Index: trunk/psModules/src/detrend/pmPattern.c
===================================================================
--- trunk/psModules/src/detrend/pmPattern.c	(revision 24905)
+++ trunk/psModules/src/detrend/pmPattern.c	(revision 26893)
@@ -1,3 +1,4 @@
 #include <stdio.h>
+#include <string.h>
 #include <pslib.h>
 
@@ -9,5 +10,5 @@
 // Mask a row as bad
 static void patternMaskRow(pmReadout *ro, // Readout to mask
-                           int y,         // Row to mask
+                           int y,       // Row to mask
                            psImageMaskType bad // Mask value to give
                            )
@@ -17,5 +18,5 @@
     psAssert(y < image->numRows, "Row not in image");
 
-    int numCols = image->numCols;       // Size of image
+    int numCols = image->numCols;       // Number of columns
     for (int x = 0; x < numCols; x++) {
         image->data.F32[y][x] = NAN;
@@ -29,4 +30,8 @@
     return;
 }
+
+//////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Measurement and application
+//////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
 bool pmPatternRow(pmReadout *ro, int order, int iter, float rej, float thresh,
@@ -63,4 +68,5 @@
     float lower = stats->robustMedian - thresh * stats->robustStdev; // Lower bound for data
     float upper = stats->robustMedian + thresh * stats->robustStdev; // Upper bound for data
+    float background = stats->robustMedian;
     psFree(stats);
     psFree(rng);
@@ -79,4 +85,7 @@
     psPolynomial1D *poly = psPolynomial1DAlloc(PS_POLYNOMIAL_ORD, order); // Polynomial to fit
     psVector *data = psVectorAlloc(numCols, PS_TYPE_F32); // Data to fit
+
+    psImage *corr = psImageAlloc(order + 1, numRows, PS_TYPE_F64); // Corrections applied
+    psImageInit(corr, NAN);
 
     for (int y = 0; y < numRows; y++) {
@@ -104,4 +113,7 @@
             continue;
         }
+
+        poly->coeff[0] -= background;
+        memcpy(corr->data.F64[y], poly->coeff, (order + 1) * PSELEMTYPE_SIZEOF(PS_TYPE_F64));
         psVector *solution = psPolynomial1DEvalVector(poly, indices); // Solution vector
         if (!solution) {
@@ -117,4 +129,8 @@
         psFree(solution);
     }
+
+    psMetadataAddImage(ro->analysis, PS_LIST_TAIL, PM_PATTERN_ROW_CORRECTION, PS_META_REPLACE,
+                       "Pattern row correction", corr);
+    psFree(corr);
 
     psFree(indices);
@@ -126,2 +142,239 @@
     return true;
 }
+
+bool pmPatternRowApply(pmReadout *ro, psImageMaskType maskBad)
+{
+    PM_ASSERT_READOUT_NON_NULL(ro, false);
+    PM_ASSERT_READOUT_IMAGE(ro, false);
+
+    bool mdok;                          // Status of MD lookup
+    psImage *corr = psMetadataLookupPtr(&mdok, ro->analysis, PM_PATTERN_ROW_CORRECTION); // Correction
+    if (!mdok) {
+        // No correction to apply
+        return true;
+    }
+
+    psImage *image = ro->image; // Image of interest
+    int numCols = image->numCols, numRows = image->numRows; // Size of image
+
+    if (corr->numRows != numRows) {
+        psError(PS_ERR_BAD_PARAMETER_SIZE, true,
+                "Number of rows of image (%d) does not match number of rows of pattern correction (%d)\n",
+                numRows, corr->numRows);
+        return false;
+    }
+
+    int order = corr->numCols - 1;                                        // Polynomial order
+    psPolynomial1D *poly = psPolynomial1DAlloc(PS_POLYNOMIAL_ORD, order); // Polynomial to apply
+    psVector *indices = psVectorAlloc(numCols, PS_TYPE_F32); // Indices for polynomial
+    float norm = 2.0 / (float)numCols;  // Normalisation for indices
+    for (int x = 0; x < numCols; x++) {
+        indices->data.F32[x] = x * norm - 1.0;
+    }
+
+    for (int y = 0; y < numRows; y++) {
+        memcpy(poly->coeff, corr->data.F64[y], (order + 1) * PSELEMTYPE_SIZEOF(PS_TYPE_F64));
+        psVector *solution = psPolynomial1DEvalVector(poly, indices); // Solution vector
+        if (!solution) {
+            psWarning("Unable to evaluate polynomial for row %d", y);
+            psErrorClear();
+            patternMaskRow(ro, y, maskBad);
+            continue;
+        }
+
+        for (int x = 0; x < numCols; x++) {
+            image->data.F32[y][x] -= solution->data.F32[x];
+        }
+        psFree(solution);
+    }
+
+    psFree(poly);
+    psFree(indices);
+
+    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));
+            psMetadataAddF32(ro->analysis, PS_LIST_TAIL, PM_PATTERN_CELL_CORRECTION, PS_META_REPLACE,
+                             "Pattern cell correction solution", NAN);
+            continue;
+        }
+        float correction = background - mean->data.F32[i]; // Correction to apply
+        const char *cellName = psMetadataLookupStr(NULL, cell->concepts, "CELL.NAME"); // Name of cell
+        psLogMsg("psModules.detrend", PS_LOG_DETAIL, "Correcting background of cell %s by %f",
+                 cellName, correction);
+        psBinaryOp(ro->image, ro->image, "+", psScalarAlloc(correction, PS_TYPE_F32));
+        psMetadataAddF32(ro->analysis, PS_LIST_TAIL, PM_PATTERN_CELL_CORRECTION, PS_META_REPLACE,
+                         "Pattern cell correction solution", correction);
+    }
+
+    psFree(mean);
+    psFree(meanMask);
+
+    return true;
+}
+
+bool pmPatternCellApply(pmReadout *ro, psImageMaskType maskBad)
+{
+    PM_ASSERT_READOUT_NON_NULL(ro, false);
+    PM_ASSERT_READOUT_IMAGE(ro, false);
+
+    bool mdok;                          // Status of MD lookup
+    float corr = psMetadataLookupF32(&mdok, ro->analysis, PM_PATTERN_CELL_CORRECTION); // Correction to apply
+    if (!mdok) {
+        // No correction to apply
+        return true;
+    }
+
+    psImage *image = ro->image, *mask = ro->mask; // Image and mask of interest
+    int numCols = image->numCols, numRows = image->numRows; // Size of image
+
+    if (!isfinite(corr)) {
+        for (int y = 0; y < numRows; y++) {
+            for (int x = 0; x < numCols; x++) {
+                image->data.F32[y][x] = NAN;
+            }
+        }
+        if (mask) {
+            for (int y = 0; y < numRows; y++) {
+                for (int x = 0; x < numCols; x++) {
+                    mask->data.PS_TYPE_IMAGE_MASK_DATA[y][x] |= maskBad;
+                }
+            }
+        }
+    } else {
+        for (int y = 0; y < numRows; y++) {
+            for (int x = 0; x < numCols; x++) {
+                image->data.F32[y][x] += corr;
+            }
+        }
+    }
+
+    return true;
+}
+
+