Move a load more stuff into libcrystfel

1 files changed, 487 insertions, 0 deletions

diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
new file mode 100644
index 00000000..a7cdc2d9
--- /dev/null
+++ b/libcrystfel/src/stream.c
@@ -0,0 +1,487 @@
+/*
+ * stream.c
+ *
+ * Stream tools
+ *
+ * (c) 2006-2011 Thomas White <taw@physics.org>
+ * (c) 2011 Rick Kirian <rkirian@asu.edu>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+
+#include "cell.h"
+#include "utils.h"
+#include "image.h"
+#include "stream.h"
+#include "reflist.h"
+#include "reflist-utils.h"
+
+
+#define CHUNK_START_MARKER "----- Begin chunk -----"
+#define CHUNK_END_MARKER "----- End chunk -----"
+#define PEAK_LIST_START_MARKER "Peaks from peak search"
+#define PEAK_LIST_END_MARKER "End of peak list"
+#define REFLECTION_START_MARKER "Reflections measured after indexing"
+/* REFLECTION_END_MARKER is over in reflist-utils.h because it is also
+ * used to terminate a standalone list of reflections */
+
+static void exclusive(const char *a, const char *b)
+{
+	ERROR("The stream options '%s' and '%s' are mutually exclusive.\n",
+	      a, b);
+}
+
+
+int parse_stream_flags(const char *a)
+{
+	int n, i;
+	int ret = STREAM_NONE;
+	char **flags;
+
+	n = assplode(a, ",", &flags, ASSPLODE_NONE);
+
+	for ( i=0; i<n; i++ ) {
+
+		if ( strcmp(flags[i], "integrated") == 0) {
+
+			ret |= STREAM_INTEGRATED;
+
+		} else if ( strcmp(flags[i], "peaks") == 0) {
+			if ( ret & STREAM_PEAKS_IF_INDEXED ) {
+				exclusive("peaks", "peaksifindexed");
+				return -1;
+			}
+			if ( ret & STREAM_PEAKS_IF_NOT_INDEXED ) {
+				exclusive("peaks", "peaksifnotindexed");
+				return -1;
+			}
+			ret |= STREAM_PEAKS;
+
+		} else if ( strcmp(flags[i], "peaksifindexed") == 0) {
+			if ( ret & STREAM_PEAKS ) {
+				exclusive("peaks", "peaksifindexed");
+				return -1;
+			}
+			if ( ret & STREAM_PEAKS_IF_NOT_INDEXED ) {
+				exclusive("peaksifnotindexed",
+				          "peaksifindexed");
+				return -1;
+			}
+			ret |= STREAM_PEAKS_IF_INDEXED;
+
+		} else if ( strcmp(flags[i], "peaksifnotindexed") == 0) {
+			if ( ret & STREAM_PEAKS ) {
+				exclusive("peaks", "peaksifnotindexed");
+				return -1;
+			}
+			if ( ret & STREAM_PEAKS_IF_INDEXED ) {
+				exclusive("peaksifnotindexed",
+				          "peaksifindexed");
+				return -1;
+			}
+			ret |= STREAM_PEAKS_IF_NOT_INDEXED;
+
+		} else {
+			ERROR("Unrecognised stream flag '%s'\n", flags[i]);
+			return -1;
+		}
+
+		free(flags[i]);
+
+	}
+	free(flags);
+
+	return ret;
+}
+
+
+int count_patterns(FILE *fh)
+{
+	char *rval;
+
+	int n_total_patterns = 0;
+	do {
+		char line[1024];
+
+		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) continue;
+		chomp(line);
+		if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_total_patterns++;
+
+	} while ( rval != NULL );
+
+	if ( ferror(fh) ) {
+		ERROR("Read error while counting patterns.\n");
+		return 0;
+	}
+
+	return n_total_patterns;
+}
+
+
+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 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");
+}
+
+
+void write_chunk(FILE *ofh, struct image *i, struct hdfile *hdfile, int f)
+{
+	double asx, asy, asz;
+	double bsx, bsy, bsz;
+	double csx, csy, csz;
+	double a, b, c, al, be, ga;
+
+	fprintf(ofh, CHUNK_START_MARKER"\n");
+
+	fprintf(ofh, "Image filename: %s\n", i->filename);
+
+	if ( i->indexed_cell != NULL ) {
+
+		cell_get_parameters(i->indexed_cell, &a, &b, &c,
+		                                         &al, &be, &ga);
+		fprintf(ofh, "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(i->indexed_cell, &asx, &asy, &asz,
+			                  &bsx, &bsy, &bsz,
+			                  &csx, &csy, &csz);
+		fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+			asx/1e9, asy/1e9, asz/1e9);
+		fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+			bsx/1e9, bsy/1e9, bsz/1e9);
+		fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
+		        csx/1e9, csy/1e9, csz/1e9);
+
+	} else {
+
+		fprintf(ofh, "No unit cell from indexing.\n");
+
+	}
+
+	if ( i->i0_available ) {
+		fprintf(ofh, "I0 = %7.5f (arbitrary units)\n", i->i0);
+	} else {
+		fprintf(ofh, "I0 = invalid\n");
+	}
+
+	fprintf(ofh, "photon_energy_eV = %f\n",
+	        J_to_eV(ph_lambda_to_en(i->lambda)));
+
+	if ( i->det != NULL ) {
+
+		int j;
+
+		for ( j=0; j<i->det->n_panels; j++ ) {
+			fprintf(ofh, "camera_length_%s = %f\n",
+			        i->det->panels[j].name, i->det->panels[j].clen);
+		}
+
+	}
+
+	copy_hdf5_fields(hdfile, i->copyme, ofh);
+
+	if ( (f & STREAM_PEAKS)
+	  || ((f & STREAM_PEAKS_IF_INDEXED) && (i->indexed_cell != NULL))
+	  || ((f & STREAM_PEAKS_IF_NOT_INDEXED) && (i->indexed_cell == NULL)) )
+	{
+		fprintf(ofh, "\n");
+		write_peaks(i, ofh);
+	}
+
+	if ( f & STREAM_INTEGRATED ) {
+
+		fprintf(ofh, "\n");
+
+		if ( i->reflections != NULL ) {
+
+			fprintf(ofh, REFLECTION_START_MARKER"\n");
+			write_reflections_to_file(ofh, i->reflections,
+			                               i->indexed_cell);
+			fprintf(ofh, REFLECTION_END_MARKER"\n");
+
+		} else {
+
+			fprintf(ofh, "No integrated reflections.\n");
+
+		}
+	}
+
+	fprintf(ofh, CHUNK_END_MARKER"\n\n");
+}
+
+
+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;
+}
+
+
+/* Read the next chunk from a stream and fill in 'image' */
+int read_chunk(FILE *fh, struct image *image)
+{
+	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_filename = 0;
+	int have_cell = 0;
+	int have_ev = 0;
+
+	if ( find_start_of_chunk(fh) ) return 1;
+
+	image->i0_available = 0;
+	image->i0 = 1.0;
+	image->lambda = -1.0;
+	image->features = NULL;
+	image->reflections = NULL;
+	image->indexed_cell = NULL;
+
+	do {
+
+		float u, v, w;
+
+		rval = fgets(line, 1023, 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, "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 ( strncmp(line, "I0 = ", 5) == 0 ) {
+			image->i0 = atof(line+5);
+			image->i0_available = 1;
+		}
+
+		if ( 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 ( 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 ( 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 ( have_as && have_bs && have_cs ) {
+			if ( image->indexed_cell != NULL ) {
+				ERROR("Duplicate cell found in stream!\n");
+				cell_free(image->indexed_cell);
+			}
+			image->indexed_cell = cell_new_from_reciprocal_axes(as,
+			                                                    bs,
+			                                                    cs);
+			have_cell = 1;
+			have_as = 0;  have_bs = 0;  have_cs = 0;
+		}
+
+		if ( strncmp(line, "photon_energy_eV = ", 19) == 0 ) {
+			image->lambda = ph_en_to_lambda(eV_to_J(atof(line+19)));
+			have_ev = 1;
+		}
+
+		if ( strcmp(line, PEAK_LIST_START_MARKER) == 0 ) {
+			if ( read_peaks(fh, image) ) {
+				ERROR("Failed while reading peaks\n");
+				return 1;
+			}
+		}
+
+		if ( strcmp(line, REFLECTION_START_MARKER) == 0 ) {
+			image->reflections = read_reflections_from_file(fh);
+			if ( image->reflections == NULL ) {
+				ERROR("Failed while reading reflections\n");
+				return 1;
+			}
+		}
+
+		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 );
+
+	return 1;  /* Either error or EOF, don't care because we will complain
+	            * on the terminal if it was an error. */
+}
+
+
+void write_stream_header(FILE *ofh, int argc, char *argv[])
+{
+	int i;
+
+	fprintf(ofh, "CrystFEL stream format 2.0\n");
+	fprintf(ofh, "Command line:");
+	for ( i=0; i<argc; i++ ) {
+		fprintf(ofh, " %s", argv[i]);
+	}
+	fprintf(ofh, "\n");
+	fflush(ofh);
+}
+
+
+int skip_some_files(FILE *fh, int n)
+{
+	char *rval = NULL;
+	int n_patterns = 0;
+
+	do {
+
+		char line[1024];
+
+		if ( n_patterns == n ) return 0;
+
+		rval = fgets(line, 1023, fh);
+		if ( rval == NULL ) continue;
+		if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_patterns++;
+
+	} while ( rval != NULL );
+
+	return 1;
+}
+
+int is_stream(const char *filename) {
+	FILE *fh;
+	char line[1024];
+	char *rval = NULL;
+	fh = fopen(filename, "r");
+	rval = fgets(line, 1023, fh);
+	fclose(fh);
+	if ( rval == NULL ) {
+		return -1;
+	}
+	if ( strncmp(line, "CrystFEL stream format 2.0", 26) == 0 ) {
+		return 1;
+	}
+	else {
+		return 0;
+	}
+	return -1;
+}