Add image_create_for_simulation()

...and factorise common code

5 files changed, 144 insertions, 164 deletions

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index 5941109e..43313441 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -1383,107 +1383,6 @@ void data_template_add_copy_header(DataTemplate *dt,
 }
 
 
-static double unit_string_to_unit(const char *str)
-{
-	if ( strcmp(str, "mm") == 0 ) return 1e-3;
-	if ( strcmp(str, "m") == 0 ) return 1.0;
-	ERROR("Invalid length unit '%s'\n", str);
-	return NAN;
-}
-
-
-static double dt_get_length(const char *from)
-{
-	double units;
-	char *sp;
-	char *fromcpy;
-	double val;
-	char *rval;
-
-	if ( from == NULL ) return NAN;
-
-	fromcpy = strdup(from);
-	if ( fromcpy == NULL ) return NAN;
-
-	sp = strchr(fromcpy, ' ');
-	if ( sp == NULL ) {
-		units = 1.0e-3;
-	} else {
-		units = unit_string_to_unit(sp+1);
-	}
-
-	sp[0] = '\0';
-	val = strtod(fromcpy, &rval);
-	if ( !( (*rval == '\0') && (rval != fromcpy)) ) {
-		ERROR("Invalid length value: %s\n", fromcpy);
-		free(fromcpy);
-		return NAN;
-	}
-
-	return val * units;
-}
-
-
-/* If possible, i.e. if there are no references to image headers in
- * 'dt', generate a detgeom structure from it.
- *
- * NB This is probably not the function you're looking for!
- * The detgeom structure should normally come from loading an image,
- * reading a stream or similar.  This function should only be used
- * when there is really no data involved, e.g. in make_pixelmap.
- */
-struct detgeom *data_template_to_detgeom(const DataTemplate *dt)
-{
-	struct detgeom *detgeom;
-	int i;
-
-	if ( dt == NULL ) return NULL;
-
-	detgeom = malloc(sizeof(struct detgeom));
-	if ( detgeom == NULL ) return NULL;
-
-	detgeom->panels = malloc(dt->n_panels*sizeof(struct detgeom_panel));
-	if ( detgeom->panels == NULL ) return NULL;
-
-	detgeom->n_panels = dt->n_panels;
-
-	for ( i=0; i<dt->n_panels; i++ ) {
-
-		detgeom->panels[i].name = safe_strdup(dt->panels[i].name);
-
-		detgeom->panels[i].pixel_pitch = dt->panels[i].pixel_pitch;
-
-		/* NB cnx,cny are in pixels, cnz is in m */
-		detgeom->panels[i].cnx = dt->panels[i].cnx;
-		detgeom->panels[i].cny = dt->panels[i].cny;
-		detgeom->panels[i].cnz = dt_get_length(dt->panels[i].cnz_from);
-
-		/* Apply offset (in m) and then convert cnz from
-		 * m to pixels */
-		detgeom->panels[i].cnz += dt->panels[i].cnz_offset;
-		detgeom->panels[i].cnz /= detgeom->panels[i].pixel_pitch;
-
-		detgeom->panels[i].max_adu = dt->panels[i].max_adu;
-		detgeom->panels[i].adu_per_photon = 1.0;  /* FIXME ! */
-
-		detgeom->panels[i].w = dt->panels[i].orig_max_fs
-		                        - dt->panels[i].orig_min_fs + 1;
-		detgeom->panels[i].h = dt->panels[i].orig_max_ss
-		                        - dt->panels[i].orig_min_ss + 1;
-
-		detgeom->panels[i].fsx = dt->panels[i].fsx;
-		detgeom->panels[i].fsy = dt->panels[i].fsy;
-		detgeom->panels[i].fsz = dt->panels[i].fsz;
-		detgeom->panels[i].ssx = dt->panels[i].ssx;
-		detgeom->panels[i].ssy = dt->panels[i].ssy;
-		detgeom->panels[i].ssz = dt->panels[i].ssz;
-
-	}
-
-	return detgeom;
-}
-
-
 static int dt_num_placeholders(const struct panel_template *p)
 {
 	int i;
diff --git a/libcrystfel/src/datatemplate.h b/libcrystfel/src/datatemplate.h
index c6054409..88a002f0 100644
--- a/libcrystfel/src/datatemplate.h
+++ b/libcrystfel/src/datatemplate.h
@@ -69,8 +69,6 @@ extern int data_template_panel_to_file_coords(const DataTemplate *dt,
 extern void data_template_add_copy_header(DataTemplate *dt,
                                           const char *header);
 
-extern struct detgeom *data_template_to_detgeom(const DataTemplate *dt);
-
 extern int data_template_get_slab_extents(const DataTemplate *dt, int *pw, int *ph);
 
 extern int data_template_in_bad_region(const DataTemplate *dtempl,
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 2e9249e8..d2fb30ba 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -397,21 +397,21 @@ static double convert_to_m(double val, int units)
 }
 
 
-void create_detgeom(struct image *image, const DataTemplate *dtempl)
+int create_detgeom(struct image *image, const DataTemplate *dtempl)
 {
 	struct detgeom *detgeom;
 	int i;
 
 	if ( dtempl == NULL ) {
 		ERROR("NULL data template!\n");
-		return;
+		return 1;
 	}
 
 	detgeom = malloc(sizeof(struct detgeom));
-	if ( detgeom == NULL ) return;
+	if ( detgeom == NULL ) return 1;
 
 	detgeom->panels = malloc(dtempl->n_panels*sizeof(struct detgeom_panel));
-	if ( detgeom->panels == NULL ) return;
+	if ( detgeom->panels == NULL ) return 1;
 
 	detgeom->n_panels = dtempl->n_panels;
 
@@ -483,7 +483,7 @@ void create_detgeom(struct image *image, const DataTemplate *dtempl)
 
 	image->detgeom = detgeom;
 
-	/* FIXME: spectrum */
+	return 0;
 }
 
 
@@ -572,43 +572,9 @@ int image_read_image_data(struct image *image,
 }
 
 
-struct image *image_read(DataTemplate *dtempl,
-                         const char *filename,
-                         const char *event,
-                         int no_image_data,
-                         int no_mask_data)
+static void set_image_parameters(struct image *image,
+                                 const DataTemplate *dtempl)
 {
-	struct image *image;
-	int i;
-	int r;
-
-	if ( dtempl == NULL ) {
-		ERROR("NULL data template!\n");
-		return NULL;
-	}
-
-	image = image_new();
-	if ( image == NULL ) {
-		ERROR("Couldn't allocate image structure.\n");
-		return NULL;
-	}
-
-	if ( !no_image_data ) {
-
-		r = image_read_image_data(image, dtempl,
-		                          filename, event);
-
-	} else {
-
-		r = image_set_zero_data(image, dtempl);
-
-	}
-
-	if ( r ) {
-		image_free(image);
-		return NULL;
-	}
-
 	/* Wavelength might be needed to create detgeom (adu_per_eV) */
 	image->lambda = convert_to_m(get_value(image,
 	                                       dtempl->wavelength_from),
@@ -620,12 +586,19 @@ struct image *image_read(DataTemplate *dtempl,
 	image->spectrum = spectrum_generate_gaussian(image->lambda,
 	                                             image->bw);
 
-	create_detgeom(image, dtempl);
+}
+
+
+static int create_badmap(struct image *image,
+                         const DataTemplate *dtempl,
+                         int no_mask_data)
+{
+	int i;
 
 	image->bad = malloc(dtempl->n_panels * sizeof(int *));
 	if ( image->bad == NULL ) {
 		ERROR("Failed to allocate bad pixel mask\n");
-		return NULL;
+		return 1;
 	}
 
 	for ( i=0; i<dtempl->n_panels; i++ ) {
@@ -640,7 +613,7 @@ struct image *image_read(DataTemplate *dtempl,
 		image->bad[i] = calloc(p_w*p_h, sizeof(int));
 		if ( image->bad[i] == NULL ) {
 			ERROR("Failed to allocate bad pixel mask\n");
-			return NULL;
+			return 1;
 		}
 
 		/* Panel marked as bad? */
@@ -669,37 +642,142 @@ struct image *image_read(DataTemplate *dtempl,
 		if ( (!no_mask_data) && (!p->bad) && (p->mask != NULL) )
 		{
 			if ( p->mask_file == NULL ) {
-				mask_fn = filename;
+				mask_fn = image->filename;
 			} else {
 				mask_fn = p->mask_file;
 			}
 			if ( is_hdf5_file(mask_fn) ) {
-				image_hdf5_read_mask(p, mask_fn, event,
+				image_hdf5_read_mask(p, mask_fn,
+				                     image->ev,
 				                     image->bad[i],
 				                     dtempl->mask_good,
 				                     dtempl->mask_bad);
 
-			} else if ( is_cbf_file(filename) ) {
-				image_cbf_read_mask(p, mask_fn, event,
+			} else if ( is_cbf_file(mask_fn) ) {
+				image_cbf_read_mask(p, mask_fn,
+				                    image->ev,
 				                    0, image->bad[i],
 				                    dtempl->mask_good,
 				                    dtempl->mask_bad);
 
-			} else if ( is_cbfgz_file(filename) ) {
-				image_cbf_read_mask(p, mask_fn, event,
+			} else if ( is_cbfgz_file(mask_fn) ) {
+				image_cbf_read_mask(p, mask_fn,
+				                    image->ev,
 				                    1, image->bad[i],
 				                    dtempl->mask_good,
 				                    dtempl->mask_bad);
 
 			} else {
 				ERROR("Unrecognised mask file type"
-				      " (%s)\n", filename);
-				return NULL;
+				      " (%s)\n", mask_fn);
+				return 1;
 			}
 		}
 	}
+	return 0;
+}
+
+
+static int create_satmap(struct image *image,
+                         const DataTemplate *dtempl)
+{
+	/* FIXME: Implementation */
+	return 0;
+}
+
+
+struct image *image_create_for_simulation(const DataTemplate *dtempl)
+{
+	struct image *image;
+
+	if ( dtempl == NULL ) {
+		ERROR("NULL data template!\n");
+		return NULL;
+	}
+
+	image = image_new();
+	if ( image == NULL ) {
+		ERROR("Couldn't allocate image structure.\n");
+		return NULL;
+	}
+
+	if ( image_set_zero_data(image, dtempl) ) {
+		image_free(image);
+		return NULL;
+	}
 
-	/* FIXME: Load saturation map */
+	set_image_parameters(image, dtempl);
+
+	if ( create_detgeom(image, dtempl) ) {
+		image_free(image);
+		return NULL;
+	}
+
+	if ( create_badmap(image, dtempl, 1) ) {
+		image_free(image);
+		return NULL;
+	}
+
+	if ( create_satmap(image, dtempl) ) {
+		image_free(image);
+		return NULL;
+	}
+
+	return image;
+}
+
+
+struct image *image_read(const DataTemplate *dtempl,
+                         const char *filename,
+                         const char *event,
+                         int no_image_data,
+                         int no_mask_data)
+{
+	struct image *image;
+	int r;
+
+	if ( dtempl == NULL ) {
+		ERROR("NULL data template!\n");
+		return NULL;
+	}
+
+	image = image_new();
+	if ( image == NULL ) {
+		ERROR("Couldn't allocate image structure.\n");
+		return NULL;
+	}
+
+	image->filename = strdup(filename);
+	image->ev = strdup(event);
+
+	/* Load the image data */
+	if ( !no_image_data ) {
+		r = image_read_image_data(image, dtempl,
+		                          filename, event);
+	} else {
+		r = image_set_zero_data(image, dtempl);
+	}
+	if ( r ) {
+		image_free(image);
+		return NULL;
+	}
+
+	set_image_parameters(image, dtempl);
+
+	if ( create_detgeom(image, dtempl) ) {
+		image_free(image);
+		return NULL;
+	}
+
+	if ( create_badmap(image, dtempl, no_mask_data) ) {
+		image_free(image);
+		return NULL;
+	}
+
+	if ( create_satmap(image, dtempl) ) {
+		image_free(image);
+		return NULL;
+	}
 
 	return image;
 }
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 9f88d0e7..a2f160af 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -186,11 +186,12 @@ extern void mark_resolution_range_as_bad(struct image *image,
                                          double min, double max);
 
 extern struct image *image_new(void);
-extern struct image *image_read(DataTemplate *dtempl,
+extern struct image *image_read(const DataTemplate *dtempl,
                                 const char *filename,
                                 const char *event,
                                 int no_image_data,
                                 int no_mask_data);
+extern struct image *image_create_for_simulation(const DataTemplate *dtempl);
 extern void image_free(struct image *image);
 
 extern ImageFeatureList *image_read_peaks(const DataTemplate *dtempl,
@@ -208,9 +209,10 @@ extern int image_set_zero_mask(struct image *image,
                                const DataTemplate *dtempl);
 
 /* Use within libcrystfel only */
-extern void create_detgeom(struct image *image,
-                           const DataTemplate *dtempl);
+extern int create_detgeom(struct image *image,
+                          const DataTemplate *dtempl);
 
+/* Use within libcrystfel only */
 extern int image_read_image_data(struct image *image,
                                  const DataTemplate *dtempl,
                                  const char *filename,
diff --git a/src/make_pixelmap.c b/src/make_pixelmap.c
index cb5afcac..099ba79f 100644
--- a/src/make_pixelmap.c
+++ b/src/make_pixelmap.c
@@ -46,6 +46,7 @@
 #include <utils.h>
 #include <datatemplate.h>
 #include <detgeom.h>
+#include <image.h>
 
 #include "version.h"
 
@@ -181,6 +182,7 @@ int main(int argc, char *argv[])
 	float *x, *y, *z;
 	uint16_t *b;
 	float res;
+	struct image *image;
 	int badmap = 0;
 	int good_pixel_val = 1;
 	int bad_pixel_val = 0;
@@ -268,13 +270,13 @@ int main(int argc, char *argv[])
 	}
 	free(input_file);
 
-	detgeom = data_template_to_detgeom(dtempl);
-	if ( detgeom == NULL ) {
-		ERROR("Could not make detector structure.\n");
-		ERROR("Geometry file must not contain references to "
-		      "image header values\n");
+	image = image_create_for_simulation(dtempl);
+	if ( image == NULL ) {
+		ERROR("Geometry file seems to contain references to "
+		      "image header values.\n");
 		return 1;
 	}
+	detgeom = image->detgeom;
 
 	/* Determine max orig fs and ss */
 	if ( data_template_get_slab_extents(dtempl, &w, &h) ) {
@@ -346,6 +348,7 @@ int main(int argc, char *argv[])
 	}
 
 	data_template_free(dtempl);
+	image_free(image);
 
 	return 0;
 }