From 9da7f1b3f6a4245eb0c35fb32d32c60d60538eb2 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 16 Dec 2020 16:01:58 +0100
Subject: Add flag_{lessthan,morethan,equal} in geometry file

This makes handling Pilatus/Eiger files, as well as many others, much
easier.
---
 libcrystfel/src/datatemplate.c      | 35 ++++++++++++++++++++++++++++
 libcrystfel/src/datatemplate_priv.h | 13 +++++++++++
 libcrystfel/src/image.c             | 46 +++++++++++++++++++++++++++++++++++--
 3 files changed, 92 insertions(+), 2 deletions(-)

(limited to 'libcrystfel')

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index 76a61893..18b09c12 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -466,6 +466,25 @@ int set_dim(struct panel_template *panel, int dimension,
 }
 
 
+static int add_flag_value(struct panel_template *p,
+                          float val,
+                          enum flag_value_type type)
+{
+	int i;
+
+	for ( i=0; i<MAX_FLAG_VALUES; i++ ) {
+		if ( p->flag_types[i] == FLAG_NOTHING ) {
+			p->flag_types[i] = type;
+			p->flag_values[i] = val;
+			return 0;
+		}
+	}
+
+	ERROR("Too many flag values.\n");
+	return 1;
+}
+
+
 static int parse_field_for_panel(struct panel_template *panel, const char *key,
                                  const char *val, DataTemplate *det)
 {
@@ -531,6 +550,20 @@ static int parse_field_for_panel(struct panel_template *panel, const char *key,
 		panel->pixel_pitch = 1.0/atof(val);
 	} else if ( strcmp(key, "max_adu") == 0 ) {
 		panel->max_adu = atof(val);
+
+	} else if ( strcmp(key, "flag_equal") == 0 ) {
+		if ( add_flag_value(panel, atof(val), FLAG_EQUAL) ) {
+			reject = -1;
+		}
+	} else if ( strcmp(key, "flag_lessthan") == 0 ) {
+		if ( add_flag_value(panel, atof(val), FLAG_LESSTHAN) ) {
+			reject = -1;
+		}
+	} else if ( strcmp(key, "flag_morethan") == 0 ) {
+		if ( add_flag_value(panel, atof(val), FLAG_MORETHAN) ) {
+			reject = -1;
+		}
+
 	} else if ( strcmp(key, "badrow_direction") == 0 ) {
 		ERROR("WARNING 'badrow_direction' is ignored in this version.\n");
 	} else if ( strcmp(key, "no_index") == 0 ) {
@@ -915,6 +948,8 @@ DataTemplate *data_template_new_from_string(const char *string_in)
         defaults.clen_for_centering = NAN;
 	defaults.adu_scale = NAN;
 	defaults.adu_scale_unit = ADU_PER_PHOTON;
+	for ( i=0; i<MAX_FLAG_VALUES; i++ ) defaults.flag_values[i] = 0;
+	for ( i=0; i<MAX_FLAG_VALUES; i++ ) defaults.flag_types[i] = FLAG_NOTHING;
 	defaults.max_adu = +INFINITY;
 	defaults.mask = NULL;
 	defaults.mask_file = NULL;
diff --git a/libcrystfel/src/datatemplate_priv.h b/libcrystfel/src/datatemplate_priv.h
index 9d4f8f26..593ebaa8 100644
--- a/libcrystfel/src/datatemplate_priv.h
+++ b/libcrystfel/src/datatemplate_priv.h
@@ -55,6 +55,15 @@ enum wavelength_unit
 	WAVELENGTH_PHOTON_EV
 };
 
+#define MAX_FLAG_VALUES (16)
+
+enum flag_value_type
+{
+	FLAG_NOTHING,
+	FLAG_EQUAL,
+	FLAG_MORETHAN,
+	FLAG_LESSTHAN
+};
 
 /* Special values for dimension IDs */
 #define DIM_FS (-1)
@@ -107,6 +116,10 @@ struct panel_template
 	/** Treat pixel as unreliable if higher than this */
 	double max_adu;
 
+	/** Pixels with exactly this value will be marked as bad */
+	enum flag_value_type flag_types[MAX_FLAG_VALUES];
+	signed int flag_values[MAX_FLAG_VALUES];
+
 	/** Location of data in file (possibly with placeholders) */
 	char *data;
 
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 2b609e51..d50bcf43 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -36,6 +36,7 @@
 #include <math.h>
 #include <stdio.h>
 #include <sys/stat.h>
+#include <fenv.h>
 
 #include "image.h"
 #include "utils.h"
@@ -629,6 +630,36 @@ static void set_image_parameters(struct image *image,
 }
 
 
+static int flag_value(float pixel, struct panel_template *p)
+{
+	int i;
+	for ( i=0; i<MAX_FLAG_VALUES; i++ ) {
+
+		float fv = p->flag_values[i];
+
+		switch ( p->flag_types[i] ) {
+
+			case FLAG_NOTHING:
+			break;
+
+			case FLAG_LESSTHAN:
+			if ( pixel < fv ) return 1;
+			break;
+
+			case FLAG_MORETHAN:
+			if ( pixel > fv ) return 1;
+			break;
+
+			case FLAG_EQUAL:
+			if ( rint(pixel) == fv) return 1;
+			break;
+
+		}
+	}
+	return 0;
+}
+
+
 static int create_badmap(struct image *image,
                          const DataTemplate *dtempl,
                          int no_mask_data)
@@ -665,17 +696,28 @@ static int create_badmap(struct image *image,
 
 		/* Add bad regions (skip if panel is bad anyway) */
 		if ( !p->bad ) {
+
 			int fs, ss;
+			fenv_t envp;
+
+			fegetenv(&envp);
+			fesetround(1);  /* Round to nearest
+			                 * (for flag_value) */
+
 			for ( fs=0; fs<p_w; fs++ ) {
 			for ( ss=0; ss<p_h; ss++ ) {
+				float val = image->dp[i][fs+ss*p_w];
 				if ( data_template_in_bad_region(dtempl, i, fs, ss)
-				     || isnan(image->dp[i][fs+ss*p_w])
-				     || isinf(image->dp[i][fs+ss*p_w]) )
+				  || isnan(val)
+				  || isinf(val)
+				  || flag_value(val, p) )
 				{
 					image->bad[i][fs+ss*p_w] = 1;
 				}
 			}
 			}
+
+			fesetenv(&envp);
 		}
 
 		/* Load mask (skip if panel is bad anyway) */
-- 
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