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-rw-r--r--libcrystfel/src/stream.c438
-rw-r--r--libcrystfel/src/stream.h4
2 files changed, 122 insertions, 320 deletions
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index be8a2c0d..b8433f31 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -8,7 +8,7 @@
* Copyright © 2012 Richard Kirian
*
* Authors:
- * 2010-2019 Thomas White <taw@physics.org>
+ * 2010-2020 Thomas White <taw@physics.org>
* 2014-2016 Valerio Mariani
* 2011 Richard Kirian
* 2011 Andrew Aquila
@@ -89,124 +89,84 @@ int stream_has_old_indexers(Stream *st)
}
-static int read_peaks(Stream *st, struct image *image)
+static ImageFeatureList *read_peaks(Stream *st,
+ const DataTemplate *dtempl,
+ struct image *image)
{
char *rval = NULL;
int first = 1;
+ ImageFeatureList *features;
- image->features = image_feature_list_new();
+ features = image_feature_list_new();
do {
char line[1024];
float x, y, d, intensity;
- int r;
- float add_x, add_y;
+ int r, exp_n;
+ char *panel_name = NULL;
rval = fgets(line, 1023, st->fh);
st->ln++;
if ( rval == NULL ) continue;
chomp(line);
- if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0;
+ if ( strcmp(line, STREAM_PEAK_LIST_END_MARKER) == 0 ) {
+ return features;
+ }
- r = sscanf(line, "%f %f %f %f", &x, &y, &d, &intensity);
- if ( (r != 4) && (!first) ) {
+ if ( AT_LEAST_VERSION(st, 2, 3) ) {
+ r = sscanf(line, "%f %f %f %f %s",
+ &x, &y, &d, &intensity, panel_name);
+ exp_n = 5;
+ } else {
+ r = sscanf(line, "%f %f %f %f",
+ &x, &y, &d, &intensity);
+ exp_n = 4;
+ }
+ if ( (r != exp_n) && (!first) ) {
ERROR("Failed to parse peak list line.\n");
ERROR("The failed line was: '%s'\n", line);
- return 1;
+ image_feature_list_free(features);
+ return NULL;
}
first = 0;
- if ( r == 4 ) {
-
- if ( image->det != NULL ) {
-
- int pn;
- struct panel *p = NULL;
- p = find_orig_panel(image->det, x, y);
- if ( p == NULL ) {
- ERROR("Panel not found\n");
- return 1;
- }
-
- add_x = x-p->orig_min_fs;
- add_y = y-p->orig_min_ss;
- pn = panel_number(image->det, p);
+ if ( (panel_name != NULL) && (dtempl != NULL) ) {
- image_add_feature(image->features, add_x, add_y,
- pn, image, intensity, NULL);
+ int pn;
+ if ( data_template_panel_name_to_number(dtempl, panel_name, &pn) ) {
+ ERROR("No such panel '%s'\n",
+ panel_name);
} else {
- image_add_feature(image->features, x, y,
- 0, image, intensity, NULL);
- }
- }
-
- } while ( rval != NULL );
-
- /* Got read error of some kind before finding PEAK_LIST_END_MARKER */
- return 1;
-}
-
+ data_template_file_to_panel_coords(dtempl,
+ &x, &y, &pn);
-static int read_peaks_2_3(Stream *st, 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;
- float add_x, add_y;
+ image_add_feature(features, x, y,
+ pn, image, intensity,
+ NULL);
- rval = fgets(line, 1023, st->fh);
- st->ln++;
- 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 ) {
-
- int pnum;
- struct panel *p;
- 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;
- add_y = y-p->orig_min_ss;
-
- pnum = panel_number(image->det, p);
+ } else {
- image_add_feature(image->features,
- add_x, add_y, pnum,
+ /* Either it's an old format stream (in which
+ * case the data is probably "slabby", so no
+ * coordinate conversion is needed), or
+ * the caller isn't interested in panel
+ * locations */
+ image_add_feature(features, x, y, 0,
image, intensity, NULL);
}
} while ( rval != NULL );
- /* Got read error of some kind before finding PEAK_LIST_END_MARKER */
- return 1;
+ /* Got read error of some kind before finding STREAM_PEAK_LIST_END_MARKER */
+ image_feature_list_free(features);
+ return NULL;
}
@@ -215,7 +175,7 @@ static int write_peaks(struct image *image,
{
int i;
- fprintf(ofh, PEAK_LIST_START_MARKER"\n");
+ fprintf(ofh, STREAM_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++ ) {
@@ -241,11 +201,11 @@ static int write_peaks(struct image *image,
fprintf(ofh, "%7.2f %7.2f %10.2f %10.2f %s\n",
write_fs, write_ss, q/1.0e9, f->intensity,
- data_template_panel_name(dtempl, f->pn));
+ data_template_panel_number_to_name(dtempl, f->pn));
}
- fprintf(ofh, PEAK_LIST_END_MARKER"\n");
+ fprintf(ofh, STREAM_PEAK_LIST_END_MARKER"\n");
return 0;
}
@@ -277,7 +237,7 @@ static RefList *read_stream_reflections_2_3(Stream *st,
if ( rval == NULL ) continue;
chomp(line);
- if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
+ if ( strcmp(line, STREAM_REFLECTION_END_MARKER) == 0 ) return out;
r = sscanf(line, "%i %i %i %f %f %f %f %f %f %s",
&h, &k, &l, &intensity, &sigma, &pk, &bg,
@@ -316,7 +276,7 @@ static RefList *read_stream_reflections_2_3(Stream *st,
} while ( rval != NULL );
- /* Got read error of some kind before finding PEAK_LIST_END_MARKER */
+ /* Got read error of some kind before finding STREAM_PEAK_LIST_END_MARKER */
return NULL;
}
@@ -349,7 +309,7 @@ static RefList *read_stream_reflections_2_1(Stream *st,
if ( rval == NULL ) continue;
chomp(line);
- if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
+ if ( strcmp(line, STREAM_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,
@@ -398,7 +358,7 @@ static RefList *read_stream_reflections_2_1(Stream *st,
} while ( rval != NULL );
- /* Got read error of some kind before finding PEAK_LIST_END_MARKER */
+ /* Got read error of some kind before finding STREAM_PEAK_LIST_END_MARKER */
return NULL;
}
@@ -425,7 +385,7 @@ static RefList *read_stream_reflections_2_2(Stream *st,
if ( rval == NULL ) continue;
chomp(line);
- if ( strcmp(line, REFLECTION_END_MARKER) == 0 ) return out;
+ if ( strcmp(line, STREAM_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);
@@ -473,7 +433,7 @@ static RefList *read_stream_reflections_2_2(Stream *st,
} while ( rval != NULL );
- /* Got read error of some kind before finding REFLECTION_END_MARKER */
+ /* Got read error of some kind before finding STREAM_REFLECTION_END_MARKER */
return NULL;
}
@@ -516,7 +476,7 @@ static int write_stream_reflections(FILE *fh, RefList *list,
fprintf(fh, "%4i %4i %4i %10.2f %10.2f %10.2f %10.2f "
"%6.1f %6.1f %s\n",
h, k, l, intensity, esd_i, pk, bg,
- fs, ss, data_template_panel_name(dtempl, pn));
+ fs, ss, data_template_panel_number_to_name(dtempl, pn));
}
return 0;
@@ -554,7 +514,7 @@ static int write_crystal(Stream *st, Crystal *cr,
double det_shift_x, det_shift_y;
int ret = 0;
- fprintf(st->fh, CRYSTAL_START_MARKER"\n");
+ fprintf(st->fh, STREAM_CRYSTAL_START_MARKER"\n");
cell = crystal_get_cell(cr);
assert(cell != NULL);
@@ -613,10 +573,10 @@ static int write_crystal(Stream *st, Crystal *cr,
if ( reflist != NULL ) {
- fprintf(st->fh, REFLECTION_START_MARKER"\n");
+ fprintf(st->fh, STREAM_REFLECTION_START_MARKER"\n");
ret = write_stream_reflections(st->fh, reflist,
dtempl);
- fprintf(st->fh, REFLECTION_END_MARKER"\n");
+ fprintf(st->fh, STREAM_REFLECTION_END_MARKER"\n");
} else {
@@ -625,7 +585,7 @@ static int write_crystal(Stream *st, Crystal *cr,
}
}
- fprintf(st->fh, CRYSTAL_END_MARKER"\n");
+ fprintf(st->fh, STREAM_CRYSTAL_END_MARKER"\n");
return ret;
}
@@ -634,22 +594,24 @@ static int write_crystal(Stream *st, Crystal *cr,
/**
* \param st A \ref Stream
* \param i An \ref image structure
- * \param include_peaks Whether to include peak search results in stream
+ * \param srf A \ref StreamFlags enum saying what to write
* \param include_reflections Whether to include integration results in stream
*
* Writes a new chunk to \p st.
*
* \returns non-zero on error.
*/
-int write_chunk(Stream *st, struct image *i,
- const DataTemplate *dtempl,
- int include_peaks, int include_reflections)
+int stream_write_chunk(Stream *st, struct image *i,
+ const DataTemplate *dtempl, StreamFlags srf)
{
int j;
char *indexer;
int ret = 0;
- fprintf(st->fh, CHUNK_START_MARKER"\n");
+ if ( srf & STREAM_REFLECTIONS ) srf |= STREAM_CRYSTALS;
+ if ( srf & STREAM_UNITCELL ) srf |= STREAM_CRYSTALS;
+
+ fprintf(st->fh, STREAM_CHUNK_START_MARKER"\n");
fprintf(st->fh, "Image filename: %s\n", i->filename);
fprintf(st->fh, "Event: %s\n", i->ev);
@@ -672,34 +634,38 @@ int write_chunk(Stream *st, struct image *i,
/* FIXME: Better way of doing this */
//imagefile_copy_fields(imfile, i->copyme, st->fh, ev);
- if ( i->det != NULL ) {
+ if ( i->detgeom != NULL ) {
int j;
double tclen = 0.0;
- for ( j=0; j<i->det->n_panels; j++ ) {
- tclen += i->det->panels[j].clen;
+ for ( j=0; j<i->detgeom->n_panels; j++ ) {
+ tclen += i->detgeom->panels[j].cnz
+ * i->detgeom->panels[j].pixel_pitch;
}
fprintf(st->fh, "average_camera_length = %f m\n",
- tclen / i->det->n_panels);
+ tclen / i->detgeom->n_panels);
}
fprintf(st->fh, "num_peaks = %i\n", image_feature_count(i->features));
fprintf(st->fh, "peak_resolution = %f nm^-1 or %f A\n",
i->peak_resolution/1e9, 1e10/i->peak_resolution);
- if ( include_peaks ) {
+ if ( srf & STREAM_PEAKS ) {
ret = write_peaks(i, dtempl, st->fh);
}
- for ( j=0; j<i->n_crystals; j++ ) {
- if ( crystal_get_user_flag(i->crystals[j]) == 0 ) {
+ if ( srf & STREAM_CRYSTALS ) {
+ for ( j=0; j<i->n_crystals; j++ ) {
+ if ( crystal_get_user_flag(i->crystals[j]) ) {
+ continue;
+ }
ret = write_crystal(st, i->crystals[j], dtempl,
- include_reflections);
+ srf & STREAM_REFLECTIONS);
}
}
- fprintf(st->fh, CHUNK_END_MARKER"\n");
+ fprintf(st->fh, STREAM_CHUNK_END_MARKER"\n");
fflush(st->fh);
@@ -730,14 +696,14 @@ static int find_start_of_chunk(Stream *st)
chomp(line);
- } while ( strcmp(line, CHUNK_START_MARKER) != 0 );
+ } while ( strcmp(line, STREAM_CHUNK_START_MARKER) != 0 );
return 0;
}
static void read_crystal(Stream *st, struct image *image,
- const DataTemplate *dtempl, StreamReadFlags srf)
+ const DataTemplate *dtempl, StreamFlags srf)
{
char line[1024];
char *rval = NULL;
@@ -778,28 +744,28 @@ static void read_crystal(Stream *st, struct image *image,
if ( rval == NULL ) break;
chomp(line);
- if ( (srf & STREAM_READ_UNITCELL)
+ if ( (srf & STREAM_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)
+ if ( (srf & STREAM_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)
+ if ( (srf & STREAM_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)
+ if ( (srf & STREAM_UNITCELL)
&& (sscanf(line, "centering = %c", &c) == 1) )
{
if ( !have_cen ) {
@@ -811,7 +777,7 @@ static void read_crystal(Stream *st, struct image *image,
}
}
- if ( (srf & STREAM_READ_UNITCELL)
+ if ( (srf & STREAM_UNITCELL)
&& (sscanf(line, "unique_axis = %c", &c) == 1) )
{
if ( !have_ua ) {
@@ -823,7 +789,7 @@ static void read_crystal(Stream *st, struct image *image,
}
}
- if ( (srf & STREAM_READ_UNITCELL)
+ if ( (srf & STREAM_UNITCELL)
&& (strncmp(line, "lattice_type = ", 15) == 0) )
{
if ( !have_latt ) {
@@ -855,8 +821,8 @@ static void read_crystal(Stream *st, struct image *image,
}
- if ( (strcmp(line, REFLECTION_START_MARKER) == 0)
- && (srf & STREAM_READ_REFLECTIONS) )
+ if ( (strcmp(line, STREAM_REFLECTION_START_MARKER) == 0)
+ && (srf & STREAM_REFLECTIONS) )
{
RefList *reflist;
@@ -884,7 +850,7 @@ static void read_crystal(Stream *st, struct image *image,
}
- if ( strcmp(line, CRYSTAL_END_MARKER) == 0 ) break;
+ if ( strcmp(line, STREAM_CRYSTAL_END_MARKER) == 0 ) break;
} while ( 1 );
@@ -940,7 +906,7 @@ static void read_crystal(Stream *st, struct image *image,
* Read the next chunk from a stream and fill in 'image'
*/
int read_chunk(Stream *st, struct image *image,
- const DataTemplate *dtempl, StreamReadFlags srf)
+ const DataTemplate *dtempl, StreamFlags srf)
{
char line[1024];
char *rval = NULL;
@@ -956,8 +922,8 @@ int read_chunk(Stream *st, struct image *image,
image->ev = NULL;
image->copied_headers = NULL;
- if ( (srf & STREAM_READ_REFLECTIONS) || (srf & STREAM_READ_UNITCELL) ) {
- srf |= STREAM_READ_CRYSTALS;
+ if ( (srf & STREAM_REFLECTIONS) || (srf & STREAM_UNITCELL) ) {
+ srf |= STREAM_CRYSTALS;
}
do {
@@ -1009,56 +975,24 @@ int read_chunk(Stream *st, struct image *image,
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_PEAKS)
+ && strcmp(line, STREAM_PEAK_LIST_START_MARKER) == 0 ) {
- }
- }
-
- 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, image);
- } else {
- fail = read_peaks(st, image);
- }
- if ( fail ) {
+ if ( read_peaks(st, dtempl, image) ) {
ERROR("Failed while reading peaks\n");
return 1;
}
}
- if ( (srf & STREAM_READ_CRYSTALS)
- && (strcmp(line, CRYSTAL_START_MARKER) == 0) ) {
+ if ( (srf & STREAM_CRYSTALS)
+ && (strcmp(line, STREAM_CRYSTAL_START_MARKER) == 0) ) {
read_crystal(st, image, dtempl, srf);
}
/* A chunk must have at least a filename and a wavelength,
* otherwise it's incomplete */
- if ( strcmp(line, CHUNK_END_MARKER) == 0 ) {
+ if ( strcmp(line, STREAM_CHUNK_END_MARKER) == 0 ) {
if ( have_filename && have_ev ) return 0;
ERROR("Incomplete chunk found in input file.\n");
return 1;
@@ -1127,7 +1061,7 @@ static void read_audit_lines(Stream *st)
rval = fgets(line, 1023, st->fh);
if ( rval == NULL ) {
ERROR("Failed to read stream audit info.\n");
- close_stream(st);
+ stream_close(st);
return;
}
@@ -1175,23 +1109,23 @@ static void read_geometry_file(Stream *st)
rval = fgets(line, 1023, st->fh);
if ( rval == NULL ) {
ERROR("Failed to read stream geometry file.\n");
- close_stream(st);
+ stream_close(st);
free(st->geometry_file);
st->geometry_file = NULL;
return;
}
- if ( strcmp(line, GEOM_START_MARKER"\n") == 0 ) {
+ if ( strcmp(line, STREAM_GEOM_START_MARKER"\n") == 0 ) {
started = 1;
continue;
}
- if ( strcmp(line, GEOM_END_MARKER"\n") == 0 ) {
+ if ( strcmp(line, STREAM_GEOM_END_MARKER"\n") == 0 ) {
done = 1;
continue;
}
- if ( strcmp(line, CHUNK_START_MARKER"\n") == 0 ) {
+ if ( strcmp(line, STREAM_CHUNK_START_MARKER"\n") == 0 ) {
done = 1;
st->in_chunk = 1;
continue;
@@ -1242,7 +1176,7 @@ Stream *open_stream_for_read(const char *filename)
rval = fgets(line, 1023, st->fh);
if ( rval == NULL ) {
ERROR("Failed to read stream version.\n");
- close_stream(st);
+ stream_close(st);
return NULL;
}
@@ -1260,7 +1194,7 @@ Stream *open_stream_for_read(const char *filename)
st->minor_version = 3;
} else {
ERROR("Invalid stream, or stream format is too new.\n");
- close_stream(st);
+ stream_close(st);
return NULL;
}
@@ -1310,102 +1244,27 @@ Stream *open_stream_fd_for_write(int fd)
}
-static void write_cell_to_stream(Stream *st, UnitCell *cell)
+void stream_write_target_cell(Stream *st, const UnitCell *cell)
{
- fprintf(st->fh, CELL_START_MARKER"\n");
+ fprintf(st->fh, STREAM_CELL_START_MARKER"\n");
write_cell(cell, st->fh);
fprintf(st->fh, "; Please note: this is the target unit cell.\n");
fprintf(st->fh, "; The actual unit cells produced by indexing "
"depend on many other factors.\n");
- fprintf(st->fh, CELL_END_MARKER"\n");
- fflush(st->fh);
-}
-
-
-/**
- * \param filename Filename of new stream
- * \param geom_filename The geometry filename to copy
- * \param cell A \ref UnitCell to write into the stream
- * \param argc The number of arguments to the program
- * \param argv The arguments to the program
- * \param indm_str The list of indexing methods
- *
- * Creates a new stream with name \p filename, and adds the stream format
- * and version header, plus a verbatim copy of the geometry file and the unit
- * cell in CrystFEL format.
- *
- * \returns A \ref Stream, or NULL on failure.
- */
-Stream *open_stream_for_write_4(const char *filename,
- const char *geom_filename, UnitCell *cell,
- int argc, char *argv[], const char *indm_str)
-
-{
- Stream *st;
-
- st = malloc(sizeof(struct _stream));
- if ( st == NULL ) return NULL;
- st->old_indexers = 0;
- st->audit_info = NULL;
- st->geometry_file = NULL;
- st->in_chunk = 0;
-
- 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");
+ fprintf(st->fh, STREAM_CELL_END_MARKER"\n");
fflush(st->fh);
-
- if ( (argc > 0) && (argv != NULL) ) {
- write_command(st, argc, argv);
- }
-
- if ( indm_str != NULL ) {
- fprintf(st->fh, "Indexing methods selected: %s\n", indm_str);
- }
- if ( geom_filename != NULL ) {
- write_geometry_file(st, geom_filename);
- }
- if ( cell != NULL ) {
- write_cell_to_stream(st, cell);
- }
-
- return st;
-}
-
-
-Stream *open_stream_for_write_3(const char *filename,
- const char *geom_filename, UnitCell *cell,
- int argc, char *argv[])
-{
- return open_stream_for_write_4(filename, geom_filename, cell,
- argc, argv, NULL);
}
/**
* \param filename Filename of new stream
- * \param geom_filename The geometry filename to copy
- * \param argc The number of arguments to the program
- * \param argv The arguments to the program
*
- * Creates a new stream with name \p filename, and adds the stream format
- * and version header, plus a verbatim copy of the geometry file
+ * Creates a new stream with name \p filename. If \p filename already
+ * exists, it will be overwritten.
*
* \returns A \ref Stream, or NULL on failure.
*/
-Stream *open_stream_for_write_2(const char *filename,
- const char *geom_filename, int argc,
- char *argv[])
+Stream *stream_open_for_write(const char *filename)
{
Stream *st;
@@ -1432,47 +1291,11 @@ Stream *open_stream_for_write_2(const char *filename,
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;
}
-/**
- * \param filename Filename of new stream
- *
- * Creates a new stream with name \p filename, and adds the stream format
- * and version headers.
- *
- * You may want to follow this with a call to \ref write_command to record the
- * command line.
- *
- * \returns A \ref Stream, or NULL on failure.
- */
-Stream *open_stream_for_write(const char *filename)
-{
- return open_stream_for_write_2(filename, NULL, 0, NULL);
-}
-
-
-/**
- * \param st A \ref Stream
- *
- * This function gets the integer file descriptor for \p st, a bit like fileno().
- *
- * This is useful in conjunction with \ref 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 \p st are \ref open_stream_for_write and \ref close_stream.
- *
- * \returns An integer file descriptor
- */
-int get_stream_fd(Stream *st)
+int stream_get_fd(Stream *st)
{
return fileno(st->fh);
}
@@ -1483,7 +1306,7 @@ int get_stream_fd(Stream *st)
*
* Closes the stream
*/
-void close_stream(Stream *st)
+void stream_close(Stream *st)
{
free(st->audit_info);
free(st->geometry_file);
@@ -1492,37 +1315,16 @@ void close_stream(Stream *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;
-}
-
-
/**
* \param st A \ref Stream
* \param argc number of arguments
* \param argv command-line arguments
*
- * Writes the command line to \p st. \p argc and \p argv should be exactly as were
- * given to main(). This should usually be called immediately after
- * ref open_stream_for_write.
+ * Writes the command line to \p st. \p argc and \p argv should be
+ * exactly as were given to main(). This should usually be called
+ * immediately after \ref stream_open_for_write.
*/
-void write_command(Stream *st, int argc, char *argv[])
+void stream_write_commandline_args(Stream *st, int argc, char *argv[])
{
int i;
@@ -1544,8 +1346,8 @@ void write_command(Stream *st, int argc, char *argv[])
* Writes the content of the geometry file to \p st. This should usually be
* called immediately after \ref write_command.
*/
-void write_geometry_file(Stream *st, const char *geom_filename) {
-
+void stream_write_geometry_file(Stream *st, const char *geom_filename)
+{
char line[2014];
FILE *geom_fh;
char *rval;
@@ -1559,7 +1361,7 @@ void write_geometry_file(Stream *st, const char *geom_filename) {
"'%s'\n", geom_filename);
return;
}
- fprintf(st->fh, GEOM_START_MARKER"\n");
+ fprintf(st->fh, STREAM_GEOM_START_MARKER"\n");
do {
rval = fgets(line, 1023, geom_fh);
@@ -1574,7 +1376,7 @@ void write_geometry_file(Stream *st, const char *geom_filename) {
fclose(geom_fh);
- fprintf(st->fh, GEOM_END_MARKER"\n");
+ fprintf(st->fh, STREAM_GEOM_END_MARKER"\n");
fflush(st->fh);
}
diff --git a/libcrystfel/src/stream.h b/libcrystfel/src/stream.h
index ed850b0b..6970ea02 100644
--- a/libcrystfel/src/stream.h
+++ b/libcrystfel/src/stream.h
@@ -68,8 +68,8 @@ typedef struct _stream Stream;
* Use this (and \ref read_chunk) to read the stream faster if you
* don't need the entire contents of the stream.
*
- * When reading, using either of \p STREAM_REFLECTIONS or
- * \p STREAM_UNITCELL implies \p STREAM_CRYSTALS.
+ * Using either of \p STREAM_REFLECTIONS or * \p STREAM_UNITCELL
+ * implies \p STREAM_CRYSTALS.
**/
typedef enum {
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 20:41:43 +0000