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-rw-r--r--libcrystfel/src/detector.c47
-rw-r--r--libcrystfel/src/detector.h3
-rw-r--r--libcrystfel/src/hdf5-file.c57
-rw-r--r--libcrystfel/src/hdf5-file.h4
-rw-r--r--libcrystfel/src/image.c668
-rw-r--r--libcrystfel/src/image.h43
-rw-r--r--libcrystfel/src/stream.c6
-rw-r--r--libcrystfel/src/stream.h12
8 files changed, 776 insertions, 64 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index e160d1e1..e3b351ff 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -528,37 +528,15 @@ int panel_number(struct detector *det, struct panel *p)
}
-void fill_in_values(struct detector *det, struct hdfile *f, struct event* ev)
+void adjust_centering_for_rail(struct panel *p)
{
- int i;
-
- for ( i=0; i<det->n_panels; i++ ) {
-
- double offs;
- struct panel *p = &det->panels[i];
+ double offs;
- if ( p->clen_from != NULL ) {
-
- double val;
- int r;
-
- r = hdfile_get_value(f, p->clen_from, ev, &val,
- H5T_NATIVE_DOUBLE);
- if ( r ) {
- ERROR("Failed to read '%s'\n", p->clen_from);
- } else {
- p->clen = val * 1.0e-3;
- }
-
- }
-
- /* Offset in +z direction from calibrated clen to actual */
- offs = p->clen - p->clen_for_centering;
- p->cnx += p->rail_x * offs;
- p->cny += p->rail_y * offs;
- p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs;
-
- }
+ /* Offset in +z direction from calibrated clen to actual */
+ offs = p->clen - p->clen_for_centering;
+ p->cnx += p->rail_x * offs;
+ p->cny += p->rail_y * offs;
+ p->clen = p->clen_for_centering + p->coffset + p->rail_z * offs;
}
@@ -1076,12 +1054,15 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam,
} else if ( strcmp(key, "photon_energy") == 0 ) {
if ( beam != NULL ) {
- if ( strncmp(val, "/", 1) == 0 ) {
+ double v;
+ char *end;
+ v = strtod(val, &end);
+ if ( (val[0] != '\0') && (end[0] == '\0') ) {
+ beam->photon_energy = v;
+ beam->photon_energy_from = NULL;
+ } else {
beam->photon_energy = 0.0;
beam->photon_energy_from = strdup(val);
- } else {
- beam->photon_energy = atof(val);
- beam->photon_energy_from = NULL;
}
}
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 04e3c1ec..e9dd1154 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -224,9 +224,8 @@ extern void get_pixel_extents(struct detector *det,
double *min_x, double *min_y,
double *max_x, double *max_y);
-extern void fill_in_values(struct detector *det, struct hdfile *f,
- struct event* ev);
extern void fill_in_adu(struct image *image);
+extern void adjust_centering_for_rail(struct panel *p);
extern int panel_is_in_rigid_group(const struct rigid_group *rg,
struct panel *p);
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index c36a58b3..dc86d641 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -134,8 +134,7 @@ struct hdfile *hdfile_open(const char *filename)
}
-int hdfile_set_image(struct hdfile *f, const char *path,
- struct panel *p)
+int hdfile_set_image(struct hdfile *f, const char *path)
{
f->dh = H5Dopen2(f->fh, path, H5P_DEFAULT);
if ( f->dh < 0 ) {
@@ -1391,8 +1390,10 @@ int hdfile_get_value(struct hdfile *f, const char *name,
}
-void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
- struct event *ev, struct image *image)
+static void hdfile_fill_in_beam_parameters(struct beam_params *beam,
+ struct hdfile *f,
+ struct event *ev,
+ struct image *image)
{
double eV;
@@ -1405,8 +1406,8 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
int r;
- r = hdfile_get_value(f, beam->photon_energy_from, ev, &eV,
- H5T_NATIVE_DOUBLE);
+ r = hdfile_get_value(f, beam->photon_energy_from,
+ ev, &eV, H5T_NATIVE_DOUBLE);
if ( r ) {
ERROR("Failed to read '%s'\n",
beam->photon_energy_from);
@@ -1418,6 +1419,36 @@ void fill_in_beam_parameters(struct beam_params *beam, struct hdfile *f,
}
+static void hdfile_fill_in_clen(struct detector *det, struct hdfile *f,
+ struct event *ev)
+{
+ int i;
+
+ for ( i=0; i<det->n_panels; i++ ) {
+
+ struct panel *p = &det->panels[i];
+
+ if ( p->clen_from != NULL ) {
+
+ double val;
+ int r;
+
+ r = hdfile_get_value(f, p->clen_from, ev, &val,
+ H5T_NATIVE_DOUBLE);
+ if ( r ) {
+ ERROR("Failed to read '%s'\n", p->clen_from);
+ } else {
+ p->clen = val * 1.0e-3;
+ }
+
+ }
+
+ adjust_centering_for_rail(p);
+
+ }
+}
+
+
int hdf5_read(struct hdfile *f, struct image *image, const char *element,
int satcorr)
{
@@ -1433,7 +1464,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element,
if ( element == NULL ) {
fail = hdfile_set_first_image(f, "/");
} else {
- fail = hdfile_set_image(f, element, NULL);
+ fail = hdfile_set_image(f, element);
}
if ( fail ) {
@@ -1482,7 +1513,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char *element,
if ( image->beam != NULL ) {
- fill_in_beam_parameters(image->beam, f, NULL, image);
+ hdfile_fill_in_beam_parameters(image->beam, f, NULL, image);
if ( image->lambda > 1000 ) {
/* Error message covers a silly value in the beam file
@@ -1747,7 +1778,7 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev,
return 1;
}
- fail = hdfile_set_image(f, panel_full_path, p);
+ fail = hdfile_set_image(f, panel_full_path);
free(panel_full_path);
@@ -1769,7 +1800,7 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev,
free(image->sat);
return 1;
}
- fail = hdfile_set_image(f, p->data, p);
+ fail = hdfile_set_image(f, p->data);
}
@@ -1886,13 +1917,13 @@ int hdf5_read2(struct hdfile *f, struct image *image, struct event *ev,
H5Dclose(f->dh);
f->data_open = 0;
- fill_in_values(image->det, f, ev);
+ hdfile_fill_in_clen(image->det, f, ev);
if ( satcorr ) debodge_saturation(f, image);
if ( image->beam != NULL ) {
- fill_in_beam_parameters(image->beam, f, ev, image);
+ hdfile_fill_in_beam_parameters(image->beam, f, ev, image);
if ( (image->lambda > 1.0) || (image->lambda < 1e-20) ) {
@@ -2299,7 +2330,7 @@ int hdfile_set_first_image(struct hdfile *f, const char *group)
for ( i=0; i<n; i++ ) {
if ( is_image[i] ) {
- hdfile_set_image(f, names[i], NULL);
+ hdfile_set_image(f, names[i]);
for ( j=0; j<n; j++ ) free(names[j]);
free(is_image);
free(is_group);
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index f22d4d54..ab53dd2e 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -67,8 +67,8 @@ extern int hdf5_read2(struct hdfile *f, struct image *image,
extern int check_path_existence(hid_t fh, const char *path);
extern struct hdfile *hdfile_open(const char *filename);
-int hdfile_set_image(struct hdfile *f, const char *path,
- struct panel *p);
+int hdfile_set_image(struct hdfile *f, const char *path);
+
extern int16_t *hdfile_get_image_binned(struct hdfile *hdfile,
int binning, int16_t *maxp);
extern char **hdfile_read_group(struct hdfile *f, int *n, const char *parent,
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 09f4958d..4e1a8b86 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -3,12 +3,12 @@
*
* Handle images and image features
*
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
- * 2011-2016 Thomas White <taw@physics.org>
+ * 2011-2017 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -31,9 +31,14 @@
#include <assert.h>
#include <math.h>
#include <stdio.h>
+#include <hdf5.h>
+#include <cbflib/cbf.h>
#include "image.h"
#include "utils.h"
+#include "events.h"
+#include "hdf5-file.h"
+#include "detector.h"
/**
* SECTION:image
@@ -50,6 +55,14 @@
*/
+struct imagefile
+{
+ enum imagefile_type type;
+ char *filename;
+ struct hdfile *hdfile;
+};
+
+
struct _imagefeaturelist
{
struct imagefeature *features;
@@ -299,3 +312,654 @@ void free_all_crystals(struct image *image)
free(image->crystals);
image->n_crystals = 0;
}
+
+
+/**************************** Image field lists *******************************/
+
+struct imagefile_field_list
+{
+ char **fields;
+ int n_fields;
+ int max_fields;
+};
+
+
+struct imagefile_field_list *new_imagefile_field_list()
+{
+ struct imagefile_field_list *n;
+
+ n = calloc(1, sizeof(struct imagefile_field_list));
+ if ( n == NULL ) return NULL;
+
+ n->max_fields = 32;
+ n->fields = malloc(n->max_fields*sizeof(char *));
+ if ( n->fields == NULL ) {
+ free(n);
+ return NULL;
+ }
+
+ return n;
+}
+
+
+void free_imagefile_field_list(struct imagefile_field_list *n)
+{
+ int i;
+ for ( i=0; i<n->n_fields; i++ ) {
+ free(n->fields[i]);
+ }
+ free(n->fields);
+ free(n);
+}
+
+
+void add_imagefile_field(struct imagefile_field_list *copyme, const char *name)
+{
+ int i;
+
+ /* Already on the list? Don't re-add if so. */
+ for ( i=0; i<copyme->n_fields; i++ ) {
+ if ( strcmp(copyme->fields[i], name) == 0 ) return;
+ }
+
+ /* Need more space? */
+ if ( copyme->n_fields == copyme->max_fields ) {
+
+ char **nfields;
+ int nmax = copyme->max_fields + 32;
+
+ nfields = realloc(copyme->fields, nmax*sizeof(char *));
+ if ( nfields == NULL ) {
+ ERROR("Failed to allocate space for new HDF5 field.\n");
+ return;
+ }
+
+ copyme->max_fields = nmax;
+ copyme->fields = nfields;
+
+ }
+
+ copyme->fields[copyme->n_fields] = strdup(name);
+ if ( copyme->fields[copyme->n_fields] == NULL ) {
+ ERROR("Failed to add field for copying '%s'\n", name);
+ return;
+ }
+
+ copyme->n_fields++;
+}
+
+
+/******************************* 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 data_height)
+{
+ 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");
+ }
+
+ if ( (p->orig_min_fs + p->w > data_width)
+ || (p->orig_min_ss + p->h > data_height) )
+ {
+ ERROR("Panel %s is outside range of data in CBF file\n",
+ p->name);
+ return 1;
+ }
+
+ 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 void cbf_fill_in_beam_parameters(struct beam_params *beam,
+ struct imagefile *f,
+ struct image *image)
+{
+ double eV;
+
+ if ( beam->photon_energy_from == NULL ) {
+
+ /* Explicit value given */
+ eV = beam->photon_energy;
+
+ } else {
+
+ ERROR("Can't get photon energy from CBF yet.\n");
+ eV = 0.0;
+
+ }
+
+ image->lambda = ph_en_to_lambda(eV_to_J(eV))*beam->photon_energy_scale;
+}
+
+
+static void cbf_fill_in_clen(struct detector *det, struct imagefile *f)
+{
+ int i;
+
+ for ( i=0; i<det->n_panels; i++ ) {
+
+ struct panel *p = &det->panels[i];
+
+ if ( p->clen_from != NULL ) {
+
+ ERROR("Can't get clen from CBF yet.\n");
+
+ }
+
+ adjust_centering_for_rail(p);
+
+ }
+}
+
+
+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 ( image->det == NULL ) {
+ ERROR("read_cbf() needs a geometry\n");
+ return 1;
+ }
+
+ if ( cbf_make_handle(&cbfh) ) {
+ ERROR("Failed to allocate CBF handle\n");
+ return 1;
+ }
+
+ 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 '%s'\n", f->filename);
+ 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, dimmid);
+ free(data);
+
+ if ( image->beam != NULL ) {
+ cbf_fill_in_beam_parameters(image->beam, f, image);
+ if ( image->lambda > 1000 ) {
+ ERROR("WARNING: Missing or nonsensical wavelength "
+ "(%e m) for %s.\n",
+ image->lambda, image->filename);
+ }
+ }
+ cbf_fill_in_clen(image->det, f);
+ fill_in_adu(image);
+
+ cbf_free_handle(cbfh);
+ return 0;
+}
+
+
+static float *convert_float(signed int *data, int w, int h)
+{
+ float *df;
+ long int i;
+
+ df = malloc(sizeof(float)*w*h);
+ if ( df == NULL ) return NULL;
+
+ for ( i=0; i<w*h; i++ ) {
+ df[i] = data[i];
+ }
+
+ return df;
+}
+
+
+static int read_cbf_simple(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;
+ }
+
+ 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 '%s'\n", f->filename);
+ 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;
+ }
+
+ image->det = simple_geometry(image, dimfast, dimmid);
+ image->dp = malloc(sizeof(float *));
+ if ( image->dp == NULL ) {
+ ERROR("Failed to allocate dp array\n");
+ return 1;
+ }
+ image->dp[0] = convert_float(data, dimfast, dimmid);
+ if ( image->dp[0] == NULL ) {
+ ERROR("Failed to allocate dp array\n");
+ return 1;
+ }
+
+ if ( image->beam != NULL ) {
+ cbf_fill_in_beam_parameters(image->beam, f, image);
+ if ( image->lambda > 1000 ) {
+ ERROR("WARNING: Missing or nonsensical wavelength "
+ "(%e m) for %s.\n",
+ image->lambda, image->filename);
+ }
+ }
+ cbf_fill_in_clen(image->det, f);
+ fill_in_adu(image);
+
+ cbf_free_handle(cbfh);
+ return 0;
+}
+
+
+/****************************** Image files ***********************************/
+
+
+static signed int is_cbf_file(const char *filename)
+{
+ FILE *fh;
+ char line[1024];
+
+ fh = fopen(filename, "r");
+ if ( fh == NULL ) return -1;
+
+ if ( fgets(line, 1024, fh) == NULL ) return -1;
+ fclose(fh);
+
+ if ( strstr(line, "CBF") == NULL ) {
+ return 0;
+ }
+
+ return 1;
+}
+
+
+struct imagefile *imagefile_open(const char *filename)
+{
+ struct imagefile *f;
+
+ f = malloc(sizeof(struct imagefile));
+ if ( f == NULL ) return NULL;
+
+ if ( H5Fis_hdf5(filename) > 0 ) {
+
+ /* This is an HDF5, pass through to HDF5 layer */
+ f->type = IMAGEFILE_HDF5;
+ f->hdfile = hdfile_open(filename);
+
+ if ( f->hdfile == NULL ) {
+ free(f);
+ return NULL;
+ }
+
+ } else if ( is_cbf_file(filename) > 0 ) {
+
+ f->type = IMAGEFILE_CBF;
+
+ }
+
+ f->filename = strdup(filename);
+ return f;
+}
+
+
+int imagefile_read(struct imagefile *f, struct image *image,
+ struct event *event)
+{
+ if ( f->type == IMAGEFILE_HDF5 ) {
+ return hdf5_read2(f->hdfile, image, event, 0);
+ } else if ( f->type == IMAGEFILE_CBF ) {
+ return read_cbf(f, image);
+ } else {
+ ERROR("Unknown file type %i\n", f->type);
+ return 1;
+ }
+}
+
+
+/* Read a simple file, no multi-event, no prior geometry etc, and
+ * generate a geometry for it */
+int imagefile_read_simple(struct imagefile *f, struct image *image)
+{
+ if ( f->type == IMAGEFILE_HDF5 ) {
+ return hdf5_read(f->hdfile, image, NULL, 0);
+ } else {
+ return read_cbf_simple(f, image);
+ }
+}
+
+
+enum imagefile_type imagefile_get_type(struct imagefile *f)
+{
+ assert(f != NULL);
+ return f->type;
+}
+
+
+struct hdfile *imagefile_get_hdfile(struct imagefile *f)
+{
+ if ( f->type != IMAGEFILE_HDF5 ) {
+ ERROR("Not an HDF5 file!\n");
+ return NULL;
+ }
+
+ return f->hdfile;
+}
+
+
+void imagefile_copy_fields(struct imagefile *f,
+ const struct imagefile_field_list *copyme,
+ FILE *fh, struct event *ev)
+{
+ int i;
+
+ if ( copyme == NULL ) return;
+
+ for ( i=0; i<copyme->n_fields; i++ ) {
+
+ char *val;
+ char *field;
+
+ field = copyme->fields[i];
+
+ if ( f->type == IMAGEFILE_HDF5 ) {
+ val = hdfile_get_string_value(f->hdfile, field, ev);
+ if ( field[0] == '/' ) {
+ fprintf(fh, "hdf5%s = %s\n", field, val);
+ } else {
+ fprintf(fh, "hdf5/%s = %s\n", field, val);
+ }
+ free(val);
+
+ } else {
+ STATUS("Mock CBF variable\n");
+ fprintf(fh, "cbf/%s = %s\n", field, "(FIXME)");
+ }
+
+
+ }
+}
+
+
+void imagefile_close(struct imagefile *f)
+{
+ if ( f->type == IMAGEFILE_HDF5 ) {
+ hdfile_close(f->hdfile);
+ }
+ free(f->filename);
+ free(f);
+}
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 9fd9b495..ead5cd4d 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -3,11 +3,11 @@
*
* Handle images and image features
*
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2009-2016 Thomas White <taw@physics.org>
+ * 2009-2017 Thomas White <taw@physics.org>
* 2014 Valerio Mariani
*
*
@@ -44,6 +44,8 @@ struct detector;
struct imagefeature;
struct sample;
struct image;
+struct imagefile;
+struct imagefile_field_list;
#include "utils.h"
#include "cell.h"
@@ -51,6 +53,7 @@ struct image;
#include "reflist.h"
#include "crystal.h"
#include "index.h"
+#include "events.h"
/**
* SpectrumType:
@@ -87,6 +90,15 @@ struct imagefeature {
const char *name;
};
+
+/* An enum representing the image file formats we can handle */
+enum imagefile_type
+{
+ IMAGEFILE_HDF5,
+ IMAGEFILE_CBF
+};
+
+
/* An opaque type representing a list of image features */
typedef struct _imagefeaturelist ImageFeatureList;
@@ -120,7 +132,7 @@ struct beam_params
* struct detector *det;
* struct beam_params *beam;
* char *filename;
- * const struct copy_hdf5_field *copyme;
+ * const struct imagefile_field_list *copyme;
*
* int id;
*
@@ -152,8 +164,8 @@ struct beam_params
* returned by the low-level indexing system. <structfield>n_crystals</structfield>
* is the number of crystals which were found in the image.
*
- * <structfield>copyme</structfield> represents a list of HDF5 fields to copy
- * to the output stream.
+ * <structfield>copyme</structfield> represents a list of fields in the image
+ * file (e.g. HDF5 fields or CBF headers) to copy to the output stream.
**/
struct image;
@@ -171,7 +183,7 @@ struct image {
struct beam_params *beam; /* The nominal beam parameters */
char *filename;
struct event *event;
- const struct copy_hdf5_field *copyme;
+ const struct imagefile_field_list *copyme;
struct stuff_from_stream *stuff_from_stream;
double avg_clen; /* Average camera length extracted
@@ -233,6 +245,25 @@ extern void image_add_crystal(struct image *image, Crystal *cryst);
extern void remove_flagged_crystals(struct image *image);
extern void free_all_crystals(struct image *image);
+/* Image files */
+extern struct imagefile *imagefile_open(const char *filename);
+extern int imagefile_read(struct imagefile *f, struct image *image,
+ struct event *event);
+extern int imagefile_read_simple(struct imagefile *f, struct image *image);
+extern struct hdfile *imagefile_get_hdfile(struct imagefile *f);
+extern enum imagefile_type imagefile_get_type(struct imagefile *f);
+extern void imagefile_copy_fields(struct imagefile *f,
+ const struct imagefile_field_list *copyme,
+ FILE *fh, struct event *ev);
+extern void imagefile_close(struct imagefile *f);
+
+/* Field lists */
+extern struct imagefile_field_list *new_imagefile_field_list(void);
+extern void free_imagefile_field_list(struct imagefile_field_list *f);
+
+extern void add_imagefile_field(struct imagefile_field_list *copyme,
+ const char *name);
+
#ifdef __cplusplus
}
#endif
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 17da74b2..fb4b0c70 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -806,8 +806,8 @@ static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
}
-int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
- int include_peaks, int include_reflections, struct event* ev)
+int write_chunk(Stream *st, struct image *i, struct imagefile *imfile,
+ int include_peaks, int include_reflections, struct event *ev)
{
int j;
char *indexer;
@@ -832,7 +832,7 @@ int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
fprintf(st->fh, "beam_divergence = %.2e rad\n", i->div);
fprintf(st->fh, "beam_bandwidth = %.2e (fraction)\n", i->bw);
- copy_hdf5_fields(hdfile, i->copyme, st->fh, ev);
+ imagefile_copy_fields(imfile, i->copyme, st->fh, ev);
if ( i->det != NULL ) {
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index ff8628c0..764e3e36 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -3,11 +3,11 @@
*
* Stream tools
*
- * Copyright © 2013-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2013-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2014 Thomas White <taw@physics.org>
+ * 2010-2017 Thomas White <taw@physics.org>
* 2014 Valerio Mariani
* 2011 Andrew Aquila
*
@@ -39,6 +39,7 @@
struct image;
struct hdfile;
struct event;
+struct imagefile;
#include "cell.h"
#define GEOM_START_MARKER "----- Begin geometry file -----"
@@ -106,10 +107,15 @@ extern int read_chunk(Stream *st, struct image *image);
extern int read_chunk_2(Stream *st, struct image *image,
StreamReadFlags srf);
-extern int write_chunk(Stream *st, struct image *image, struct hdfile *hdfile,
+extern int write_chunk(Stream *st, struct image *image, struct imagefile *imfile,
int include_peaks, int include_reflections,
struct event *ev);
+extern int write_chunk_2(Stream *st, struct image *image,
+ struct imagefile *imfile,
+ int include_peaks, int include_reflections,
+ struct event *ev);
+
extern void write_command(Stream *st, int argc, char *argv[]);
extern void write_geometry_file(Stream *st, const char *geom_filename);
extern int rewind_stream(Stream *st);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 08:09:40 +0000