULL) { + if (! readout->data_exists) { continue; } + + if (file->fileLevel == PM_FPA_LEVEL_READOUT) { + // call addstar on this file + setFilename (file, view); + addstarFile (addstarCommand, file->filename); + continue; + } else { + psError (PS_ERR_IO, true, "inconsistent fileLevel for %s: %d\n", file->name, file->fileLevel); + return false; + } + } + } + } + return true; +} + +bool setFilename (pmFPAfile *file, pmFPAview *view) { + + // determine the file name + // free a name allocated earlier + psFree (file->filename); + file->filename = pmFPAfileNameFromRule (file->filerule, file, view); + if (file->filename == NULL) { + psError(PS_ERR_IO, true, "Filename is NULL"); + return false; + } + + // indirect filenames are not allowed for output + if (!strcasecmp (file->filename, "@FILES")) { + psError(PS_ERR_IO, true, "indirect filenames are not allowed for output : %s\n", file->name); + return false; + } + if (!strcasecmp (file->filename, "@DETDB")) { + psError(PS_ERR_IO, true, "detrend db filenames are not allowed for output : %s\n", file->name); + return false; + } + return true; +} + +bool addstarFile (char *addstarCommand, char *filename) { + + bool status; + char *addstarLine = psStringCopy(addstarCommand); + psStringSubstitute(&addstarCommand, filename, "%s"); + + // catch addstar stderr/stdout and do what? + psIOBuffer *buffer = psIOBufferAlloc (512); + psPipe *pipe = psPipeOpen (addstarLine); + status = psIOBufferReadEmpty (buffer, 100, pipe->fd_stdout); + if (!status) { + psError (PS_ERR_IO, false, "detselect is not responding"); + } + psFree (addstarLine); + psFree (buffer); + psPipeClose (pipe); + psFree (pipe); + return status; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageArguments.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageArguments.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageArguments.c (revision 23312) @@ -0,0 +1,163 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +static void usage (void) { + fprintf(stderr, "USAGE: ppImage [-file INPUT.fits] [-list INPUT.txt] OUTPUT\n\n"); + fprintf(stderr, "Optional arguments:\n"); + fprintf(stderr, "\t-stats STATS.mdc: Output statistics into STATS.mdc\n"); + fprintf(stderr, "\t-isfringe: The input image contains fringe data.\n"); + fprintf(stderr, "\t-isdark: The input image contains dark data.\n"); + fprintf(stderr, "\t-usemask MASKVAL: Use this mask value (override recipe).\n"); + fprintf(stderr, "\t-chip CHIPNUM: Only process this chip number.\n"); + fprintf(stderr, "\t-norm VALUE: Divide through by this value when done.\n"); + fprintf(stderr, "\t-normlist file.mdc: normalizations by class_id.\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "Input options (single file / file list):\n"); + fprintf(stderr, "\t-bias/-biaslist: Bias image.\n"); + fprintf(stderr, "\t-dark/-darklist: Dark image.\n"); + fprintf(stderr, "\t-shutter/-shutterlist: Shutter image.\n"); + fprintf(stderr, "\t-flat/-flatlist: Flat image.\n"); + fprintf(stderr, "\t-mask/-masklist: Mask image.\n"); + fprintf(stderr, "\t-fringe/-fringelist: Fringe image and data.\n"); + fprintf(stderr, "\n"); + exit (2); +} + +pmConfig *ppImageArguments(int argc, char **argv) +{ + int argnum; // Argument number of interest + + if (argc == 1) { + usage(); + } + + if (psArgumentGet (argc, argv, "-version")) { + psString version; + version = ppImageVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = ppStatsVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psphotVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psastroVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psModulesVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + version = psLibVersionLong(); fprintf (stdout, "%s\n", version); psFree (version); + exit (0); + } + + // load the site-wide configuration information + pmConfig *config = pmConfigRead(&argc, argv, RECIPE_NAME); + if (config == NULL) { + psErrorStackPrint(stderr, "Can't find site configuration!\n"); + exit(EXIT_FAILURE); + } + + // save the following additional recipe values based on command-line options + // these options override the PPIMAGE recipe values loaded from recipe files + psMetadata *options = pmConfigRecipeOptions (config, RECIPE_NAME); + + // save these recipe options until we have loaded the options + // psMetadata *options = psMetadataAlloc (); + // psMetadataAddPtr (config->arguments, PS_LIST_TAIL, "PPIMAGE.OPTIONS", PS_DATA_METADATA, "", options); + + if ((argnum = psArgumentGet(argc, argv, "-stats"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "STATS", PS_META_REPLACE, + "Filename for summary statistics", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-isfringe"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUT_IS_FRINGE", PS_META_REPLACE, + "Input is fringe image", true); + } + if ((argnum = psArgumentGet(argc, argv, "-isdark"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(config->arguments, PS_LIST_TAIL, "INPUT_IS_DARK", PS_META_REPLACE, + "Input is dark image", true); + } + + if ((argnum = psArgumentGet(argc, argv, "-visual"))) { + psArgumentRemove(argnum, &argc, argv); + pmVisualSetVisual(true); + } + + // Number of threads + if ((argnum = psArgumentGet(argc, argv, "-threads"))) { + psArgumentRemove(argnum, &argc, argv); + int nThreads = atoi(argv[argnum]); + psMetadataAddS32(config->arguments, PS_LIST_TAIL, "NTHREADS", 0, "number of warp threads", nThreads); + psArgumentRemove(argnum, &argc, argv); + + // create the thread pool with number of desired threads, supplying our thread launcher function + // XXX need to determine the number of threads from the config data + psThreadPoolInit (nThreads); + } + + // the following options override the PPIMAGE recipe options + + // recipe option: -usemask : override MASK setting in recipe + if ((argnum = psArgumentGet(argc, argv, "-usemask"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddBool(options, PS_LIST_TAIL, "MASK", PS_META_REPLACE, "", true); + psArgumentRemove(argnum, &argc, argv); + } + + // XXX add other PPIMAGE recipe options here + + // the input file is a required argument; if not found, we will exit + pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list"); + + // if these command-line options are supplied, load the file name lists into config->arguments + // override any configuration-specified source for these files + pmConfigFileSetsMD (config->arguments, &argc, argv, "BIAS", "-bias", "-biaslist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "DARK", "-dark", "-darklist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "SHUTTER", "-shutter", "-shutterlist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "FLAT", "-flat", "-flatlist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "MASK", "-mask", "-masklist"); + pmConfigFileSetsMD (config->arguments, &argc, argv, "FRINGE", "-fringe", "-fringelist"); + + // chip selection is used to limit chips to be processed + if ((argnum = psArgumentGet (argc, argv, "-chip"))) { + psArgumentRemove (argnum, &argc, argv); + psMetadataAddStr (config->arguments, PS_LIST_TAIL, "CHIP_SELECTIONS", PS_DATA_STRING, "", argv[argnum]); + psArgumentRemove (argnum, &argc, argv); + } + + // Optional normalization factor + if ((argnum = psArgumentGet(argc, argv, "-norm"))) { + psArgumentRemove(argnum, &argc, argv); + float norm = atof(argv[argnum]); + psMetadataAddF32(config->arguments, PS_LIST_TAIL, "NORMALIZATION", 0, + "Normalisation to apply", norm); + psArgumentRemove(argnum, &argc, argv); + } + + // Optional per-class normalization table + if ((argnum = psArgumentGet(argc, argv, "-normlist"))) { + psArgumentRemove(argnum, &argc, argv); + + unsigned int nFail = 0; + psMetadata *normlist = psMetadataConfigRead (NULL, &nFail, argv[argnum], false); + // XXX allow this file to be in nebulous? + + psMetadataAddMetadata(config->arguments, PS_LIST_TAIL, "NORMALIZATION.TABLE", 0, "Normalization to apply", normlist); + psFree (normlist); + psArgumentRemove(argnum, &argc, argv); + } + + if ((argnum = psArgumentGet(argc, argv, "-dumpconfig"))) { + psArgumentRemove(argnum, &argc, argv); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "DUMP_CONFIG", PS_META_REPLACE, + "Filename for configuration dump", argv[argnum]); + psArgumentRemove(argnum, &argc, argv); + } + + if (argc != 2) usage (); + + // Add the input and output images (which remain on the command-line) to the arguments list + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "Name of the output image", argv[1]); + + return config; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageAstrom.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageAstrom.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageAstrom.c (revision 23312) @@ -0,0 +1,66 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +// this function is mostly equivalent to the top-level of psastro, with some +// modifications since the data has already been loaded. +bool ppImageAstrom (pmConfig *config) { + + bool status; + + // select recipe options supplied on command line + // XXX move these options to the "PSASTRO" recipe? + psMetadata *recipe = psMetadataLookupPtr (&status, config->recipes, PSASTRO_RECIPE); + + // find or define a pmFPAfile PSPHOT.INPUT + pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSASTRO.INPUT"); + PS_ASSERT (input, false); + + ppImageMemoryDump("astrom"); + + // convert the output sources created by psphot into astrometry objects + if (!psastroConvertFPA (input->fpa, recipe)) { + psError (PSASTRO_ERR_UNKNOWN, false, "error reading input data\n"); + return false; + } + + if (!psastroAnalysis (config)) { + psError (PSASTRO_ERR_UNKNOWN, false, "failure in psastro analysis\n"); + return false; + } + + // deactivate the psastro files, reactive when needed + pmFPAfileActivate (config->files, false, NULL); + pmFPAfileActivate (config->files, true, "PSASTRO.OUTPUT"); + + // loop over all chips and perform IO needed + pmChip *chip = NULL; + pmFPAview *view = pmFPAviewAlloc(0);// View for level of interest + while ((chip = pmFPAviewNextChip(view, input->fpa, 1)) != NULL) { + psLogMsg ("ppImageLoop", 4, "Chip %d: %x %x\n", view->chip, chip->file_exists, chip->process); + + ppImageMemoryDump("astrom"); + + // Output and Close at Chip level + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + psFree(view); + return false; + } + } + + // Output and Close FPA + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + psFree(view); + return false; + } + + // deactivate the PSASTRO files, re-active all else + // XXX do we need a way to activate / deactivate other groups? + pmFPAfileActivate (config->files, true, NULL); + pmFPAfileActivate (config->files, false, "PSASTRO.OUTPUT"); + + psFree(view); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageCleanup.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageCleanup.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageCleanup.c (revision 23312) @@ -0,0 +1,30 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +void ppImageCleanup (pmConfig *config, ppImageOptions *options) +{ + // Free memory used by ppImage + psFree(options); + psFree(config); + + // Free memory used by psModules + pmSourceFitSetDone (); + pmConceptsDone(); + pmConfigDone(); + pmModelClassCleanup(); + + // Free memory used by psLib + psLibFinalize(); + + // psMemBlock **memblocks; + // int Nleaks = psMemCheckLeaks (0, &memblocks, stderr, false); + // fprintf (stderr, "Found %d leaks at %s\n", Nleaks, "ppImage"); + + // fprintf(stderr, "Found %d leaks at %s\n", psMemCheckLeaks (0, NULL, NULL, false), "ppImage"); + fprintf(stderr, "Found %d leaks at %s\n", psMemCheckLeaks (0, NULL, stdout, false), "ppImage"); + + return; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDefineFile.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDefineFile.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDefineFile.c (revision 23312) @@ -0,0 +1,56 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +bool ppImageDefineFile(pmConfig *config, pmFPA *input, char *filerule, char *argname, + pmFPAfileType fileType, pmDetrendType detrendType) +{ + bool status; + pmFPAfile *file = NULL; // File to be defined + + if (!file) { + // look for the file on the RUN metadata + file = pmFPAfileDefineFromRun(&status, config, filerule); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition"); + return false; + } + } + if (!file) { + // look for the file on the argument list + file = pmFPAfileDefineFromArgs(&status, config, filerule, argname); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition"); + return false; + } + } + if (!file) { + // look for the file in the camera config table + file = pmFPAfileDefineFromConf(&status, config, filerule); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition"); + return false; + } + } + if (!file) { + // look for the file to be loaded from the detrend database + file = pmFPAfileDefineFromDetDB(&status, config, filerule, input, detrendType); + if (!status) { + psError(PS_ERR_UNKNOWN, false, "failed to load file definition"); + return false; + } + } + + if (!file) { + return false; + } + + if (file->type != fileType) { + psError(PS_ERR_IO, true, "%s is not of type %s", filerule, pmFPAfileStringFromType(fileType)); + return false; + } + return true; +} + Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendFree.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendFree.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendFree.c (revision 23312) @@ -0,0 +1,69 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +// list of the detrend types to free +static char *detrendTypes[] = { + "PPIMAGE.MASK", + "PPIMAGE.BIAS", + "PPIMAGE.DARK", + "PPIMAGE.FLAT", + "PPIMAGE.SHUTTER", + NULL +}; + +bool ppImageDetrendFree (pmConfig *config, pmFPAview *view) { + + bool status; + + for (int i = 0; detrendTypes[i] != NULL; i++) { + + pmFPAfile *file = psMetadataLookupPtr(&status, config->files, detrendTypes[i]); // File of interest + if (!file) continue; // not all detrends are used in any given run + + // this only returns false on a failure. if we are not ready to write or close, it is not an error + if (!pmFPAfileWrite (file, view, config)) { + psError(PS_ERR_IO, false, "failed to WRITE %s", file->name); + return false; + } + if (!pmFPAfileClose(file, view)) { + psError(PS_ERR_IO, false, "failed to CLOSE for %s", file->name); + return false; + } + if (!pmFPAfileFreeData(file, view)) { + if (!psMetadataRemoveKey(config->files, file->name)) { + psError(PS_ERR_IO, false, "failed to remove %s in FPA_AFTER block", file->name); + return false; + } + } + } + return true; +} + +bool ppImageFringeFree (pmConfig *config, pmFPAview *view) { + + bool status; + + pmFPAfile *file = psMetadataLookupPtr(&status, config->files, "PPIMAGE.FRINGE"); // File of interest + if (!file) return true; + + // this only returns false on a failure. if we are not ready to write or close, it is not an error + if (!pmFPAfileWrite (file, view, config)) { + psError(PS_ERR_IO, false, "failed to WRITE %s", file->name); + return false; + } + if (!pmFPAfileClose(file, view)) { + psError(PS_ERR_IO, false, "failed to CLOSE for %s", file->name); + return false; + } + if (!pmFPAfileFreeData(file, view)) { + if (!psMetadataRemoveKey(config->files, file->name)) { + psError(PS_ERR_IO, false, "failed to remove %s in FPA_AFTER block", file->name); + return false; + } + } + + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendFringe.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendFringe.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendFringe.c (revision 23312) @@ -0,0 +1,351 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +bool ppImageDetrendFringeMeasure(pmReadout *readout, pmCell *fringe, const bool isResidual, const ppImageOptions *options) +{ + PS_ASSERT_PTR_NON_NULL(readout, false); + PS_ASSERT_PTR_NON_NULL(fringe, false); + PS_ASSERT_PTR_NON_NULL(options, false); + + // Reference fringe measurements + psArray *references = psMemIncrRefCounter(psMetadataLookupPtr(NULL, fringe->analysis, + "FRINGE.MEASUREMENTS")); + if (!references) { + references = pmFringesParse(fringe); // Reference fringes + if (!references) { + psError(PS_ERR_IO, false, "Unable to find fringe references.\n"); + return false; + } + psMetadataAdd(fringe->analysis, PS_LIST_TAIL, "FRINGE.MEASUREMENTS", PS_DATA_UNKNOWN, + "Fringe measurements", references); + } + + pmFringeStats *reference = references->data[0]; // Take the first as representative + pmFringeRegions *regions = reference->regions; // Regions to measure + pmFringeStats *measurements = pmFringeStatsMeasure(regions, readout, options->maskValue); // Fringe stats + + // Normalise measurements by the exposure time + bool mdok; // Status of MD lookup + float expTime = psMetadataLookupF32(&mdok, readout->parent->concepts, "CELL.EXPOSURE"); // Exp. time + if (!mdok || !isfinite(expTime)) { + psError(PS_ERR_UNKNOWN, false, "CELL.EXPOSURE is not set for --- can't normalise fringes\n"); + psFree(measurements); + return false; + } + if (expTime == 0) { + psWarning("Exposure time is zero --- are you sure you want fringe subtraction?\n"); + expTime = 1.0; + } + // normalize by exposure time : NOTE df is 1/sigma + psBinaryOp(measurements->f, measurements->f, "*", psScalarAlloc(1.0 / expTime, PS_TYPE_F32)); + psBinaryOp(measurements->df, measurements->df, "*", psScalarAlloc(expTime, PS_TYPE_F32)); + + char *scienceFringes = NULL; + if (isResidual) { + scienceFringes = psStringCopy ("FRINGE.RESIDUALS"); + } else { + scienceFringes = psStringCopy ("FRINGE.MEASUREMENTS"); + } + + // Science fringe measurements + pmFringeStats *previous = psMetadataLookupPtr(NULL, readout->parent->analysis, scienceFringes); + if (previous) { + // Multiple readouts: concatenate + psArray *concatenate = psArrayAlloc(2); // Array to hold fringes + + // Concatenate science measurements + concatenate->data[0] = previous; + concatenate->data[1] = measurements; + pmFringeStats *new = pmFringeStatsConcatenate(concatenate, NULL, NULL); // New measurements + psFree(measurements); + measurements = new; + + // Concatenate reference measurements (duplication, so the science and reference line up) + for (int i = 0; i < references->n; i++) { + concatenate->data[0] = concatenate->data[1] = references->data[i]; + pmFringeStats *refNew = pmFringeStatsConcatenate(concatenate, NULL, NULL); + psFree(references->data[i]); + references->data[i] = refNew; + } + concatenate->data[0] = concatenate->data[1] = NULL; + psFree(concatenate); + } + + psMetadataAdd(readout->parent->analysis, PS_LIST_TAIL, scienceFringes, + PS_DATA_UNKNOWN | PS_META_REPLACE, "Fringe measurements", measurements); + psFree(measurements); + psFree(scienceFringes); + psFree(references); + + return true; +} + + +// Pull the fringes out of the cell analysis FRINGE.MEASUREMENTS for a chip +// XXX need some error checks +static psArray *getFringes(const pmChip *chip, const char *source) +{ + psArray *cells = chip->cells; // Component cells + psArray *fringes = psArrayAlloc(cells->n); // Fringes, to return + for (int i = 0; i < cells->n; i++) { + pmCell *cell = cells->data[i]; // Cell of interest + + // XXX for now, skip the video cells (cell->readouts->n > 1) + if (cell->readouts->n > 1) { + psWarning ("Skipping Video Cell for ppImageDetrendFringe.c:getFringes"); + continue; + } + + fringes->data[i] = psMemIncrRefCounter(psMetadataLookupPtr(NULL, cell->analysis, source)); + } + + return fringes; +} + + +// Solve the fringe system: we have science fringe measurements for each cell, and an array of reference +// fringe measurements for each cell. Need to concatenate these together first, and then solve. +bool ppImageDetrendFringeSolve(pmChip *scienceChip, const pmChip *refChip, const bool isResidual, const ppImageOptions *options) +{ + PS_ASSERT_PTR_NON_NULL(scienceChip, NULL); + PS_ASSERT_PTR_NON_NULL(refChip, NULL); + PS_ASSERT_PTR_NON_NULL(options, NULL); + + psArray *science = NULL; + if (isResidual) { + science = getFringes(scienceChip, "FRINGE.RESIDUALS"); // Fringe residuals on science chip + } else { + science = getFringes(scienceChip, "FRINGE.MEASUREMENTS"); // Fringe measurements on science chip + } + + pmFringeStats *scienceCat = pmFringeStatsConcatenate(science, NULL, NULL); // Science fringes + psFree(science); + + // Need to transform the array of cells each with an array of fringes --> array of fringes for the chip as + // a whole + psArray *references = getFringes(refChip, "FRINGE.MEASUREMENTS"); // Fringe measurements on reference chip + int numRefs = ((psArray*)references->data[0])->n; // Number of reference fringes + psArray *referencesCat = psArrayAlloc(numRefs); // Reference fringes + for (int i = 0; i < numRefs; i++) { // Iterate over fringes + psArray *refs = psArrayAlloc(references->n); // Array of fringes for each cell + for (int j = 0; j < references->n; j++) { // Iterate over cells + psArray *ref = references->data[j]; // Array of references for this cell + refs->data[j] = psMemIncrRefCounter(ref->data[i]); + } + referencesCat->data[i] = pmFringeStatsConcatenate(refs, NULL, NULL); + psFree(refs); + } + psFree(references); + + // Now we can solve + psTrace("ppImage", 3, "Solving fringe system...\n"); + pmFringeScale *solution = pmFringeScaleMeasure(scienceCat, referencesCat, options->fringeRej, + options->fringeIter, options->fringeKeep); + + if (isResidual) { + psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.RESIDUAL.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); + } else { + psMetadataAdd(scienceChip->analysis, PS_LIST_TAIL, "FRINGE.SOLUTION", PS_DATA_UNKNOWN, "Fringe solution", solution); + } + +# if (0) + // write the fringe amplitude or residual amplitude to the header + // XXX this is measured per cell, but we only have headers per chip + pmHDU *hdu = pmHDUFromCell(science);// HDU of interest + for (int i = 0; i < solution->nFringeFrames; i++) { + // write metadata header value + psString keyword = NULL; + if (isResidual) { + psStringAppend (&keyword, "FRES_%02dV", i); + } else { + psStringAppend (&keyword, "FRNG_%02dV", i); + } + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); + psFree (keyword); + + keyword = NULL; + if (isResidual) { + psStringAppend (&keyword, "FRES_%02dE", i); + } else { + psStringAppend (&keyword, "FRNG_%02dE", i); + } + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); + psFree (keyword); + } +# endif + + psFree(solution); + psFree(scienceCat); + psFree(referencesCat); + + return true; +} + + +bool ppImageDetrendFringeGenerate(pmCell *science, pmCell *fringes, const ppImageOptions *options) +{ + PS_ASSERT_PTR_NON_NULL(science, false); + PS_ASSERT_PTR_NON_NULL(fringes, false); + + pmFringeScale *solution = psMetadataLookupPtr(NULL, science->parent->analysis, "FRINGE.SOLUTION"); + if (!solution) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find fringe solution.\n"); + return false; + } + assert(fringes->readouts->n == solution->nFringeFrames); + + bool mdok; // Status of MD lookup + float expTime = psMetadataLookupF32(&mdok, science->concepts, "CELL.EXPOSURE"); // Exp. time + if (!mdok || !isfinite(expTime)) { + psError(PS_ERR_UNKNOWN, true, "CELL.EXPOSURE is not set --- can't renormalise fringes\n"); + return false; + } + if (expTime == 0) { + psWarning("Exposure time is zero --- are you sure you want fringe subtraction?\n"); + expTime = 1.0; + } + + pmHDU *hdu = pmHDUFromCell(science);// HDU of interest + + // Construct the fringe image from the scale + psTrace("ppImage", 3, "Generating fringe correction...\n"); + psImage *sumFringe = NULL; // Sum of the fringes + for (int i = 0; i < solution->nFringeFrames; i++) { + pmReadout *fringeRO = fringes->readouts->data[i]; // Fringe readout + psImage *fringe = fringeRO->image; // Fringe image + psTrace("ppImage", 5, "Scale for fringe component %d is %f\n", + i, solution->coeff->data.F32[i + 1]); + psBinaryOp(fringe, fringe, "*", psScalarAlloc(solution->coeff->data.F32[i + 1], PS_TYPE_F32)); + if (!sumFringe) { + sumFringe = psImageCopy(NULL, fringe, PS_TYPE_F32); + } else { + psBinaryOp(sumFringe, sumFringe, "+", fringe); + } + + psVector *md5 = psImageMD5(fringe); // md5 hash + psString md5string = psMD5toString(md5); // String + psFree(md5); + psStringPrepend(&md5string, "Fringe image %d (scale %.3f) MD5: ", + i, solution->coeff->data.F32[i + 1]); + psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, + md5string, ""); + psFree(md5string); + +# if (0) + // write metadata header value + // XXX this is measured per cell, but we only have headers per chip + psString keyword = NULL; + psStringAppend (&keyword, "FRNG_%02dV", i); + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude", solution->coeff->data.F32[i + 1]); + psFree (keyword); + + keyword = NULL; + psStringAppend (&keyword, "FRNG_%02dE", i); + psMetadataAddF32(hdu->header, PS_LIST_TAIL, keyword, PS_META_REPLACE, "Fringe Amplitude error", solution->coeffErr->data.F32[i + 1]); + psFree (keyword); +# endif + + } + if (expTime != 1.0) { + psBinaryOp(sumFringe, sumFringe, "*", psScalarAlloc(expTime, PS_TYPE_F32)); + } + + // Apply the correction to all readouts + psArray *readouts = science->readouts; // Array of science readouts + for (int i = 0; i < readouts->n; i++) { + pmReadout *readout = readouts->data[i]; // Readout of interest + if (!readout || !readout->data_exists) { + continue; + } + + // XXX: Make generic, so subregions may be subtracted as well + if (!psBinaryOp(readout->image, readout->image, "-", sumFringe)) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to subtract fringe.\n"); + return false; + } + + // measure residual fringe amplitude. results go to FRINGE.RESIDUALS + ppImageDetrendFringeMeasure (readout, fringes, true, options); + } + psFree(sumFringe); + + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now, used for reporting + psString timeString = psTimeToISO(time); // String with time + psFree(time); + psStringPrepend(&timeString, "Fringe correction completed at "); + psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, + timeString, ""); + psFree(timeString); + + return sumFringe; +} + +bool ppImageDetrendFringeApply (pmConfig *config, pmChip *chip, const pmFPAview *inputView, const ppImageOptions *options) { + + pmCell *cell = NULL; + + assert (options->doFringe); // do not call if not needed + assert (inputView->chip != -1); + assert (inputView->cell == -1); + assert (inputView->readout == -1); + + pmFPAview *view = pmFPAviewAlloc(0); // View for local processing + *view = *inputView; + + // select the reference chip + pmChip *fringe = pmFPAfileThisChip(config->files, view, "PPIMAGE.FRINGE"); + if (!fringe) { + psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); + psFree (view); + return false; + } + + // Solve the fringe system + if (!ppImageDetrendFringeSolve(chip, fringe, false, options)) { + psError(PS_ERR_UNKNOWN, false, "failed to solve the fringe system.\n"); + psFree (view); + return false; + } + + // Go back over the cells to apply the fringe correction + view->cell = view->readout = -1; + while ((cell = pmFPAviewNextCell(view, chip->parent, 1)) != NULL) { + if (!cell->process || !cell->file_exists) { + continue; + } + + // Apply the fringe correction + psTrace("ppImage", 3, "Applying fringe correction...\n"); + pmCell *fringeCell = pmFPAfileThisCell(config->files, view, "PPIMAGE.FRINGE"); + if (!fringeCell) { + psError(PS_ERR_UNKNOWN, false, "missing fringe reference data.\n"); + psFree (view); + return false; + } + + // XXX for now, skip the video cells (cell->readouts->n > 1) + if (cell->readouts->n > 1) { + psWarning ("Skipping Video Cell for ppImageDetrendFringeApply"); + continue; + } + + if (!ppImageDetrendFringeGenerate(cell, fringeCell, options)) { + psError(PS_ERR_UNKNOWN, false, "failed to apply fringe image.\n"); + psFree (view); + return false; + } + } + + // Solve the residual fringe system + if (!ppImageDetrendFringeSolve(chip, fringe, true, options)) { + psError(PS_ERR_UNKNOWN, false, "failed to solve the residual fringe system.\n"); + psFree (view); + return false; + } + + psFree (view); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendNonLinear.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendNonLinear.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendNonLinear.c (revision 23312) @@ -0,0 +1,114 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +bool ppImageDetrendNonLinearPolynomial(pmReadout *input, psMetadataItem *dataItem) { + + // These are the polynomial coefficients + psVector *coeff = dataItem->data.V; // The coefficient vector + if (coeff->type.type != PS_TYPE_F64) { + psVector *temp = psVectorCopy(NULL, coeff, PS_TYPE_F64); // F64 version + psFree (coeff); + coeff = temp; + } + psPolynomial1D *correction = psPolynomial1DAlloc(coeff->n - 1, PS_POLYNOMIAL_ORD); + psFree(correction->coeff); + correction->coeff = psMemIncrRefCounter(coeff->data.F64); + pmNonLinearityPolynomial(input, correction); + psFree(coeff); + psFree(correction); + return true; +} + +bool ppImageDetrendNonLinearLookup(pmReadout *input, psMetadataItem *dataItem) { + + // This is a filename: lookup table + char *name = dataItem->data.V; // Filename + psLookupTable *table = psLookupTableAlloc(name, "%f %f", 0); + if (psLookupTableRead(table) <= 0) { + psErrorStackPrint(stderr, "Unable to read non-linearity correction file " + "%s --- ignored\n", name); + return false; + } +#ifdef PRODUCTION + pmNonLinearityLookup(input, table); +#else + psVector *influx = table->values->data[0]; + psVector *outflux = table->values->data[1]; + pmNonLinearityLookup(input, influx, outflux); +#endif + psFree(table); + return true; +} + +bool ppImageDetrendNonLinear(pmReadout *input, ppImageOptions *options) { + + psMetadataItem *concept; + pmCell *cell = input->parent; + + switch (options->nonLinearType) { + case PS_DATA_VECTOR: + ppImageDetrendNonLinearPolynomial (input, options->nonLinearData); + return true; + + case PS_DATA_STRING: + ppImageDetrendNonLinearLookup (input, options->nonLinearData); + return true; + + case PS_DATA_METADATA: + // XXX EAM: this is somewhat confusing : let's wrap in a function when i understand it + + // Go looking for the value in the hierarchy + concept = psMetadataLookup(cell->concepts, options->nonLinearSource); + if (! concept) { + pmChip *chip = cell->parent;// Parent chip + concept = psMetadataLookup(chip->concepts, options->nonLinearSource); + if (! concept) { + pmFPA *fpa = chip->parent; // Parent FPA + concept = psMetadataLookup(fpa->concepts, options->nonLinearSource); + if (! concept) { + psLogMsg("phase2", PS_LOG_WARN, "Unable to find value of concept %s " + "for non-linearity correction --- ignored.\n", (char *)options->nonLinearSource); + return false; + } + } + } + + if (concept->type != PS_DATA_STRING) { + psLogMsg("phase2", PS_LOG_WARN, "Type for concept %p isn't STRING, as" + " expected for non-linearity correction --- ignored.\n", + concept); + return false; + } + + // Get the value of the concept + psString conceptValue = concept->data.V; + psMetadata *folder = (psMetadata *)options->nonLinearData->data.V; + psMetadataItem *optionItem = psMetadataLookup(folder, conceptValue); + if (!optionItem) { + psLogMsg("phase2", PS_LOG_WARN, "Unable to find %s in NONLIN.DATA" + " --- ignored.\n", conceptValue); + return false; + } + + switch (optionItem->type) { + case PS_DATA_VECTOR: + ppImageDetrendNonLinearPolynomial (input, optionItem); + return true; + case PS_DATA_STRING: + ppImageDetrendNonLinearLookup (input, optionItem); + return true; + default: + psLogMsg("phase2", PS_LOG_WARN, "Non-linearity correction " + "desired but unable to interpret NONLIN.DATA for %s" + " --- ignored\n", conceptValue); + return false; + } + default: + psAbort("Invalid options->nonLinearType"); + } + return true; +} + Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendReadout.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendReadout.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendReadout.c (revision 23312) @@ -0,0 +1,171 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +bool ppImageDetrendReadout(pmConfig *config, ppImageOptions *options, pmFPAview *view) +{ + // construct a view for the detrend images (which have only one readout) + pmFPAview *detview = pmFPAviewAlloc(0); + *detview = *view; + detview->readout = 0; + + // find the currently selected readout + pmReadout *input = pmFPAfileThisReadout(config->files, view, "PPIMAGE.INPUT"); + + // Masking on the basis of pixel value needs to be done before anything else, so the values are pristine. + if (options->doMaskBuild) { + pmReadoutGenerateMask(input, options->satMask, options->badMask); + } + // apply the externally supplied mask to the input->mask pixels + if (options->doMask) { + pmReadout *mask = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.MASK"); + pmMaskBadPixels(input, mask, options->maskValue); + } + +# if 0 + // Non-linearity correction + if (options->doNonLin) { + ppImageDetrendNonLinear(detrend->input, input, options); + } +# endif + + // set up the dark and bias + pmCell *dark = NULL; // Multi-dark + pmReadout *oldDark = NULL; // Old-fashioned dark + pmReadout *bias = NULL; + if (options->doBias) { + bias = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.BIAS"); + } + if (options->doDark) { + bool mdok; // Status of MD lookup + psMetadata *recipe = psMetadataLookupPtr (&mdok, config->recipes, RECIPE_NAME); + assert(mdok && recipe); + if (psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { + oldDark = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.DARK"); + } else { + dark = pmFPAfileThisCell(config->files, detview, "PPIMAGE.DARK"); + } + } + + // Bias, dark and overscan subtraction are all merged. + if (options->doBias || options->doOverscan) { + if (!pmBiasSubtract(input, options->overscan, bias, oldDark, view)) { + psError(PS_ERR_UNKNOWN, false, "Unable to subtract bias."); + psFree(detview); + return false; + } + } + + // Weight on the basis of pixel value needs to be done after the overscan has been subtracted + if (options->doVarianceBuild) { + // create the target mask and variance images + pmReadoutGenerateVariance(input, true); + } + + if (options->doDark && dark) { + if (!pmDarkApply(input, dark, options->maskValue)) { + psError(PS_ERR_UNKNOWN, false, "Unable to subtract dark."); + psFree(detview); + return false; + } + } + + if (options->doRemnance) { + if (!pmRemnance(input, options->maskValue, options->badMask, + options->remnanceSize, options->remnanceThresh)) { + psError(PS_ERR_UNKNOWN, false, "Unable to mask remnance."); + psFree(detview); + return false; + } + } + + // Shutter correction + if (options->doShutter) { + pmReadout *shutter = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.SHUTTER"); + if (!pmShutterCorrectionApply(input, shutter, pmConfigMaskGet("FLAT", config))) { + psFree(detview); + return false; + } + } + + // Flat-field correction (no options used?) + if (options->doFlat) { + pmReadout *flat = pmFPAfileThisReadout(config->files, detview, "PPIMAGE.FLAT"); + if (!pmFlatField(input, flat, options->flatMask)) { + psFree(detview); + return false; + } + } + + // Normalization by a single (known) constant + bool mdok; // Status of MD lookup + float norm = psMetadataLookupF32(&mdok, config->arguments, "NORMALIZATION"); + if (mdok && isfinite(norm) && norm != 1.0) { + pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest + psString comment = NULL; // Comment to add + psStringAppend(&comment, "Normalization: %f", norm); + psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, comment, ""); + psFree(comment); + + psBinaryOp(input->image, input->image, "*", psScalarAlloc(norm, PS_TYPE_F32)); + } + +# if (1) + // Normalization by per-class values + psMetadata *normlist = psMetadataLookupMetadata(&mdok, config->arguments, "NORMALIZATION.TABLE"); + if (normlist) { + pmFPAfile *inputFile = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.INPUT"); + + // get the menu of class IDs + psMetadata *menu = psMetadataLookupMetadata(&mdok, inputFile->camera, "CLASSID"); + if (!menu) { + psError(PS_ERR_IO, false, "Unable to find CLASSID metadata in camera configuration"); + psFree(detview); + return false; + } + // get the rule for class_id for the desired class + const char *rule = psMetadataLookupStr(&mdok, menu, options->normClass); + if (!rule) { + psError(PS_ERR_IO, false, "Unable to find NORM.CLASS value %s in CLASSID in camera configuration", options->normClass); + psFree(detview); + return false; + } + // get the class_id from the rule + char *classID = pmFPAfileNameFromRule(rule, inputFile, view); + if (!classID) { + psError(PS_ERR_IO, false, "error converting CLASSID rule %s to name\n", rule); + psFree(detview); + return false; + } + + // get normalization from the class_id + float norm = psMetadataLookupF32 (&mdok, normlist, classID); + + pmHDU *hdu = pmHDUFromReadout(input); // HDU of interest + psString comment = NULL; // Comment to add + psStringAppend(&comment, "Normalization: %f", norm); + psMetadataAddStr(hdu->header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, comment, ""); + psFree(comment); + + // apply the normalization + psBinaryOp(input->image, input->image, "*", psScalarAlloc(norm, PS_TYPE_F32)); + + psFree (classID); + } +# endif + + if (options->doFringe) { + pmCell *fringe = pmFPAfileThisCell(config->files, detview, "PPIMAGE.FRINGE"); + if (!ppImageDetrendFringeMeasure(input, fringe, false, options)) { + psFree(detview); + return false; + } + } + + ppImageMemoryDump("detrend"); + + psFree(detview); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendRecord.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendRecord.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageDetrendRecord.c (revision 23312) @@ -0,0 +1,80 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +static void detrendRecord( + bool doThis, // Are we supposed to do this? + psMetadata *target, // Target metadata + const pmConfig *config, // Configuration + const pmFPAview *view, // View to cell + const char *filename, // Name of file + const char *name, // Name in header + const char *desc // Description + ) +{ + psAssert(config, "Need configuration"); + psAssert(view, "Need view to cell"); + psAssert(name, "Need file name"); + + if (!doThis) { + return; + } + + pmFPAfile *file = psMetadataLookupPtr(NULL, config->files, filename); // File of interest + psAssert(file, "Should be there"); + + if (target) { + psMetadataAddStr(target, PS_LIST_TAIL, name, 0, desc, file->filename); + } + + pmCell *input = pmFPAfileThisCell(config->files, view, "PPIMAGE.INPUT"); // File we're processing + psAssert(input, "Should be there"); + pmHDU *hdu = pmHDUGetHighest(input->parent->parent, input->parent, input); // HDU for cell + + // Strip off path and Nebulous bits + char *base = file->filename; // Base name of file + for (char *new = base; (new = strpbrk(base, "/:")); base = new + 1); // No action + + // We don't want multiple listings in the header saying the same thing, so make sure we haven't put the + // same entry there. Usually (if the detrend and the image have the same file level) there'll only end up + // being one entry. + psString regexp = NULL; // Regular expression + psStringAppend(®exp, "^%s$", name); + psMetadataIterator *iter = psMetadataIteratorAlloc(hdu->header, PS_LIST_HEAD, regexp); // Iterator for hdr + psFree(regexp); + psMetadataItem *item; // Item from iteration + bool found = false; + while (!found && (item = psMetadataGetAndIncrement(iter))) { + if (item->type == PS_DATA_STRING && strcmp(item->data.str, base) == 0) { + found = true; + } + } + psFree(iter); + if (!found) { + psMetadataAddStr(hdu->header, PS_LIST_TAIL, name, PS_META_DUPLICATE_OK, desc, base); + } + + return; +} + + +bool ppImageDetrendRecord(pmCell *cell, const pmConfig *config, const ppImageOptions *options, + const pmFPAview *view) +{ + psMetadata *detrend = psMetadataAlloc(); // Detrend information + psMetadataAddMetadata(cell->analysis, PS_LIST_TAIL, "DETREND", 0, "Detrend information", detrend); + + detrendRecord(options->doMask, detrend, config, view, "PPIMAGE.MASK", "DETREND.MASK", "Mask filename"); + detrendRecord(options->doBias, detrend, config, view, "PPIMAGE.BIAS", "DETREND.BIAS", "Bias filename"); + detrendRecord(options->doDark, detrend, config, view, "PPIMAGE.DARK", "DETREND.DARK", "Dark filename"); + detrendRecord(options->doShutter, detrend, config, view, "PPIMAGE.SHUTTER", "DETREND.SHUTTER", + "Shutter correction filename"); + detrendRecord(options->doFlat, detrend, config, view, "PPIMAGE.FLAT", "DETREND.FLAT", "Flat filename"); + detrendRecord(options->doFringe, detrend, config, view, "PPIMAGE.FRINGE", "DETREND.FRINGE", + "Fringe filename"); + + psFree (detrend); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.c.in =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.c.in (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.c.in (revision 23312) @@ -0,0 +1,26 @@ +/* + * The line + { PPIMAGE_ERR_$X{ErrorCode}, "$X{ErrorDescription}"}, + * (without the Xs) + * will be replaced by values from errorCodes.dat + */ +#include "pslib.h" +#include "ppImageErrorCodes.h" + +void ppImageErrorRegister(void) +{ + static psErrorDescription errors[] = { + { PPIMAGE_ERR_BASE, "First value we use; lower values belong to psLib" }, + { PPIMAGE_ERR_${ErrorCode}, "${ErrorDescription}"}, + }; + static int nerror = PPIMAGE_ERR_NERROR - PPIMAGE_ERR_BASE; // number of values in enum + + for (int i = 0; i < nerror; i++) { + psErrorDescription *tmp = psAlloc(sizeof(psErrorDescription)); + p_psMemSetPersistent(tmp, true); + *tmp = errors[i]; + psErrorRegister(tmp, 1); + psFree(tmp); /* it's on the internal list */ + } + nerror = 0; // don't register more than once +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.dat =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.dat (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.dat (revision 23312) @@ -0,0 +1,10 @@ +# +# This file is used to generate ppImageErrorClasses.h +# +BASE = 500 First value we use; lower values belong to psLib +# these errors correspond to standard exit conditions +ARGUMENTS Incorrect arguments +SYS System error +CONFIG Problem in configure files +PROG Programming error +DATA invalid data Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.h.in =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.h.in (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageErrorCodes.h.in (revision 23312) @@ -0,0 +1,18 @@ +#if !defined(PPIMAGE_ERROR_CODES_H) +#define PPIMAGE_ERROR_CODES_H +/* + * The line + * PPIMAGE_ERR_$X{ErrorCode}, + * (without the X) + * + * will be replaced by values from errorCodes.dat + */ +typedef enum { + PPIMAGE_ERR_BASE = 512, + PPIMAGE_ERR_${ErrorCode}, + PPIMAGE_ERR_NERROR +} ppImageErrorCode; + +void ppImageErrorRegister(void); + +#endif Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageFileCheck.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageFileCheck.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageFileCheck.c (revision 23312) @@ -0,0 +1,60 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +void ppImageFileCheck (pmConfig *config) { + + // add the output names to the output-type files + psMetadataItem *item = NULL; + psMetadataIterator *iter = psMetadataIteratorAlloc (config->files, PS_LIST_HEAD, NULL); + while ((item = psMetadataGetAndIncrement (iter)) != NULL) { + pmFPAfile *file = item->data.V; + pmFPA *fpa = file->fpa; + fprintf (stderr, "file %s\n", file->name); + if (!fpa) { + fprintf (stderr, " has no FPA\n"); + continue; + } + if (fpa->hdu) { + if (fpa->hdu->images) fprintf (stderr, " (%d,%d) images\n", -1, -1); + if (fpa->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", -1, -1); + if (fpa->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", -1, -1); + if (fpa->hdu->header) fprintf (stderr, " (%d,%d) header\n", -1, -1); + } else { + // fprintf (stderr, " has no fpa data (%d,%d)\n", -1, -1); + } + for (int i = 0; i < fpa->chips->n; i++) { + pmChip *chip = fpa->chips->data[i]; + if (chip->hdu) { + if (chip->hdu->images) fprintf (stderr, " (%d,%d) images\n", i, -1); + if (chip->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", i, -1); + if (chip->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", i, -1); + if (chip->hdu->header) fprintf (stderr, " (%d,%d) header\n", i, -1); + } else { + // fprintf (stderr, " has no chip data (%d,%d)\n", i, -1); + } + for (int j = 0; j < chip->cells->n; j++) { + pmCell *cell = chip->cells->data[j]; + if (cell->hdu) { + if (cell->hdu->images) fprintf (stderr, " (%d,%d) images\n", i, j); + if (cell->hdu->variances) fprintf (stderr, " (%d,%d) variances\n", i, j); + if (cell->hdu->masks) fprintf (stderr, " (%d,%d) masks\n", i, j); + if (cell->hdu->header) fprintf (stderr, " (%d,%d) header\n", i, j); + } else { + // fprintf (stderr, " has no cell data (%d,%d)\n", i, j); + } + for (int k = 0; k < cell->readouts->n; k++) { + pmReadout *readout = cell->readouts->data[k]; + if (readout) { + if (readout->image) fprintf (stderr, " (%d,%d,%d) image\n", i, j, k); + if (readout->variance) fprintf (stderr, " (%d,%d,%d) variance\n", i, j, k); + if (readout->mask) fprintf (stderr, " (%d,%d,%d) masks\n", i, j, k); + } + } + } + } + } + psFree (iter); +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageLoop.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageLoop.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageLoop.c (revision 23312) @@ -0,0 +1,235 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +#define ESCAPE(MESSAGE) { \ + psError(PS_ERR_UNKNOWN, false, MESSAGE); \ + psFree(view); \ + return false; \ +} + +bool ppImageLoop(pmConfig *config, ppImageOptions *options) +{ + psMetadata *stats = options->doStats ? psMetadataAlloc() : NULL; // Statistics to output + float timeDetrend = 0; // Amount of time spent in detrend + float timePhot = 0; // Amount of time spent in photometry + + bool status; // Status of MD lookup + pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.INPUT"); + if (!status) { + psErrorStackPrint(stderr, "Can't find input data!\n"); + ppImageCleanup(config, options); + exit(PS_EXIT_PROG_ERROR); + } + + pmConfigCamerasCull(config, NULL); + pmConfigRecipesCull(config, "PPIMAGE,PPSTATS,PSPHOT,MASKS,PSASTRO,JPEG"); + + pmFPAview *view = pmFPAviewAlloc(0);// View for level of interest + pmHDU *lastHDU = NULL; // Last HDU that was updated + + // files associated with the science image + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE("load failure for FPA"); + } + + pmChip *chip; // Chip from FPA + while ((chip = pmFPAviewNextChip(view, input->fpa, 1)) != NULL) { + psLogMsg ("ppImageLoop", 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("load failure for Chip"); + } + + psTimerStart(TIMER_DETREND); + pmCell *cell; // Cell from chip + while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { + psLogMsg ("ppImageLoop", 5, "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("load failure for Cell"); + } + + // Put version information into the header + pmHDU *hdu = pmHDUGetHighest(input->fpa, chip, cell); + if (hdu && hdu != lastHDU) { + ppImageVersionHeader(hdu->header); + lastHDU = hdu; + } + + // XXX for now, skip the video cells (cell->readouts->n > 1) + if (cell->readouts->n > 1) { + psWarning ("Skipping Video Cell for ppImageDetrendReadout"); + continue; + } + + // process each of the readouts + pmReadout *readout; // Readout from cell + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + if (!pmFPAfileIOChecks(config, view, PM_FPA_BEFORE)) { + ESCAPE("load failure for Readout"); + } + if (!readout->data_exists) { + continue; + } + + // XXX set the options->*Mask values here (after the mask images have been loaded + // and before any of the value are used) + if (!ppImageSetMaskBits(config, options)) { + ESCAPE("Unable to set bit masks"); + } + + // perform the detrend analysis + if (!ppImageDetrendReadout(config, options, view)) { + ESCAPE("Unable to detrend readout"); + } + + // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT + if (!ppImageDetrendFree (config, view)) { + ESCAPE("Unable to free detrend images"); + } + } + + if (cell->data_exists) { + ppImageDetrendRecord(cell, config, options, view); + } + // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT + if (!ppImageDetrendFree (config, view)) { + ESCAPE("Unable to free detrend images"); + } + } + // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT + if (!ppImageDetrendFree (config, view)) { + ESCAPE("Unable to free detrend images"); + } + + // Apply the fringe correction + if (options->doFringe) { + if (!ppImageDetrendFringeApply(config, chip, view, options)) { + ESCAPE("Unable to defringe"); + } + } + // free detrend images potentially in use: MASK, BIAS, DARK, SHUTTER, FLAT + if (!ppImageFringeFree (config, view)) { + ESCAPE("Unable to free fringe images"); + } + + // measure various pixel-based statistics for this image + if (!ppImagePixelStats(config, stats, options, view)) { + ESCAPE("Unable to measures pixel stats for image"); + } + if (!ppImageMosaicChip(config, options, view, "PPIMAGE.CHIP", "PPIMAGE.OUTPUT")) { + ESCAPE("Unable to mosaic chip"); + } + timeDetrend += psTimerClear(TIMER_DETREND); + + + // we perform photometry on the readouts of this chip in the output + psTimerStart(TIMER_PHOT); + if (options->doPhotom) { + if (!ppImagePhotom(config, view)) { + ESCAPE("error running photometry."); + } + } + timePhot += psTimerClear(TIMER_PHOT); + + // replace the masked pixels with the background level + if (options->doBG) { + if (!ppImageSubtractBackground(config, view, options)) { + ESCAPE("Unable to subtract background"); + } + } + + // these may be used by ppImageSubtractBackground. + // if these are defined as internal files, drop them here + status = true; + status &= pmFPAfileDropInternal (config->files, "PSPHOT.BACKMDL"); + status &= pmFPAfileDropInternal (config->files, "PSPHOT.BACKMDL.STDEV"); + status &= pmFPAfileDropInternal (config->files, "PSPHOT.BACKGND"); + if (!status) { + psError(PSPHOT_ERR_PROG, false, "trouble dropping internal files"); + psFree (view); + return false; + } + + // binning (used for display) must take place after the background is replaced, if desired + if (!ppImageRebinChip(config, view, options, "PPIMAGE.BIN1")) { + ESCAPE("Unable to bin chip (level 1)."); + } + if (!ppImageRebinChip(config, view, options, "PPIMAGE.BIN2")) { + ESCAPE("Unable to bin chip (level 2)."); + } + + // Close cells (XXX shouldn't pmFPAfileClose iterate down as needed?) + view->cell = -1; + while ((cell = pmFPAviewNextCell(view, input->fpa, 1)) != NULL) { + if (!cell->process || !cell->file_exists) { + continue; + } + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for Cell"); + } + } + + // Close chip + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for Chip"); + } + } + + // generate the full-scale FPA mosaic + if (!ppImageMosaicFPA(config, options, "PPIMAGE.OUTPUT.FPA1", "PPIMAGE.BIN1")) { + ESCAPE("failure in FPA Mosaic (level 1)"); + } + if (!ppImageMosaicFPA(config, options, "PPIMAGE.OUTPUT.FPA2", "PPIMAGE.BIN2")) { + ESCAPE("failure in FPA Mosaic (level 2)"); + } + + // we perform astrometry on all chips after sources have been detected + // this also performs the psastro file IO + if (options->doAstromChip || options->doAstromMosaic) { + if (!ppImageAstrom(config)) { + ESCAPE("error running astrometry."); + } + } + + if (psTraceGetLevel("ppImage") >= 3) { + ppImageFileCheck(config); + } + + // Calculate summary statistics from FPA Metadata + if (!ppImageMetadataStats(config, stats, options)) { + ESCAPE("Unable to determine FPA-level metadata statistics."); + } + + // Output and Close FPA + if (!pmFPAfileIOChecks(config, view, PM_FPA_AFTER)) { + ESCAPE("save failure for FPA"); + } + psFree(view); + + // Dump configuration + psString dump_file = psMetadataLookupStr(&status, config->arguments, "DUMP_CONFIG"); + if (dump_file) { + pmConfigDump(config, input->fpa, dump_file); + } + + // Write out summary statistics + if (options->doStats) { + psMetadataAddF32(stats, PS_LIST_TAIL, "DT_DET", 0, "Time spent detrending (sec)", timeDetrend); + psMetadataAddF32(stats, PS_LIST_TAIL, "DT_PHOT", 0, "Time spent photometering (sec)", timePhot); + psMetadataAddF32(stats, PS_LIST_TAIL, "DT_TOTAL", 0, "Total time (sec)", psTimerMark(TIMER_TOTAL)); + if (!ppImageStatsOutput(config, stats, options)) { + ESCAPE("Unable to write statistics file."); + } + } + psFree (stats); + + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMemory.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMemory.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMemory.c (revision 23312) @@ -0,0 +1,38 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include + +#include "ppImage.h" + +//#define TESTING + +void ppImageMemoryDump(const char *description) +{ +#ifndef TESTING + return; +#else + psMemBlock **leaks = NULL; + int numLeaks = psMemCheckLeaks(0, &leaks, NULL, true); + + static int num = 0; + psString filename = NULL; + psStringAppend(&filename, "%s_%d.txt", description, num++); + FILE *fp = fopen(filename, "w"); + psFree(filename); + + for (int i = 0; i < numLeaks; i++) { + psMemBlock *memBlock = leaks[i]; + fprintf(fp, "%ld : %s at (%s:%d) ID: %lu Ref: %lu\n", + (unsigned long)memBlock->userMemorySize, memBlock->func, memBlock->file, + (int)memBlock->lineno, (unsigned long)memBlock->id, memBlock->refCounter); + } + psFree(leaks); + + fclose(fp); + + return; +#endif +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMetadataStats.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMetadataStats.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMetadataStats.c (revision 23312) @@ -0,0 +1,46 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +// calculate stats from headers and concepts +bool ppImageMetadataStats(pmConfig *config, psMetadata *stats, const ppImageOptions *options) +{ + bool mdok; // Status of MD lookup + + if (!options->doStats) { + return true; + } + + // Extract statistics from the last output fpa + pmFPAfile *outImage = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.OUTPUT"); + pmFPAfile *outPhotom = psMetadataLookupPtr(&mdok, config->files, "PSPHOT.OUTPUT"); + pmFPAfile *outAstrom = psMetadataLookupPtr(&mdok, config->files, "PSASTRO.OUTPUT"); + + if (!outImage && !outPhotom && !outAstrom) { + psError(PS_ERR_UNEXPECTED_NULL, true, + "Unable to find any output file (PPIMAGE.OUTPUT, PSPHOT.OUTPUT, PSASTRO.OUTPUT)."); + return false; + } + + // get the latest output product available + pmFPAfile *output = outAstrom; + if (!output) { + output = outPhotom; + } + if (!output) { + output = outImage; + } + + // extract stats for the complete fpa + pmFPAview *view = pmFPAviewAlloc(0); + if (!ppStatsMetadata(stats, output->fpa, view, options->maskValue, config)) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to generate stats for image."); + psFree(view); + return false; + } + + psFree(view); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMosaic.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMosaic.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageMosaic.c (revision 23312) @@ -0,0 +1,77 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +bool ppImageMosaicChip(pmConfig *config, const ppImageOptions *options, const pmFPAview *view, + const char *outFile, const char *inFile) +{ + bool status; // Status of MD lookup + + pmFPAfile *in = psMetadataLookupPtr(&status, config->files, inFile); // Input file + if (!status) { + psErrorStackPrint(stderr, "Can't find required I/O file!\n"); + exit(EXIT_FAILURE); + } + + pmFPAfile *out = psMetadataLookupPtr(&status, config->files, outFile); // Output file + if (!status) { + psErrorStackPrint(stderr, "Can't find required I/O file!\n"); + exit(EXIT_FAILURE); + } + + pmChip *outChip = pmFPAviewThisChip(view, out->fpa); + pmChip *inChip = pmFPAviewThisChip(view, in->fpa); + if (!outChip->hdu && !outChip->parent->hdu) { + const char *name = psMetadataLookupStr(&status, in->fpa->concepts, "FPA.OBS"); // Name of FPA + pmFPAAddSourceFromView(out->fpa, name, view, out->format); + } + + psTrace("pmChipMosaic", 5, "mosaic chip %s to %s (xbin,ybin: %d,%d to %d,%d)\n", + in->name, out->name, in->xBin, in->yBin, out->xBin, out->yBin); + + // Mosaic the chip, making a deep copy. This has the side effect of making the output + // image products pure trimmed images, but also increases the memory footprint. + status = pmChipMosaic(outChip, inChip, true, options->blankMask); + return status; +} + +bool ppImageMosaicFPA (pmConfig *config, const ppImageOptions *options, const char *outFile, + const char *inFile) +{ + bool status; // Status of MD lookup + + pmFPAfile *in = psMetadataLookupPtr(&status, config->files, inFile); // Input file + if (!status) { + psErrorStackPrint(stderr, "Can't find required I/O file!\n"); + exit(EXIT_FAILURE); + } + + pmFPAfile *out = psMetadataLookupPtr(&status, config->files, outFile); // Output file + if (!status) { + psErrorStackPrint(stderr, "Can't find required I/O file!\n"); + exit(EXIT_FAILURE); + } + + // XXX test printing of all concepts + #if 0 + for (int i = 0; i < in->fpa->chips->n; i++) { + pmChip *chip = in->fpa->chips->data[i]; + for (int j = 0; j < chip->cells->n; j++) { + pmCell *cell = chip->cells->data[j]; + psMetadataPrint(stdout, cell->concepts, 2); + } + } + #endif + + const char *name = psMetadataLookupStr(&status, in->fpa->concepts, "FPA.OBS"); // Name of FPA + + pmFPAview *view = pmFPAviewAlloc(0); + pmFPAAddSourceFromView(out->fpa, name, view, out->format); + psFree(view); + + psTrace ("pmFPAMosaic", 5, "mosaic fpa %s to %s (xbin,ybin: %d,%d to %d,%d)\n", + in->name, out->name, in->xBin, in->yBin, out->xBin, out->yBin); + return pmFPAMosaic(out->fpa, in->fpa, false, options->blankMask); +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageOptions.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageOptions.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageOptions.c (revision 23312) @@ -0,0 +1,287 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +static void imageOptionsFree(ppImageOptions *options) +{ + psFree(options->overscan); + psFree(options->nonLinearData); + psFree(options->nonLinearSource); +} + +ppImageOptions *ppImageOptionsAlloc(void) +{ + ppImageOptions *options = psAlloc(sizeof(ppImageOptions)); + psMemSetDeallocator(options, (psFreeFunc)imageOptionsFree); + + // actions which ppImage should perform + options->doMaskBuild = false; // Build internal mask + options->doVarianceBuild = false; // Build internal variance + options->doMask = false; // Mask bad pixels + options->doNonLin = false; // Non-linearity correction + options->doOverscan = false; // Overscan subtraction + options->doBias = false; // Bias subtraction + options->doDark = false; // Dark subtraction + options->doRemnance = false; // Remnance masking + options->doShutter = false; // Shutter correction + options->doFlat = false; // Flat-field normalisation + options->doFringe = false; // Fringe subtraction + options->doPhotom = false; // Source identification and photometry + options->doAstromChip = false; // Astrometry (per-chip) + options->doAstromMosaic = false; // Astrometry (full-mosaic) + options->doStats = false; // Measure and save image statistics + + // output files requested + options->BaseFITS = false; // create output image + options->BaseMaskFITS = false; // create output mask image + options->BaseVarianceFITS = false; // create output variance image + + options->ChipFITS = false; // create output chip-mosaic image + options->ChipMaskFITS = false; // create output chip-mosaic mask image + options->ChipVarianceFITS = false; // create output chip-mosaic variance image + + options->FPA1FITS = false; // create fpa-mosaic binned image (scale 1) + options->FPA2FITS = false; // create fpa-mosaic binned image (scale 2) + options->Bin1FITS = false; // create binned image (scale 1) + options->Bin2FITS = false; // create binned image (scale 2) + options->Bin1JPEG = false; // create jpeg of binned image (scale 1) + options->Bin2JPEG = false; // create jpeg of binned image (scale 2) + + // default flags for various activities + options->maskValue = 0x00; // Default mask value (used to skip / ignore pixels) + options->satMask = 0x00; // Saturated pixels (supplied to pmReadoutGenerateMask) + options->badMask = 0x00; // Bad (low) pixels (supplied to pmReadoutGenerateMask) + options->flatMask = 0x00; // Bad flat pixels (supplied to pmFlatField) + options->blankMask = 0x00; // Blank (no data, cell gap) pixels (supplied to pmChipMosaic, pmFPAMosaic) + options->markValue = 0x00; // A safe bit for internal marking + + // Non-linearity default options + options->nonLinearType = 0; // Type of non-linearity data (vector, string or metadata) + options->nonLinearData = NULL; // The non-linearity data + options->nonLinearSource = NULL; // If the non-linearity data is a menu, this provides the key + + // Overscan defaults + options->overscan = NULL; // Overscan options + + // binning parameters + options->xBin1 = 16; // x-binning, scale 1 + options->yBin1 = 16; // y-binning, scale 1 + options->xBin2 = 16; // x-binning, scale 2 + options->yBin2 = 16; // y-binning, scale 2 + + // Fringe defaults + options->fringeRej = NAN; // Fringe rejection limit + options->fringeIter = 0; // Fringe iterations + options->fringeKeep = 1.0; // Fringe keep fraction + + // Remnance values + options->remnanceSize = 30; // Size for remnance detection + options->remnanceThresh = 25.0; // Threshold for remnance detection + + // per-class normalization source + options->normClass = NULL; // per-class normalizations refer to this class + + return options; +} + +ppImageOptions *ppImageOptionsParse(pmConfig *config) +{ + bool status; + ppImageOptions *options = ppImageOptionsAlloc (); + + // select the recipe for this analysis + bool mdStatus = false; // Result of MD lookup + psMetadata *recipe = psMetadataLookupMetadata(&mdStatus, config->recipes, RECIPE_NAME); + if (! mdStatus || !recipe) { + psLogMsg("ppImage", PS_LOG_ERROR, "Can't find recipe %s in the RECIPES.\n", RECIPE_NAME); + exit(EXIT_FAILURE); + } + + // Non-linearity recipe options + if (psMetadataLookupBool(NULL, recipe, "NONLIN")) { + psMetadataItem *dataItem = psMetadataLookup(recipe, "NONLIN.DATA"); + if (! dataItem) { + psLogMsg(__func__, PS_LOG_ERROR, "Non-linearity correction desired, but unable to " + "find NONLIN.DATA in recipe %s.", RECIPE_NAME); + exit(EXIT_FAILURE); + } + + options->doNonLin = true; + options->nonLinearType = dataItem->type; + options->nonLinearData = dataItem; + + switch (dataItem->type) { + // No immediate action required + case PS_DATA_VECTOR: + case PS_DATA_STRING: + break; + + // This is a menu; we need the key + case PS_DATA_METADATA: + { + bool status; + options->nonLinearSource = psMetadataLookupStr(&status, recipe, "NONLIN.SOURCE"); + if (! status || ! options->nonLinearSource) { + psLogMsg(__func__, PS_LOG_ERROR, "Non-linearity correction desired, but unable to " + "find NONLIN.SOURCE in recipe %s.", RECIPE_NAME); + exit(EXIT_FAILURE); + } + } + break; + default: + psLogMsg(__func__, PS_LOG_ERROR, "Non-linearity correction desired, but " + "NONLIN.DATA is of invalid type in recipe %s.", RECIPE_NAME); + exit(EXIT_FAILURE); + } + } + + // XXX PAP: The overscan stuff needs to be updated following the reworked API + + // Overscan recipe options + // XXX EAM : we should abort on invalid options. default options? + if (psMetadataLookupBool(NULL, recipe, "OVERSCAN")) { + options->doOverscan = true; + + // Do the overscan as a single value? + bool overscanSingle = psMetadataLookupBool(NULL, recipe, "OVERSCAN.SINGLE"); + + // How do we fit it? + pmFit overscanFit = PM_FIT_NONE; // Fit type for overscan + int overscanOrder = 0; // Order for overscan fit + psString fit = psMetadataLookupStr(NULL, recipe, "OVERSCAN.FIT"); + if (! strcasecmp(fit, "POLYNOMIAL")) { + overscanFit = PM_FIT_POLY_ORD; + overscanOrder = psMetadataLookupS32(NULL, recipe, "OVERSCAN.ORDER"); + } else if (! strcasecmp(fit, "CHEBYSHEV")) { + overscanFit = PM_FIT_POLY_CHEBY; + overscanOrder = psMetadataLookupS32(NULL, recipe, "OVERSCAN.ORDER"); + } else if (! strcasecmp(fit, "SPLINE")) { + overscanFit = PM_FIT_SPLINE; + } else if (strcasecmp(fit, "NONE")) { + psLogMsg(__func__, PS_LOG_WARN, + "OVERSCAN.FIT (%s) in recipe %s is not one of NONE, POLYNOMIAL, or SPLINE", + fit, RECIPE_NAME); + exit(EXIT_FAILURE); + } + + // What method do we use to measure the overscan statistics? + // XXX allow user to specify psStats types by name + psStats *overscanStats = NULL; // Statistics for overscan + psString stat = psMetadataLookupStr(NULL, recipe, "OVERSCAN.STAT"); + if (! strcasecmp(stat, "MEAN")) { + // overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN); + overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEAN); + } else if (! strcasecmp(stat, "MEDIAN")) { + overscanStats = psStatsAlloc(PS_STAT_SAMPLE_MEDIAN); + } else { + psErrorStackPrint(stderr, "OVERSCAN.STAT (%s) in recipe %s is not one of MEAN or MEDIAN", + stat, RECIPE_NAME); + exit(EXIT_FAILURE); + } + + int boxcar = psMetadataLookupS32(NULL, recipe, "OVERSCAN.BOXCAR"); + float gauss = psMetadataLookupF32(NULL, recipe, "OVERSCAN.GAUSS"); + + // Fill in the options + options->overscan = pmOverscanOptionsAlloc(overscanSingle, overscanFit, overscanOrder, + overscanStats, boxcar, gauss); + + options->overscan->constant = psMetadataLookupBool(NULL, recipe, "OVERSCAN.CONSTANT"); + options->overscan->value = psMetadataLookupF32(NULL, recipe, "OVERSCAN.VALUE"); + + psFree(overscanStats); + } + + // for these images, even if not required otherwise + options->doMaskBuild = psMetadataLookupBool(NULL, recipe, "MASK.BUILD"); + options->doVarianceBuild = psMetadataLookupBool(NULL, recipe, "VARIANCE.BUILD"); + + // Mask recipe options (note that mask bit values are set in ppImageSetMaskBits.c) + options->doMask = psMetadataLookupBool(NULL, recipe, "MASK"); + + options->doBias = psMetadataLookupBool(NULL, recipe, "BIAS"); + options->doDark = psMetadataLookupBool(NULL, recipe, "DARK"); + options->doRemnance = psMetadataLookupBool(NULL, recipe, "REMNANCE"); + options->doFlat = psMetadataLookupBool(NULL, recipe, "FLAT"); + options->doFringe = psMetadataLookupBool(NULL, recipe, "FRINGE"); + options->doShutter = psMetadataLookupBool(NULL, recipe, "SHUTTER"); + + options->doStats = false; + char *statsName = psMetadataLookupStr(&status, config->arguments, "STATS"); // Filename for statistics + if (statsName) { + options->doStats = true; + } + + // binned image options + options->xBin1 = psMetadataLookupS32(&status, recipe, "BIN1.XBIN"); + if (!status) { + psWarning("BIN1.XBIN not found in recipe: setting to default value.\n"); + } + options->yBin1 = psMetadataLookupS32(&status, recipe, "BIN1.YBIN"); + if (!status) { + psWarning("BIN1.YBIN not found in recipe: setting to default value.\n"); + options->yBin1 = 16; + } + + options->xBin2 = psMetadataLookupS32(&status, recipe, "BIN2.XBIN"); + if (!status) { + psWarning("BIN2.XBIN not found in recipe: setting to default value.\n"); + options->xBin1 = 16; + } + options->yBin2 = psMetadataLookupS32(&status, recipe, "BIN2.YBIN"); + if (!status) { + psWarning("BIN2.YBIN not found in recipe: setting to default value.\n"); + options->yBin1 = 16; + } + + options->BaseFITS = psMetadataLookupBool(NULL, recipe, "BASE.FITS"); + options->BaseMaskFITS = psMetadataLookupBool(NULL, recipe, "BASE.MASK.FITS"); + options->BaseVarianceFITS = psMetadataLookupBool(NULL, recipe, "BASE.VARIANCE.FITS"); + + options->ChipFITS = psMetadataLookupBool(NULL, recipe, "CHIP.FITS"); + options->ChipMaskFITS = psMetadataLookupBool(NULL, recipe, "CHIP.MASK.FITS"); + options->ChipVarianceFITS = psMetadataLookupBool(NULL, recipe, "CHIP.VARIANCE.FITS"); + + options->FPA1FITS = psMetadataLookupBool(NULL, recipe, "FPA1.FITS"); + options->FPA2FITS = psMetadataLookupBool(NULL, recipe, "FPA2.FITS"); + + options->Bin1FITS = psMetadataLookupBool(NULL, recipe, "BIN1.FITS"); + options->Bin1JPEG = psMetadataLookupBool(NULL, recipe, "BIN1.JPEG"); + options->Bin2FITS = psMetadataLookupBool(NULL, recipe, "BIN2.FITS"); + options->Bin2JPEG = psMetadataLookupBool(NULL, recipe, "BIN2.JPEG"); + + options->doPhotom = psMetadataLookupBool(NULL, recipe, "PHOTOM"); + options->doAstromChip = psMetadataLookupBool(NULL, recipe, "ASTROM.CHIP"); + options->doAstromMosaic = psMetadataLookupBool(NULL, recipe, "ASTROM.MOSAIC"); + options->doBG = psMetadataLookupBool(NULL, recipe, "BACKGROUND"); + + // even if not requested explicitly, if any of these are set, build an internal mask and variance: + if (options->doBias || options->doOverscan || options->doDark || options->doShutter || options->doFlat || + options->doPhotom) { + options->doMaskBuild = true; + options->doVarianceBuild = true; + } else if (options->doMask || options->doBG) { + options->doMaskBuild = true; + } + + if ((options->doAstromChip || options->doAstromMosaic) && !options->doPhotom) { + psLogMsg(__func__, PS_LOG_ERROR, "Invalid PPIMAGE options: cannot do ASTROMetry without PHOTOMetry"); + exit(EXIT_FAILURE); + } + + // Fringe options + options->fringeRej = psMetadataLookupF32(NULL, recipe, "FRINGE.REJ"); + options->fringeIter = psMetadataLookupS32(NULL, recipe, "FRINGE.ITER"); + options->fringeKeep = psMetadataLookupF32(NULL, recipe, "FRINGE.KEEP"); + + // Remnance options + options->remnanceSize = psMetadataLookupF32(NULL, recipe, "REMNANCE.SIZE"); + options->remnanceThresh = psMetadataLookupS32(NULL, recipe, "REMNANCE.THRESH"); + + // per-class normalization source (just a reference; don't free) + options->normClass = psMetadataLookupStr(NULL, recipe, "NORM.CLASS"); + + return options; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageParseCamera.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageParseCamera.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageParseCamera.c (revision 23312) @@ -0,0 +1,465 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +ppImageOptions *ppImageParseCamera(pmConfig *config) +{ + bool status = false; + + if (!ppImageDefineFile(config, NULL, "PPIMAGE.INPUT", "INPUT", PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_NONE)) { + psError(PS_ERR_IO, false, "Can't find an input image source"); + return NULL; + } + pmFPAfile *input = psMetadataLookupPtr(NULL, config->files, "PPIMAGE.INPUT"); // Input file + psAssert(input, "We just put it there!"); + + // add recipe options supplied on command line + psMetadata *recipe = psMetadataLookupPtr(&status, config->recipes, RECIPE_NAME); + + // parse the options from the metadata format to the ppImageOptions structure + ppImageOptions *options = ppImageOptionsParse(config); + + // the following are defined from the argument list, if given, + // otherwise they revert to the config information + // not all input or output images are used in a given recipe + if (options->doBias) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.BIAS", "BIAS", + PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_BIAS)) { + psError(PS_ERR_IO, false, "Can't find a bias image source"); + psFree(options); + return NULL; + } + } + if (options->doDark) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.DARK", "DARK", + PM_FPA_FILE_DARK, PM_DETREND_TYPE_DARK)) { + psError(PS_ERR_IO, false, "Can't find a dark image source"); + psFree(options); + return NULL; + } + } + if (options->doMask) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.MASK", "MASK", + PM_FPA_FILE_MASK, PM_DETREND_TYPE_MASK)) { + psError(PS_ERR_IO, false, "Can't find a mask image source"); + psFree(options); + return NULL; + } + +#if 0 + // I think this is now done automatically in the pmFPAfileDefine and pmFPAfileIOChecks -- PAP. + + // XXX have ppImageDefineFile return the pmFPAfile? + pmFPAfile *mask = psMetadataLookupPtr(&status, config->files, "PPIMAGE.MASK"); + psAssert(mask, "Just defined the mask!"); + + // Need to read the names of bit masks from the mask header and set them in the + // recipe. If we are loading this from the detrend db, this action will happen + // when the file is resolved. + if (!mask->detrend) { + // XXX need to load the mask bit names from one of the headers + // this grabs the first available hdu : no guarantee that it will be valid, though + pmHDU *hdu = pmHDUGetFirst(mask->fpa); + if (!hdu) { + psError(PS_ERR_IO, true, "no valid HDU for PPIMAGE.INPUT.MASK"); + return NULL; + } + // XXX is this consistent with the pmConfigMaskReadHeader call above? + if (!pmConfigMaskReadHeader(config, hdu->header)) { + psError(PS_ERR_IO, false, "error in mask bits"); + return NULL; + } + } +#endif + } + if (options->doShutter) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.SHUTTER", "SHUTTER", + PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_SHUTTER)) { + psError(PS_ERR_IO, false, "Can't find a shutter image source"); + psFree(options); + return NULL; + } + } + + if (options->doFlat) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.FLAT", "FLAT", + PM_FPA_FILE_IMAGE, PM_DETREND_TYPE_FLAT)) { + psError(PS_ERR_IO, false, "Can't find a flat image source"); + psFree(options); + return NULL; + } + } + + int nThreads = psMetadataLookupS32(&status, config->arguments, "NTHREADS"); + if (nThreads > 0) { + int nScanRows = psMetadataLookupS32(&status, recipe, "SCAN.ROWS"); + pmDetrendSetThreadTasks(nScanRows); + } + + // fringe frame are only applied for a subset of the filters. + // if the filter is one of those identified by a FRINGE.FILTERS metadata entry + // in ppImage.config, apply the fringe frame + if (options->doFringe) { + // determine filter from the concepts + const char *filter = psMetadataLookupStr(&status, input->fpa->concepts, "FPA.FILTER"); + if (!status || !filter || strlen(filter) == 0) { + psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find FPA.FILTER.\n"); + psFree(options); + return NULL; + } + + // select FRINGE.FILTERS from the recipe and test if the filter matches + // is the mdi saved with psList or string? + psMetadataItem *mdi = psMetadataLookup (recipe, "FRINGE.FILTERS"); + if (mdi == NULL) { + // no valid filters for fringe data for this camera + options->doFringe = false; + goto skip_fringe; + } + // place entry on a list regardless of type + psList *filters = NULL; + if (mdi->type == PS_DATA_STRING) { + filters = psListAlloc(NULL); + psListAdd (filters, PS_LIST_HEAD, mdi); + } else if (mdi->type == PS_DATA_METADATA_MULTI) { + filters = psMemIncrRefCounter(mdi->data.list); + } else { + psError(PS_ERR_BAD_PARAMETER_TYPE, true, + "FRINGE.FILTERS in recipe %s is not of type METADATA", RECIPE_NAME); + psFree(options); + return NULL; + } + + // search through list to find the current filter + psListIterator *iter = psListIteratorAlloc (filters, PS_LIST_HEAD, FALSE); + options->doFringe = false; + for (int i = 0; !options->doFringe && (i < filters->n); i++) { + psMetadataItem *item = psListGetAndIncrement (iter); + char *validFilter = item->data.V; + if (strcmp (validFilter, filter)) continue; + options->doFringe = true; + } + psFree(iter); + psFree(filters); + } +skip_fringe: + if (options->doFringe) { + if (!ppImageDefineFile(config, input->fpa, "PPIMAGE.FRINGE", "FRINGE", + PM_FPA_FILE_FRINGE, PM_DETREND_TYPE_FRINGE)) { + psError (PS_ERR_IO, false, "Can't find a fringe image source"); + return NULL; + } + } + + // the following files are output targets + pmFPAfile *outImage = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT"); + if (!outImage) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.OUTPUT")); + psFree(options); + return NULL; + } + if (outImage->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT is not of type IMAGE"); + psFree(options); + return NULL; + } + pmFPAfile *outMask = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.MASK"); + if (!outMask) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.OUTPUT.MASK")); + psFree(options); + return NULL; + } + if (outMask->type != PM_FPA_FILE_MASK) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.MASK is not of type MASK"); + psFree(options); + return NULL; + } + pmFPAfile *outVariance = pmFPAfileDefineOutput(config, input->fpa, "PPIMAGE.OUTPUT.VARIANCE"); + if (!outVariance) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.OUTPUT.VARIANCE")); + psFree(options); + return NULL; + } + if (outVariance->type != PM_FPA_FILE_VARIANCE) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.VARIANCE is not of type VARIANCE"); + psFree(options); + return NULL; + } + + // XXX should these be bound explicitly to the outImage->fpa rather than the input->fpa? + pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, input->fpa, "PPIMAGE.CHIP"); + if (!chipImage) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.CHIP")); + psFree(options); + return NULL; + } + if (chipImage->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "PPIMAGE.CHIP is not of type IMAGE"); + psFree(options); + return NULL; + } + pmFPAfile *chipMask = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.MASK"); + if (!chipMask) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.CHIP.MASK")); + psFree(options); + return NULL; + } + if (chipMask->type != PM_FPA_FILE_MASK) { + psError(PS_ERR_IO, true, "PPIMAGE.CHIP.MASK is not of type MASK"); + psFree(options); + return NULL; + } + pmFPAfile *chipVariance = pmFPAfileDefineOutput(config, chipImage->fpa, "PPIMAGE.CHIP.VARIANCE"); + if (!chipVariance) { + psError(PS_ERR_IO, false, _("Unable to generate output file from PPIMAGE.CHIP.VARIANCE")); + psFree(options); + return NULL; + } + if (chipVariance->type != PM_FPA_FILE_VARIANCE) { + psError(PS_ERR_IO, true, "PPIMAGE.CHIP.VARIANCE is not of type VARIANCE"); + psFree(options); + return NULL; + } + + pmFPAfile *byFPA1 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA1"); + if (!byFPA1) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.OUTPUT.FPA1")); + psFree(options); + return NULL; + } + if (byFPA1->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.FPA1 is not of type IMAGE"); + psFree(options); + return NULL; + } + pmFPAfile *byFPA2 = pmFPAfileDefineFPAMosaic(config, input->fpa, "PPIMAGE.OUTPUT.FPA2"); + if (!byFPA2) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.OUTPUT.FPA2")); + psFree(options); + return NULL; + } + if (byFPA2->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.FPA2 is not of type IMAGE"); + psFree(options); + return NULL; + } + + // chipImage -> psphotInput (pmFPAfileDefineFromFile) : fpa is constructed + // psphotInput -> psphotOutput (pmFPAfileDefineOutputFromFile) : fpa is equated + // psphotOutput -> psastroInput (pmFPAfileDefineInput) : fpa is ref-copied + // psastroInput -> psastroModel (pmFPAfileDefineFromArgs : fpa is ref-copied + // psastroInput -> psastroModel (pmFPAfileDefineFromConf : fpa is constructed + // psastroInput -> psastroModel (pmFPAfileDefineFromDetDB : fpa is constructed (pmDetrendSelect uses input concepts ) + + // For photometry, we operate on the chip-mosaicked image + // we create a copy of the mosaicked image for psphot so we can write out a clean image + if (options->doPhotom || options->doBG) { + + // this file is just used as a carrier; output files (eg, PSPHOT.RESID) are defined by + // psphotDefineFiles + pmFPAfile *psphotInput = pmFPAfileDefineFromFile (config, chipImage, 1, 1, "PSPHOT.INPUT"); + PS_ASSERT (psphotInput, false); + + // define associated psphot input/output files + if (!psphotDefineFiles (config, psphotInput)) { + psError(PSPHOT_ERR_CONFIG, false, + "Trouble defining the additional input/output files for psphot"); + return false; + } + } + + // For photometry, we operate on the chip-mosaicked image + if (options->doAstromChip || options->doAstromMosaic) { + if (!options->doPhotom) { + psError(PSASTRO_ERR_CONFIG, false, + "Photometry mode is not selected; it is required for astrometry"); + return false; + } + + pmFPAfile *psphotOutput = psMetadataLookupPtr(&status, config->files, "PSPHOT.OUTPUT"); + PS_ASSERT(psphotOutput, false); + + pmFPAfile *psastroInput = pmFPAfileDefineInput(config, psphotOutput->fpa, NULL, "PSASTRO.INPUT"); + PS_ASSERT(psastroInput, false); + psastroInput->mode = PM_FPA_MODE_REFERENCE; + + // define associated psphot input/output files + if (!psastroDefineFiles(config, psastroInput)) { + psError(PSPHOT_ERR_CONFIG, false, + "Trouble defining the additional input/output files for psastro"); + return false; + } + + // deactivate the psastro files, reactive when needed + pmFPAfileActivate(config->files, false, "PSASTRO.OUTPUT"); + } + + // save any of these files? + outImage->save = options->BaseFITS; + outMask->save = options->BaseMaskFITS; + outVariance->save = options->BaseVarianceFITS; + + chipImage->save = options->ChipFITS; + chipMask->save = options->ChipMaskFITS; + chipVariance->save = options->ChipVarianceFITS; + + byFPA1->save = options->FPA1FITS; + byFPA2->save = options->FPA2FITS; + + // outImage is used as a carrier: input to chipImage -> require the data to remain at the CHIP level + outImage->freeLevel = PS_MIN(outImage->freeLevel, PM_FPA_LEVEL_CHIP); + outImage->dataLevel = outImage->freeLevel; + outImage->fileLevel = PS_MIN(outImage->fileLevel, outImage->dataLevel); + + // outMask and outVariance must be freed at the same level as outImage (all freed by pmFPAFreeData) + outMask->freeLevel = outImage->freeLevel; + outVariance->freeLevel = outImage->freeLevel; + outMask->dataLevel = outImage->dataLevel; + outVariance->dataLevel = outImage->dataLevel; + + // Ditto for the chip-mosaicked version + chipMask->freeLevel = chipImage->freeLevel; + chipVariance->freeLevel = chipImage->freeLevel; + chipMask->dataLevel = chipImage->dataLevel; + chipVariance->dataLevel = chipImage->dataLevel; + + // the input data is the same as the outImage data : force the free levels to match + input->freeLevel = PS_MIN(outImage->freeLevel, input->freeLevel); + + // define the binned target files (which may just be carriers for some camera configurations) + pmFPAfile *bin1 = pmFPAfileDefineFromFPA(config, chipImage->fpa, options->xBin1, options->yBin1, + "PPIMAGE.BIN1"); + if (!bin1) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.BIN1")); + psFree(options); + return NULL; + } + if (bin1->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.BIN1 is not of type IMAGE"); + psFree(options); + return NULL; + } + + pmFPAfile *bin2 = pmFPAfileDefineFromFPA(config, chipImage->fpa, options->xBin2, options->yBin2, + "PPIMAGE.BIN2"); + if (!bin2) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.BIN2")); + psFree(options); + return NULL; + } + if (bin2->type != PM_FPA_FILE_IMAGE) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.BIN2 is not of type IMAGE"); + psFree(options); + return NULL; + } + + // bin1 and bin2 are used as carriers: input for byFPA1, byFPA2 + bin1->freeLevel = PM_FPA_LEVEL_FPA; + bin2->freeLevel = PM_FPA_LEVEL_FPA; + + pmFPAfile *jpg1 = pmFPAfileDefineOutput(config, byFPA1->fpa, "PPIMAGE.JPEG1"); + if (!jpg1) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.JPEG1")); + psFree(options); + return NULL; + } + if (jpg1->type != PM_FPA_FILE_JPEG) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.JPEG1 is not of type JPEG"); + psFree(options); + return NULL; + } + pmFPAfile *jpg2 = pmFPAfileDefineOutput(config, byFPA2->fpa, "PPIMAGE.JPEG2"); + if (!jpg2) { + psError(PS_ERR_IO, false, _("Unable to generate new file from PPIMAGE.JPEG2")); + psFree(options); + return NULL; + } + if (jpg2->type != PM_FPA_FILE_JPEG) { + psError(PS_ERR_IO, true, "PPIMAGE.OUTPUT.JPEG2 is not of type JPEG"); + psFree(options); + return NULL; + } + + // XXX we could potentially not define these pmFPAfiles if no output is requested... + bin1->save = options->Bin1FITS; + bin2->save = options->Bin2FITS; + jpg1->save = options->Bin1JPEG; + jpg2->save = options->Bin2JPEG; + + // Chip selection: turn on only the chips specified (pass status to suppress missing-key log msg) + char *chipLine = psMetadataLookupStr(&status, config->arguments, "CHIP_SELECTIONS"); + psArray *chips = psStringSplitArray(chipLine, ",", false); + if (chips->n > 0) { + pmFPASelectChip (input->fpa, -1, true); // deselect all chips + for (int i = 0; i < chips->n; i++) { + int chipNum = atoi(chips->data[i]); + if (! pmFPASelectChip(input->fpa, chipNum, false)) { + psError(PS_ERR_IO, false, "Chip number %d doesn't exist in camera.\n", chipNum); + psFree(options); + return false; + } + } + } + psFree (chips); + + if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_FRINGE")) { + // It's a fringe file, so change the file type + input->type = PM_FPA_FILE_FRINGE; + outImage->type = PM_FPA_FILE_FRINGE; + } + if (psMetadataLookupBool(NULL, config->arguments, "INPUT_IS_DARK")) { + // It's a dark file, so change the file type + input->type = PM_FPA_FILE_DARK; + outImage->type = PM_FPA_FILE_DARK; + // Turn off compression --- there are just too many nasties that can happen + psFree(outImage->compression); + outImage->compression = NULL; + psFree(outImage->options); + outImage->options = NULL; + } + + // Turn off mask and variance output if we're not doing anything interesting + if (!options->doMaskBuild && outMask->save) { + psWarning("output mask image (BASE.MASK.FITS) requested, but not generated: skipping.\n"); + outMask->save = false; + } + if (!options->doVarianceBuild && outVariance->save) { + psWarning("output variance image (BASE.VARIANCE.FITS) requested, but not generated: skipping.\n"); + outVariance->save = false; + } + if (!options->doMaskBuild && chipMask->save) { + psWarning("output mask image (CHIP.MASK.FITS) requested, but not generated: skipping.\n"); + chipMask->save = false; + } + if (!options->doVarianceBuild && chipVariance->save) { + psWarning("output variance image (CHIP.VARIANCE.FITS) requested, but not generated: skipping.\n"); + chipVariance->save = false; + } + + if (psTraceGetLevel("ppImage.config") > 0) { + // Get a look inside all the files. + psMetadataIterator *filesIter = psMetadataIteratorAlloc(config->files, PS_LIST_HEAD, NULL); + psMetadataItem *item; // Item from iteration + fprintf(stderr, "Files:\n"); + while ((item = psMetadataGetAndIncrement(filesIter))) { + pmFPAfile *file = item->data.V; // File of interest + fprintf(stderr, "%s: %p %p %p (%p) %p\n", file->name, + file->src, file->fpa, + file->camera, file->fpa->camera, file->format); + } + psFree(filesIter); + } + + // Change the input dark type between the old (IMAGE) and new (multi-DARK). + // Hopefully this is a temporary change until we all move over to using the new dark types + bool mdok; // Status of MD lookup + if (options->doDark && psMetadataLookupBool(&mdok, recipe, "OLDDARK")) { + pmFPAfile *dark = psMetadataLookupPtr(NULL, config->files, "PPIMAGE.DARK"); + assert(dark); + dark->type = PM_FPA_FILE_IMAGE; + } + + return (options); +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImagePhotom.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImagePhotom.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImagePhotom.c (revision 23312) @@ -0,0 +1,61 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +# include "ppImage.h" + +// In this function, we perform the psphot analysis routine for the chip-mosaicked images +bool ppImagePhotom (pmConfig *config, pmFPAview *view) { + + bool status; + pmCell *cell; + pmReadout *readout; + + psphotInit (); + + // find or define a pmFPAfile PSPHOT.INPUT + pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSPHOT.INPUT"); + if (!status) { + psError(PSPHOT_ERR_CONFIG, false, "PSPHOT.INPUT I/O file is not defined"); + return false; + } + + // we make a new copy of the output chip to keep psphot from modifying the output image + pmChip *oldChip = pmFPAviewThisChip (view, input->src); + pmChip *newChip = pmFPAviewThisChip (view, input->fpa); + pmChipCopy (newChip, oldChip); + + // iterate over the cells and readout for this chip + while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) { + psLogMsg ("ppImagePhotom", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (! cell->process || ! cell->file_exists) { continue; } + + // process each of the readouts + while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) { + if (! readout->data_exists) { continue; } + + // run the actual photometry analysis + if (!psphotReadout (config, view)) { + psError(psErrorCodeLast(), false, "failure in psphotReadout for chip %d, cell %d, readout %d\n", view->chip, view->cell, view->readout); + return false; + } + + // we want to save the MASK as modified by psphot, but not the data or weight + // free the old mask and replace with a memory copy of the new mask + pmReadout *oldReadout = pmFPAviewThisReadout (view, input->src); + pmReadout *newReadout = pmFPAviewThisReadout (view, input->fpa); + psFree (oldReadout->mask); + oldReadout->mask = psMemIncrRefCounter (newReadout->mask); + } + } + + ppImageMemoryDump("photom"); + + // the PSPHOT.INPUT file is a temporary file used to carry PPIMAGE.CHIP to psphotReadout + // XXX not sure that this is needed... +// pmFPAfileActivate (config->files, false, "PSPHOT.INPUT"); + + return true; +} + +// XXX do we need to deactivate all files and activate the psphot ones explicitly? Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImagePixelStats.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImagePixelStats.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImagePixelStats.c (revision 23312) @@ -0,0 +1,85 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +// calculate stats, including MD5 +bool ppImagePixelStats(pmConfig *config, psMetadata *stats, const ppImageOptions *options, + const pmFPAview *inputView) +{ + bool mdok; // Status of MD lookup + + // loop over the cells/readouts for this chip + pmFPAview *view = pmFPAviewAlloc(0); // View for local processing + *view = *inputView; + + // perform the analysis of for this FPA + pmFPAfile *output = psMetadataLookupPtr(&mdok, config->files, "PPIMAGE.OUTPUT"); + if (!output) { + psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find output file (PPIMAGE.OUTPUT)."); + psFree(view); + return false; + } + + // select the corresponding chip + pmChip *chip = pmFPAviewThisChip(view, output->fpa); + if (!chip) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find requested chip."); + psFree(view); + return false; + } + + // Perform statistics for this chip + if (options->doStats) { + if (!ppStatsPixels(stats, output->fpa, view, options->maskValue, config)) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to generate stats for image."); + psFree(view); + return false; + } + + // extract the fringe amplitude from the analysis + if (options->doFringe && !ppStatsFringe(stats, chip, "FRINGE", "FRINGE.SOLUTION")) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to extract fringe solution for image."); + psFree(view); + return false; + } + + // extract the fringe residual amplitude from the analysis + if (options->doFringe && !ppStatsFringe(stats, chip, "FRINGE_RESID", "FRINGE.RESIDUAL.SOLUTION")) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to extract fringe solution for image."); + psFree(view); + return false; + } + } + + + view->cell = view->readout = -1; + pmCell *cell = NULL; // Cell from iteration + while ((cell = pmFPAviewNextCell(view, output->fpa, 1)) != NULL) { + if (!cell->process || !cell->file_exists) { + continue; + } + + // Add MD5 information for cell + pmHDU *hdu = pmHDUFromCell(cell); // HDU that owns the cell + pmReadout *readout = NULL; // Readout from iteration + while ((readout = pmFPAviewNextReadout(view, output->fpa, 1)) != NULL) { + const char *chipName = psMetadataLookupStr(NULL, chip->concepts, "CHIP.NAME"); + const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); + + psString headerName = NULL; // Header name for MD5 + psStringAppend(&headerName, "MD5_%s_%s_%d", chipName, cellName, view->readout); + + psVector *md5 = psImageMD5(readout->image); // md5 hash + psString md5string = psMD5toString(md5); // String + psFree(md5); + psMetadataAddStr(hdu->header, PS_LIST_TAIL, headerName, PS_META_REPLACE, "Image MD5", md5string); + psFree(md5string); + psFree(headerName); + } + } + + psFree (view); + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageRebinReadout.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageRebinReadout.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageRebinReadout.c (revision 23312) @@ -0,0 +1,44 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +bool ppImageRebinChip (pmConfig *config, pmFPAview *view, ppImageOptions *options, char *outName) { + + pmCell *cell; + pmReadout *inReadout, *outReadout; + + pmFPAfile *outFile = psMetadataLookupPtr(NULL, config->files, outName); + if (outFile == NULL) return false; + + // XXX double check that chip != -1? + + pmChip *inChip = pmFPAviewThisChip (view, outFile->src); + pmChip *outChip = pmFPAviewThisChip (view, outFile->fpa); + if (!pmChipCopyStructure (outChip, inChip, outFile->xBin, outFile->yBin)) { + psError(PS_ERR_UNKNOWN, false, "Unable to copy chip structure."); + return false; + } + + while ((cell = pmFPAviewNextCell (view, outFile->src, 1)) != NULL) { + psLogMsg ("ppImageRebinChip", 5, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process); + if (! cell->process || ! cell->file_exists) { continue; } + + // process each of the readouts + while ((inReadout = pmFPAviewNextReadout (view, outFile->src, 1)) != NULL) { + if (! inReadout->data_exists) { continue; } + + outReadout = pmFPAviewThisReadout (view, outFile->fpa); + + // run the rebin code + if (!pmReadoutRebin(outReadout, inReadout, options->maskValue, outFile->xBin, outFile->yBin)) { + psError(PS_ERR_UNKNOWN, false, "Unable to rebin readout."); + return false; + } + } + } + + return true; +} + Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageReplaceBackground.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageReplaceBackground.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageReplaceBackground.c (revision 23312) @@ -0,0 +1,180 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +// In this function, we perform the psphot analysis routine for the chip-mosaicked images +bool ppImageSubtractBackground(pmConfig *config, const pmFPAview *view, const ppImageOptions *options) +{ + psAssert(config, "Need configuration"); + psAssert(view, "Need view to chip"); + psAssert(options, "Need options"); + + if (!options->doBG) { + return true; + } + + bool status; // Status of MD lookup + pmFPAfile *input = psMetadataLookupPtr(&status, config->files, "PPIMAGE.CHIP"); // File to correct + if (!status) { + psError(PS_ERR_UNEXPECTED_NULL, true, "PPIMAGE.CHIP file is not defined"); + return false; + } + + psMetadata *ppImageRecipe = psMetadataLookupPtr(NULL, config->recipes, RECIPE_NAME); + psAssert(ppImageRecipe, "Need PPIMAGE recipe"); + psMetadata *psphotRecipe = psMetadataLookupPtr(NULL, config->recipes, PSPHOT_RECIPE); + psAssert(psphotRecipe, "Need PSPHOT recipe"); + + // XXX Should this be options->maskValue or options->maskValue & ~options->satMask? + // The latter will leave saturated pixels high + psImageMaskType maskVal = options->maskValue; + + // user-defined masks to test for good/bad pixels (build from recipe list if not yet set) + psMetadataAddImageMask(psphotRecipe, PS_LIST_TAIL, "MASK.PSPHOT", PS_META_REPLACE, "user-defined mask", maskVal); + + // Since we are working on a chip-mosaicked image, there should only be a single cell and readout + pmChip *chip = pmFPAviewThisChip(view, input->fpa); // Chip of interest + if (!chip) { + psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find chip"); + return false; + } + if (chip->cells->n == 0) { + psWarning("Chip has no cells"); + return true; + } + if (chip->cells->n > 1) { + psWarning("Chip has %ld cells; only the first will be processed", chip->cells->n); + } + pmCell *cell = chip->cells->data[0]; // Cell of interest + if (!cell || !cell->process || !cell->file_exists) { + // Nothing to process + return true; + } + if (cell->readouts->n == 0) { + psWarning("Cell has no readouts"); + return true; + } + if (cell->readouts->n > 1) { + psWarning("Cell has %ld readouts; only the first will be processed", cell->readouts->n); + } + pmReadout *ro = cell->readouts->data[0]; // Readout of interest + if (!ro || !ro->data_exists) { + // Nothing to process + return true; + } + psImage *image = ro->image, *mask = ro->mask; // Image and mask of interest + + // View corresponding to this readout + pmFPAview roView = *view; + roView.cell = roView.readout = 0; + + // If the background model file has not been defined, psphotModelBackground will generate it + pmReadout *modelRO = NULL; + pmFPAfile *modelFile = psMetadataLookupPtr(&status, config->files, "PSPHOT.BACKMDL"); // Background model + if (modelFile) { + modelRO = pmFPAviewThisReadout(&roView, modelFile->fpa); // Background model + } + + // the background model has not been defined, or at least not generated + if (!modelFile || !modelRO) { + if (!psphotModelBackground(config, &roView, "PPIMAGE.CHIP")) { + psError(PS_ERR_UNKNOWN, false, "Unable to model background"); + return false; + } + // the model file should now at least be defined + modelFile = psMetadataLookupPtr(&status, config->files, "PSPHOT.BACKMDL"); // Background model + if (!modelFile) { + psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to define background model I/O file"); + return false; + } + // now grab the readout from the correct location: + if (modelFile->mode == PM_FPA_MODE_INTERNAL) { + modelRO = modelFile->readout; + } else { + modelRO = pmFPAviewThisReadout(&roView, modelFile->fpa); + } + if (!modelRO) { + psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find background model"); + return false; + } + } + psImageBinning *binning = psMetadataLookupPtr(&status, modelRO->analysis, + "PSPHOT.BACKGROUND.BINNING"); // Binning for model + if (!binning) { + psError(PS_ERR_UNEXPECTED_NULL, true, "Unable to find background binning"); + return false; + } + +# define USE_UNBIN 1 +# if (USE_UNBIN) + // select background pixels, from output background file, or create + pmReadout *background = NULL; + pmFPAfile *backfile = psMetadataLookupPtr (&status, config->files, "PSPHOT.BACKGND"); + if (backfile) { + // we are using PSPHOT.BACKGND as an I/O file: select readout or create + if (backfile->mode == PM_FPA_MODE_INTERNAL) { + background = backfile->readout; + } else { + background = pmFPAviewThisReadout (&roView, backfile->fpa); + } + if (background == NULL) { + // readout does not yet exist: create from input + pmFPAfileCopyStructureView (backfile->fpa, input->fpa, 1, 1, &roView); + background = pmFPAviewThisReadout (&roView, backfile->fpa); + if ((image->numCols != background->image->numCols) || (image->numRows != background->image->numRows)) { + psError (PSPHOT_ERR_PROG, true, "inconsistent sizes for background dimensions"); + return false; + } + } + } else { + background = pmFPAfileDefineInternal (config->files, "PSPHOT.BACKGND", image->numCols, image->numRows, PS_TYPE_F32); + } + psF32 **backData = background->image->data.F32; + + // linear interpolation to full-scale + if (!psImageUnbin (background->image, modelRO->image, binning)) { + psError (PSPHOT_ERR_PROG, true, "inconsistent sizes for unbinning"); + return false; + } + + // Do the background subtraction + int numCols = image->numCols, numRows = image->numRows; // Size of image + for (int y = 0; y < numRows; y++) { + for (int x = 0; x < numCols; x++) { + float value = backData[y][x]; + if (!isfinite(value)) { + image->data.F32[y][x] = NAN; + mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= options->badMask; + } else { + image->data.F32[y][x] -= value; + } + } + } +# else + // Do the background subtraction + int numCols = image->numCols, numRows = image->numRows; // Size of image + for (int y = 0; y < numRows; y++) { + for (int x = 0; x < numCols; x++) { + if (mask && mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] & maskVal) { + image->data.F32[y][x] = 0.0; + } else { + float value = psImageUnbinPixel(x + 0.5, y + 0.5, modelRO->image, binning); // Background value + if (!isfinite(value)) { + image->data.F32[y][x] = NAN; + mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= options->badMask; + } else { + image->data.F32[y][x] -= value; + } + } + } + } +# endif + + // XXX should these really be here?? (probably not...) + // pmFPAfileDropInternal(config->files, "PSPHOT.BACKMDL"); + // pmFPAfileDropInternal(config->files, "PSPHOT.BACKMDL.STDEV"); + + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageSetMaskBits.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageSetMaskBits.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageSetMaskBits.c (revision 23312) @@ -0,0 +1,46 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +bool ppImageSetMaskBits (pmConfig *config, ppImageOptions *options) { + + if (!pmConfigMaskSetBits(&options->maskValue, &options->markValue, config)) { + psError (PS_ERR_UNKNOWN, true, "Unable to define the mask bit values"); + return false; + } + + // at this point we know we have valid values for required entries SAT, BAD, FLAT, BLANK: + + // mask for non-linear flat corrections + options->flatMask = pmConfigMaskGet("FLAT", config); + psAssert (options->flatMask, "flat mask not set"); + + // mask for non-existent data (default to DETECTOR if not defined) + options->blankMask = pmConfigMaskGet("BLANK", config); + psAssert (options->blankMask, "blank mask not set"); + + // mask for saturated data (default to RANGE if not defined) + options->satMask = pmConfigMaskGet("SAT", config); + psAssert (options->satMask, "sat mask not set"); + + // mask for below-range data (default to RANGE if not defined) + options->badMask = pmConfigMaskGet("BAD", config); + psAssert (options->badMask, "bad mask not set"); + + // save MASK and MARK on the PSPHOT recipe + psMetadata *recipe = psMetadataLookupPtr (NULL, config->recipes, PSPHOT_RECIPE); + if (!recipe) { + psError(PSPHOT_ERR_CONFIG, false, "missing recipe %s", PSPHOT_RECIPE); + return false; + } + + // set maskValue and markValue in the psphot recipe + psMetadataAddImageMask(recipe, PS_LIST_TAIL, "MASK.PSPHOT", PS_META_REPLACE, "user-defined mask", + options->maskValue); + psMetadataAddImageMask(recipe, PS_LIST_TAIL, "MARK.PSPHOT", PS_META_REPLACE, "user-defined mask", + options->markValue); + + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageSetThreads.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageSetThreads.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageSetThreads.c (revision 23312) @@ -0,0 +1,26 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +bool ppImageThread_ppImageDetrendReadout (psThreadJob *job) { + + pmConfig *config = job->args->data[0]; + ppImageOptions *options = job->args->data[1]; + pmFPAview *view = job->args->data[2]; + + bool status = ppImageDetrendReadout(config, options, view); + return status; +} + +bool ppImageSetThreads () { + + psThreadTask *task = NULL; + + task = psThreadTaskAlloc ("PPIMAGE_DETREND_READOUT", 3); + task->function = &ppImageThread_ppImageDetrendReadout; + psThreadTaskAdd (task); + + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageStatsOutput.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageStatsOutput.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageStatsOutput.c (revision 23312) @@ -0,0 +1,34 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +// write stats to output file +bool ppImageStatsOutput(pmConfig *config, psMetadata *stats, const ppImageOptions *options) +{ + bool mdok; + + // measure statistics, or ignore? + if (!options->doStats) { + return true; + } + + // get the output stats filename + const char *statsName = psMetadataLookupStr(&mdok, config->arguments, "STATS"); // Filename for statistics + if (!statsName && !strlen(statsName)) { + psError(PS_ERR_UNEXPECTED_NULL, false, "missing STATS entry in arguments list."); + return false; + } + + // Write out + psString resolved = pmConfigConvertFilename(statsName, config, true, true); // Resolved filename + if (!psMetadataConfigWrite(stats, resolved)) { + psError(PS_ERR_IO, false, "Unable to serialize stats metadata.\n"); + psFree(resolved); + return false; + } + psFree(resolved); + + return true; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageVersion.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageVersion.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppImageVersion.c (revision 23312) @@ -0,0 +1,115 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "ppImage.h" + +#ifndef PPIMAGE_VERSION +#error "PPIMAGE_VERSION is not set" +#endif +#ifndef PPIMAGE_BRANCH +#error "PPIMAGE_BRANCH is not set" +#endif +#ifndef PPIMAGE_SOURCE +#error "PPIMAGE_SOURCE is not set" +#endif + +#define xstr(s) str(s) +#define str(s) #s + +psString ppImageVersion(void) +{ + char *value = NULL; + psStringAppend(&value, "%s@%s", xstr(PPIMAGE_BRANCH), xstr(PPIMAGE_VERSION)); + return value; +} + +psString ppImageSource(void) +{ + return psStringCopy (xstr(PPIMAGE_SOURCE)); +} + +psString ppImageVersionLong(void) +{ + psString version = ppImageVersion(); // Version, to return + psString source = ppImageSource(); // Source + + psStringPrepend(&version, "ppImage "); + 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 ppImageVersionHeader(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, "ppImage at %s", timeString); + psFree(timeString); + psMetadataAddStr(header, PS_LIST_TAIL, "HISTORY", PS_META_DUPLICATE_OK, NULL, history); + psFree(history); + + psLibVersionHeader(header); + psModulesVersionHeader(header); + psphotVersionHeader(header); + psastroVersionHeader(header); + ppStatsVersionHeader(header); + + psString version = ppImageVersion(); // ppImage software version + psString source = ppImageSource(); // ppImage software source + + psStringPrepend(&version, "ppImage version: "); + psStringPrepend(&source, "ppImage 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; +} + + +void ppImageVersionPrint(void) +{ + psTime *time = psTimeGetNow(PS_TIME_TAI); // The time now + psString timeString = psTimeToISO(time); // The time in an ISO string + psFree(time); + psLogMsg("ppImage", PS_LOG_INFO, "ppImage at %s", timeString); + psFree(timeString); + + psString pslib = psLibVersionLong();// psLib version + psString psmodules = psModulesVersionLong(); // psModules version + psString psphot = psphotVersionLong(); // psphot version + psString psastro = psastroVersionLong(); // psastro version + psString ppStats = ppStatsVersionLong(); // ppStats version + psString ppImage = ppImageVersionLong(); // ppImage version + + psLogMsg("ppImage", PS_LOG_INFO, "%s", pslib); + psLogMsg("ppImage", PS_LOG_INFO, "%s", psmodules); + psLogMsg("ppImage", PS_LOG_INFO, "%s", psphot); + psLogMsg("ppImage", PS_LOG_INFO, "%s", psastro); + psLogMsg("ppImage", PS_LOG_INFO, "%s", ppStats); + psLogMsg("ppImage", PS_LOG_INFO, "%s", ppImage); + + psFree(pslib); + psFree(psmodules); + psFree(psphot); + psFree(psastro); + psFree(ppStats); + psFree(ppImage); + + return; +} Index: /branches/eam_branches/eam_branch_20090312/ppImage/src/ppTest.c =================================================================== --- /branches/eam_branches/eam_branch_20090312/ppImage/src/ppTest.c (revision 23312) +++ /branches/eam_branches/eam_branch_20090312/ppImage/src/ppTest.c (revision 23312) @@ -0,0 +1,190 @@ +#ifdef HAVE_CONFIG_H +#include +#endif + +#include + +#include "pslib.h" +#include "psmodules.h" + +int main(int argc, char *argv[]) +{ + psLibInit(NULL); + + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// ppImageConfig.c +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + pmConfig *config = pmConfigRead(&argc, argv, "PPIMAGE"); + if (! config) { + psErrorStackPrint(stderr, "Can't find site configuration!\n"); + exit(EXIT_FAILURE); + } + + // Parse other command-line arguments + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-key", 0, "exposure ID", ""); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-bias", 0, "Name of the bias image", ""); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-dark", 0, "Name of the dark image", ""); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-flat", 0, "Name of the flat-field image", ""); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-mask", 0, "Name of the mask image", ""); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-fringe", 0, "Name of the fringe image", ""); + psMetadataAddS32(config->arguments, PS_LIST_TAIL, "-chip", 0, "Chip number to process (if positive)", -1); + + if (! psArgumentParse(config->arguments, &argc, argv) || argc != 3) { + printf("\nPan-STARRS Phase 2 processing\n\n"); + printf("Usage: %s INPUT.fits OUTPUT.fits\n\n", argv[0]); + psArgumentHelp(config->arguments); + psFree(config->arguments); + exit(EXIT_FAILURE); + } + + // Add the input and output images (which remain on the command-line) to the arguments list + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-input", 0, "Name of the input image", argv[1]); + psMetadataAddStr(config->arguments, PS_LIST_TAIL, "-output", 0, "Name of the output image", argv[2]); + + // Define database handle, if used +#if 0 + config->database = pmConfigDB(config->site); +#endif + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// ppImageParseCamera.c extract with some alterations +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + + const char *inName = psMetadataLookupStr(NULL, config->arguments, "-input"); + psLogMsg("ppImage", PS_LOG_INFO, "Opening input image: %s\n", inName); + psFits *inFile = psFitsOpen(inName, "r"); // File handle for FITS file + if (! inFile) { + // There's no point in continuing if we can't open the input + psErrorStackPrint(stderr, "Can't open input image: %s\n", inName); + exit(EXIT_FAILURE); + } + psMetadata *phu = psFitsReadHeader(NULL, inFile); // FITS primary header + + psMetadata *cameraFormat = pmConfigCameraFormatFromHeader(NULL, NULL, config, phu, true); + if (! config->camera) { + cameraFormat = pmConfigCameraFormatFromHeader(NULL, NULL, config, phu, true); + if (! config->camera) { + // There's no point in continuing if we can't recognise what we've got + psErrorStackPrint(stderr, "Can't find camera configuration!\n"); + exit(EXIT_FAILURE); + } + } + // Determine the correct recipe to use + if (! config->recipes && !pmConfigReadRecipes(config, PM_RECIPE_SOURCE_CAMERA | PM_RECIPE_SOURCE_CL)) { + // There's no point in continuing if we can't work out what recipes to use + psErrorStackPrint(stderr, "Can't find recipe configuration!\n"); + exit(EXIT_FAILURE); + } + +#if 1 + const char *outName = psMetadataLookupStr(NULL, config->arguments, "-output"); + psLogMsg("ppImage", PS_LOG_INFO, "Opening output image: %s\n", outName); + psFits *outFile = psFitsOpen(outName, "w"); + if (!outFile) { + // There's no point in continuing if we can't open the output + psErrorStackPrint(stderr, "Can't open output image: %s\n", outName); + exit(EXIT_FAILURE); + } +#endif + + // Construct camera in preparation for reading + pmFPA *fpa = pmFPAConstruct(config->camera, config->cameraName); + pmFPAview *view = pmFPAAddSourceFromHeader(fpa, phu, cameraFormat); + printf("View chip: %d\n", view->chip); + printf("View cell: %d\n", view->cell); + +////////////////////////////////////////////////////////////////////////////////////////////////////////////// +// The action happens here +////////////////////////////////////////////////////////////////////////////////////////////////////////////// + +#if 0 + pmFPAPrint(stdout, fpa, false, false); + exit(0); +#endif + +#if 0 + // A mosaic + psMetadata *mosaicCamera = psMetadataConfigRead(NULL, NULL, "/home/mithrandir/price/ipp/config/mcshort_mosaic/camera.config", true); + pmFPA *mosaicFPA = pmFPAConstruct(mosaicCamera); + psMetadata *mosaicFormat = psMetadataConfigRead(NULL, NULL, "/home/mithrandir/price/ipp/config/mcshort_mosaic/format_mosaic.config", true); + pmFPAview *mosaicView = pmFPAviewAlloc(0); + pmFPAAddSourceFromView(mosaicFPA, mosaicView, mosaicFormat); + psFree(mosaicView); +#endif + + // Read the FPA + pmFPARead(fpa, inFile, NULL); + +#if 1 + psArray *chips = fpa->chips; + pmFPAWrite(fpa, outFile, NULL, true, false); + for (int i = 0; i < chips->n; i++) { + pmChip *chip = chips->data[i]; +#if 1 + //pmChipRead(chip, inFile, NULL); + pmChipWrite(chip, outFile, NULL, true, false); + psArray *cells = chip->cells; + for (int j = 0; j < cells->n; j++) { + pmCell *cell = cells->data[j]; + pmCellWrite(cell, outFile, NULL, true); +#if 0 // Read bit by bit + pmReadout *readout = pmReadoutAlloc(cell); + for (int z = 0; pmReadoutReadNext(readout, inFile, z, 512); z++) { + do { + printf("Chip %d, Cell %d, Plane %d, row0 = %d\n", i, j, z, readout->row0); + pmReadoutWriteNext(readout, outFile, z); + //pmFPAPrint(stdout, fpa, false, true); + } while (pmReadoutReadNext(readout, inFile, z, 512)); + } + psFree(readout); +#else // Read the whole cell at once + // pmCellRead(cell, inFile, NULL); + // pmCellWrite(cell, outFile, NULL, false); + // pmCellFreeData(cell); +#endif + } + pmChipWrite(chip, outFile, NULL, false, false); +#endif + +#if 0 + pmChipMosaic(mosaicFPA->chips->data[i], chip); + pmChipWrite(mosaicFPA->chips->data[i], outFile, NULL, true, true); + pmChipFreeData(chip); + pmChipFreeData(mosaicFPA->chips->data[i]); +#endif + } + pmFPAWrite(fpa, outFile, NULL, false, false); +#endif + +#if 0 + pmFPAMosaic(mosaicFPA, fpa); + pmFPAWrite(mosaicFPA, outFile, NULL, true, true); + //pmFPAPrint(stdout, mosaicFPA, true, true); + psFree(mosaicCamera); + psFree(mosaicFormat); + psFree(mosaicView); + //psFree(mosaicFPA); +#endif + +#if 1 + pmFPAPrint(stdout, fpa, false, false); +#endif + +#if 1 + psFitsClose(outFile); +#endif + + psFree(view); + psFree(phu); + psFree(fpa); + psFree(config); + psFitsClose(inFile); + psFree(cameraFormat); + + pmConceptsDone(); + pmConfigDone(); + psLibFinalize(); + + // Pau. +}