fromfile indexer in a separate file

4 files changed, 442 insertions, 311 deletions

diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt
index 9f79b0c4..b0f29543 100644
--- a/libcrystfel/CMakeLists.txt
+++ b/libcrystfel/CMakeLists.txt
@@ -75,6 +75,7 @@ set(LIBCRYSTFEL_SOURCES
     src/pinkindexer.c
     src/rational.c
     src/spectrum.c
+    src/fromfile.c
     ${BISON_symopp_OUTPUTS}
     ${FLEX_symopl_OUTPUTS}
 )
@@ -117,6 +118,7 @@ set(LIBCRYSTFEL_HEADERS
     src/pinkindexer.h
     src/rational.h
     src/spectrum.h
+    src/fromfile.h
 )
 
 if (DOXYGEN_FOUND)
diff --git a/libcrystfel/src/fromfile.c b/libcrystfel/src/fromfile.c
new file mode 100644
index 00000000..8dcb92c1
--- /dev/null
+++ b/libcrystfel/src/fromfile.c
@@ -0,0 +1,364 @@
+/*
+ * fromfile.c
+ *
+ * Perform indexing from solution file
+ *
+ *
+ * Authors:
+ *   2020 Pascal Hogan-Lamarre <pascal.hogan.lamarre@mail.utoronto.ca>
+ *
+ * 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/>.
+ *
+ */
+
+#include "image.h"
+#include "detector.h"
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include <fenv.h>
+#include <unistd.h>
+
+#include "uthash.h"
+
+/** \file fromfile.h */
+
+/* There are 9 vector components, 
+ * 2 detector shifts, 1 profile radius,
+ *  1 resolution limit */
+#define NPARAMS_PER_LINE 13  
+/* The keys are the filename, 
+ * event path, event dim and crystal number */
+#define NKEYS_PER_LINE 4  
+
+struct fromfile_private
+{
+	UnitCell *cellTemplate;
+	struct fromfile_entries *sol_hash;
+};
+
+struct fromfile_keys
+{			 	
+  char filename[100];
+  char event_path[100];
+  int event_dim;
+  int crystal_number;
+};
+
+struct fromfile_entries
+{			 		
+    struct fromfile_keys key;
+    float solution[NPARAMS_PER_LINE];
+    UT_hash_handle hh;
+};
+
+void print_struct(struct fromfile_entries *sol_hash) 
+{
+    struct fromfile_entries *s;
+    s = (struct fromfile_entries *)malloc(sizeof *s);
+    memset(s, 0, sizeof *s);
+
+    for( s=sol_hash; s != NULL; s=(struct fromfile_entries*)(s->hh.next) ) {
+        printf("File %s, event %s//%d and crystal_number %d \n",
+		       s->key.filename, s->key.event_path, 
+			   s->key.event_dim, s->key.crystal_number);
+    }
+}
+
+void full_print_struct(struct fromfile_entries *sol_hash)
+{
+    struct fromfile_entries *s;
+    s = (struct fromfile_entries *)malloc(sizeof *s);
+    memset(s, 0, sizeof *s);
+
+    for( s=sol_hash; s != NULL; s=(struct fromfile_entries*)(s->hh.next) ) {
+        printf("File %s, event %s//%d and crystal_number %d \n",
+		       s->key.filename, s->key.event_path, 
+			   s->key.event_dim, s->key.crystal_number);
+		
+		printf("Solution parameters:\n");
+        for( int i = 0; i < NPARAMS_PER_LINE; i++ ){
+		    printf("%e", s->solution[i]);
+        }
+        printf("\n");
+    }
+}
+
+int ncrystals_in_sol(char *path)
+{
+	FILE *fh;
+	int count = 0;  /* Line counter (result) */
+    char c;         /* To store a character read from file */
+
+	fh = fopen(path, "r");
+
+	if ( fh == NULL ) {
+		ERROR("%s not found by ncrystals_in_sol\n",path);
+		return 0;
+	}
+
+	for ( c = getc(fh); c != EOF; c = getc(fh) ){
+        if ( c == '\n' ){
+            count = count + 1; 
+		}
+	}
+	
+	/* For the last line, which has no \n at the end*/
+	count = count + 1;
+  
+    fclose(fh); 
+
+	return count;
+
+}
+
+void *fromfile_prepare(char *solution_filename, UnitCell *cell)
+{	
+	FILE *fh;
+	int nlines;
+	int nparams_in_solution;
+	int nentries;
+	char filename[100];   					
+	char event_path[100];   
+	int event_dim;                
+	int crystal_number;
+	int current_line;
+	int position_in_current_line;
+	struct fromfile_entries *sol_hash = NULL;
+	struct fromfile_entries *item = NULL;
+	float params[NPARAMS_PER_LINE];
+	char path_to_sol[50],extension[10];
+	char cwd[PATH_MAX];
+
+	/* Assembling solution file name from input file name*/
+	strcpy(path_to_sol, "../");
+	strcpy(extension, ".sol");
+	strcat(path_to_sol, strtok(solution_filename, "."));
+	strcat(path_to_sol, extension);
+
+	if (getcwd(cwd, sizeof(cwd)) != NULL) {
+		ERROR("Cannot identify current directory\n");
+	}
+
+	fh = fopen(path_to_sol, "r");
+
+	if ( fh == NULL ) {
+		ERROR("%s not found by fromfile_prepare in %s\n", path_to_sol, cwd);
+		return 0;
+	}
+	else {
+		STATUS("Found solution file %s at %s\n", path_to_sol, cwd);
+	}
+
+	nlines = ncrystals_in_sol(path_to_sol);
+	/* Total crystal parameters in solution file */
+	nparams_in_solution = nlines*NPARAMS_PER_LINE; 
+	/* Total entries in solution file */
+	nentries = nlines*(NPARAMS_PER_LINE+NKEYS_PER_LINE); 
+  
+	STATUS("Parsing solution file containing %d lines...\n", nlines);
+
+	/* Reads indexing solutions */
+	int j = 0; /* follows the solution parameter [0,NPARAMS_PER_LINE] */
+	for(int i = 0; i < nentries; i++)
+	{	
+
+		current_line = i/(NPARAMS_PER_LINE+NKEYS_PER_LINE);
+		
+		position_in_current_line = (i)%(NPARAMS_PER_LINE+NKEYS_PER_LINE);
+
+		if ( position_in_current_line == 0 ){
+			if ( fscanf(fh, "%s", filename) != 1 ) {
+				if ( current_line == (nlines-1) ){
+					break;
+				}
+				else{
+				printf("Failed to read a filename\n");
+				return 0;
+				}
+			}
+		}
+
+		if ( position_in_current_line == 1 ){
+
+			if ( fscanf(fh, "%s", event_path) != 1 ) {
+				printf("Failed to read an event path\n");
+				return 0;
+			}
+		}
+
+		if ( position_in_current_line == 2 ){
+
+			if ( fscanf(fh, "%d", &event_dim) != 1 ) {
+				printf("Failed to read an event dim\n");
+				return 0;
+			}
+		}
+			
+		if ( position_in_current_line == 3 ){
+			if ( fscanf(fh, "%d", &crystal_number) != 1 ) {
+				printf("Failed to read a crystal number\n");
+				return 0;
+			}			
+		}
+
+		if ( position_in_current_line > 3 ){
+			if ( fscanf(fh, "%e", &params[j]) != 1 ) {
+				printf("Failed to read a parameter\n");
+				return 0;
+			}
+			j+=1;			
+		}
+
+		if ( j == (NPARAMS_PER_LINE) ){
+
+			/* Prepare to add to the hash table */
+			item = (struct fromfile_entries *)malloc(sizeof *item);
+			memset(item, 0, sizeof *item);
+			strcpy(item->key.filename, filename);
+			strcpy(item->key.event_path, event_path);
+			item->key.event_dim = event_dim;
+			item->key.crystal_number = crystal_number;
+			for ( int k = 0; k < NPARAMS_PER_LINE; k++){
+    			item->solution[k] = params[k];
+			}
+
+			/* Verify the uniqueness of the key */
+			struct fromfile_entries *uniqueness_test;
+			HASH_FIND(hh, sol_hash, &item->key, 
+			          sizeof(struct fromfile_keys), uniqueness_test); 
+    		if (uniqueness_test==NULL) {
+				HASH_ADD(hh, sol_hash, key, sizeof(struct fromfile_keys), item);
+			}
+			else{
+				printf("Keys must be unique! Verify the combinations");
+				return 0;
+			}
+
+		j=0;		
+
+		}
+	}
+	
+	fclose(fh);
+	
+	STATUS("Solution parsing done. Have %d parameters and %d total entries.\n",
+	       nparams_in_solution, nentries);
+
+	struct fromfile_private *dp;
+	dp = (struct fromfile_private *) malloc( sizeof(struct fromfile_private));
+
+	if ( dp == NULL ){
+		return NULL;
+	}
+    
+    dp->cellTemplate = cell;
+	dp->sol_hash = sol_hash;
+	
+	STATUS("Solution lookup table initialized!\n");
+
+	return (void *)dp;
+}
+
+static void update_detector(struct detector *det, double xoffs, double yoffs)
+{
+	int i;
+
+	for ( i = 0; i < det->n_panels; i++ ) {
+		struct panel *p = &det->panels[i];
+		p->cnx += xoffs * p->res;
+		p->cny += yoffs * p->res;
+	}
+}
+
+int fromfile_index(struct image *image, void *mpriv, int crystal_number)
+{
+	Crystal *cr;
+	UnitCell *cell;
+	float asx, asy, asz, bsx, bsy, bsz, csx, csy, csz;
+	float xshift, yshift, profile_radius, resolution_limit;
+	struct fromfile_entries *item, *p, *pprime;
+	float *sol;
+	
+	struct fromfile_private *dp = (struct fromfile_private *)mpriv;
+
+	/* Look up the hash table */
+	item = (struct fromfile_entries *)malloc(sizeof *item);
+	memset(item, 0, sizeof *item);
+	strcpy(item->key.filename, image->filename);
+	strcpy(item->key.event_path, *image->event->path_entries);
+	item->key.event_dim = *image->event->dim_entries;
+	item->key.crystal_number = crystal_number;
+
+	/* key already in the hash? */
+    HASH_FIND(hh,  dp->sol_hash, &item->key, sizeof(struct fromfile_keys), p);
+    if ( p == NULL ) {
+		return 0;
+	}
+
+	sol = &(p->solution)[0];
+	
+	asx = sol[0] * 1e9;
+	asy = sol[1] * 1e9;
+	asz = sol[2] * 1e9;
+	bsx = sol[3] * 1e9;
+	bsy = sol[4] * 1e9;
+	bsz = sol[5] * 1e9;
+	csx = sol[6] * 1e9;
+	csy = sol[7] * 1e9;
+	csz = sol[8] * 1e9;
+	xshift = sol[9] * 1e-3;
+	yshift = sol[10] * 1e-3;
+	profile_radius = sol[11] * 1e9;
+	resolution_limit = sol[12] * 1e9;
+
+	cr = crystal_new();
+	cell = cell_new();
+	cell_set_reciprocal(cell, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+    cell_set_lattice_type(cell, cell_get_lattice_type(dp->cellTemplate));
+	cell_set_centering(cell, cell_get_centering(dp->cellTemplate));
+	cell_set_unique_axis(cell, cell_get_unique_axis(dp->cellTemplate));
+	
+	crystal_set_cell(cr, cell);
+	crystal_set_det_shift(cr, xshift , yshift);
+	update_detector(image->det, xshift , yshift);
+	crystal_set_profile_radius(cr, profile_radius);
+	crystal_set_resolution_limit(cr, resolution_limit);
+	image_add_crystal(image, cr);
+
+	/*Look for additional crystals*/
+	item->key.crystal_number = crystal_number+1;
+	HASH_FIND(hh,  dp->sol_hash, &item->key, 
+	          sizeof(struct fromfile_keys), pprime);
+
+    if ( pprime == NULL ) {
+		
+		/* If no more crystal, done */
+		return 1;
+	}
+	else{
+		/* If more crystals, recursive call for next crystal in line */
+		fromfile_index(image, mpriv, crystal_number+1);
+	}
+	
+	dp->sol_hash = NULL; /* Clean up local copy */
+	
+	return 1;
+	
+}
\ No newline at end of file
diff --git a/libcrystfel/src/fromfile.h b/libcrystfel/src/fromfile.h
new file mode 100644
index 00000000..dda976b5
--- /dev/null
+++ b/libcrystfel/src/fromfile.h
@@ -0,0 +1,73 @@
+/*
+ * fromfile.h
+ *
+ * Perform indexing from solution file
+ *
+ *
+ * Authors:
+ *   2020 Pascal Hogan-Lamarre <pascal.hogan.lamarre@mail.utoronto.ca>
+ *
+ * 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/>.
+ *
+ */
+
+#ifndef FROMFILE_H
+#define FROMFILE_H
+
+
+#include "image.h"
+#include "cell.h"
+#include "uthash.h"
+
+/* There are 9 vector components, 
+ * 2 detector shifts, 1 profile radius,
+ *  1 resolution limit */
+#define NPARAMS_PER_LINE 13  
+/* The keys are the filename, 
+ * event path, event dim and crystal number */
+#define NKEYS_PER_LINE 4     
+
+struct fromfile_private
+{
+	UnitCell *cellTemplate;
+	struct fromfile_entries *sol_hash;
+};
+
+struct fromfile_keys
+{			 	
+  char filename[100];
+  char event_path[100];
+  int event_dim;
+  int crystal_number;
+};
+
+struct fromfile_entries
+{			 		
+    struct fromfile_keys key;
+    float solution[NPARAMS_PER_LINE];
+    UT_hash_handle hh;
+};
+
+extern void print_struct(struct fromfile_entries *sol_hash);
+
+extern void full_print_struct(struct fromfile_entries *sol_hash);
+
+extern void *fromfile_prepare(char *solution_filename, UnitCell *cell);
+
+extern int fromfile_index(struct image *image, void *mpriv, int crystal_number);
+
+
+#endif	/* FROMFILE_H */
\ No newline at end of file
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 0150787a..c8e34b23 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -60,34 +60,13 @@
 #include "taketwo.h"
 #include "xgandalf.h"
 #include "pinkindexer.h"
+#include "fromfile.h"
 
 #include "uthash.h"
 
 
 /** \file index.h */
 
-#define NPARAMS_PER_LINE 13  // There are 9 vector components, 2 detector shifts, 1 profile radius, 1 resolution limit 
-#define NKEYS_PER_LINE 4  // The keys are the filename, event path, event dim and crystal number 
-
-struct skip_private
-{
-	UnitCell *cellTemplate;
-	struct record_t *sol_hash;
-};
-
-struct record_key_t{			 	//Hash table keys
-  char filename[100];
-  char event_path[100];
-  int event_dim;
-  int crystal_number;
-};
-
-struct record_t{			 		//Hash table
-    struct record_key_t key;
-    float solution[NPARAMS_PER_LINE];
-    UT_hash_handle hh;
-};
-
 struct _indexingprivate
 {
 	IndexingFlags flags;
@@ -99,27 +78,6 @@ struct _indexingprivate
 	void **engine_private;
 };
 
-void print_struct(struct record_t *sol_hash) {
-    struct record_t *s;
-    s = (struct record_t *)malloc(sizeof *s);
-    memset(s, 0, sizeof *s);
-
-    for(s=sol_hash; s != NULL; s=(struct record_t*)(s->hh.next)) {
-        printf("This entry corresponds to event %s//%d and crystal_number %d in file %s \n", s->key.event_path, s->key.event_dim, s->key.crystal_number, s->key.filename);
-    }
-}
-
-void full_print_struct(struct record_t *sol_hash) {
-    struct record_t *s;
-    s = (struct record_t *)malloc(sizeof *s);
-    memset(s, 0, sizeof *s);
-
-    for(s=sol_hash; s != NULL; s=(struct record_t*)(s->hh.next)) {
-        printf("This entry corresponds to event %s//%d and crystal_number %d in file %s \n", s->key.event_path, s->key.event_dim, s->key.crystal_number, s->key.filename);
-		printf("The solution parameters are %e %e %e %e %e %e %e %e %e %e %e %e %e \n", s->solution[0], s->solution[1], s->solution[2], s->solution[3], s->solution[4], s->solution[5], s->solution[6], s->solution[7], s->solution[8], s->solution[9], s->solution[10], s->solution[11], s->solution[12]);
-    }
-}
-
 static const char *onoff(int a)
 {
 	if ( a ) return "on";
@@ -155,272 +113,6 @@ static void show_indexing_flags(IndexingFlags flags)
 	       onoff(flags & INDEXING_RETRY));
 }
 
-int ncrystals_in_sol(char *path)
-{
-	FILE *fh;
-	int count = 0;  // Line counter (result) 
-    char c;  // To store a character read from file 
-
-	fh = fopen(path, "r");
-
-	if ( fh == NULL ) {
-		ERROR("%s not found by ncrystals_in_sol\n",path);
-		return 0;
-	}
-
-	for (c = getc(fh); c != EOF; c = getc(fh)) 
-        if (c == '\n') // Increment count if this character is newline 
-            count = count + 1; 
-	
-	//For the last line, which has no \n at the end
-	count = count + 1;
-  
-    // Close the file 
-    fclose(fh); 
-
-	// STATUS("Found indexing file %s containing %d lines. \n", path, count);
-
-	return count;
-
-}
-
-
-void *skip_prepare(char *solution_filename, UnitCell *cell)
-{	
-	FILE *fh;
-	int nlines;
-	int nparams_in_solution;
-	int nentries;
-	char filename[100];   					
-	char event_path[100];   
-	int event_dim;                
-	int crystal_number;
-	int current_line;
-	int position_in_current_line;
-	struct record_t *sol_hash = NULL;
-	struct record_t *item = NULL;
-	float params[NPARAMS_PER_LINE];
-	char path_to_sol[50],extension[10];
-	char cwd[PATH_MAX];
-
-	//Assembling solution file name from input file name to crystfel
-	strcpy(path_to_sol,"../");
-	strcpy(extension,".sol");
-	strcat(path_to_sol, strtok(solution_filename, ".") );     //Add .sol at the previously splitted name
-	strcat(path_to_sol, extension );
-
-	if (getcwd(cwd, sizeof(cwd)) != NULL) {
-		//printf("Path where skip_prepare is ran: %s\n", cwd);
-	}
-
-	fh = fopen(path_to_sol, "r");
-
-	if ( fh == NULL ) {
-		ERROR("%s not found by skip_prepare in %s\n", path_to_sol, cwd);
-		return 0;
-	}
-	else {
-		STATUS("Found solution file %s at %s\n", path_to_sol, cwd);
-	}
-
-	nlines = ncrystals_in_sol(path_to_sol);
-	nparams_in_solution = nlines*NPARAMS_PER_LINE; /* total crystal parameters in solution file */
-	nentries = nlines*(NPARAMS_PER_LINE+NKEYS_PER_LINE); /* total entries in solution file */
-  
-	STATUS("Parsing solution file containing %d lines...\n", nlines);
-
-	//Reads indexing solutions
-	int j = 0; //index that follows the solution parameter [0,NPARAMS_PER_LINE]
-	for(int i = 0; i < nentries; i++)
-	{	
-
-		current_line = i/(NPARAMS_PER_LINE+NKEYS_PER_LINE);
-		
-		position_in_current_line = (i)%(NPARAMS_PER_LINE+NKEYS_PER_LINE);
-
-		if (position_in_current_line == 0){
-
-			if ( fscanf(fh, "%s", filename) != 1 ) {
-				if (current_line == (nlines-1)){
-					break;
-				}
-				else{
-				printf("Failed to read a filename from indexing.sol with skip_prepare\n");
-				return 0;
-				}
-			}
-		}
-
-		if (position_in_current_line == 1){
-
-			if ( fscanf(fh, "%s", event_path) != 1 ) {
-				printf("Failed to read an event path from indexing.sol with skip_prepare\n");
-				return 0;
-			}
-		}
-
-		if (position_in_current_line == 2){
-
-			if ( fscanf(fh, "%d", &event_dim) != 1 ) {
-				printf("Failed to read an event dim from indexing.sol with skip_prepare\n");
-				return 0;
-			}
-		}
-			
-		if (position_in_current_line == 3){
-			if ( fscanf(fh, "%d", &crystal_number) != 1 ) {
-				printf("Failed to read a crystal number from indexing.sol with skip_prepare\n");
-				return 0;
-			}			
-		}
-
-		if (position_in_current_line > 3){
-			if ( fscanf(fh, "%e", &params[j]) != 1 ) {
-				printf("Failed to read a parameter from indexing.sol with skip_prepare\n");
-				return 0;
-			}
-			j+=1;
-
-			
-		}
-
-		if (j == (NPARAMS_PER_LINE) ){
-
-			//Prepare to add to the hash table
-			item = (struct record_t *)malloc(sizeof *item);
-			memset(item, 0, sizeof *item);
-			strcpy(item->key.filename, filename);
-			strcpy(item->key.event_path, event_path);
-			item->key.event_dim = event_dim;
-			item->key.crystal_number = crystal_number;
-			for (int k = 0; k < NPARAMS_PER_LINE; k++){
-    			item->solution[k] = params[k];
-			}
-
-			//Verify the uniqueness of the key
-			struct record_t *uniqueness_test;
-			HASH_FIND(hh, sol_hash, &item->key, sizeof(struct record_key_t), uniqueness_test);  // id already in the hash? 
-    		if (uniqueness_test==NULL) {
-				//If not in the table, add
-				HASH_ADD(hh, sol_hash, key, sizeof(struct record_key_t), item);
-			}
-			else{
-				//If already in the table, break with error
-				printf("Keys to the data must be unique! Verify the combination filename, event, crystal_number");
-				return 0;
-			}
-
-		j=0;		
-
-		}
-	}
-	
-	fclose(fh);
-	
-	STATUS("Solution file parsing done. Have %d parameters and %d total entries.\n", nparams_in_solution, nentries)
-
-	struct skip_private *dp;
-	dp = (struct skip_private *) malloc( sizeof(struct skip_private));
-
-	if ( dp == NULL ) return NULL;
-    
-    dp->cellTemplate = cell;
-	dp->sol_hash = sol_hash;
-	
-	STATUS("Solution lookup table initialized!\n");
-
-	return (void *)dp;
-}
-
-//Fonction from pinkindexer.c to update the detector center of individual crystals
-//hack for electron crystallography while crystal_set_det_shift is not working approprietly
-static void update_detector(struct detector *det, double xoffs, double yoffs)
-{
-	int i;
-
-	for (i = 0; i < det->n_panels; i++) {
-		struct panel *p = &det->panels[i];
-		p->cnx += xoffs * p->res;
-		p->cny += yoffs * p->res;
-	}
-}
-
-static int skip_index(struct image *image, void *mpriv, int crystal_number)
-{
-	Crystal *cr;
-	UnitCell *cell;
-	float asx, asy, asz, bsx, bsy, bsz, csx, csy, csz, xshift, yshift, profile_radius, resolution_limit;
-	struct record_t *item, *p, *pprime;
-	float *sol;
-	
-	struct skip_private *dp = (struct skip_private *)mpriv;
-
-	//Look up the hash table
-	item = (struct record_t *)malloc(sizeof *item);
-	memset(item, 0, sizeof *item);
-	strcpy(item->key.filename, image->filename);
-	strcpy(item->key.event_path, *image->event->path_entries);
-	item->key.event_dim = *image->event->dim_entries;
-	item->key.crystal_number = crystal_number;
-
-    HASH_FIND(hh,  dp->sol_hash, &item->key, sizeof(struct record_key_t), p);  //id already in the hash?
-    if (p==NULL) {
-		//STATUS("Not indexing file %s, event %s %d \n", image->filename, *image->event->path_entries, *image->event->dim_entries);
-		return 0;
-	}
-
-	sol = &(p->solution)[0];
-	
-	asx = sol[0];
-	asy = sol[1];
-	asz = sol[2];
-	bsx = sol[3];
-	bsy = sol[4];
-	bsz = sol[5];
-	csx = sol[6];
-	csy = sol[7];
-	csz = sol[8];
-	xshift = sol[9];
-	yshift = sol[10];
-	profile_radius = sol[11];
-	resolution_limit = sol[12];
-
-	cr = crystal_new();
-	cell = cell_new();
-	cell_set_reciprocal(cell, asx * 1e9, asy * 1e9, asz* 1e9, bsx * 1e9, bsy * 1e9, bsz * 1e9, csx * 1e9, csy * 1e9, csz* 1e9);
-    cell_set_lattice_type(cell, cell_get_lattice_type(dp->cellTemplate));
-	cell_set_centering(cell, cell_get_centering(dp->cellTemplate));
-	cell_set_unique_axis(cell, cell_get_unique_axis(dp->cellTemplate));
-	
-	crystal_set_cell(cr, cell);
-	crystal_set_det_shift(cr, xshift * 1e-3, yshift * 1e-3);
-	update_detector(image->det, xshift * 1e-3, yshift * 1e-3);
-	crystal_set_profile_radius(cr, profile_radius*1e9);
-	crystal_set_resolution_limit(cr, resolution_limit*1e9);
-	image_add_crystal(image, cr);
-
-	//Look for additional crystals
-	item->key.crystal_number = crystal_number+1;
-	HASH_FIND(hh,  dp->sol_hash, &item->key, sizeof(struct record_key_t), pprime);  //id already in the hash?
-    if (pprime==NULL) {
-		
-		//If no more crystal, done
-		return 1;
-	}
-	else{
-		//If more crystals, recursive call for next crystal in line
-		skip_index(image,mpriv,crystal_number+1);
-	}
-
-	
-	dp->sol_hash = NULL; //Clean up local copy of the hash table
-	
-
-	return 1;
-	
-}
-
-
 static char *base_indexer_str(IndexingMethod indm)
 {
 	char *str;
@@ -541,7 +233,7 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
 		break;
 
 		case INDEXING_FILE :
-		priv = skip_prepare(filename, cell);
+		priv = fromfile_prepare(filename, cell);
 		break;
 
 		case INDEXING_FELIX :
@@ -924,7 +616,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		case INDEXING_FILE :
 		set_last_task(last_task, "indexing:file");
 		int crystal_number = 0;
-		r = skip_index(image,mpriv,crystal_number);
+		r = fromfile_index(image, mpriv, crystal_number);
 		break;
 
 		case INDEXING_FELIX :