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-rw-r--r--libcrystfel/src/image.c235
1 files changed, 228 insertions, 7 deletions
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 29e5d5e1..a8c278fc 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -38,6 +38,7 @@
#include "utils.h"
#include "events.h"
#include "hdf5-file.h"
+#include "detector.h"
/**
* SECTION:image
@@ -54,6 +55,14 @@
*/
+struct imagefile
+{
+ enum imagefile_type type;
+ char *filename;
+ struct hdfile *hdfile;
+};
+
+
struct _imagefeaturelist
{
struct imagefeature *features;
@@ -382,16 +391,231 @@ void add_imagefile_field(struct imagefile_field_list *copyme, const char *name)
/******************************* CBF files ************************************/
+
+static char *cbf_strerr(int e)
+{
+ char *err;
+
+ err = malloc(1024);
+ if ( err == NULL ) return NULL;
+
+ err[0] = '\0';
+
+ /* NB Sum of lengths of all strings must be less than 1024 */
+ if ( e & CBF_FORMAT ) strcat(err, "Invalid format");
+ if ( e & CBF_ALLOC ) strcat(err, "Memory allocation failed");
+ if ( e & CBF_ARGUMENT ) strcat(err, "Invalid argument");
+ if ( e & CBF_ASCII ) strcat(err, "Value is ASCII");
+ if ( e & CBF_BINARY ) strcat(err, "Value is binary");
+ if ( e & CBF_BITCOUNT ) strcat(err, "Wrong number of bits");
+ if ( e & CBF_ENDOFDATA ) strcat(err, "End of data");
+ if ( e & CBF_FILECLOSE ) strcat(err, "File close error");
+ if ( e & CBF_FILEOPEN ) strcat(err, "File open error");
+ if ( e & CBF_FILEREAD ) strcat(err, "File read error");
+ if ( e & CBF_FILETELL ) strcat(err, "File tell error");
+ if ( e & CBF_FILEWRITE ) strcat(err, "File write error");
+ if ( e & CBF_IDENTICAL ) strcat(err, "Name already exists");
+ if ( e & CBF_NOTFOUND ) strcat(err, "Not found");
+ if ( e & CBF_OVERFLOW ) strcat(err, "Overflow");
+ if ( e & CBF_UNDEFINED ) strcat(err, "Number undefined");
+ if ( e & CBF_NOTIMPLEMENTED ) strcat(err, "Not implemented");
+
+ return err;
+}
+
+
+static int unpack_panels(struct image *image, signed int *data, int data_width)
+{
+ int pi;
+
+ /* FIXME: Load these masks from an HDF5 file, if filenames are
+ * given in the geometry file */
+ uint16_t *flags = NULL;
+ float *sat = NULL;
+
+ image->dp = malloc(image->det->n_panels * sizeof(float *));
+ image->bad = malloc(image->det->n_panels * sizeof(int *));
+ image->sat = malloc(image->det->n_panels * sizeof(float *));
+ if ( (image->dp == NULL) || (image->bad == NULL)
+ || (image->sat == NULL) )
+ {
+ ERROR("Failed to allocate panels.\n");
+ return 1;
+ }
+
+ for ( pi=0; pi<image->det->n_panels; pi++ ) {
+
+ struct panel *p;
+ int fs, ss;
+
+ p = &image->det->panels[pi];
+ image->dp[pi] = malloc(p->w*p->h*sizeof(float));
+ image->bad[pi] = calloc(p->w*p->h, sizeof(int));
+ image->sat[pi] = malloc(p->w*p->h*sizeof(float));
+ if ( (image->dp[pi] == NULL) || (image->bad[pi] == NULL)
+ || (image->sat[pi] == NULL) )
+ {
+ ERROR("Failed to allocate panel\n");
+ return 1;
+ }
+
+ if ( p->mask != NULL ) {
+ ERROR("WARNING: Bad pixel masks do not currently work "
+ "with CBF files\n");
+ ERROR(" (bad pixel regions specified in the geometry "
+ "file will be used, however)\n");
+ }
+
+ if ( p->satmap != NULL ) {
+ ERROR("WARNING: Saturation maps do not currently work "
+ "with CBF files\n");
+ }
+
+ for ( ss=0; ss<p->h; ss++ ) {
+ for ( fs=0; fs<p->w; fs++ ) {
+
+ int idx;
+ int cfs, css;
+ int bad = 0;
+
+ cfs = fs+p->orig_min_fs;
+ css = ss+p->orig_min_ss;
+ idx = cfs + css*data_width;
+
+ image->dp[pi][fs+p->w*ss] = data[idx];
+
+ if ( sat != NULL ) {
+ image->sat[pi][fs+p->w*ss] = sat[idx];
+ } else {
+ image->sat[pi][fs+p->w*ss] = INFINITY;
+ }
+
+ if ( p->no_index ) bad = 1;
+
+ if ( in_bad_region(image->det, p, cfs, css) ) {
+ bad = 1;
+ }
+
+ if ( flags != NULL ) {
+
+ int f;
+
+ f = flags[idx];
+
+ /* Bad if it's missing any of the "good" bits */
+ if ( (f & image->det->mask_good)
+ != image->det->mask_good ) bad = 1;
+
+ /* Bad if it has any of the "bad" bits. */
+ if ( f & image->det->mask_bad ) bad = 1;
+
+ }
+ image->bad[pi][fs+p->w*ss] = bad;
+
+ }
+ }
+
+ }
+
+ return 0;
+}
+
+
static int read_cbf(struct imagefile *f, struct image *image)
{
cbf_handle cbfh;
+ FILE *fh;
+ int r;
+ unsigned int compression;
+ int binary_id, minelement, maxelement, elsigned, elunsigned;
+ size_t elsize, elements, elread, dimfast, dimmid, dimslow, padding;
+ const char *byteorder;
+ signed int *data;
if ( cbf_make_handle(&cbfh) ) {
ERROR("Failed to allocate CBF handle\n");
return 1;
}
- ERROR("Mock CBF read\n");
+ fh = fopen(f->filename, "rb");
+ if ( fh == NULL ) {
+ ERROR("Failed to open '%s'\n", f->filename);
+ return 1;
+ }
+ /* CBFlib calls fclose(fh) when it's ready */
+
+ if ( cbf_read_widefile(cbfh, fh, 0) ) {
+ ERROR("Failed to read CBF file\n");
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ /* Select row 0 in data column inside array_data */
+ cbf_find_category(cbfh, "array_data");
+ cbf_find_column(cbfh, "data");
+ cbf_select_row(cbfh, 0);
+
+ /* Get parameters for array read */
+ r = cbf_get_integerarrayparameters_wdims(cbfh, &compression, &binary_id,
+ &elsize, &elsigned, &elunsigned,
+ &elements,
+ &minelement, &maxelement,
+ &byteorder,
+ &dimfast, &dimmid, &dimslow,
+ &padding);
+ if ( r ) {
+ char *err = cbf_strerr(r);
+ ERROR("Failed to read CBF array parameters: %s\n", err);
+ free(err);
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ if ( dimslow != 0 ) {
+ ERROR("CBF data array is 3D - don't know what to do with it\n");
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ if ( dimfast*dimmid*elsize > 10e9 ) {
+ ERROR("CBF data is far too big (%i x %i x %i bytes).\n",
+ (int)dimfast, (int)dimmid, (int)elsize);
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ if ( elsize != 4 ) {
+ STATUS("Don't know what to do with element size %i\n",
+ (int)elsize);
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ if ( strcmp(byteorder, "little_endian") != 0 ) {
+ STATUS("Don't know what to do with non-little-endian datan\n");
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ data = malloc(elsize*dimfast*dimmid);
+ if ( data == NULL ) {
+ ERROR("Failed to allocate memory for CBF data\n");
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ r = cbf_get_integerarray(cbfh, &binary_id, data, elsize, 1,
+ elsize*dimfast*dimmid, &elread);
+ if ( r ) {
+ char *err = cbf_strerr(r);
+ ERROR("Failed to read CBF array: %s\n", err);
+ free(err);
+ cbf_free_handle(cbfh);
+ return 1;
+ }
+
+ unpack_panels(image, data, dimfast);
+ free(data);
cbf_free_handle(cbfh);
return 0;
@@ -400,12 +624,6 @@ static int read_cbf(struct imagefile *f, struct image *image)
/****************************** Image files ***********************************/
-struct imagefile
-{
- enum imagefile_type type;
- struct hdfile *hdfile;
-};
-
static signed int is_cbf_file(const char *filename)
{
@@ -450,6 +668,7 @@ struct imagefile *imagefile_open(const char *filename)
}
+ f->filename = strdup(filename);
return f;
}
@@ -538,4 +757,6 @@ void imagefile_close(struct imagefile *f)
if ( f->type == IMAGEFILE_HDF5 ) {
hdfile_close(f->hdfile);
}
+ free(f->filename);
+ free(f);
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 21:41:37 +0000