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/*
* image.c
*
* Handle images and image features
*
* Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2014 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
* 2011-2017 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
* CrystFEL is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* CrystFEL is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include <stdlib.h>
#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
* @short_description: Data structure representing an image
* @title: Image
* @section_id:
* @see_also:
* @include: "image.h"
* @Image:
*
* The <structname>image</structname> structure represents an image, usually one
* frame from a large series of diffraction patterns, which might be from the
* same or different crystals.
*/
struct imagefile
{
enum imagefile_type type;
char *filename;
struct hdfile *hdfile;
};
struct _imagefeaturelist
{
struct imagefeature *features;
int n_features;
};
void image_add_feature(ImageFeatureList *flist, double fs, double ss,
struct panel *p,
struct image *parent, double intensity, const char *name)
{
if ( flist->features ) {
flist->features = realloc(flist->features,
(flist->n_features+1)
*sizeof(struct imagefeature));
} else {
assert(flist->n_features == 0);
flist->features = malloc(sizeof(struct imagefeature));
}
flist->features[flist->n_features].fs = fs;
flist->features[flist->n_features].ss = ss;
flist->features[flist->n_features].p = p;
flist->features[flist->n_features].intensity = intensity;
flist->features[flist->n_features].parent = parent;
flist->features[flist->n_features].name = name;
flist->features[flist->n_features].valid = 1;
flist->n_features++;
}
ImageFeatureList *image_feature_list_new()
{
ImageFeatureList *flist;
flist = malloc(sizeof(ImageFeatureList));
flist->n_features = 0;
flist->features = NULL;
return flist;
}
static int comp(const void *a, const void *b)
{
const struct imagefeature *ap = a;
const struct imagefeature *bp = b;
return ap->intensity < bp->intensity;
}
/* Strongest first. Returned list is guaranteed not to have any holes
* (feature->valid = 0) */
ImageFeatureList *sort_peaks(ImageFeatureList *flist)
{
ImageFeatureList *n = image_feature_list_new();
int nf, i;
if ( n == NULL ) return NULL;
n->features = malloc(flist->n_features*sizeof(struct imagefeature));
if ( n->features == NULL ) {
free(n);
return NULL;
}
nf = 0;
for ( i=0; i<flist->n_features; i++ ) {
struct imagefeature *f;
f = image_get_feature(flist, i);
if ( f == NULL ) continue;
n->features[nf++] = flist->features[i];
}
n->n_features = nf;
qsort(n->features, nf, sizeof(struct imagefeature), comp);
return n;
}
void image_feature_list_free(ImageFeatureList *flist)
{
if ( !flist ) return;
if ( flist->features ) free(flist->features);
free(flist);
}
struct imagefeature *image_feature_closest(ImageFeatureList *flist,
double fs, double ss,
struct panel *p, double *d, int *idx)
{
int i;
double dmin = +HUGE_VAL;
int closest = 0;
for ( i=0; i<flist->n_features; i++ ) {
double ds;
if ( p != flist->features[i].p ) continue;
ds = distance(flist->features[i].fs, flist->features[i].ss,
fs, ss);
if ( ds < dmin ) {
dmin = ds;
closest = i;
}
}
if ( dmin < +HUGE_VAL ) {
*d = dmin;
*idx = closest;
return &flist->features[closest];
}
*d = +INFINITY;
return NULL;
}
Reflection *image_reflection_closest(RefList *rlist,
double fs, double ss, struct panel *p,
struct detector *det,
double *d)
{
double dmin = HUGE_VAL;
Reflection *closest = NULL;
Reflection *refl;
RefListIterator *iter;
for ( refl = first_refl(rlist, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
double ds;
struct panel *p2;
double rfs, rss;
get_detector_pos(refl, &rfs, &rss);
p2 = get_panel(refl);
if ( p != p2 ) continue;
ds = distance(rfs, rss, fs, ss);
if ( ds < dmin ) {
dmin = ds;
closest = refl;
}
}
if ( dmin < +HUGE_VAL ) {
*d = dmin;
return closest;
}
*d = +INFINITY;
return NULL;
}
int image_feature_count(ImageFeatureList *flist)
{
if ( flist == NULL ) return 0;
return flist->n_features;
}
struct imagefeature *image_get_feature(ImageFeatureList *flist, int idx)
{
/* Sanity check */
if ( flist == NULL ) return NULL;
if ( idx >= flist->n_features ) return NULL;
if ( flist->features[idx].valid == 0 ) return NULL;
return &flist->features[idx];
}
void image_remove_feature(ImageFeatureList *flist, int idx)
{
flist->features[idx].valid = 0;
}
void image_add_crystal(struct image *image, Crystal *cryst)
{
Crystal **crs;
int n;
n = image->n_crystals;
crs = realloc(image->crystals, (n+1)*sizeof(Crystal *));
if ( crs == NULL ) {
ERROR("Failed to allocate memory for crystals.\n");
return;
}
crs[n] = cryst;
image->crystals = crs;
image->n_crystals = n+1;
}
void remove_flagged_crystals(struct image *image)
{
int i;
for ( i=0; i<image->n_crystals; i++ ) {
if ( crystal_get_user_flag(image->crystals[i]) ) {
int j;
Crystal *deleteme = image->crystals[i];
cell_free(crystal_get_cell(deleteme));
crystal_free(deleteme);
for ( j=i; j<image->n_crystals-1; j++ ) {
image->crystals[j] = image->crystals[j+1];
}
image->n_crystals--;
}
}
}
/* Free all crystals, including their RefLists and UnitCells */
void free_all_crystals(struct image *image)
{
int i;
if ( image->crystals == NULL ) return;
for ( i=0; i<image->n_crystals; i++ ) {
Crystal *cr = image->crystals[i];
reflist_free(crystal_get_reflections(cr));
cell_free(crystal_get_cell(cr));
crystal_free(image->crystals[i]);
}
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 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 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 ( 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);
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;
}
/****************************** 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 {
STATUS("Mock CBF simple read\n");
return 0;
}
}
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);
}
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