Index: trunk/psLib/src/imageops/psImageConvolve.c
===================================================================
--- trunk/psLib/src/imageops/psImageConvolve.c	(revision 30078)
+++ trunk/psLib/src/imageops/psImageConvolve.c	(revision 30595)
@@ -67,5 +67,8 @@
 }
 
-psKernel *psKernelAlloc(int xMin, int xMax, int yMin, int yMax)
+psKernel *p_psKernelAlloc(const char *file,
+			  unsigned int lineno,
+			  const char *func,
+			  int xMin, int xMax, int yMin, int yMax)
 {
     // Check the inputs to make sure max > min; if not, switch.
@@ -91,5 +94,5 @@
     int numCols = xMax - xMin + 1;      // Number of columns for kernel image
 
-    psKernel *kernel = psAlloc(sizeof(psKernel)); // The kernel, to be returned
+    psKernel *kernel = p_psAlloc(file, lineno, func, sizeof(psKernel)); // The kernel, to be returned
     psMemSetDeallocator(kernel,(psFreeFunc)kernelFree);
 
@@ -272,7 +275,9 @@
     float threshold = sumKernel * (1.0 - frac); // Threshold for truncation
 
+    int truncateRadius = maxSize;	// Truncation radius
+    bool truncate = false;
+
     // Find truncation size
-    int truncate = 0;                     // Truncation radius
-    for (int radius = 1; truncate == 0 && radius < maxSize; radius++) {
+    for (int radius = 1; !truncate && (radius < maxSize); radius++) {
         int uMin = PS_MAX(-radius, xMin);
         int uMax = PS_MIN(radius, xMax);
@@ -290,11 +295,13 @@
             }
         }
+	// This is the truncation radius
         if (sum > threshold) {
-            // This is the truncation radius
-            truncate = radius;
-        }
-    }
-    if (truncate == maxSize) {
-        // No truncation possible
+	    truncate = true;
+            truncateRadius = radius;
+        }
+    }
+
+    // Do nothing if no truncation is possible
+    if (!truncate) {
         return true;
     }
@@ -302,9 +309,9 @@
     // Truncate the kernel
     {
-        int uMin = PS_MAX(-truncate, xMin);
-        int uMax = PS_MIN(truncate, xMax);
-        int vMin = PS_MAX(-truncate, yMin);
-        int vMax = PS_MIN(truncate, yMax);
-        int r2 = PS_SQR(truncate);
+        int uMin = PS_MAX(-truncateRadius, xMin);
+        int uMax = PS_MIN(truncateRadius, xMax);
+        int vMin = PS_MAX(-truncateRadius, yMin);
+        int vMax = PS_MIN(truncateRadius, yMax);
+        int r2 = PS_SQR(truncateRadius);
         for (int v = vMin; v <= vMax; v++) {
             int v2 = PS_SQR(v);
@@ -317,8 +324,8 @@
         }
     }
-    kernel->xMin = PS_MAX(-truncate, kernel->xMin);
-    kernel->xMax = PS_MIN(truncate, kernel->xMax);
-    kernel->yMin = PS_MAX(-truncate, kernel->yMin);
-    kernel->yMax = PS_MIN(truncate, kernel->yMax);
+    kernel->xMin = PS_MAX(-truncateRadius, kernel->xMin);
+    kernel->xMax = PS_MIN(truncateRadius, kernel->xMax);
+    kernel->yMin = PS_MAX(-truncateRadius, kernel->yMin);
+    kernel->yMax = PS_MIN(truncateRadius, kernel->yMax);
 
     return true;
Index: trunk/psLib/src/imageops/psImageConvolve.h
===================================================================
--- trunk/psLib/src/imageops/psImageConvolve.h	(revision 30078)
+++ trunk/psLib/src/imageops/psImageConvolve.h	(revision 30595)
@@ -84,4 +84,5 @@
 /// @return psKernel*          A new kernel object
 ///
+#ifdef DOXYGEN
 psKernel *psKernelAlloc(
     int xMin,                          ///< Most negative x index
@@ -89,5 +90,18 @@
     int yMin,                          ///< Most negative y index
     int yMax                           ///< Most positive y index
+);
+#else // ifdef DOXYGEN
+psKernel *p_psKernelAlloc(
+    const char *file,                   ///< File of caller
+    unsigned int lineno,                ///< Line number of caller
+    const char *func,                   ///< Function name of caller
+    int xMin,                          ///< Most negative x index
+    int xMax,                          ///< Most positive x index
+    int yMin,                          ///< Most negative y index
+    int yMax                           ///< Most positive y index
 ) PS_ATTR_MALLOC;
+#define psKernelAlloc(xMin, xMax, yMin, yMax)				\
+    p_psKernelAlloc(__FILE__, __LINE__, __func__, (xMin), (xMax), (yMin), (yMax))
+#endif // ifdef DOXYGEN
 
 /// Allocate a convolution kernel from a provided image
Index: trunk/psLib/src/imageops/psImageCovariance.c
===================================================================
--- trunk/psLib/src/imageops/psImageCovariance.c	(revision 30078)
+++ trunk/psLib/src/imageops/psImageCovariance.c	(revision 30595)
@@ -30,4 +30,15 @@
     return covar;
 }
+
+/** 
+
+ * changes from 28666
+ ** add scale to imageCovarianceCalculate (& multiply at return)
+ ** add scale to imageCovarianceCalculateThread
+
+ ** accumulate scale (sum kernel^2) in psImageCovarianceCalculate and pass to imageCovarianceCalculate
+ ** accumulate scale (sum kernel^2) in psImageCovarianceCalculateFactor and pass to imageCovarianceCalculate
+
+ **/
 
 /// Calculation of covariance matrix element when convolving
Index: trunk/psLib/src/sys/psLogMsg.c
===================================================================
--- trunk/psLib/src/sys/psLogMsg.c	(revision 30078)
+++ trunk/psLib/src/sys/psLogMsg.c	(revision 30595)
@@ -291,10 +291,11 @@
         head_ptr += strlen(head_ptr);
     }
-    // Hostname should be 20 characters.
+
+    // Hostname should be 10 characters.
     if (logHost) {
         if (head_ptr > head) {
             *head_ptr++ = '|';
         }
-        maxLength -= snprintf(head_ptr, maxLength, "%-20s", hostname);
+        maxLength -= snprintf(head_ptr, maxLength, " %s ", hostname);
         head_ptr += strlen(head_ptr);
     }
@@ -310,12 +311,15 @@
             *head_ptr++ = '|';
         }
-        maxLength -= snprintf(head_ptr, maxLength, "%s", name);
+        maxLength -= snprintf(head_ptr, maxLength, "%s|\n", name);
 
         head_ptr += strlen(head_ptr);
-    }
-
-    if (head_ptr > head) {
-        *head_ptr++ = '\n';
-    } else if (!logMsg) {                  // no output desired
+    } else {
+      if (head_ptr > head) {
+	*head_ptr++ = '|';
+      }
+    }
+
+    // rather than putting in a return for the message, let's only put in the return if we asked for the function name
+    if ((head_ptr == head) && !logMsg) { // no output desired
         return;
     }
@@ -332,5 +336,5 @@
         char *line = strtok_r(msg, "\n", &msgPtr);
         while (line) {
-            if(write(logFD, "    ", 4)) {;} // ignore return value
+            if(write(logFD, "          ", PS_MIN(2*level, 10))) {;} // ignore return value
             if(write(logFD, line, strlen(line))) {;} // ignore return value
             if(write(logFD, "\n", 1)) {;} // ignore return value
Index: trunk/psLib/src/sys/psMemory.c
===================================================================
--- trunk/psLib/src/sys/psMemory.c	(revision 30078)
+++ trunk/psLib/src/sys/psMemory.c	(revision 30595)
@@ -626,5 +626,6 @@
             nleak++;
 
-            if (fd != NULL) {
+	    // only print a max of 500 leaks (make this an argument)
+            if ((nleak < 500) && (fd != NULL)) {
                 if (nleak == 1) {
                     fprintf(fd, "# func at (file:line)  ID: X  Ref: X\n");
Index: trunk/psLib/test/imageops/Makefile.am
===================================================================
--- trunk/psLib/test/imageops/Makefile.am	(revision 30078)
+++ trunk/psLib/test/imageops/Makefile.am	(revision 30595)
@@ -26,5 +26,6 @@
 	tap_psImageMapFit \
 	tap_psImageMapFit2 \
-	tap_psImageMaskOps
+	tap_psImageMaskOps \
+	tap_psImageCovariance
 
 #	tap_psImageShiftKernel
Index: trunk/psLib/test/imageops/samples/conv.sample1.001.fits
===================================================================
--- trunk/psLib/test/imageops/samples/conv.sample1.001.fits	(revision 30595)
+++ trunk/psLib/test/imageops/samples/conv.sample1.001.fits	(revision 30595)
@@ -0,0 +1,140 @@
+SIMPLE  =                    T / file does conform to FITS standard             BITPIX  =                  -32 / number of bits per data pixel                  NAXIS   =                    2 / number of data axes                            NAXIS1  =                   37 / length of data axis 1                          NAXIS2  =                   37 / length of data axis 2                          EXTEND  =                    T / FITS dataset may contain extensions            COMMENT   FITS (Flexible Image Transport System) format is defined in 'AstronomyCOMMENT   and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H BZERO   =   0.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          BSCALE  =   1.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          END                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             .I­.ÍpÇ/‹:œ01/r0ÓÀÓ1m²–1ú¬ô2xmŒ2çmR3J¶?3§
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Index: trunk/psLib/test/imageops/samples/conv.sample1.002.fits
===================================================================
--- trunk/psLib/test/imageops/samples/conv.sample1.002.fits	(revision 30595)
+++ trunk/psLib/test/imageops/samples/conv.sample1.002.fits	(revision 30595)
@@ -0,0 +1,19 @@
+SIMPLE  =                    T / file does conform to FITS standard             BITPIX  =                  -32 / number of bits per data pixel                  NAXIS   =                    2 / number of data axes                            NAXIS1  =                   17 / length of data axis 1                          NAXIS2  =                   17 / length of data axis 2                          EXTEND  =                    T / FITS dataset may contain extensions            COMMENT   FITS (Flexible Image Transport System) format is defined in 'AstronomyCOMMENT   and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H BZERO   =   0.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          BSCALE  =   1.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          END                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             8ªïŽ8ÿCé92åÇ9kïÛ9’ÙÁ9¬óŽ9À˜9ÉðÈ9Æd†9¶Z9u˜9€œG9HÅr9ș8՞O8‘(R8;`ƒ8ûßØ9;) 9‚ú{9­ß‡9Üǘ:‡•:
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+;#,;*³t;/"w;H¿:疥:šÂh:?wË9éöf9”Qr9By8ýø
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9ùöT9jX9š4Ÿ:Ì:‰Y;Û$;ô#<èÞ<Ó
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Index: trunk/psLib/test/imageops/samples/incovar.sample1.001.fits
===================================================================
--- trunk/psLib/test/imageops/samples/incovar.sample1.001.fits	(revision 30595)
+++ trunk/psLib/test/imageops/samples/incovar.sample1.001.fits	(revision 30595)
@@ -0,0 +1,19 @@
+SIMPLE  =                    T / file does conform to FITS standard             BITPIX  =                  -32 / number of bits per data pixel                  NAXIS   =                    2 / number of data axes                            NAXIS1  =                   11 / length of data axis 1                          NAXIS2  =                   11 / length of data axis 2                          EXTEND  =                    T / FITS dataset may contain extensions            COMMENT   FITS (Flexible Image Transport System) format is defined in 'AstronomyCOMMENT   and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H BZERO   =   0.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          BSCALE  =   1.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          END                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             4„¶×“&7=ò¶µÛ›Qž­æ9ºvÌž­æ:µÛ›”7=òŠ¶×“4„Ÿ¶Õ©9.mṙ±ç81¯;
+Ä?<ÇÐ;
+Ä?81¯¹™±Û9.mÙ¶Õ©ó7<-G¹™ :]$žœ}L»wõ­œ/üg»wõ­žœ}L:]¹™ 
7<.µÙ·81»žœš€75Ù:n;˗
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Index: trunk/psLib/test/imageops/samples/incovar.sample1.002.fits
===================================================================
--- trunk/psLib/test/imageops/samples/incovar.sample1.002.fits	(revision 30595)
+++ trunk/psLib/test/imageops/samples/incovar.sample1.002.fits	(revision 30595)
@@ -0,0 +1,8 @@
+SIMPLE  =                    T / file does conform to FITS standard             BITPIX  =                  -32 / number of bits per data pixel                  NAXIS   =                    2 / number of data axes                            NAXIS1  =                   11 / length of data axis 1                          NAXIS2  =                   11 / length of data axis 2                          EXTEND  =                    T / FITS dataset may contain extensions            COMMENT   FITS (Flexible Image Transport System) format is defined in 'AstronomyCOMMENT   and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H BZERO   =   0.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          BSCALE  =   1.000000000000E+00 / Scaling: TRUE = BZERO + BSCALE * DISK          END                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             4š«¶ìƒŸ7P-ѵëå8žŒO³ºƒ}$žŒO²µëä'7P-Ѷ샧4š««¶ì'ƒ94ù¹žì^84â;Ì<ÈÖ2;Ì84
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Index: trunk/psLib/test/imageops/tap_psImageCovariance.c
===================================================================
--- trunk/psLib/test/imageops/tap_psImageCovariance.c	(revision 30595)
+++ trunk/psLib/test/imageops/tap_psImageCovariance.c	(revision 30595)
@@ -0,0 +1,70 @@
+/** @file  tap_psImageCovariance.c
+ *
+ *  @brief Contains the tests for psImageCovariance.[ch]
+ *
+ *  @version $Revision: 1.2 $
+ *  @date $Date: 2007-05-02 04:14:33 $
+ *
+ *  Copyright 2011 Institute for Astronomy, University of Hawaii
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include <pslib.h>
+#include "tap.h"
+#include "pstap.h"
+
+psKernel *psKernelReadSimple(char *filename) {
+
+    psRegion region = {0, 0, 0, 0};
+
+    psFits *fits = psFitsOpen(filename, "r");
+    psFitsDumpErrors(0, "foo");
+    ok(fits, "opened FITS file");
+
+    psImage *image = psFitsReadImage(fits, region, 0);
+    psFitsDumpErrors(0, "foo");
+    ok(image, "read image from FITS file");
+
+    psFitsClose(fits);
+
+    int x0 = image->numCols / 2;
+    int y0 = image->numRows / 2;
+    psKernel *kernel = psKernelAllocFromImage(image, x0, y0);
+    ok(kernel, "allocated kernel from image");
+
+    psFree(image);
+
+    return kernel;
+}
+
+int main(int argc, char **argv) {
+
+    plan_tests(4);
+
+    // return null for null input image
+    {
+        psMemId id = psMemGetId();
+
+	// read in the kernel and the covariance matrix
+	psKernel *kernel = psKernelReadSimple("kernel.fits");
+        ok(kernel, "read kernel");
+
+	psKernel *inputCov = psKernelReadSimple("cov.input.fits");
+        ok(inputCov, "read input covariance");
+
+	psKernel *outputCov = psImageCovarianceCalculate(kernel, inputCov);
+        ok(outputCov, "calculated covariance");
+
+	psFits *fits = psFitsOpen("cov.output.fits", "w");
+	psFitsWriteImage(fits, NULL, outputCov->image, 0, NULL);
+	psFitsClose(fits);
+
+	psFree(kernel);
+        psFree(inputCov);
+        psFree(outputCov);
+        ok(!psMemCheckLeaks (id, NULL, NULL, false), "no memory leaks");
+    }
+}
+
+