Kick powder_plot out (to crystfel-programs)

4 files changed, 3 insertions, 1370 deletions

diff --git a/.gitignore b/.gitignore
index 30a8bdee..86e2415d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,7 +29,6 @@ src/get_hkl
 src/hdfsee
 src/indexamajig
 src/compare_hkl
-src/powder_plot
 src/render_hkl
 src/partialator
 src/check_hkl
diff --git a/Makefile.am b/Makefile.am
index 8feebadc..bf353e2e 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,10 +1,10 @@
+docdir = ${datadir}/doc/${PACKAGE}
 EXTRA_DIST = configure m4/gnulib-cache.m4
 SUBDIRS = lib doc/reference libcrystfel
 ACLOCAL_AMFLAGS = -I m4
 
 bin_PROGRAMS = src/pattern_sim src/process_hkl src/get_hkl src/indexamajig \
-               src/compare_hkl src/powder_plot \
-               src/partialator src/check_hkl src/partial_sim
+               src/compare_hkl  src/partialator src/check_hkl src/partial_sim
 
 noinst_PROGRAMS = tests/list_check tests/integration_check \
                   tests/pr_gradient_check tests/symmetry_check \
@@ -60,8 +60,6 @@ src_compare_hkl_SOURCES = src/compare_hkl.c
 
 src_check_hkl_SOURCES = src/check_hkl.c
 
-src_powder_plot_SOURCES = src/powder_plot.c
-
 if HAVE_CAIRO
 src_render_hkl_SOURCES = src/render_hkl.c
 endif
@@ -108,8 +106,7 @@ EXTRA_DIST += $(crystfel_DATA)
 man_MANS = doc/man/crystfel.7 doc/man/check_hkl.1 doc/man/compare_hkl.1 \
            doc/man/crystfel_geometry.5 doc/man/get_hkl.1 doc/man/hdfsee.1 \
            doc/man/indexamajig.1 doc/man/partialator.1 doc/man/partial_sim.1 \
-           doc/man/pattern_sim.1 doc/man/powder_plot.1 doc/man/process_hkl.1 \
-           doc/man/render_hkl.1
+           doc/man/pattern_sim.1 doc/man/process_hkl.1 doc/man/render_hkl.1
 
 
 EXTRA_DIST += $(man_MANS)
diff --git a/doc/man/powder_plot.1 b/doc/man/powder_plot.1
deleted file mode 100644
index 6dac163f..00000000
--- a/doc/man/powder_plot.1
+++ /dev/null
@@ -1,159 +0,0 @@
-.\" powder_plot man page
-.\"
-.\" Copyright © 2012 Andrew Aquila <andrew.aquila@cfel.de>
-.\" Copyright © 2012 Thomas White <taw@physics.org>
-.\"
-.\" Part of CrystFEL - crystallography with a FEL
-.\"
-
-.TH POWDER_PLOT 1
-.SH NAME
-powder_plot \- generate 1D powder patterns
-.SH SYNOPSIS
-.PP
-.B powder_plot
-\fB-i\fR \fIinput.hkl\fR | \fB-i\fR \fIinput.h5\fR | \fB-i\fR \fIinput.stream\fR
-\fB-o\fR \fIoutput.dat\fR
-[\fB--min=\fR\fI1/d\fR \fB--max=\fR\fI1/d\fR]
-[\fIoptions\fR\] \fB...\fR
-
-.PP
-.BR powder_plot
-\fB-i\fR \fIfile.hkl\fR [\fIoptions\fR\] \fB...\fR [\fB--use-redundancy\fR] [\fB--no-d-scaling\fR]
-
-.PP
-.BR powder_plot
-\fB-i\fR \fIfile.h5\fR [\fIoptions\fR\] \fB...\fR
-\fB-g\fR \fIgeometry.geom\fR
-\fB-b\fR \fIbeam.beam\fR [\fB--no-sat-corr\fR] [\fB--ring-corr\fR]
-
-.PP
-.BR powder_plot
-\fB-i\fR \fIfile.stream\fR [\fIoptions\fR\] \fB...\fR --data=\fItype\fR
-[-g \fIgeometry.geom\fR] [-b \fIbeam.beam\fR] [\fB--no-sat-corr\fR] [\fB--only-indexed\fR]
-[\fB--use-redundancy\fR] [\fB--ring-corr\fR] [\fB--no-d-scaling\fR]
-
-.PP
-.BR powder_plot
-\fB--help\fR
-
-.SH DESCRIPTION
-
-powder_plot calculates one dimensional powder traces by summing many individual intensities, Bragg peaks or pixels.  Its input can come from a CrystFEL stream (such as that written by "indexamajig"), an reflection list in CrystFEL format (".hkl" format), or an HDF5 file.
-
-The output of powder_plot consists of a three line header followed by a tab-delimited list of six values:
-
- 1/d of the histogram bin, where d is the Bragg law d spacing in meters
- the total number of peaks (N)
- the total intensity in the N peaks
- the mean intensity of the N peaks
- the standard deviation of the distribution
- the standard deviation of the mean of the data
-
-The sigma of the mean is not the same as the sigma of the intensities
-themselves.  The former quantity measures how accurately the mean intensity has
-been determined, whereas the latter quantity measures the spread of the
-intensities.
-
-.SH DATA TYPE OPTIONS WHEN READING FROM A STREAM
-
-When taking input from stream, the d-spacing for a particular intensity can be
-generated in a variety of different ways.  You can choose which one with
-\fB--data=\fR\fItype\fR.  Possibilities for \fItype\fR are:
-.RS
-.IP \fBreflection\fR
-.PD
-Use peak positions from indexed reflections
-.IP \fBhkl\fR
-.PD
-Use the Miller indices from indexed reflections, combined with a unit cell from PDB file provided with -p.
-.IP \fBpeaks\fR
-.PD
-Use peak positions from peak search
-.IP \fBh5\fR
-.PD
-Use all pixels in the HDF5 file, excluding bad regions
-.RE
-.PP
-The default is \fB--data=hkl\fR.
-
-
-.SH HISTOGRAM OPTIONS
-
-You can set the mininum and maximum 1/d values, in units of inverse meters,
-with the options \fB-min=\fR\fIn\fR and \fB--max=\fR\fIn\fR.
-When taking input from peak positions, The default behaviour is to use the entire detector extent from the geometry description file, which you  with the \fB-g\fR flag.
-
-You can also adjust the number of histogram bins with the option --bins=<n>,
-where n is an integer.
-
-Scaling can be set to produce linearly, quadratically or cubically spaced 1/d
-values using \fB--spacing=\fR\fItype\fR.  Possibilities for \fItype\fR are:
-.RS
-.IP \fBlinear\fR
-.PD
-The resolution shells will have equal widths in terms of 1/d.
-.IP \fBwilson\fR
-.PD
-The resolution shells will be quadratically spaced, giving even spacing in a plot against 1/d^2 (a Wilson plot).
-.IP \fBvolume\fR
-.PD
-The resolution shells will all have equal volumes in reciprocal space.
-.RE
-.PP
-The default is \fB--spacing=linear\fR.
-
-.SH OPTIONS FOR MORE CONTROL
-
-.B
-.IP --no-sat-corr
-Don't correct values of saturated peaks using the table included in the HDF5 file.
-See the help for indexamajig for more information.
-
-.B
-.IP --only-indexed
-Use with --data=peaks or h5 if you want to use the peak list of only indexed patterns.
-This is useful for finding differences between patterns which could be indexed and
-those which could not.
-
-.B
-.IP --no-d-scaling
-Do not scale the intensities in the powder plot by d^2.  This should be used when
-creating a powder plot from a reflection list.
-
-.B
-.IP --ring-corr
-Do not correct for the fractional area sampled of the powder ring.  This might be
-useful for detectors with gaps.
-
-.B
-.IP --use-redundancy
-Divide intensities by the number of measurements (the redundancy column in the
-reflection list), and not the number of symmetrical equivalent reflections as the
-number of times a reflection occurs in the powder.
-
-.SH AUTHOR
-This page was written by Andrew Aquila and Thomas White.
-
-.SH REPORTING BUGS
-Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
-
-.SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
-.PD
-.P
-powder_plot, and this manual, are part of CrystFEL.
-.P
-CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-.P
-CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-.P
-You should have received a copy of the GNU General Public License along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
-
-.SH SEE ALSO
-.BR crystfel (7),
-.BR indexamajig (1),
-.BR process_hkl (1),
-.BR check_hkl (1),
-.BR crystfel_geometry (5),
-.BR render_hkl (1) .
diff --git a/src/powder_plot.c b/src/powder_plot.c
deleted file mode 100644
index 7917ccd0..00000000
--- a/src/powder_plot.c
+++ /dev/null
@@ -1,1204 +0,0 @@
-/*
- * powder_plot.c
- *
- * Plot powder patterns
- *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
- * Copyright © 2012 Richard Kirian
- *
- * Authors:
- *   2010-2012 Thomas White <taw@physics.org>
- *   2011-2012 Andrew Aquila <andrew.aquila@cfel.de>
- *   2011      Richard Kirian
- *
- * This file is part of CrystFEL.
- *
- * CrystFEL is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * CrystFEL is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdarg.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <unistd.h>
-#include <getopt.h>
-
-#include "stream.h"
-#include "reflist.h"
-#include "utils.h"
-#include "image.h"
-#include "detector.h"
-#include "index.h"
-#include "hdf5-file.h"
-#include "beam-parameters.h"
-#include "reflist-utils.h"
-#include "symmetry.h"
-#include "cell-utils.h"
-
-
-struct bin_stats {
-	unsigned int N;
-	double total;
-	double mean;
-	double std_dev;
-	double q_min;
-	double q_max;
-	double q_value;
-	double fract;
-};
-
-struct histogram_info {
-	double q_max;
-	double q_min;
-	double q_delta;
-	unsigned int histsize;
-	int spacing; //linear, q^2, & equal volume
-};
-
-enum {
-	PLOT_PEAKS,
-	PLOT_HKL,
-	PLOT_REFL,
-	PLOT_H5
-};
-
-enum {
-	FILE_STREAM,
-	FILE_HKL,
-	FILE_H5
-};
-
-enum {
-	LINEAR,
-	q2,
-	VOLUME
-};
-
-
-static int find_q_bin_index(double q, struct histogram_info *info,
-                            struct bin_stats *hist)
-{
-	/* bisection search alg. find q_bin index of order Log(n) time */
-	int mid;
-	int min = 0;
-	int max = info->histsize-1;
-	if (q < hist[min].q_max) return min;
-	if (q > hist[max].q_min) return max;
-	do {
-		mid = (min + max) / 2;
-		if (q < hist[mid].q_min) {
-			max = mid;
-		} else if (q > hist[mid].q_max){
-			min = mid ;
-		} else {
-			return mid;
-		}
-	} while(max - min > 1);
-	return mid;
-}
-
-
-/* Used for HDF5 files, peak list and stream positions */
-static int add_peak_to_histogram(double fs, double ss, double intensity,
-                                 struct image *image,
-                                 struct histogram_info *info,
-                                 struct bin_stats *hist)
-{
-	struct rvec r;
-	double q, delta;
-	int i;
-
-	r = get_q(image, fs, ss, NULL, 1.0/ image->lambda);
-	q = modulus(r.u, r.v, r.w);
-
-	/* Ignore q value if outside of range */
-	if ( (q<info->q_min) || (q>info->q_max) ) return 1;
-
-	i = find_q_bin_index(q, info, hist);
-
-	/* See Knuth TAOCP vol 2, 3rd ed, pg 232 for running variance */
-	delta = intensity - hist[i].mean;
-	hist[i].N++;
-	hist[i].total += intensity;
-	hist[i].mean = hist[i].mean + delta /hist[i].N;
-	hist[i].std_dev = hist[i].std_dev + (delta *(intensity - hist[i].mean));
-
-	return 0;
-}
-
-
-/* Used for d and hkl of stream files where redundancy = 1 */
-static int add_d_to_histogram(double q, double intensity,
-                              struct histogram_info *info,
-                              struct bin_stats *hist)
-{
-	double delta;
-	int i;
-
-	/* Ignore q value if outside of range */
-	if ( (q<info->q_min) || (q>info->q_max) ) return 1;
-
-	i = find_q_bin_index(q, info, hist);
-
-	delta = intensity - hist[i].mean;
-	hist[i].N++;
-	hist[i].total += intensity;
-	hist[i].mean = hist[i].mean + delta /hist[i].N;
-	hist[i].std_dev = hist[i].std_dev + (delta *(intensity - hist[i].mean));
-
-	return 0;
-}
-
-
-static int add_hkl_to_histogram(double q, double intensity, int redundancy,
-                                int q_scaling, struct histogram_info *info,
-                                struct bin_stats *hist)
-{
-	int i = 0;
-
-	/* Ignore q value if outside of range */
-	if ( (q<info->q_min) || (q>info->q_max) ) {
-		return 1;
-	}
-
-	/* The accounting is the intensity of the reflection times the
-	 * number of occurance of that reflection smeared out over the
-	 * surface area which is 4*pi*q^2  the 4*pi is left out since it is a
-	 * common constant and the total is in arbitrary units.
-	 */
-	for ( i=0; i<redundancy; i++ ) {
-		if ( q_scaling ) {
-			add_d_to_histogram(q, intensity/(q*q), info, hist);
-		} else {
-			add_d_to_histogram(q, intensity, info, hist);
-		}
-	}
-
-	return 0;
-}
-
-
-static int histogram_setup(struct histogram_info *info,
-                           struct bin_stats *histdata)
-{
-	int i;
-	double x;
-
-	if ( info->spacing == LINEAR ) {
-		x = 1.0;
-	} else if ( info->spacing == q2 ) {
-		x = 2.0;
-	} else {
-		x = 3.0;
-	}
-
-	for ( i=0; i<info->histsize; i++ ) {
-
-		double qd, qm;
-
-		histdata[i].N  = 0;
-		histdata[i].total = 0.0;
-		histdata[i].mean = 0.0;
-		histdata[i].std_dev = 0.0;
-		histdata[i].fract = 0.0;
-
-		qd = info->q_delta;
-		qm = info->q_min;
-
-		histdata[i].q_min = pow( (i*qd) + pow(qm, x), 1.0/x);
-
-		histdata[i].q_max = pow( ((i+1.0)*qd) + pow(qm, x), 1.0/x);
-
-		histdata[i].q_value= pow( ((i+0.5)*qd) + pow(qm, x), 1.0/x);
-
-	}
-	return 0;
-}
-
-
-static int ring_fraction_calc(struct histogram_info *info,
-                              struct bin_stats *hist, struct image *image)
-{
-	int fs,ss;
-	int bin;
-
-	/* Check that detector geometry is present and wavelength is valid */
-	if ( (image->det == NULL) || (image->lambda < 0.0) ) return 1;
-
-	/* Loop over all pixels */
-	for ( ss=0; ss<image->height; ss++ ) {
-	for ( fs=0; fs<image->width;  fs++ ) {
-
-		struct panel *p;
-		struct rvec r;
-		int i;
-		double q, q_fs, q_ss;
-
-		r = get_q(image, fs, ss, NULL, 1.0/image->lambda);
-		q = modulus(r.u, r.v, r.w);
-
-		/* If pixel is valid (not a bad pixel and not out of range) */
-		if ( (q>info->q_min) && (q<info->q_max) &&
-		     (in_bad_region(image->det,fs,ss) == 0) ) {
-
-			/* Select the panel, then (sometimes) ask for the q
-			 * of the (corner of the) pixel one step beyond the
-			 * edge, to get the exact size of the required pixel.
-			 */
-			p = find_panel(image->det, fs, ss);
-
-			r = get_q_for_panel(p, (fs+1)-(double)p->min_fs,
-			                       ss-(double)p->min_ss,
-			                       NULL, 1.0/image->lambda);
-			q_fs =  modulus(r.u, r.v, r.w);
-
-			r = get_q_for_panel(p, fs-(double)p->min_fs,
-			                       (ss+1) -(double)p->min_ss,
-			                       NULL, 1.0/image->lambda);
-			q_ss =  modulus(r.u, r.v, r.w);
-
-			i = find_q_bin_index(q, info, hist);
-
-			hist[i].fract = hist[i].fract + fabs((q_fs-q)*(q_ss-q));
-
-		}
-
-	}
-	}
-
-	/* Divide measured area by ring area */
-	for ( bin=0; bin<info->histsize; bin++ ) {
-
-		double inner_area, outer_area, ring_area;
-
-		outer_area = pow(hist[bin].q_max, 2.0);
-		inner_area = pow(hist[bin].q_min, 2.0);
-		ring_area = M_PI*(outer_area - inner_area);
-
-		hist[bin].fract = hist[bin].fract / ring_area;
-
-	}
-
-	return 0;
-}
-
-
-static unsigned int process_h5(struct image *image, struct histogram_info *info,
-                               struct bin_stats *histdata)
-{
-	int fs, ss;
-	double intensity;
-
-	for ( ss=0; ss<image->height; ss++ ) {
-	for ( fs=0; fs<image->width; fs++ ) {
-
-		intensity = image->data[fs + image->width*ss];
-		if ( !in_bad_region(image->det,fs,ss) ) {
-			add_peak_to_histogram(fs, ss, intensity,
-		                              image, info, histdata);
-		}
-	}
-	progress_bar(ss, image->height, "Processing");
-	}
-	return 0;
-}
-
-
-static unsigned int process_hkl(struct image *image, const SymOpList *sym,
-                                UnitCell *cell,
-                                struct histogram_info *info,
-                                struct bin_stats *histdata,
-                                int q_scaling, int use_redundancy)
-{
-	Reflection *refl;
-	RefListIterator *iter;
-	unsigned int i = 0;
-	unsigned int n_peaks = 0;
-	int h, k, l, redundancy;
-	double q, intensity;
-	unsigned int nref;
-	SymOpMask *m;
-
-	m = new_symopmask(sym);
-
-	nref = num_reflections(image->reflections);
-
-	for ( refl = first_refl(image->reflections, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) )
-	{
-		get_indices(refl, &h, &k, &l);
-		intensity = get_intensity(refl);
-		if ( use_redundancy ) {
-			redundancy = get_redundancy(refl);
-		} else {
-			special_position(sym, m, h, k, l);
-			redundancy = num_equivs(sym, m);
-		}
-
-		/* Multiply by 2 to get 1/d (in m^-1) */
-		q = 2.0 * resolution(cell, h, k, l);
-
-		add_hkl_to_histogram(q, intensity, redundancy, q_scaling,
-		                     info, histdata);
-
-		n_peaks += redundancy;
-
-		i++;
-		progress_bar(i, nref, "Processing");
-
-	}
-
-	free_symopmask(m);
-
-	return n_peaks;
-}
-
-
-static unsigned int process_stream_reflection(FILE *fh, struct image *image,
-                                              struct histogram_info *info,
-                                              struct bin_stats *histdata,
-                                              unsigned int *n_patterns)
-{
-	int rval;
-	unsigned int i = 0;
-	unsigned int n_peaks = 0;
-	Reflection *refl;
-	RefListIterator *iter;
-	double intensity, fs_double, ss_double;
-	unsigned int processing_total;
-
-	processing_total = count_patterns(fh);
-	rewind(fh);
-
-	do {
-		/* Get data from next chunk */
-		rval = read_chunk(fh, image);
-		if ( rval ) continue;
-
-		/* Check if the pattern indexed, if so use those peaks */
-		if ( image->reflections != NULL ) {
-
-			(*n_patterns)++;
-			for ( refl = first_refl(image->reflections, &iter);
-			      refl != NULL;
-		      	      refl = next_refl(refl, iter) ) {
-				/* note added fs_double as fs is an int */
-				intensity = get_intensity(refl);
-				get_detector_pos(refl, &fs_double, &ss_double);
-
-				if ( !add_peak_to_histogram(fs_double,
-				                            ss_double,
-				                            intensity,
-				                            image, info,
-				                            histdata) )
-				{
-					n_peaks++;
-				}
-
-			}
-
-		}
-
-		free(image->filename);
-		reflist_free(image->reflections);
-		image_feature_list_free(image->features);
-		cell_free(image->indexed_cell);
-
-		i++;
-		progress_bar(i, processing_total, "Processing");
-
-	} while ( rval == 0 );
-
-	return n_peaks;
-}
-
-
-static unsigned int process_stream_hkl(FILE *fh, struct image *image,
-                                       struct histogram_info *info,
-                                       struct bin_stats *histdata,
-                                       UnitCell *cell, unsigned int *n_patterns)
-{
-	int rval;
-	unsigned int i = 0;
-	unsigned int n_peaks = 0;
-	Reflection *refl;
-	RefListIterator *iter;
-	double intensity, q;
-	unsigned int processing_total;
-
-	processing_total = count_patterns(fh);
-	rewind(fh);
-
-	do {
-
-		/* Get data from next chunk */
-		rval = read_chunk(fh, image);
-		if ( rval ) continue;
-		if ( image->reflections != NULL ) {
-
-			(*n_patterns)++;
-
-			for ( refl = first_refl(image->reflections, &iter);
-		      	      refl != NULL;
-			      refl = next_refl(refl, iter) )
-			{
-				int h, k, l;
-
-				get_indices(refl, &h, &k, &l);
-				intensity = get_intensity(refl);
-				q = 2.0 * resolution(cell, h, k, l);
-
-				if ( !add_d_to_histogram(q, intensity, info,
-				                         histdata) ) n_peaks++;
-			}
-		}
-
-		free(image->filename);
-		reflist_free(image->reflections);
-		image_feature_list_free(image->features);
-		cell_free(image->indexed_cell);
-
-		i++;
-		progress_bar(i, processing_total, "Processing");
-
-	} while ( rval == 0 );
-
-	return n_peaks;
-}
-
-
-static int add_features_to_histogram(struct image *image,
-                                     struct histogram_info *info,
-                                     struct bin_stats *histdata)
-{
-	int j;
-	int n_peaks;
-
-	n_peaks = 0;
-	for ( j=0; j<image_feature_count(image->features); j++) {
-
-		struct imagefeature *f;
-
-		f = image_get_feature(image->features, j);
-		if ( !f->valid ) continue;
-
-		if ( !in_bad_region(image->det, f->fs,f->ss) ) {
-
-			int r;
-
-			r = add_peak_to_histogram(f->fs, f->ss, f->intensity,
-			                          image, info, histdata);
-
-			if ( !r ) n_peaks++;
-
-		}
-
-	}
-
-	return n_peaks;
-}
-
-
-static unsigned int process_stream_peaks(FILE *fh, struct image *image,
-                                         struct histogram_info *info,
-                                         struct bin_stats *histdata,
-                                         unsigned int *n_patterns,
-                                         int only_indexed)
-{
-	int rval;
-	unsigned int i = 0;
-	unsigned int n_peaks = 0;
-	unsigned int processing_total;
-
-	processing_total = count_patterns(fh);
-	rewind(fh);
-
-	do {
-
-		/* Get data from next chunk */
-		rval = read_chunk(fh, image);
-		if ( rval ) continue;
-
-		if ( image->features != NULL ) {
-
-			if ( (!only_indexed)
-			  || ( only_indexed && (image->reflections != NULL)) )
-			{
-				(*n_patterns)++;
-				n_peaks += add_features_to_histogram(image,
-				                                     info,
-				                                     histdata);
-			}
-		}
-
-		free(image->filename);
-		reflist_free(image->reflections);
-		image_feature_list_free(image->features);
-		cell_free(image->indexed_cell);
-
-		i++;
-		progress_bar(i, processing_total, "Processing");
-
-	} while ( rval == 0 );
-
-	return n_peaks;
-}
-
-
-static unsigned int process_stream_h5(FILE *fh, struct image *image,
-                                      struct histogram_info *info,
-                                      struct bin_stats *histdata,
-                                      int config_satcorr, int only_indexed,
-                                      unsigned int *n_patterns,
-                                      const char *element)
-{
-	int fs, ss, rval;
-	double intensity;
-	unsigned int i = 0;
-	unsigned int n_peaks = 0;
-	struct hdfile *hdfile = NULL;
-	unsigned int processing_total;
-
-	processing_total = count_patterns(fh);
-	rewind(fh);
-
-	do {
-
-		/* Get data from next chunk */
-		rval = read_chunk(fh, image);
-		if ( rval ) continue;
-		if ( !only_indexed ||
-		   ( only_indexed && (image->reflections != NULL) ) )
-		{
-			hdfile = hdfile_open(image->filename);
-			if ( element != NULL ) {
-				int r;
-				r = hdfile_set_image(hdfile, element);
-				if ( r ) {
-					ERROR("Couldn't select path '%s'\n",
-					     element);
-					hdfile_close(hdfile);
-					return 0;
-				}
-			} else {
-				int r;
-				r = hdfile_set_first_image(hdfile, "/");
-				if ( r ) {
-					ERROR("Couldn't select first path\n");
-					hdfile_close(hdfile);
-					return 0;
-				}
-
-			}
-			hdf5_read(hdfile, image, config_satcorr);
-			hdfile_close(hdfile);
-			n_patterns++;
-			for ( ss=0; ss<image->height; ss++ ) {
-			for ( fs=0; fs<image->width;  fs++ ) {
-
-				intensity = image->data[fs + image->width*ss];
-				if ( !in_bad_region(image->det,fs,ss) ) {
-
-					add_peak_to_histogram(fs, ss, intensity,
-					                      image, info,
-					                      histdata);
-
-				}
-
-			}
-			}
-		}
-
-		free(image->data);
-		free(image->filename);
-		reflist_free(image->reflections);
-		image_feature_list_free(image->features);
-		cell_free(image->indexed_cell);
-
-		i++;
-		progress_bar(i, processing_total, "Processing");
-
-	} while ( rval == 0 );
-
-	return n_peaks;
-}
-
-
-static void show_help(const char *s)
-{
-	printf("Syntax: %s [options]\n\n", s);
-	printf(
-"Plot a powder pattern as a 1D graph using the detector geometry.\n"
-"\n"
-"  -h, --help              Display this help message.\n"
-"  -i, --input=<file>      Input filename. (*.stream, *.hkl, or *.h5)\n"
-"  -o, --output=<file>     Output filename. Default: stdout.\n"
-"  -g. --geometry=<file>   Get detector geometry from <file>.\n"
-"  -b, --beam=<file>       Get beam parameters (wavelength) from <file>.\n"
-"  -p, --pdb=<file>        Get unit cell from PDB file. (.hkl files only)\n"
-"  -y, --symmetry=<sym>    The symmetry of crystal (.hkl files only)\n"
-"  -s, --bins=n            Makes histogram with n bins (default is 100).\n"
-"      --spacing=<type>    Use 'type' to select the 1/d spacing.\n"
-"                          Choose from:\n"
-"                            linear      : linear (default)\n"
-"                            wilson      : even spacing in Wilson plots\n"
-"                            volume      : constant volume\n"
-"      --max=n             The maximum 1/d to be considered in plot.\n"
-"      --min=n             The minimum 1/d to be considered in plot.\n"
-"  -d, --data=<type>       Use to select the kind of stream data in histogram.\n"
-"                          Choose from:\n"
-"                            reflection  : uses peak positons from indexed\n"
-"                                          reflection \n"
-"                            hkl         : uses the hkl list from indexed\n"
-"                                          reflections (requires pdb file)\n"
-"                            peaks       : uses all peaks found from peak\n"
-"                                          search\n"
-"                            h5          : all points in h5, excluding bad\n"
-"                                          regions\n"
-"                          The default is 'hkl'.\n"
-"     --no-sat-corr        Don't correct values of saturated peaks using a\n"
-"                            table included in the HDF5 file.\n"
-"     --only-indexed       Use with -data=peaks or h5 if you want to use the\n"
-"                            peak list of only indexed patterns\n"
-"     --no-d-scaling       Use with .hkl files if you want to not scale the\n"
-"                            powder by d^2\n"
-"     --ring-corr          Use if you want to scale the powder plot to\n"
-"                            correct for the fractional area sampled of the\n"
-"                            powder ring\n"
-"     --use-redundancy     Use with .hkl files if you want to use the number\n"
-"                            of measurements and not the number of symetrical\n"
-"                            equivelent reflections as the number of time a\n"
-"                            reflection occurs in the powder\n"
-" -e, --image=<element>    Use this image when reading an HDF5 file.\n"
-"                           Example: /data/data0.\n"
-"                           Default: The first one found.\n"
-"\n");
-}
-
-
-static void rlim_bailout()
-{
-	ERROR("Unable to automatically determine the resolution limits.\n");
-	ERROR("Try again with --min and --max.\n");
-	exit(1);
-}
-
-
-int main(int argc, char *argv[])
-{
-	FILE *fh = NULL;
-	UnitCell *cell = NULL;
-	struct image image;
-	struct hdfile *hdfile = NULL;
-	struct bin_stats *histdata = NULL;
-	struct histogram_info hist_info;
-	SymOpList *sym;
-
-	/* Default settings */
-	hist_info.histsize =  100;
-	hist_info.q_min    = -1.0;
-	hist_info.q_max    = -1.0;
-	hist_info.spacing  = LINEAR;
-	image.lambda = -1.0;
-	image.beam = NULL;
-	image.det  = NULL;
-	char *element = NULL;
-
-	unsigned int n_patterns = 0;
-	unsigned int n_peaks    = 0;
-
-	int c, file_type, data_type;
-	int config_satcorr = 1;
-	int need_geometry  = 0;
-	int need_beam      = 0;
-	int need_pdb       = 0;
-	int only_indexed   = 0;
-	int q_scaling      = 1;
-	int ring_corr      = 0;
-	int use_redundancy = 0;
-	unsigned int i;
-
-	char *filename = NULL;
-	char *geometry = NULL;
-	char *beamf    = NULL;
-	char *pdb      = NULL;
-	char *output   = NULL;
-	char *datatype = NULL;
-	char *sym_str  = NULL;
-
-	/* Long options */
-	const struct option longopts[] = {
-		{"help",               0, NULL,               'h'},
-		{"input",              1, NULL,               'i'},
-		{"output",             1, NULL,               'o'},
-		{"geometry",           1, NULL,               'g'},
-		{"beam",               1, NULL,               'b'},
-		{"pdb",                1, NULL,               'p'},
-		{"symmetry",           1, NULL,               'y'},
-		{"bins",               1, NULL,               's'},
-		{"max",                1, NULL,                1 },
-		{"min",                1, NULL,                2 },
-		{"spacing",            1, NULL,                3 },
-		{"no-sat-corr",        0, &config_satcorr,     0 },
-		{"sat-corr",           0, &config_satcorr,     1 },
-		{"only-indexed",       0, &only_indexed,       1 },
-		{"no-d-scaling",       0, &q_scaling,          0 },
-		{"ring-corr",          0, &ring_corr,          1 },
-		{"use-redundancy",     0, &use_redundancy,     1 },
-		{"data",               1, NULL,               'd'},
-		{"image",              1, NULL,               'e'},
-		{0, 0, NULL, 0}
-	};
-
-	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:o:g:b:p:y:s:e:d:",
-	        longopts, NULL)) != -1)
-	{
-
-		switch (c) {
-
-			case 'h' :
-			show_help(argv[0]);
-			return 0;
-
-			case 'i' :
-			filename = strdup(optarg);
-			break;
-
-			case 'o' :
-			output = strdup(optarg);
-			break;
-
-			case 'g' :
-			geometry = strdup(optarg);
-			break;
-
-			case 'b' :
-			beamf = strdup(optarg);
-			break;
-
-			case 'p' :
-			pdb = strdup(optarg);
-			break;
-
-			case 'y' :
-			sym_str = strdup(optarg);
-			break;
-
-			case 's' :
-			hist_info.histsize = atoi(optarg);
-			break;
-
-			case 'e' :
-			element = strdup(optarg);
-			break;
-
-			case 1 :
-			hist_info.q_max = atof(optarg);
-			break;
-
-			case 2 :
-			hist_info.q_min = atof(optarg);
-			break;
-
-			case 3 :
-			if (strcmp(optarg, "linear") == 0 ) {
-				hist_info.spacing = LINEAR;
-			} else if (strcmp(optarg, "wilson") == 0 ) {
-				hist_info.spacing = q2;
-			} else if (strcmp(optarg, "volume") == 0) {
-				hist_info.spacing = VOLUME;
-			} else {
-				ERROR("Invalid spacing type: '%s'\n", optarg);
-				return 1;
-			}
-			break;
-
-			case 'd' :
-			datatype = strdup(optarg);
-			break;
-
-			case 0 :
-			break;
-
-			default :
-			ERROR("Unhandled option '%c'\n", c);
-			break;
-		}
-
-	}
-
-	/* Process input file type */
-	if ( filename == NULL ) {
-
-		ERROR("You must specify the input filename with -i\n");
-		return 1;
-
-	}
-
-	if ( is_stream(filename) == 1 ) {
-
-		file_type = FILE_STREAM;
-
-	} else if ( H5Fis_hdf5(filename) > 0 ) {
-
-		file_type = FILE_H5;
-		need_geometry = 1;
-
-	} else {
-
-		image.reflections = read_reflections(filename);
-
-		if ( image.reflections != NULL ) {
-			file_type = FILE_HKL;
-			need_pdb = 1;
-			need_geometry = 0;
-			need_beam = 0;
-			image.lambda = 0.0;
-		} else {
-			ERROR("Couldn't recognise %s as reflection list,"
-			      " stream or image.\n", filename);
-			return 1;
-		}
-
-	}
-
-	if ( datatype == NULL ) {
-		data_type = PLOT_HKL;
-		if ((hist_info.q_min < 0.0) || (hist_info.q_max < 0.0)) {
-			need_geometry = 1;
-		}
-		need_pdb = 1;
-
-	} else if ( strcmp(datatype, "reflection") == 0 ) {
-		data_type = PLOT_REFL;
-		need_geometry = 1;
-
-	} else if ( strcmp(datatype, "hkl") == 0 ) {
-		data_type = PLOT_HKL;
-		need_pdb = 1;
-
-	} else if ( strcmp(datatype, "peaks") == 0 ) {
-		data_type = PLOT_PEAKS;
-		need_geometry = 1;
-
-	} else if ( strcmp(datatype, "h5") == 0 ) {
-		data_type = PLOT_H5;
-		need_geometry = 1;
-
-	} else {
-
-		ERROR("Failed to read data plot type: '%s'\n", datatype);
-		return 1;
-	}
-
-	/* doubt this is needed, but double check just in case */
-	if ( file_type == FILE_HKL ) {
-		need_geometry = 0;
-		need_beam = 0;
-	}
-
-	/* Logic checks */
-	if ( need_geometry && (image.lambda < 0.0) ) {
-		need_beam = 1;
-	}
-	if ( hist_info.histsize <= 0 ) {
-		ERROR("You need to specify a histogram with more then 0 "
-                      "bins\n");
-		return 1;
-	}
-
-	/* Get geometry, beam and pdb files and parameters as needed */
-	if ( need_geometry ) {
-		if ( geometry == NULL ) {
-			ERROR("You need to specify a geometry file with "
-		              "--geometry\n");
-			return 1;
-		} else {
-			image.det = get_detector_geometry(geometry);
-			if ( image.det == NULL ) {
-				ERROR("Failed to read detector geometry "
-				      "from '%s'\n", geometry);
-				return 1;
-			}
-			image.width  = image.det->max_fs;
-			image.height = image.det->max_ss;
-		}
-	}
-	free(geometry);
-
-	/* Open files to get wavelength if it exists & camera length
-	   if they are not found in the geometry file */
-	if (file_type == FILE_STREAM) {
-		fh = fopen(filename, "r");
-		if ( fh == NULL ) {
-			ERROR("Failed to open input file\n");
-			return 1;
-		}
-		/* Use wavelength from first chunk */
-		read_chunk(fh, &image);
-		rewind(fh);
-	} else if (file_type == FILE_H5) {
-		hdfile = hdfile_open(filename);
-		if ( element != NULL ) {
-			int r;
-			r = hdfile_set_image(hdfile, element);
-			if ( r ) {
-				ERROR("Couldn't select path '%s'\n",
-				     element);
-				hdfile_close(hdfile);
-				return 0;
-			}
-		} else {
-			int r;
-			r = hdfile_set_first_image(hdfile, "/");
-			if ( r ) {
-				ERROR("Couldn't select first path\n");
-				hdfile_close(hdfile);
-				return 0;
-			}
-
-		}
-		hdf5_read(hdfile, &image, config_satcorr);
-		hdfile_close(hdfile);
-	}
-	free(filename);
-
-	/* Logic checks */
-	if ( need_geometry && (image.lambda < 0.0) ) {
-		need_beam = 1;
-	}
-	if ( hist_info.histsize <= 0 ) {
-		ERROR("You need to specify a histogram with more then 0 "
-                      "bins\n");
-		return 1;
-	}
-
-	if ( need_beam ) {
-
-		if ( beamf == NULL ) {
-			ERROR("No wavelength in file, so you need to specify "
-			      "a beam parameters file with --beam\n");
-			return 1;
-		} else {
-			image.beam = get_beam_parameters(beamf);
-			if ( image.beam == NULL ) {
-				ERROR("Failed to read beam from '%s'\n",
-				      beamf);
-				return 1;
-			}
-			image.lambda = ph_en_to_lambda(eV_to_J(
-			                 image.beam->photon_energy));
-		}
-
-	}
-	free(beamf);
-
-	if ( need_pdb ) {
-
-		if (pdb == NULL) {
-			ERROR("You need to specify a pdb file with --pdb.\n");
-			return 1;
-		} else {
-			cell = load_cell_from_pdb(pdb);
-			if ( cell == NULL ) {
-				ERROR("Couldn't read unit cell (from %s)\n",
-				       pdb);
-				return 1;
-			}
-		}
-	}
-	free(pdb);
-
-	if ( sym_str == NULL ) {
-		sym_str = strdup("1");
-	}
-	sym = get_pointgroup(sym_str);
-	free(sym_str);
-
-	/* Set up histogram info*/
-	if ( file_type == FILE_HKL || data_type == PLOT_HKL) {
-		/* get q range from Miller indices in hkl
-		   file. */
-		if ((hist_info.q_min < 0.0) && (hist_info.q_max < 0.0)) {
-			if ( image.reflections == NULL ) rlim_bailout();
-			resolution_limits(image.reflections, cell,
-		                  &hist_info.q_min, &hist_info.q_max);
-		} else if (hist_info.q_min < 0.0) {
-			double dummy;
-			if ( image.reflections == NULL ) rlim_bailout();
-			resolution_limits(image.reflections, cell,
-		                  &hist_info.q_min, &dummy);
-		} else if (hist_info.q_max < 0.0) {
-			double dummy;
-			if ( image.reflections == NULL ) rlim_bailout();
-			resolution_limits(image.reflections, cell,
-		                  &dummy, &hist_info.q_max);
-		}
-	} else {
-		if ( hist_info.q_min < 0.0 ) {
-			hist_info.q_min = smallest_q(&image);
-		}
-		if ( hist_info.q_max < 0.0 ) {
-			hist_info.q_max = largest_q(&image);
-		}
-	}
-
-	if ( hist_info.q_min >= hist_info.q_max ) {
-		ERROR("the minimum 1/d value (%e) "
-	              "is greater then your max 1/d value (%e).\n",
-                      hist_info.q_min, hist_info.q_max);
-		return 1;
-	}
-
-	if ( hist_info.spacing == LINEAR) {
-		hist_info.q_delta = (hist_info.q_max - hist_info.q_min)/
-		                    hist_info.histsize;
-	} else if ( hist_info.spacing == q2) {
-		hist_info.q_delta = (pow(hist_info.q_max, 2.0) -
-		                     pow(hist_info.q_min, 2.0)) /
-		                     hist_info.histsize;
-	} else {  //by default must be in VOLUME
-		hist_info.q_delta = (pow(hist_info.q_max, 3.0) -
-		                     pow(hist_info.q_min, 3.0)) /
-		                     hist_info.histsize;
-	}
-	/* Set up histogram data */
-	histdata = malloc((hist_info.histsize) * sizeof(struct bin_stats));
-	histogram_setup(&hist_info, histdata);
-
-	/* Set up ring scaling */
-	if ( ring_corr ) {
-
-		if ( ring_fraction_calc(&hist_info, histdata, &image) ) {
-
-			ERROR("Detector geometry is required to correct for"
-			      " finite ring area.\n");
-			return 1;
-		}
-	}
-
-	/* Process reflections based on file type and data type */
-	switch ( file_type ) {
-		case FILE_H5 :
-		n_patterns++;
-		n_peaks = process_h5(&image, &hist_info, histdata);
-		free(image.data);
-		break;
-
-		case FILE_HKL :
-		n_patterns++; //inc number of patterns used
-		n_peaks = process_hkl(&image, sym, cell, &hist_info, histdata,
-                                      q_scaling, use_redundancy);
-		break;
-
-		case FILE_STREAM :
-		switch ( data_type ) {
-
-			case PLOT_REFL :
-			n_peaks = process_stream_reflection(fh, &image,
-			             &hist_info, histdata, &n_patterns);
-			break;
-
-			case PLOT_HKL :
-			n_peaks = process_stream_hkl(fh, &image, &hist_info,
-
-				     histdata, cell, &n_patterns);
-			break;
-			case PLOT_PEAKS :
-			n_peaks = process_stream_peaks(fh, &image, &hist_info,
-			             histdata, &n_patterns, only_indexed);
-			break;
-
-			case PLOT_H5 :
-			n_peaks =  process_stream_h5(fh, &image, &hist_info,
-			             histdata, config_satcorr, only_indexed,
-			             &n_patterns, element);
-			break;
-
-			default :
-			break;
-		}
-		fclose(fh);
-		break;
-
-		default :
-		break;
-
-	}
-
-	/* Sqrt the variance to get the std_dev */
-	for( i=0; i<hist_info.histsize; i++ ) {
-		if (histdata[i].N > 1) {
-			histdata[i].std_dev = sqrt(histdata[i].std_dev/
-			                          (histdata[i].N-1));
-		}
-	}
-	if ( ring_corr ) {
-		for( i=0; i<hist_info.histsize; i++ ) {
-			histdata[i].N       = histdata[i].N      /
-			                      histdata[i].fract;
-			histdata[i].total   = histdata[i].total  /
-			                      histdata[i].fract;
-			histdata[i].mean    = histdata[i].mean   /
-			                      histdata[i].fract;
-			histdata[i].std_dev = histdata[i].total  /
-			                      histdata[i].fract;
-		}
-	}
-
-	/* Print out the results */
-	if ( output != NULL ) {
-		fh = fopen(output, "w");
-		if ( fh == NULL ) {
-			ERROR("Failed to open output file\n");
-			return 1;
-		}
-	} else {
-		fh = stdout;
-	}
-
-	/* Print header */
-	fprintf(fh, "Command line:");
-	for ( i=0; i<argc; i++ ) {
-		fprintf(fh, " %s", argv[i]);
-	}
-	fprintf(fh, "\n");
-	fprintf(fh, "I read %i patterns with %i peaks\n", n_patterns, n_peaks);
-	fprintf(fh, "1/d(m^-1)\tN\ttotal\tmean\tstd dev\t std dev of mean\n");
-
-	for( i=0; i<hist_info.histsize; i++ ) {
-		fprintf(fh, "%5e\t%i\t%5e\t%5e\t%5e\t%5e\n",
-		        histdata[i].q_min, histdata[i].N,
-		        histdata[i].total, histdata[i].mean,
-		        histdata[i].std_dev,
-		        histdata[i].std_dev/sqrt(histdata[i].N));
-	}
-
-	if ( cell != NULL ) cell_free(cell);
-	if ( image.det  != NULL ) free(image.det);
-	if ( image.beam != NULL ) free(image.beam);
-	fclose(fh);
-	free(histdata);
-
-	return 0;
-}