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Better handling of (usually) unsigned data arrays when calling routine

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to convert to (signed) int and apply pixel mask. The environment
variable DURIN_RESET_UNMASKED_PIXEL can now be used to set non-masked
saturated pixels in order to process them correctly with e.g. XDS.
This commit is contained in:
Clemens Vonrhein
2021-04-08 14:46:48 +01:00
parent 0f27832f78
commit 77d2b84957
2 changed files with 127 additions and 44 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/file.c
+12 -2
View File
@@ -104,7 +104,13 @@ int get_nxs_dataset_dims(struct ds_desc_t *desc) {
ERROR_JUMP(-1, close_space, "Error getting dataset dimensions");
}
desc->data_width = width;
if ( H5Tequal(t_id,H5T_NATIVE_CHAR)>0 || H5Tequal(t_id,H5T_NATIVE_INT)>0 || H5Tequal(t_id,H5T_NATIVE_SHORT)>0 || H5Tequal(t_id,H5T_NATIVE_LONG)>0 || H5Tequal(t_id,H5T_NATIVE_LLONG)>0 ) {
// signed
desc->data_width = -width;
} else {
// unsigned
desc->data_width = width;
}
close_space:
H5Sclose(s_id);
@@ -233,7 +239,7 @@ int get_frame_from_chunk(const struct ds_desc_t *desc, const char *ds_name,
if (o_eiger_desc->bs_applied) {
if (bslz4_decompress(o_eiger_desc->bs_params, c_bytes, c_buffer,
desc->data_width * frame_size[1] * frame_size[2],
abs(desc->data_width) * frame_size[1] * frame_size[2],
buffer) < 0) {
char message[128];
sprintf(message,
@@ -351,6 +357,10 @@ int get_dectris_eiger_dataset_dims(struct ds_desc_t *desc) {
if (data_width <= 0) {
ERROR_JUMP(-1, close_space, "Unable to get type size");
}
if ( H5Tequal(t_id,H5T_NATIVE_CHAR)>0 || H5Tequal(t_id,H5T_NATIVE_INT)>0 || H5Tequal(t_id,H5T_NATIVE_SHORT)>0 || H5Tequal(t_id,H5T_NATIVE_LONG)>0 || H5Tequal(t_id,H5T_NATIVE_LLONG)>0 ) {
// signed
data_width = -data_width;
}
ndims = H5Sget_simple_extent_ndims(s_id);
if (ndims != 3) {
src/plugin.c
+115 -42
View File
@@ -17,24 +17,41 @@
/* 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 uses the value -2 if bit 1, 2 or 3 are set */
#define COPY_AND_MASK(in, out, size, mask) \
/* CV-GPhL-20210408: we want more control over the value non-masked
pixels should be set to. */
#define COPY_AND_MASK(in, value, setValue, 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; \
if (value!=0) { \
if (mask) { \
for (i = 0; i < size; ++i) { \
out[i] = (in[i] == value) ? setValue : 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] == value) ? setValue : in[i]; \
} \
} \
} else { \
for (i = 0; i < size; i++) { \
out[i] = in[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; \
@@ -58,36 +75,97 @@ void fill_info_array(int info[1024]) {
info[2] = VERSION_MINOR;
info[3] = VERSION_PATCH;
info[4] = VERSION_TIMESTAMP;
info[5] = 0; // image number offset
info[6] = -1; // marked pixels not already in pixel_mask: reset to this value
char *cenv;
cenv = getenv("DURIN_IMAGE_NUMBER_OFFSET");
if (cenv!=NULL) {
info[5] = atoi(cenv);
}
cenv = getenv("DURIN_RESET_UNMASKED_PIXEL");
if (cenv!=NULL) {
info[6] = atoi(cenv);
}
}
int convert_to_int_and_mask(void *in_buffer, int d_width, int *out_buffer,
int convert_to_int_and_mask(void *in_buffer, int width, int setValue, 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);
int d_width = abs(width);
// CV-20210407
// Dealing with a signed data array: no extra check for marker
// value needed (since data can already take advantage of the
// negative data range). It is unclear though why/when data would
// come in as a signed array in the first place ...
if (width<0) {
if (d_width == sizeof(signed char)) {
// 8-bit
signed char *in = in_buffer;
COPY_AND_MASK(in, 0, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(short)) {
// 16-bit
short *in = in_buffer;
COPY_AND_MASK(in, 0, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(int)) {
// 16-bit
int *in = in_buffer;
COPY_AND_MASK(in, 0, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(long int)) {
// 32-bit
long int *in = in_buffer;
COPY_AND_MASK(in, 0, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(long long int)) {
// 64-bit
long long int *in = in_buffer;
COPY_AND_MASK(in, 0, setValue, 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);
}
}
// CV-20210407
// Dealing with an unsigned data array: extra check for marker
// value required (to handle overloaded pixels correctly if wanted
// - see also DURIN_RESET_UNMASKED_PIXEL environment variable).
else {
if (d_width == sizeof(unsigned char)) {
// 8-bit
unsigned char *in = in_buffer;
COPY_AND_MASK(in, UINT8_MAX, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(unsigned short)) {
// 16-bit
unsigned short *in = in_buffer;
COPY_AND_MASK(in, UINT16_MAX, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(unsigned int)) {
// 16-bit
unsigned int *in = in_buffer;
COPY_AND_MASK(in, UINT16_MAX, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(unsigned long)) {
// 32-bit
unsigned long *in = in_buffer;
COPY_AND_MASK(in, UINT32_MAX, setValue, out_buffer, length, mask);
} else if (d_width == sizeof(unsigned long long)) {
// 64-bit
unsigned long long *in = in_buffer;
COPY_AND_MASK(in, UINT32_MAX, setValue, 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;
}
@@ -124,12 +202,7 @@ void plugin_open(const char *filename, int info[1024], int *error_flag) {
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);
}
data_desc->image_number_offset = info[5];
mask_buffer = malloc(data_desc->dims[1] * data_desc->dims[2] * sizeof(int));
if (mask_buffer) {
@@ -172,7 +245,7 @@ void plugin_get_header(int *nx, int *ny, int *nbytes, float *qx, float *qy,
*nx = data_desc->dims[2];
*ny = data_desc->dims[1];
*nbytes = data_desc->data_width;
*nbytes = abs(data_desc->data_width);
*number_of_frames = data_desc->dims[0];
*qx = (float)x_pixel_size;
*qy = (float)y_pixel_size;
@@ -193,10 +266,10 @@ void plugin_get_data(int *frame_number, int *nx, int *ny, int *data_array,
fill_info_array(info);
void *buffer = NULL;
if (sizeof(*data_array) == data_desc->data_width) {
if (sizeof(*data_array) == abs(data_desc->data_width)) {
buffer = data_array;
} else {
buffer = malloc(data_desc->data_width * frame_size_px);
buffer = malloc(abs(data_desc->data_width) * frame_size_px);
if (!buffer) {
ERROR_JUMP(-1, done, "Unable to allocate data buffer");
}
@@ -209,7 +282,7 @@ void plugin_get_data(int *frame_number, int *nx, int *ny, int *data_array,
}
if (buffer != data_array) {
if (convert_to_int_and_mask(buffer, data_desc->data_width, data_array,
if (convert_to_int_and_mask(buffer, data_desc->data_width, info[6], data_array,
frame_size_px, mask_buffer) < 0) {
char message[64];
sprintf(message, "Error converting data for frame %d", *frame_number);