Individual panel arrays

5 files changed, 107 insertions, 26 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 37328e5f..09f33d5d 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -1003,8 +1003,12 @@ out:
 		p->xss = -p->fsy / d;
 		p->yss = p->fsx / d;
 
+		p->w = p->max_fs - p->min_fs + 1;
+		p->h = p->max_ss - p->min_ss + 1;
+
 	}
 
+
 	find_min_max_d(det);
 
 	if ( reject ) return NULL;
@@ -1129,6 +1133,9 @@ struct detector *simple_geometry(const struct image *image)
 	geom->panels[0].yfs = 0;
 	geom->panels[0].yss = 1;
 
+	geom->panels[0].w = image->width;
+	geom->panels[0].h = image->height;
+
 	find_min_max_d(geom);
 
 	return geom;
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 43bdc42d..c8d36396 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -75,6 +75,9 @@ struct panel
 	double yfs;
 	double xss;
 	double yss;
+
+	int w;  /* Width, calculated as max_fs-min_fs+1 */
+	int h;  /* Height, calculated as max_ss-min_ss+1 */
 };
 
 
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index bb11adac..3c4066be 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -501,6 +501,73 @@ static void debodge_saturation(struct hdfile *f, struct image *image)
 }
 
 
+static int unpack_panels(struct image *image, struct detector *det)
+{
+	int pi;
+
+	image->dp = malloc(det->n_panels * sizeof(float *));
+	image->bad = malloc(det->n_panels * sizeof(int *));
+	if ( (image->dp == NULL) || (image->bad == NULL) ) {
+		ERROR("Failed to allocate panels.\n");
+		return 1;
+	}
+
+	for ( pi=0; pi<det->n_panels; pi++ ) {
+
+		struct panel *p;
+		int fs, ss;
+
+		p = &det->panels[pi];
+		image->dp[pi] = malloc(p->w*p->h*sizeof(float));
+		image->bad[pi] = calloc(p->w*p->h, sizeof(int));
+		if ( (image->dp[pi] == NULL) || (image->bad[pi] == NULL) ) {
+			ERROR("Failed to allocate panel\n");
+			return 1;
+		}
+
+		for ( fs=0; fs<p->w; fs++ ) {
+		for ( ss=0; ss<p->h; ss++ ) {
+
+			int idx;
+			int cfs, css;
+			int bad = 0;
+
+			cfs = fs+p->min_fs;
+			css = ss+p->min_ss;
+			idx = cfs + css*image->width;
+
+			image->dp[pi][fs+p->w*ss] = image->data[idx];
+
+			if ( in_bad_region(det, cfs, css) ) {
+				bad = 1;
+			}
+
+			if ( image->flags != NULL ) {
+
+				int flags;
+
+				flags = image->flags[idx];
+
+				/* Bad if it's missing any of the "good" bits */
+				if ( !((flags & image->det->mask_good)
+			                   == image->det->mask_good) ) bad = 1;
+
+				/* Bad if it has any of the "bad" bits. */
+				if ( flags & image->det->mask_bad ) bad = 1;
+
+			}
+
+			image->bad[pi][fs+p->w*ss] = bad;
+
+		}
+		}
+
+	}
+
+	return 0;
+}
+
+
 int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
 {
 	herr_t r;
@@ -551,6 +618,32 @@ int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
 
 	if ( satcorr ) debodge_saturation(f, image);
 
+	if ( (image->width != image->det->max_fs + 1 )
+	  || (image->height != image->det->max_ss + 1))
+	{
+		ERROR("Image size doesn't match geometry size"
+			" - rejecting image.\n");
+		ERROR("Image size: %i,%i.  Geometry size: %i,%i\n",
+		      image->width, image->height,
+		      image->det->max_fs + 1, image->det->max_ss + 1);
+		return 1;
+	}
+
+	fill_in_values(image->det, f);
+	fill_in_beam_parameters(image->beam, f);
+	image->lambda = ph_en_to_lambda(eV_to_J(image->beam->photon_energy));
+
+	if ( (image->beam->photon_energy < 0.0) || (image->lambda > 1000) ) {
+		/* Error message covers a silly value in the beam file or in
+		 * the HDF5 file. */
+		ERROR("Nonsensical wavelength (%e m or %e eV) value for %s.\n",
+		      image->lambda, image->beam->photon_energy,
+		      image->filename);
+		return 1;
+	}
+
+	unpack_panels(image, image->det);
+
 	return 0;
 }
 
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 0d131451..a1ac75a3 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -124,10 +124,14 @@ struct image;
 
 struct image {
 
+	/* The following three fields will be going away in the future */
 	float                   *data;
 	uint16_t                *flags;
 	double                  *twotheta;
 
+	float                   **dp;    /* Data in panel */
+	int                     **bad;   /* Bad pixels by panel */
+
 	Crystal                 **crystals;
 	int                     n_crystals;
 	IndexingMethod          indexed_by;
diff --git a/src/process_image.c b/src/process_image.c
index bf694623..65deace5 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -109,32 +109,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		return;
 	}
 
-	if ( (image.width != image.det->max_fs + 1 )
-	  || (image.height != image.det->max_ss + 1))
-	{
-		ERROR("Image size doesn't match geometry size"
-			" - rejecting image.\n");
-		ERROR("Image size: %i,%i.  Geometry size: %i,%i\n",
-		      image.width, image.height,
-		      image.det->max_fs + 1, image.det->max_ss + 1);
-		hdfile_close(hdfile);
-		return;
-	}
-
-	fill_in_values(image.det, hdfile);
-	fill_in_beam_parameters(image.beam, hdfile);
-
-	image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy));
-
-	if ( (image.beam->photon_energy < 0.0) || (image.lambda > 1000) ) {
-		/* Error message covers a silly value in the beam file or in
-		 * the HDF5 file. */
-		ERROR("Nonsensical wavelength (%e m or %e eV) value for %s.\n",
-		      image.lambda, image.beam->photon_energy, image.filename);
-		hdfile_close(hdfile);
-		return;
-	}
-
 	/* Take snapshot of image after CM subtraction but before applying
 	 * horrible noise filters to it */
 	data_size = image.width * image.height * sizeof(float);