Initial DataTemplate parser (copied from get_detector_geometry)

2 files changed, 1367 insertions, 99 deletions

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index 22bad02c..bff8eccf 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -31,133 +31,1212 @@
 #endif
 
 #include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
 
+#include "utils.h"
 #include "datatemplate.h"
+#include "events.h"
+
+#include "datatemplate_priv.h"
 
 
 /**
  * \file datatemplate.h
  */
 
-enum adu_per_unit
-{
-	ADU_PER_PHOTON,
-	ADU_PER_EV
+struct rg_definition {
+	char *name;
+	char *pns;
 };
 
 
-/**
- * Represents one panel of a detector
- */
-struct panel_template
-{
-	/** Text name for panel (fixed length array) */
-	char     name[1024];
-
-	/** \name Location of corner in units of the pixel size of this panel */
-	/**@{*/
-	double   cnx;
-	double   cny;
-	/**@}*/
-
-	/** Location to get \ref cnz from, e.g. from HDF5 file */
-	char    *cnz_from;
-
-	/** The offset to be applied from \ref clen */
-	double   coffset;
-
-	/** Location of mask data */
-	char    *mask;
-
-	/** Filename for mask data */
-	char    *mask_file;
-
-	/** Location of per-pixel saturation map */
-	char    *satmap;
-
-	/** Filename for saturation map */
-	char    *satmap_file;
-
-	/** Resolution in pixels per metre  */
-	double   pixel_pitch;
-
-	/** Readout direction (for filtering out clusters of peaks)
-	  * ('x' or 'y') */
-	char     badrow;
-
-	/** Number of detector intensity units per photon, or eV */
-	double   adu_scale;
-	enum adu_per_unit adu_scale_unit;
-
-	/** Treat pixel as unreliable if higher than this */
-	double   max_adu;
-
-	/** Location of data in file */
-	char    *data;
-
-	/** Dimension structure */
-	struct dim_structure *dim_structure;
-
-	/** \name Transformation matrix from pixel coordinates to lab frame */
-	/*@{*/
-	double fsx;
-	double fsy;
-	double fsz;
-	double ssx;
-	double ssy;
-	double ssz;
-	/*@}*/
-
-	/** \name Rail direction */
-	/*@{*/
-	double rail_x;
-	double rail_y;
-	double rail_z;
-	/*@}*/
-
-	/* Value of clen (without coffset) at which beam is centered */
-	double clen_for_centering;
-
-	/** \name Position of the panel in the data block in the file. */
-	/*@{*/
-	int orig_min_fs;
-	int orig_max_fs;
-	int orig_min_ss;
-	int orig_max_ss;
-	/*@}*/
+struct rgc_definition {
+	char *name;
+	char *rgs;
 };
 
 
-struct _datatemplate
+static struct panel_template *new_panel(DataTemplate *det, const char *name)
 {
-	struct panel_template     *panels;
-	int                        n_panels;
+	struct panel_template *new;
 
-	struct badregion          *bad;
-	int                        n_bad;
+	det->n_panels++;
+	det->panels = realloc(det->panels,
+	                      det->n_panels*sizeof(struct panel_template));
 
-	unsigned int               mask_bad;
-	unsigned int               mask_good;
+	new = &det->panels[det->n_panels-1];
+	memcpy(new, &det->defaults, sizeof(struct panel_template));
 
-	struct rigid_group       **rigid_groups;
-	int                        n_rigid_groups;
+	new->name = strdup(name);
 
-	struct rg_collection     **rigid_group_collections;
-	int                        n_rg_collections;
+	/* Copy strings */
+	if ( new->cnz_from != NULL ) new->cnz_from = strdup(new->cnz_from);
+	if ( new->data != NULL ) new->data = strdup(new->data);
+	if ( new->mask != NULL ) new->mask = strdup(new->mask);
 
-	int                        path_dim;
-	int                        dim_dim;
+	/* Create a new copy of the dim_structure if needed */
+	if ( new->dim_structure != NULL ) {
 
-	struct panel_template      defaults;
-};
+		struct dim_structure *dim_copy;
+		int di;
 
+		dim_copy = initialize_dim_structure();
+		dim_copy->num_dims = new->dim_structure->num_dims;
+		dim_copy->dims = malloc(dim_copy->num_dims*sizeof(int));
+		for ( di=0; di<dim_copy->num_dims; di++ ) {
+			dim_copy->dims[di] = new->dim_structure->dims[di];
+		}
 
-DataTemplate *data_template_new_from_file(const char *filename)
+		new->dim_structure = dim_copy;
+	}
+
+	return new;
+}
+
+
+static struct dt_badregion *new_bad_region(DataTemplate *det, const char *name)
+{
+	struct dt_badregion *new;
+
+	det->n_bad++;
+	det->bad = realloc(det->bad, det->n_bad*sizeof(struct dt_badregion));
+
+	new = &det->bad[det->n_bad-1];
+	new->min_x = NAN;
+	new->max_x = NAN;
+	new->min_y = NAN;
+	new->max_y = NAN;
+	new->min_fs = 0;
+	new->max_fs = 0;
+	new->min_ss = 0;
+	new->max_ss = 0;
+	new->is_fsss = 99; /* Slightly nasty: means "unassigned" */
+	new->panel = NULL;
+	strcpy(new->name, name);
+
+	return new;
+}
+
+
+static struct panel_template *find_panel_by_name(DataTemplate *det, const char *name)
 {
+	int i;
+
+	for ( i=0; i<det->n_panels; i++ ) {
+		if ( strcmp(det->panels[i].name, name) == 0 ) {
+			return &det->panels[i];
+		}
+	}
+
+	return NULL;
+}
+
+
+static struct dt_badregion *find_bad_region_by_name(DataTemplate *det,
+                                                 const char *name)
+{
+	int i;
+
+	for ( i=0; i<det->n_bad; i++ ) {
+		if ( strcmp(det->bad[i].name, name) == 0 ) {
+			return &det->bad[i];
+		}
+	}
+
 	return NULL;
 }
 
 
+static struct dt_rigid_group *find_or_add_rg(DataTemplate *det,
+                                          const char *name)
+{
+	int i;
+	struct dt_rigid_group **new;
+	struct dt_rigid_group *rg;
+
+	for ( i=0; i<det->n_rigid_groups; i++ ) {
+
+		if ( strcmp(det->rigid_groups[i]->name, name) == 0 ) {
+			return det->rigid_groups[i];
+		}
+
+	}
+
+	new = realloc(det->rigid_groups,
+	              (1+det->n_rigid_groups)*sizeof(struct dt_rigid_group *));
+	if ( new == NULL ) return NULL;
+
+	det->rigid_groups = new;
+
+	rg = malloc(sizeof(struct dt_rigid_group));
+	if ( rg == NULL ) return NULL;
+
+	det->rigid_groups[det->n_rigid_groups++] = rg;
+
+	rg->name = strdup(name);
+	rg->panels = NULL;
+	rg->n_panels = 0;
+
+	return rg;
+}
+
+
+static struct dt_rg_collection *find_or_add_rg_coll(DataTemplate *det,
+                                                    const char *name)
+{
+	int i;
+	struct dt_rg_collection **new;
+	struct dt_rg_collection *rgc;
+
+	for ( i=0; i<det->n_rg_collections; i++ ) {
+		if ( strcmp(det->rigid_group_collections[i]->name, name) == 0 )
+		{
+			return det->rigid_group_collections[i];
+		}
+	}
+
+	new = realloc(det->rigid_group_collections,
+	              (1+det->n_rg_collections)*sizeof(struct dt_rg_collection *));
+	if ( new == NULL ) return NULL;
+
+	det->rigid_group_collections = new;
+
+	rgc = malloc(sizeof(struct dt_rg_collection));
+	if ( rgc == NULL ) return NULL;
+
+	det->rigid_group_collections[det->n_rg_collections++] = rgc;
+
+	rgc->name = strdup(name);
+	rgc->rigid_groups = NULL;
+	rgc->n_rigid_groups = 0;
+
+	return rgc;
+}
+
+
+static void add_to_rigid_group(struct dt_rigid_group *rg, struct panel_template *p)
+{
+	struct panel_template **pn;
+
+	pn = realloc(rg->panels, (1+rg->n_panels)*sizeof(struct panel_template *));
+	if ( pn == NULL ) {
+		ERROR("Couldn't add panel to rigid group.\n");
+		return;
+	}
+
+	rg->panels = pn;
+	rg->panels[rg->n_panels++] = p;
+}
+
+
+static void add_to_rigid_group_coll(struct dt_rg_collection *rgc,
+                                    struct dt_rigid_group *rg)
+{
+	struct dt_rigid_group **r;
+
+	r = realloc(rgc->rigid_groups, (1+rgc->n_rigid_groups)*
+	            sizeof(struct dt_rigid_group *));
+	if ( r == NULL ) {
+		ERROR("Couldn't add rigid group to collection.\n");
+		return;
+	}
+
+	rgc->rigid_groups = r;
+	rgc->rigid_groups[rgc->n_rigid_groups++] = rg;
+}
+
+
+/* Free all rigid groups in detector */
+static void free_all_rigid_groups(DataTemplate *det)
+{
+	int i;
+
+	if ( det->rigid_groups == NULL ) return;
+	for ( i=0; i<det->n_rigid_groups; i++ ) {
+		free(det->rigid_groups[i]->name);
+		free(det->rigid_groups[i]->panels);
+		free(det->rigid_groups[i]);
+	}
+	free(det->rigid_groups);
+}
+
+
+/* Free all rigid groups in detector */
+static void free_all_rigid_group_collections(DataTemplate *det)
+{
+	int i;
+
+	if ( det->rigid_group_collections == NULL ) return;
+	for ( i=0; i<det->n_rg_collections; i++ ) {
+		free(det->rigid_group_collections[i]->name);
+		free(det->rigid_group_collections[i]->rigid_groups);
+		free(det->rigid_group_collections[i]);
+	}
+	free(det->rigid_group_collections);
+}
+
+
+static struct dt_rigid_group *find_rigid_group_by_name(DataTemplate *det,
+                                                       char *name)
+{
+	int i;
+
+	for ( i=0; i<det->n_rigid_groups; i++ ) {
+		if ( strcmp(det->rigid_groups[i]->name, name) == 0 ) {
+			return det->rigid_groups[i];
+		}
+	}
+
+	return NULL;
+}
+
+
+static int atob(const char *a)
+{
+	if ( strcasecmp(a, "true") == 0 ) return 1;
+	if ( strcasecmp(a, "false") == 0 ) return 0;
+	return atoi(a);
+}
+
+
+static int assplode_algebraic(const char *a_orig, char ***pbits)
+{
+	int len, i;
+	int nexp;
+	char **bits;
+	char *a;
+	int idx, istr;
+
+	len = strlen(a_orig);
+
+	/* Add plus at start if no sign there already */
+	if ( (a_orig[0] != '+') && (a_orig[0] != '-') ) {
+		len += 1;
+		a = malloc(len+1);
+		snprintf(a, len+1, "+%s", a_orig);
+		a[len] = '\0';
+
+	} else {
+		a = strdup(a_orig);
+	}
+
+	/* Count the expressions */
+	nexp = 0;
+	for ( i=0; i<len; i++ ) {
+		if ( (a[i] == '+') || (a[i] == '-') ) nexp++;
+	}
+
+	bits = calloc(nexp, sizeof(char *));
+
+	/* Break the string up */
+	idx = -1;
+	istr = 0;
+	assert((a[0] == '+') || (a[0] == '-'));
+	for ( i=0; i<len; i++ ) {
+
+		char ch;
+
+		ch = a[i];
+
+		if ( (ch == '+') || (ch == '-') ) {
+			if ( idx >= 0 ) bits[idx][istr] = '\0';
+			idx++;
+			bits[idx] = malloc(len+1);
+			istr = 0;
+		}
+
+		if ( !isdigit(ch) && (ch != '.') && (ch != '+') && (ch != '-')
+		  && (ch != 'x') && (ch != 'y') && (ch != 'z') )
+		{
+			ERROR("Invalid character '%c' found.\n", ch);
+			return 0;
+		}
+
+		assert(idx >= 0);
+		bits[idx][istr++] = ch;
+
+	}
+	if ( idx >= 0 ) bits[idx][istr] = '\0';
+
+	*pbits = bits;
+	free(a);
+
+	return nexp;
+}
+
+
+/* Parses the scan directions (accounting for possible rotation)
+ * Assumes all white spaces have been already removed */
+static int dir_conv(const char *a, double *sx, double *sy, double *sz)
+{
+	int n;
+	char **bits;
+	int i;
+
+	*sx = 0.0;  *sy = 0.0;  *sz = 0.0;
+
+	n = assplode_algebraic(a, &bits);
+
+	if ( n == 0 ) {
+		ERROR("Invalid direction '%s'\n", a);
+		return 1;
+	}
+
+	for ( i=0; i<n; i++ ) {
+
+		int len;
+		double val;
+		char axis;
+		int j;
+
+		len = strlen(bits[i]);
+		assert(len != 0);
+		axis = bits[i][len-1];
+		if ( (axis != 'x') && (axis != 'y') && (axis != 'z') ) {
+			ERROR("Invalid symbol '%c' - must be x, y or z.\n",
+			      axis);
+			return 1;
+		}
+
+		/* Chop off the symbol now it's dealt with */
+		bits[i][len-1] = '\0';
+
+		/* Check for anything that isn't part of a number */
+		for ( j=0; j<strlen(bits[i]); j++ ) {
+			if ( isdigit(bits[i][j]) ) continue;
+			if ( bits[i][j] == '+' ) continue;
+			if ( bits[i][j] == '-' ) continue;
+			if ( bits[i][j] == '.' ) continue;
+			ERROR("Invalid coefficient '%s'\n", bits[i]);
+		}
+
+		if ( strlen(bits[i]) == 0 ) {
+			val = 1.0;
+		} else {
+			val = atof(bits[i]);
+		}
+		if ( strlen(bits[i]) == 1 ) {
+			if ( bits[i][0] == '+' ) val = 1.0;
+			if ( bits[i][0] == '-' ) val = -1.0;
+		}
+		switch ( axis ) {
+
+			case 'x' :
+			*sx += val;
+			break;
+
+			case 'y' :
+			*sy += val;
+			break;
+
+			case 'z' :
+			*sz += val;
+			break;
+		}
+
+		free(bits[i]);
+
+	}
+	free(bits);
+
+	return 0;
+}
+
+
+static int parse_field_for_panel(struct panel_template *panel, const char *key,
+                                 const char *val, DataTemplate *det)
+{
+	int reject = 0;
+
+	if ( strcmp(key, "min_fs") == 0 ) {
+		panel->orig_min_fs = atof(val);
+	} else if ( strcmp(key, "max_fs") == 0 ) {
+		panel->orig_max_fs = atof(val);
+	} else if ( strcmp(key, "min_ss") == 0 ) {
+		panel->orig_min_ss = atof(val);
+	} else if ( strcmp(key, "max_ss") == 0 ) {
+		panel->orig_max_ss = atof(val);
+	} else if ( strcmp(key, "corner_x") == 0 ) {
+		panel->cnx = atof(val);
+	} else if ( strcmp(key, "corner_y") == 0 ) {
+		panel->cny = atof(val);
+	} else if ( strcmp(key, "rail_direction") == 0 ) {
+		if ( dir_conv(val, &panel->rail_x,
+		                   &panel->rail_y,
+		                   &panel->rail_z) )
+		{
+			ERROR("Invalid rail direction '%s'\n", val);
+			reject = 1;
+		}
+	} else if ( strcmp(key, "clen_for_centering") == 0 ) {
+		panel->clen_for_centering = atof(val);
+	} else if ( strcmp(key, "adu_per_eV") == 0 ) {
+		panel->adu_per_eV = atof(val);
+	} else if ( strcmp(key, "adu_per_photon") == 0 ) {
+		panel->adu_per_photon = atof(val);
+	} else if ( strcmp(key, "rigid_group") == 0 ) {
+		add_to_rigid_group(find_or_add_rg(det, val), panel);
+	} else if ( strcmp(key, "clen") == 0 ) {
+		/* Gets expanded when image is loaded */
+		panel->cnz_from = strdup(val);
+
+	} else if ( strcmp(key, "data") == 0 ) {
+		if ( strncmp(val,"/",1) != 0 ) {
+			ERROR("Invalid data location '%s'\n", val);
+			reject = -1;
+		}
+		panel->data = strdup(val);
+
+	} else if ( strcmp(key, "mask") == 0 ) {
+		if ( strncmp(val,"/",1) != 0 ) {
+			ERROR("Invalid mask location '%s'\n", val);
+			reject = -1;
+		}
+		panel->mask = strdup(val);
+
+	} else if ( strcmp(key, "mask_file") == 0 ) {
+		panel->mask_file = strdup(val);
+
+	} else if ( strcmp(key, "saturation_map") == 0 ) {
+		panel->satmap = strdup(val);
+	} else if ( strcmp(key, "saturation_map_file") == 0 ) {
+		panel->satmap_file = strdup(val);
+
+	} else if ( strcmp(key, "coffset") == 0) {
+		panel->cnz_offset = atof(val);
+	} else if ( strcmp(key, "res") == 0 ) {
+		panel->pixel_pitch = 1.0/atof(val);
+	} else if ( strcmp(key, "max_adu") == 0 ) {
+		panel->max_adu = atof(val);
+	} else if ( strcmp(key, "badrow_direction") == 0 ) {
+		ERROR("WARNING 'badrow_direction' is ignored in this version.\n");
+	} else if ( strcmp(key, "no_index") == 0 ) {
+		panel->bad = atob(val);
+	} else if ( strcmp(key, "fs") == 0 ) {
+		if ( dir_conv(val, &panel->fsx, &panel->fsy, &panel->fsz) != 0 )
+		{
+			ERROR("Invalid fast scan direction '%s'\n", val);
+			reject = 1;
+		}
+	} else if ( strcmp(key, "ss") == 0 ) {
+		if ( dir_conv(val, &panel->ssx, &panel->ssy, &panel->ssz) != 0 )
+		{
+			ERROR("Invalid slow scan direction '%s'\n", val);
+			reject = 1;
+		}
+	} else if ( strncmp(key, "dim", 3) == 0) {
+		int dim_entry;
+		char *endptr;
+		if ( key[3] != '\0' ) {
+			if  ( panel->dim_structure == NULL ) {
+				panel->dim_structure = initialize_dim_structure();
+			}
+			dim_entry = strtoul(key+3, &endptr, 10);
+			if ( endptr[0] != '\0' ) {
+				ERROR("Invalid dimension number %s\n", key+3);
+			} else {
+				if ( set_dim_structure_entry(panel->dim_structure,
+				                        dim_entry, val) )
+				{
+					ERROR("Failed to set dim structure entry\n");
+				}
+			}
+		} else {
+			ERROR("'dim' must be followed by a number, e.g. 'dim0'\n");
+		}
+	} else {
+		ERROR("Unrecognised field '%s'\n", key);
+	}
+
+	return reject;
+}
+
+
+static int check_badr_fsss(struct dt_badregion *badr, int is_fsss)
+{
+	/* First assignment? */
+	if ( badr->is_fsss == 99 ) {
+		badr->is_fsss = is_fsss;
+		return 0;
+	}
+
+	if ( is_fsss != badr->is_fsss ) {
+		ERROR("You can't mix x/y and fs/ss in a bad region.\n");
+		return 1;
+	}
+
+	return 0;
+}
+
+
+static int parse_field_bad(struct dt_badregion *badr, const char *key,
+                           const char *val)
+{
+	int reject = 0;
+
+	if ( strcmp(key, "min_x") == 0 ) {
+		badr->min_x = atof(val);
+		reject = check_badr_fsss(badr, 0);
+	} else if ( strcmp(key, "max_x") == 0 ) {
+		badr->max_x = atof(val);
+		reject = check_badr_fsss(badr, 0);
+	} else if ( strcmp(key, "min_y") == 0 ) {
+		badr->min_y = atof(val);
+		reject = check_badr_fsss(badr, 0);
+	} else if ( strcmp(key, "max_y") == 0 ) {
+		badr->max_y = atof(val);
+		reject = check_badr_fsss(badr, 0);
+	} else if ( strcmp(key, "min_fs") == 0 ) {
+		badr->min_fs = atof(val);
+		reject = check_badr_fsss(badr, 1);
+	} else if ( strcmp(key, "max_fs") == 0 ) {
+		badr->max_fs = atof(val);
+		reject = check_badr_fsss(badr, 1);
+	} else if ( strcmp(key, "min_ss") == 0 ) {
+		badr->min_ss = atof(val);
+		reject = check_badr_fsss(badr, 1);
+	} else if ( strcmp(key, "max_ss") == 0 ) {
+		badr->max_ss = atof(val);
+		reject = check_badr_fsss(badr, 1);
+	} else if ( strcmp(key, "panel") == 0 ) {
+		badr->panel = strdup(val);
+	} else {
+		ERROR("Unrecognised field '%s'\n", key);
+	}
+
+	return reject;
+}
+
+static void parse_toplevel(DataTemplate *dt,
+                           const char *key, const char *val,
+                           struct rg_definition ***rg_defl,
+                           struct rgc_definition ***rgc_defl, int *n_rg_defs,
+                           int *n_rgc_defs)
+{
+
+	if ( strcmp(key, "mask_bad") == 0 ) {
+
+		char *end;
+		double v = strtod(val, &end);
+
+		if ( end != val ) {
+			dt->mask_bad = v;
+		}
+
+	} else if ( strcmp(key, "mask_good") == 0 ) {
+
+		char *end;
+		double v = strtod(val, &end);
+
+		if ( end != val ) {
+			dt->mask_good = v;
+		}
+
+	} else if ( strcmp(key, "coffset") == 0 ) {
+		dt->defaults.cnz_offset = atof(val);
+
+	} else if ( strcmp(key, "photon_energy") == 0 ) {
+		/* Will be expanded when image is loaded */
+		dt->wavelength_from = strdup(val);
+
+	} else if ( strcmp(key, "photon_energy_bandwidth") == 0 ) {
+		double v;
+		char *end;
+		v = strtod(val, &end);
+		if ( (val[0] != '\0') && (end[0] == '\0') ) {
+			dt->photon_energy_bandwidth = v;
+		} else {
+			ERROR("Invalid value for photon_energy_bandwidth\n");
+		}
+
+	} else if ( strcmp(key, "photon_energy_scale") == 0 ) {
+		dt->photon_energy_scale = atof(val);
+
+	} else if ( strcmp(key, "peak_info_location") == 0 ) {
+		dt->hdf5_peak_path = strdup(val);
+
+	} else if (strncmp(key, "rigid_group", 11) == 0
+	        && strncmp(key, "rigid_group_collection", 22) != 0 ) {
+
+		struct rg_definition **new;
+
+		new = realloc(*rg_defl,
+		             ((*n_rg_defs)+1)*sizeof(struct rg_definition*));
+		*rg_defl = new;
+
+		(*rg_defl)[*n_rg_defs] = malloc(sizeof(struct rg_definition));
+		(*rg_defl)[*n_rg_defs]->name = strdup(key+12);
+		(*rg_defl)[*n_rg_defs]->pns = strdup(val);
+		*n_rg_defs = *n_rg_defs+1;
+
+	} else if ( strncmp(key, "rigid_group_collection", 22) == 0 ) {
+
+		struct rgc_definition **new;
+
+		new = realloc(*rgc_defl, ((*n_rgc_defs)+1)*
+		      sizeof(struct rgc_definition*));
+		*rgc_defl = new;
+
+		(*rgc_defl)[*n_rgc_defs] =
+		                   malloc(sizeof(struct rgc_definition));
+		(*rgc_defl)[*n_rgc_defs]->name = strdup(key+23);
+		(*rgc_defl)[*n_rgc_defs]->rgs = strdup(val);
+		*n_rgc_defs = *n_rgc_defs+1;
+
+	} else if ( parse_field_for_panel(&dt->defaults, key, val, dt) ) {
+		ERROR("Unrecognised top level field '%s'\n", key);
+	}
+}
+
+
+DataTemplate *data_template_new_from_string(const char *string_in)
+{
+	DataTemplate *dt;
+	char **bits;
+	int done = 0;
+	int i;
+	int rgi, rgci;
+	int reject = 0;
+	int path_dim, mask_path_dim;
+	int dim_dim;
+	int dim_reject = 0;
+	int dim_dim_reject = 0;
+	struct rg_definition **rg_defl = NULL;
+	struct rgc_definition **rgc_defl = NULL;
+	int n_rg_definitions = 0;
+	int n_rgc_definitions = 0;
+	char *string;
+	char *string_orig;
+	size_t len;
+
+	dt = calloc(1, sizeof(DataTemplate));
+	if ( dt == NULL ) return NULL;
+
+	dt->n_panels = 0;
+	dt->panels = NULL;
+	dt->n_bad = 0;
+	dt->bad = NULL;
+	dt->mask_good = 0;
+	dt->mask_bad = 0;
+	dt->n_rigid_groups = 0;
+	dt->rigid_groups = NULL;
+	dt->path_dim = 0;
+	dt->dim_dim = 0;
+	dt->n_rg_collections = 0;
+	dt->rigid_group_collections = NULL;
+	dt->photon_energy_bandwidth = -1.0;
+	dt->photon_energy_scale = -1.0;
+	dt->peak_info_location = NULL;
+
+	/* The default defaults... */
+	dt->defaults.orig_min_fs = -1;
+	dt->defaults.orig_min_ss = -1;
+	dt->defaults.orig_max_fs = -1;
+	dt->defaults.orig_max_ss = -1;
+	dt->defaults.cnx = NAN;
+	dt->defaults.cny = NAN;
+	dt->defaults.cnz_from = NULL;
+	dt->defaults.cnz_offset = 0.0;
+	dt->defaults.pixel_pitch = -1.0;
+	dt->defaults.bad = 0;
+	dt->defaults.fsx = 1.0;
+	dt->defaults.fsy = 0.0;
+	dt->defaults.fsz = 0.0;
+	dt->defaults.ssx = 0.0;
+	dt->defaults.ssy = 1.0;
+	dt->defaults.ssz = 0.0;
+        dt->defaults.rail_x = NAN;  /* The actual default rail direction */
+        dt->defaults.rail_y = NAN;  /*  is below */
+        dt->defaults.rail_z = NAN;
+        dt->defaults.clen_for_centering = NAN;
+	dt->defaults.adu_scale = NAN;
+	dt->defaults.adu_scale_unit = ADU_PER_PHOTON;
+	dt->defaults.max_adu = +INFINITY;
+	dt->defaults.mask = NULL;
+	dt->defaults.mask_file = NULL;
+	dt->defaults.satmap = NULL;
+	dt->defaults.satmap_file = NULL;
+	dt->defaults.data = NULL;
+	dt->defaults.dim_structure = NULL;
+	dt->defaults.name = NULL;
+
+	string = strdup(string_in);
+	if ( string == NULL ) return NULL;
+	len = strlen(string);
+	for ( i=0; i<len; i++ ) {
+		if ( string_in[i] == '\r' ) string[i] = '\n';
+	}
+
+	/* Becaue 'string' will get modified */
+	string_orig = string;
+
+	do {
+
+		int n1, n2;
+		char **path;
+		char *line;
+		struct dt_badregion *badregion = NULL;
+		struct panel_template *panel = NULL;
+		char wholeval[1024];
+
+		const char *nl = strchr(string, '\n');
+		if ( nl != NULL ) {
+		       size_t len = nl - string;
+			line = strndup(string, nl-string);
+			line[len] = '\0';
+			string += len+1;
+		} else {
+			line = strdup(string);
+			done = 1;
+		}
+
+		if ( line[0] == ';' ) {
+			free(line);
+			continue;
+		}
+
+		n1 = assplode(line, " \t", &bits, ASSPLODE_NONE);
+		if ( n1 < 3 ) {
+			for ( i=0; i<n1; i++ ) free(bits[i]);
+			free(bits);
+			free(line);
+			continue;
+		}
+
+		/* Stitch the pieces of the "value" back together */
+		wholeval[0] = '\0';  /* Empty string */
+		for ( i=2; i<n1; i++ ) {
+			if ( bits[i][0] == ';' ) break;  /* Stop on comment */
+			strncat(wholeval, bits[i], 1023);
+		}
+
+		if ( bits[1][0] != '=' ) {
+			for ( i=0; i<n1; i++ ) free(bits[i]);
+			free(bits);
+			free(line);
+			continue;
+		}
+
+		n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE);
+		if ( n2 < 2 ) {
+
+			/* This was a top-level option, not handled above. */
+			parse_toplevel(dt, bits[0], wholeval, &rg_defl,
+			               &rgc_defl, &n_rg_definitions,
+				       &n_rgc_definitions);
+			for ( i=0; i<n1; i++ ) free(bits[i]);
+			free(bits);
+			for ( i=0; i<n2; i++ ) free(path[i]);
+			free(path);
+			free(line);
+			continue;
+		}
+
+		if ( strncmp(path[0], "bad", 3) == 0 ) {
+			badregion = find_bad_region_by_name(dt, path[0]);
+			if ( badregion == NULL ) {
+				badregion = new_bad_region(dt, path[0]);
+			}
+		} else {
+			panel = find_panel_by_name(dt, path[0]);
+			if ( panel == NULL ) {
+				panel = new_panel(dt, path[0]);
+			}
+		}
+
+		if ( panel != NULL ) {
+			if ( parse_field_for_panel(panel, path[1],
+			                           wholeval, dt) )
+			{
+				reject = 1;
+			}
+		} else {
+			if ( parse_field_bad(badregion, path[1], wholeval) ) {
+				reject = 1;
+			}
+		}
+
+		for ( i=0; i<n1; i++ ) free(bits[i]);
+		for ( i=0; i<n2; i++ ) free(path[i]);
+		free(bits);
+		free(path);
+		free(line);
+
+	} while ( !done );
+
+	if ( dt->n_panels == -1 ) {
+		ERROR("No panel descriptions in geometry file.\n");
+		free(dt);
+		return NULL;
+	}
+
+	path_dim = -1;
+	dim_reject = 0;
+
+	for ( i=0; i<dt->n_panels; i++ ) {
+
+		int panel_dim = 0;
+		char *next_instance;
+
+		next_instance = dt->panels[i].data;
+
+		while ( next_instance ) {
+			next_instance = strstr(next_instance, "%");
+			if ( next_instance != NULL ) {
+				next_instance += 1*sizeof(char);
+				panel_dim += 1;
+			}
+		}
+
+		if ( path_dim == -1 ) {
+			path_dim = panel_dim;
+		} else {
+			if ( panel_dim != path_dim ) {
+				dim_reject = 1;
+			}
+		}
+
+	}
+
+	mask_path_dim = -1;
+	for ( i=0; i<dt->n_panels; i++ ) {
+
+		int panel_mask_dim = 0;
+		char *next_instance;
+
+		if ( dt->panels[i].mask != NULL ) {
+
+			next_instance = dt->panels[i].mask;
+
+			while ( next_instance ) {
+				next_instance = strstr(next_instance, "%");
+				if ( next_instance != NULL ) {
+					next_instance += 1*sizeof(char);
+					panel_mask_dim += 1;
+				}
+			}
+
+			if ( mask_path_dim == -1 ) {
+				mask_path_dim = panel_mask_dim;
+			} else {
+				if ( panel_mask_dim != mask_path_dim ) {
+					dim_reject = 1;
+				}
+			}
+
+		}
+	}
+
+	if ( dim_reject ==  1 ) {
+		ERROR("All panels' data and mask entries must have the same "
+		      "number of placeholders\n");
+		reject = 1;
+	}
+
+	if ( mask_path_dim > path_dim ) {
+		ERROR("Number of placeholders in mask cannot be larger than "
+		      "for data\n");
+		reject = 1;
+	}
+
+	dt->path_dim = path_dim;
+
+	dim_dim_reject = 0;
+	dim_dim = -1;
+
+	for ( i=0; i<dt->n_panels; i++ ) {
+
+		int di;
+		int found_ss = 0;
+		int found_fs = 0;
+		int panel_dim_dim = 0;
+
+		if ( dt->panels[i].dim_structure == NULL ) {
+			dt->panels[i].dim_structure = default_dim_structure();
+		}
+
+		for ( di=0; di<dt->panels[i].dim_structure->num_dims; di++ ) {
+
+			if ( dt->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_UNDEFINED  ) {
+				dim_dim_reject = 1;
+				ERROR("Dimension %i for panel %s is undefined.\n",
+				      di, dt->panels[i].name);
+			}
+			if ( dt->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_PLACEHOLDER  ) {
+				panel_dim_dim += 1;
+			}
+			if ( dt->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_SS  ) {
+				found_ss += 1;
+			}
+			if ( dt->panels[i].dim_structure->dims[di] ==
+			                                   HYSL_FS  ) {
+				found_fs += 1;
+			}
+
+		}
+
+		if ( found_ss != 1 ) {
+			ERROR("Exactly one slow scan dim coordinate is needed "
+			      "(found %i for panel %s)\n", found_ss,
+			      dt->panels[i].name);
+			dim_dim_reject = 1;
+		}
+
+		if ( found_fs != 1 ) {
+			ERROR("Exactly one fast scan dim coordinate is needed "
+			      "(found %i for panel %s)\n", found_fs,
+			      dt->panels[i].name);
+			dim_dim_reject = 1;
+		}
+
+		if ( panel_dim_dim > 1 ) {
+			ERROR("Maximum one placeholder dim coordinate is "
+			      "allowed (found %i for panel %s)\n",
+			      panel_dim_dim, dt->panels[i].name);
+			dim_dim_reject = 1;
+		}
+
+		if ( dim_dim == -1 ) {
+			dim_dim = panel_dim_dim;
+		} else {
+			if ( panel_dim_dim != dim_dim ) {
+				dim_dim_reject = 1;
+			}
+		}
+
+	}
+
+	if ( dim_dim_reject ==  1) {
+		reject = 1;
+	}
+
+	dt->dim_dim = dim_dim;
+
+	for ( i=0; i<dt->n_panels; i++ ) {
+
+		struct panel_template *p = &dt->panels[i];
+
+		if ( p->orig_min_fs < 0 ) {
+			ERROR("Please specify the minimum FS coordinate for"
+			      " panel %s\n", dt->panels[i].name);
+			reject = 1;
+		}
+		if ( p->orig_max_fs < 0 ) {
+			ERROR("Please specify the maximum FS coordinate for"
+			      " panel %s\n", dt->panels[i].name);
+			reject = 1;
+		}
+		if ( p->orig_min_ss < 0 ) {
+			ERROR("Please specify the minimum SS coordinate for"
+			      " panel %s\n", dt->panels[i].name);
+			reject = 1;
+		}
+		if ( p->orig_max_ss < 0 ) {
+			ERROR("Please specify the maximum SS coordinate for"
+			      " panel %s\n", dt->panels[i].name);
+			reject = 1;
+		}
+		if ( isnan(p->cnx) ) {
+			ERROR("Please specify the corner X coordinate for"
+			      " panel %s\n", dt->panels[i].name);
+			reject = 1;
+		}
+		if ( isnan(p->cny) ) {
+			ERROR("Please specify the corner Y coordinate for"
+			      " panel %s\n", dt->panels[i].name);
+			reject = 1;
+		}
+		if ( p->cnz_from == NULL ) {
+			ERROR("Please specify the camera length for panel %s\n",
+			      dt->panels[i].name);
+			reject = 1;
+		}
+		if ( p->pixel_pitch < 0 ) {
+			ERROR("Please specify the pixel size for"
+			      " panel %s\n", dt->panels[i].name);
+			reject = 1;
+		}
+		if ( p->data == NULL ) {
+			ERROR("Please specify the data location for panel %s\n",
+			      p->name);
+			reject = 1;
+		}
+		if ( isnan(p->adu_per_eV) && isnan(p->adu_per_photon) ) {
+			ERROR("Please specify either adu_per_eV or "
+			      "adu_per_photon for panel %s\n",
+			      dt->panels[i].name);
+			reject = 1;
+		}
+
+		if ( isnan(p->clen_for_centering) && !isnan(p->rail_x) )
+		{
+			ERROR("You must specify clen_for_centering if you "
+			      "specify the rail direction (panel %s)\n",
+			      p->name);
+			reject = 1;
+		}
+
+		if ( (p->mask_file != NULL) && (p->mask == NULL) ) {
+			ERROR("You have specified 'mask_file' but not 'mask'.  "
+			      "'mask_file' will therefore have no effect.  "
+			      "(panel %s)\n", p->name);
+			reject = 1;
+		}
+
+		/* The default rail direction */
+		if ( isnan(p->rail_x) ) {
+			p->rail_x = 0.0;
+			p->rail_y = 0.0;
+			p->rail_z = 1.0;
+		}
+		if ( isnan(p->clen_for_centering) ) p->clen_for_centering = 0.0;
+
+	}
+
+	for ( i=0; i<dt->n_bad; i++ ) {
+		if ( dt->bad[i].is_fsss == 99 ) {
+			ERROR("Please specify the coordinate ranges for"
+			      " bad region %s\n", dt->bad[i].name);
+			reject = 1;
+		}
+	}
+
+	free(dt->defaults.cnz_from);
+	free(dt->defaults.data);
+	free(dt->defaults.mask);
+
+	for ( rgi=0; rgi<n_rg_definitions; rgi++) {
+
+		int pi, n1;
+		struct dt_rigid_group *rigidgroup = NULL;
+
+		rigidgroup = find_or_add_rg(dt, rg_defl[rgi]->name);
+
+		n1 = assplode(rg_defl[rgi]->pns, ",", &bits, ASSPLODE_NONE);
+
+		for ( pi=0; pi<n1; pi++ ) {
+
+			struct panel_template *p;
+
+			p = find_panel_by_name(dt, bits[pi]);
+			if ( p == NULL ) {
+				ERROR("Cannot add panel to rigid group\n");
+				ERROR("Panel not found: %s\n", bits[pi]);
+				return NULL;
+			}
+			add_to_rigid_group(rigidgroup, p);
+			free(bits[pi]);
+		}
+		free(bits);
+		free(rg_defl[rgi]->name);
+		free(rg_defl[rgi]->pns);
+		free(rg_defl[rgi]);
+	}
+	free(rg_defl);
+
+	for ( rgci=0; rgci<n_rgc_definitions; rgci++ ) {
+
+		int rgi, n2;
+		struct dt_rg_collection *rgcollection = NULL;
+
+		rgcollection = find_or_add_rg_coll(dt, rgc_defl[rgci]->name);
+
+		n2 = assplode(rgc_defl[rgci]->rgs, ",", &bits, ASSPLODE_NONE);
+
+		for ( rgi=0; rgi<n2; rgi++ ) {
+
+			struct dt_rigid_group *r;
+
+			r = find_rigid_group_by_name(dt, bits[rgi]);
+			if ( r == NULL ) {
+				ERROR("Cannot add rigid group to collection\n");
+				ERROR("Rigid group not found: %s\n", bits[rgi]);
+				return NULL;
+			}
+			add_to_rigid_group_coll(rgcollection, r);
+			free(bits[rgi]);
+		}
+		free(bits);
+		free(rgc_defl[rgci]->name);
+		free(rgc_defl[rgci]->rgs);
+		free(rgc_defl[rgci]);
+
+	}
+	free(rgc_defl);
+
+	if ( n_rg_definitions == 0 ) {
+
+		int pi;
+
+		for ( pi=0; pi<dt->n_panels; pi++ ) {
+
+			struct dt_rigid_group *rigidgroup = NULL;
+
+			rigidgroup = find_or_add_rg(dt, dt->panels[pi].name);
+			add_to_rigid_group(rigidgroup, &dt->panels[pi]);
+
+		}
+	}
+
+	if ( n_rgc_definitions == 0 ) {
+
+		int rgi;
+		struct dt_rg_collection *rgcollection = NULL;
+
+		rgcollection = find_or_add_rg_coll(dt, "default");
+
+		for ( rgi=0; rgi<dt->n_rigid_groups; rgi++ ) {
+
+			add_to_rigid_group_coll(rgcollection,
+			                        dt->rigid_groups[rgi]);
+
+		}
+	}
+
+	free(string_orig);
+
+	if ( reject ) return NULL;
+
+	return dt;
+}
+
+
+DataTemplate *data_template_new_from_file(const char *filename)
+{
+	char *contents;
+	DataTemplate *dt;
+
+	contents = load_entire_file(filename);
+	if ( contents == NULL ) {
+		ERROR("Failed to load geometry file '%s'\n", filename);
+		return NULL;
+	}
+
+	dt = data_template_new_from_string(contents);
+	free(contents);
+	return dt;
+}
+
+
 void data_template_free(DataTemplate *dt)
 {
+	int i;
+
+	free_all_rigid_groups(dt);
+	free_all_rigid_group_collections(dt);
+
+	for ( i=0; i<dt->n_panels; i++ ) {
+		free(dt->panels[i].cnz_from);
+		free_dim_structure(dt->panels[i].dim_structure);
+	}
+
+	free(dt->panels);
+	free(dt->bad);
+	free(dt);
 }
diff --git a/libcrystfel/src/datatemplate_priv.h b/libcrystfel/src/datatemplate_priv.h
new file mode 100644
index 00000000..e8da4193
--- /dev/null
+++ b/libcrystfel/src/datatemplate_priv.h
@@ -0,0 +1,189 @@
+/*
+ * datatemplate_priv.h
+ *
+ * Data template structure (private parts)
+ *
+ * Copyright © 2019-2020 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2019-2020 Thomas White <taw@physics.org>
+ *
+ * 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/>.
+ *
+ */
+
+
+enum adu_per_unit
+{
+	ADU_PER_PHOTON,
+	ADU_PER_EV
+};
+
+
+struct dt_rigid_group
+{
+	char *name;
+	struct panel_template **panels;
+	int n_panels;
+};
+
+
+struct dt_rg_collection
+{
+	char *name;
+	struct dt_rigid_group **rigid_groups;
+	int n_rigid_groups;
+};
+
+
+/**
+ * Represents one panel of a detector
+ */
+struct panel_template
+{
+	/** Text name for panel */
+	char *name;
+
+	/** \name Location of corner in units of the pixel size of this panel */
+	/**@{*/
+	double cnx;
+	double cny;
+	/**@}*/
+
+	/** Location to get \ref cnz from, e.g. from HDF5 file */
+	char *cnz_from;
+
+	/** The offset to be applied from \ref clen */
+	double cnz_offset;
+
+	/** Location of mask data */
+	char *mask;
+
+	/** Filename for mask data */
+	char *mask_file;
+
+	/** Location of per-pixel saturation map */
+	char *satmap;
+
+	/** Filename for saturation map */
+	char *satmap_file;
+
+	/** Mark entire panel as bad if set */
+	int bad;
+
+	/** Resolution in pixels per metre  */
+	double pixel_pitch;
+
+	/** Number of detector intensity units per photon, or eV */
+	double adu_scale;
+	enum adu_per_unit adu_scale_unit;
+
+	/** Treat pixel as unreliable if higher than this */
+	double max_adu;
+
+	/** Location of data in file */
+	char *data;
+
+	/** Dimension structure */
+	struct dim_structure *dim_structure;
+
+	/** \name Transformation matrix from pixel coordinates to lab frame */
+	/*@{*/
+	double fsx;
+	double fsy;
+	double fsz;
+	double ssx;
+	double ssy;
+	double ssz;
+	/*@}*/
+
+	/** \name Rail direction */
+	/*@{*/
+	double rail_x;
+	double rail_y;
+	double rail_z;
+	/*@}*/
+
+	/* Value of clen (without coffset) at which beam is centered */
+	double clen_for_centering;
+
+	/** \name Position of the panel in the data block in the file. */
+	/*@{*/
+	int orig_min_fs;
+	int orig_max_fs;
+	int orig_min_ss;
+	int orig_max_ss;
+	/*@}*/
+
+
+	/* FIXME: Should only be one */
+	double                     adu_per_eV;
+	double                     adu_per_photon;
+
+};
+
+
+struct dt_badregion
+{
+	char name[1024];
+	int is_fsss;
+	char *panel;
+
+	double min_x;
+	double max_x;
+	double min_y;
+	double max_y;
+
+	/* Specified INCLUSIVELY */
+	int      min_fs;
+	int      max_fs;
+	int      min_ss;
+	int      max_ss;
+
+};
+
+
+struct _datatemplate
+{
+	struct panel_template     *panels;
+	int                        n_panels;
+
+	struct dt_badregion       *bad;
+	int                        n_bad;
+
+	char                      *wavelength_from;
+	double                     photon_energy_bandwidth;  /* Eww */
+	double                     photon_energy_scale;      /* Eww */
+
+	char                      *peak_info_location;
+
+	unsigned int               mask_bad;
+	unsigned int               mask_good;
+
+	struct dt_rigid_group    **rigid_groups;
+	int                        n_rigid_groups;
+
+	struct dt_rg_collection  **rigid_group_collections;
+	int                        n_rg_collections;
+
+	int                        path_dim;
+	int                        dim_dim;
+
+	char                      *hdf5_peak_path;
+
+	struct panel_template      defaults;
+};