First cut: use H5_USE_110_API

For #18 - compile against 1.10 API (may need to do more work to make sure this
does what we actually want)

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=c89 -shlib
 
 .PHONY: plugin
 plugin: $(BUILD_DIR)/durin-plugin.so

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/file.c

@@ -339,7 +339,7 @@ int get_dectris_eiger_dataset_dims(struct ds_desc_t *desc) {
 		ds_id = H5Dopen2(desc->data_g_id, ds_name, H5P_DEFAULT);
 		if (ds_id < 0) {
 			char message[64];
-			sprintf("Unable to open dataset %.16s", ds_name);
+			sprintf(message, "Unable to open dataset %.16s", ds_name);
 			ERROR_JUMP(-1, loop_end, message);
 		}
 		t_id = H5Dget_type(ds_id);
@@ -410,14 +410,14 @@ int read_pixel_info(hid_t g_id, const char *path, double *size) {
 	ds_id = H5Dopen2(g_id, path, H5P_DEFAULT);
 	if (ds_id < 0) {
 		char message[64];
-		sprintf("Error opening dataset %.32s", path);
+		sprintf(message, "Error opening dataset %.32s", path);
 		ERROR_JUMP(-1, done, message);
 	}
 
 	err = H5Dread(ds_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &value);
 	if (err < 0) {
 		char message[64];
-		sprintf("Error reading dataset %.32s", path);
+		sprintf(message, "Error reading dataset %.32s", path);
 		ERROR_JUMP(-1, close_dataset, message);
 	}
 
@@ -429,8 +429,8 @@ int read_pixel_info(hid_t g_id, const char *path, double *size) {
 		double scale = 1;
 		a_id = H5Aopen(ds_id, "units", H5P_DEFAULT);
 		if (a_id < 0) {
-			char message[64];
-			sprintf("Error openeing units attribute for %.32s after existence check", path);
+			char message[100];
+			sprintf(message, "Error openeing units attribute for %.32s after existence check", path);
 			ERROR_JUMP(-1, close_dataset, message);
 		}
 

src/plugin.c

@@ -238,7 +238,10 @@ void plugin_close(int *error_flag) {
 	}
 	file_id = 0;
 
-	if (mask_buffer) free(mask_buffer);
+	if (mask_buffer) {
+	        free(mask_buffer);
+		mask_buffer = NULL;
+	}
 	if (data_desc->free_desc) {
 		data_desc->free_desc(data_desc);
 		data_desc = NULL;