Bugfixes to refactored hdf5 reading and writing functions

4 files changed, 48 insertions, 32 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index a7829474..e17c51a0 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -497,13 +497,13 @@ static struct panel *new_panel(struct detector *det, const char *name)
 	}
 
 	/* Create a new copy of the data location if needed */
-	if ( new->data_from != NULL ) {
-		new->data_from = strdup(new->data_from);
+	if ( new->data != NULL ) {
+		new->data = strdup(new->data);
 	}
 
 	/* Create a new copy of the bad pixel mask location */
 	if ( new->mask != NULL ) {
-		new->mask = strdup(new->data_from);
+		new->mask = strdup(new->mask);
 	}
 
 	return new;
@@ -676,12 +676,12 @@ static int parse_field_for_panel(struct panel *panel, const char *key,
 			panel->clen_from = NULL;
 		}
 
-	} else if ( strcmp(key, "data_from") == 0 ) {
+	} else if ( strcmp(key, "data") == 0 ) {
 		if ( strncmp(val,"/",1) != 0 ) {
 			ERROR("Invalid data location '%s'\n", val);
 			reject = -1;
 		}
-		panel->data_from = strdup(val);
+		panel->data = strdup(val);
 
 	} else if ( strcmp(key, "mask") == 0 ) {
 		if ( strncmp(val,"/",1) != 0 ) {
@@ -911,7 +911,7 @@ struct detector *get_detector_geometry(const char *filename)
 	det->defaults.adu_per_eV = NAN;
 	det->defaults.max_adu = +INFINITY;
 	det->defaults.mask = NULL;
-	det->defaults.data_from = NULL;
+	det->defaults.data = NULL;
 	strncpy(det->defaults.name, "", 1023);
 
 	do {
@@ -1100,7 +1100,7 @@ out:
 	det->max_ss = max_ss;
 
 	free(det->defaults.clen_from);
-	free(det->defaults.data_from);
+	free(det->defaults.data);
 	free(det->defaults.mask);
 
 	/* Calculate matrix inverses and other stuff */
@@ -1190,8 +1190,8 @@ struct detector *copy_geom(const struct detector *in)
 			p->clen_from = strdup(p->clen_from);
 		}
 
-		if ( p->data_from != NULL ) {
-			/* Make a copy of the data_from fields unique to this
+		if ( p->data != NULL ) {
+			/* Make a copy of the data fields unique to this
 			 * copy of the structure. */
 			p->clen_from = strdup(p->clen_from);
 		}
@@ -1436,9 +1436,9 @@ int write_detector_geometry(const char *filename, struct detector *det)
 			        p->name, p->rigid_group->name);
 		}
 
-		if ( p->data_from != NULL ) {
-			fprintf(fh, "%s/data_from = %s\n",
-			        p->name, p->data_from);
+		if ( p->data != NULL ) {
+			fprintf(fh, "%s/data = %s\n",
+					p->name, p->data);
 		}
 
 		if ( p->mask != NULL ) {
@@ -1490,32 +1490,32 @@ void mark_resolution_range_as_bad(struct image *image,
 }
 
 
-extern int single_source (struct detector *det, char *element)
+extern int single_panel_data_source (struct detector *det, const char *element)
 {
 	int pi;
 	char *first_datafrom = NULL;
 	char *curr_datafrom = NULL;
 
-	if ( det->panels[0].data_from == NULL ) {
+	if ( det->panels[0].data == NULL ) {
 		if ( element != NULL ) {
 			first_datafrom = strdup(element);
 		} else {
 			first_datafrom = strdup("/data/data");
 		}
 	} else {
-		first_datafrom = strdup(det->panels[0].data_from);
+		first_datafrom = strdup(det->panels[0].data);
 	}
 
 	for ( pi=1;pi<det->n_panels;pi++ ) {
 
-		if ( det->panels[pi].data_from == NULL ) {
+		if ( det->panels[pi].data == NULL ) {
 			if ( element != NULL ) {
 				curr_datafrom = strdup(element);
 			} else {
 				curr_datafrom = strdup("/data/data");
 			}
 		} else {
-			curr_datafrom = strdup(det->panels[pi].data_from);
+			curr_datafrom = strdup(det->panels[pi].data);
 		}
 
 		if ( strcmp(curr_datafrom, first_datafrom) != 0 ) {
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 6dc398d7..9245849f 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -87,7 +87,7 @@ struct panel
 	struct rigid_group *rigid_group;  /* Rigid group */
 	double   adu_per_eV;   /* Number of ADU per eV */
 	double   max_adu;  /* Treat pixel as unreliable if higher than this */
-	char    *data_from;
+	char    *data;
 
 	double fsx;
 	double fsy;
@@ -209,7 +209,8 @@ extern int write_detector_geometry(const char *filename, struct detector *det);
 extern void mark_resolution_range_as_bad(struct image *image,
                                          double min, double max);
 
-extern int single_source (struct detector *det, char *element);
+
+extern int single_panel_data_source (struct detector *det, const char *element);
 
 
 #ifdef __cplusplus
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 3f90117d..a0fa8866 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -365,8 +365,8 @@ int hdf5_write_image(const char *filename, struct image *image, char *element)
 	}
 	locations[0].max_ss = 0;
 	locations[0].max_fs = 0;
-	if ( image->det->panels[0].data_from != NULL ) {
-		locations[0].location = image->det->panels[0].data_from;
+	if ( image->det->panels[0].data != NULL ) {
+		locations[0].location = image->det->panels[0].data;
 	} else {
 		locations[0].location = default_location;
 	}
@@ -383,10 +383,10 @@ int hdf5_write_image(const char *filename, struct image *image, char *element)
 
 		p = image->det->panels[pi];
 
-		if ( p.data_from == NULL ) {
+		if ( p.data == NULL ) {
 			p_location = default_location;
 		} else {
-			p_location = p.data_from;
+			p_location = p.data;
 		}
 
 		panel_processed = 0;
@@ -846,6 +846,12 @@ static int unpack_panels(struct image *image, struct detector *det)
 
 int hdf5_read(struct hdfile *f, struct image *image, const char* element, int satcorr)
 {
+	return hdf5_read2(f, image, element, satcorr, 0);
+}
+
+
+int hdf5_read2(struct hdfile *f, struct image *image, const char* element, int satcorr, int override_data_and_mask)
+{
 	herr_t r;
 	float *buf;
 	uint16_t *flags;
@@ -857,6 +863,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char* element, int sa
 	int pi;
 	hid_t mask_dh = NULL;
 
+
 	if ( image->det == NULL ) {
 		ERROR("Geometry not available\n");
 		return 1;
@@ -908,12 +915,16 @@ int hdf5_read(struct hdfile *f, struct image *image, const char* element, int sa
 		if ( p->orig_min_ss == -1 ) p->orig_min_ss = p->min_ss;
 		if ( p->orig_max_ss == -1 ) p->orig_max_ss = p->max_ss;
 
-		if ( p->data_from != NULL ) {
-			fail = hdfile_set_image(f, p->data_from);
-		} else if ( element != NULL ) {
+		if ( override_data_and_mask ) {
 			fail = hdfile_set_image(f, element);
 		} else {
-			fail = hdfile_set_first_image(f,"/");
+			if ( p->data != NULL ) {
+				fail = hdfile_set_image(f, p->data);
+			} else if ( element != NULL ) {
+				fail = hdfile_set_image(f, element);
+			} else {
+				fail = hdfile_set_first_image(f,"/");
+			}
 		}
 		if ( fail ) {
 			ERROR("Couldn't select path for panel %s\n",
@@ -974,10 +985,8 @@ int hdf5_read(struct hdfile *f, struct image *image, const char* element, int sa
 		H5Dclose(f->dh);
 		f->data_open = 0;
 		H5Sclose(dataspace);
-		H5Sclose(memspace);
 
 		if ( p->mask != NULL ) {
-
 			mask_dh = H5Dopen2(f->fh, p->mask, H5P_DEFAULT);
 			if ( mask_dh <= 0 ) {
 				ERROR("Couldn't open flags for panel %s\n",
@@ -985,7 +994,7 @@ int hdf5_read(struct hdfile *f, struct image *image, const char* element, int sa
 				image->flags = NULL;
 			} else {
 
-				mask_dataspace = H5Dget_space(H5Dget_space(mask_dh));
+				mask_dataspace = H5Dget_space(mask_dh);
 				check = H5Sselect_hyperslab(mask_dataspace, H5S_SELECT_SET,
 				                            f_offset, NULL, f_count, NULL);
 				if ( check < 0 ) {
@@ -1000,12 +1009,16 @@ int hdf5_read(struct hdfile *f, struct image *image, const char* element, int sa
 				} else {
 					no_mask_loaded = 0;
 				}
-				H5Dclose(mask_dataspace);
+
+				H5Sclose(mask_dataspace);
 				H5Dclose(mask_dh);
-		      }
+
+			}
 
 		}
 
+		H5Sclose(memspace);
+
 		p->min_fs = m_min_fs;
 		p->max_fs = m_max_fs;
 		p->min_ss = curr_ss;
diff --git a/libcrystfel/src/hdf5-file.h b/libcrystfel/src/hdf5-file.h
index 1cac71a5..b5159fcf 100644
--- a/libcrystfel/src/hdf5-file.h
+++ b/libcrystfel/src/hdf5-file.h
@@ -52,6 +52,8 @@ extern int hdf5_write_image(const char *filename, struct image *image, char *ele
 
 extern int hdf5_read(struct hdfile *f, struct image *image, const char *element, int satcorr);
 
+extern int hdf5_read2(struct hdfile *f, struct image *image, const char* element, int satcorr, int override_data_and_mask);
+
 extern struct hdfile *hdfile_open(const char *filename);
 extern int hdfile_set_image(struct hdfile *f, const char *path);
 extern int16_t *hdfile_get_image_binned(struct hdfile *hdfile,