fix reading ids

Author: jonaslandsgesell

h5mdplugin.c

@@ -71,7 +71,7 @@ static int read_h5md_timestep(void *_file, int natoms, molfile_timestep_t *ts) {
 	h5md_get_ntime(file,&ntime);
 	if(current_time>=ntime)
 		return MOLFILE_ERROR;
-	if ((ts != NULL ||current_time==0)) { //skip reading if ts is NULL pointer (needs modification of the timestep below)
+	if (ts != NULL) { //skip reading if ts is NULL pointer (needs modification of the timestep below)
 		h5md_get_natoms(file, &natoms);
 
 		//read boxinformation
@@ -94,14 +94,12 @@ static int read_h5md_timestep(void *_file, int natoms, molfile_timestep_t *ts) {
 
 	}
 
-
 	int status_seek=h5md_seek_timestep(file, current_time+1); //modify timestep in the internal state of the plugin for this file
 	if(status_seek!=0){
 		status= MOLFILE_SUCCESS;
 	}else if(status_seek!=0 ){
 		status= MOLFILE_ERROR;
 	}
-
 	return status;
 }
 
@@ -156,7 +154,6 @@ int check_consistency_species_index_of_species(struct h5md_file *file, int len_d
 
 //load whole VMD structure
 int read_h5md_structure_vmd_structure(void *_file, int *optflags,molfile_atom_t *atoms) {
-	printf("read structure\n");
 	molfile_atom_t *atom;
 	*optflags = MOLFILE_ATOMICNUMBER | MOLFILE_MASS | MOLFILE_RADIUS |  MOLFILE_INSERTION | MOLFILE_CHARGE; // we read the optional attributes atomicnumber, mass, radius and charge
 	struct h5md_file* file=_file;
@@ -306,7 +303,7 @@ int read_h5md_structure_vmd_structure(void *_file, int *optflags,molfile_atom_t
 	//After assignment free used resources
 	if(status_index_species==0)
 		h5md_free_timeindependent_dataset_automatically(type_class_index_species,data_index_species, 0);
-	if(status_read_species==0)	
+	if(status_read_species>=0)	
 		h5md_free_timeindependent_dataset_automatically(type_class_species,data_species_float, 0);
 	if(status_read_name==0)
 		h5md_free_timeindependent_dataset_automatically(type_class_name,data_name, len_data_index_species);

libh5md.c

@@ -344,7 +344,7 @@ void sort_data_according_to_id_dataset(struct h5md_file* file, int group_number,
 	int i= group_number;
 	/////////////////
 	//read in id_data of group
-	if(file->groups[i].id_dataset_id>0){
+	if(file->groups[i].id_dataset_id>=0){
 		int data_out_local_id[file->groups[i].natoms_group];
 		hid_t dataspace_id_id=H5Dget_space(file->groups[i].id_dataset_id); //Define dataset dataspace (for id_dataset) in file.
 		/* 
@@ -354,17 +354,37 @@ void sort_data_according_to_id_dataset(struct h5md_file* file, int group_number,
 		hsize_t dataset_slab_offset[rank_dataset];
 		dataset_slab_offset[0]=file->current_time;
 		dataset_slab_offset[1]=0;
+		if(rank_dataset==3)
+			dataset_slab_offset[2]=0;
 
 		hsize_t dataset_slab_count[rank_dataset];
 		dataset_slab_count[0] = 1;
 		dataset_slab_count[1] = file->groups[i].natoms_group;
+		if(rank_dataset==3)
+			dataset_slab_count[2]=1;
 		H5Sselect_hyperslab(dataspace_id_id, H5S_SELECT_SET, dataset_slab_offset, NULL, dataset_slab_count, NULL);
+		/*
+		* Define memory dataspace.
+		*/
+		int rank=1; //linear data representation
+		hsize_t dimsm[rank];
+		dimsm[0]=file->groups[i].natoms_group;
+
+		hid_t memspace_id = H5Screate_simple(rank,dimsm,NULL);
 
+		/* 
+		* Define memory hyperslab. 
+		*/
+		hsize_t offset_out[rank];
+		hsize_t count_out[rank];
+		offset_out[0]=0;
+		count_out[0]=file->groups[i].natoms_group;	
+		H5Sselect_hyperslab(memspace_id, H5S_SELECT_SET, offset_out, NULL, count_out, NULL);
 		/*
 		* Read data from hyperslab in the file into the hyperslab in memory
 		*/
 		hid_t wanted_memory_datatype = H5T_NATIVE_INT;
-		H5Dread (file->groups[i].id_dataset_id, wanted_memory_datatype, H5S_SELECT_SET, dataspace_id_id, H5P_DEFAULT, data_out_local_id); 
+		H5Dread (file->groups[i].id_dataset_id, wanted_memory_datatype, memspace_id, dataspace_id_id, H5P_DEFAULT, data_out_local_id); 
 		H5Sclose(dataspace_id_id);
 		//use id data to sort particle positions (use binary tree)
 		//create binary tree
@@ -491,7 +511,7 @@ int h5md_unfold_positions(struct h5md_file* file, float* unsorted_folded_pos){
 		/////////////////
 		//read in image_data of group
 		int data_out_local_image[file->groups[i].natoms_group*file->groups[i].nspacedims];
-		if(file->groups[i].image_dataset_id>0){
+		if(file->groups[i].image_dataset_id>=0){
 			hid_t dataspace_image_id=H5Dget_space(file->groups[i].image_dataset_id); //Define dataset dataspace (for image_dataset) in file.
 			if(dataspace_image_id<0)
 				continue;
@@ -572,7 +592,7 @@ int get_box_vectors(struct h5md_file* file,  int group_i, int time_i, float* vec
 	hid_t box_timeindependent_dataset_id=H5Dopen2(file->file_id, full_path_box_dataset_timeindependent ,H5P_DEFAULT);
 
 
-	if(box_timedependent_dataset_id>0){
+	if(box_timedependent_dataset_id>=0){
 		//timedependent dataset exists, use it
 		//read timedependent dataset 
 		float *data_box = malloc(file->ntime*3*3*sizeof(float));
@@ -588,7 +608,7 @@ int get_box_vectors(struct h5md_file* file,  int group_i, int time_i, float* vec
 		vector_c[2]=data_box[time_i*9+8];
 		free (data_box);
 		status=0;
-	}else if(box_timeindependent_dataset_id>0){
+	}else if(box_timeindependent_dataset_id>=0){
 		//read timeindependent dataset
 		//decided whether box is cubic (dataset contains a vector) or triclinic (dataset contains a matrix)
 		int dims_box;
@@ -660,7 +680,7 @@ int get_box_information(struct h5md_file* file, int group_number, int time_i, h5
 	float vector_a[3];
 	float vector_b[3];
 	float vector_c[3];
-	if(box_timedependent_dataset_id>0){
+	if(box_timedependent_dataset_id>=0){
 		//timedependent dataset exists, use it
 		//read timedependent dataset 
 		status=get_box_vectors(file, group_number, time_i, vector_a,vector_b,vector_c);
@@ -673,7 +693,7 @@ int get_box_information(struct h5md_file* file, int group_number, int time_i, h5
 		box->beta= calculate_angle_between_vectors(vector_a,vector_c,3);
 		box->gamma= calculate_angle_between_vectors(vector_a,vector_b,3);
 	}else{
-		if(box_timeindependent_dataset_id>0){
+		if(box_timeindependent_dataset_id>=0){
 			time_i=FALSE;
 			//read timeindependent dataset
 			//decided whether box is cubic (dataset contains a vector) or triclinic (dataset contains a matrix)
@@ -962,7 +982,7 @@ void h5md_show_hdf5_error_messages(){
 
 int h5md_get_file_id(struct h5md_file *file, hid_t *file_id){
 	*file_id=file->file_id;
-	if(file_id !=0)
+	if(file_id != NULL)
 		return 0;
 	else
 		return -1;
@@ -1056,7 +1076,7 @@ int h5md_append_dataset(struct h5md_file *file, char* absolute_name_of_dataset,
 	int status;
 	//check existence of dataset
 	hid_t dataset_id = H5Dopen2(file->file_id, absolute_name_of_dataset, H5P_DEFAULT);
-	if(dataset_id>0){
+	if(dataset_id>=0){
 		hid_t datatype_read  = H5Dget_type(dataset_id);     // datatype handle
 		H5T_class_t type_class_read     = H5Tget_class(datatype_read);
 		hid_t dataspace_id = H5Dget_space(dataset_id);    //dataspace handle
@@ -1178,7 +1198,7 @@ int h5md_set_author(struct h5md_file* file, char* name, char* email_address){
 		status_email=H5LTset_attribute_string(file->file_id, "/h5md/author", "email", email_address);
 	}
 
-	if( status_name>0 && status_email>0 )
+	if( status_name>=0 && status_email>=0 )
 		return 0;
 	else
 		return -1;
@@ -1204,7 +1224,7 @@ int h5md_set_creator(struct h5md_file* file, char* name, char* version){
 		status_version=H5LTset_attribute_string(file->file_id, "/h5md/creator", "version", version);
 	}
 
-	if(status_name>0  && status_version>0 )
+	if(status_name>=0  && status_version>=0 )
 		return 0;
 	else
 		return -1;

tests/libh5md_test.cc

@@ -210,7 +210,7 @@ int test_appending_to_dataset_position_style(){//depends on test_create_file() s
 					{1, 1, 1.6} };
 	hid_t datatype3= H5T_NATIVE_FLOAT;
 
-	h5md_append_dataset(file, "/testappend", datatype3, (void*) data_in3, rank_in3, dims_in3);
+	h5md_append_dataset(file, "testappend", datatype3, (void*) data_in3, rank_in3, dims_in3);
 
 
 	int rank_in4=3; //should be 3 for positions : time_i, atom_i, x_i
@@ -219,7 +219,7 @@ int test_appending_to_dataset_position_style(){//depends on test_create_file() s
 					{5, 6.0, 2},
 					{5, 5, 5.6} };
 	hid_t datatype4= H5T_NATIVE_FLOAT;
-	int status=h5md_append_dataset(file, "/testappend", datatype4, (void*) data_in4, rank_in4, dims_in4);
+	int status=h5md_append_dataset(file, "testappend", datatype4, (void*) data_in4, rank_in4, dims_in4);
 	h5md_close(file);
 	return status;
 }
@@ -299,12 +299,12 @@ int test_appending_to_onedimensional_string_dataset(){
 }
 
 
-int test_h5md_read_timestep(){
+int test_h5md_get_timestep(){
 	struct h5md_file* file;
  	h5md_open(&file, "../samples/full_vmd_structure.h5", -1);
 	h5md_seek_timestep(file, 1);
-	float* coords= (float*) malloc(100*3*sizeof(float));
-	h5md_read_timestep(file, 100, coords);
+	float* coords= (float*) malloc(3*sizeof(float));
+	h5md_get_timestep(file, coords);
 	int status;
 	if(coords[3*2+0]-0.109156<0.0001)
 		status= 0;

tests/libh5md_test.hpp

@@ -1,7 +1,7 @@
 #ifndef GTEST_LIBH5MD_H_
 #define GTEST_LIBH5MD_H_
 
-int test_h5md_read_timestep();
+int test_h5md_get_timestep();
 int test_create_file();
 int test_write_file_with_datasets();
 int test_write_fixed_length_string_dataset();

tests/libh5md_unittest.cc

@@ -54,8 +54,8 @@ TEST(h5mdWriteTest, test_get_fill_value_float) {
 	EXPECT_EQ(-1, test_get_fill_value_float());
 }
 
-TEST(h5mdReadTest, test_read_timestep){
-	EXPECT_EQ(0, test_h5md_read_timestep());
+TEST(h5mdReadTest, test_h5md_get_timestep){
+	EXPECT_EQ(0, test_h5md_get_timestep());
 }