Index: branches/eam_branches/20091201/psModules/src/detrend/pmPattern.c
===================================================================
--- branches/eam_branches/20091201/psModules/src/detrend/pmPattern.c	(revision 26770)
+++ branches/eam_branches/20091201/psModules/src/detrend/pmPattern.c	(revision 26776)
@@ -127,2 +127,142 @@
     return true;
 }
+
+
+
+
+bool pmPatternCell(pmChip *chip, const psVector *tweak, psStatsOptions bgStat, psStatsOptions cellStat,
+                   psImageMaskType maskVal, psImageMaskType maskBad)
+{
+    PS_ASSERT_PTR_NON_NULL(chip, false);
+    PS_ASSERT_VECTOR_NON_NULL(tweak, false);
+    PS_ASSERT_VECTOR_SIZE(tweak, chip->cells->n, false);
+    PS_ASSERT_VECTOR_TYPE(tweak, PS_TYPE_U8, false);
+
+    int numCells = tweak->n;            // Number of cells
+
+    psVector *mean = psVectorAlloc(numCells, PS_TYPE_F32); // Mean for each cell
+    psVector *meanMask = psVectorAlloc(numCells, PS_TYPE_VECTOR_MASK); // Mask for means
+    psVectorInit(mean, NAN);
+    psVectorInit(meanMask, 0);
+
+    // Mask bits
+    enum {
+        PM_PATTERN_IGNORE = 0x01,       // Ignore this cell
+        PM_PATTERN_TWEAK  = 0x02,       // Tweak this cell
+        PM_PATTERN_ERROR  = 0x04,       // Error in calculating background
+        PM_PATTERN_ALL    = 0xFF,       // All causes
+    };
+
+    // Count number of cells to tweak
+    int numTweak = 0;                   // Number of cells to tweak
+    int numIgnore = 0;                  // Number of cells to ignore
+    for (int i = 0; i < numCells; i++) {
+        pmCell *cell = chip->cells->data[i]; // Cell of interest
+        if (!cell || !cell->data_exists || !cell->process ||
+            cell->readouts->n == 0 || cell->readouts->n > 1 || !cell->readouts->data[0]) {
+            numIgnore++;
+            meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] = PM_PATTERN_IGNORE;
+            continue;
+        }
+        if (tweak->data.U8[i]) {
+            meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] = PM_PATTERN_TWEAK;
+            numTweak++;
+        }
+    }
+    if (numTweak == 0) {
+        // Nothing to do
+        psFree(mean);
+        psFree(meanMask);
+        return true;
+    }
+    if (numTweak >= numCells - numIgnore) {
+        psError(PS_ERR_BAD_PARAMETER_VALUE, true, "Cannot pattern-correct all cells within a chip.");
+        psFree(mean);
+        psFree(meanMask);
+        return false;
+    }
+
+    // Measure mean of each cell
+    // This is not really the perfect thing to do, which would be to take a common mean for the set of cells
+    // which aren't being tweaked (because some cells will be heavily masked, so shouldn't be weighted the
+    // same as pure cells), but it's simple and fast.
+    psStats *bgStats = psStatsAlloc(bgStat); // Statistics on background
+    psRandom *rng = psRandomAlloc(PS_RANDOM_TAUS); // Random number generator
+    for (int i = 0; i < numCells; i++) {
+        if (meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PM_PATTERN_IGNORE) {
+            continue;
+        }
+        pmCell *cell = chip->cells->data[i]; // Cell of interest
+        pmReadout *ro = cell->readouts->data[0]; // Readout of interest
+
+        psStatsInit(bgStats);
+#if 1
+        if (!psImageBackground(bgStats, NULL, ro->image, ro->mask, maskVal, rng)) {
+            psWarning("Unable to measure background for cell %d\n", i);
+            psErrorClear();
+            meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] |= PM_PATTERN_ERROR;
+            continue;
+        }
+#else
+        if (!psImageStats(bgStats, ro->image, ro->mask, maskVal)) {
+            psWarning("Unable to measure background for cell %d\n", i);
+            psErrorClear();
+            meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] |= PM_PATTERN_ERROR;
+            continue;
+        }
+#endif
+        mean->data.F32[i] = psStatsGetValue(bgStats, bgStat);
+        if (!isfinite(mean->data.F32[i])) {
+            psWarning("Non-finite background for cell %d\n", i);
+            psErrorClear();
+            meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] |= PM_PATTERN_ERROR;
+            continue;
+        }
+    }
+    psFree(bgStats);
+    psFree(rng);
+
+    psStats *cellStats = psStatsAlloc(cellStat); // Statistics on cells
+    if (!psVectorStats(cellStats, mean, NULL, meanMask, PM_PATTERN_ALL)) {
+        psError(PS_ERR_UNKNOWN, false, "Unable to calculate mean cell background.");
+        psFree(mean);
+        psFree(meanMask);
+        psFree(cellStats);
+        return false;
+    }
+
+    float background = psStatsGetValue(cellStats, cellStat); // Background value for chip
+    psFree(cellStats);
+    if (!isfinite(background)) {
+        psError(PS_ERR_UNKNOWN, false, "Non-finite mean cell background.");
+        psFree(mean);
+        psFree(meanMask);
+        return false;
+    }
+
+    psLogMsg("psModules.detrend", PS_LOG_DETAIL, "Mean chip background is %f", background);
+
+    for (int i = 0; i < numCells; i++) {
+        if (meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PM_PATTERN_IGNORE) {
+            continue;
+        }
+        if (!(meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PM_PATTERN_TWEAK)) {
+            continue;
+        }
+        pmCell *cell = chip->cells->data[i]; // Cell of interest
+        pmReadout *ro = cell->readouts->data[0]; // Readout of interest
+        if (meanMask->data.PS_TYPE_VECTOR_MASK_DATA[i] & PM_PATTERN_ERROR) {
+            psImageInit(ro->image, NAN);
+            psBinaryOp(ro->mask, ro->mask, "|", psScalarAlloc(maskBad, PS_TYPE_IMAGE_MASK));
+            continue;
+        }
+        float correction = background - mean->data.F32[i]; // Correction to apply
+        psLogMsg("psModules.detrend", PS_LOG_DETAIL, "Correcting background of cell %d by %f", i, correction);
+        psBinaryOp(ro->image, ro->image, "+", psScalarAlloc(correction, PS_TYPE_F32));
+    }
+
+    psFree(mean);
+    psFree(meanMask);
+
+    return true;
+}
Index: branches/eam_branches/20091201/psModules/src/detrend/pmPattern.h
===================================================================
--- branches/eam_branches/20091201/psModules/src/detrend/pmPattern.h	(revision 26770)
+++ branches/eam_branches/20091201/psModules/src/detrend/pmPattern.h	(revision 26776)
@@ -31,4 +31,15 @@
     );
 
+/// Fix the background on cells known to be troublesome
+bool pmPatternCell(
+    pmChip *chip,                       ///< Chip to correct
+    const psVector *tweak,              ///< U8 vector indicating whether to tweak the corresponding cell
+    psStatsOptions bgStat,              ///< Statistic to use for background measurement
+    psStatsOptions cellStat,            ///< Statistic to use for combination of cell background measurements
+    psImageMaskType maskVal,            ///< Mask value to use
+    psImageMaskType maskBad             ///< Mask value to give bad pixels
+    );
+
+
 /// @}
 #endif