Null terminate buffer in file.c

Ensure the buffer is null terminated after allocation - otherwise correct results from strcmp below is undefined.

Makefile

@@ -8,7 +8,7 @@ BSLZ4_BUILD_DIR = ./bslz4/build
 BSLZ4_INC_DIR = $(BSLZ4_SRC_DIR)
 
 CC=h5cc
-CFLAGS=-Wall -g -O2 -fpic -I$(INC_DIR) -I$(BSLZ4_INC_DIR) -std=c89
+CFLAGS=-DH5_USE_110_API -Wall -g -O2 -fpic -I$(INC_DIR) -I$(BSLZ4_INC_DIR) -std=c99 -shlib
 
 .PHONY: plugin
 plugin: $(BUILD_DIR)/durin-plugin.so
@@ -42,7 +42,7 @@ $(BSLZ4_BUILD_DIR)/bitshuffle_core.o $(BSLZ4_BUILD_DIR)/iochain.o
 $(BUILD_DIR)/durin-plugin.so: $(BUILD_DIR)/plugin.o $(BUILD_DIR)/file.o $(BUILD_DIR)/err.o $(BUILD_DIR)/filters.o \
 $(BUILD_DIR)/bslz4.a
 	mkdir -p $(BUILD_DIR)
-	$(CC) $(CFLAGS) -shared $^ -o $(BUILD_DIR)/durin-plugin.so
+	$(CC) $(CFLAGS) -shared -noshlib $^ -o $(BUILD_DIR)/durin-plugin.so
 
 $(BUILD_DIR)/example: $(BUILD_DIR)/test.o $(BUILD_DIR)/file.o $(BUILD_DIR)/err.o $(BUILD_DIR)/filters.o \
 $(BUILD_DIR)/bslz4.a

README.md

@@ -8,6 +8,9 @@ See:
 * https://www.dectris.com/features/features-eiger-x/hdf5-and-nexus
 * https://strucbio.biologie.uni-konstanz.de/xdswiki
 
+## Get Durin
+
+Latest release at https://github.com/DiamondLightSource/durin/releases/tag/2019v1
 
 ## Usage
 In your XDS.INP add:
@@ -29,26 +32,47 @@ series of datasets named `data_000001`, `data_000002`, etc.
 
 
 ## Building
-First ensure that the HDF5 libraries are compiled with:
 
+### Building HDF5 library
+The HDF5 library used when building durin must have been compiled with specific switches enabled
+to allow the durin plugin to be built and used.
+
+Download the HDF5 source code (https://www.hdfgroup.org/downloads/hdf5/source-code) and extract
+to any directory (referred to as `/hdf5_dir`), and run the following commands.
 ```
+cd /hdf5_dir
+mkdir build
+cd build
 export CFLAGS=-fPIC
-./configure --enable-threadsafe=yes --enable-unsupported
+../configure --enable-threadsafe --enable-deprecated-symbols --enable-hl --enable-unsupported
+make
+make check
+make install
 ```
+The hdf5 tools and libraries should now be located in `/hdf5_dir/build/hdf5`
 
-former is neeed to ensure that XDS in parallel mode will work, latter
-to ensure that the chunk read (which for opaque reasons is defined to
-be _high level_) works. Then make sure that wherever this was
-installed, the h5cc is in PATH before:
+For reference, the plugin requires the thread-safe switch and the optimised chunk read function.
+The chunk read function may be defined in the high level library instead of the regular library,
+depending on the exact HDF5 version downloaded (hence the --enable-deprecated-symbols _and_ --enable-hl).
+The unsupported flag enables building with both threadsafe and high-level enabled.
 
+
+### Building durin plugin
+The plugin makefile will use the "h5cc" compiler wrapper, provided by the HDF5 library, which
+must be on your PATH.
+Download or clone the plugin source code (https://github.com/DiamondLightSource/durin)
+into any directory (referred to as `/durin_dir`) and run the following commands.
 ```
-cd durin
+cd /durin_dir
+PATH=/hdf5_dir/build/hdf5/bin:$PATH
 make
 ```
+The plugin is located at `/durin_dir/build/durin-plugin.so` and should be added to the
+XDS.INP file as `LIB=/durin_dir/build/durin-plugin.so`
 
-Plugin file is `build/durin-plugin.so` - this should be added to the
-XDS.INP file i.e. as:
 
+
+## Example XDS.INP
 ```
 DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=4096
 LIB=/opt/durin/build/durin-plugin.so
@@ -57,7 +81,6 @@ SENSOR_THICKNESS= 0.450
 !SILICON= 3.953379
 DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
-NX=2070 NY=2164 QX=0.0750 QY=0.0750
 DETECTOR_DISTANCE= 194.633000
 ORGX= 1041.30 ORGY= 1160.90
 ROTATION_AXIS= 0.00000 -1.00000 -0.00000
@@ -74,4 +97,4 @@ JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 ```
 
 N.B. the master file is needed, not the .nxs one which follows the
-standard. 
+standard.

src/err.c

@@ -3,19 +3,18 @@
  * Author: Charles Mita
  */
 
-
-#include <stdio.h>
 #include <hdf5.h>
+#include <stdio.h>
+
 #include "err.h"
 
-
 struct error_stack_t {
-	char **files;
-	char **funcs;
-	int *lines;
-	int *errors;
-	char **messages;
-	int size;
+  char **files;
+  char **funcs;
+  int *lines;
+  int *errors;
+  char **messages;
+  int size;
 };
 
 static char files_buffer[ERR_MAX_FILENAME_LENGTH * ERR_MAX_STACK_SIZE] = {0};
@@ -30,89 +29,89 @@ static char *messages[ERR_MAX_STACK_SIZE] = {0};
 
 static struct error_stack_t stack = {files, funcs, lines, errors, messages, 0};
 
+void push_error_stack(const char *file, const char *func, int line, int err,
+                      const char *message) {
+  if (stack.size >= ERR_MAX_STACK_SIZE)
+    return; /* unfortunate */
+  int idx = stack.size;
 
-void push_error_stack(const char *file, const char *func, int line, int err, const char *message) {
-	if (stack.size >= ERR_MAX_STACK_SIZE) return; /* unfortunate */
-	int idx = stack.size;
+  /* subtract 1 to ensure room for null byte in buffer */
+  sprintf(stack.funcs[idx], "%.*s", ERR_MAX_FUNCNAME_LENGTH - 1, func);
+  sprintf(stack.files[idx], "%.*s", ERR_MAX_FILENAME_LENGTH - 1, file);
+  sprintf(stack.messages[idx], "%.*s", ERR_MAX_MESSAGE_LENGTH - 1, message);
+  stack.lines[idx] = line;
+  stack.errors[idx] = err;
 
-	/* subtract 1 to ensure room for null byte in buffer */
-	sprintf(stack.funcs[idx], "%.*s", ERR_MAX_FUNCNAME_LENGTH - 1, func);
-	sprintf(stack.files[idx], "%.*s", ERR_MAX_FILENAME_LENGTH - 1, file);
-	sprintf(stack.messages[idx], "%.*s", ERR_MAX_MESSAGE_LENGTH - 1, message);
-	stack.lines[idx] = line;
-	stack.errors[idx] = err;
-
-	stack.size++;
+  stack.size++;
 }
 
-
-herr_t h5e_walk_callback(unsigned int n, const struct H5E_error2_t *err, void *client_data) {
-	herr_t retval = 0;
-	/* only read the message for the innermost stack frame - the rest are just noise */
-	if (n == 0) {
-		char message[ERR_MAX_MESSAGE_LENGTH] = {0};
-		sprintf(message, "%.*s", ERR_MAX_MESSAGE_LENGTH - 1, err->desc);
-		push_error_stack(err->file_name, err->func_name, err->line, -1, message);
-	} else {
-		push_error_stack(err->file_name, err->func_name, err->line, -1, "");
-	}
-	return retval;
+herr_t h5e_walk_callback(unsigned int n, const struct H5E_error2_t *err,
+                         void *client_data) {
+  herr_t retval = 0;
+  /* only read the message for the innermost stack frame - the rest are just
+   * noise */
+  if (n == 0) {
+    char message[ERR_MAX_MESSAGE_LENGTH] = {0};
+    sprintf(message, "%.*s", ERR_MAX_MESSAGE_LENGTH - 1, err->desc);
+    push_error_stack(err->file_name, err->func_name, err->line, -1, message);
+  } else {
+    push_error_stack(err->file_name, err->func_name, err->line, -1, "");
+  }
+  return retval;
 }
 
-
 int h5e_error_callback(hid_t stack_id, void *client_data) {
-	int retval = 0;
-	herr_t err = 0;
-	err = H5Ewalk2(stack_id, H5E_WALK_UPWARD, &h5e_walk_callback, client_data);
-	if (err < 0) {
-		ERROR_JUMP(err, done, "Error walking HDF5 Error stack");
-	}
+  int retval = 0;
+  herr_t err = 0;
+  err = H5Ewalk2(stack_id, H5E_WALK_UPWARD, &h5e_walk_callback, client_data);
+  if (err < 0) {
+    ERROR_JUMP(err, done, "Error walking HDF5 Error stack");
+  }
 done:
-	return retval;
+  return retval;
 }
 
-
 void reset_error_stack() {
-	stack.size = 0;
-	H5Eclear2(H5E_DEFAULT); /* almost certainly unnecessary */
+  stack.size = 0;
+  H5Eclear2(H5E_DEFAULT); /* almost certainly unnecessary */
 }
 
-
 void dump_error_stack(FILE *out) {
-	int idx = stack.size;
-	if (idx > 0) fprintf(out, "Durin plugin error:\n");
-	while (idx-- > 0) {
-		const char *file = stack.files[idx];
-		const char *func = stack.funcs[idx];
-		const char *message = stack.messages[idx];
-		const int line = stack.lines[idx];
-		if (message[0] != '\0') {
-			fprintf(out, "\t%s - line %d in %s:\n\t\t%s\n", file, line, func, message);
-		} else {
-			fprintf(out, "\t%s - line %d in %s\n", file, line, func);
-		}
-	}
+  int idx = stack.size;
+  if (idx > 0)
+    fprintf(out, "Durin plugin error:\n");
+  while (idx-- > 0) {
+    const char *file = stack.files[idx];
+    const char *func = stack.funcs[idx];
+    const char *message = stack.messages[idx];
+    const int line = stack.lines[idx];
+    if (message[0] != '\0') {
+      fprintf(out, "\t%s - line %d in %s:\n\t\t%s\n", file, line, func,
+              message);
+    } else {
+      fprintf(out, "\t%s - line %d in %s\n", file, line, func);
+    }
+  }
 }
 
-
 int init_h5_error_handling() {
-	int retval = 0;
-	hid_t err = 0;
-	if ((err = H5Eset_auto2(H5E_DEFAULT, &h5e_error_callback, NULL)) < 0) {
-		ERROR_JUMP(err, done, "Error configuring HDF5 error callback");
-	}
+  int retval = 0;
+  hid_t err = 0;
+  if ((err = H5Eset_auto2(H5E_DEFAULT, &h5e_error_callback, NULL)) < 0) {
+    ERROR_JUMP(err, done, "Error configuring HDF5 error callback");
+  }
 done:
-	return retval;
+  return retval;
 }
 
 int init_error_handling() {
-	int retval = 0;
-	int idx = 0;
-	while (idx < ERR_MAX_STACK_SIZE) {
-		stack.files[idx] = files_buffer + (idx * ERR_MAX_FILENAME_LENGTH);
-		stack.funcs[idx] = funcs_buffer + (idx * ERR_MAX_FUNCNAME_LENGTH);
-		stack.messages[idx] = messages_buffer + (idx * ERR_MAX_MESSAGE_LENGTH);
-		idx++;
-	}
-	return retval;
+  int retval = 0;
+  int idx = 0;
+  while (idx < ERR_MAX_STACK_SIZE) {
+    stack.files[idx] = files_buffer + (idx * ERR_MAX_FILENAME_LENGTH);
+    stack.funcs[idx] = funcs_buffer + (idx * ERR_MAX_FUNCNAME_LENGTH);
+    stack.messages[idx] = messages_buffer + (idx * ERR_MAX_MESSAGE_LENGTH);
+    idx++;
+  }
+  return retval;
 }

src/err.h

@@ -3,46 +3,44 @@
  * Author: Charles Mita
  */
 
-
 #ifndef NXS_XDS_ERR_H
 #define NXS_XDS_ERR_H
 
-
 #define ERR_MAX_FILENAME_LENGTH 64
 #define ERR_MAX_FUNCNAME_LENGTH 128
 #define ERR_MAX_MESSAGE_LENGTH 1024
 #define ERR_MAX_STACK_SIZE 128
 
-
 /* obtain __func__ from GCC if no C99 */
 #if __STDC_VERSION__ < 199901L
-# if __GNUC__ >= 2
-#  define __func__ __FUNCTION__
-# else
-#  define __func__ "<unknown>"
-# endif
+#if __GNUC__ >= 2
+#define __func__ __FUNCTION__
+#else
+#define __func__ "<unknown>"
+#endif
 #endif
 
 #if __GNUC__ >= 2
-# define __line__ __LINE__
+#define __line__ __LINE__
 #else
-# define __line__ 0
+#define __line__ 0
 #endif
 
 #if __GNUC__ >= 2
-# define __file__ __FILE__
+#define __file__ __FILE__
 #else
-# define __file__ "unknown"
+#define __file__ "unknown"
 #endif
 
-#define ERROR_JUMP(err, target, message) \
-{ \
-	push_error_stack(__file__, __func__, __line__, err, message); \
-	retval = err; \
-	goto target; \
-}
+#define ERROR_JUMP(err, target, message)                                       \
+  {                                                                            \
+    push_error_stack(__file__, __func__, __line__, err, message);              \
+    retval = err;                                                              \
+    goto target;                                                               \
+  }
 
-void push_error_stack(const char *file, const char *func, int line, int err, const char *message);
+void push_error_stack(const char *file, const char *func, int line, int err,
+                      const char *message);
 
 void dump_error_stack(FILE *out);
 

src/file.h

@@ -3,48 +3,47 @@
  * Author: Charles Mita
  */
 
-
 #ifndef NXS_XDS_FILE_H
 #define NXS_XDS_FILE_H
 
-#include <hdf5.h>
 #include "err.h"
 #include "filters.h"
-
+#include <hdf5.h>
 
 struct ds_desc_t {
-	hid_t det_g_id;
-	hid_t data_g_id;
-	hsize_t dims[3];
-	int data_width;
-	int (*get_pixel_properties)(const struct ds_desc_t*, double*, double*);
-	int (*get_pixel_mask)(const struct ds_desc_t*, int*);
-	int (*get_data_frame)(const struct ds_desc_t*, const int, void*);
-	void (*free_desc)(struct ds_desc_t*);
+  hid_t det_g_id;
+  hid_t data_g_id;
+  hsize_t dims[3];
+  int data_width;
+  int (*get_pixel_properties)(const struct ds_desc_t *, double *, double *);
+  int (*get_pixel_mask)(const struct ds_desc_t *, int *);
+  int (*get_data_frame)(const struct ds_desc_t *, const int, void *);
+  void (*free_desc)(struct ds_desc_t *);
 };
 
 struct nxs_ds_desc_t {
-	struct ds_desc_t base;
+  struct ds_desc_t base;
 };
 
 struct eiger_ds_desc_t {
-	struct ds_desc_t base;
-	int n_data_blocks;
-	int *block_sizes;
-	int (*frame_func)(const struct ds_desc_t*, const char*, const hsize_t*, const hsize_t*, void*);
+  struct ds_desc_t base;
+  int n_data_blocks;
+  int *block_sizes;
+  int (*frame_func)(const struct ds_desc_t *, const char *, const hsize_t *,
+                    const hsize_t *, void *);
 };
 
 struct opt_eiger_ds_desc_t {
-	struct eiger_ds_desc_t base;
-	int bs_applied;
-	unsigned int bs_params[BS_H5_N_PARAMS];
+  struct eiger_ds_desc_t base;
+  int bs_applied;
+  unsigned int bs_params[BS_H5_N_PARAMS];
 };
 
 int get_detector_info(const hid_t fid, struct ds_desc_t **desc);
 
 struct det_visit_objects_t {
-	hid_t nxdata;
-	hid_t nxdetector;
+  hid_t nxdata;
+  hid_t nxdetector;
 };
 
 #endif /* NXS_XDS_FILE_H */

src/filters.c

@@ -4,55 +4,55 @@
  */
 
 #include <stdio.h>
-#include "filters.h"
-#include "err.h"
+
 #include "bitshuffle.h"
+#include "err.h"
+#include "filters.h"
 
 /* Required prototypes from bitshuffle.c but not included in header */
 uint64_t bshuf_read_uint64_BE(const void *buffer);
 uint32_t bshuf_read_uint32_BE(const void *buffer);
 
-
 /*
- * Derived from the h5 filter code from the bitshuffle project (not included here)
+ * Derived from the h5 filter code from the bitshuffle project (not included
+ * here)
  */
-int bslz4_decompress(
-		const unsigned int* bs_params,
-		size_t in_size,
-		void *in_buffer,
-		size_t out_size,
-		void *out_buffer) {
+int bslz4_decompress(const unsigned int *bs_params, size_t in_size,
+                     void *in_buffer, size_t out_size, void *out_buffer) {
 
-	int retval = 0;
-	size_t size, elem_size, block_size, u_bytes;
+  int retval = 0;
+  size_t size, elem_size, block_size, u_bytes;
 
-	elem_size = bs_params[2];
-	u_bytes = bshuf_read_uint64_BE(in_buffer);
+  elem_size = bs_params[2];
+  u_bytes = bshuf_read_uint64_BE(in_buffer);
 
-	if (u_bytes != out_size) {
-		char message[64];
-		sprintf(message, "Decompressed chunk is %lu bytes, expected %lu", u_bytes, out_size);
-		ERROR_JUMP(-1, done, message);
-	}
+  if (u_bytes != out_size) {
+    char message[64];
+    sprintf(message, "Decompressed chunk is %lu bytes, expected %lu", u_bytes,
+            out_size);
+    ERROR_JUMP(-1, done, message);
+  }
 
-	block_size = bshuf_read_uint32_BE((const char *) in_buffer + 8) / elem_size;
-	if (!block_size) {
-		ERROR_JUMP(-1, done, "Read block bitshuffle lz4 block size as 0");
-	}
-	/* skip over header */
-	in_buffer += 12;
-	size = u_bytes / elem_size;
+  block_size = bshuf_read_uint32_BE((const char *)in_buffer + 8) / elem_size;
+  if (!block_size) {
+    ERROR_JUMP(-1, done, "Read block bitshuffle lz4 block size as 0");
+  }
+  /* skip over header */
+  in_buffer += 12;
+  size = u_bytes / elem_size;
 
-	if (bs_params[4] == BS_H5_PARAM_LZ4_COMPRESS) {
-		if (bshuf_decompress_lz4(in_buffer, out_buffer, size, elem_size, block_size) < 0) {
-			ERROR_JUMP(-1, done, "Error performing bitshuffle_lz4 decompression");
-		}
-	} else {
-		if (bshuf_bitunshuffle(in_buffer, out_buffer, size, elem_size, block_size) < 0) {
-			ERROR_JUMP(-1, done, "Error performing bit unshuffle");
-		}
-	}
+  if (bs_params[4] == BS_H5_PARAM_LZ4_COMPRESS) {
+    if (bshuf_decompress_lz4(in_buffer, out_buffer, size, elem_size,
+                             block_size) < 0) {
+      ERROR_JUMP(-1, done, "Error performing bitshuffle_lz4 decompression");
+    }
+  } else {
+    if (bshuf_bitunshuffle(in_buffer, out_buffer, size, elem_size, block_size) <
+        0) {
+      ERROR_JUMP(-1, done, "Error performing bit unshuffle");
+    }
+  }
 
 done:
-	return retval;
+  return retval;
 }

src/filters.h

@@ -10,13 +10,7 @@
 #define BS_H5_FILTER_ID 32008
 #define BS_H5_PARAM_LZ4_COMPRESS 2
 
-
-
-int bslz4_decompress(
-		const unsigned int* bs_params,
-		size_t in_size,
-		void *in_buffer,
-		size_t out_size,
-		void *out_buffer);
+int bslz4_decompress(const unsigned int *bs_params, size_t in_size,
+                     void *in_buffer, size_t out_size, void *out_buffer);
 
 #endif /* NXS_XDS_FILTER_H */

src/plugin.c

@@ -3,249 +3,244 @@
  * 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 */
+/* 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 uses 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];                                                        \
+      }                                                                        \
+    }                                                                          \
+  }
 
-
-/* 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; \
-		} \
-	} \
-}
-
+#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;
+  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);
-	}
+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;
+  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;
+void plugin_open(const char *filename, int info[1024], int *error_flag) {
+  int retval = 0;
+  *error_flag = 0;
 
-	init_error_handling();
+  init_error_handling();
 
-	if (H5dont_atexit() < 0) {
-		ERROR_JUMP(-2, done, "Failed configuring HDF5 library behaviour");
-	}
+  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");
-	}
+  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);
-	}
+  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, "");
-	}
+  reset_error_stack();
+  retval = get_detector_info(file_id, &data_desc);
+  if (retval < 0) {
+    ERROR_JUMP(-4, done, "");
+  }
 
-	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;
+  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);
-	}
+  *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);
 
-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");
+  }
 
-	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;
+  *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);
-	}
+  *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) {
 
-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);
 
-	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");
+    }
+  }
 
-	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 (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);
-	}
+  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);
+  *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 (file_id) {
+    if (H5Fclose(file_id) < 0) {
+      /* TODO: backtrace */
+      *error_flag = -1;
+    }
+  }
+  file_id = 0;
 
-	if (mask_buffer) free(mask_buffer);
-	if (data_desc->free_desc) {
-		data_desc->free_desc(data_desc);
-		data_desc = NULL;
-	}
-	if (H5close() < 0) {
-		*error_flag = -1;
-	}
+  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

src/plugin.h

@@ -15,39 +15,23 @@
 extern "C" {
 #endif
 
-#define DLS_CUSTOMER_ID 0x01 /* pretend we're Dectris, otherwise XDS doesn't work */
+#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_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_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

src/test.c

@@ -1,134 +1,141 @@
+#include "err.h"
+#include "file.h"
+#include <hdf5.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <hdf5.h>
-#include "file.h"
-#include "err.h"
 
-#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] & 0xFE) out[i] = -2; \
-			if (mask[i] & 0x01) out[i] = -1; \
-		} \
-	} else { \
-		for (i = 0; i < size; i++) { \
-			out[i] = in[i]; \
-		} \
-	} \
-}
+#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] & 0xFE)                                                    \
+          out[i] = -2;                                                         \
+        if (mask[i] & 0x01)                                                    \
+          out[i] = -1;                                                         \
+      }                                                                        \
+    } else {                                                                   \
+      for (i = 0; i < size; i++) {                                             \
+        out[i] = in[i];                                                        \
+      }                                                                        \
+    }                                                                          \
+  }
 
 int parse_args(int argc, char **argv, char **file_name, int *frame_idx) {
-	int retval = 0;
-	if (argc == 2) {
-		*frame_idx = 0;
-		*file_name = argv[1];
-	} else if (argc >= 2) {
-		*file_name = argv[1];
-		*frame_idx = atoi(argv[2]);
-	} else {
-		ERROR_JUMP(-1, done, "Require filename argument");
-	}
+  int retval = 0;
+  if (argc == 2) {
+    *frame_idx = 0;
+    *file_name = argv[1];
+  } else if (argc >= 2) {
+    *file_name = argv[1];
+    *frame_idx = atoi(argv[2]);
+  } else {
+    ERROR_JUMP(-1, done, "Require filename argument");
+  }
 done:
-	return retval;
+  return retval;
 }
 
-
 int main(int argc, char **argv) {
-	int err = 0;
-	int retval = 0;
-	char *test_file = "";
-	struct ds_desc_t *desc;
-	int dims[3] = {0};
-	hid_t fid = 0;
-	int frame_idx = 0;
-	int *mask = NULL;
-	int *data = NULL;
-	void *buffer = NULL;
+  int err = 0;
+  int retval = 0;
+  char *test_file = "";
+  struct ds_desc_t *desc;
+  int dims[3] = {0};
+  hid_t fid = 0;
+  int frame_idx = 0;
+  int *mask = NULL;
+  int *data = NULL;
+  void *buffer = NULL;
 
-	init_error_handling();
-	if (init_h5_error_handling() < 0) {
-		ERROR_JUMP(-1, done, "");
-	}
+  init_error_handling();
+  if (init_h5_error_handling() < 0) {
+    ERROR_JUMP(-1, done, "");
+  }
 
-	if (parse_args(argc, argv, &test_file, &frame_idx) < 0) {
-		ERROR_JUMP(-1, done, "Failure parsing arguments");
-	}
+  if (parse_args(argc, argv, &test_file, &frame_idx) < 0) {
+    ERROR_JUMP(-1, done, "Failure parsing arguments");
+  }
 
-	fid = H5Fopen(test_file, H5F_ACC_RDONLY, H5P_DEFAULT);
-	if (fid < 0) ERROR_JUMP(-1, done, "Error opening file");
+  fid = H5Fopen(test_file, H5F_ACC_RDONLY, H5P_DEFAULT);
+  if (fid < 0)
+    ERROR_JUMP(-1, done, "Error opening file");
 
-	err = get_detector_info(fid, &desc);
-	if (err < 0) {
-		ERROR_JUMP(err, done, "");
-	}
-	dims[0] = desc->dims[0];
-	dims[1] = desc->dims[1];
-	dims[2] = desc->dims[2];
+  err = get_detector_info(fid, &desc);
+  if (err < 0) {
+    ERROR_JUMP(err, done, "");
+  }
+  dims[0] = desc->dims[0];
+  dims[1] = desc->dims[1];
+  dims[2] = desc->dims[2];
 
-	printf("Dims: %d, %d, %d\n", dims[0], dims[1], dims[2]);
+  printf("Dims: %d, %d, %d\n", dims[0], dims[1], dims[2]);
 
-	mask = malloc(dims[1] * dims[2] * sizeof(*mask));
-	if (!mask) {
-		ERROR_JUMP(err, done, "Failed to allocate space for pixel mask");
-	}
-	err = desc->get_pixel_mask(desc, mask);
-	if (err < 0) {
-		ERROR_JUMP(err, done, "");
-	}
+  mask = malloc(dims[1] * dims[2] * sizeof(*mask));
+  if (!mask) {
+    ERROR_JUMP(err, done, "Failed to allocate space for pixel mask");
+  }
+  err = desc->get_pixel_mask(desc, mask);
+  if (err < 0) {
+    ERROR_JUMP(err, done, "");
+  }
 
-	data = malloc(dims[1] * dims[2] * sizeof(*data));
-	if (sizeof(*data) != desc->data_width) {
-		buffer = malloc(dims[1] * dims[2] * desc->data_width);
-	} else {
-		buffer = data;
-	}
+  data = malloc(dims[1] * dims[2] * sizeof(*data));
+  if (sizeof(*data) != desc->data_width) {
+    buffer = malloc(dims[1] * dims[2] * desc->data_width);
+  } else {
+    buffer = data;
+  }
 
-	err = desc->get_data_frame(desc, frame_idx, buffer);
-	if (err < 0) {
-		ERROR_JUMP(err, done, "");
-	}
+  err = desc->get_data_frame(desc, frame_idx, buffer);
+  if (err < 0) {
+    ERROR_JUMP(err, done, "");
+  }
 
-	if (buffer != data) {
-		if (desc->data_width == sizeof(signed char)) {
-			signed char *in = buffer;
-			COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
-		} else if (desc->data_width == sizeof(short)) {
-			short *in = buffer;
-			COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
-		} else if (desc->data_width == sizeof(int)) {
-			int *in = buffer;
-			COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
-		} else if (desc->data_width == sizeof(long int)) {
-			long int *in = buffer;
-			COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
-		} else if (desc->data_width == sizeof(long long int)) {
-			long long int *in = buffer;
-			COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
-		}
-	}
+  if (buffer != data) {
+    if (desc->data_width == sizeof(signed char)) {
+      signed char *in = buffer;
+      COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
+    } else if (desc->data_width == sizeof(short)) {
+      short *in = buffer;
+      COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
+    } else if (desc->data_width == sizeof(int)) {
+      int *in = buffer;
+      COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
+    } else if (desc->data_width == sizeof(long int)) {
+      long int *in = buffer;
+      COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
+    } else if (desc->data_width == sizeof(long long int)) {
+      long long int *in = buffer;
+      COPY_AND_MASK(in, data, dims[1] * dims[2], mask);
+    }
+  }
 
-	{
-		int i, j;
-		int max_i = 30;
-		int max_j = 10;
-		max_j = max_j < dims[1] ? max_j : dims[1];
-		max_i = max_i < dims[2] ? max_i : dims[2];
-		for (j = 0; j < max_j; j++) {
-			for (i = 0; i < max_i; i++) {
-				printf("%3d ", data[i + j*dims[2]]);
-			}
-			printf("\n");
-		}
-	}
+  {
+    int i, j;
+    int max_i = 30;
+    int max_j = 10;
+    max_j = max_j < dims[1] ? max_j : dims[1];
+    max_i = max_i < dims[2] ? max_i : dims[2];
+    for (j = 0; j < max_j; j++) {
+      for (i = 0; i < max_i; i++) {
+        printf("%3d ", data[i + j * dims[2]]);
+      }
+      printf("\n");
+    }
+  }
 
 done:
-	if (fid > 0) H5Fclose(fid);
-	if (data) free(data);
-	if (buffer && (data != buffer)) free(buffer);
-	if (mask) free(mask);
-	if (retval != 0) dump_error_stack(stderr);
-	return retval;
+  if (fid > 0)
+    H5Fclose(fid);
+  if (data)
+    free(data);
+  if (buffer && (data != buffer))
+    free(buffer);
+  if (mask)
+    free(mask);
+  if (retval != 0)
+    dump_error_stack(stderr);
+  return retval;
 }