Merge pull request #106 from jamienoss/infrastructure-changes-from-#101

Infrastructure changes, inc. hstio

hstio/keyword.c

@@ -228,7 +228,7 @@ static int insertname(FitsKwInfo *kw, char *nm) {
         int orig_nlines = 0;
 
         if (kw->hdr->nalloc == 0) {
-            if (allocHdr(kw->hdr,HdrUnit) != 0)
+            if (allocHdr(kw->hdr,HdrUnit, True) != 0)
             return -1;
         }
         if (kw->hdr->nlines == kw->hdr->nalloc) {
@@ -275,7 +275,7 @@ static int addcommentary(Hdr *h, char *text, char *type) {
         int  nblankline  = 0;
         char *t;
         if (h->nalloc == 0) {
-            if (allocHdr(h,HdrUnit) != 0)
+            if (allocHdr(h,HdrUnit, True) != 0)
                 return -1;
         }
         if (h->nlines == h->nalloc) {
@@ -1165,7 +1165,7 @@ FitsKw  insertFitsCard(FitsKw kw_, char *card) {
 
         /* make sure we have room */
         if (kw->hdr->nalloc == 0) {
-            if (allocHdr(kw->hdr,HdrUnit) != 0)
+            if (allocHdr(kw->hdr,HdrUnit, True) != 0)
                 { error(NOMEM,""); return NULL; }
         }
         if (kw->hdr->nlines == kw->hdr->nalloc) {

include/hstio.h

@@ -5,6 +5,8 @@
 extern "C" {
 # endif
 
+# include <stdlib.h>
+
 # define HSTIO_VERSION "HSTIO Version 2.6 (11-Mar-2010)"
 
 /*
@@ -117,8 +119,6 @@ extern "C" {
 **
 */
 
-# include <stdlib.h>
-
 /* Below is a general use pointer register (book keeping) to allow easy cleanup upon exit (pseudo C++ destructor)
  * Use example:
  *
@@ -166,13 +166,24 @@ enum Bool_ { False = 0, True = 1 };
 typedef enum Bool_ Bool;
 # endif
 
+enum StorageOrder
+{
+    ROWMAJOR,
+    COLUMNMAJOR
+};
+
+#define SCIEXT 0x01
+#define ERREXT 0x02
+#define DQEXT 0x04
+
 typedef struct {
         short *buffer;          /* the pointer to the beg. of the buffer */
         int buffer_size;        /* the size of the full 2-d array in the */
         int tot_nx;             /* buffer.                               */
         int tot_ny;             /*     buffer_size = tot_nx*tot_ny       */
         int nx;                 /* The size of the current "view" of the */
         int ny;                 /* full 2-d array.                       */
+        enum StorageOrder storageOrder;
         short *data;            /* The pointer to the beginning of the   */
                                 /* subsection of the full 2-d array.     */
 } ShortTwoDArray;
@@ -184,6 +195,7 @@ typedef struct {
         int tot_ny;
         int nx;
         int ny;
+        enum StorageOrder storageOrder;
         float *data;
 } FloatTwoDArray;
 
@@ -208,10 +220,12 @@ typedef struct {
 */
 
 # define Pix(a,i,j)      (a).data[(j)*(a).tot_nx + (i)]
+# define PixColumnMajor(a,i,j) (a).data[(j)*(a).tot_ny + (i)]
 # define DQPix(a,i,j)    (a).data[(j)*(a).tot_nx + (i)]
 # define DQSetPix(a,i,j,value) (a).data[(j)*(a).tot_nx + (i)] = (value)
 
 # define PPix(a,i,j)      (a)->data[(j)*(a)->tot_nx + (i)]
+# define PPixColumnMajor(a,i,j) (a)->data[(j)*(a)->tot_ny + (i)]
 # define PDQPix(a,i,j)    (a)->data[(j)*(a)->tot_nx + (i)]
 # define PDQSetPix(a,i,j,value) (a)->data[(j)*(a)->tot_nx + (i)] = (value)
 
@@ -251,6 +265,8 @@ typedef struct {
         int sx;                 /* The sizes of the X and Y dimensions  */
         int sy;                 /* of the section.                      */
 } DataSection;
+void copyDataSection(DataSection * dest, const DataSection * src);
+
 
 # define HDRSize 81
 typedef char HdrArray[HDRSize]; /* Headers are simply an array of fixed */
@@ -707,12 +723,14 @@ void updateWCS (Hdr *hdr, int xbeg, int ybeg);
 */
 # define IFloatData { NULL, 0, 0, 0, 0, 0, NULL }
 void initFloatData(FloatTwoDArray *);
-int allocFloatData(FloatTwoDArray *, int, int);
+int allocFloatData(FloatTwoDArray *, int, int, Bool zeroInitialize);
 void freeFloatData(FloatTwoDArray *);
+int swapFloatStorageOrder(FloatTwoDArray * target, const FloatTwoDArray * source, enum StorageOrder targetStorageOrder);
 # define IShortData { NULL, 0, 0, 0, 0, 0, NULL }
 void initShortData(ShortTwoDArray *);
-int allocShortData(ShortTwoDArray *, int, int);
+int allocShortData(ShortTwoDArray *, int, int, Bool zeroInitialize);
 void freeShortData(ShortTwoDArray *);
+int swapShortStorageOrder(ShortTwoDArray * target, const ShortTwoDArray * source, enum StorageOrder targetStorageOrder);
 
 # define IFloatLine { NULL, 0 }
 void initFloatLine  (FloatHdrLine *);
@@ -729,18 +747,20 @@ int  allocDQLine  (SingleGroupLine *);
 
 # define IHdr { 0, 0, NULL }
 void initHdr(Hdr *);
-int allocHdr(Hdr *, int);
+int allocHdr(Hdr *, int, Bool zeroInitialize);
 int reallocHdr(Hdr *, int);
 void freeHdr(Hdr *);
-int copyHdr(Hdr *to, Hdr *from);
+int copyHdr(Hdr *to, const Hdr *from);
 
 # define IFloatHdrData { NULL, { 0, 0, 0, 0 }, IHdr, IFloatData }
 void initFloatHdrData(FloatHdrData *);
-int allocFloatHdrData(FloatHdrData *, int, int);
+int allocFloatHdrData(FloatHdrData *, int, int, Bool zeroInitialize);
+int copyFloatHdrData(FloatHdrData * target, const FloatHdrData * src, enum StorageOrder targetStorageOrder);
 void freeFloatHdrData(FloatHdrData *);
 # define IShortHdrData { NULL, { 0, 0, 0, 0 }, IHdr, IShortData }
 void initShortHdrData(ShortHdrData *);
-int allocShortHdrData(ShortHdrData *, int, int);
+int allocShortHdrData(ShortHdrData *, int, int, Bool zeroInitialize);
+int copyShortHdrData(ShortHdrData * target, const ShortHdrData * src, enum StorageOrder targetStorageOrder);
 void freeShortHdrData(ShortHdrData *);
 
 # define IFloatHdrLine { NULL, IHdr, False, 0, NULL }
@@ -755,13 +775,23 @@ void freeShortHdrLine  (ShortHdrLine *);
 # define ISingleGroup { NULL, 0, NULL, IFloatHdrData, IFloatHdrData, \
 IShortHdrData }
 void initSingleGroup(SingleGroup *);
-int allocSingleGroup(SingleGroup *, int, int);
+int allocSingleGroup(SingleGroup *, int, int, Bool zeroInitialize);
+int allocSingleGroupHeader(Hdr ** hdr, Bool zeroInitialize);
+int allocSingleGroupExts(SingleGroup *x, int i, int j, unsigned extension, Bool zeroInitialize);
 void freeSingleGroup(SingleGroup *);
+void setStorageOrder(SingleGroup * group, enum StorageOrder storageOrder);
+int copySingleGroup(SingleGroup * target, const SingleGroup * source, enum StorageOrder targetStorageOrder);
+void copyOffsetSingleGroup(SingleGroup * output, const SingleGroup * input, unsigned nRows, unsigned nColumns, unsigned outputOffset, unsigned inputOffset, unsigned outputSkipLength, unsigned inputSkipLength);
 # define IMultiGroup { 0, NULL }
 void initMultiGroup(MultiGroup *);
 int allocMultiGroup(MultiGroup *, int);
 void freeMultiGroup(MultiGroup *);
 
+int copyFloatData(FloatTwoDArray * target, const FloatTwoDArray * source, enum StorageOrder targetStorageOrder);
+void copyOffsetFloatData(float * output, const float * input, unsigned nRows, unsigned nColumns, unsigned outputOffset, unsigned inputOffset, unsigned outputSkipLength, unsigned inputSkipLength);
+int copyShortData(ShortTwoDArray * target, const ShortTwoDArray * source, enum StorageOrder targetStorageOrder);
+void copyOffsetShortData(short * output, const short * input, unsigned nRows, unsigned nColumns, unsigned outputOffset, unsigned inputOffset, unsigned outputSkipLength, unsigned inputSkipLength);
+
 # define ISingleNicmosGroup { NULL, 0, NULL, IFloatHdrData, IFloatHdrData, \
 IShortHdrData, IShortHdrData, IFloatHdrData }
 void initSingleNicmosGroup(SingleNicmosGroup *);

include/xtables.h

@@ -57,6 +57,8 @@ void c_imtclose (IRAFPointer imt);
 IRAFPointer c_tbtopn (char *tablename, int iomode, IRAFPointer template);
 void c_tbtcre (IRAFPointer tp);
 void c_tbtclo (IRAFPointer tp);
+void c_tbtClose (IRAFPointer * tp);
+
 int c_tbtacc (char *tablename);
 void c_tbtnam (IRAFPointer tp, char *tablename, int maxch);
 void c_tbfpri (char *intable, char *outtable, int *copied);
@@ -68,6 +70,7 @@ int c_tbpsta (IRAFPointer tp, int param);
 void c_tbcdef1 (IRAFPointer tp, IRAFPointer *cp,
         char *colname, char *colunits, char *colfmt, int datatype, int nelem);
 void c_tbcfnd1 (IRAFPointer tp, const char *colname, IRAFPointer *cp);
+IRAFPointer c_tbcfnd1_retPtr (IRAFPointer tp, const char *colname);
 IRAFPointer c_tbcnum (IRAFPointer tp, int colnum);
 
 int c_tbcigi (IRAFPointer cp, int param);
@@ -102,13 +105,16 @@ void c_tbrcsc (IRAFPointer itp, IRAFPointer otp,
                 int irow, int orow, int ncols);
 void c_tbrudf (IRAFPointer tp, IRAFPointer *cp, int numcols, int row);
 
-void c_tbegtb (IRAFPointer tp, IRAFPointer cp, int rownum, Bool *buffer);
-void c_tbegtd (IRAFPointer tp, IRAFPointer cp, int rownum, double *buffer);
-void c_tbegtr (IRAFPointer tp, IRAFPointer cp, int rownum, float *buffer);
-void c_tbegti (IRAFPointer tp, IRAFPointer cp, int rownum, int *buffer);
-void c_tbegts (IRAFPointer tp, IRAFPointer cp, int rownum, short *buffer);
-void c_tbegtt (IRAFPointer tp, IRAFPointer cp, int rownum, char *buffer,
+void c_tbegtb (const IRAFPointer tp, const IRAFPointer cp, int rownum, Bool *buffer);
+void c_tbegtd (const IRAFPointer tp, const IRAFPointer cp, int rownum, double *buffer);
+void c_tbegtr (const IRAFPointer tp, const IRAFPointer cp, int rownum, float *buffer);
+void c_tbegti (const IRAFPointer tp, const IRAFPointer cp, int rownum, int *buffer);
+void c_tbegts (const IRAFPointer tp, const IRAFPointer cp, int rownum, short *buffer);
+void c_tbegtt (const IRAFPointer tp, const IRAFPointer cp, int rownum, char *buffer,
                 int maxch);
+int c_tbeGetInt(const IRAFPointer tp, const IRAFPointer cp, int rownum);
+double c_tbeGetDouble(const IRAFPointer tp, const IRAFPointer cp, int rownum);
+
 void c_tbeptb (IRAFPointer tp, IRAFPointer cp, int rownum, Bool buffer);
 void c_tbeptd (IRAFPointer tp, IRAFPointer cp, int rownum, double buffer);
 void c_tbeptr (IRAFPointer tp, IRAFPointer cp, int rownum, float buffer);

pkg/acs/calacs/acs2d/doflat.c

@@ -258,7 +258,7 @@ static int divFlat (SingleGroup *x, char *flatname, ACSInfo *acs2d) {
 
     /* Initialize shifted spot arrays */
     initSingleGroup(&outspot);
-    allocSingleGroup(&outspot, inspot.sci.data.nx, inspot.sci.data.ny);
+    allocSingleGroup(&outspot, inspot.sci.data.nx, inspot.sci.data.ny, True);
 
     parseObsDate(x->globalhdr, &date);
     status = GetSpotTab(acs2d->spot.name, date, &shiftx, &shifty);

pkg/acs/calacs/acsrej/acsrej_loop.c

@@ -315,7 +315,7 @@ int acsrej_loop (IODescPtr ipsci[], IODescPtr ipdq[],
        back into the input DQ arrays at the end of processing, while dq
        will hold values to write to the output CRJ DQ extension */
     initShortData (&dq2);
-    allocShortData (&dq2, dim_x, dim_y);
+    allocShortData (&dq2, dim_x, dim_y, True);
     for (j = 0; j < dim_y; j++) {
         for (i = 0; i < dim_x; i++) {
             PDQSetPix(dq,i,j,crflag);

pkg/stis/calstis/cs1/dobias.c

@@ -90,7 +90,7 @@ SingleGroup *x    io: image to be calibrated; written to in-place
 	    /* First bin the bias image down to the actual size of x. */
 
 	    initSingleGroup (&z);
-	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny);
+	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny, True);
 	    if ((status = bin2d (&y, x0, y0, rx, ry, avg, &z))) {
 		printf ("ERROR    (biascorr) size mismatch.\n");
 		return (status);

pkg/stis/calstis/cs1/doblev.c

@@ -140,7 +140,7 @@ int *driftcorr    o: true means correction for drift along lines was applied
 	initSingleGroup (out);
 	allocSingleGroup (out,
 		in->sci.data.nx - (trimx1 + trimx2),
-		in->sci.data.ny - (trimy1 + trimy2));
+		in->sci.data.ny - (trimy1 + trimy2), True);
 	if (hstio_err())
 	    return (OUT_OF_MEMORY);
 

pkg/stis/calstis/cs1/dodark.c

@@ -217,7 +217,7 @@ int sci_extver     i: IMSET number in input (science) file
 	    /* Bin the dark image down to the actual size of x. */
 
 	    initSingleGroup (&z);
-	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny);
+	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny, True);
 	    if ((status = bin2d (&y, x0, y0, rx, ry, avg, &z))) {
 		printf ("ERROR    (darkcorr) size mismatch.\n");
 		return (status);

pkg/stis/calstis/cs1/dodqi.c

@@ -347,7 +347,7 @@ SingleGroup *x    io: image to be calibrated; DQ array written to in-place
 
 	if (!in_place) {
 	    /* Allocate space for a scratch array. */
-	    allocShortData (&ydq, snpix[0], snpix[1]);
+	    allocShortData (&ydq, snpix[0], snpix[1], True);
 	    if (hstio_err()) {
 		printf (
 		"ERROR    (doDQI) couldn't allocate data quality array.\n");

pkg/stis/calstis/cs1/doflat.c

@@ -98,7 +98,7 @@ SingleGroup *x    io: image to be calibrated; written to in-place
 		if (hstio_err())
 		    return (OPEN_FAILED);
 
-		allocSingleGroup (&z, y.sci.data.nx, y.sci.data.ny);
+		allocSingleGroup (&z, y.sci.data.nx, y.sci.data.ny, True);
 		if (hstio_err())
 		    return (ALLOCATION_PROBLEM);
 
@@ -126,7 +126,7 @@ SingleGroup *x    io: image to be calibrated; written to in-place
 		*/
 		nx = rx * z.sci.data.nx;
 		ny = ry * z.sci.data.ny;
-		allocSingleGroup (&y, nx, ny);
+		allocSingleGroup (&y, nx, ny, True);
 		if (hstio_err())
 		    return (ALLOCATION_PROBLEM);
 
@@ -198,7 +198,7 @@ SingleGroup *x    io: image to be calibrated; written to in-place
 
 	    /* Bin the flat field down to the actual size of x. */
 
-	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny);
+	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny, True);
 	    if ((status = bin2d (&y, x0, y0, rx, ry, avg, &z))) {
 		printf ("ERROR    (doFlat) size mismatch\n");
 		return (status);

pkg/stis/calstis/cs1/dolores.c

@@ -68,7 +68,7 @@ int *done         o: true if input image has been binned
 	if ((out = calloc (1, sizeof (SingleGroup))) == NULL)
 	    return (OUT_OF_MEMORY);
 	initSingleGroup (out);
-	allocSingleGroup (out, (in->sci.data.nx) / mx, (in->sci.data.ny) / my);
+	allocSingleGroup (out, (in->sci.data.nx) / mx, (in->sci.data.ny) / my, True);
 	if (hstio_err())
 	    return (OUT_OF_MEMORY);
 

pkg/stis/calstis/cs1/doshad.c

@@ -86,7 +86,7 @@ SingleGroup *x    io: image to be calibrated; written to in-place
 	    /* Bin the reference image down to the actual size of x. */
 
 	    initSingleGroup (&z);
-	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny);
+	    allocSingleGroup (&z, x->sci.data.nx, x->sci.data.ny, True);
 	    if ((status = bin2d (&y, x0, y0, rx, ry, avg, &z))) {
 		printf ("ERROR    (doShad) size mismatch.\n");
 		return (status);

pkg/stis/calstis/cs4/maketemplate.c

@@ -230,7 +230,7 @@ static void debugimg (char *dbgfile, CmplxArray *z) {
 	int i, j;
 
 	initFloatHdrData (&x);
-	allocFloatHdrData (&x, z->nx, z->ny);
+	allocFloatHdrData (&x, z->nx, z->ny, True);
 
 	for (j = 0;  j < z->ny;  j++) {
 	    for (i = 0;  i < z->nx;  i++)

pkg/stis/calstis/cs6/do1dx.c

@@ -649,7 +649,7 @@ StisInfo6 *sts    i: calibration switches and info
             */
 	    if (sts->scatter) {
 	        if (allocSingleGroup (&holdraw, in.sci.data.nx,
-                                      in.sci.data.ny) == -1)
+                                      in.sci.data.ny, True) == ALLOCATION_PROBLEM)
 	            return (OUT_OF_MEMORY);
 	        for (i = 0; i < holdraw.sci.data.nx; i++) {
 	            for (j = 0; j < holdraw.sci.data.ny; j++) {
@@ -1158,7 +1158,7 @@ StisInfo6 *sts    i: calibration switches and info
                     */
 	            if (!outw_exists) {
 	                if (allocSingleGroup (&outw, in.sci.data.nx,
-                                                     in.sci.data.ny) == -1)
+                                                     in.sci.data.ny, True) == ALLOCATION_PROBLEM)
 	                    return (OUT_OF_MEMORY);
 	                outw_exists = 1;
 	            }

pkg/stis/calstis/cs6/idtalg/calstis6idt.c

@@ -459,12 +459,12 @@ int bks_order;		i: backgr. smoothing polynomial order
 	        return (OUT_OF_MEMORY);
 	    if (ltm[0] > 1.0) {
 	        allocSingleGroup (&win, in.sci.data.nx / 2,
-                                        in.sci.data.ny / 2);
+                                        in.sci.data.ny / 2, True);
 	        if (RebinData (&in, &win, x1d, wx1d, 2, tabptr.nrows))
 	            return (ERROR_RETURN);
 	    } else {
 	        allocSingleGroup (&win, in.sci.data.nx,
-                                        in.sci.data.ny);
+                                        in.sci.data.ny, True);
 	        if (RebinData (&in, &win, x1d, wx1d, 1, tabptr.nrows))
 	            return (ERROR_RETURN);
 	    }
@@ -1211,7 +1211,7 @@ int bks_order;		i: backgr. smoothing polynomial order
 	        }
 	        remove (temp_ima);
 	        initSingleGroup (&wout);
-	        allocSingleGroup (&wout, win.sci.data.nx, win.sci.data.ny);
+	        allocSingleGroup (&wout, win.sci.data.nx, win.sci.data.ny, True);
 	        for (j = 0; j < wout.sci.data.ny; j++) {
 	            for (i = 0; i < wout.sci.data.nx; i++)
 	                Pix (wout.sci.data, i, j) = im_mod[j][i];
@@ -1377,7 +1377,7 @@ int bks_order;		i: backgr. smoothing polynomial order
 	    initSingleGroup (&wout);
 	    if ((wx1d2 = AllocX1DTable (tabptr.nrows)) == NULL)
 	        return (OUT_OF_MEMORY);
-	    allocSingleGroup (&wout, in.sci.data.nx, in.sci.data.ny);
+	    allocSingleGroup (&wout, in.sci.data.nx, in.sci.data.ny, True);
 	    if (ltm[0] > 1.0) {
 	        if (RebinData (&win, &wout, wx1d, wx1d2, -2, tabptr.nrows))
 	            return (ERROR_RETURN);

pkg/stis/calstis/cs7/do2dx.c

@@ -446,7 +446,7 @@ StisInfo7 *sts    i: calibration switches and info
 		AddOffsets (sts, &slit);
 
 		/* Create output imset. */
-		allocSingleGroup (out, coord_o->npix[0], coord_o->npix[1]);
+		allocSingleGroup (out, coord_o->npix[0], coord_o->npix[1], True);
 		if (hstio_err())
 		    return (OUT_OF_MEMORY);
 

pkg/wfc3/calwf3/lib/dodqi.c

@@ -249,7 +249,7 @@ SingleGroup *x    io: image to be calibrated; DQ array written to in-place
 	/* Allocate space for scratch array */
 	initShortHdrData (&ydq);
 	if (!in_place) {
-	    allocShortHdrData (&ydq, snpix[0], snpix[1]);
+	    allocShortHdrData (&ydq, snpix[0], snpix[1], True);
 	    if (hstio_err()) {
 		trlerror ("doDQI couldn't allocate data quality array.");
 		return (status = OUT_OF_MEMORY);

pkg/wfc3/calwf3/wf3ccd/doccd.c

@@ -343,7 +343,7 @@ int DoCCD (WF3Info *wf3, int extver) {
                 sub2full will reset the pixel values
                 */
                 initSingleGroup(&fullarray);
-                allocSingleGroup(&fullarray,RAZ_COLS/2,RAZ_ROWS);
+                allocSingleGroup(&fullarray,RAZ_COLS/2,RAZ_ROWS, True);
                 fullarray.group_num=x.group_num;
                 CreateEmptyChip(wf3, &fullarray);
                 if (x.group_num == 2){ /*post blev*/