indexamajig: --peaks=cxi instead of --peaks=hdf5 --cxi-hdf5-peaks

6 files changed, 154 insertions, 143 deletions

diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index daaacd9f..25e700ab 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -378,169 +378,170 @@ static float *read_hdf5_data(struct hdfile *f, char *path, int line)
 }
 
 
-int get_peaks(struct image *image, struct hdfile *f, const char *p,
-              int cxi_format, struct filename_plus_event *fpe)
+/* Get peaks from HDF5, in "CXI format" (as in "CXIDB") */
+int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p,
+                  struct filename_plus_event *fpe)
 {
-	if ( cxi_format ) {
-
-		char path_n[1024];
-		char path_x[1024];
-		char path_y[1024];
-		char path_i[1024];
-		int r;
-		int pk;
-
-		int line = 0;
-		int num_peaks;
+	char path_n[1024];
+	char path_x[1024];
+	char path_y[1024];
+	char path_i[1024];
+	int r;
+	int pk;
 
-		float *buf_x;
-		float *buf_y;
-		float *buf_i;
+	int line = 0;
+	int num_peaks;
 
-		if ( (fpe != NULL) && (fpe->ev != NULL)
-		  && (fpe->ev->dim_entries != NULL) )
-		{
-			line = fpe->ev->dim_entries[0];
-		} else {
-			ERROR("CXI format peak list format selected,"
-			      "but file has no event structure");
-			return 1;
-		}
+	float *buf_x;
+	float *buf_y;
+	float *buf_i;
 
-		snprintf(path_n, 1024, "%s/nPeaks", p);
-		snprintf(path_x, 1024, "%s/peakXPosRaw", p);
-		snprintf(path_y, 1024, "%s/peakYPosRaw", p);
-		snprintf(path_i, 1024, "%s/peakTotalIntensity", p);
+	if ( (fpe != NULL) && (fpe->ev != NULL)
+	  && (fpe->ev->dim_entries != NULL) )
+	{
+		line = fpe->ev->dim_entries[0];
+	} else {
+		ERROR("CXI format peak list format selected,"
+		      "but file has no event structure");
+		return 1;
+	}
 
-		r = read_peak_count(f, path_n, line, &num_peaks);
-		if ( r != 0 ) return 1;
+	snprintf(path_n, 1024, "%s/nPeaks", p);
+	snprintf(path_x, 1024, "%s/peakXPosRaw", p);
+	snprintf(path_y, 1024, "%s/peakYPosRaw", p);
+	snprintf(path_i, 1024, "%s/peakTotalIntensity", p);
 
-		buf_x = read_hdf5_data(f, path_x, line);
-		if ( r != 0 ) return 1;
+	r = read_peak_count(f, path_n, line, &num_peaks);
+	if ( r != 0 ) return 1;
 
-		buf_y = read_hdf5_data(f, path_y, line);
-		if ( r != 0 ) return 1;
+	buf_x = read_hdf5_data(f, path_x, line);
+	if ( r != 0 ) return 1;
 
-		buf_i = read_hdf5_data(f, path_i, line);
-		if ( r != 0 ) return 1;
+	buf_y = read_hdf5_data(f, path_y, line);
+	if ( r != 0 ) return 1;
 
-		if ( image->features != NULL ) {
-			image_feature_list_free(image->features);
-		}
-		image->features = image_feature_list_new();
+	buf_i = read_hdf5_data(f, path_i, line);
+	if ( r != 0 ) return 1;
 
-		for ( pk=0; pk<num_peaks; pk++ ) {
+	if ( image->features != NULL ) {
+		image_feature_list_free(image->features);
+	}
+	image->features = image_feature_list_new();
 
-			float fs, ss, val;
-			struct panel *p;
+	for ( pk=0; pk<num_peaks; pk++ ) {
 
-			fs = buf_x[pk];
-			ss = buf_y[pk];
-			val = buf_i[pk];
+		float fs, ss, val;
+		struct panel *p;
 
-			p = find_orig_panel(image->det, fs, ss);
-			if ( p == NULL ) continue;
-			if ( p->no_index ) continue;
+		fs = buf_x[pk];
+		ss = buf_y[pk];
+		val = buf_i[pk];
 
-			/* Convert coordinates to match rearranged
-			 * panels in memory */
-			fs = fs - p->orig_min_fs + p->min_fs;
-			ss = ss - p->orig_min_ss + p->min_ss;
+		p = find_orig_panel(image->det, fs, ss);
+		if ( p == NULL ) continue;
+		if ( p->no_index ) continue;
 
-			image_add_feature(image->features, fs, ss, image,
-			                  val, NULL);
+		/* Convert coordinates to match rearranged
+		 * panels in memory */
+		fs = fs - p->orig_min_fs + p->min_fs;
+		ss = ss - p->orig_min_ss + p->min_ss;
 
-		}
+		image_add_feature(image->features, fs, ss, image,
+		                  val, NULL);
 
-	} else {
+	}
 
-		hid_t dh, sh;
-		hsize_t size[2];
-		hsize_t max_size[2];
-		int i;
-		float *buf;
-		herr_t r;
-		int tw;
+	return 0;
+}
 
-		dh = H5Dopen2(f->fh, p, H5P_DEFAULT);
-		if ( dh < 0 ) {
-			ERROR("Peak list (%s) not found.\n", p);
-			return 1;
-		}
 
-		sh = H5Dget_space(dh);
-		if ( sh < 0 ) {
-			H5Dclose(dh);
-			ERROR("Couldn't get dataspace for peak list.\n");
-			return 1;
-		}
+int get_peaks(struct image *image, struct hdfile *f, const char *p)
+{
+	hid_t dh, sh;
+	hsize_t size[2];
+	hsize_t max_size[2];
+	int i;
+	float *buf;
+	herr_t r;
+	int tw;
 
-		if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
-			ERROR("Peak list has the wrong dimensionality (%i).\n",
-			H5Sget_simple_extent_ndims(sh));
-			H5Sclose(sh);
-			H5Dclose(dh);
-			return 1;
-		}
+	dh = H5Dopen2(f->fh, p, H5P_DEFAULT);
+	if ( dh < 0 ) {
+		ERROR("Peak list (%s) not found.\n", p);
+		return 1;
+	}
 
-		H5Sget_simple_extent_dims(sh, size, max_size);
+	sh = H5Dget_space(dh);
+	if ( sh < 0 ) {
+		H5Dclose(dh);
+		ERROR("Couldn't get dataspace for peak list.\n");
+		return 1;
+	}
 
-		tw = size[1];
-		if ( (tw != 3) && (tw != 4) ) {
-			H5Sclose(sh);
-			H5Dclose(dh);
-			ERROR("Peak list has the wrong dimensions.\n");
-			return 1;
-		}
+	if ( H5Sget_simple_extent_ndims(sh) != 2 ) {
+		ERROR("Peak list has the wrong dimensionality (%i).\n",
+		H5Sget_simple_extent_ndims(sh));
+		H5Sclose(sh);
+		H5Dclose(dh);
+		return 1;
+	}
 
-		buf = malloc(sizeof(float)*size[0]*size[1]);
-		if ( buf == NULL ) {
-			H5Sclose(sh);
-			H5Dclose(dh);
-			ERROR("Couldn't reserve memory for the peak list.\n");
-			return 1;
-		}
-		r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
-		            H5P_DEFAULT, buf);
-		if ( r < 0 ) {
-			ERROR("Couldn't read peak list.\n");
-			free(buf);
-			return 1;
-		}
+	H5Sget_simple_extent_dims(sh, size, max_size);
 
-		if ( image->features != NULL ) {
-			image_feature_list_free(image->features);
-		}
-		image->features = image_feature_list_new();
+	tw = size[1];
+	if ( (tw != 3) && (tw != 4) ) {
+		H5Sclose(sh);
+		H5Dclose(dh);
+		ERROR("Peak list has the wrong dimensions.\n");
+		return 1;
+	}
 
-		for ( i=0; i<size[0]; i++ ) {
+	buf = malloc(sizeof(float)*size[0]*size[1]);
+	if ( buf == NULL ) {
+		H5Sclose(sh);
+		H5Dclose(dh);
+		ERROR("Couldn't reserve memory for the peak list.\n");
+		return 1;
+	}
+	r = H5Dread(dh, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
+	            H5P_DEFAULT, buf);
+	if ( r < 0 ) {
+		ERROR("Couldn't read peak list.\n");
+		free(buf);
+		return 1;
+	}
 
-			float fs, ss, val;
-			struct panel *p;
+	if ( image->features != NULL ) {
+		image_feature_list_free(image->features);
+	}
+	image->features = image_feature_list_new();
 
-			fs = buf[tw*i+0];
-			ss = buf[tw*i+1];
-			val = buf[tw*i+2];
+	for ( i=0; i<size[0]; i++ ) {
 
-			p = find_orig_panel(image->det, fs, ss);
-			if ( p == NULL ) continue;
-			if ( p->no_index ) continue;
+		float fs, ss, val;
+		struct panel *p;
 
-			/* Convert coordinates to match rearranged panels in memory */
-			fs = fs - p->orig_min_fs + p->min_fs;
-			ss = ss - p->orig_min_ss + p->min_ss;
+		fs = buf[tw*i+0];
+		ss = buf[tw*i+1];
+		val = buf[tw*i+2];
 
-			image_add_feature(image->features, fs, ss, image, val,
-			                  NULL);
+		p = find_orig_panel(image->det, fs, ss);
+		if ( p == NULL ) continue;
+		if ( p->no_index ) continue;
 
-		}
+		/* Convert coordinates to match rearranged panels in memory */
+		fs = fs - p->orig_min_fs + p->min_fs;
+		ss = ss - p->orig_min_ss + p->min_ss;
 
-		free(buf);
-		H5Sclose(sh);
-		H5Dclose(dh);
+		image_add_feature(image->features, fs, ss, image, val,
+		                  NULL);
 
 	}
 
+	free(buf);
+	H5Sclose(sh);
+	H5Dclose(dh);
+
 	return 0;
 }
 
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index 4d7b223c..2988b929 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -3,11 +3,11 @@
  *
  * Read/write HDF5 data files
  *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2009-2012 Thomas White <taw@physics.org>
+ *   2009-2015 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
 
  *
@@ -79,8 +79,10 @@ extern void hdfile_close(struct hdfile *f);
 extern int hdfile_is_scalar(struct hdfile *f, const char *name, int verbose);
 char *hdfile_get_string_value(struct hdfile *f, const char *name,
                               struct event* ev);
-extern int get_peaks(struct image *image, struct hdfile *f, const char *p,
-                     int cxi_format, struct filename_plus_event *fpe);
+extern int get_peaks(struct image *image, struct hdfile *f, const char *p);
+
+extern int get_peaks_cxi(struct image *image, struct hdfile *f, const char *p,
+                         struct filename_plus_event *fpe);
 extern double get_value(struct hdfile *f, const char *name);
 
 extern double get_ev_based_value(struct hdfile *f, const char *name,
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 9900c232..ba724419 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -3,11 +3,11 @@
  *
  * Peak search and other image analysis
  *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2014 Thomas White <taw@physics.org>
+ *   2010-2015 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 4f28aec5..627dfa67 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -97,11 +97,9 @@ static void show_help(const char *s)
 "                           zaef  : Use Zaefferer (2000) gradient detection.\n"
 "                                    This is the default method.\n"
 "                           hdf5  : Get from a table in HDF5 file.\n"
+"                           cxi   : Get from CXI format HDF5 file.\n"
 "     --hdf5-peaks=<p>     Find peaks table in HDF5 file here.\n"
 "                           Default: /processing/hitfinder/peakinfo\n"
-"     --cxi-hdf5-peaks     Peaks in the HDF5 file are in CXI file format.\n"
-"                           Only used in conjunction with the --hdf5-peaks,\n"
-"                           ignored otherwise."
 "     --integration=<meth> Perform final pattern integration using <meth>.\n"
 "\n\n"
 "For more control over the process, you might need:\n\n"
@@ -219,7 +217,6 @@ int main(int argc, char *argv[])
 	iargs.peaks = PEAK_ZAEF;
 	iargs.beam = &beam;
 	iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
-	iargs.cxi_hdf5_peaks = 0;
 	iargs.copyme = NULL;
 	iargs.pk_inn = -1.0;
 	iargs.pk_mid = -1.0;
@@ -271,7 +268,6 @@ int main(int argc, char *argv[])
 		{"no-use-saturated",   0, &iargs.use_saturated,      0},
 		{"no-revalidate",      0, &iargs.no_revalidate,      1},
 		{"check-hdf5-snr",     0, &iargs.check_hdf5_snr,     1},
-		{"cxi-hdf5-peaks",     0, &iargs.cxi_hdf5_peaks,     1},
 
 		/* Long-only options which don't actually do anything */
 		{"no-sat-corr",        0, &iargs.satcorr,            0},
@@ -513,6 +509,8 @@ int main(int argc, char *argv[])
 		iargs.peaks = PEAK_ZAEF;
 	} else if ( strcmp(speaks, "hdf5") == 0 ) {
 		iargs.peaks = PEAK_HDF5;
+	} else if ( strcmp(speaks, "cxi") == 0 ) {
+		iargs.peaks = PEAK_CXI;
 	} else {
 		ERROR("Unrecognised peak detection method '%s'\n", speaks);
 		return 1;
diff --git a/src/process_image.c b/src/process_image.c
index d5133a0c..847cc9f4 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -225,10 +225,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	switch ( iargs->peaks ) {
 
 		case PEAK_HDF5:
-		/* Get peaks from HDF5 */
-
-		if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path,
-		               iargs->cxi_hdf5_peaks, pargs->filename_p_e) ) {
+		if ( get_peaks(&image, hdfile, iargs->hdf5_peak_path) ) {
 			ERROR("Failed to get peaks from HDF5 file.\n");
 		}
 		if ( !iargs->no_revalidate ) {
@@ -239,6 +236,19 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		}
 		break;
 
+		case PEAK_CXI:
+		if ( get_peaks_cxi(&image, hdfile, iargs->hdf5_peak_path,
+		                   pargs->filename_p_e) ) {
+			ERROR("Failed to get peaks from CXI file.\n");
+		}
+		if ( !iargs->no_revalidate ) {
+			validate_peaks(&image, iargs->min_snr,
+				       iargs->pk_inn, iargs->pk_mid,
+		                       iargs->pk_out, iargs->use_saturated,
+				       iargs->check_hdf5_snr);
+		}
+		break;
+
 		case PEAK_ZAEF:
 		search_peaks(&image, iargs->threshold,
 		             iargs->min_gradient, iargs->min_snr,
diff --git a/src/process_image.h b/src/process_image.h
index 53e2c66a..68254485 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -41,6 +41,7 @@
 enum {
 	PEAK_ZAEF,
 	PEAK_HDF5,
+	PEAK_CXI,
 };
 
 
@@ -63,7 +64,6 @@ struct index_args
 	float tols[4];
 	struct beam_params *beam;
 	char *hdf5_peak_path;
-	int cxi_hdf5_peaks;
 	float pk_inn;
 	float pk_mid;
 	float pk_out;