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|
/*
* stream.c
*
* Stream tools
*
* Copyright © 2013-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
*
* Authors:
* 2010-2014 Thomas White <taw@physics.org>
* 2014 Valerio Mariani
* 2011 Richard Kirian
* 2011 Andrew Aquila
* 2014 Takanori Nakane <nakane.t@gmail.com>
*
* 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/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include "version.h"
#include "cell.h"
#include "cell-utils.h"
#include "utils.h"
#include "image.h"
#include "stream.h"
#include "reflist.h"
#include "reflist-utils.h"
#define LATEST_MAJOR_VERSION (2)
#define LATEST_MINOR_VERSION (3)
#define AT_LEAST_VERSION(st, a, b) ((st->major_version>=(a)) \
&& (st->minor_version>=(b)))
struct _stream
{
FILE *fh;
int major_version;
int minor_version;
};
static int read_peaks(FILE *fh, struct image *image)
{
char *rval = NULL;
int first = 1;
image->features = image_feature_list_new();
do {
char line[1024];
float x, y, d, intensity;
int r;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0;
r = sscanf(line, "%f %f %f %f", &x, &y, &d, &intensity);
if ( (r != 4) && (!first) ) {
ERROR("Failed to parse peak list line.\n");
ERROR("The failed line was: '%s'\n", line);
return 1;
}
first = 0;
if ( r == 4 ) {
image_add_feature(image->features, x, y,
image, intensity, NULL);
}
} while ( rval != NULL );
/* Got read error of some kind before finding PEAK_LIST_END_MARKER */
return 1;
}
static int read_peaks_2_3(FILE *fh, struct image *image)
{
char *rval = NULL;
int first = 1;
image->features = image_feature_list_new();
do {
char line[1024];
char pn[32];
float x, y, d, intensity;
int r;
struct panel *p = NULL;
int add_x, add_y;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0;
r = sscanf(line, "%f %f %f %f %s", &x, &y, &d, &intensity, pn);
if ( (r != 5) && (!first) ) {
ERROR("Failed to parse peak list line.\n");
ERROR("The failed line was: '%s'\n", line);
return 1;
}
first = 0;
if ( r == 5 ) {
p = find_panel_by_name(image->det, pn);
if ( p == NULL ) {
ERROR("Panel not found: %s\n", pn);
return 1;
}
add_x = x-p->orig_min_fs+p->min_fs;
add_y = x-p->orig_min_ss+p->min_ss;
image_add_feature(image->features, add_x, add_y,
image, intensity, NULL);
}
} while ( rval != NULL );
/* Got read error of some kind before finding PEAK_LIST_END_MARKER */
return 1;
}
static void write_peaks(struct image *image, FILE *ofh)
{
int i;
fprintf(ofh, PEAK_LIST_START_MARKER"\n");
fprintf(ofh, " fs/px ss/px (1/d)/nm^-1 Intensity\n");
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
struct rvec r;
double q;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
q = modulus(r.u, r.v, r.w);
fprintf(ofh, "%7.2f %7.2f %10.2f %10.2f\n",
f->fs, f->ss, q/1.0e9, f->intensity);
}
fprintf(ofh, PEAK_LIST_END_MARKER"\n");
}
static void write_peaks_2_3(struct image *image, FILE *ofh)
{
int i;
fprintf(ofh, PEAK_LIST_START_MARKER"\n");
fprintf(ofh, " fs/px ss/px (1/d)/nm^-1 Intensity Panel\n");
for ( i=0; i<image_feature_count(image->features); i++ ) {
struct imagefeature *f;
struct rvec r;
double q;
struct panel *p;
double write_fs, write_ss;
f = image_get_feature(image->features, i);
if ( f == NULL ) continue;
r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
q = modulus(r.u, r.v, r.w);
p = find_panel(image->det,f->fs,f->ss);
write_fs = f->fs-p->min_fs+p->orig_min_fs;
write_ss = f->ss-p->min_ss+p->orig_min_ss;
fprintf(ofh, "%7.2f %7.2f %10.2f %10.2f %s\n",
write_fs, write_ss, q/1.0e9, f->intensity, p->name);
}
fprintf(ofh, PEAK_LIST_END_MARKER"\n");
}
static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det)
{
char *rval = NULL;
int first = 1;
RefList *out;
out = reflist_new();
do {
char line[1024];
signed int h, k, l;
float intensity, sigma, fs, ss;
char phs[1024];
char pn[32];
int cts;
int r;
Reflection *refl;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
r = sscanf(line, "%i %i %i %f %s %f %i %f %f %s",
&h, &k, &l, &intensity, phs, &sigma, &cts,
&fs, &ss, pn);
if ( (r != 10) && (!first) ) {
reflist_free(out);
return NULL;
}
first = 0;
if ( r == 10 ) {
double ph;
char *v;
struct panel *p;
float write_fs, write_ss;
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
if ( det != NULL ) {
p = find_panel_by_name(det,pn);
set_detector_pos(refl, 0.0, write_fs, write_ss);
write_ss = ss-p->orig_min_ss+p->min_ss;
write_fs = fs-p->orig_min_fs+p->min_fs;
}
set_esd_intensity(refl, sigma);
set_redundancy(refl, cts);
ph = strtod(phs, &v);
if ( v != phs ) set_phase(refl, deg2rad(ph));
}
} while ( rval != NULL );
/* Got read error of some kind before finding PEAK_LIST_END_MARKER */
return NULL;
}
static RefList *read_stream_reflections_2_1(FILE *fh)
{
char *rval = NULL;
int first = 1;
RefList *out;
out = reflist_new();
do {
char line[1024];
signed int h, k, l;
float intensity, sigma, fs, ss;
char phs[1024];
int cts;
int r;
Reflection *refl;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
r = sscanf(line, "%i %i %i %f %s %f %i %f %f",
&h, &k, &l, &intensity, phs, &sigma, &cts, &fs, &ss);
if ( (r != 9) && (!first) ) {
reflist_free(out);
return NULL;
}
first = 0;
if ( r == 9 ) {
double ph;
char *v;
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
set_detector_pos(refl, 0.0, fs, ss);
set_esd_intensity(refl, sigma);
set_redundancy(refl, cts);
ph = strtod(phs, &v);
if ( v != phs ) set_phase(refl, deg2rad(ph));
}
} while ( rval != NULL );
/* Got read error of some kind before finding PEAK_LIST_END_MARKER */
return NULL;
}
static RefList *read_stream_reflections_2_2(FILE *fh)
{
char *rval = NULL;
int first = 1;
RefList *out;
out = reflist_new();
do {
char line[1024];
signed int h, k, l;
float intensity, sigma, fs, ss, pk, bg;
int r;
Reflection *refl;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
r = sscanf(line, "%i %i %i %f %f %f %f %f %f",
&h, &k, &l, &intensity, &sigma, &pk, &bg, &fs, &ss);
if ( (r != 9) && (!first) ) {
reflist_free(out);
return NULL;
}
first = 0;
if ( r == 9 ) {
refl = add_refl(out, h, k, l);
set_intensity(refl, intensity);
set_detector_pos(refl, 0.0, fs, ss);
set_esd_intensity(refl, sigma);
set_redundancy(refl, 1);
set_peak(refl, pk);
set_mean_bg(refl, bg);
}
} while ( rval != NULL );
/* Got read error of some kind before finding PEAK_LIST_END_MARKER */
return NULL;
}
static void write_stream_reflections_2_2(FILE *fh, RefList *list)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I sigma(I) peak background"
" fs/px ss/px\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, bg, pk;
double fs, ss;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
pk = get_peak(refl);
bg = get_mean_bg(refl);
/* Reflections with redundancy = 0 are not written */
if ( get_redundancy(refl) == 0 ) continue;
fprintf(fh,
"%4i %4i %4i %10.2f %10.2f %10.2f %10.2f %6.1f %6.1f\n",
h, k, l, intensity, esd_i, pk, bg, fs, ss);
}
}
static void write_stream_reflections_2_1(FILE *fh, RefList *list)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I phase sigma(I) "
" counts fs/px ss/px\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, ph;
int red;
double fs, ss;
char phs[16];
int have_phase;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
red = get_redundancy(refl);
ph = get_phase(refl, &have_phase);
/* Reflections with redundancy = 0 are not written */
if ( red == 0 ) continue;
if ( have_phase ) {
snprintf(phs, 16, "%8.2f", rad2deg(ph));
} else {
strncpy(phs, " -", 15);
}
fprintf(fh,
"%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f\n",
h, k, l, intensity, phs, esd_i, red, fs, ss);
}
}
static void write_stream_reflections_2_3(FILE *fh, RefList *list,
struct image *image)
{
Reflection *refl;
RefListIterator *iter;
fprintf(fh, " h k l I phase sigma(I) "
" counts fs/px ss/px panel\n");
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
double intensity, esd_i, ph;
int red;
double fs, ss;
double write_fs, write_ss;
char phs[16];
int have_phase;
struct panel *p = NULL;
get_indices(refl, &h, &k, &l);
get_detector_pos(refl, &fs, &ss);
intensity = get_intensity(refl);
esd_i = get_esd_intensity(refl);
red = get_redundancy(refl);
ph = get_phase(refl, &have_phase);
/* Reflections with redundancy = 0 are not written */
if ( red == 0 ) continue;
if ( have_phase ) {
snprintf(phs, 16, "%8.2f", rad2deg(ph));
} else {
strncpy(phs, " -", 15);
}
p = find_panel(image->det,fs,ss);
write_fs = fs-p->min_fs+p->orig_min_fs;
write_ss = ss-p->min_ss+p->orig_min_ss;
fprintf(fh,
"%3i %3i %3i %10.2f %s %10.2f %7i %6.1f %6.1f %s\n",
h, k, l, intensity, phs, esd_i, red,
write_fs, write_ss, p->name);
}
}
static int num_integrated_reflections(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
int n = 0;
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
if ( get_redundancy(refl) > 0 ) n++;
}
return n;
}
static void write_crystal(Stream *st, Crystal *cr, int include_reflections)
{
UnitCell *cell;
RefList *reflist;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double a, b, c, al, be, ga;
double rad;
fprintf(st->fh, CRYSTAL_START_MARKER"\n");
cell = crystal_get_cell(cr);
assert(cell != NULL);
cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
fprintf(st->fh, "Cell parameters %7.5f %7.5f %7.5f nm,"
" %7.5f %7.5f %7.5f deg\n",
a*1.0e9, b*1.0e9, c*1.0e9,
rad2deg(al), rad2deg(be), rad2deg(ga));
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
fprintf(st->fh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
asx/1e9, asy/1e9, asz/1e9);
fprintf(st->fh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
bsx/1e9, bsy/1e9, bsz/1e9);
fprintf(st->fh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
csx/1e9, csy/1e9, csz/1e9);
fprintf(st->fh, "lattice_type = %s\n",
str_lattice(cell_get_lattice_type(cell)));
fprintf(st->fh, "centering = %c\n", cell_get_centering(cell));
fprintf(st->fh, "unique_axis = %c\n", cell_get_unique_axis(cell));
rad = crystal_get_profile_radius(cr);
fprintf(st->fh, "profile_radius = %.5f nm^-1\n", rad/1e9);
reflist = crystal_get_reflections(cr);
if ( reflist != NULL ) {
fprintf(st->fh, "diffraction_resolution_limit"
" = %.2f nm^-1 or %.2f A\n",
crystal_get_resolution_limit(cr)/1e9,
1e9 / crystal_get_resolution_limit(cr));
fprintf(st->fh, "num_reflections = %i\n",
num_integrated_reflections(reflist));
fprintf(st->fh, "num_saturated_reflections = %lli\n",
crystal_get_num_saturated_reflections(cr));
}
if ( include_reflections ) {
if ( reflist != NULL ) {
fprintf(st->fh, REFLECTION_START_MARKER"\n");
if ( AT_LEAST_VERSION(st, 2, 3) ) {
write_stream_reflections_2_3(st->fh, reflist,
crystal_get_image(cr));
} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
write_stream_reflections_2_2(st->fh, reflist);
} else {
/* This function writes like a normal reflection
* list was written in stream 2.1 */
write_stream_reflections_2_1(st->fh, reflist);
}
fprintf(st->fh, REFLECTION_END_MARKER"\n");
} else {
fprintf(st->fh, "No integrated reflections.\n");
}
}
fprintf(st->fh, CRYSTAL_END_MARKER"\n");
}
void write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
int include_peaks, int include_reflections, struct event* ev)
{
int j;
char *indexer;
fprintf(st->fh, CHUNK_START_MARKER"\n");
fprintf(st->fh, "Image filename: %s\n", i->filename);
if ( i->event != NULL ) {
fprintf(st->fh, "Event: %s\n", get_event_string(i->event));
}
fprintf(st->fh, "Image serial number: %i\n", i->serial);
indexer = indexer_str(i->indexed_by);
fprintf(st->fh, "indexed_by = %s\n", indexer);
free(indexer);
fprintf(st->fh, "photon_energy_eV = %f\n",
J_to_eV(ph_lambda_to_en(i->lambda)));
fprintf(st->fh, "beam_divergence = %.5f mrad\n", i->div*1e3);
fprintf(st->fh, "beam_bandwidth = %.5f %%\n", i->bw*100.0);
copy_hdf5_fields(hdfile, i->copyme, st->fh, ev);
if ( i->det != NULL ) {
int j;
double tclen = 0.0;
for ( j=0; j<i->det->n_panels; j++ ) {
tclen += i->det->panels[j].clen;
}
fprintf(st->fh, "average_camera_length = %f m\n",
tclen / i->det->n_panels);
for ( j=0; j<i->det->n_rigid_groups; j++ ) {
struct rigid_group *rg = i->det->rigid_groups[j];
if ( !rg->have_deltas ) continue;
fprintf(st->fh, "rg_delta_%s_fsx = %f\n",
rg->name, rg->d_fsx);
fprintf(st->fh, "rg_delta_%s_ssx = %f\n",
rg->name, rg->d_ssx);
fprintf(st->fh, "rg_delta_%s_cnx = %f\n",
rg->name, rg->d_cnx);
fprintf(st->fh, "rg_delta_%s_fsy = %f\n",
rg->name, rg->d_fsy);
fprintf(st->fh, "rg_delta_%s_ssy = %f\n",
rg->name, rg->d_ssy);
fprintf(st->fh, "rg_delta_%s_cny = %f\n",
rg->name, rg->d_cny);
}
}
fprintf(st->fh, "num_peaks = %lli\n", i->num_peaks);
fprintf(st->fh, "num_saturated_peaks = %lli\n", i->num_saturated_peaks);
if ( include_peaks ) {
if ( AT_LEAST_VERSION(st, 2, 3) ) {
write_peaks_2_3(i, st->fh);
} else {
write_peaks(i, st->fh);
}
}
for ( j=0; j<i->n_crystals; j++ ) {
write_crystal(st, i->crystals[j], include_reflections);
}
fprintf(st->fh, CHUNK_END_MARKER"\n");
fflush(st->fh);
}
static int find_start_of_chunk(FILE *fh)
{
char *rval = NULL;
char line[1024];
do {
rval = fgets(line, 1023, fh);
/* Trouble? */
if ( rval == NULL ) return 1;
chomp(line);
} while ( strcmp(line, CHUNK_START_MARKER) != 0 );
return 0;
}
static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
{
char line[1024];
char *rval = NULL;
struct rvec as, bs, cs;
int have_as = 0;
int have_bs = 0;
int have_cs = 0;
int have_latt = 0;
int have_cen = 0;
int have_ua = 0;
char centering = 'P';
char unique_axis = '*';
LatticeType lattice_type = L_TRICLINIC;
Crystal *cr;
int n;
Crystal **crystals_new;
cr = crystal_new();
if ( cr == NULL ) {
ERROR("Failed to allocate crystal!\n");
return;
}
do {
float u, v, w, lim, rad;
char c;
rval = fgets(line, 1023, st->fh);
/* Trouble? */
if ( rval == NULL ) break;
chomp(line);
if ( (srf & STREAM_READ_UNITCELL)
&& (sscanf(line, "astar = %f %f %f", &u, &v, &w) == 3) )
{
as.u = u*1e9; as.v = v*1e9; as.w = w*1e9;
have_as = 1;
}
if ( (srf & STREAM_READ_UNITCELL)
&& (sscanf(line, "bstar = %f %f %f", &u, &v, &w) == 3) )
{
bs.u = u*1e9; bs.v = v*1e9; bs.w = w*1e9;
have_bs = 1;
}
if ( (srf & STREAM_READ_UNITCELL)
&& (sscanf(line, "cstar = %f %f %f", &u, &v, &w) == 3) )
{
cs.u = u*1e9; cs.v = v*1e9; cs.w = w*1e9;
have_cs = 1;
}
if ( (srf & STREAM_READ_UNITCELL)
&& (sscanf(line, "centering = %c", &c) == 1) )
{
if ( !have_cen ) {
centering = c;
have_cen = 1;
} else {
ERROR("Duplicate centering ignored.\n");
}
}
if ( (srf & STREAM_READ_UNITCELL)
&& (sscanf(line, "unique_axis = %c", &c) == 1) )
{
if ( !have_ua ) {
unique_axis = c;
have_ua = 1;
} else {
ERROR("Duplicate unique axis ignored.\n");
}
}
if ( (srf & STREAM_READ_UNITCELL)
&& (strncmp(line, "lattice_type = ", 15) == 0) )
{
if ( !have_latt ) {
lattice_type = lattice_from_str(line+15);
have_latt = 1;
} else {
ERROR("Duplicate lattice type ignored.\n");
}
}
if ( strncmp(line, "num_saturated_reflections = ", 28) == 0 ) {
int n = atoi(line+28);
crystal_set_num_saturated_reflections(cr, n);
}
if ( sscanf(line, "diffraction_resolution_limit = %f nm^-1",
&lim) == 1 ) {
crystal_set_resolution_limit(cr, lim*1e9);
}
if ( sscanf(line, "profile_radius = %f nm^-1", &rad) == 1 ) {
crystal_set_profile_radius(cr, rad*1e9);
}
if ( (strcmp(line, REFLECTION_START_MARKER) == 0)
&& (srf & STREAM_READ_REFLECTIONS) )
{
RefList *reflist;
/* The reflection list format in the stream diverges
* after 2.2 */
if ( AT_LEAST_VERSION(st, 2, 3) ) {
reflist = read_stream_reflections_2_3(st->fh, image->det);
} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
reflist = read_stream_reflections_2_2(st->fh);
} else {
reflist = read_stream_reflections_2_1(st->fh);
}
if ( reflist == NULL ) {
ERROR("Failed while reading reflections\n");
break;
}
crystal_set_reflections(cr, reflist);
}
if ( strcmp(line, CRYSTAL_END_MARKER) == 0 ) break;
} while ( 1 );
if ( have_as && have_bs && have_cs ) {
UnitCell *cell;
cell = crystal_get_cell(cr);
if ( cell != NULL ) {
ERROR("Duplicate cell found in stream!\n");
ERROR("I'll use the most recent one.\n");
cell_free(cell);
}
cell = cell_new_from_reciprocal_axes(as, bs, cs);
if ( have_cen && have_ua && have_latt ) {
cell_set_centering(cell, centering);
cell_set_unique_axis(cell, unique_axis);
cell_set_lattice_type(cell, lattice_type);
} /* else keep default triclinic P */
crystal_set_cell(cr, cell);
have_as = 0; have_bs = 0; have_cs = 0;
have_latt = 0; have_ua = 0; have_cen = 0;
}
/* Unused at the moment */
crystal_set_mosaicity(cr, 0.0);
/* Add crystal to the list for this image */
n = image->n_crystals+1;
crystals_new = realloc(image->crystals, n*sizeof(Crystal *));
if ( crystals_new == NULL ) {
ERROR("Failed to expand crystal list!\n");
} else {
image->crystals = crystals_new;
image->crystals[image->n_crystals++] = cr;
}
}
/* Read the next chunk from a stream and fill in 'image' */
int read_chunk_2(Stream *st, struct image *image, StreamReadFlags srf)
{
char line[1024];
char *rval = NULL;
int have_filename = 0;
int have_ev = 0;
if ( find_start_of_chunk(st->fh) ) return 1;
image->lambda = -1.0;
image->features = NULL;
image->crystals = NULL;
image->n_crystals = 0;
if ( (srf & STREAM_READ_REFLECTIONS) || (srf & STREAM_READ_UNITCELL) ) {
srf |= STREAM_READ_CRYSTALS;
}
do {
long long num_peaks;
int ser;
float div, bw;
rval = fgets(line, 1023, st->fh);
/* Trouble? */
if ( rval == NULL ) break;
chomp(line);
if ( strncmp(line, "Image filename: ", 16) == 0 ) {
image->filename = strdup(line+16);
have_filename = 1;
}
if ( strncmp(line, "indexed_by = ", 13) == 0 ) {
IndexingMethod *list;
list = build_indexer_list(line+13);
image->indexed_by = list[0];
free(list);
have_filename = 1;
}
if ( strncmp(line, "photon_energy_eV = ", 19) == 0 ) {
image->lambda = ph_en_to_lambda(eV_to_J(atof(line+19)));
have_ev = 1;
}
if ( sscanf(line, "beam_divergence = %f mrad", &div) == 1 ) {
image->div = div/1e3;
}
if ( sscanf(line, "beam_bandwidth = %f %%", &bw) == 1 ) {
image->bw = bw/100.0;
}
if ( sscanf(line, "num_peaks = %lld %%", &num_peaks) == 1 ) {
image->num_peaks = num_peaks;
}
if ( sscanf(line, "Image serial number: %i", &ser) == 1 ) {
image->serial = ser;
}
if ( strncmp(line, "camera_length_", 14) == 0 ) {
if ( image->det != NULL ) {
int k;
char name[1024];
struct panel *p;
for ( k=0; k<strlen(line)-14; k++ ) {
char ch = line[k+14];
name[k] = ch;
if ( (ch == ' ') || (ch == '=') ) {
name[k] = '\0';
break;
}
}
p = find_panel_by_name(image->det, name);
if ( p == NULL ) {
ERROR("No panel '%s'\n", name);
} else {
p->clen = atof(line+14+k+3);
}
}
}
if ( (srf & STREAM_READ_PEAKS)
&& strcmp(line, PEAK_LIST_START_MARKER) == 0 ) {
int fail;
if ( AT_LEAST_VERSION(st, 2, 3) ) {
fail = read_peaks_2_3(st->fh, image);
} else {
fail = read_peaks(st->fh, image);
}
if ( fail ) {
ERROR("Failed while reading peaks\n");
return 1;
}
}
if ( (srf & STREAM_READ_CRYSTALS)
&& (strcmp(line, CRYSTAL_START_MARKER) == 0) ) {
read_crystal(st, image, srf);
}
/* A chunk must have at least a filename and a wavelength,
* otherwise it's incomplete */
if ( strcmp(line, CHUNK_END_MARKER) == 0 ) {
if ( have_filename && have_ev ) return 0;
ERROR("Incomplete chunk found in input file.\n");
return 1;
}
} while ( 1 );
if ( !feof(st->fh) ) {
ERROR("Error reading stream.\n");
}
return 1; /* Either error or EOF, don't care because we will complain
* on the terminal if it was an error. */
}
int read_chunk(Stream *st, struct image *image)
{
return read_chunk_2(st, image, STREAM_READ_UNITCELL
| STREAM_READ_REFLECTIONS
| STREAM_READ_PEAKS);
}
void write_stream_header(FILE *ofh, int argc, char *argv[])
{
int i;
fprintf(ofh, "Command line:");
for ( i=0; i<argc; i++ ) {
fprintf(ofh, " %s", argv[i]);
}
fprintf(ofh, "\n");
fflush(ofh);
}
Stream *open_stream_for_read(const char *filename)
{
Stream *st;
st = malloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
st->fh = fopen(filename, "r");
if ( st->fh == NULL ) {
free(st);
return NULL;
}
char line[1024];
char *rval;
rval = fgets(line, 1023, st->fh);
if ( rval == NULL ) {
ERROR("Failed to read stream version.\n");
close_stream(st);
return NULL;
}
if ( strncmp(line, "CrystFEL stream format 2.0", 26) == 0 ) {
st->major_version = 2;
st->minor_version = 0;
} else if ( strncmp(line, "CrystFEL stream format 2.1", 26) == 0 ) {
st->major_version = 2;
st->minor_version = 1;
} else if ( strncmp(line, "CrystFEL stream format 2.2", 26) == 0 ) {
st->major_version = 2;
st->minor_version = 2;
} else if ( strncmp(line, "CrystFEL stream format 2.3", 26) == 0 ) {
st->major_version = 2;
st->minor_version = 3;
} else {
ERROR("Invalid stream, or stream format is too new.\n");
close_stream(st);
return NULL;
}
return st;
}
/**
* open_stream_fd_for_write
* @fd: File descriptor (e.g. from open()) to use for stream data.
*
* Creates a new %Stream from @fd, so that stream data can be written to @fd
* using write_chunk().
*
* In contrast to open_stream_for_write(), this function does not write any of
* the usual headers. This function is mostly for use when multiple substreams
* need to be multiplexed into a single master stream. The master would be
* opened using open_stream_for_write(), and the substreams using this function.
*
* Returns: a %Stream, or NULL on failure.
*/
Stream *open_stream_fd_for_write(int fd)
{
Stream *st;
st = malloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
st->fh = fdopen(fd, "w");
if ( st->fh == NULL ) {
free(st);
return NULL;
}
st->major_version = LATEST_MAJOR_VERSION;
st->minor_version = LATEST_MINOR_VERSION;
return st;
}
/**
* open_stream_for_write_2
* @filename: Filename of new stream
* @geom_filename: The geometry filename to copy
* @argc: The number of arguments to the program
* @argv: The arguments to the program
*
* Creates a new stream with name @filename, and adds the stream format
* and version header, plus a verbatim copy of the geometry file
*
* You may want to follow this with a call to write_command() to record the
* command line.
*
* Returns: a %Stream, or NULL on failure.
*/
Stream *open_stream_for_write_2(const char *filename,
const char *geom_filename, int argc,
char *argv[])
{
Stream *st;
st = malloc(sizeof(struct _stream));
if ( st == NULL ) return NULL;
st->fh = fopen(filename, "w");
if ( st->fh == NULL ) {
ERROR("Failed to open stream.\n");
free(st);
return NULL;
}
st->major_version = LATEST_MAJOR_VERSION;
st->minor_version = LATEST_MINOR_VERSION;
fprintf(st->fh, "CrystFEL stream format %i.%i\n",
st->major_version, st->minor_version);
fprintf(st->fh, "Generated by CrystFEL "CRYSTFEL_VERSIONSTRING"\n");
fflush(st->fh);
if ( (argc > 0) && (argv != NULL) ) {
write_command(st, argc, argv);
}
if ( geom_filename != NULL ) {
write_geometry_file(st, geom_filename);
}
return st;
}
/**
* open_stream_for_write
* @filename: Filename of new stream
*
* Creates a new stream with name @filename, and adds the stream format
* and version headers.
*
* You may want to follow this with a call to write_command() to record the
* command line.
*
* Returns: a %Stream, or NULL on failure.
*/
Stream *open_stream_for_write(const char *filename)
{
return open_stream_for_write_2(filename, NULL, 0, NULL);
}
/**
* get_stream_fd
* @st: A %Stream
*
* This function gets the integer file descriptor for @st, a bit like fileno().
*
* This is useful in conjunction with open_stream_fd_for_write(), to get the
* underlying file descriptor to which the multiplexed stream data should be
* written. In this case, the only other operations you should ever do (or have
* done) on @st are open_stream_for_write() and close_stream().
*
* Returns: an integer file descriptor
*/
int get_stream_fd(Stream *st)
{
return fileno(st->fh);
}
void close_stream(Stream *st)
{
fclose(st->fh);
free(st);
}
int is_stream(const char *filename)
{
FILE *fh;
char line[1024];
char *rval;
fh = fopen(filename, "r");
if ( fh == NULL ) return 0;
rval = fgets(line, 1023, fh);
fclose(fh);
if ( rval == NULL ) return 0;
if ( strncmp(line, "CrystFEL stream format 2.0", 26) == 0 ) return 1;
if ( strncmp(line, "CrystFEL stream format 2.1", 26) == 0 ) return 1;
if ( strncmp(line, "CrystFEL stream format 2.2", 26) == 0 ) return 1;
return 0;
}
/**
* write_command
* @st: A %Stream
* @argc: number of arguments
* @argv: command-line arguments
*
* Writes the command line to @st. @argc and @argv should be exactly as were
* given to main(). This should usually be called immediately after
* open_stream_for_write().
*/
void write_command(Stream *st, int argc, char *argv[])
{
int i;
if ( argc == 0 ) return;
for ( i=0; i<argc; i++ ) {
if ( i > 0 ) fprintf(st->fh, " ");
fprintf(st->fh, "%s", argv[i]);
}
fprintf(st->fh, "\n");
fflush(st->fh);
}
/**
* write_geometry_file
* @st: A %Stream
* @geom_filename: geomtry file name
*
* Writes the content of the geometry file to @st. This should usually be
* called immediately after write_command().
*/
void write_geometry_file(Stream *st, const char *geom_filename) {
char line[2014];
FILE *geom_fh;
char *rval;
if ( geom_filename == NULL ) return;
geom_fh = fopen(geom_filename, "r");
if ( geom_fh == NULL ) {
ERROR("Failed to read detector geometry from "
"'%s'\n", geom_filename);
return;
}
fprintf(st->fh, GEOM_START_MARKER"\n");
do {
rval = fgets(line, 1023, geom_fh);
fputs(line, st->fh);
} while ( rval != NULL );
fprintf(st->fh, GEOM_END_MARKER"\n");
fflush(st->fh);
}
/**
* rewind_stream:
* @st: A %Stream
*
* Attempts to set the file pointer for @st to the start of the stream, so that
* later calls to read_chunk() will repeat the sequence of chunks from the
* start.
*
* Programs must not assume that this operation always succeeds!
*
* Returns: non-zero if the stream could not be rewound.
*/
int rewind_stream(Stream *st)
{
return fseek(st->fh, 0, SEEK_SET);
}
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