diff options
| -rwxr-xr-x | scripts/check-near-bragg | 23 | ||||
| -rwxr-xr-x | scripts/check-peak-detection | 54 | ||||
| -rw-r--r-- | src/dw-hdfsee.c | 19 | ||||
| -rw-r--r-- | src/stream.c | 105 |
4 files changed, 177 insertions, 24 deletions
diff --git a/scripts/check-near-bragg b/scripts/check-near-bragg index 6c46fde6..17141fc4 100755 --- a/scripts/check-near-bragg +++ b/scripts/check-near-bragg @@ -14,36 +14,37 @@ while ( $line = <FH> ) { chomp $line; my $handled = 0; - if ( $line =~ /^\s*[0-9\-]+\s+[0-9\-]+\s+[0-9\-]+\s+[0-9\.\-]+/ ) { + if ( $in_image ) { printf(TMP "%s\n", $line); $handled = 1; } - if ( $line =~ /^\s*[0-9\-\.]+\s+[0-9\-\.]+\s+[0-9\-\.]+\s+[0-9\.\-]+/ ) { - printf(TMP "%s\n", $line); + if ( $line =~ /^Reflections\ measured\ after\ indexing$/ ) { + $in_image = 1; $handled = 1; } - if ( $line =~ /^Reflections\ from\ indexing\ in\ (.+)$/ ) { + if ( $line =~ /^Image\ filename:\ (.+)$/ ) { $filename = $1; $handled = 1; } - if ( $line =~ /^Peaks\ from\ peak search\ in\ (.+)$/ ) { - $filename = $1; - $handled = 1; - } + if ( $line =~ /^End\ of\ reflections$/ ) { - if ( $line =~ /^$/ ) { close(TMP); - #$filename = "images-old/".basename($filename); + + # Example of how to do "basename" and "prefix": + # $filename = "images-old/".basename($filename); + printf(STDERR "Viewing %s\n", $filename); system("hdfsee ".$filename. - " --peak-overlay=list.tmp --binning=1 --int-boost=10"); + " --peak-overlay=list.tmp --binning=2 --int-boost=10"); if ( $? != 0 ) { exit; } unlink("list.tmp"); open(TMP, "> list.tmp"); $handled = 1; + $in_image = 0; + } if ( !$handled ) { diff --git a/scripts/check-peak-detection b/scripts/check-peak-detection new file mode 100755 index 00000000..16fe53d3 --- /dev/null +++ b/scripts/check-peak-detection @@ -0,0 +1,54 @@ +#!/usr/bin/perl -w + +use strict; +use File::Basename; + +open(FH, $ARGV[0]); +open(TMP, "> list.tmp"); + +my $in_image = 0; +my $line; +my $filename; +while ( $line = <FH> ) { + + chomp $line; + my $handled = 0; + + if ( $in_image ) { + printf(TMP "%s\n", $line); + $handled = 1; + } + + if ( $line =~ /^Peaks\ from\ peak\ search$/ ) { + $in_image = 1; + $handled = 1; + } + + if ( $line =~ /^Image\ filename:\ (.+)$/ ) { + $filename = $1; + $handled = 1; + } + + if ( $line =~ /^End\ of\ peak\ list$/ ) { + + close(TMP); + + # Example of how to do "basename" and "prefix": + # $filename = "images-old/".basename($filename); + + printf(STDERR "Viewing %s\n", $filename); + system("hdfsee ".$filename. + " --peak-overlay=list.tmp --binning=2 --int-boost=10"); + if ( $? != 0 ) { exit; } + unlink("list.tmp"); + open(TMP, "> list.tmp"); + $handled = 1; + $in_image = 0; + + } + + if ( !$handled ) { + printf(STDERR "Unhandled: '%s'\n", $line); + } + +} diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c index 55a06fef..4d8f586c 100644 --- a/src/dw-hdfsee.c +++ b/src/dw-hdfsee.c @@ -695,29 +695,32 @@ static void load_features_from_file(struct image *image, const char *filename) do { char line[1024]; - float x, y, df; + float intensity, sigma, res, fs, ss; + char phs[1024]; int r; + int cts; signed int h, k, l; rval = fgets(line, 1023, fh); if ( rval == NULL ) continue; chomp(line); - /* Try long format (output of pattern_sim --near-bragg) */ - r = sscanf(line, "%i %i %i %f (at %f,%f)", - &h, &k, &l, &df, &x, &y); - if ( r == 6 ) { + /* Try long format (from stream) */ + r = sscanf(line, "%i %i %i %f %s %f %f %i %f %f", + &h, &k, &l, &intensity, phs, &sigma, &res, &cts, + &fs, &ss); + if ( r == 10 ) { char name[32]; snprintf(name, 31, "%i %i %i", h, k, l); - image_add_feature(image->features, x, y, image, 1.0, + image_add_feature(image->features, fs, ss, image, 1.0, strdup(name)); continue; } - r = sscanf(line, "%f %f", &x, &y); + r = sscanf(line, "%f %f", &fs, &ss); if ( r != 2 ) continue; - image_add_feature(image->features, x, y, image, 1.0, NULL); + image_add_feature(image->features, fs, ss, image, 1.0, NULL); } while ( rval != NULL ); } diff --git a/src/stream.c b/src/stream.c index 9c2d0c7e..2a75216d 100644 --- a/src/stream.c +++ b/src/stream.c @@ -22,10 +22,15 @@ #include "utils.h" #include "image.h" #include "stream.h" +#include "reflist.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" +#define REFLECTION_END_MARKER "End of reflections" static void exclusive(const char *a, const char *b) @@ -139,15 +144,55 @@ static UnitCell *read_orientation_matrix(FILE *fh) } +static int read_reflections(FILE *fh, struct image *image) +{ + char *rval = NULL; + + image->reflections = reflist_new(); + + do { + + char line[1024]; + signed int h, k, l; + float intensity, sigma, res, 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, PEAK_LIST_END_MARKER) == 0 ) return 0; + + r = sscanf(line, "%i %i %i %f %s %f %f %i %f %f", + &h, &k, &l, &intensity, phs, &sigma, &res, &cts, + &fs, &ss); + if ( r != 10 ) return 1; + + refl = add_refl(image->reflections, h, k, l); + set_int(refl, intensity); + set_detector_pos(refl, fs, ss, 0.0); + /* FIXME: Set ESD */ + + } while ( rval != NULL ); + + /* Got read error of some kind before finding PEAK_LIST_END_MARKER */ + return 1; + +} + + static void write_reflections(struct image *image, FILE *ofh) { Reflection *refl; RefListIterator *iter; - fprintf(ofh, "Reflections measured after indexing\n"); + fprintf(ofh, REFLECTION_START_MARKER"\n"); /* FIXME: Unify this with write_reflections() over in reflections.c */ fprintf(ofh, " h k l I phase sigma(I) " - " 1/d(nm^-1) counts\n"); + " 1/d(nm^-1) counts fs/px ss/px\n"); for ( refl = first_refl(image->reflections, &iter); refl != NULL; @@ -155,17 +200,53 @@ static void write_reflections(struct image *image, FILE *ofh) signed int h, k, l; double intensity, esd_i, s; + double fs, ss; get_indices(refl, &h, &k, &l); + get_detector_pos(refl, &fs, &ss); intensity = get_intensity(refl); esd_i = 0.0; /* FIXME! */ s = 0.0; /* FIXME! */ /* h, k, l, I, sigma(I), s */ - fprintf(ofh, "%3i %3i %3i %10.2f %s %10.2f %10.2f %7i\n", - h, k, l, intensity, " -", esd_i, s/1.0e9, 1); + fprintf(ofh, + "%3i %3i %3i %10.2f %s %10.2f %10.2f %7i %6.1f %6.1f\n", + h, k, l, intensity, " -", esd_i, s/1.0e9, 1, + fs, ss); } + + fprintf(ofh, REFLECTION_END_MARKER"\n"); +} + + +static int read_peaks(FILE *fh, struct image *image) +{ + char *rval = NULL; + + 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 ) return 1; + + image_add_feature(image->features, x, y, image, 1.0, NULL); + + } while ( rval != NULL ); + + /* Got read error of some kind before finding PEAK_LIST_END_MARKER */ + return 1; } @@ -173,7 +254,7 @@ static void write_peaks(struct image *image, FILE *ofh) { int i; - fprintf(ofh, "Peaks from peak search\n"); + 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++ ) { @@ -192,6 +273,8 @@ static void write_peaks(struct image *image, FILE *ofh) f->fs, f->ss, q/1.0e9, f->intensity); } + + fprintf(ofh, PEAK_LIST_END_MARKER"\n"); } @@ -291,6 +374,10 @@ int read_chunk(FILE *fh, struct image *image) if ( find_start_of_chunk(fh) ) return 1; image->i0_available = 0; + if ( image->features != NULL ) { + image_feature_list_free(image->features); + image->features = NULL; + } do { @@ -338,6 +425,14 @@ int read_chunk(FILE *fh, struct image *image) have_ev = 1; } + if ( strcmp(line, PEAK_LIST_START_MARKER) == 0 ) { + if ( read_peaks(fh, image) ) return 1; + } + + if ( strcmp(line, REFLECTION_START_MARKER) == 0 ) { + if ( read_reflections(fh, image) ) return 1; + } + } while ( strcmp(line, CHUNK_END_MARKER) != 0 ); if ( have_filename && have_cell && have_ev ) return 0; |