Initial code commit.
Little to no error reporting, still fairly brittle and not very well tested.
This commit is contained in:
Charles Mita
@@ -0,0 +1,7 @@
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||||
*.swp
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*.*~
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||||
*.bak
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||||
*.tmp
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||||
|
||||
*.o
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||||
*.so
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||||
@@ -0,0 +1,24 @@
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||||
Copyright (c) 2018, Diamond Light Source
|
||||
All rights reserved.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions are met:
|
||||
* Redistributions of source code must retain the above copyright
|
||||
notice, this list of conditions and the following disclaimer.
|
||||
* Redistributions in binary form must reproduce the above copyright
|
||||
notice, this list of conditions and the following disclaimer in the
|
||||
documentation and/or other materials provided with the distribution.
|
||||
* Neither the name of the <organization> nor the
|
||||
names of its contributors may be used to endorse or promote products
|
||||
derived from this software without specific prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
|
||||
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
|
||||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
||||
DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
|
||||
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
|
||||
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
|
||||
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
|
||||
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
|
||||
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
||||
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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||||
@@ -0,0 +1,18 @@
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||||
BUILD_DIR ?= ./build
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SRC_DIR = ./src
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||||
INC_DIR = $(SRC_DIR)
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CC=h5cc
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CFLAGS=-Wall -g -O2 -fpic -I$(INC_DIR)
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|
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$(BUILD_DIR)/%.o: $(SRC_DIR)/%.c
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mkdir -p $(BUILD_DIR)
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$(CC) $(CFLAGS) -c $< -o $@
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plugin: $(BUILD_DIR)/plugin.o $(BUILD_DIR)/file.o
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mkdir -p $(BUILD_DIR)
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$(CC) $(CFLAGS) -shared $^ -o $(BUILD_DIR)/plugin.so
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.PHONY: clean
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clean:
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rm -r $(BUILD_DIR)
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+668
@@ -0,0 +1,668 @@
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/*
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* Copyright (c) 2018 Diamond Light Source Ltd.
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* Author: Charles Mita
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*/
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#include <hdf5.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <strings.h>
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#include "file.h"
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hid_t h5_int_type_from_width(const int width) {
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if (width == sizeof(char)) {
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return H5T_NATIVE_SCHAR;
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} else if (width == sizeof(short)) {
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return H5T_NATIVE_SHORT;
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} else if (width == sizeof(int)) {
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return H5T_NATIVE_INT;
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} else if (width == sizeof(long)) {
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return H5T_NATIVE_LONG;
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} else if (width == sizeof(long long)) {
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return H5T_NATIVE_LLONG;
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} else {
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/* TODO: error */
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return -1;
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}
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}
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void clear_det_visit_objects(struct det_visit_objects_t *objects) {
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if (objects->nxdata) {
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H5Oclose(objects->nxdata);
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objects->nxdata = 0;
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}
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if (objects->nxdetector) {
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H5Oclose(objects->nxdetector);
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objects->nxdetector = 0;
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}
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}
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void free_dataset_properties(struct dataset_properties_t *p) {
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if (p->dims) {
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free(p->dims);
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p->dims = NULL;
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}
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p->ndims = 0;
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}
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void free_nxs_data_description(struct data_description_t *desc) {
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if (desc->extra) free(desc->extra); /* should just be NULL */
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desc->extra = NULL;
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}
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void free_eiger_data_description(struct data_description_t *desc) {
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if (!desc->extra) return;
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struct eiger_data_description_t *extra = desc->extra;
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if (extra->block_sizes) free(extra->block_sizes);
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free(extra);
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desc->extra = NULL;
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}
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double scale_from_units(const char* unit_string) {
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if (strcasecmp("m", unit_string) == 0 ||
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strcasecmp("metres", unit_string) == 0 ||
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strcasecmp("meters", unit_string) == 0) {
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return 1.;
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} else if (strcasecmp("cm", unit_string) == 0 ||
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strcasecmp("centimetres", unit_string) == 0 ||
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strcasecmp("centimeters", unit_string) == 0) {
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return 0.01;
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} else if (strcasecmp("mm", unit_string) == 0 ||
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strcasecmp("millimetres", unit_string) == 0 ||
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strcasecmp("millimeters", unit_string) == 0) {
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return 0.001;
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} else if (strcasecmp("um", unit_string) == 0 ||
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strcasecmp("microns", unit_string) == 0 ||
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strcasecmp("micrometres", unit_string) == 0 ||
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strcasecmp("micrometers", unit_string) == 0) {
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return 0.000001;
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} else {
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fprintf(stderr, "Unrecognised unit string %s", unit_string);
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return 1;
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}
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||||
}
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int get_nxs_dataset_dims(const struct data_description_t *desc, struct dataset_properties_t *properties) {
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hid_t g_id, ds_id, s_id, t_id;
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int retval = 0;
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int ndims = 0;
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int width = 0;
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hsize_t *dims = NULL;
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g_id = desc->data_group_id;;
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ds_id = H5Dopen2(g_id, "data", H5P_DEFAULT);
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if (ds_id <= 0) {
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retval = -1;
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return retval;
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}
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t_id = H5Dget_type(ds_id);
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if (t_id <= 0) {
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retval = -1;
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goto close_dataset;
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}
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width = H5Tget_size(t_id);
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if (width <= 0) {
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retval = -1;
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goto close_type;
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||||
}
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s_id = H5Dget_space(ds_id);
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||||
if (s_id <= 0) {
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||||
retval = -1;
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||||
goto close_dataset;
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||||
}
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||||
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||||
ndims = H5Sget_simple_extent_ndims(s_id);
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||||
if (ndims <= 0) {
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retval = -1;
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||||
goto close_space;
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||||
}
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dims = malloc(ndims * sizeof(hsize_t));
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||||
if (!dims) {
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||||
retval = -1;
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||||
goto close_space;
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||||
}
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||||
if (H5Sget_simple_extent_dims(s_id, dims, NULL) < 0) {
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||||
retval = -1;
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||||
free(dims);
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||||
goto close_space;
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||||
}
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||||
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properties->ndims = ndims;
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||||
properties->dims = dims;
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properties->data_width = width;
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||||
close_space:
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H5Sclose(s_id);
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close_type:
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H5Tclose(t_id);
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||||
close_dataset:
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H5Dclose(ds_id);
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||||
return retval;
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}
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int get_frame(hid_t g_id, const char* name, hsize_t *frame_idx, hsize_t *frame_size, int data_width, void *buffer) {
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int retval = 0;
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herr_t err = 0;
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hid_t ds_id, s_id, ms_id, t_id;
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||||
ds_id = H5Dopen2(g_id, name, H5P_DEFAULT);
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if (ds_id <= 0) {
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retval = -1;
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||||
return retval;
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||||
}
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s_id = H5Dget_space(ds_id);
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||||
if (s_id <= 0) {
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retval = -1;
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goto close_dataset;
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||||
}
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err = H5Sselect_hyperslab(s_id, H5S_SELECT_SET, frame_idx, NULL, frame_size, NULL);
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if (err < 0) {
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retval = -1;
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goto close_space;
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||||
}
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ms_id = H5Screate_simple(3, frame_size, frame_size);
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if (ms_id < 0) {
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retval = -1;
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goto close_space;
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}
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t_id = h5_int_type_from_width(data_width);
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if (t_id < 0) {
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retval = -1;
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goto close_mspace;
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}
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err = H5Dread(ds_id, t_id, ms_id, s_id, H5P_DEFAULT, buffer);
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if (err < 0) {
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retval = -1;
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goto close_mspace;
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}
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close_mspace:
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H5Sclose(ms_id);
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close_space:
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H5Sclose(s_id);
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close_dataset:
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H5Dclose(ds_id);
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return retval;
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}
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int get_nxs_frame(
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const struct data_description_t *desc,
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const struct dataset_properties_t *ds_prop,
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int n,
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int data_width,
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void *buffer) {
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/* detector data are the two inner most indices */
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/* n is indexed from one - hdf5 slices start at zero */
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/* TODO: handle ndims > 3 and select appropriately */
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int retval = 0;
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hsize_t frame_idx[3] = {n - 1, 0, 0};
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hsize_t frame_size[3] = {1, ds_prop->dims[1], ds_prop->dims[2]};
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retval = get_frame(desc->data_group_id, "data", frame_idx, frame_size, data_width, buffer);
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return retval;
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}
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||||
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int get_dectris_eiger_frame(
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const struct data_description_t *desc,
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const struct dataset_properties_t *ds_prop,
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int n,
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||||
int data_width,
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||||
void *buffer) {
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||||
|
||||
int retval = 0;
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||||
int block, frame_count, idx;
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||||
struct eiger_data_description_t *eiger_desc = desc->extra;
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char data_name[16] = {0};
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hsize_t frame_idx[3] = {0, 0, 0};
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hsize_t frame_size[3] = {1, ds_prop->dims[1], ds_prop->dims[2]};
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||||
|
||||
/* determine the relevant data block */
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||||
frame_count = 0;
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||||
block = 0;
|
||||
while ((frame_count += eiger_desc->block_sizes[block]) < (n-1)) block++;
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||||
idx = n - (frame_count - eiger_desc->block_sizes[block]) - 1; /* index in current block */
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||||
printf("n: %d -> Block: %d, idx: %d\n", n, block, idx);
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frame_idx[0] = idx;
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sprintf(data_name, "data_%06d", block + 1);
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||||
retval = get_frame(desc->data_group_id, data_name, frame_idx, frame_size, data_width, buffer);
|
||||
return retval;
|
||||
}
|
||||
|
||||
|
||||
int get_dectris_eiger_dataset_dims(const struct data_description_t *desc, struct dataset_properties_t *properties) {
|
||||
int retval = 0;
|
||||
int n_datas = 0;
|
||||
int n = 0;
|
||||
int data_width = 0;
|
||||
int ndims = 3;
|
||||
char ds_name[16] = {0}; /* 12 chars in "data_xxxxxx\0" */
|
||||
int *frame_counts = NULL;
|
||||
hsize_t *dims = malloc(3 * sizeof(hsize_t));
|
||||
if (!dims) {
|
||||
retval = -1;
|
||||
return retval;
|
||||
}
|
||||
memset(dims, 0, sizeof(hsize_t) * ndims);
|
||||
|
||||
/* datasets are "data_%06d % n" - need to determine how many of these there are and what the ranges are */
|
||||
|
||||
sprintf(ds_name, "data_%06d", n_datas + 1);
|
||||
while (H5Lexists(desc->data_group_id, ds_name, H5P_DEFAULT) > 0) {
|
||||
sprintf(ds_name, "data_%06d", ++n_datas + 1);
|
||||
}
|
||||
|
||||
frame_counts = malloc(n_datas * sizeof(*frame_counts));
|
||||
|
||||
for (n = 0; n < n_datas; n++) {
|
||||
hid_t ds_id, t_id, s_id;
|
||||
hsize_t block_dims[3] = {0};
|
||||
sprintf(ds_name, "data_%06d", n + 1);
|
||||
ds_id = H5Dopen2(desc->data_group_id, ds_name, H5P_DEFAULT);
|
||||
if (ds_id < 0) {
|
||||
retval = -1;
|
||||
break;
|
||||
}
|
||||
t_id = H5Dget_type(ds_id);
|
||||
if (t_id < 0) {
|
||||
retval = -1;
|
||||
goto close_dataset;
|
||||
}
|
||||
s_id = H5Dget_space(ds_id);
|
||||
if (s_id < 0) {
|
||||
retval = -1;
|
||||
goto close_type;
|
||||
}
|
||||
|
||||
data_width = H5Tget_size(t_id);
|
||||
if (data_width <= 0) {
|
||||
retval = -1;
|
||||
goto close_space;
|
||||
}
|
||||
|
||||
if (H5Sget_simple_extent_dims(s_id, block_dims, NULL) < 0) {
|
||||
retval = -1;
|
||||
goto close_space;
|
||||
}
|
||||
|
||||
dims[1] = block_dims[1];
|
||||
dims[2] = block_dims[2];
|
||||
|
||||
dims[0] += block_dims[0];
|
||||
frame_counts[n] = block_dims[0];
|
||||
|
||||
close_space:
|
||||
H5Sclose(s_id);
|
||||
close_type:
|
||||
H5Tclose(t_id);
|
||||
close_dataset:
|
||||
H5Dclose(ds_id);
|
||||
}
|
||||
|
||||
if (retval < 0) {
|
||||
free(dims);
|
||||
free(frame_counts);
|
||||
} else {
|
||||
properties->ndims = ndims;
|
||||
properties->dims = dims;
|
||||
properties->data_width = data_width;
|
||||
((struct eiger_data_description_t *) desc->extra)->n_data_blocks = n_datas;
|
||||
((struct eiger_data_description_t *) desc->extra)->block_sizes = frame_counts;
|
||||
}
|
||||
return retval;
|
||||
}
|
||||
|
||||
|
||||
int read_pixel_info(hid_t g_id, const char *path, double *size) {
|
||||
/*
|
||||
* NXdetector allows pixel size to be an array (for varied pixel size),
|
||||
* however XDS only allows for a single value.
|
||||
* TODO: handle array case (return first value maybe?)
|
||||
*/
|
||||
|
||||
/* read the scalar dataset value and scale according to the unit in the attribute */
|
||||
/* returned value is in metres */
|
||||
int retval = 0;
|
||||
herr_t err = 0;
|
||||
hid_t ds_id;
|
||||
double value = 0;
|
||||
ds_id = H5Dopen2(g_id,path, H5P_DEFAULT);
|
||||
if (ds_id < 0) {
|
||||
retval = -1;
|
||||
return retval;;
|
||||
}
|
||||
|
||||
err = H5Dread(ds_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &value);
|
||||
if (err < 0) {
|
||||
retval = -1;
|
||||
goto close_dataset;
|
||||
}
|
||||
|
||||
if (H5Aexists(ds_id, "units") > 0) {
|
||||
/* string may be variable length */
|
||||
hid_t a_id, t_id, mt_id;
|
||||
void *str_buffer = NULL;
|
||||
int str_size = -1;
|
||||
double scale = 1;
|
||||
a_id = H5Aopen(ds_id, "units", H5P_DEFAULT);
|
||||
if (a_id < 0) {
|
||||
retval = -1;
|
||||
goto close_dataset;
|
||||
}
|
||||
|
||||
t_id = H5Aget_type(a_id);
|
||||
if (t_id < 0) {
|
||||
retval = -1;
|
||||
goto close_attribute;
|
||||
}
|
||||
/* TODO: handle multiple strings in attribute (just detect and error) */
|
||||
if (H5Tis_variable_str(t_id) > 0) {
|
||||
str_size = -1;
|
||||
str_buffer = malloc(sizeof(char*));
|
||||
} else {
|
||||
str_size = H5Tget_size(t_id);
|
||||
/* do not assume room has been left for null-byte in fixed length string */
|
||||
str_buffer = malloc(str_size + 1);
|
||||
}
|
||||
if (str_buffer == NULL) {
|
||||
retval = -1;
|
||||
goto close_datatype;
|
||||
}
|
||||
mt_id = H5Tcopy(H5T_C_S1);
|
||||
if (mt_id < 0) {
|
||||
retval = -1;
|
||||
goto free_string;
|
||||
}
|
||||
err = H5Tset_size(mt_id, str_size == -1 ? H5T_VARIABLE : str_size);
|
||||
if (err < 0) {
|
||||
retval = -1;
|
||||
goto close_mem_datatype;
|
||||
}
|
||||
|
||||
err = H5Aread(a_id, mt_id, str_buffer);
|
||||
if (err < 0) {
|
||||
retval = -1;
|
||||
goto close_mem_datatype;
|
||||
}
|
||||
/* ensure last byte is null */
|
||||
if (str_size > 0) ((char*) str_buffer)[str_size] = '\0';
|
||||
|
||||
scale = scale_from_units(str_size == -1 ? *(char**)str_buffer : (char*)str_buffer);
|
||||
value *= scale;
|
||||
|
||||
if (str_size == -1) {
|
||||
/* we have to create this dataspace just to indicate we want
|
||||
* to clear the entire vlen dataset (all 1 element - good job HDF5)
|
||||
*/
|
||||
hsize_t dims[1] = {1};
|
||||
hid_t s_id = H5Screate_simple(1, dims, NULL);
|
||||
H5Sselect_all(s_id);
|
||||
H5Dvlen_reclaim(mt_id, s_id, H5P_DEFAULT, str_buffer);
|
||||
H5Sclose(s_id);
|
||||
}
|
||||
close_mem_datatype:
|
||||
H5Tclose(mt_id);
|
||||
free_string:
|
||||
free(str_buffer);
|
||||
close_datatype:
|
||||
H5Tclose(t_id);
|
||||
close_attribute:
|
||||
H5Aclose(a_id);
|
||||
}
|
||||
|
||||
*size = value;
|
||||
|
||||
close_dataset:
|
||||
H5Dclose(ds_id);
|
||||
|
||||
return retval;
|
||||
}
|
||||
|
||||
|
||||
int get_nxs_pixel_info(const struct data_description_t *desc, double *x_size, double *y_size) {
|
||||
if (read_pixel_info(desc->det_group_id, "x_pixel_size", x_size) < 0) {
|
||||
return -1;
|
||||
}
|
||||
if (read_pixel_info(desc->det_group_id, "y_pixel_size", y_size) < 0) {
|
||||
return -1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
int get_dectris_eiger_pixel_info(const struct data_description_t *desc, double *x_size, double *y_size) {
|
||||
if (read_pixel_info(desc->det_group_id, "detectorSpecific/x_pixel_size", x_size) < 0) {
|
||||
return -1;
|
||||
}
|
||||
if (read_pixel_info(desc->det_group_id, "detectorSpecific/y_pixel_size", y_size) < 0) {
|
||||
return -1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
int get_nxs_pixel_mask(const struct data_description_t *desc, int *buffer) {
|
||||
int retval = 0;
|
||||
hid_t ds_id;
|
||||
herr_t err = 0;
|
||||
|
||||
ds_id = H5Dopen2(desc->det_group_id, "pixel_mask", H5P_DEFAULT);
|
||||
if (ds_id < 0) {
|
||||
retval = -1;
|
||||
return retval;
|
||||
}
|
||||
|
||||
err = H5Dread(ds_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
|
||||
if (err < 0) {
|
||||
retval = -1;
|
||||
goto close_dataset;
|
||||
}
|
||||
|
||||
close_dataset:
|
||||
H5Dclose(ds_id);
|
||||
return retval;
|
||||
}
|
||||
|
||||
|
||||
int get_dectris_eiger_pixel_mask(const struct data_description_t *desc, int *buffer) {
|
||||
int retval = 0;
|
||||
hid_t ds_id;
|
||||
herr_t err = 0;
|
||||
|
||||
ds_id = H5Dopen2(desc->det_group_id, "detectorSpecific/pixel_mask", H5P_DEFAULT);
|
||||
if (ds_id < 0) {
|
||||
retval = -1;
|
||||
return retval;
|
||||
}
|
||||
|
||||
err = H5Dread(ds_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
|
||||
if (err < 0) {
|
||||
retval = -1;
|
||||
goto close_dataset;
|
||||
}
|
||||
|
||||
close_dataset:
|
||||
H5Dclose(ds_id);
|
||||
return retval;
|
||||
|
||||
}
|
||||
|
||||
|
||||
herr_t det_visit_callback(hid_t root_id, const char *name, const H5O_info_t *info, void *op_data) {
|
||||
struct det_visit_objects_t *output_data = op_data;
|
||||
hid_t g_id;
|
||||
herr_t retval = 0;
|
||||
if (info->type != H5O_TYPE_GROUP) return 0;
|
||||
g_id = H5Oopen(root_id, name, H5P_DEFAULT);
|
||||
|
||||
/* check for an "NX_class" attribute */
|
||||
{
|
||||
char* buffer = NULL;
|
||||
hid_t a_id, t_id;
|
||||
H5A_info_t a_info;
|
||||
if (H5Aexists(g_id, "NX_class") <= 0) {
|
||||
retval = 0;
|
||||
goto close_group;
|
||||
}
|
||||
a_id = H5Aopen(g_id, "NX_class", H5P_DEFAULT);
|
||||
if (a_id <= 0) {
|
||||
/* TODO: error trace */
|
||||
retval = -1;
|
||||
goto close_group;
|
||||
}
|
||||
if (H5Aget_info(a_id, &a_info) < 0) {
|
||||
/* TODO: handle error */
|
||||
retval = -1;
|
||||
goto close_attr;
|
||||
}
|
||||
t_id = H5Tcreate(H5T_STRING, a_info.data_size);
|
||||
if (t_id <= 0) {
|
||||
retval = -1;
|
||||
goto close_attr;
|
||||
}
|
||||
buffer = malloc(a_info.data_size + 1);
|
||||
if (buffer == NULL) {
|
||||
/* TODO: OOM error */
|
||||
retval =- 1;
|
||||
goto close_type;
|
||||
}
|
||||
|
||||
if (H5Aread(a_id, t_id, buffer) < 0) {
|
||||
/*TODO: handle*/
|
||||
retval = -1;
|
||||
goto free_buffer;
|
||||
}
|
||||
|
||||
/* at least one file has been seen where the NX_class attribute was not null terminated
|
||||
* and extraneous bytes where being read by strcmp - set the end byte to null
|
||||
*/
|
||||
buffer[a_info.data_size] = '\0';
|
||||
if (strcmp("NXdata", buffer) == 0) {
|
||||
hid_t out_id = H5Gopen(root_id, name, H5P_DEFAULT);
|
||||
output_data->nxdata = out_id;
|
||||
} else if (strcmp("NXdetector", buffer) == 0) {
|
||||
hid_t out_id = H5Gopen(root_id, name, H5P_DEFAULT);
|
||||
output_data->nxdetector = out_id;
|
||||
}
|
||||
|
||||
free_buffer:
|
||||
free(buffer);
|
||||
close_type:
|
||||
H5Tclose(t_id);
|
||||
close_attr:
|
||||
H5Aclose(a_id);
|
||||
}
|
||||
|
||||
close_group:
|
||||
if (H5Gclose(g_id) < 0) {
|
||||
/* TODO: error trace */
|
||||
retval = -1;
|
||||
}
|
||||
return retval;
|
||||
}
|
||||
|
||||
|
||||
int fill_data_descriptor(struct data_description_t *data_desc, struct det_visit_objects_t *visit_result) {
|
||||
int retval = 0;
|
||||
data_desc->det_group_id = visit_result->nxdetector;
|
||||
|
||||
/* determine the pixel information location */
|
||||
if (H5Lexists(data_desc->det_group_id, "x_pixel_size", H5P_DEFAULT) > 0 &&
|
||||
H5Lexists(data_desc->det_group_id, "y_pixel_size", H5P_DEFAULT)) {
|
||||
data_desc->get_pixel_properties = &get_nxs_pixel_info;
|
||||
} else if (H5Lexists(data_desc->det_group_id, "detectorSpecific", H5P_DEFAULT) > 0 &&
|
||||
H5Lexists(data_desc->det_group_id, "detectorSpecifc/x_pixel_size", H5P_DEFAULT) > 0 &&
|
||||
H5Lexists(data_desc->det_group_id, "detectorSpecifc/y_pixel_size", H5P_DEFAULT) > 0) {
|
||||
data_desc->get_pixel_properties = &get_dectris_eiger_pixel_info;
|
||||
} else {
|
||||
data_desc->get_pixel_properties = NULL;
|
||||
retval = -1;
|
||||
}
|
||||
|
||||
/* determine pixel mask location */
|
||||
if (H5Lexists(data_desc->det_group_id, "pixel_mask", H5P_DEFAULT) > 0) {
|
||||
data_desc->get_pixel_mask = &get_nxs_pixel_mask;
|
||||
} else if (H5Lexists(data_desc->det_group_id, "detectorSpecific", H5P_DEFAULT) > 0 &&
|
||||
H5Lexists(data_desc->det_group_id, "detectorSpecific/pixel_mask", H5P_DEFAULT) > 0) {
|
||||
data_desc->get_pixel_mask = &get_dectris_eiger_pixel_mask;
|
||||
} else {
|
||||
data_desc->get_pixel_mask = NULL;
|
||||
retval = -1;
|
||||
}
|
||||
|
||||
/* determine where the data is stored and what strategy to use */
|
||||
/* we select the "dectris-eiger" strategy if both are valid due to
|
||||
* potential confusion with the sizes of a virtual dataset (and possible
|
||||
* failure opening it if the library version is not up to date)
|
||||
*/
|
||||
if (H5Lexists(visit_result->nxdetector, "data_000001", H5P_DEFAULT) > 0) {
|
||||
data_desc->data_group_id = visit_result->nxdetector;
|
||||
data_desc->get_data_properties = &get_dectris_eiger_dataset_dims;
|
||||
data_desc->get_data_frame = &get_dectris_eiger_frame;
|
||||
} else if (H5Lexists(visit_result->nxdetector, "data", H5P_DEFAULT) > 0) {
|
||||
data_desc->data_group_id = visit_result->nxdetector;
|
||||
data_desc->get_data_properties = &get_nxs_dataset_dims;
|
||||
data_desc->get_data_frame = &get_nxs_frame;
|
||||
} else if (H5Lexists(visit_result->nxdata, "data_000001", H5P_DEFAULT) > 0) {
|
||||
data_desc->data_group_id = visit_result->nxdata;
|
||||
data_desc->get_data_properties = &get_dectris_eiger_dataset_dims;
|
||||
data_desc->get_data_frame = &get_dectris_eiger_frame;
|
||||
} else if (H5Lexists(visit_result->nxdata, "data", H5P_DEFAULT) > 0) {
|
||||
data_desc->data_group_id = visit_result->nxdata;
|
||||
data_desc->get_data_properties = &get_nxs_dataset_dims;
|
||||
data_desc->get_data_frame = &get_nxs_frame;
|
||||
} else {
|
||||
data_desc->data_group_id = 0;
|
||||
data_desc->get_data_properties = NULL;
|
||||
data_desc->get_data_frame = NULL;
|
||||
retval = -1;
|
||||
}
|
||||
|
||||
if (data_desc->get_data_properties == &get_dectris_eiger_dataset_dims) {
|
||||
/* setup the "extra eiger info" struct */
|
||||
struct eiger_data_description_t *eiger_desc = malloc(sizeof(*eiger_desc));
|
||||
memset(eiger_desc, 0, sizeof(*eiger_desc));
|
||||
if (!eiger_desc) {
|
||||
retval = -1;
|
||||
return retval;
|
||||
}
|
||||
data_desc->extra = eiger_desc;
|
||||
data_desc->free_extra = free_eiger_data_description;
|
||||
} else {
|
||||
data_desc->free_extra = free_nxs_data_description;
|
||||
}
|
||||
|
||||
return retval;
|
||||
}
|
||||
|
||||
|
||||
int extract_detector_info(
|
||||
const hid_t fid,
|
||||
struct data_description_t *data_desc,
|
||||
struct dataset_properties_t *dataset_prop) {
|
||||
herr_t err = 0;
|
||||
struct det_visit_objects_t objects = {0};
|
||||
err = H5Ovisit(fid, H5_INDEX_NAME, H5_ITER_INC, &det_visit_callback, &objects);
|
||||
if (err < 0) {
|
||||
clear_det_visit_objects(&objects);
|
||||
return -1;
|
||||
}
|
||||
if (objects.nxdata == 0) {
|
||||
fprintf(stderr, "WARNING: Could not locate an NXdata entry\n");
|
||||
}
|
||||
if (objects.nxdetector == 0) {
|
||||
fprintf(stderr, "WARNING: Could not locate an NXdetector entry\n");
|
||||
}
|
||||
|
||||
fill_data_descriptor(data_desc, &objects);
|
||||
data_desc->get_data_properties(data_desc, dataset_prop);
|
||||
return 0;
|
||||
}
|
||||
+53
@@ -0,0 +1,53 @@
|
||||
/*
|
||||
* Copyright (c) 2018 Diamond Light Source Ltd.
|
||||
* Author: Charles Mita
|
||||
*/
|
||||
|
||||
|
||||
#ifndef NXS_XDS_FILE_H
|
||||
#define NXS_XDS_FILE_H
|
||||
|
||||
#include <hdf5.h>
|
||||
|
||||
struct dataset_properties_t {
|
||||
int ndims;
|
||||
int data_width;
|
||||
hsize_t *dims;
|
||||
};
|
||||
|
||||
void free_dataset_properties(struct dataset_properties_t *p);
|
||||
|
||||
struct data_description_t {
|
||||
hid_t det_group_id;
|
||||
hid_t data_group_id;
|
||||
int (*get_pixel_properties)(const struct data_description_t*, double*, double*);
|
||||
int (*get_pixel_mask)(const struct data_description_t*, int*);
|
||||
int (*get_data_properties)(const struct data_description_t*, struct dataset_properties_t*);
|
||||
int (*get_data_frame)(const struct data_description_t*, const struct dataset_properties_t*, int, int, void*);
|
||||
void *extra;
|
||||
void (*free_extra)(struct data_description_t*);
|
||||
};
|
||||
|
||||
void free_nxs_data_description(struct data_description_t *desc);
|
||||
|
||||
struct eiger_data_description_t {
|
||||
int n_data_blocks;
|
||||
int *block_sizes;
|
||||
};
|
||||
|
||||
void free_eiger_data_description(struct data_description_t *desc);
|
||||
|
||||
struct det_visit_objects_t {
|
||||
hid_t nxdata;
|
||||
hid_t nxdetector;
|
||||
};
|
||||
|
||||
void clear_det_visit_objects(struct det_visit_objects_t *objects);
|
||||
|
||||
int get_nxs_dataset_dims(const struct data_description_t *desc, struct dataset_properties_t *properties);
|
||||
|
||||
int fill_data_descriptor(struct data_description_t *data_desc, struct det_visit_objects_t *visit_result);
|
||||
|
||||
int extract_detector_info(const hid_t fid, struct data_description_t *data_desc, struct dataset_properties_t *ds_prop);
|
||||
|
||||
#endif /* NXS_XDS_FILE_H */
|
||||
+138
@@ -0,0 +1,138 @@
|
||||
/*
|
||||
* Copyright (c) 2018 Diamond Light Source Ltd.
|
||||
* Author: Charles Mita
|
||||
*/
|
||||
|
||||
|
||||
#include <hdf5.h>
|
||||
#include <stdlib.h>
|
||||
#include "file.h"
|
||||
#include "plugin.h"
|
||||
|
||||
|
||||
static hid_t file_id = 0;
|
||||
static struct data_description_t data_desc = {0};
|
||||
static struct dataset_properties_t ds_prop = {0};
|
||||
static int *mask_buffer = NULL;
|
||||
|
||||
|
||||
void apply_mask(int *data, int *mask, int size) {
|
||||
int *dptr, *mptr;
|
||||
dptr = data;
|
||||
mptr = mask;
|
||||
while (dptr < data + size && mptr < mask + size) {
|
||||
/* mask bits loosely based on what Neggia does and what NeXus says should be done */
|
||||
/* basically - anything in the low byte (& 0xFF) means "ignore this" */
|
||||
if (*mptr & 0x01) *dptr = -1;
|
||||
if (*mptr & 0xFE) *dptr = -2;
|
||||
dptr++;
|
||||
mptr++;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
void plugin_open(
|
||||
const char *filename,
|
||||
int info[1024],
|
||||
int *error_flag) {
|
||||
int err = 0;
|
||||
info[0] = DLS_CUSTOMER_ID;
|
||||
info[1] = VERSION_MAJOR;
|
||||
info[2] = VERSION_MINOR;
|
||||
info[3] = VERSION_PATCH;
|
||||
info[4] = VERSION_TIMESTAMP;
|
||||
file_id = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
|
||||
if (file_id < 0) {
|
||||
/* TODO: backtrace */
|
||||
*error_flag = -4;
|
||||
return;
|
||||
}
|
||||
|
||||
err = extract_detector_info(file_id, &data_desc, &ds_prop);
|
||||
if (err < 0) {
|
||||
*error_flag = -4;
|
||||
return;
|
||||
}
|
||||
|
||||
mask_buffer = malloc(ds_prop.dims[1] * ds_prop.dims[2] * sizeof(int));
|
||||
if (mask_buffer) {
|
||||
err = data_desc.get_pixel_mask(&data_desc, mask_buffer);
|
||||
if (err < 0) {
|
||||
fprintf(stderr, "WARNING: Could not read pixel mask - no masking will be applied\n");
|
||||
free(mask_buffer);
|
||||
mask_buffer = NULL;
|
||||
}
|
||||
}
|
||||
|
||||
*error_flag = 0;
|
||||
}
|
||||
|
||||
|
||||
void plugin_get_header(
|
||||
int *nx, int *ny,
|
||||
int *nbytes,
|
||||
float *qx, float *qy,
|
||||
int *number_of_frames,
|
||||
int info[1024],
|
||||
int *error_flag) {
|
||||
int err = 0;
|
||||
double x_pixel_size, y_pixel_size;
|
||||
|
||||
err = data_desc.get_pixel_properties(&data_desc, &x_pixel_size, &y_pixel_size);
|
||||
if (err < 0) {
|
||||
*error_flag = -4;
|
||||
return;
|
||||
}
|
||||
|
||||
*nx = ds_prop.dims[2];
|
||||
*ny = ds_prop.dims[1];
|
||||
*nbytes = ds_prop.dims[1] * ds_prop.dims[2] * ds_prop.data_width;
|
||||
*number_of_frames = ds_prop.dims[0];
|
||||
*qx = (float) x_pixel_size;
|
||||
*qy = (float) y_pixel_size;
|
||||
*error_flag = 0;
|
||||
}
|
||||
|
||||
|
||||
void plugin_get_data(
|
||||
int *frame_number,
|
||||
int *nx, int *ny,
|
||||
int *data_array,
|
||||
int info[1024],
|
||||
int *error_flag) {
|
||||
int err = 0;
|
||||
err = data_desc.get_data_frame(&data_desc, &ds_prop, *frame_number, sizeof(int), data_array);
|
||||
if (err < 0) {
|
||||
*error_flag = -2;
|
||||
return;
|
||||
}
|
||||
if (mask_buffer) {
|
||||
apply_mask(data_array, mask_buffer, ds_prop.dims[1] * ds_prop.dims[2]);
|
||||
}
|
||||
*error_flag = 0;
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
void plugin_close(int *error_flag) {
|
||||
if (file_id) {
|
||||
herr_t err = H5Fclose(file_id);
|
||||
if (err) {
|
||||
/* TODO: backtrace */
|
||||
*error_flag = -1;
|
||||
}
|
||||
}
|
||||
file_id = 0;
|
||||
|
||||
if (mask_buffer) free(mask_buffer);
|
||||
if (data_desc.free_extra) data_desc.free_extra(&data_desc);
|
||||
free_dataset_properties(&ds_prop);
|
||||
}
|
||||
|
||||
#ifdef __cplusplus
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
@@ -0,0 +1,55 @@
|
||||
/*
|
||||
* Copyright (c) 2018 Diamond Light Source Ltd.
|
||||
* Author: Charles Mita
|
||||
*/
|
||||
|
||||
/*
|
||||
* External library interface for XDS.
|
||||
* Ref: https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/LIB
|
||||
*/
|
||||
|
||||
#ifndef NXS_XDS_PLUGIN_H
|
||||
#define NXS_XDS_PLUGIN_H
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
#define DLS_CUSTOMER_ID 0x01 /* pretend we're Dectris, otherwise XDS doesn't work */
|
||||
#define VERSION_MAJOR 0
|
||||
#define VERSION_MINOR 0
|
||||
#define VERSION_PATCH 0
|
||||
#define VERSION_TIMESTAMP -1 /* good enough for Dectris apparantely */
|
||||
|
||||
|
||||
void plugin_open(
|
||||
const char *filename,
|
||||
int info[1024],
|
||||
int *error_flag);
|
||||
|
||||
|
||||
void plugin_get_header(
|
||||
int *nx, int *ny,
|
||||
int *nbytes,
|
||||
float *qx, float *qy,
|
||||
int *number_of_frames,
|
||||
int info[1024],
|
||||
int *error_flag);
|
||||
|
||||
|
||||
void plugin_get_data(
|
||||
int *frame_number,
|
||||
int *nx, int *ny,
|
||||
int *data_array,
|
||||
int info[1024],
|
||||
int *error_flag);
|
||||
|
||||
|
||||
void plugin_close(int *error_flag);
|
||||
|
||||
|
||||
#ifdef __cplusplus
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#endif /* NXS_XDS_PLUGIN_H */
|
||||
Reference in New Issue
Block a user