aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--configure.ac32
-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
-rw-r--r--src/dw-hdfsee.c66
-rw-r--r--src/dw-hdfsee.h8
-rw-r--r--src/im-sandbox.c2
-rw-r--r--src/indexamajig.c18
-rw-r--r--src/process_image.c32
-rw-r--r--src/process_image.h2
15 files changed, 885 insertions, 115 deletions
diff --git a/configure.ac b/configure.ac
index a570abe4..d02fff2a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -37,6 +37,34 @@ AC_ARG_WITH(gsl,
GSL_LIBS="-L$withval/lib -lgsl -lgslcblas -lm"],
[PKG_CHECK_MODULES([GSL], [gsl])])
+AC_ARG_ENABLE(cbf, AS_HELP_STRING([--enable-cbf], [Enable CBF file support]))
+AC_ARG_WITH(cbflib_dir, AS_HELP_STRING([--with-cbflib],
+ [Specify location of CBFlib headers and libraries]))
+AC_MSG_CHECKING([whether to use CBFlib])
+AS_IF([test "x$enable_cbf" = "xyes"],
+[
+ AC_MSG_RESULT([yes])
+ AS_IF([test "x$with_cbflib_dir" != "x"],
+ [
+ dnl NB not ${with_cbflib_dir}/include/cbflib, because cbflib installs
+ dnl its own HDF5 headers which we do not want in the include path
+ CBF_CFLAGS="-I${with_cbflib_dir}/include"
+ dnl Fortunately no libhdf5.so in this folder
+ CBF_LIBS="-lcbf -L${with_cbflib_dir}/lib"
+ have_cbflib=true
+ ], [
+ AC_CHECK_LIB([cbf], [cbf_make_handle], [
+ have_cbflib=true
+ CBF_LIBS="-lcbf"
+ ])
+ ])
+], [
+ AC_MSG_RESULT([no])
+])
+AS_IF([test x$have_cbflib = xtrue],
+[
+ AC_DEFINE([HAVE_CBFLIB], [1], [Define to 1 if CBFlib is available])
+])
AC_ARG_WITH(opencl, AS_HELP_STRING([--with-opencl], [Use OpenCL]))
AC_ARG_WITH(opencl_dir, AS_HELP_STRING([--with-opencl-dir],
@@ -325,7 +353,7 @@ MAIN_CFLAGS="$MAIN_CFLAGS $GDK_pixbuf_2_CFLAGS $FFTW_CFLAGS $Pango_CFLAGS"
MAIN_CFLAGS="$MAIN_CFLAGS $PangoCairo_CFLAGS"
AC_SUBST([MAIN_CFLAGS])
-LIBCRYSTFEL_CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $FFTW_CFLAGS"
+LIBCRYSTFEL_CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $FFTW_CFLAGS $CBF_CFLAGS"
AC_SUBST([LIBCRYSTFEL_CFLAGS])
MAIN_LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
@@ -335,7 +363,7 @@ MAIN_LIBS="$MAIN_LIBS $Pango_LIBS $PangoCairo_LIBS $LDFLAGS"
AC_SUBST([MAIN_LIBS])
LIBCRYSTFEL_LIBS="$LIBS $HDF5_LIBS $GSL_LIBS $FFTW_LIBS $CURSES_LIB $LDFLAGS"
-LIBCRYSTFEL_LIBS="$LIBCRYSTFEL_LIBS -pthread"
+LIBCRYSTFEL_LIBS="$LIBCRYSTFEL_LIBS -pthread $CBF_LIBS"
AC_SUBST([LIBCRYSTFEL_LIBS])
GTK_DOC_CHECK([1.9],[--flavour no-tmpl])
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);
diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index 87c23f4e..0336f25e 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -74,8 +74,8 @@ static void displaywindow_error(DisplayWindow *dw, const char *message)
static gint displaywindow_closed(GtkWidget *window, DisplayWindow *dw)
{
- if ( dw->hdfile != NULL ) {
- hdfile_close(dw->hdfile);
+ if ( dw->imagefile != NULL ) {
+ imagefile_close(dw->imagefile);
}
if ( dw->surf != NULL ) cairo_surface_destroy(dw->surf);
@@ -725,7 +725,7 @@ static gint displaywindow_set_binning(GtkWidget *widget, DisplayWindow *dw)
return 0;
}
- if ( dw->hdfile == NULL ) {
+ if ( dw->imagefile == NULL ) {
return 0;
}
@@ -852,8 +852,8 @@ static gint displaywindow_set_boostint(GtkWidget *widget, DisplayWindow *dw)
return 0;
}
- if ( dw->hdfile == NULL ) {
- return 0;
+ if ( dw->imagefile == NULL ) {
+ return 0;
}
bd = malloc(sizeof(BoostIntDialog));
@@ -927,8 +927,8 @@ static gint displaywindow_newevent(DisplayWindow *dw, int new_event)
float **old_dp = dw->image->dp;
int **old_bad = dw->image->bad;
- fail = hdf5_read2(dw->hdfile, dw->image,
- dw->ev_list->events[new_event], 0);
+ fail = imagefile_read(dw->imagefile, dw->image,
+ dw->ev_list->events[new_event]);
if ( fail ) {
ERROR("Couldn't load image");
dw->image->dp = old_dp;
@@ -1046,8 +1046,8 @@ static gint displaywindow_set_newevent(GtkWidget *widget, DisplayWindow *dw)
return 0;
}
- if ( dw->hdfile == NULL ) {
- return 0;
+ if ( dw->imagefile == NULL ) {
+ return 0;
}
ed = malloc(sizeof(EventDialog));
@@ -1162,7 +1162,7 @@ static gint displaywindow_set_ringradius(GtkWidget *widget, DisplayWindow *dw)
return 0;
}
- if ( dw->hdfile == NULL ) {
+ if ( dw->imagefile == NULL ) {
return 0;
}
@@ -1796,7 +1796,7 @@ static gint displaywindow_show_numbers(GtkWidget *widget, DisplayWindow *dw)
return 0;
}
- if ( dw->hdfile == NULL ) {
+ if ( dw->imagefile == NULL ) {
return 0;
}
@@ -2306,12 +2306,14 @@ struct newhdf {
char name[1024];
};
+/* New HDF5 element selected from menu */
static gint displaywindow_newhdf(GtkMenuItem *item, struct newhdf *nh)
{
gboolean a;
int fail;
if ( nh->dw->not_ready_yet ) return 0;
+ assert(imagefile_get_type(nh->dw->imagefile) == IMAGEFILE_HDF5);
a = gtk_check_menu_item_get_active(GTK_CHECK_MENU_ITEM(nh->widget));
if ( !a ) return 0;
@@ -2320,7 +2322,8 @@ static gint displaywindow_newhdf(GtkMenuItem *item, struct newhdf *nh)
* one */
free_detector_geometry(nh->dw->image->det);
nh->dw->image->det = NULL;
- fail = hdf5_read(nh->dw->hdfile, nh->dw->image, nh->name, 0);
+ fail = hdf5_read(imagefile_get_hdfile(nh->dw->imagefile),
+ nh->dw->image, nh->name, 0);
if ( fail ) {
ERROR("Couldn't load image");
return 1;
@@ -2456,7 +2459,12 @@ static int displaywindow_update_menus(DisplayWindow *dw, const char *selectme)
GtkWidget *ms;
GtkWidget *w;
- ms = displaywindow_createhdfmenus(dw->hdfile, dw, selectme);
+ if ( imagefile_get_type(dw->imagefile) != IMAGEFILE_HDF5 ) {
+ return 0;
+ }
+
+ ms = displaywindow_createhdfmenus(imagefile_get_hdfile(dw->imagefile),
+ dw, selectme);
if ( ms == NULL ) return 1;
@@ -2828,8 +2836,8 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
dw->image->lambda = 0.0;
dw->image->filename = filename;
- dw->hdfile = hdfile_open(filename);
- if ( dw->hdfile == NULL ) {
+ dw->imagefile = imagefile_open(filename);
+ if ( dw->imagefile == NULL ) {
ERROR("Couldn't open file: %s\n", filename);
free(dw->geom_filename);
free(dw);
@@ -2842,11 +2850,19 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
}
if ( dw->image->det != NULL && ( dw->image->det->path_dim != 0 ||
- dw->image->det->dim_dim != 0 )) {
+ dw->image->det->dim_dim != 0 ))
+ {
+ struct hdfile *hdfile;
+
+ if ( imagefile_get_type(dw->imagefile) != IMAGEFILE_HDF5 ) {
+ ERROR("Multi-event geometry, but not HDF5 file!\n");
+ return NULL;
+ }
+ hdfile = imagefile_get_hdfile(dw->imagefile);
dw->multi_event = 1;
- dw->ev_list = fill_event_list(dw->hdfile, dw->image->det);
+ dw->ev_list = fill_event_list(hdfile, dw->image->det);
if ( dw->ev_list == NULL ) {
ERROR("Error while parsing file structure\n");
@@ -2883,18 +2899,26 @@ DisplayWindow *displaywindow_open(char *filename, char *geom_filename,
dw->curr_event = 0;
ev = dw->ev_list->events[dw->curr_event];
}
- check = hdf5_read2(dw->hdfile, dw->image, ev, 0);
+ check = imagefile_read(dw->imagefile, dw->image, ev);
} else {
- check = hdf5_read2(dw->hdfile, dw->image, NULL, 0);
+ check = imagefile_read(dw->imagefile, dw->image, NULL);
}
} else {
- check = hdf5_read(dw->hdfile, dw->image, element, 0);
+ if ( element != NULL ) {
+ if ( imagefile_get_type(dw->imagefile) != IMAGEFILE_HDF5 ) {
+ ERROR("-e/--image requiest an HDF5 file\n");
+ return NULL;
+ }
+ hdfile_set_image(imagefile_get_hdfile(dw->imagefile),
+ element);
+ }
+ check = imagefile_read_simple(dw->imagefile, dw->image);
dw->simple = 1;
}
if ( check ) {
ERROR("Couldn't load file\n");
- hdfile_close(dw->hdfile);
+ imagefile_close(dw->imagefile);
free(dw->geom_filename);
return NULL;
}
diff --git a/src/dw-hdfsee.h b/src/dw-hdfsee.h
index 85c82ac7..fdbea231 100644
--- a/src/dw-hdfsee.h
+++ b/src/dw-hdfsee.h
@@ -3,12 +3,12 @@
*
* Quick yet non-crappy HDF viewer
*
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
*
* Authors:
- * 2009-2014 Thomas White <taw@physics.org>
+ * 2009-2017 Thomas White <taw@physics.org>
* 2014 Valerio Mariani
* 2014 Takanori Nakane <nakane.t@gmail.com>
* 2012 Richard Kirian
@@ -101,8 +101,8 @@ typedef struct {
int simple;
- struct hdfile *hdfile;
- struct image *image;
+ struct imagefile *imagefile;
+ struct image *image;
char *geom_filename;
char *rg_coll_name;
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 2dabf3e9..60400ad8 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -375,7 +375,7 @@ static void run_work(const struct index_args *iargs, Stream *st,
cleanup_indexing(iargs->ipriv);
free_detector_geometry(iargs->det);
free(iargs->hdf5_peak_path);
- free_copy_hdf5_field_list(iargs->copyme);
+ free_imagefile_field_list(iargs->copyme);
cell_free(iargs->cell);
if ( iargs->profile ) time_accounts_print(taccs);
time_accounts_free(taccs);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f48fac17..439f9be3 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -172,9 +172,9 @@ static void show_help(const char *s)
}
-static void add_geom_beam_stuff_to_copy_hdf5(struct copy_hdf5_field *copyme,
- struct detector *det,
- struct beam_params *beam)
+static void add_geom_beam_stuff_to_field_list(struct imagefile_field_list *copyme,
+ struct detector *det,
+ struct beam_params *beam)
{
int i;
@@ -183,12 +183,12 @@ static void add_geom_beam_stuff_to_copy_hdf5(struct copy_hdf5_field *copyme,
struct panel *p = &det->panels[i];
if ( p->clen_from != NULL ) {
- add_copy_hdf5_field(copyme, p->clen_from);
+ add_imagefile_field(copyme, p->clen_from);
}
}
if ( beam->photon_energy_from != NULL ) {
- add_copy_hdf5_field(copyme, beam->photon_energy_from);
+ add_imagefile_field(copyme, beam->photon_energy_from);
}
}
@@ -257,7 +257,7 @@ int main(int argc, char *argv[])
iargs.stream_peaks = 1;
iargs.stream_refls = 1;
iargs.int_diag = INTDIAG_NONE;
- iargs.copyme = new_copy_hdf5_field_list();
+ iargs.copyme = new_imagefile_field_list();
if ( iargs.copyme == NULL ) {
ERROR("Couldn't allocate HDF5 field list.\n");
return 1;
@@ -431,7 +431,7 @@ int main(int argc, char *argv[])
break;
case 10 :
- add_copy_hdf5_field(iargs.copyme, optarg);
+ add_imagefile_field(iargs.copyme, optarg);
break;
case 11 :
@@ -627,7 +627,7 @@ int main(int argc, char *argv[])
geom_filename);
return 1;
}
- add_geom_beam_stuff_to_copy_hdf5(iargs.copyme, iargs.det, iargs.beam);
+ add_geom_beam_stuff_to_field_list(iargs.copyme, iargs.det, iargs.beam);
/* If no peak path from geometry file, use these (but see later) */
if ( iargs.hdf5_peak_path == NULL ) {
@@ -806,7 +806,7 @@ int main(int argc, char *argv[])
create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
st, tempdir);
- free_copy_hdf5_field_list(iargs.copyme);
+ free_imagefile_field_list(iargs.copyme);
cell_free(iargs.cell);
free(iargs.beam->photon_energy_from);
free(prefix);
diff --git a/src/process_image.c b/src/process_image.c
index cd5c0866..d3177d82 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -102,7 +102,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
int serial, struct sb_shm *sb_shared, TimeAccounts *taccs)
{
int check;
- struct hdfile *hdfile;
+ struct imagefile *imfile;
struct image image;
int i;
int r;
@@ -125,15 +125,15 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
time_accounts_set(taccs, TACC_HDF5OPEN);
sb_shared->pings[cookie]++;
- hdfile = hdfile_open(image.filename);
- if ( hdfile == NULL ) {
+ imfile = imagefile_open(image.filename);
+ if ( imfile == NULL ) {
ERROR("Couldn't open file: %s\n", image.filename);
return;
}
time_accounts_set(taccs, TACC_HDF5READ);
sb_shared->pings[cookie]++;
- check = hdf5_read2(hdfile, &image, image.event, 0);
+ check = imagefile_read(imfile, &image, image.event);
if ( check ) {
return;
}
@@ -159,9 +159,13 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
sb_shared->pings[cookie]++;
switch ( iargs->peaks ) {
+ struct hdfile *hdfile;
+
case PEAK_HDF5:
- if ( get_peaks_2(&image, hdfile, iargs->hdf5_peak_path,
- iargs->half_pixel_shift) )
+ hdfile = imagefile_get_hdfile(imfile);
+ if ( (hdfile == NULL)
+ || (get_peaks_2(&image, hdfile, iargs->hdf5_peak_path,
+ iargs->half_pixel_shift)) )
{
ERROR("Failed to get peaks from HDF5 file.\n");
}
@@ -174,9 +178,11 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
break;
case PEAK_CXI:
- if ( get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path,
- pargs->filename_p_e,
- iargs->half_pixel_shift) )
+ hdfile = imagefile_get_hdfile(imfile);
+ if ( (hdfile == NULL)
+ || (get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path,
+ pargs->filename_p_e,
+ iargs->half_pixel_shift)) )
{
ERROR("Failed to get peaks from CXI file.\n");
}
@@ -227,7 +233,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
if ( r ) {
ERROR("Failed to chdir to temporary folder: %s\n",
strerror(errno));
- hdfile_close(hdfile);
+ imagefile_close(imfile);
return;
}
@@ -250,7 +256,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
r = chdir(rn);
if ( r ) {
ERROR("Failed to chdir: %s\n", strerror(errno));
- hdfile_close(hdfile);
+ imagefile_close(imfile);
return;
}
free(rn);
@@ -288,7 +294,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
time_accounts_set(taccs, TACC_WRITESTREAM);
sb_shared->pings[cookie]++;
- ret = write_chunk(st, &image, hdfile,
+ ret = write_chunk(st, &image, imfile,
iargs->stream_peaks, iargs->stream_refls,
pargs->filename_p_e->ev);
if ( ret != 0 ) {
@@ -338,5 +344,5 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
image_feature_list_free(image.features);
free_detector_geometry(image.det);
- hdfile_close(hdfile);
+ imagefile_close(imfile);
}
diff --git a/src/process_image.h b/src/process_image.h
index d63679cf..14f90c78 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -80,7 +80,7 @@ struct index_args
int min_pix_count;
int max_pix_count;
int local_bg_radius;
- struct copy_hdf5_field *copyme;
+ struct imagefile_field_list *copyme;
int integrate_saturated;
int use_saturated;
int no_revalidate;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 21:28:51 +0000