Index: /branches/eam_branches/ipp-dev-20210817/psastro/src/Makefile.am
===================================================================
--- /branches/eam_branches/ipp-dev-20210817/psastro/src/Makefile.am	(revision 41798)
+++ /branches/eam_branches/ipp-dev-20210817/psastro/src/Makefile.am	(revision 41799)
@@ -10,5 +10,5 @@
 libpsastro_la_LDFLAGS = $(PSASTRO_LIBS) $(PPSTATS_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
 
-bin_PROGRAMS = psastro psastroExtract psastroModel psastroModelFit gpcModel
+bin_PROGRAMS = psastro psastroExtract psastroModel psastroModelFit gpcModel psastroTIO
 
 psastro_CFLAGS = $(PSASTRO_CFLAGS) $(PPSTATS_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
@@ -31,4 +31,8 @@
 gpcModel_LDFLAGS = $(PSASTRO_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
 gpcModel_LDADD = libpsastro.la
+
+psastroTIO_CFLAGS = $(PSASTRO_CFLAGS) $(PSMODULE_CFLAGS) $(PSLIB_CFLAGS)
+psastroTIO_LDFLAGS = $(PSASTRO_LIBS) $(PSMODULE_LIBS) $(PSLIB_LIBS)
+psastroTIO_LDADD = libpsastro.la
 
 psastro_SOURCES = \
@@ -62,4 +66,12 @@
 	psastroModelAdjust.c        \
 	psastroModelDataSave.c      \
+	psastroCleanup.c
+
+psastroTIO_SOURCES = \
+	psastroTIO.c		    \
+        psastroTIOArguments.c	    \
+	psastroTIOParseCamera.c   \
+	psastroTIODataLoad.c      \
+	psastroTIODataSave.c      \
 	psastroCleanup.c
 
Index: /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIO.c
===================================================================
--- /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIO.c	(revision 41799)
+++ /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIO.c	(revision 41799)
@@ -0,0 +1,60 @@
+/** @file psastroTIO.c
+ *
+ *  @brief
+ *
+ *  @ingroup psastroTIO
+ *
+ *  @author IfA
+ *  @version $Revision: 1.3 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-07 02:03:34 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+# include "psastroStandAlone.h"
+
+pmConfig *psastroTIOArguments (int argc, char **argv);
+bool psastroTIOParseCamera (pmConfig *config);
+bool psastroTIODataLoad (pmConfig *config);
+bool psastroTIODataSave (pmConfig *config);
+
+int main (int argc, char **argv) {
+
+    pmConfig *config = NULL;
+
+    psTimerStart ("complete");
+
+    // model inits are needed in pmSourceIO
+    // models defined in psphot/src/models are not available in psastro
+    pmModelClassInit ();
+
+    // load configuration information
+    config = psastroTIOArguments (argc, argv);
+
+    // load identify the data sources
+    if (!psastroTIOParseCamera (config)) {
+	psErrorStackPrint(stderr, "error setting up the camera\n");
+	exit (1);
+    }
+
+    psLogMsg ("psastro", 3, "parsed camera: %f sec\n", psTimerMark ("complete"));
+
+    // load the raw pixel data (from PSPHOT.SOURCES)
+    // select subset of stars for astrometry
+    if (!psastroTIODataLoad (config)) {
+	psErrorStackPrint(stderr, "error loading input data\n");
+	exit (1);
+    }
+
+    psLogMsg ("psastro", 3, "read data: %f sec\n", psTimerMark ("complete"));
+
+    // save the model
+    if (!psastroTIODataSave (config)) {
+	psErrorStackPrint(stderr, "error saving output data\n");
+	exit (1);
+    }
+
+    psLogMsg ("psastro", 3, "save data: %f sec\n", psTimerMark ("complete"));
+
+    // psastroCleanup (config);
+    exit (EXIT_SUCCESS);
+}
Index: /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIOArguments.c
===================================================================
--- /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIOArguments.c	(revision 41799)
+++ /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIOArguments.c	(revision 41799)
@@ -0,0 +1,73 @@
+/** @file psastroTIOArguments.c
+ *
+ *  @brief
+ *
+ *  @ingroup psastroTIO
+ *
+ *  @author IfA
+ *  @version $Revision: 1.3 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-07 02:03:34 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+# include "psastroStandAlone.h"
+
+static char *usage = "USAGE: psastroTIO -file (filename) -output (root)";
+
+pmConfig *psastroTIOArguments (int argc, char **argv) {
+
+    int N;
+
+    if (argc == 1) {
+        psError(PSASTRO_ERR_ARGUMENTS, true, "No arguments supplied");
+        psErrorStackPrint(stderr, "%s", usage);
+	exit (1);
+    }
+
+    // load config data from default locations
+    pmConfig *config = pmConfigRead(&argc, argv, PSASTRO_RECIPE);
+    if (config == NULL) {
+        psError(PSASTRO_ERR_CONFIG, false, "Can't read site configuration");
+        psErrorStackPrint(stderr, "%s", usage);
+	exit (1);
+    }
+
+    // save the following additional recipe values based on command-line options
+    // these options override the PSASTRO recipe values loaded from recipe files
+
+    // define the output filename
+    if ((N = psArgumentGet (argc, argv, "-output")) == FALSE) {
+        psError(PSASTRO_ERR_ARGUMENTS, true, "Missing -output (root)");
+        psErrorStackPrint(stderr, "%s", usage);
+	exit (1);
+    }
+    psArgumentRemove (N, &argc, argv);
+    psMetadataAddStr (config->arguments, PS_LIST_TAIL, "OUTPUT", 0, "", argv[N]);
+    psArgumentRemove (N, &argc, argv);
+
+    int status = pmConfigFileSetsMD (config->arguments, &argc, argv, "INPUT", "-file", "-list");
+    if (!status) {
+        psError(PSASTRO_ERR_ARGUMENTS, true, "Missing -file (input) or -list (input)");
+        psErrorStackPrint(stderr, "exit");
+        return NULL;
+    }
+
+    // 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_META_REPLACE, "", argv[N]);
+        psArgumentRemove (N, &argc, argv);
+    }
+    
+    if (argc != 1) {
+	psError(PSASTRO_ERR_ARGUMENTS, true, "Incorrect arguments supplied: argc = %d", argc);
+	if (argc) {
+	    for (int i = 1; i < argc; i++){
+		fprintf (stderr, "argc %d : %s\n", i, argv[i]);
+	    }
+	}
+	psErrorStackPrint(stderr, "exit");
+	exit (1);
+    }
+    return (config);
+}
Index: /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIODataLoad.c
===================================================================
--- /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIODataLoad.c	(revision 41799)
+++ /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIODataLoad.c	(revision 41799)
@@ -0,0 +1,82 @@
+/** @file psastroTIODataLoad.c
+ *
+ *  @brief
+ *
+ *  @ingroup psastro
+ *
+ *  @author IfA
+ *  @version $Revision: 1.12 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-07 02:03:34 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+# include "psastroStandAlone.h"
+
+# define ESCAPE { \
+  psError(PS_ERR_UNKNOWN, false, "Failure in psastroTIODataLoad"); \
+  psFree (view); \
+  return false; \
+}
+  
+bool psastroTIODataLoad (pmConfig *config) {
+
+    pmChip *chip;
+    pmCell *cell;
+    pmReadout *readout;
+
+    psTimerStart ("psastroDataLoad");
+
+    // select the current recipe
+    psMetadata *recipe  = psMetadataLookupPtr (NULL, config->recipes, PSASTRO_RECIPE);
+    if (!recipe) {
+	psError(PSASTRO_ERR_CONFIG, true, "Can't find PSASTRO recipe!\n");
+	return false;
+    }
+
+    // select the input data sources
+    pmFPAfile *input = psMetadataLookupPtr (NULL, config->files, "PSASTRO.INPUT");
+    if (!input) {
+	psError(PSASTRO_ERR_CONFIG, true, "Can't find input data!\n");
+	return false;
+    }
+
+    // de-activate all files except PSASTRO.INPUT
+    pmFPAfileActivate (config->files, false, NULL);
+    pmFPAfileActivate (config->files, true, "PSASTRO.INPUT");
+
+    pmFPAview *view = pmFPAviewAlloc (0);
+
+    // files associated with the science image
+    if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE;
+
+    while ((chip = pmFPAviewNextChip (view, input->fpa, 1)) != NULL) {
+        psTrace ("psastro", 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;
+
+	while ((cell = pmFPAviewNextCell (view, input->fpa, 1)) != NULL) {
+            psTrace ("psastro", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process);
+            if (!cell->process || !cell->file_exists) { continue; }
+	    if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE;
+
+	    // process each of the readouts
+	    while ((readout = pmFPAviewNextReadout (view, input->fpa, 1)) != NULL) {
+		if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE;
+		if (!readout->data_exists) { continue; }
+
+		// if (!psastroConvertReadout (config, view, readout, recipe)) ESCAPE;
+
+		if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+	    }
+	    if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+	}
+	if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+    }
+    if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+
+    psLogMsg ("psastro", 3, "load data : %f sec\n", psTimerMark ("psastroDataLoad"));
+
+    psFree (view);
+    return true;
+}
+
Index: /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIODataSave.c
===================================================================
--- /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIODataSave.c	(revision 41799)
+++ /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIODataSave.c	(revision 41799)
@@ -0,0 +1,84 @@
+/** @file psastroTIODataSave.c
+ *
+ *  @brief
+ *
+ *  @ingroup psastro
+ *
+ *  @author IfA
+ *  @version $Revision: 1.15 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-07 02:03:34 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+# include "psastroInternal.h"
+
+# define ESCAPE { \
+  psError(PS_ERR_UNKNOWN, false, "Failure in psastroTIODataSave"); \
+  psFree (view); \
+  return false; \
+}
+
+void pmSourceIO_ShowTiming(void);
+
+bool psastroTIODataSave (pmConfig *config) {
+
+    pmChip *chip;
+    pmCell *cell;
+    pmReadout *readout;
+
+    psTimerStart ("psastroDataSave");
+
+    // select the current recipe
+    psMetadata *recipe  = psMetadataLookupPtr (NULL, config->recipes, PSASTRO_RECIPE);
+    if (!recipe) {
+        psError(PSASTRO_ERR_CONFIG, true, "Can't find PSASTRO recipe!\n");
+        return false;
+    }
+
+    // select the output data sources
+    pmFPAfile *output = psMetadataLookupPtr (NULL, config->files, "PSASTRO.OUTPUT");
+    if (!output) {
+        psError(PSASTRO_ERR_CONFIG, true, "Can't find or interpret output file rule PSASTRO.OUTPUT!\n");
+        return false;
+    }
+
+    // de-activate all files except PSASTRO.OUTPUT, PSASTRO.OUT.ASTROM, and PSPHOT.OUTPUT.CFF
+    pmFPAfileActivate (config->files, false, NULL);
+    pmFPAfileActivate (config->files, true, "PSASTRO.OUTPUT");
+
+    pmFPAview *view = pmFPAviewAlloc (0);
+
+    // open/load files as needed
+    if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE;
+
+    while ((chip = pmFPAviewNextChip (view, output->fpa, 1)) != NULL) {
+        psTrace ("psastro", 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;
+
+        while ((cell = pmFPAviewNextCell (view, output->fpa, 1)) != NULL) {
+            psTrace ("psastro", 4, "Cell %d: %x %x\n", view->cell, cell->file_exists, cell->process);
+            if (!cell->process || !cell->file_exists) { continue; }
+            if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE;
+
+            // process each of the readouts
+            while ((readout = pmFPAviewNextReadout (view, output->fpa, 1)) != NULL) {
+                if (!pmFPAfileIOChecks (config, view, PM_FPA_BEFORE)) ESCAPE;
+                if (!readout->data_exists) { continue; }
+
+                if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+            }
+            if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+        }
+        if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+    }
+    if (!pmFPAfileIOChecks (config, view, PM_FPA_AFTER)) ESCAPE;
+
+    psLogMsg ("psastro", 3, "save data : %f sec\n", psTimerMark ("psastroDataSave"));
+
+    psFree (view);
+
+    pmSourceIO_ShowTiming();
+
+    return true;
+}
Index: /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIOParseCamera.c
===================================================================
--- /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIOParseCamera.c	(revision 41799)
+++ /branches/eam_branches/ipp-dev-20210817/psastro/src/psastroTIOParseCamera.c	(revision 41799)
@@ -0,0 +1,51 @@
+/** @file psastroTIOParseCamera.c
+ *
+ *  @brief
+ *
+ *  @ingroup psastroTIO
+ *
+ *  @author IfA
+ *  @version $Revision: 1.3 $ $Name: not supported by cvs2svn $
+ *  @date $Date: 2009-02-07 02:03:34 $
+ *  Copyright 2009 Institute for Astronomy, University of Hawaii
+ */
+
+# include "psastroInternal.h"
+
+bool psastroTIOParseCamera (pmConfig *config) {
+
+    bool status = false;
+
+    // the input image(s) are required arguments; they define the camera
+    pmFPAfile *input = pmFPAfileDefineFromArgs (&status, config, "PSASTRO.INPUT", "INPUT");
+    if (!status) {
+	psError(PSASTRO_ERR_CONFIG, false, "Failed to build FPA from PSASTRO.INPUT");
+	return false;
+    }
+
+    pmFPAfile *output = pmFPAfileDefineOutput (config, input->fpa, "PSASTRO.OUTPUT");
+    if (!output) {
+	psError(PSASTRO_ERR_CONFIG, false, "Failed to build FPA from PSASTRO.INPUT");
+	return false;
+    }
+    output->save = true;
+
+
+    // Chip selection: turn on only the chips specified (option is not required)
+    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(PSASTRO_ERR_CONFIG, true, "Chip number %d doesn't exist in camera.\n", chipNum);
+		return false;
+	    }
+        }
+    }
+    psFree (chips);
+
+    psTrace("psastro", 1, "Done with psastroTIOParseCamera...\n");
+    return true;
+}