Changeset 29833 for trunk/psModules/src/detrend/pmNonLinear.c

Timestamp:

Nov 25, 2010, 9:45:07 PM (15 years ago)

Author:

watersc1

Message:

Merge of czw_branch/20100817 into trunk. This includes the non-linearity correction application code.

Location:

trunk

Files:

• . (modified) (1 prop)
• psModules/src/detrend/pmNonLinear.c (modified) (3 diffs)

trunk/psModules/src/detrend/pmNonLinear.c

@@ -10 +10 @@
 #include "pmNonLinear.h"
 
+psF32 pmNonLinearityMeasureNoisy(psF32 flux, psVector *correction_fluxes, psVector *correction_factors);
 pmReadout *pmNonLinearityPolynomial(pmReadout *inputReadout, const psPolynomial1D *input1DPoly)
 {
@@ -27 +28 @@
 
 // set the bin closest to the corresponding value.  
-#define PS_BIN_FOR_VALUE(RESULT, VECTOR, VALUE) { \
-        psVectorBinaryDisectResult result; \
-        psScalar tmpScalar; \
-        tmpScalar.type.type = PS_TYPE_F32; \
-        tmpScalar.data.F32 = (VALUE); \
-        RESULT = psVectorBinaryDisect (&result, VECTOR, &tmpScalar); \
-        switch (result) { \
-          case PS_BINARY_DISECT_PASS: \
-            break; \
-          case PS_BINARY_DISECT_OUTSIDE_RANGE: \
-            numPixels ++; \
-            break; \
-          case PS_BINARY_DISECT_INVALID_INPUT: \
-          case PS_BINARY_DISECT_INVALID_TYPE: \
-            psAbort ("programming error"); \
-            break; \
+#define PS_BIN_FOR_VALUE(RESULT, VECTOR, VALUE) {                       \
+        psVectorBinaryDisectResult result;                              \
+        psScalar tmpScalar;                                             \
+        tmpScalar.type.type = PS_TYPE_F32;                              \
+        tmpScalar.data.F32 = (VALUE);                                   \
+        RESULT = psVectorBinaryDisect (&result, VECTOR, &tmpScalar);    \
+        switch (result) {                                               \
+          case PS_BINARY_DISECT_PASS:                                   \
+            break;                                                      \
+          case PS_BINARY_DISECT_OUTSIDE_RANGE:                          \
+            numPixels ++;                                               \
+            break;                                                      \
+          case PS_BINARY_DISECT_INVALID_INPUT:                          \
+          case PS_BINARY_DISECT_INVALID_TYPE:                           \
+            psAbort ("programming error");                              \
+            break;                                                      \
         } }
+
+
+# define PS_BIN_INTERPOLATE(RESULT, VECTOR, BOUNDS, BIN, VALUE) {       \
+        float dX, dY, Xo, Yo, Xt;                                       \
+        if (BIN == BOUNDS->n - 1) {                                     \
+            dX = 0.5*(BOUNDS->data.F32[BIN+1] - BOUNDS->data.F32[BIN-1]); \
+            dY = VECTOR->data.F32[BIN] - VECTOR->data.F32[BIN-1];       \
+            Xo = 0.5*(BOUNDS->data.F32[BIN+1] + BOUNDS->data.F32[BIN]); \
+            Yo = VECTOR->data.F32[BIN];                                 \
+        } else {                                                        \
+            dX = 0.5*(BOUNDS->data.F32[BIN+2] - BOUNDS->data.F32[BIN]); \
+            dY = VECTOR->data.F32[BIN+1] - VECTOR->data.F32[BIN];       \
+            Xo = 0.5*(BOUNDS->data.F32[BIN+1] + BOUNDS->data.F32[BIN]); \
+            Yo = VECTOR->data.F32[BIN];                                 \
+        }                                                               \
+        if (dY != 0) {                                                  \
+            Xt = (VALUE - Yo)*dX/dY + Xo;                               \
+        } else {                                                        \
+            Xt = Xo;                                                    \
+        }                                                               \
+        Xt = PS_MIN (BOUNDS->data.F32[BIN+1], PS_MAX(BOUNDS->data.F32[BIN], Xt)); \
+        psTrace("pmNonLinear", 6, "(Xo, Yo, dX, dY, Xt, Yt) is (%.2f %.2f %.2f %.2f %.2f %.2f)\n", \
+                Xo, Yo, dX, dY, Xt, VALUE);                             \
+        RESULT = Xt; }
 
 pmReadout *pmNonLinearityLookup(pmReadout *inputReadout, const psVector *inFlux, const psVector *outFlux)
@@ -92 +117 @@
     return inputReadout;
 }
+
+bool pmNonLinearityApply(pmReadout *inputReadout, psArray *Ltab)
+{
+    PS_ASSERT_PTR_NON_NULL(inputReadout, false);
+    PS_ASSERT_PTR_NON_NULL(inputReadout->image, false);
+    PS_ASSERT_IMAGE_TYPE(inputReadout->image, PS_TYPE_F32, false);
+    PS_ASSERT_PTR_NON_NULL(Ltab, false);
+
+    psTimerStart ("nonlinear");
+
+    psS32 numSamples = 39;
+    psS32 numBorder  = 10;
+
+    //  psS32 tableSize = Ltab->n;
+
+    psImage *image = inputReadout->image;
+
+    // Load default data.
+    psVector *default_row_correction_fluxes = psVectorAlloc(numSamples,PS_TYPE_F32);
+    psVector *default_col_correction_fluxes = psVectorAlloc(numSamples,PS_TYPE_F32);
+
+    psVector *default_row_correction_factors = psVectorAlloc(numSamples,PS_TYPE_F32);
+    psVector *default_col_correction_factors = psVectorAlloc(numSamples,PS_TYPE_F32);
+
+    // pre-allocate the correction vectors
+    psVector *row_correction_fluxes  = NULL;
+    psVector *col_correction_fluxes  = NULL;
+    psVector *row_correction_factors = NULL;
+    psVector *col_correction_factors = NULL;
+
+    int n = 0;
+    int m = 0;
+    for (int k = 0; k < Ltab->n; k++) { // Begin load default tables
+        psMetadata *row = Ltab->data[k];        
+        if (psMetadataLookupS32(NULL,row,"POSITION") != -1) {
+            continue;
+        }
+        if (psMetadataLookupS32(NULL,row,"DIRECTION") == 0) {
+            psVectorSet(default_row_correction_fluxes,n,psMetadataLookupF32(NULL,row,"FLUX"));
+            psVectorSet(default_row_correction_factors,n,psMetadataLookupF32(NULL,row,"FACTOR"));
+            n++;
+        }
+        else {
+            psVectorSet(default_col_correction_fluxes,m,psMetadataLookupF32(NULL,row,"FLUX"));
+            psVectorSet(default_col_correction_factors,m,psMetadataLookupF32(NULL,row,"FACTOR"));
+            m++;
+        }
+    } // End load default tables
+  
+    psLogMsg ("psModules", PS_LOG_MINUTIA, "load default data from table: %f sec\n", psTimerMark ("nonlinear"));
+
+    // pre-allocate arrays with the correction vectors for the borders
+    psArray *x_lo_flux = psArrayAlloc(numBorder);
+    psArray *x_hi_flux = psArrayAlloc(numBorder);
+    psArray *y_lo_flux = psArrayAlloc(numBorder);
+    psArray *y_hi_flux = psArrayAlloc(numBorder);
+
+    psArray *x_lo_fact = psArrayAlloc(numBorder);
+    psArray *x_hi_fact = psArrayAlloc(numBorder);
+    psArray *y_lo_fact = psArrayAlloc(numBorder);
+    psArray *y_hi_fact = psArrayAlloc(numBorder);
+    for (int i = 0; i < numBorder; i++) {
+        // pre-allocate the correction vectors
+        x_lo_flux->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+        x_hi_flux->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+        y_lo_flux->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+        y_hi_flux->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+
+        x_lo_fact->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+        x_hi_fact->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+        y_lo_fact->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+        y_hi_fact->data[i] = psVectorAllocEmpty(numSamples,PS_TYPE_F32);
+    }   
+
+    // parse out the full table:
+    for (int k = 0; k < Ltab->n; k++) {
+        psMetadata *row = Ltab->data[k];        
+        int dir = psMetadataLookupS32(NULL,row,"DIRECTION");
+        int pos = psMetadataLookupS32(NULL,row,"POSITION");
+
+        psVector *fluxVector = NULL;
+        psVector *factVector = NULL;
+
+        int seq = -1;
+        if ((dir == 0) && (pos < image->numCols/2)) {
+          seq = pos ;
+            if (seq < 0) continue;
+            fluxVector = x_lo_flux->data[seq];
+            factVector = x_lo_fact->data[seq];
+        } 
+        if ((dir == 0) && (pos > image->numCols/2)) {
+            seq = pos + numBorder - image->numCols;
+            if (seq >= image->numCols) continue;
+            fluxVector = x_hi_flux->data[seq];
+            factVector = x_hi_fact->data[seq];
+        }
+        if ((dir == 1) && (pos < image->numRows/2)) {
+            seq = pos;
+            if (seq < 0) continue;
+            fluxVector = y_lo_flux->data[seq];
+            factVector = y_lo_fact->data[seq];
+        } 
+        if ((dir == 1) && (pos > image->numRows/2)) {
+            seq = pos + numBorder - image->numRows;
+            if (seq >= image->numRows) continue;
+            fluxVector = y_hi_flux->data[seq];
+            factVector = y_hi_fact->data[seq];
+        }
+
+        float flux = psMetadataLookupF32(NULL,row,"FLUX");
+        float factor = psMetadataLookupF32(NULL,row,"FACTOR");
+
+        psVectorAppend(fluxVector, flux);
+        psVectorAppend(factVector, factor);
+    }
+    psLogMsg ("psModules", PS_LOG_MINUTIA, "load border data from table: %f sec\n", psTimerMark ("nonlinear"));
+
+    for (int i = 0; i < image->numRows; i++) { // Loop over rows : note: problem with discontinuity here
+        row_correction_fluxes = NULL;
+        if (i < numBorder) {
+            row_correction_fluxes  = y_lo_flux->data[i];
+            row_correction_factors = y_lo_fact->data[i];
+        }
+        if (i > image->numRows - numBorder) {
+            row_correction_fluxes  = y_hi_flux->data[i + numBorder - image->numRows];
+            row_correction_factors = y_hi_fact->data[i + numBorder - image->numRows];
+        }
+        if (row_correction_fluxes == NULL) {
+          row_correction_factors = default_row_correction_factors;
+            row_correction_fluxes = default_row_correction_fluxes;
+        }
+
+        for (int j = 0; j < image->numCols; j++) { // Loop over columns
+            col_correction_fluxes = NULL;
+            if (j < numBorder) {
+                col_correction_fluxes  = x_lo_flux->data[j];
+                col_correction_factors = x_lo_fact->data[j];
+            }
+            if (j > image->numCols - numBorder) {
+                col_correction_fluxes  = x_hi_flux->data[j + numBorder - image->numCols];
+                col_correction_factors = x_hi_fact->data[j + numBorder - image->numCols];
+            }
+            if (col_correction_fluxes == NULL) {
+              col_correction_factors = default_col_correction_factors;
+              col_correction_fluxes = default_col_correction_fluxes;
+            }
+
+            // Calculate correction factor contribution for this pixel.
+            psF32 factor_row = pmNonLinearityMeasure(image->data.F32[i][j], row_correction_fluxes,row_correction_factors);
+            psF32 factor_col = pmNonLinearityMeasure(image->data.F32[i][j], col_correction_fluxes,col_correction_factors);
+#if (0)
+            if (((i == 200)&&(j == 200))||((i == 9)&&(j == 5))) { // Print out if we're looking at a test case.
+              psF32 factor_row = pmNonLinearityMeasureNoisy(image->data.F32[i][j], row_correction_fluxes,row_correction_factors);
+              psF32 factor_col = pmNonLinearityMeasureNoisy(image->data.F32[i][j], col_correction_fluxes,col_correction_factors);
+              
+                psTrace("psModules.nonlin",6,"Linearity: %d %d %s %f %f %f %d %d\n",i,j,
+                        psMetadataLookupStr(NULL,inputReadout->parent->concepts,"CELL.NAME"),
+                        image->data.F32[i][j],factor_row,factor_col,numBorder,numSamples);
+                psTrace("psModules.nonlin",6,"Linearity: R: %d %d %d C: %d %d %d\n",
+                        i,(i < numBorder),(image->numRows - i),
+                        j,(j < numBorder),(image->numCols - j));
+
+                psTrace("psModules.nonlin",6,"Linearity: V: ");
+                for (int k = 0; k < numSamples; k++) {
+                    psTrace("psModules.nonlin",6,"(%f %f) (%f %f) DDDD> (%f %f) (%f %f)",
+                            col_correction_fluxes->data.F32[k],col_correction_factors->data.F32[k],
+                            row_correction_fluxes->data.F32[k],row_correction_factors->data.F32[k],
+                            default_col_correction_fluxes->data.F32[k],default_col_correction_factors->data.F32[k],
+                            default_row_correction_fluxes->data.F32[k],default_row_correction_factors->data.F32[k]);
+                }
+                psTrace("psModules.nonlin",6,"\n");
+            } // End Test case
+#endif
+            // Apply correction to image data
+#if (0)
+            if (((i == 200)&&(j == 200))||((i == 9)&&(j == 5))) { // Print out if we're looking at a test case.
+              psTrace("psModules.nonlin",4,"Applied Linearity Correction: %s %d %d : %f %f -> %f\n",
+                      psMetadataLookupStr(NULL,inputReadout->parent->concepts,"CELL.NAME"),
+                      i,j,image->data.F32[i][j],(factor_row + factor_col) / 2.0,
+                      image->data.F32[i][j] + (factor_row + factor_col) / 2.0);
+            }
+# endif
+            image->data.F32[i][j] = image->data.F32[i][j] - ( factor_row + factor_col ) / 2.0;
+
+        } // End loop over columns
+    } // End loop over rows
+    psLogMsg ("psModules", PS_LOG_MINUTIA, "apply correction: %f sec\n", psTimerMark ("nonlinear"));
+
+    psFree(x_lo_flux);
+    psFree(x_hi_flux);
+    psFree(y_lo_flux);
+    psFree(y_hi_flux);
+
+    psFree(x_lo_fact);
+    psFree(x_hi_fact);
+    psFree(y_lo_fact);
+    psFree(y_hi_fact);
+
+    psFree(default_row_correction_fluxes);
+    psFree(default_row_correction_factors);
+    psFree(default_col_correction_fluxes);
+    psFree(default_col_correction_factors);
+  
+    return(true);
+}
+
+psF32 pmNonLinearityMeasure(psF32 flux, psVector *correction_fluxes, psVector *correction_factors) {
+    //  psS32 numPixels = 0;
+    psF32 result = 0;
+    psU32 bin = 0;
+
+    bin = correction_fluxes->n - 1;
+    if (flux < correction_fluxes->data.F32[0]) {
+        return(0.0);
+    }
+/*     if (flux > correction_fluxes->data.F32[bin]) { */
+/*      return(0.0); */
+/*     } */
+  
+    for (int i = 0; i < correction_fluxes->n - 1; i++) {
+        if ((flux >= correction_fluxes->data.F32[i])&&
+            (flux <  correction_fluxes->data.F32[i+1])) {
+            result = correction_factors->data.F32[i] +
+                (flux - correction_fluxes->data.F32[i]) *
+                ((correction_factors->data.F32[i+1] - correction_factors->data.F32[i]) /
+                 (correction_fluxes->data.F32[i+1] - correction_fluxes->data.F32[i]));
+            continue;
+        }
+    }
+
+/*   PS_BIN_FOR_VALUE(bin,correction_fluxes,flux); */
+/*   if ((bin < 0)||(bin > correction_fluxes->n)) { */
+/*     return(1.0); */
+/*   } */
+  
+/*   PS_BIN_INTERPOLATE(result,correction_fluxes,correction_factors,bin,flux); */
+    if (!isfinite(result)) {
+        result = 0.0;
+    }
+/*     if (result <= 0) { */
+/*      result = 1.0; */
+/*     } */
+    return(result);
+}
+
+psF32 pmNonLinearityMeasureNoisy(psF32 flux, psVector *correction_fluxes, psVector *correction_factors) {
+    //  psS32 numPixels = 0;
+    psF32 result = 0;
+    psU32 bin = 0;
+
+    bin = correction_fluxes->n - 1;
+    psTrace("psModules.nonlin",6,"NLMN: %f %d %f %f\n",flux,bin,correction_fluxes->data.F32[0],correction_fluxes->data.F32[bin]);
+    if (flux < correction_fluxes->data.F32[0]) {
+        return(0.0);
+    }
+/*     if (flux > correction_fluxes->data.F32[bin]) { */
+/*      return(0.0); */
+/*     } */
+
+    for (int i = 0; i < correction_fluxes->n - 1; i++) {
+      psTrace("psModules.nonlin",6,"NLMN: %f %d %f %f %f %f\n",flux,i,correction_fluxes->data.F32[i],correction_fluxes->data.F32[i],
+              correction_factors->data.F32[i],correction_factors->data.F32[i+1]);
+        if ((flux >= correction_fluxes->data.F32[i])&&
+            (flux <  correction_fluxes->data.F32[i+1])) {
+            result = correction_factors->data.F32[i] +
+                (flux - correction_fluxes->data.F32[i]) *
+                ((correction_factors->data.F32[i+1] - correction_factors->data.F32[i]) /
+                 (correction_fluxes->data.F32[i+1] - correction_fluxes->data.F32[i]));
+            continue;
+        }
+    }
+
+/*   PS_BIN_FOR_VALUE(bin,correction_fluxes,flux); */
+/*   if ((bin < 0)||(bin > correction_fluxes->n)) { */
+/*     return(1.0); */
+/*   } */
+  
+/*   PS_BIN_INTERPOLATE(result,correction_fluxes,correction_factors,bin,flux); */
+    if (!isfinite(result)) {
+        result = 0.0;
+    }
+/*     if (result <= 0) { */
+/*      result = 1.0; */
+/*     } */
+    return(result);
+}
+
+  
+