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-rw-r--r--libcrystfel/src/detector.c7
-rw-r--r--libcrystfel/src/detector.h3
-rw-r--r--libcrystfel/src/hdf5-file.c93
-rw-r--r--libcrystfel/src/image.h4
-rw-r--r--src/process_image.c26
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);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 22:24:35 +0000