From d9dd0cefca108ec5dc7f08aad4be9b5c2ded4389 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@bitwiz.org.uk>
Date: Sun, 27 Jun 2010 16:55:02 +0200
Subject: indexamajig: Make saturation correction optional and default to off

---
 src/calibrate_detector.c | 2 +-
 src/hdf5-file.c          | 4 ++--
 src/hdf5-file.h          | 2 +-
 src/indexamajig.c        | 8 +++++++-
 src/powder_plot.c        | 2 +-
 src/render.c             | 6 +++---
 6 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index 044cc93d..70b70c71 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -175,7 +175,7 @@ static void *process_image(void *pargsv)
 		return NULL;
 	}
 
-	hdf5_read(hdfile, &image);
+	hdf5_read(hdfile, &image, 1);
 
 	if ( pargs->config_cmfilter ) {
 		filter_cm(&image);
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index a5fc7d26..71ab0354 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -326,7 +326,7 @@ static void debodge_saturation(struct hdfile *f, struct image *image)
 }
 
 
-int hdf5_read(struct hdfile *f, struct image *image)
+int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
 {
 	herr_t r;
 	float *buf;
@@ -379,7 +379,7 @@ int hdf5_read(struct hdfile *f, struct image *image)
 		image->f0_available = 1;
 	}
 
-	debodge_saturation(f, image);
+	if ( satcorr ) debodge_saturation(f, image);
 
 	return 0;
 }
diff --git a/src/hdf5-file.h b/src/hdf5-file.h
index 455628bd..7e662799 100644
--- a/src/hdf5-file.h
+++ b/src/hdf5-file.h
@@ -27,7 +27,7 @@ struct hdfile;
 extern int hdf5_write(const char *filename, const void *data,
                       int width, int height, int type);
 
-extern int hdf5_read(struct hdfile *f, struct image *image);
+extern int hdf5_read(struct hdfile *f, struct image *image, int satcorr);
 
 extern struct hdfile *hdfile_open(const char *filename);
 extern int hdfile_set_image(struct hdfile *f, const char *path);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 89003b34..1e005ceb 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -59,6 +59,7 @@ struct process_args
 	int config_nomatch;
 	int config_unpolar;
 	int config_sanity;
+	int config_satcorr;
 	struct detector *det;
 	IndexingMethod indm;
 	const double *intensities;
@@ -126,6 +127,8 @@ static void show_help(const char *s)
 "      --unpolarized       Don't correct for the polarisation of the X-rays.\n"
 "      --check-sanity      Check that indexed locations approximately correspond\n"
 "                           with detected peaks.\n"
+"      --sat-corr          Correct values of saturated peaks using a table\n"
+"                           included in the HDF5 file.\n"
 "\n\nOptions for greater performance or verbosity:\n\n"
 "      --verbose           Be verbose about indexing.\n"
 "      --gpu               Use the GPU to speed up the simulation.\n"
@@ -288,7 +291,7 @@ static void *process_image(void *pargsv)
 		return result;
 	}
 
-	hdf5_read(hdfile, &image);
+	hdf5_read(hdfile, &image, pargs->config_satcorr);
 
 	if ( config_cmfilter ) {
 		filter_cm(&image);
@@ -409,6 +412,7 @@ int main(int argc, char *argv[])
 	int config_alternate = 0;
 	int config_unpolar = 0;
 	int config_sanity = 0;
+	int config_satcorr = 0;
 	struct detector *det;
 	char *geometry = NULL;
 	IndexingMethod indm;
@@ -449,6 +453,7 @@ int main(int argc, char *argv[])
 		{"prefix",             1, NULL,               'x'},
 		{"unpolarized",        0, &config_unpolar,     1},
 		{"check-sanity",       0, &config_sanity,      1},
+		{"sat-corr",           0, &config_satcorr,     1},
 		{0, 0, NULL, 0}
 	};
 
@@ -609,6 +614,7 @@ int main(int argc, char *argv[])
 		pargs->config_nomatch = config_nomatch;
 		pargs->config_unpolar = config_unpolar;
 		pargs->config_sanity = config_sanity;
+		pargs->config_satcorr = config_satcorr;
 		pargs->cell = cell;
 		pargs->det = det;
 		pargs->indm = indm;
diff --git a/src/powder_plot.c b/src/powder_plot.c
index f0d30553..f721d02e 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -102,7 +102,7 @@ int main(int argc, char *argv[])
 
 	hdfile = hdfile_open(filename);
 	hdfile_set_image(hdfile, "/data/data");
-	hdf5_read(hdfile, &image);
+	hdf5_read(hdfile, &image, 1);
 
 	for ( x=0; x<image.width; x++ ) {
 	for ( y=0; y<image.height; y++ ) {
diff --git a/src/render.c b/src/render.c
index efbbfcb9..faad77dc 100644
--- a/src/render.c
+++ b/src/render.c
@@ -77,7 +77,7 @@ float *render_get_image_binned(DisplayWindow *dw, int binning, float *max)
 		image->features = NULL;
 		image->data = NULL;
 
-		hdf5_read(dw->hdfile, image);
+		hdf5_read(dw->hdfile, image, 1);
 		dw->image_dirty = 0;
 		if ( dw->cmfilter ) filter_cm(image);
 		if ( dw->noisefilter ) filter_noise(image, NULL);
@@ -482,7 +482,7 @@ int render_tiff_fp(DisplayWindow *dw, const char *filename)
 	if ( image == NULL ) return 1;
 	image->features = NULL;
 	image->data = NULL;
-	hdf5_read(dw->hdfile, image);
+	hdf5_read(dw->hdfile, image, 1);
 	if ( dw->cmfilter ) filter_cm(image);
 	if ( dw->noisefilter ) filter_noise(image, NULL);
 
@@ -527,7 +527,7 @@ int render_tiff_int16(DisplayWindow *dw, const char *filename)
 	if ( image == NULL ) return 1;
 	image->features = NULL;
 	image->data = NULL;
-	hdf5_read(dw->hdfile, image);
+	hdf5_read(dw->hdfile, image, 1);
 	if ( dw->cmfilter ) filter_cm(image);
 	if ( dw->noisefilter ) filter_noise(image, NULL);
 
-- 
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