durin/src/plugin.c

/*
 * Copyright (c) 2018 Diamond Light Source Ltd.
 * Author: Charles Mita
 */


#include <hdf5.h>
#include <stdlib.h>
#include "file.h"
#include "filters.h"
#include "plugin.h"


/* XDS does not provide an error callback facility, so just write to stderr for now */
/* generally regarded as poor practice */
#define ERROR_OUTPUT stderr



/* 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" */
/* Neggia usses the value -2 if bit 1, 2 or 3 are set */
#define COPY_AND_MASK(in, out, size, mask) \
{ \
	int i; \
	if (mask) { \
		for (i = 0; i < size; ++i) { \
			out[i] = in[i]; \
			if (mask[i] & 0xFF) out[i] = -1; \
			if (mask[i] & 30) out[i] = -2; \
		} \
	} else { \
		for (i = 0; i < size; i++) { \
			out[i] = in[i]; \
		} \
	} \
}

#define APPLY_MASK(buffer, mask, size) \
{ \
	int i; \
	if (mask) { \
		for (i = 0; i < size; ++i) { \
			if (mask[i] & 0xFF) buffer[i] = -1; \
			if (mask[i] & 30) buffer[i] = -2; \
		} \
	} \
}


static hid_t file_id = 0;
static struct ds_desc_t *data_desc = NULL;
static int *mask_buffer = NULL;


void fill_info_array(int info[1024]) {
	info[0] = DLS_CUSTOMER_ID;
	info[1] = VERSION_MAJOR;
	info[2] = VERSION_MINOR;
	info[3] = VERSION_PATCH;
	info[4] = VERSION_TIMESTAMP;
}

int convert_to_int_and_mask(void *in_buffer, int d_width, int *out_buffer, int length, int *mask) {
	/* transfer data to output buffer, performing data conversion as required */
	int retval = 0;
	/* TODO: decide how conversion of data should work */
	/* Should we sign extend? Neggia doesn't (casts from uint*), but may be more intuitive */
	if (d_width == sizeof(signed char)) {
		signed char *in = in_buffer;
		COPY_AND_MASK(in, out_buffer, length, mask);
	} else if (d_width == sizeof(short)) {
		short *in = in_buffer;
		COPY_AND_MASK(in, out_buffer, length, mask);
	} else if (d_width == sizeof(int)) {
		int *in = in_buffer;
		COPY_AND_MASK(in, out_buffer, length, mask);
	} else if (d_width == sizeof(long int)) {
		long int *in = in_buffer;
		COPY_AND_MASK(in, out_buffer, length, mask);
	} else if (d_width == sizeof(long long int)) {
		long long int *in = in_buffer;
		COPY_AND_MASK(in, out_buffer, length, mask);
	} else {
		char message[128];
		sprintf(message, "Unsupported conversion of data width %d to %ld (int)", d_width, sizeof(int));
		ERROR_JUMP(-1, done, message);
	}
done:
	return retval;
}

#ifdef __cplusplus
extern "C" {
#endif

void plugin_open(
		const char *filename,
		int info[1024],
		int *error_flag) {
	int retval = 0;
	*error_flag = 0;

	init_error_handling();

	if (H5dont_atexit() < 0) {
		ERROR_JUMP(-2, done, "Failed configuring HDF5 library behaviour");
	}

	if (init_h5_error_handling() < 0) {
		ERROR_JUMP(-2, done, "Failed to configure HDF5 error handling");
	}

	fill_info_array(info);
	file_id = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
	if (file_id < 0) {
		char message[128] = {0};
		sprintf(message, "Could not open %.100s", filename);
		ERROR_JUMP(-4, done, message);
	}

	reset_error_stack();
	retval = get_detector_info(file_id, &data_desc);
	if (retval < 0) {
		ERROR_JUMP(-4, done, "");
	}

	data_desc->image_number_offset = 0;
	char *cenv;
	cenv = getenv("DURIN_IMAGE_NUMBER_OFFSET");
	if (cenv!=NULL) {
	  data_desc->image_number_offset = atoi(cenv);
	}

	mask_buffer = malloc(data_desc->dims[1] * data_desc->dims[2] * sizeof(int));
	if (mask_buffer) {
		retval = data_desc->get_pixel_mask(data_desc, mask_buffer);
		if (retval < 0) {
			fprintf(ERROR_OUTPUT, "WARNING: Could not read pixel mask - no masking will be applied\n");
			dump_error_stack(ERROR_OUTPUT);
			free(mask_buffer);
			mask_buffer = NULL;
		}
	}
	retval = 0;

done:
	*error_flag = retval;
	if (retval < 0) {
		if ((data_desc) && (data_desc->free_desc)) {
			data_desc->free_desc(data_desc);
			data_desc = NULL;
		}
		dump_error_stack(ERROR_OUTPUT);
	}
}


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;
	int retval = 0;
	double x_pixel_size, y_pixel_size;
	reset_error_stack();
	fill_info_array(info);

	err = data_desc->get_pixel_properties(data_desc, &x_pixel_size, &y_pixel_size);
	if (err < 0) {
		ERROR_JUMP(err, done, "Failed to retrieve pixel information");
	}

	*nx = data_desc->dims[2];
	*ny = data_desc->dims[1];
	*nbytes = data_desc->data_width;
	*number_of_frames = data_desc->dims[0];
	*qx = (float) x_pixel_size;
	*qy = (float) y_pixel_size;

done:
	*error_flag = retval;
	if (retval < 0) {
		dump_error_stack(ERROR_OUTPUT);
	}
}


void plugin_get_data(
		int *frame_number,
		int *nx, int *ny,
		int *data_array,
		int info[1024],
		int *error_flag) {

	int retval = 0;
	int frame_size_px = data_desc->dims[1] * data_desc->dims[2];
	reset_error_stack();
	fill_info_array(info);

	void *buffer = NULL;
	if (sizeof(*data_array) == data_desc->data_width) {
		buffer = data_array;
	} else {
		buffer = malloc(data_desc->data_width * frame_size_px);
		if (!buffer) {
			ERROR_JUMP(-1, done, "Unable to allocate data buffer");
		}
	}

	if (data_desc->get_data_frame(data_desc, (*frame_number) - 1, buffer) < 0) {
		char message[64] = {0};
		sprintf(message, "Failed to retrieve data for frame %d", *frame_number);
		ERROR_JUMP(-2, done, message);
	}

	if (buffer != data_array) {
		if (convert_to_int_and_mask(buffer, data_desc->data_width, data_array, frame_size_px, mask_buffer) < 0) {
			char message[64];
			sprintf(message, "Error converting data for frame %d", *frame_number);
			ERROR_JUMP(-2, done, message);
		}
	} else {
		APPLY_MASK(data_array, mask_buffer, frame_size_px);
	}

done:
	*error_flag = retval;
	if (retval < 0) {
		dump_error_stack(ERROR_OUTPUT);
	}
	if (buffer && (buffer != data_array)) free(buffer);
}


void plugin_close(int *error_flag) {
	if (file_id) {
		if (H5Fclose(file_id) < 0) {
			/* TODO: backtrace */
			*error_flag = -1;
		}
	}
	file_id = 0;

	if (mask_buffer) {
	        free(mask_buffer);
		mask_buffer = NULL;
	}
	if (data_desc->free_desc) {
		data_desc->free_desc(data_desc);
		data_desc = NULL;
	}
	if (H5close() < 0) {
		*error_flag = -1;
	}
}

#ifdef __cplusplus
} /* extern "C" */
#endif