hdfsee.c 6.24 KB
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/*
 * hdfsee.c
 *
 * Quick yet non-crappy HDF viewer
 *
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 * (c) 2006-2010 Thomas White <taw@physics.org>
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 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */


#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <gtk/gtk.h>
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#include <getopt.h>
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#include "dw-hdfsee.h"
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#include "utils.h"
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#include "render.h"
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/* Global program state */
DisplayWindow *main_window_list[64];
size_t main_n_windows = 0;


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static void show_help(const char *s)
{
	printf("Syntax: %s [options] image.h5\n\n", s);
	printf(
"Quick HDF5 image viewer.\n"
"\n"
"  -h, --help                       Display this help message.\n"
"\n"
"  -p, --peak-overlay=<filename>    Draw circles in positions listed in file.\n"
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"      --ring-size=<n>              Set the size for those circles.\n"
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"  -i, --int-boost=<n>              Multiply intensity by <n>.\n"
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"  -b, --binning=<n>                Set display binning to <n>.\n"
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"      --filter-cm                  Perform common-mode noise subtraction.\n"
"      --filter-noise               Apply an aggressive noise filter which\n"
"                                    sets all pixels in each 3x3 region to\n"
"                                    zero if any of them have negative\n"
"                                    values.\n"
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"      --show-rings                 Overlay rings that indicate resolution.\n"
"      --simple-rings=XX,YY,...     Overlay rings at specified radii XX, YY, ...\n"
"                                    in pixel units.\n" 
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"  -c, --colscale=<scale>           Use the given colour scale.  Choose from:\n"
"                                    mono    : Greyscale, black is zero.\n"
"                                    invmono : Greyscale, white is zero.\n"
"                                    colour  : Colour scale:\n"
"                                               black-blue-pink-red-orange-\n"
"                                               -yellow-white.\n"
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"  -e, --image=<element>            Start up displaying this image from the\n"
"                                    HDF5 file.  Example: /data/data0.\n"
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"  -g, --geometry=<filename>        Use geometry from file for display.\n"
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"\n");
}


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/* Called to notify that an image display window has been closed */
void hdfsee_window_closed(DisplayWindow *dw)
{
	size_t i;

	for ( i=0; i<main_n_windows; i++ ) {

		if ( main_window_list[i] == dw ) {

			size_t j;

			for ( j=i+1; j<main_n_windows; j++ ) {
				main_window_list[j] = main_window_list[j+1];
			}

		}

	}

	main_n_windows--;

	if ( main_n_windows == 0 ) gtk_exit(0);

}


int main(int argc, char *argv[])
{
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	int c;
	size_t i;
	int nfiles;
	char *peaks = NULL;
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	int boost = 1;
	int binning = 2;
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	int config_cmfilter = 0;
	int config_noisefilter = 0;
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	int config_showrings = 0;
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	int colscale = SCALE_COLOUR;
	char *cscale = NULL;
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	char *element = NULL;
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	char *geometry = NULL;
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	double ring_size = 5.0;
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	char *reslist = NULL;
	double ring_radii[128];
	int n_rings = -1;
	
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	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"peak-overlay",       1, NULL,               'p'},
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		{"int-boost",          1, NULL,               'i'},
		{"binning",            1, NULL,               'b'},
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		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
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		{"colscale",           1, NULL,               'c'},
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		{"image",              1, NULL,               'e'},
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		{"geometry",           1, NULL,               'g'},
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		{"show-rings",         0, &config_showrings,   1},
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		{"ring-size",          1, NULL,                2},
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		{"simple-rings",       1, NULL,               'r'},
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		{0, 0, NULL, 0}
	};

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	gtk_init(&argc, &argv);

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	/* Short options */
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	while ((c = getopt_long(argc, argv, "hp:b:i:c:e:g:2:",
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	                        longopts, NULL)) != -1) {
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		char *test;

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		switch (c) {
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		case 'h' :
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			show_help(argv[0]);
			return 0;
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		case 'p' :
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			peaks = strdup(optarg);
			break;
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		case 'i' :
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			boost = atoi(optarg);
			if ( boost < 1 ) {
				ERROR("Intensity boost must be a positive"
				      " integer.\n");
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				return 1;
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			}
			break;

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		case 'b' :
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			binning = atoi(optarg);
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			if ( binning < 1 ) {
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				ERROR("Binning must be a positive integer.\n");
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				return 1;
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			}
			break;

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		case 'c' :
			cscale = strdup(optarg);
			break;

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		case 'e' :
			element = strdup(optarg);
			break;

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		case 'g' :
			geometry = strdup(optarg);
			break;

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		case 2 :
			ring_size = strtod(optarg, &test);
			if ( test == optarg ) {
				ERROR("Ring size must be numerical.\n");
				return 1;
			}
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		case 'r' :
			config_showrings = 1;
			reslist = strdup(optarg);
			int nchar = strlen(reslist);
			char thisvalue[128];
			int i;
			int j=0;
			n_rings = 0;
			for ( i=0; i<=nchar; i++ ) {
				if ( ( reslist[i] != ',' ) && ( reslist[i] != '\0' ) ) {
					thisvalue[j] = reslist[i];
					j++;
				} else {
					j=0;
					thisvalue[i] = '\0';
					ring_radii[n_rings] = atof(thisvalue);
					n_rings++;
				}
			}
			break;
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		case 0 :
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			break;
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		default :
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			return 1;
		}
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	}

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	nfiles = argc-optind;

	if ( nfiles < 1 ) {
		ERROR("You need to give me a file to open!\n");
		return -1;
	}

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	if ( cscale == NULL ) cscale = strdup("colour");
	if ( strcmp(cscale, "mono") == 0 ) {
		colscale = SCALE_MONO;
	} else if ( strcmp(cscale, "invmono") == 0 ) {
		colscale = SCALE_INVMONO;
	} else if ( strcmp(cscale, "colour") == 0 ) {
		colscale = SCALE_COLOUR;
	} else if ( strcmp(cscale, "color") == 0 ) {
		colscale = SCALE_COLOUR;
	} else {
		ERROR("Unrecognised colour scale '%s'\n", cscale);
		return 1;
	}
	free(cscale);

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	for ( i=0; i<nfiles; i++ ) {
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		main_window_list[i] = displaywindow_open(argv[optind+i], peaks,
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		                                         boost, binning,
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		                                         config_cmfilter,
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		                                         config_noisefilter,
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		                                         colscale, element,
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		                                         geometry,
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		                                         config_showrings,
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		                                         ring_radii,
		                                         n_rings,
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		                                         ring_size);
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		if ( main_window_list[i] == NULL ) {
			ERROR("Couldn't open display window\n");
		} else {
			main_n_windows++;
		}
	}
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	if ( main_n_windows == 0 ) return 0;
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	gtk_main();

	return 0;
}