Changeset 17818

Timestamp:

May 27, 2008, 7:12:46 PM (18 years ago)

Author:

eugene

Message:

working on the photometry of fake sources

Location:

branches/eam_branch_20080511/ppSim

Files:

• notes.txt (modified) (1 diff)
• src/Makefile.am (modified) (1 diff)
• src/ppSim.h (modified) (3 diffs)
• src/ppSimCreate.c (modified) (1 diff)
• src/ppSimDetectionLimits.c (added)
• src/ppSimDetections.c (added)
• src/ppSimInsertStars.c (modified) (2 diffs)
• src/ppSimLoadForceSources.c (modified) (2 diffs)
• src/ppSimLoop.c (modified) (3 diffs)
• src/ppSimMergeReadouts.c (modified) (2 diffs)
• src/ppSimMergeSources.c (added)
• src/ppSimPhotom.c (modified) (2 diffs)
• src/ppSimPhotomFiles.c (added)
• src/ppSimPhotomReadout.c (modified) (8 diffs)

branches/eam_branch_20080511/ppSim/notes.txt

@@ +1 @@
+
+
+2008.05.17
+
+  pmFPAfiles used in ppSim:
+
+  PPSIM.INPUT : an input image loaded by ppSim; the simulated features
+                may be added to this image.  In fact, the features are
+                generated in the output image, and the two images are
+                added (as images) together.
+
+  PPSIM.OUTPUT  : the output image.  this file is used for the main
+                  ppSimLoop function
+
+  PPSIM.CHIP    : chip-mosaiced version of the output image.  only
+                  generated if photometry is requested.  Is this
+                  actually used as an output image?
+
+  PPSIM.REAL.SOURCES : real sources loaded by PPSIM.  these sources
+                       are subtracted from the image before testing
+                       for the detectability of the fake sources and
+                       before measuring the flux of fake or forced
+                       soures.  They should be the sources measured in
+                       a previous psphot run, though any input list
+                       could be used.  Results are very ill-defined if
+                       the sources do not correspond to actual image
+                       sources!
+
+  PSPHOT.PSF.LOAD : input PSF model used to measure the input sources
+
+  PPSIM.SOURCES : output fake sources (injected fake sources with real values) 
+  PPSIM.FAKE.SOURCES : output fake photometry (measured photometry for all fake sources)
+  PPSIM.FORCE.SOURCES : output force photometry
+  
+  ** used within psphot functions:
+  PSPHOT.BACKMDL : model background generated by psphotModelBackground
+  PSPHOT.BACKMDL.STDEV : model background error generated by psphotModelBackground
+  PSPHOT.BACKGND : full-scale model background generated by psphotSubtractBackground
+  PSPHOT.BACKSUB : background-subtracted image
 
 2008.05.15

branches/eam_branch_20080511/ppSim/src/Makefile.am

@@ -26 +26 @@
         ppSimLoadSpots.c        \
         ppSimPhotom.c           \
+        ppSimPhotomReadout.c    \
+        ppSimPhotomFiles.c      \
+        ppSimLoadForceSources.c \
         ppSimMergeReadouts.c    \
+        ppSimDetections.c       \
+        ppSimMergeSources.c     \
         ppSimMosaicChip.c       \
         ppSimRandomGaussian.c   \

branches/eam_branch_20080511/ppSim/src/ppSim.h

@@ -16 +16 @@
 
 #define PPSIM_RECIPE "PPSIM"
-#define OUTPUT_FILE "PPSIM.OUTPUT"
+// #define OUTPUT_FILE "PPSIM.OUTPUT"
 
 // Compare a value with minimum and maximum values, replacing where required.
@@ -174 +174 @@
 float ppSimGetZeroPoint (psMetadata *recipe, char *filter);
 
-bool ppSimMergeReadouts (pmReadout *outReadout, pmReadout *inReadout);
+bool ppSimMergeReadouts (pmConfig *config, pmFPAview *view);
 
 double ppSimRandomGaussian (const psRandom *rnd, double mean, double sigma);
@@ -180 +180 @@
 void ppSimRandomGaussianFree();
 
+bool ppSimPhotomFiles (pmConfig *config, pmFPAfile *input);
+bool ppSimPhotomReadout(pmConfig *config, const pmFPAview *view);
+psArray *ppSimLoadForceSources(pmConfig *config, const pmFPAview *view);
+bool ppSimDetections (psImage *significance, psMetadata *recipe, psArray *sources);
+psArray *ppSimMergeSources (psArray *in1, psArray *in2);
+
 #endif

branches/eam_branch_20080511/ppSim/src/ppSimCreate.c

@@ -3 +3 @@
 pmFPAfile *ppSimCreate(pmConfig *config)
 {
-    bool status;
-    bool simImage = false;
-    PS_ASSERT_PTR_NON_NULL(config, NULL);
-    pmFPA *fpa = NULL;
+  bool status;
+  bool simImage = false;
+  PS_ASSERT_PTR_NON_NULL(config, NULL);
+  pmFPA *fpa = NULL;
 
-    // the input image defines the camera.  if it is not supplied, the user must have
-    // supplied a camera and other metadata on the command line
-    pmFPAfile *input = pmFPAfileDefineFromArgs (&status, config, "PPIMAGE.INPUT", "INPUT");
-    if (!input) {
-        // if we have not specified the camera already, we need to interpolate the recipes associated with this camera, and read other command-line recipes
-        if (!pmConfigReadRecipes(config, PM_RECIPE_SOURCE_CL)) {
-            psError(PS_ERR_IO, false, "Error merging recipes from camera config for %s", config->cameraName);
-            return NULL;
-        }
-    } else {
-      // If an image is supplied, we still generate a fake image and merge them together downstream
-      // (otherwise, we get the variance wrong).
-        simImage = false;
-        if (input->type != PM_FPA_FILE_IMAGE) {
-            psError(PS_ERR_IO, true, "PPIMAGE.INPUT is not of type IMAGE");
-            return NULL;
-        }
+  // the input image defines the camera.  if it is not supplied, the user must have
+  // supplied a camera and other metadata on the command line
+  pmFPAfile *input = pmFPAfileDefineFromArgs (&status, config, "PPSIM.INPUT", "INPUT");
+  if (!input) {
+    // if we have not specified the camera already, we need to interpolate the recipes associated with this camera, and read other command-line recipes
+    if (!pmConfigReadRecipes(config, PM_RECIPE_SOURCE_CL)) {
+      psError(PS_ERR_IO, false, "Error merging recipes from camera config for %s", config->cameraName);
+      return NULL;
     }
+  } else {
+    // If an image is supplied, we still generate a fake image and merge them together downstream
+    // (otherwise, we get the variance wrong).
+    simImage = false;
+    if (input->type != PM_FPA_FILE_IMAGE) {
+      psError(PS_ERR_IO, true, "PPSIM.INPUT is not of type IMAGE");
+      return NULL;
+    }
+  }
 
-    // generate the fpa structure used by the output camera (determined from INPUT or specified)
-    assert (config->camera);
-    fpa = pmFPAConstruct(config->camera); // FPA to contain the observation
-    if (!fpa) {
-      psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to construct an FPA from camera configuration.");
+  // generate the fpa structure used by the output camera (determined from INPUT or specified)
+  assert (config->camera);
+  fpa = pmFPAConstruct(config->camera); // FPA to contain the observation
+  if (!fpa) {
+    psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to construct an FPA from camera configuration.");
+    return NULL;
+  }
+
+  // define the output image file -- this is the basis for the ppSimLoop
+  pmFPAfile *output = pmFPAfileDefineOutput(config, fpa, "PPSIM.OUTPUT");
+  if (!output) {
+    psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to create output file from PPSIM.OUTPUT. Did you forget to specify the format?");
+    return NULL;
+  }
+  if (output->type != PM_FPA_FILE_IMAGE) {
+    psError(PS_ERR_BAD_PARAMETER_TYPE, true, "PPSIM.OUTPUT type is not IMAGE");
+    psFree(fpa);
+    return NULL;
+  }
+  // XXX we should not require the output image to be written
+  output->save = true;
+
+  config->format = psMemIncrRefCounter (output->format);
+  config->formatName = psStringCopy (output->formatName);
+
+  // the recipe is now fully realized for the desired camera
+  psMetadata *recipe = psMetadataLookupMetadata(&status, config->recipes, PPSIM_RECIPE); // Recipe
+
+  char *typeStr = psMetadataLookupStr(NULL, recipe, "IMAGE.TYPE"); // Type of image to simulate
+  ppSimType type = ppSimTypeFromString (typeStr); // Type of image to simulate
+
+  if (type == PPSIM_TYPE_OBJECT) {
+    // adjust the seeing by the scale
+    float seeing = psMetadataLookupF32(&status, recipe, "SEEING");
+    if (isnan(seeing)) {
+      psError(PS_ERR_BAD_PARAMETER_TYPE, true, "seeing is not defined");
+      psFree(fpa);
+      return NULL;
+    }
+    float scale = psMetadataLookupF32(&status, recipe, "PIXEL.SCALE");
+    if (isnan(scale)) {
+      psError(PS_ERR_BAD_PARAMETER_TYPE, true, "pixel scale is not defined");
+      psFree(fpa);
+      return NULL;
+    }
+    psMetadataAddF32(recipe, PS_LIST_TAIL, "SEEING", PS_META_REPLACE, "Seeing SIGMA (pixels)", seeing / 2.0 / sqrt(2.0 * log(2.0)) / scale);
+  }
+
+  if ((type == PPSIM_TYPE_OBJECT) || (type == PPSIM_TYPE_FLAT)) {
+    // determine the zeropoint from the filter
+    float zp = psMetadataLookupF32(&status, recipe, "ZEROPOINT");
+    if (isnan(zp)) {
+      char *filter = psMetadataLookupStr(&status, recipe, "FILTER");
+      float zp = ppSimGetZeroPoint (recipe, filter);
+      psMetadataAddF32(recipe, PS_LIST_TAIL, "ZEROPOINT", PS_META_REPLACE, "Photometric zeropoint", zp);
+    }
+  }
+
+  // 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
+  bool doPhotom = psMetadataLookupBool(&status, recipe, "PHOTOM"); // Density of fakes
+  if (doPhotom) {
+
+    // we need a chip image if we perform photometry (is it necessary to build it if we don't use it?)
+    pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, output->fpa, "PPSIM.CHIP");
+    if (!chipImage) {
+      psError(PS_ERR_IO, false, _("Unable to generate new file from PPSIM.CHIP"));
+      psFree(fpa);
+      return NULL;
+    }
+    if (chipImage->type != PM_FPA_FILE_IMAGE) {
+      psError(PS_ERR_IO, true, "PPSIM.CHIP is not of type IMAGE");
+      psFree(fpa);
       return NULL;
     }
 
-    // define the output image file -- this is the basis for the ppSimLoop
-    pmFPAfile *output = pmFPAfileDefineOutput(config, fpa, OUTPUT_FILE);
-    if (!output) {
-        psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to create output file from %s.  "
-                "Did you forget to specify the format?", OUTPUT_FILE);
-        return NULL;
+    // define associated psphot input/output files
+    if (!ppSimPhotomFiles (config, chipImage)) {
+      psError(PSPHOT_ERR_CONFIG, false, "Trouble defining the additional input/output files for psphot");
+      psFree(fpa);
+      return NULL;
     }
-    if (output->type != PM_FPA_FILE_IMAGE) {
-        psError(PS_ERR_BAD_PARAMETER_TYPE, true, "%s type is not IMAGE", OUTPUT_FILE);
+  } else {
+    // have we supplied a psf model?  this happens in ppSimPhotomFiles if we request a photometry
+    // analysis.  however, even if we do not, a psf model may be used to generate the fake
+    // sources.
+    if (psMetadataLookupPtr(NULL, config->arguments, "PSPHOT.PSF")) {
+      // tie the psf file to the chipMosaic 
+      pmFPAfileBindFromArgs(&status, output, config, "PSPHOT.PSF.LOAD", "PSPHOT.PSF");
+      if (!status) {
+        psError(PS_ERR_UNKNOWN, false, "Failed to find/build PSPHOT.PSF.LOAD");
         psFree(fpa);
-        return NULL;
+        return NULL;
+      }
     }
-    // XXX we should not require the output image to be written
-    output->save = true;
+  }
 
-    config->format = psMemIncrRefCounter (output->format);
-    config->formatName = psStringCopy (output->formatName);
+  // PPSIM.SOURCES carries the constructed, fake sources with their true parameters
+  // XXX only invoke this code for OBJECT types of images?
+  pmFPAfile *simSources = pmFPAfileDefineOutput (config, output->fpa, "PPSIM.SOURCES");
+  if (!simSources) {
+    psError(PS_ERR_UNKNOWN, false, "Cannot find a rule for PPSIM.SOURCES");
+    return false;
+  }
+  simSources->save = true;
 
-    // the recipe is now fully realized for the desired camera
+  // if we have loaded an input image, we derive certain values from the image, if possible
+  if (input) {
+    // we need to extract certain metadata from the image and populate the recipe.
+    // or else we need to set the fpa concepts based on the recipe options...
+
     psMetadata *recipe = psMetadataLookupMetadata(&status, config->recipes, PPSIM_RECIPE); // Recipe
 
-    char *typeStr = psMetadataLookupStr(NULL, recipe, "IMAGE.TYPE"); // Type of image to simulate
-    ppSimType type = ppSimTypeFromString (typeStr); // Type of image to simulate
+    ppSimArgToRecipeF32(&status, recipe, "EXPTIME", input->fpa->concepts, "FPA.EXPOSURE");
+    char *filter = ppSimArgToRecipeStr(&status, recipe, "FILTER", input->fpa->concepts, "FPA.FILTER");
 
-    if (type == PPSIM_TYPE_OBJECT) {
-        // adjust the seeing by the scale
-        float seeing = psMetadataLookupF32(&status, recipe, "SEEING");
-        if (isnan(seeing)) {
-            psError(PS_ERR_BAD_PARAMETER_TYPE, true, "seeing is not defined");
-            psFree(fpa);
-            return NULL;
-        }
-        float scale = psMetadataLookupF32(&status, recipe, "PIXEL.SCALE");
-        if (isnan(scale)) {
-            psError(PS_ERR_BAD_PARAMETER_TYPE, true, "pixel scale is not defined");
-            psFree(fpa);
-            return NULL;
-        }
-        psMetadataAddF32(recipe, PS_LIST_TAIL, "SEEING", PS_META_REPLACE, "Seeing SIGMA (pixels)", seeing / 2.0 / sqrt(2.0 * log(2.0)) / scale);
+    float zp = ppSimGetZeroPoint (recipe, filter);
+    psMetadataAddF32(recipe, PS_LIST_TAIL, "ZEROPOINT", PS_META_REPLACE, "Photometric zeropoint", zp);
+  }
+
+  pmFPALevel phuLevel = pmFPAPHULevel(output->format); // Level at which PHU goes
+
+  pmFPAview *view = pmFPAviewAlloc(0);// View for current level
+
+  if (phuLevel == PM_FPA_LEVEL_FPA) {
+    if (!pmFPAAddSourceFromView(fpa, "Simulation", view, output->format)) {
+      psError(PS_ERR_UNKNOWN, false, "Unable to add PHU to FPA.");
+      psFree(fpa);
+      psFree(view);
+      return NULL;
+    }
+  }
+
+  pmChip *chip;                       // Chip from FPA
+  while ((chip = pmFPAviewNextChip(view, fpa, 1))) {
+    if (phuLevel == PM_FPA_LEVEL_CHIP) {
+      if (!pmFPAAddSourceFromView(fpa, "Simulation", view, output->format)) {
+        psError(PS_ERR_UNKNOWN, false, "Unable to add PHU to FPA.");
+        psFree(fpa);
+        psFree(view);
+        return NULL;
+      }
     }
 
-    if ((type == PPSIM_TYPE_OBJECT) || (type == PPSIM_TYPE_FLAT)) {
-        // determine the zeropoint from the filter
-        float zp = psMetadataLookupF32(&status, recipe, "ZEROPOINT");
-        if (isnan(zp)) {
-            char *filter = psMetadataLookupStr(&status, recipe, "FILTER");
-            float zp = ppSimGetZeroPoint (recipe, filter);
-            psMetadataAddF32(recipe, PS_LIST_TAIL, "ZEROPOINT", PS_META_REPLACE, "Photometric zeropoint", zp);
+    pmCell *cell;                   // Cell from chip
+    while ((cell = pmFPAviewNextCell(view, fpa, 1))) {
+      if (phuLevel == PM_FPA_LEVEL_CELL) {
+        if (!pmFPAAddSourceFromView(fpa, "Simulation", view, output->format)) {
+          psError(PS_ERR_UNKNOWN, false, "Unable to add PHU to FPA.");
+          psFree(fpa);
+          psFree(view);
+          return NULL;
         }
+      }
     }
+  }
 
-    // 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
-    bool doPhotom = psMetadataLookupBool(&status, recipe, "PHOTOM"); // Density of fakes
-    if (doPhotom) {
+  psFree(fpa);
+  psFree(view);
 
-        // we need a chip image if we perform photometry (is it necessary to build it if we don't use it?)
-        pmFPAfile *chipImage = pmFPAfileDefineChipMosaic(config, output->fpa, "PPSIM.CHIP");
-        if (!chipImage) {
-            psError(PS_ERR_IO, false, _("Unable to generate new file from PPSIM.CHIP"));
-            psFree(fpa);
-            return NULL;
-        }
-        if (chipImage->type != PM_FPA_FILE_IMAGE) {
-            psError(PS_ERR_IO, true, "PPSIM.CHIP is not of type IMAGE");
-            psFree(fpa);
-            return NULL;
-        }
-
-        // *** Define two input files:
-        // PPSIM.REAL.SOURCES
-
-        // the input image(s) are required arguments; they define the camera
-        pmFPAfile *realSources = pmFPAfileDefineFromArgs (&status, config, "PPSIM.REAL.SOURCES", "REAL.SOURCES");
-        if (!status) {
-          psError(PS_ERR_UNKNOWN, false, "Failed to build FPA from PPSIM.REAL.SOURCES");
-          return false;
-        }
-
-        // 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");
-            psFree(fpa);
-            return NULL;
-        }
-    } else {
-        // have we supplied a psf model?  this happens in psphotDefineFiles if we request a photometry
-        // analysis.  however, even if we do not, a psf model may be used to generate the fake
-        // sources.
-        if (psMetadataLookupPtr(NULL, config->arguments, "PSPHOT.PSF")) {
-            // tie the psf file to the chipMosaic 
-            pmFPAfileBindFromArgs(&status, output, config, "PSPHOT.PSF.LOAD", "PSPHOT.PSF");
-            if (!status) {
-                psError(PS_ERR_UNKNOWN, false, "Failed to find/build PSPHOT.PSF.LOAD");
-                psFree(fpa);
-                return NULL;
-            }
-        }
-    }
-
-    // PPSIM.SOURCES carries the constructed, fake sources with their true parameters
-    // XXX only invoke this code for OBJECT types of images?
-    pmFPAfile *simSources = pmFPAfileDefineOutput (config, output->fpa, "PPSIM.SOURCES");
-    if (!simSources) {
-        psError(PS_ERR_UNKNOWN, false, "Cannot find a rule for PPSIM.SOURCES");
-        return false;
-    }
-    simSources->save = true;
-
-    // if we have loaded an input image, we derive certain values from the image, if possible
-    if (input) {
-        // we need to extract certain metadata from the image and populate the recipe.
-        // or else we need to set the fpa concepts based on the recipe options...
-
-        psMetadata *recipe = psMetadataLookupMetadata(&status, config->recipes, PPSIM_RECIPE); // Recipe
-
-        ppSimArgToRecipeF32(&status, recipe, "EXPTIME", input->fpa->concepts, "FPA.EXPOSURE");
-        char *filter = ppSimArgToRecipeStr(&status, recipe, "FILTER", input->fpa->concepts, "FPA.FILTER");
-
-        float zp = ppSimGetZeroPoint (recipe, filter);
-        psMetadataAddF32(recipe, PS_LIST_TAIL, "ZEROPOINT", PS_META_REPLACE, "Photometric zeropoint", zp);
-    }
-
-    pmFPALevel phuLevel = pmFPAPHULevel(output->format); // Level at which PHU goes
-
-    pmFPAview *view = pmFPAviewAlloc(0);// View for current level
-
-    if (phuLevel == PM_FPA_LEVEL_FPA) {
-        if (!pmFPAAddSourceFromView(fpa, "Simulation", view, output->format)) {
-            psError(PS_ERR_UNKNOWN, false, "Unable to add PHU to FPA.");
-            psFree(fpa);
-            psFree(view);
-            return NULL;
-        }
-    }
-
-    pmChip *chip;                       // Chip from FPA
-    while ((chip = pmFPAviewNextChip(view, fpa, 1))) {
-        if (phuLevel == PM_FPA_LEVEL_CHIP) {
-            if (!pmFPAAddSourceFromView(fpa, "Simulation", view, output->format)) {
-                psError(PS_ERR_UNKNOWN, false, "Unable to add PHU to FPA.");
-                psFree(fpa);
-                psFree(view);
-                return NULL;
-            }
-        }
-
-        pmCell *cell;                   // Cell from chip
-        while ((cell = pmFPAviewNextCell(view, fpa, 1))) {
-            if (phuLevel == PM_FPA_LEVEL_CELL) {
-                if (!pmFPAAddSourceFromView(fpa, "Simulation", view, output->format)) {
-                    psError(PS_ERR_UNKNOWN, false, "Unable to add PHU to FPA.");
-                    psFree(fpa);
-                    psFree(view);
-                    return NULL;
-                }
-            }
-        }
-    }
-
-    psFree(fpa);
-    psFree(view);
-
-    return output;
+  return output;
 }

branches/eam_branch_20080511/ppSim/src/ppSimInsertStars.c

@@ -15 +15 @@
 
     if (!stars->n) { return true; }
-
-    // XXX is this needed?
-    // pmFPAfile *simSources = psMetadataLookupPtr(NULL, config->files, "PPSIM.SOURCES"); // Output sources
 
     pmCell *cell = readout->parent;
@@ -136 +133 @@
 
     // NOTE: readout must be part of the pmFPAfile named "PPSIM.OUTPUT"
-    psMetadataAdd (readout->analysis, PS_LIST_TAIL, "PSPHOT.SOURCES", PS_DATA_ARRAY, "psphot sources", sources);
+    // XXX PPSIM.SOURCES are the fake sources with their *input* values
+    psMetadataAdd (readout->analysis, PS_LIST_TAIL, "PPSIM.SOURCES", PS_DATA_ARRAY, "fake sources", sources);
     psFree(sources);
 

branches/eam_branch_20080511/ppSim/src/ppSimLoadForceSources.c

@@ +1 @@
+# include "ppSim.h"
+
+psArray *ppSimLoadForceSources(pmConfig *config, const pmFPAview *view) {
+
+# if (0)
+
     // de-activate all files except PSASTRO.REFSTARS
     pmFPAfileActivate (config->files, false, NULL);
@@ -77 +83 @@
     pmFPAfileActivate (config->files, true, NULL);
     pmFPAfileActivate (config->files, false, "PSASTRO.OUT.REFSTARS");
+# endif
+
+    return NULL;
+}

branches/eam_branch_20080511/ppSim/src/ppSimLoop.c

@@ -13 +13 @@
 
     // in this program, we are looping over the output image, rather than the input as in ppImage
-    pmFPAfile *file = psMetadataLookupPtr(NULL, config->files, OUTPUT_FILE); // Output file
+    pmFPAfile *file = psMetadataLookupPtr(NULL, config->files, "PPSIM.OUTPUT"); // Output file
     assert(file);
-
-    // if we have an input image, we need to add the synthetic data on top of it below
-    // XXX we may potentially use this input file to skip missing elements
-    pmFPAfile *input = psMetadataLookupPtr(NULL, config->files, "PPIMAGE.INPUT");
 
     pmFPA *fpa = file->fpa;             // FPA for file
@@ -111 +107 @@
 
             psVector *biasCols = ppSimMakeBiassec (cell, config);
-
-            pmCell *inputCell = NULL;
-            if (input) {
-                inputCell = pmFPAviewThisCell (view, input->fpa);
-            }
 
             for (int i = 0; i < cell->readouts->n; i++) {
@@ -169 +160 @@
                 readout->parent->parent->data_exists = true;
 
-                if (inputCell && inputCell->readouts->data[i]) {
-                    pmReadout *inReadout = inputCell->readouts->data[i];
-                    if (!inReadout->weight) {
-                        if (!pmReadoutGenerateWeight(inReadout, true)) {
-                            psError (PS_ERR_UNKNOWN, false, "trouble creating weight");
-                            return false;
-                        }
-                    }
-                    if (!ppSimMergeReadouts (readout, inReadout)) ESCAPE (PS_ERR_UNKNOWN, "problem merging input image with simulated image");
-                }
+                // if there is an input image, merge it with the simulated image
+                if (!ppSimMergeReadouts (config, view)) ESCAPE (PS_ERR_UNKNOWN, "problem merging input image with simulated image");
             }
             psFree(biasCols);

branches/eam_branch_20080511/ppSim/src/ppSimMergeReadouts.c

@@ -2 +2 @@
 
 // XXX add bounds to the inputs?
-bool ppSimMergeReadouts (pmReadout *outReadout, pmReadout *inReadout) {
+bool ppSimMergeReadouts (pmConfig *config, pmFPAview *view) {
 
     // bool mdok;
+
+    // if we have an input image, we need to add the synthetic data on top of it below
+    // XXX we may potentially use this input file to skip missing elements
+    pmFPAfile *input = psMetadataLookupPtr(NULL, config->files, "PPSIM.INPUT");
+    if (!input) return true;
+
+    pmReadout *inReadout = pmFPAviewThisReadout (view, input->fpa);
+    if (!inReadout) return true;
+
+    if (!inReadout->weight) {
+      if (!pmReadoutGenerateWeight(inReadout, true)) {
+        psError (PS_ERR_UNKNOWN, false, "trouble creating weight");
+        return false;
+      }
+    }
+
+    // output must exist or we made a programming error
+    pmFPAfile *output = psMetadataLookupPtr(NULL, config->files, "PPSIM.OUTPUT"); // Output file
+    assert(output);
+
+    // XXX require outReadout?
+    pmReadout *outReadout = pmFPAviewThisReadout (view, output->fpa);
+    if (!outReadout) return true;
 
     psImage *inSignal = inReadout->image;
@@ -12 +35 @@
     psImage *outVariance = outReadout->weight;
 
-    // psMetadata *recipe = psMetadataLookupMetadata(&mdok, config->recipes, PPSIM_RECIPE); // Recipe
     assert (inSignal->numRows == outSignal->numRows);
     assert (inSignal->numCols == outSignal->numCols);

branches/eam_branch_20080511/ppSim/src/ppSimPhotom.c

@@ -18 +18 @@
     ppSimMosaicChip(config, blankMask, view, "PPSIM.CHIP", "PPSIM.OUTPUT");
 
-    // find or define a pmFPAfile PSPHOT.INPUT
-    pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PSPHOT.INPUT");
+    // XXX have ppSimMosaicChip return the pointer?
+    pmFPAfile *input = psMetadataLookupPtr (&status, config->files, "PPSIM.CHIP");
     if (!status) {
-        psError(PSPHOT_ERR_CONFIG, false, "PSPHOT.INPUT I/O file is not defined");
+        psError(PSPHOT_ERR_CONFIG, false, "PPSIM.CHIP 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
-    // XXX is this needed for ppSim? (yes, unless we do not do photometry and make a simulated image)
+    // XXX is this needed for ppSim? only if we want to write out the image with and without subtracted sources
     pmChip *oldChip = pmFPAviewThisChip (view, input->src);
     pmChip *newChip = pmFPAviewThisChip (view, input->fpa);
@@ -45 +45 @@
                 return false;
             }
-
             ppSimDetectionLimits (config, view);
         }

branches/eam_branch_20080511/ppSim/src/ppSimPhotomReadout.c

@@ -1 @@
-# include "psphotInternal.h"
+# include "ppSim.h"
 
-bool psphotReadout(pmConfig *config, const pmFPAview *view) {
+bool ppSimPhotomReadout(pmConfig *config, const pmFPAview *view) {
 
     psTimerStart ("psphotReadout");
@@ -18 +18 @@
     }
 
-    // find the currently selected readout
-    // XXX keep this name or go with something like PPSIM.PHOT.INPUT?
-    pmReadout  *readout = pmFPAfileThisReadout (config->files, view, "PSPHOT.INPUT");
+    // find the currently selected readout. 
+    // we always perform photometry on the mosaiced chip
+    pmReadout  *readout = pmFPAfileThisReadout (config->files, view, "PPSIM.CHIP");
     PS_ASSERT_PTR_NON_NULL (readout, false);
 
@@ -27 +27 @@
 
     // load the psf model, if suppled.  FWHM_X,FWHM_Y,etc are saved in the recipe
+    // this function uses PSPHOT.PSF.LOAD as the pmFPAfile 
     pmPSF *psf = psphotLoadPSF (config, view, recipe);
     assert (psf);
@@ -33 +34 @@
     // PPSIM.REAL.SOURCES carries the pmSource objects (from psphot analysis or loaded externally)
     psArray *realSources = psMetadataLookupPtr (NULL, readout->analysis, "PPSIM.REAL.SOURCES");
-    psArray *fakeSources = psMetadataLookupPtr (NULL, readout->analysis, "PSPHOT.SOURCES");
-    forceSources = ppSimLoadForceSources (config, view);
+    psArray *forceSources = ppSimLoadForceSources (config, view);
 
-    // replace all sources
-    psphotRemoveSources (realSources, recipe);
+    // XXX make a copy of the fake-source parameters so these can be saved independently 
+    // from the measured fake-source parameters
+    psArray *injectedSources = psMetadataLookupPtr (NULL, readout->analysis, "PPSIM.SOURCES");
+    psArray *fakeSources = psArrayAlloc (injectedSources->n);
+    for (int i = 0; i < injectedSources->n; i++) {
+      fakeSources->data[i] = pmSourceCopy (injectedSources->data[i]);
+    }
+
+    // remove all sources 
+    psphotRemoveAllSources (realSources, recipe);
 
     // generate a background model (median, smoothed image)
-    if (!psphotModelBackground (config, view, "PSPHOT.INPUT")) {
+    if (!psphotModelBackground (config, view, "PPSIM.CHIP")) {
         return psphotReadoutCleanup (config, readout, recipe, NULL, NULL, NULL);
     }
-    if (!psphotSubtractBackground (config, view, "PSPHOT.INPUT")) {
+    if (!psphotSubtractBackground (config, view, "PPSIM.CHIP")) {
         return psphotReadoutCleanup (config, readout, recipe, NULL, NULL, NULL);
     }
@@ -51 +59 @@
 
     // XXX fake sources should measure peak->x,y, force sources should not
+    psMaskType maskVal = 0xff; 
     psImage *significance = psphotSignificanceImage (readout, recipe, 1, maskVal);
     ppSimDetections (significance, recipe, fakeSources);
@@ -60 +69 @@
 
     // replace all sources
-    psphotReplaceAll (realSources, recipe);
+    psphotReplaceAllSources (realSources, recipe);
 
     // construct an initial model for each object
@@ -67 +76 @@
     psphotGuessModels (readout, forceSources, recipe, psf);
     
+    psArray *sources = NULL;
+
     // linear fit to real + fake sources
-    psArray *sources = ppSimMergeSources (realSources, fakeSources);
+    sources = ppSimMergeSources (realSources, fakeSources);
     psphotFitSourcesLinear (readout, sources, recipe, psf, FALSE); // XXX option to NOT subtract
-    psphotReplaceAll (sources, recipe);
+    psphotReplaceAllSources (sources, recipe);
     psFree (sources); // only frees the merged references
 
     // linear fit to real + forced sources
-    psArray *sources = ppSimMergeSources (realSources, forceSources);
+    sources = ppSimMergeSources (realSources, forceSources);
     psphotFitSourcesLinear (readout, sources, recipe, psf, FALSE); // XXX option to NOT subtract
-    psphotReplaceAll (sources, recipe);
+    psphotReplaceAllSources (sources, recipe);
     psFree (sources); // only frees the merged references
 
@@ -85 +96 @@
     if (!psphotApResid (readout, forceSources, recipe, psf)) {
         psLogMsg ("psphot", 3, "failed on psphotApResid");
-        return psphotReadoutCleanup (config, readout, recipe, detections, psf, sources);
+        return psphotReadoutCleanup (config, readout, recipe, NULL, psf, NULL);
     }
 
-    // calculate source magnitudes
+    // calculate source magnitudes (for which set??)
     pmReadout *background = psphotSelectBackground (config, view, false);
-    psphotMagnitudes(sources, recipe, psf, background);
+    psphotMagnitudes(fakeSources, recipe, psf, background);
+    psphotMagnitudes(forceSources, recipe, psf, background);
 
     // drop the references to the image pixels held by each source
-    psphotSourceFreePixels (sources);
+    psphotSourceFreePixels (realSources);
+    psphotSourceFreePixels (fakeSources);
+    psphotSourceFreePixels (forceSources);
 
     // create the exported-metadata and free local data
-    return psphotReadoutCleanup(config, readout, recipe, detections, psf, sources);
+    // XXX this places the sources on readout->analysis as PSPHOT.SOURCES.  modify?
+    // (or don't supply the sources, and do this with a different function)
+    psphotReadoutCleanup(config, readout, recipe, NULL, psf, NULL);
+
+    // add forceSources to the readout (real and fake already there)
+    psMetadataAdd (readout->analysis, PS_LIST_TAIL, "PPSIM.FAKE.SOURCES", PS_DATA_ARRAY, "fake photometry ", fakeSources);
+    psMetadataAdd (readout->analysis, PS_LIST_TAIL, "PPSIM.FORCE.SOURCES", PS_DATA_ARRAY, "forced photometry ", forceSources);
+    psFree (forceSources);
+    return true;
 }