Changeset 42379 for trunk/psModules/src/detrend/pmPatternIO.c

Timestamp:

Feb 8, 2023, 11:54:08 AM (3 years ago)

Author:

eugene

Message:

merge from eam_branches/ipp-20220316. no_warn strncpy; avoid passing NULL to sprintf %s; add code for PATTERN_DEAD_CELLS; fix error in PSF residual image evaluation; drop detailed mask analysis for binned images (not actually used)

Location:

trunk/psModules

Files:

• . (modified) (1 prop)
• src/detrend/pmPatternIO.c (modified) (2 diffs)

trunk/psModules/src/detrend/pmPatternIO.c

@@ -482 +482 @@
 }
 
-// read the set of tables, one for each chip
+// Read the set of tables, one for each chip.  The values are saved on the cell->analysis
+// metadata of the pmFPAfile associated with the pattern file.  Later, when this is used (e.g.,
+// ppImageDetrendPatternRowApply), the values are transferred to the cell->analysis metadata of
+// the pmFPAfile for the image being processed.
 bool pmPatternRowAmpReadChips (pmFPAfile *file) {
 
@@ -560 +563 @@
     return true;
 }
+
+/**************** PatternDeadCells I/O *************************/
+
+bool pmPatternDeadCellsRead (const pmFPAview *view, pmFPAfile *file, const pmConfig *config)
+    {
+        // read the full model in one pass: require the level to be FPA
+        if (view->chip != -1) {
+            psError(PS_ERR_IO, false, "Pattern Dead Cells must be read at the FPA level");
+            return false;
+        }
+
+        if (!pmPatternDeadCellsReadFPA (file)) {
+            psError(PS_ERR_IO, false, "Failed to read Pattern Dead Cells for fpa");
+            return false;
+        }
+        return true;
+    }
+
+// read in all chip-level Pattern Dead Cells data for this FPA
+bool pmPatternDeadCellsReadFPA (pmFPAfile *file) {
+
+    if (!pmPatternDeadCellsReadChips (file)) {
+        psError(PS_ERR_IO, false, "Failed to read Pattern Dead Cells for chips");
+        return false;
+    }
+
+    return true;
+}
+
+// Read the set of dead cell image cubes, one for each chip.  The values are saved on the
+// chip->analysis metadata of the pmFPAfile associated with the pattern file.  Later, when this
+// is used (e.g., ppImageDetrendPatternDeadCellsApply), the values are transferred to the
+// chip->analysis metadata of the pmFPAfile for the image being processed.
+bool pmPatternDeadCellsReadChips (pmFPAfile *file) {
+
+    bool haveData, status;
+
+    // loop over the extensions
+    // for each extension, use the extname (eg, XY01.ded) to assign to a chip
+
+    // move to the start of the file
+    haveData = psFitsMoveExtNum (file->fits, 1, false);
+    if (!haveData) {
+        psError(PS_ERR_IO, false, "Failed to read even the first extension?");
+        return false;
+    }
+
+    int nGood = 0;
+    while (haveData) {
+
+        // load the header
+        psMetadata *header = psFitsReadHeader(NULL, file->fits); // The FITS header
+        if (!header) psAbort("cannot read dead cell header");
+
+        // load the full model in one shot
+        psImage *deadCellData = psFitsReadImage(file->fits, psRegionSet(0,0,0,0), 0); // dead cell patterns
+        if (!deadCellData) psAbort("cannot read dead cell pattern");
+        
+        // determine the chip (not all chips have DEAD CELL patterns)
+        char *extname = psMetadataLookupStr (&status, header, "EXTNAME");
+        psLogMsg ("psModules.detrend", 8, "read dead cell pattern for extname %s\n", extname);
+
+        // I expect to find a name of the form: chipName.ded (eg, XY01.ded)
+        // where chipName like 'XY01'
+        psAssert (strlen(extname) == 8, "invalid extension %s", extname);
+        psAssert (extname[5] == 'd', "invalid extension %s", extname);
+        psAssert (extname[6] == 'e', "invalid extension %s", extname);
+        psAssert (extname[7] == 'd', "invalid extension %s", extname);
+
+        char chipName[5];
+        strncpy (chipName, extname, 4);
+        chipName[4] = 0;
+
+        pmChip *chip = pmConceptsChipFromName (file->fpa, chipName);
+        if (!chip) psAbort ("invalid chip?");
+
+        psMetadataAddImage (chip->analysis, PS_LIST_TAIL, "PTN.DEAD.CELL", PS_META_REPLACE, "", deadCellData);
+        psFree (deadCellData);
+        psFree (header);
+
+        // move to the next extension
+        haveData = psFitsMoveExtNum (file->fits, 1, true);
+        nGood ++;
+    }
+    psLogMsg ("psModules.detrend", 4, "read patterns for %d chips from Pattern Dead Cells file\n", nGood);
+
+    return true;
+}