Don't hide symbols in the shared library

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

.gitea/workflows/build.yml

@@ -0,0 +1,35 @@
+name: Build Packages
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+
+jobs:
+  build-library:
+    name: Build
+    runs-on: durin
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build library
+        shell: bash
+        run: |
+          mkdir -p build
+          cd build
+          cmake -DCMAKE_BUILD_TYPE=Release ..
+          make -j
+
+      - name: Upload release assets to Gitea
+        if: github.ref_type == 'tag'
+        shell: bash
+        env:
+          GITEA_TOKEN: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}
+        run: |
+          set -euo pipefail
+          python tools/gitea_release_upload.py \
+            "${{ github.server_url }}" \
+            "${{ github.repository }}" \
+            "${{ github.ref_name }}"

CMakeLists.txt

@@ -0,0 +1,56 @@
+CMAKE_MINIMUM_REQUIRED(VERSION 3.19)
+
+PROJECT(durin VERSION 1.0.0 LANGUAGES C)
+
+include(FetchContent)
+
+SET(CMAKE_C_FLAGS_RELEASE "-O3")
+
+SET(CMAKE_C_STANDARD 99)
+SET(CMAKE_C_STANDARD_REQUIRED ON)
+SET(CMAKE_C_EXTENSIONS OFF)
+
+SET(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+SET(BUILD_SHARED_LIBS OFF)
+
+set(HDF5_USE_STATIC_LIBRARIES TRUE)
+
+SET(HDF5_BUILD_HL_LIB OFF)
+
+SET(HDF5_ENABLE_THREADSAFE ON)
+SET(HDF5_ENABLE_SZIP_SUPPORT OFF)
+SET(HDF5_ENABLE_SZIP_ENCODING OFF)
+SET(HDF5_BUILD_EXAMPLES OFF)
+SET(HDF5_BUILD_CPP_LIB OFF)
+SET(HDF5_ENABLE_Z_LIB_SUPPORT OFF)
+SET(HDF5_EXTERNALLY_CONFIGURED 1)
+
+INCLUDE_DIRECTORIES(bslz4/src)
+
+FetchContent_Declare(hdf5
+        URL https://github.com/HDFGroup/hdf5/releases/download/hdf5_1.14.6/hdf5-1.14.6.tar.gz
+        DOWNLOAD_EXTRACT_TIMESTAMP FALSE
+        EXCLUDE_FROM_ALL)
+
+FetchContent_MakeAvailable(hdf5)
+
+ADD_LIBRARY(durin-plugin SHARED
+        src/plugin.c src/plugin.h
+        src/err.c src/err.h
+        src/filters.c src/filters.h
+        src/file.c src/file.h bslz4/src/bitshuffle.c bslz4/src/bitshuffle.h
+        bslz4/src/bitshuffle_core.c bslz4/src/bitshuffle_core.h
+        bslz4/src/bitshuffle_internals.h
+        bslz4/src/bshuf_h5filter.c bslz4/src/bshuf_h5filter.h
+        bslz4/src/iochain.c bslz4/src/iochain.h
+        bslz4/src/lz4.c bslz4/src/lz4.h
+        )
+
+set_target_properties(durin-plugin PROPERTIES VERSION 1.0.0)
+
+TARGET_COMPILE_DEFINITIONS(durin-plugin PRIVATE
+        H5_USE_110_API
+        USE_BITSHUFFLE)
+
+TARGET_LINK_LIBRARIES(durin-plugin PRIVATE hdf5-static)

Dockerfile

@@ -0,0 +1,43 @@
+FROM registry.access.redhat.com/ubi7/ubi
+
+ARG HDF5_TAG="hdf5_1.14.6"
+
+LABEL authors="Filip Leonarski"
+
+ARG CMAKE_VERSION=3.31.6
+ARG NODE_MAJOR=16
+
+RUN yum -y update && \
+    yum -y install \
+        gcc \
+        gcc-c++ \
+        git \
+        make \
+        tar \
+        gzip \
+        curl && \
+    yum clean all
+
+# Install a recent Node.js (NodeSource). Change NODE_MAJOR if you want another major version.
+RUN curl -fsSL https://rpm.nodesource.com/setup_${NODE_MAJOR}.x | bash - && \
+    yum -y install nodejs && \
+    yum clean all && \
+    node --version && npm --version && (corepack enable || true)
+
+RUN set -eux; \
+    arch="$(uname -m)"; \
+    case "$arch" in \
+      x86_64) cmake_arch="x86_64" ;; \
+      aarch64) cmake_arch="aarch64" ;; \
+      *) echo "Unsupported architecture: $arch"; exit 1 ;; \
+    esac; \
+    curl -L "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}-linux-${cmake_arch}.tar.gz" \
+      -o /tmp/cmake.tar.gz; \
+    tar -xzf /tmp/cmake.tar.gz -C /opt; \
+    ln -s "/opt/cmake-${CMAKE_VERSION}-linux-${cmake_arch}/bin/cmake" /usr/local/bin/cmake; \
+    ln -s "/opt/cmake-${CMAKE_VERSION}-linux-${cmake_arch}/bin/ctest" /usr/local/bin/ctest; \
+    ln -s "/opt/cmake-${CMAKE_VERSION}-linux-${cmake_arch}/bin/cpack" /usr/local/bin/cpack; \
+    rm -f /tmp/cmake.tar.gz
+
+# Default entrypoint prints tool versions and hints.
+CMD ["/bin/bash", "-l"]

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2018, Diamond Light Source
+Copyright (c) 2018-2019, Diamond Light Source
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -8,15 +8,15 @@ modification, are permitted provided that the following conditions are met:
     * 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
+    * Neither the name of the copyright holder 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
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS 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

Makefile

@@ -1,39 +0,0 @@
-BUILD_DIR ?= ./build
-SRC_DIR = ./src
-TEST_DIR = ./test
-INC_DIR = $(SRC_DIR)
-
-CC=h5cc
-CFLAGS=-Wall -g -O2 -fpic -I$(INC_DIR)
-
-.PHONY: all
-all: plugin example test_plugin
-
-.PHONY: plugin
-plugin: $(BUILD_DIR)/durin-plugin.so
-
-.PHONY: example
-example: $(BUILD_DIR)/example
-
-.PHONY: test_plugin
-test_plugin: $(BUILD_DIR)/test_plugin
-
-$(BUILD_DIR)/test_plugin: $(TEST_DIR)/generic_data_plugin.f90 $(TEST_DIR)/test_generic_host.f90
-	mkdir -p $(BUILD_DIR)
-	gfortran -O -g -fopenmp -ldl $(TEST_DIR)/generic_data_plugin.f90 $(TEST_DIR)/test_generic_host.f90 -o $@ -J$(BUILD_DIR)
-
-$(BUILD_DIR)/%.o: $(SRC_DIR)/%.c
-	mkdir -p $(BUILD_DIR)
-	$(CC) $(CFLAGS) -c $< -o $@
-
-$(BUILD_DIR)/durin-plugin.so: $(BUILD_DIR)/plugin.o $(BUILD_DIR)/file.o $(BUILD_DIR)/err.o
-	mkdir -p $(BUILD_DIR)
-	$(CC) $(CFLAGS) -shared $^ -o $(BUILD_DIR)/durin-plugin.so
-
-$(BUILD_DIR)/example: $(BUILD_DIR)/test.o $(BUILD_DIR)/file.o $(BUILD_DIR)/err.o
-	mkdir -p $(BUILD_DIR)
-	$(CC) $(CFLAGS) $^ -o $(BUILD_DIR)/example
-
-.PHONY: clean
-clean:
-	rm -r $(BUILD_DIR)

README.md

@@ -8,11 +8,24 @@ See:
 * https://www.dectris.com/features/features-eiger-x/hdf5-and-nexus
 * https://strucbio.biologie.uni-konstanz.de/xdswiki
 
+## Paul Scherrer Institute fork
+This fork is maintained by Paul Scherrer Institute.
+The plugin is based on the code developed by the Diamond Light Source and modified by Global Phasing.
+Modifications from PSI side:
+* Using CMake for building the plugin
+* HDF5 is built as part of the CMake process
+* Bitshuffle/LZ4 is updated to the latest version
+* HDF5 filter is automatically registered for virtual dataset HDF5 files
+* Docker image to build the plugin on x86/RH7 is provided.
+* Generated versioned shared library, so the used version can be tracked.
+
+## Get Durin
+Linux x86 version is automatically built on RHEL 7 and available from the Gitea release page.
 
 ## Usage
 In your XDS.INP add:
 ```
-LIB=[path to durin-plugin.so]
+LIB=[path to libdurin-plugin.so]
 NAME_TEMPLATE_OF_DATA_FRAMES=[data_path]/data_images_??????.h5
 ```
 XDS will instruct the plugin to load `[data_path]/data_images_master.h5` and this must be the
@@ -24,13 +37,41 @@ the master file contains an `NXdata` or `NXdetector` group with either a dataset
 series of datasets named `data_000001`, `data_000002`, etc.
 
 
-## Requirements
-* HDF5 Library (https://www.hdfgroup.org/downloads)
-
-
 ## Building
+Requires CMake version 3.19 or later + GCC compiler. There is no need to build HDF5 separately.
+To build:
 ```
-cd durin
-make
+mkdir build
+cd build
+cmake ..
+make -j
+```
+
+The plugin is located at `build/libdurin-plugin.so` and should be added to the
+XDS.INP file as `LIB=<CURRENT_DIRECTORY>/build/libdurin-plugin.so`.
+Alternatively, versioned copy is also provided, e.g. `libdurin-plugin.so.1.0.0`, allowing to track 
+the current version of the plugin.
+
+## Example XDS.INP
+```
+DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=4096
+LIB=/opt/durin/build/libdurin-plugin.so
+SENSOR_THICKNESS= 0.450
+!SENSOR_MATERIAL / THICKNESS Si 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
+DETECTOR_DISTANCE= 194.633000
+ORGX= 1041.30 ORGY= 1160.90
+ROTATION_AXIS= 0.00000 -1.00000 -0.00000
+STARTING_ANGLE= -30.000
+OSCILLATION_RANGE= 0.100
+X-RAY_WAVELENGTH= 0.97891
+INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.022
+FRACTION_OF_POLARIZATION= 0.999
+POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
+NAME_TEMPLATE_OF_DATA_FRAMES= ../image_9264_??????.h5
+TRUSTED_REGION= 0.0 1.41
+DATA_RANGE= 1 600
+JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 ```
-Plugin file is `build/durin-plugin.so`

bslz4/LICENSE

@@ -0,0 +1,21 @@
+Bitshuffle - Filter for improving compression of typed binary data.
+
+Copyright (c) 2014 Kiyoshi Masui (kiyo@physics.ubc.ca)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

bslz4/src/bitshuffle.c

@@ -0,0 +1,279 @@
+/*
+ * Bitshuffle - Filter for improving compression of typed binary data.
+ *
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ *
+ */
+
+#include "bitshuffle.h"
+#include "bitshuffle_core.h"
+#include "bitshuffle_internals.h"
+#include "lz4.h"
+
+#ifdef ZSTD_SUPPORT
+#include "zstd.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+
+
+// Macros.
+#define CHECK_ERR_FREE_LZ(count, buf) if (count < 0) {                      \
+    free(buf); return count - 1000; }
+
+
+/* Bitshuffle and compress a single block. */
+int64_t bshuf_compress_lz4_block(ioc_chain *C_ptr, \
+        const size_t size, const size_t elem_size, const int option) {
+
+    int64_t nbytes, count;
+    void *tmp_buf_bshuf;
+    void *tmp_buf_lz4;
+    size_t this_iter;
+    const void *in;
+    void *out;
+
+    tmp_buf_bshuf = malloc(size * elem_size);
+    if (tmp_buf_bshuf == NULL) return -1;
+
+    int dst_capacity = LZ4_compressBound(size * elem_size);
+    tmp_buf_lz4 = malloc(dst_capacity);
+    if (tmp_buf_lz4 == NULL){
+        free(tmp_buf_bshuf);
+        return -1;
+    }
+
+
+    in = ioc_get_in(C_ptr, &this_iter);
+    ioc_set_next_in(C_ptr, &this_iter, (void*) ((char*) in + size * elem_size));
+
+    count = bshuf_trans_bit_elem(in, tmp_buf_bshuf, size, elem_size);
+    if (count < 0) {
+        free(tmp_buf_lz4);
+        free(tmp_buf_bshuf);
+        return count;
+    }
+    nbytes = LZ4_compress_default((const char*) tmp_buf_bshuf, (char*) tmp_buf_lz4, size * elem_size, dst_capacity);
+    free(tmp_buf_bshuf);
+    CHECK_ERR_FREE_LZ(nbytes, tmp_buf_lz4);
+
+    out = ioc_get_out(C_ptr, &this_iter);
+    ioc_set_next_out(C_ptr, &this_iter, (void *) ((char *) out + nbytes + 4));
+
+    bshuf_write_uint32_BE(out, nbytes);
+    memcpy((char *) out + 4, tmp_buf_lz4, nbytes);
+
+    free(tmp_buf_lz4);
+
+    return nbytes + 4;
+}
+
+
+/* Decompress and bitunshuffle a single block. */
+int64_t bshuf_decompress_lz4_block(ioc_chain *C_ptr,
+        const size_t size, const size_t elem_size, const int option) {
+
+    int64_t nbytes, count;
+    void *out, *tmp_buf;
+    const void *in;
+    size_t this_iter;
+    int32_t nbytes_from_header;
+
+    in = ioc_get_in(C_ptr, &this_iter);
+    nbytes_from_header = bshuf_read_uint32_BE(in);
+    ioc_set_next_in(C_ptr, &this_iter,
+            (void*) ((char*) in + nbytes_from_header + 4));
+
+    out = ioc_get_out(C_ptr, &this_iter);
+    ioc_set_next_out(C_ptr, &this_iter,
+            (void *) ((char *) out + size * elem_size));
+
+    tmp_buf = malloc(size * elem_size);
+    if (tmp_buf == NULL) return -1;
+
+    nbytes = LZ4_decompress_safe((const char*) in + 4, (char *) tmp_buf, nbytes_from_header,
+                                 size * elem_size);
+    CHECK_ERR_FREE_LZ(nbytes, tmp_buf);
+    if (nbytes != size * elem_size) {
+        free(tmp_buf);
+        return -91;
+    }
+    nbytes = nbytes_from_header;
+
+    count = bshuf_untrans_bit_elem(tmp_buf, out, size, elem_size);
+    CHECK_ERR_FREE(count, tmp_buf);
+    nbytes += 4;
+
+    free(tmp_buf);
+    return nbytes;
+}
+
+#ifdef ZSTD_SUPPORT
+/* Bitshuffle and compress a single block. */
+int64_t bshuf_compress_zstd_block(ioc_chain *C_ptr, \
+        const size_t size, const size_t elem_size, const int comp_lvl) {
+
+    int64_t nbytes, count;
+    void *tmp_buf_bshuf;
+    void *tmp_buf_zstd;
+    size_t this_iter;
+    const void *in;
+    void *out;
+
+    tmp_buf_bshuf = malloc(size * elem_size);
+    if (tmp_buf_bshuf == NULL) return -1;
+
+    size_t tmp_buf_zstd_size = ZSTD_compressBound(size * elem_size);
+    tmp_buf_zstd = malloc(tmp_buf_zstd_size);
+    if (tmp_buf_zstd == NULL){
+        free(tmp_buf_bshuf);
+        return -1;
+    }
+
+    in = ioc_get_in(C_ptr, &this_iter);
+    ioc_set_next_in(C_ptr, &this_iter, (void*) ((char*) in + size * elem_size));
+
+    count = bshuf_trans_bit_elem(in, tmp_buf_bshuf, size, elem_size);
+    if (count < 0) {
+        free(tmp_buf_zstd);
+        free(tmp_buf_bshuf);
+        return count;
+    }
+    nbytes = ZSTD_compress(tmp_buf_zstd, tmp_buf_zstd_size, (const void*)tmp_buf_bshuf,  size * elem_size, comp_lvl);
+    free(tmp_buf_bshuf);
+    CHECK_ERR_FREE_LZ(nbytes, tmp_buf_zstd);
+
+    out = ioc_get_out(C_ptr, &this_iter);
+    ioc_set_next_out(C_ptr, &this_iter, (void *) ((char *) out + nbytes + 4));
+
+    bshuf_write_uint32_BE(out, nbytes);
+    memcpy((char *) out + 4, tmp_buf_zstd, nbytes);
+
+    free(tmp_buf_zstd);
+
+    return nbytes + 4;
+}
+
+
+/* Decompress and bitunshuffle a single block. */
+int64_t bshuf_decompress_zstd_block(ioc_chain *C_ptr,
+        const size_t size, const size_t elem_size, const int option) {
+
+    int64_t nbytes, count;
+    void *out, *tmp_buf;
+    const void *in;
+    size_t this_iter;
+    int32_t nbytes_from_header;
+
+    in = ioc_get_in(C_ptr, &this_iter);
+    nbytes_from_header = bshuf_read_uint32_BE(in);
+    ioc_set_next_in(C_ptr, &this_iter,
+            (void*) ((char*) in + nbytes_from_header + 4));
+
+    out = ioc_get_out(C_ptr, &this_iter);
+    ioc_set_next_out(C_ptr, &this_iter,
+            (void *) ((char *) out + size * elem_size));
+
+    tmp_buf = malloc(size * elem_size);
+    if (tmp_buf == NULL) return -1;
+
+    nbytes = ZSTD_decompress(tmp_buf, size * elem_size, (void *)((char *) in + 4), nbytes_from_header);
+    CHECK_ERR_FREE_LZ(nbytes, tmp_buf);
+    if (nbytes != size * elem_size) {
+        free(tmp_buf);
+        return -91;
+    }
+
+    nbytes = nbytes_from_header;
+    count = bshuf_untrans_bit_elem(tmp_buf, out, size, elem_size);
+    CHECK_ERR_FREE(count, tmp_buf);
+    nbytes += 4;
+
+    free(tmp_buf);
+    return nbytes;
+}
+#endif // ZSTD_SUPPORT
+
+
+/* ---- Public functions ----
+ *
+ * See header file for description and usage.
+ *
+ */
+
+size_t bshuf_compress_lz4_bound(const size_t size,
+        const size_t elem_size, size_t block_size) {
+
+    size_t bound, leftover;
+
+    if (block_size == 0) {
+        block_size = bshuf_default_block_size(elem_size);
+    }
+    if (block_size % BSHUF_BLOCKED_MULT) return -81;
+
+    // Note that each block gets a 4 byte header.
+    // Size of full blocks.
+    bound = (LZ4_compressBound(block_size * elem_size) + 4) * (size / block_size);
+    // Size of partial blocks, if any.
+    leftover = ((size % block_size) / BSHUF_BLOCKED_MULT) * BSHUF_BLOCKED_MULT;
+    if (leftover) bound += LZ4_compressBound(leftover * elem_size) + 4;
+    // Size of uncompressed data not fitting into any blocks.
+    bound += (size % BSHUF_BLOCKED_MULT) * elem_size;
+    return bound;
+}
+
+
+int64_t bshuf_compress_lz4(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size) {
+    return bshuf_blocked_wrap_fun(&bshuf_compress_lz4_block, in, out, size,
+            elem_size, block_size, 0/*option*/);
+}
+
+
+int64_t bshuf_decompress_lz4(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size) {
+    return bshuf_blocked_wrap_fun(&bshuf_decompress_lz4_block, in, out, size,
+            elem_size, block_size, 0/*option*/);
+}
+
+#ifdef ZSTD_SUPPORT
+size_t bshuf_compress_zstd_bound(const size_t size,
+        const size_t elem_size, size_t block_size) {
+
+    size_t bound, leftover;
+
+    if (block_size == 0) {
+        block_size = bshuf_default_block_size(elem_size);
+    }
+    if (block_size % BSHUF_BLOCKED_MULT) return -81;
+
+    // Note that each block gets a 4 byte header.
+    // Size of full blocks.
+    bound = (ZSTD_compressBound(block_size * elem_size) + 4) * (size / block_size);
+    // Size of partial blocks, if any.
+    leftover = ((size % block_size) / BSHUF_BLOCKED_MULT) * BSHUF_BLOCKED_MULT;
+    if (leftover) bound += ZSTD_compressBound(leftover * elem_size) + 4;
+    // Size of uncompressed data not fitting into any blocks.
+    bound += (size % BSHUF_BLOCKED_MULT) * elem_size;
+    return bound;
+}
+
+
+int64_t bshuf_compress_zstd(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size, const int comp_lvl) {
+    return bshuf_blocked_wrap_fun(&bshuf_compress_zstd_block, in, out, size,
+            elem_size, block_size, comp_lvl);
+}
+
+
+int64_t bshuf_decompress_zstd(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size) {
+    return bshuf_blocked_wrap_fun(&bshuf_decompress_zstd_block, in, out, size,
+            elem_size, block_size, 0/*option*/);
+}
+#endif // ZSTD_SUPPORT

bslz4/src/bitshuffle.h

@@ -0,0 +1,205 @@
+/*
+ * Bitshuffle - Filter for improving compression of typed binary data.
+ *
+ * This file is part of Bitshuffle
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ *
+ *
+ * Header File
+ *
+ * Worker routines return an int64_t which is the number of bytes processed
+ * if positive or an error code if negative.
+ *
+ * Error codes:
+ *      -1    : Failed to allocate memory.
+ *      -11   : Missing SSE.
+ *      -12   : Missing AVX.
+ *      -80   : Input size not a multiple of 8.
+ *      -81   : block_size not multiple of 8.
+ *      -91   : Decompression error, wrong number of bytes processed.
+ *      -1YYY : Error internal to compression routine with error code -YYY.
+ */
+
+
+#ifndef BITSHUFFLE_H
+#define BITSHUFFLE_H
+
+#include <stdlib.h>
+#include "bitshuffle_core.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * ---- LZ4 Interface ----
+ */
+
+/* ---- bshuf_compress_lz4_bound ----
+ *
+ * Bound on size of data compressed with *bshuf_compress_lz4*.
+ *
+ * Parameters
+ * ----------
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Process in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *
+ * Returns
+ * -------
+ *  Bound on compressed data size.
+ *
+ */
+size_t bshuf_compress_lz4_bound(const size_t size,
+        const size_t elem_size, size_t block_size);
+
+
+/* ---- bshuf_compress_lz4 ----
+ *
+ * Bitshuffled and compress the data using LZ4.
+ *
+ * Transpose within elements, in blocks of data of *block_size* elements then
+ * compress the blocks using LZ4.  In the output buffer, each block is prefixed
+ * by a 4 byte integer giving the compressed size of that block.
+ *
+ * Output buffer must be large enough to hold the compressed data.  This could
+ * be in principle substantially larger than the input buffer.  Use the routine
+ * *bshuf_compress_lz4_bound* to get an upper limit.
+ *
+ * Parameters
+ * ----------
+ *  in : input buffer, must be of size * elem_size bytes
+ *  out : output buffer, must be large enough to hold data.
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Process in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *
+ * Returns
+ * -------
+ *  number of bytes used in output buffer, negative error-code if failed.
+ *
+ */
+int64_t bshuf_compress_lz4(const void* in, void* out, const size_t size, const size_t
+        elem_size, size_t block_size);
+
+
+/* ---- bshuf_decompress_lz4 ----
+ *
+ * Undo compression and bitshuffling.
+ *
+ * Decompress data then un-bitshuffle it in blocks of *block_size* elements.
+ *
+ * To properly unshuffle bitshuffled data, *size*, *elem_size* and *block_size*
+ * must patch the parameters used to compress the data.
+ *
+ * Parameters
+ * ----------
+ *  in : input buffer
+ *  out : output buffer, must be of size * elem_size bytes
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Process in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *
+ * Returns
+ * -------
+ *  number of bytes consumed in *input* buffer, negative error-code if failed.
+ *
+ */
+int64_t bshuf_decompress_lz4(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size);
+
+/*
+ * ---- ZSTD Interface ----
+ */
+
+#ifdef ZSTD_SUPPORT
+/* ---- bshuf_compress_zstd_bound ----
+ *
+ * Bound on size of data compressed with *bshuf_compress_zstd*.
+ *
+ * Parameters
+ * ----------
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Process in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *
+ * Returns
+ * -------
+ *  Bound on compressed data size.
+ *
+ */
+size_t bshuf_compress_zstd_bound(const size_t size,
+        const size_t elem_size, size_t block_size);
+
+/* ---- bshuf_compress_zstd ----
+ *
+ * Bitshuffled and compress the data using zstd.
+ *
+ * Transpose within elements, in blocks of data of *block_size* elements then
+ * compress the blocks using ZSTD.  In the output buffer, each block is prefixed
+ * by a 4 byte integer giving the compressed size of that block.
+ *
+ * Output buffer must be large enough to hold the compressed data.  This could
+ * be in principle substantially larger than the input buffer.  Use the routine
+ * *bshuf_compress_zstd_bound* to get an upper limit.
+ *
+ * Parameters
+ * ----------
+ *  in : input buffer, must be of size * elem_size bytes
+ *  out : output buffer, must be large enough to hold data.
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Process in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *  comp_lvl : compression level applied
+ *
+ * Returns
+ * -------
+ *  number of bytes used in output buffer, negative error-code if failed.
+ *
+ */
+int64_t bshuf_compress_zstd(const void* in, void* out, const size_t size, const size_t
+        elem_size, size_t block_size, const int comp_lvl);
+
+
+/* ---- bshuf_decompress_zstd ----
+ *
+ * Undo compression and bitshuffling.
+ *
+ * Decompress data then un-bitshuffle it in blocks of *block_size* elements.
+ *
+ * To properly unshuffle bitshuffled data, *size*, *elem_size* and *block_size*
+ * must patch the parameters used to compress the data.
+ *
+ * Parameters
+ * ----------
+ *  in : input buffer
+ *  out : output buffer, must be of size * elem_size bytes
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Process in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *
+ * Returns
+ * -------
+ *  number of bytes consumed in *input* buffer, negative error-code if failed.
+ *
+ */
+int64_t bshuf_decompress_zstd(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size);
+
+#endif // ZSTD_SUPPORT
+
+#ifdef __cplusplus
+} // extern "C"
+#endif
+
+#endif  // BITSHUFFLE_H

bslz4/src/bitshuffle_core.h

@@ -0,0 +1,182 @@
+/*
+ * Bitshuffle - Filter for improving compression of typed binary data.
+ *
+ * This file is part of Bitshuffle
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ *
+ *
+ * Header File
+ *
+ * Worker routines return an int64_t which is the number of bytes processed
+ * if positive or an error code if negative.
+ *
+ * Error codes:
+ *      -1    : Failed to allocate memory.
+ *      -11   : Missing SSE.
+ *      -12   : Missing AVX.
+ *      -13   : Missing Arm Neon.
+ *      -14   : Missing AVX512.
+ *      -80   : Input size not a multiple of 8.
+ *      -81   : block_size not multiple of 8.
+ *      -91   : Decompression error, wrong number of bytes processed.
+ *      -1YYY : Error internal to compression routine with error code -YYY.
+ */
+
+
+#ifndef BITSHUFFLE_CORE_H
+#define BITSHUFFLE_CORE_H
+
+// We assume GNU g++ defining `__cplusplus` has stdint.h
+#if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199900L) || defined(__cplusplus)
+#include <stdint.h>
+#else
+  typedef unsigned char       uint8_t;
+  typedef unsigned short      uint16_t;
+  typedef unsigned int        uint32_t;
+  typedef   signed int        int32_t;
+  typedef unsigned long long  uint64_t;
+  typedef long long           int64_t;
+#endif
+
+#include <stdlib.h>
+
+
+// These are usually set in the setup.py.
+#ifndef BSHUF_VERSION_MAJOR
+#define BSHUF_VERSION_MAJOR 0
+#define BSHUF_VERSION_MINOR 4
+#define BSHUF_VERSION_POINT 0
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* --- bshuf_using_SSE2 ----
+ *
+ * Whether routines where compiled with the SSE2 instruction set.
+ *
+ * Returns
+ * -------
+ *  1 if using SSE2, 0 otherwise.
+ *
+ */
+int bshuf_using_SSE2(void);
+
+
+/* ---- bshuf_using_NEON ----
+ *
+ * Whether routines where compiled with the NEON instruction set.
+ *
+ * Returns
+ * -------
+ *  1 if using NEON, 0 otherwise.
+ *
+ */
+int bshuf_using_NEON(void);
+
+
+/* ---- bshuf_using_AVX2 ----
+ *
+ * Whether routines where compiled with the AVX2 instruction set.
+ *
+ * Returns
+ * -------
+ *  1 if using AVX2, 0 otherwise.
+ *
+ */
+int bshuf_using_AVX2(void);
+
+
+/* ---- bshuf_using_AVX512 ----
+ *
+ * Whether routines where compiled with the AVX512 instruction set.
+ *
+ * Returns
+ * -------
+ *  1 if using AVX512, 0 otherwise.
+ *
+ */
+int bshuf_using_AVX512(void);
+
+
+/* ---- bshuf_default_block_size ----
+ *
+ * The default block size as function of element size.
+ *
+ * This is the block size used by the blocked routines (any routine
+ * taking a *block_size* argument) when the block_size is not provided
+ * (zero is passed).
+ *
+ * The results of this routine are guaranteed to be stable such that
+ * shuffled/compressed data can always be decompressed.
+ *
+ * Parameters
+ * ----------
+ *  elem_size : element size of data to be shuffled/compressed.
+ *
+ */
+size_t bshuf_default_block_size(const size_t elem_size);
+
+
+/* ---- bshuf_bitshuffle ----
+ *
+ * Bitshuffle the data.
+ *
+ * Transpose the bits within elements, in blocks of *block_size*
+ * elements.
+ *
+ * Parameters
+ * ----------
+ *  in : input buffer, must be of size * elem_size bytes
+ *  out : output buffer, must be of size * elem_size bytes
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Do transpose in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *
+ * Returns
+ * -------
+ *  number of bytes processed, negative error-code if failed.
+ *
+ */
+int64_t bshuf_bitshuffle(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size);
+
+
+/* ---- bshuf_bitunshuffle ----
+ *
+ * Unshuffle bitshuffled data.
+ *
+ * Untranspose the bits within elements, in blocks of *block_size*
+ * elements.
+ *
+ * To properly unshuffle bitshuffled data, *size*, *elem_size* and *block_size*
+ * must match the parameters used to shuffle the data.
+ *
+ * Parameters
+ * ----------
+ *  in : input buffer, must be of size * elem_size bytes
+ *  out : output buffer, must be of size * elem_size bytes
+ *  size : number of elements in input
+ *  elem_size : element size of typed data
+ *  block_size : Do transpose in blocks of this many elements. Pass 0 to
+ *  select automatically (recommended).
+ *
+ * Returns
+ * -------
+ *  number of bytes processed, negative error-code if failed.
+ *
+ */
+int64_t bshuf_bitunshuffle(const void* in, void* out, const size_t size,
+        const size_t elem_size, size_t block_size);
+
+#ifdef __cplusplus
+} // extern "C"
+#endif
+
+#endif  // BITSHUFFLE_CORE_H

bslz4/src/bitshuffle_internals.h

@@ -0,0 +1,75 @@
+/*
+ * Bitshuffle - Filter for improving compression of typed binary data.
+ *
+ * This file is part of Bitshuffle
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ */
+
+
+#ifndef BITSHUFFLE_INTERNALS_H
+#define BITSHUFFLE_INTERNALS_H
+
+// We assume GNU g++ defining `__cplusplus` has stdint.h
+#if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199900L) || defined(__cplusplus)
+#include <stdint.h>
+#else
+  typedef unsigned char       uint8_t;
+  typedef unsigned short      uint16_t;
+  typedef unsigned int        uint32_t;
+  typedef   signed int        int32_t;
+  typedef unsigned long long  uint64_t;
+  typedef long long           int64_t;
+#endif
+
+#include <stdlib.h>
+#include "iochain.h"
+
+
+// Constants.
+#ifndef BSHUF_MIN_RECOMMEND_BLOCK
+#define BSHUF_MIN_RECOMMEND_BLOCK 128
+#define BSHUF_BLOCKED_MULT 8    // Block sizes must be multiple of this.
+#define BSHUF_TARGET_BLOCK_SIZE_B 8192
+#endif
+
+
+// Macros.
+#define CHECK_ERR_FREE(count, buf) if (count < 0) { free(buf); return count; }
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* ---- Utility functions for internal use only ---- */
+
+int64_t bshuf_trans_bit_elem(const void* in, void* out, const size_t size,
+        const size_t elem_size);
+
+/* Read a 32 bit unsigned integer from a buffer big endian order. */
+uint32_t bshuf_read_uint32_BE(const void* buf);
+
+/* Write a 32 bit unsigned integer to a buffer in big endian order. */
+void bshuf_write_uint32_BE(void* buf, uint32_t num);
+
+int64_t bshuf_untrans_bit_elem(const void* in, void* out, const size_t size,
+        const size_t elem_size);
+
+/* Function definition for worker functions that process a single block. */
+typedef int64_t (*bshufBlockFunDef)(ioc_chain* C_ptr,
+        const size_t size, const size_t elem_size, const int option);
+
+/* Wrap a function for processing a single block to process an entire buffer in
+ * parallel. */
+int64_t bshuf_blocked_wrap_fun(bshufBlockFunDef fun, const void* in, void* out,
+        const size_t size, const size_t elem_size, size_t block_size, const int option);
+
+#ifdef __cplusplus
+} // extern "C"
+#endif
+
+#endif  // BITSHUFFLE_INTERNALS_H

bslz4/src/bshuf_h5filter.c

@@ -0,0 +1,260 @@
+/*
+ * Bitshuffle HDF5 filter
+ *
+ * This file is part of Bitshuffle
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ *
+ */
+
+#include "bitshuffle.h"
+#include "bshuf_h5filter.h"
+
+
+#define PUSH_ERR(func, minor, str)                                      \
+    H5Epush1(__FILE__, func, __LINE__, H5E_PLINE, minor, str)
+
+
+// Prototypes from bitshuffle.c
+void bshuf_write_uint64_BE(void* buf, uint64_t num);
+uint64_t bshuf_read_uint64_BE(void* buf);
+void bshuf_write_uint32_BE(void* buf, uint32_t num);
+uint32_t bshuf_read_uint32_BE(const void* buf);
+
+
+// Only called on compression, not on reverse.
+herr_t bshuf_h5_set_local(hid_t dcpl, hid_t type, hid_t space){
+
+    herr_t r;
+    size_t ii;
+
+    unsigned int elem_size;
+
+    unsigned int flags;
+    size_t nelements = 8;
+    size_t nelem_max = 11;
+    unsigned values[] = {0,0,0,0,0,0,0,0,0,0,0};
+    unsigned tmp_values[] = {0,0,0,0,0,0,0,0};
+    char msg[80];
+
+    r = H5Pget_filter_by_id2(dcpl, BSHUF_H5FILTER, &flags, &nelements,
+            tmp_values, 0, NULL, NULL);
+    if(r<0) return -1;
+
+    // First 3 slots reserved. Move any passed options to higher addresses.
+    for (ii=0; ii < nelements && ii + 3 < nelem_max; ii++) {
+        values[ii + 3] = tmp_values[ii];
+    }
+
+    nelements = 3 + nelements;
+
+    values[0] = BSHUF_VERSION_MAJOR;
+    values[1] = BSHUF_VERSION_MINOR;
+
+    elem_size = H5Tget_size(type);
+    if(elem_size <= 0) {
+        PUSH_ERR("bshuf_h5_set_local", H5E_CALLBACK, 
+                "Invalid element size.");
+        return -1;
+    }
+
+    values[2] = elem_size;
+
+    // Validate user supplied arguments.
+    if (nelements > 3) {
+        if (values[3] % 8 || values[3] < 0) {
+            sprintf(msg, "Error in bitshuffle. Invalid block size: %d.",
+                    values[3]);
+            PUSH_ERR("bshuf_h5_set_local", H5E_CALLBACK, msg);
+            return -1;
+        }
+    }
+    if (nelements > 4) {
+        switch (values[4]) {
+            case 0:
+                break;
+            case BSHUF_H5_COMPRESS_LZ4:
+                break;
+            #ifdef ZSTD_SUPPORT
+            case BSHUF_H5_COMPRESS_ZSTD:
+                break;
+            #endif
+            default:
+                PUSH_ERR("bshuf_h5_set_local", H5E_CALLBACK, 
+                         "Invalid bitshuffle compression.");
+        }
+    }
+
+    r = H5Pmodify_filter(dcpl, BSHUF_H5FILTER, flags, nelements, values);
+    if(r<0) return -1;
+
+    return 1;
+}
+
+
+size_t bshuf_h5_filter(unsigned int flags, size_t cd_nelmts,
+           const unsigned int cd_values[], size_t nbytes,
+           size_t *buf_size, void **buf) {
+
+    size_t size, elem_size;
+    int err = -1;
+    char msg[80];
+    size_t block_size = 0;
+    size_t buf_size_out, nbytes_uncomp, nbytes_out;
+    char* in_buf = *buf;
+    void *out_buf;
+
+    if (cd_nelmts < 3) {
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+                "Not enough parameters.");
+        return 0;
+    }
+    elem_size = cd_values[2];
+#ifdef ZSTD_SUPPORT
+    const int comp_lvl = cd_values[5]; 
+#endif
+
+    // User specified block size.
+    if (cd_nelmts > 3) block_size = cd_values[3];
+
+    if (block_size == 0) block_size = bshuf_default_block_size(elem_size);
+    
+#ifndef ZSTD_SUPPORT
+    if (cd_nelmts > 4 && (cd_values[4] == BSHUF_H5_COMPRESS_ZSTD)) {
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+                "ZSTD compression filter chosen but ZSTD support not installed.");
+        return 0;
+    }
+#endif
+
+    // Compression in addition to bitshuffle.
+    if (cd_nelmts > 4 && (cd_values[4] == BSHUF_H5_COMPRESS_LZ4 || cd_values[4] == BSHUF_H5_COMPRESS_ZSTD)) {
+        if (flags & H5Z_FLAG_REVERSE) {
+            // First eight bytes is the number of bytes in the output buffer,
+            // little endian.
+            nbytes_uncomp = bshuf_read_uint64_BE(in_buf);
+            // Override the block size with the one read from the header.
+            block_size = bshuf_read_uint32_BE((const char*) in_buf + 8) / elem_size;
+            // Skip over the header.
+            in_buf += 12;
+            buf_size_out = nbytes_uncomp;
+        } else {
+            nbytes_uncomp = nbytes;
+            // Pick which compressions library to use
+            if(cd_values[4] == BSHUF_H5_COMPRESS_LZ4) {
+              buf_size_out = bshuf_compress_lz4_bound(nbytes_uncomp / elem_size, 
+                  elem_size, block_size) + 12;
+            }
+#ifdef ZSTD_SUPPORT
+            else if (cd_values[4] == BSHUF_H5_COMPRESS_ZSTD) {
+              buf_size_out = bshuf_compress_zstd_bound(nbytes_uncomp / elem_size, 
+                  elem_size, block_size) + 12;
+            }
+#endif
+        }
+    } else {
+        nbytes_uncomp = nbytes;
+        buf_size_out = nbytes;
+    }
+
+    // TODO, remove this restriction by memcopying the extra.
+    if (nbytes_uncomp % elem_size) {
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+                "Non integer number of elements.");
+        return 0;
+    }
+    size = nbytes_uncomp / elem_size;
+
+    out_buf = malloc(buf_size_out);
+    if (out_buf == NULL) {
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, 
+                "Could not allocate output buffer.");
+        return 0;
+    }
+
+    if (cd_nelmts > 4 && (cd_values[4] == BSHUF_H5_COMPRESS_LZ4 || cd_values[4] == BSHUF_H5_COMPRESS_ZSTD)) {
+        if (flags & H5Z_FLAG_REVERSE) {
+            // Bit unshuffle/decompress.
+            // Pick which compressions library to use
+            if(cd_values[4] == BSHUF_H5_COMPRESS_LZ4) {
+              err = bshuf_decompress_lz4(in_buf, out_buf, size, elem_size, block_size);
+            }
+#ifdef ZSTD_SUPPORT
+            else if (cd_values[4] == BSHUF_H5_COMPRESS_ZSTD) {
+              err = bshuf_decompress_zstd(in_buf, out_buf, size, elem_size, block_size);
+            }
+#endif
+            nbytes_out = nbytes_uncomp;
+        } else {
+            // Bit shuffle/compress.
+            // Write the header, described in
+            // http://www.hdfgroup.org/services/filters/HDF5_LZ4.pdf.
+            // Technically we should be using signed integers instead of
+            // unsigned ones, however for valid inputs (positive numbers) these
+            // have the same representation.
+            bshuf_write_uint64_BE(out_buf, nbytes_uncomp);
+            bshuf_write_uint32_BE((char*) out_buf + 8, block_size * elem_size);
+            if(cd_values[4] == BSHUF_H5_COMPRESS_LZ4) {
+                err = bshuf_compress_lz4(in_buf, (char*) out_buf + 12, size,
+                        elem_size, block_size); 
+            }
+#ifdef ZSTD_SUPPORT
+            else if (cd_values[4] == BSHUF_H5_COMPRESS_ZSTD) {
+                err = bshuf_compress_zstd(in_buf, (char*) out_buf + 12, size,
+                        elem_size, block_size, comp_lvl); 
+            }
+#endif
+            nbytes_out = err + 12;
+        } 
+    } else {
+            if (flags & H5Z_FLAG_REVERSE) {
+            // Bit unshuffle.
+            err = bshuf_bitunshuffle(in_buf, out_buf, size, elem_size,
+                    block_size); } else {
+            // Bit shuffle.
+            err = bshuf_bitshuffle(in_buf, out_buf, size, elem_size,
+                    block_size); } nbytes_out = nbytes; }
+    //printf("nb_in %d, nb_uncomp %d, nb_out %d, buf_out %d, block %d\n",
+    //nbytes, nbytes_uncomp, nbytes_out, buf_size_out, block_size);
+
+    if (err < 0) {
+        sprintf(msg, "Error in bitshuffle with error code %d.", err);
+        PUSH_ERR("bshuf_h5_filter", H5E_CALLBACK, msg);
+        free(out_buf);
+        return 0;
+    } else {
+        free(*buf);
+        *buf = out_buf;
+        *buf_size = buf_size_out;
+
+        return nbytes_out;
+    }
+}
+
+
+
+H5Z_class_t bshuf_H5Filter[1] = {{
+    H5Z_CLASS_T_VERS,
+    (H5Z_filter_t)(BSHUF_H5FILTER),
+    1, 1,
+    "bitshuffle; see https://github.com/kiyo-masui/bitshuffle",
+    NULL,
+    (H5Z_set_local_func_t)(bshuf_h5_set_local),
+    (H5Z_func_t)(bshuf_h5_filter)
+}};
+
+
+int bshuf_register_h5filter(void){
+
+    int retval;
+
+    retval = H5Zregister(bshuf_H5Filter);
+    if(retval<0){
+        PUSH_ERR("bshuf_register_h5filter",
+                 H5E_CANTREGISTER, "Can't register bitshuffle filter");
+    }
+    return retval;
+}

bslz4/src/bshuf_h5filter.h

@@ -0,0 +1,67 @@
+/*
+ * Bitshuffle HDF5 filter
+ *
+ * This file is part of Bitshuffle
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ *
+ *
+ * Header File
+ *
+ * Filter Options
+ * --------------
+ *  block_size (option slot 0) : integer (optional)
+ *      What block size to use (in elements not bytes). Default is 0,
+ *      for which bitshuffle will pick a block size with a target of 8kb.
+ *  Compression (option slot 1) : 0 or BSHUF_H5_COMPRESS_LZ4
+ *      Whether to apply LZ4 compression to the data after bitshuffling.
+ *      This is much faster than applying compression as a second filter
+ *      because it is done when the small block of data is already in the
+ *      L1 cache.
+ *
+ *      For LZ4 compression, the compressed format of the data is the same as
+ *      for the normal LZ4 filter described in
+ *      http://www.hdfgroup.org/services/filters/HDF5_LZ4.pdf.
+ *
+ */
+
+
+#ifndef BSHUF_H5FILTER_H
+#define BSHUF_H5FILTER_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define H5Z_class_t_vers 2
+#include "hdf5.h"
+
+
+#define BSHUF_H5FILTER 32008
+
+
+#define BSHUF_H5_COMPRESS_LZ4 2
+#define BSHUF_H5_COMPRESS_ZSTD 3
+
+
+extern H5Z_class_t bshuf_H5Filter[1];
+
+
+/* ---- bshuf_register_h5filter ----
+ *
+ * Register the bitshuffle HDF5 filter within the HDF5 library.
+ *
+ * Call this before using the bitshuffle HDF5 filter from C unless
+ * using dynamically loaded filters.
+ *
+ */
+int bshuf_register_h5filter(void);
+
+#ifdef __cplusplus
+} // extern "C"
+#endif
+
+#endif // BSHUF_H5FILTER_H

bslz4/src/iochain.c

@@ -0,0 +1,90 @@
+/*
+ * IOchain - Distribute a chain of dependent IO events among threads.
+ *
+ * This file is part of Bitshuffle
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ *
+ */
+
+#include <stdlib.h>
+#include "iochain.h"
+
+
+void ioc_init(ioc_chain *C, const void *in_ptr_0, void *out_ptr_0) {
+#ifdef _OPENMP
+    omp_init_lock(&C->next_lock);
+    for (size_t ii = 0; ii < IOC_SIZE; ii ++) {
+        omp_init_lock(&(C->in_pl[ii].lock));
+        omp_init_lock(&(C->out_pl[ii].lock));
+    }
+#endif
+    C->next = 0;
+    C->in_pl[0].ptr = in_ptr_0;
+    C->out_pl[0].ptr = out_ptr_0;
+}
+
+
+void ioc_destroy(ioc_chain *C) {
+#ifdef _OPENMP
+    omp_destroy_lock(&C->next_lock);
+    for (size_t ii = 0; ii < IOC_SIZE; ii ++) {
+        omp_destroy_lock(&(C->in_pl[ii].lock));
+        omp_destroy_lock(&(C->out_pl[ii].lock));
+    }
+#endif
+}
+
+
+const void * ioc_get_in(ioc_chain *C, size_t *this_iter) {
+#ifdef _OPENMP
+    omp_set_lock(&C->next_lock);
+    #pragma omp flush
+#endif
+    *this_iter = C->next;
+    C->next ++;
+#ifdef _OPENMP
+    omp_set_lock(&(C->in_pl[*this_iter % IOC_SIZE].lock));
+    omp_set_lock(&(C->in_pl[(*this_iter + 1) % IOC_SIZE].lock));
+    omp_set_lock(&(C->out_pl[(*this_iter + 1) % IOC_SIZE].lock));
+    omp_unset_lock(&C->next_lock);
+#endif
+    return C->in_pl[*this_iter % IOC_SIZE].ptr;
+}
+
+
+void ioc_set_next_in(ioc_chain *C, size_t* this_iter, void* in_ptr) {
+    C->in_pl[(*this_iter + 1) % IOC_SIZE].ptr = in_ptr;
+#ifdef _OPENMP
+    omp_unset_lock(&(C->in_pl[(*this_iter + 1) % IOC_SIZE].lock));
+#endif
+}
+
+
+void * ioc_get_out(ioc_chain *C, size_t *this_iter) {
+#ifdef _OPENMP
+    omp_set_lock(&(C->out_pl[(*this_iter) % IOC_SIZE].lock));
+    #pragma omp flush
+#endif
+    void *out_ptr = C->out_pl[*this_iter % IOC_SIZE].ptr;
+#ifdef _OPENMP
+    omp_unset_lock(&(C->out_pl[(*this_iter) % IOC_SIZE].lock));
+#endif
+    return out_ptr;
+}
+
+
+void ioc_set_next_out(ioc_chain *C, size_t *this_iter, void* out_ptr) {
+    C->out_pl[(*this_iter + 1) % IOC_SIZE].ptr = out_ptr;
+#ifdef _OPENMP
+    omp_unset_lock(&(C->out_pl[(*this_iter + 1) % IOC_SIZE].lock));
+    // *in_pl[this_iter]* lock released at the end of the iteration to avoid being
+    // overtaken by previous threads and having *out_pl[this_iter]* corrupted.
+    // Especially worried about thread 0, iteration 0.
+    omp_unset_lock(&(C->in_pl[(*this_iter) % IOC_SIZE].lock));
+#endif
+}
+

bslz4/src/iochain.h

@@ -0,0 +1,94 @@
+/*
+ * IOchain - Distribute a chain of dependent IO events among threads.
+ *
+ * This file is part of Bitshuffle
+ * Author: Kiyoshi Masui <kiyo@physics.ubc.ca>
+ * Website: http://www.github.com/kiyo-masui/bitshuffle
+ * Created: 2014
+ *
+ * See LICENSE file for details about copyright and rights to use.
+ *
+ *
+ * Header File
+ *
+ * Similar in concept to a queue. Each task includes reading an input
+ * and writing output, but the location of the input/output (the pointers)
+ * depend on the previous item in the chain.
+ *
+ * This is designed for parallelizing blocked compression/decompression IO,
+ * where the destination of a compressed block depends on the compressed size
+ * of all previous blocks.
+ *
+ * Implemented with OpenMP locks.
+ *
+ *
+ * Usage
+ * -----
+ *  - Call `ioc_init` in serial block.
+ *  - Each thread should create a local variable *size_t this_iter* and 
+ *    pass its address to all function calls. Its value will be set
+ *    inside the functions and is used to identify the thread.
+ *  - Each thread must call each of the `ioc_get*` and `ioc_set*` methods
+ *    exactly once per iteration, starting with `ioc_get_in` and ending
+ *    with `ioc_set_next_out`.
+ *  - The order (`ioc_get_in`, `ioc_set_next_in`, *work*, `ioc_get_out`,
+ *    `ioc_set_next_out`, *work*) is most efficient.
+ *  - Have each thread call `ioc_end_pop`.
+ *  - `ioc_get_in` is blocked until the previous entry's
+ *    `ioc_set_next_in` is called.
+ *  - `ioc_get_out` is blocked until the previous entry's
+ *    `ioc_set_next_out` is called.
+ *  - There are no blocks on the very first iteration.
+ *  - Call `ioc_destroy` in serial block.
+ *  - Safe for num_threads >= IOC_SIZE (but less efficient).
+ *
+ */
+
+
+#ifndef IOCHAIN_H
+#define IOCHAIN_H
+
+
+#include <stdlib.h>
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+
+#define IOC_SIZE 33
+
+
+typedef struct ioc_ptr_and_lock {
+#ifdef _OPENMP
+    omp_lock_t lock;
+#endif
+    void *ptr;
+} ptr_and_lock;
+
+typedef struct ioc_const_ptr_and_lock {
+#ifdef _OPENMP
+    omp_lock_t lock;
+#endif
+    const void *ptr;
+} const_ptr_and_lock;
+
+
+typedef struct ioc_chain {
+#ifdef _OPENMP
+    omp_lock_t next_lock;
+#endif
+    size_t next;
+    const_ptr_and_lock in_pl[IOC_SIZE];
+    ptr_and_lock out_pl[IOC_SIZE];
+} ioc_chain;
+
+
+void ioc_init(ioc_chain *C, const void *in_ptr_0, void *out_ptr_0);
+void ioc_destroy(ioc_chain *C);
+const void * ioc_get_in(ioc_chain *C, size_t *this_iter);
+void ioc_set_next_in(ioc_chain *C, size_t* this_iter, void* in_ptr);
+void * ioc_get_out(ioc_chain *C, size_t *this_iter);
+void ioc_set_next_out(ioc_chain *C, size_t *this_iter, void* out_ptr);
+
+#endif  // IOCHAIN_H
+

bslz4/src/lz4.h

@@ -0,0 +1,774 @@
+/*
+ *  LZ4 - Fast LZ compression algorithm
+ *  Header File
+ *  Copyright (C) 2011-present, Yann Collet.
+
+   BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
+
+   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.
+
+   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 THE COPYRIGHT
+   OWNER OR CONTRIBUTORS 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.
+
+   You can contact the author at :
+    - LZ4 homepage : http://www.lz4.org
+    - LZ4 source repository : https://github.com/lz4/lz4
+*/
+#if defined (__cplusplus)
+extern "C" {
+#endif
+
+#ifndef LZ4_H_2983827168210
+#define LZ4_H_2983827168210
+
+/* --- Dependency --- */
+#include <stddef.h>   /* size_t */
+
+
+/**
+  Introduction
+
+  LZ4 is lossless compression algorithm, providing compression speed >500 MB/s per core,
+  scalable with multi-cores CPU. It features an extremely fast decoder, with speed in
+  multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.
+
+  The LZ4 compression library provides in-memory compression and decompression functions.
+  It gives full buffer control to user.
+  Compression can be done in:
+    - a single step (described as Simple Functions)
+    - a single step, reusing a context (described in Advanced Functions)
+    - unbounded multiple steps (described as Streaming compression)
+
+  lz4.h generates and decodes LZ4-compressed blocks (doc/lz4_Block_format.md).
+  Decompressing such a compressed block requires additional metadata.
+  Exact metadata depends on exact decompression function.
+  For the typical case of LZ4_decompress_safe(),
+  metadata includes block's compressed size, and maximum bound of decompressed size.
+  Each application is free to encode and pass such metadata in whichever way it wants.
+
+  lz4.h only handle blocks, it can not generate Frames.
+
+  Blocks are different from Frames (doc/lz4_Frame_format.md).
+  Frames bundle both blocks and metadata in a specified manner.
+  Embedding metadata is required for compressed data to be self-contained and portable.
+  Frame format is delivered through a companion API, declared in lz4frame.h.
+  The `lz4` CLI can only manage frames.
+*/
+
+/*^***************************************************************
+*  Export parameters
+*****************************************************************/
+/*
+*  LZ4_DLL_EXPORT :
+*  Enable exporting of functions when building a Windows DLL
+*  LZ4LIB_VISIBILITY :
+*  Control library symbols visibility.
+*/
+#ifndef LZ4LIB_VISIBILITY
+#  if defined(__GNUC__) && (__GNUC__ >= 4)
+#    define LZ4LIB_VISIBILITY __attribute__ ((visibility ("default")))
+#  else
+#    define LZ4LIB_VISIBILITY
+#  endif
+#endif
+#if defined(LZ4_DLL_EXPORT) && (LZ4_DLL_EXPORT==1)
+#  define LZ4LIB_API __declspec(dllexport) LZ4LIB_VISIBILITY
+#elif defined(LZ4_DLL_IMPORT) && (LZ4_DLL_IMPORT==1)
+#  define LZ4LIB_API __declspec(dllimport) LZ4LIB_VISIBILITY /* It isn't required but allows to generate better code, saving a function pointer load from the IAT and an indirect jump.*/
+#else
+#  define LZ4LIB_API LZ4LIB_VISIBILITY
+#endif
+
+/*------   Version   ------*/
+#define LZ4_VERSION_MAJOR    1    /* for breaking interface changes  */
+#define LZ4_VERSION_MINOR    9    /* for new (non-breaking) interface capabilities */
+#define LZ4_VERSION_RELEASE  3    /* for tweaks, bug-fixes, or development */
+
+#define LZ4_VERSION_NUMBER (LZ4_VERSION_MAJOR *100*100 + LZ4_VERSION_MINOR *100 + LZ4_VERSION_RELEASE)
+
+#define LZ4_LIB_VERSION LZ4_VERSION_MAJOR.LZ4_VERSION_MINOR.LZ4_VERSION_RELEASE
+#define LZ4_QUOTE(str) #str
+#define LZ4_EXPAND_AND_QUOTE(str) LZ4_QUOTE(str)
+#define LZ4_VERSION_STRING LZ4_EXPAND_AND_QUOTE(LZ4_LIB_VERSION)
+
+LZ4LIB_API int LZ4_versionNumber (void);  /**< library version number; useful to check dll version */
+LZ4LIB_API const char* LZ4_versionString (void);   /**< library version string; useful to check dll version */
+
+
+/*-************************************
+*  Tuning parameter
+**************************************/
+/*!
+ * LZ4_MEMORY_USAGE :
+ * Memory usage formula : N->2^N Bytes (examples : 10 -> 1KB; 12 -> 4KB ; 16 -> 64KB; 20 -> 1MB; etc.)
+ * Increasing memory usage improves compression ratio.
+ * Reduced memory usage may improve speed, thanks to better cache locality.
+ * Default value is 14, for 16KB, which nicely fits into Intel x86 L1 cache
+ */
+#ifndef LZ4_MEMORY_USAGE
+# define LZ4_MEMORY_USAGE 14
+#endif
+
+
+/*-************************************
+*  Simple Functions
+**************************************/
+/*! LZ4_compress_default() :
+ *  Compresses 'srcSize' bytes from buffer 'src'
+ *  into already allocated 'dst' buffer of size 'dstCapacity'.
+ *  Compression is guaranteed to succeed if 'dstCapacity' >= LZ4_compressBound(srcSize).
+ *  It also runs faster, so it's a recommended setting.
+ *  If the function cannot compress 'src' into a more limited 'dst' budget,
+ *  compression stops *immediately*, and the function result is zero.
+ *  In which case, 'dst' content is undefined (invalid).
+ *      srcSize : max supported value is LZ4_MAX_INPUT_SIZE.
+ *      dstCapacity : size of buffer 'dst' (which must be already allocated)
+ *     @return  : the number of bytes written into buffer 'dst' (necessarily <= dstCapacity)
+ *                or 0 if compression fails
+ * Note : This function is protected against buffer overflow scenarios (never writes outside 'dst' buffer, nor read outside 'source' buffer).
+ */
+LZ4LIB_API int LZ4_compress_default(const char* src, char* dst, int srcSize, int dstCapacity);
+
+/*! LZ4_decompress_safe() :
+ *  compressedSize : is the exact complete size of the compressed block.
+ *  dstCapacity : is the size of destination buffer (which must be already allocated), presumed an upper bound of decompressed size.
+ * @return : the number of bytes decompressed into destination buffer (necessarily <= dstCapacity)
+ *           If destination buffer is not large enough, decoding will stop and output an error code (negative value).
+ *           If the source stream is detected malformed, the function will stop decoding and return a negative result.
+ * Note 1 : This function is protected against malicious data packets :
+ *          it will never writes outside 'dst' buffer, nor read outside 'source' buffer,
+ *          even if the compressed block is maliciously modified to order the decoder to do these actions.
+ *          In such case, the decoder stops immediately, and considers the compressed block malformed.
+ * Note 2 : compressedSize and dstCapacity must be provided to the function, the compressed block does not contain them.
+ *          The implementation is free to send / store / derive this information in whichever way is most beneficial.
+ *          If there is a need for a different format which bundles together both compressed data and its metadata, consider looking at lz4frame.h instead.
+ */
+LZ4LIB_API int LZ4_decompress_safe (const char* src, char* dst, int compressedSize, int dstCapacity);
+
+
+/*-************************************
+*  Advanced Functions
+**************************************/
+#define LZ4_MAX_INPUT_SIZE        0x7E000000   /* 2 113 929 216 bytes */
+#define LZ4_COMPRESSBOUND(isize)  ((unsigned)(isize) > (unsigned)LZ4_MAX_INPUT_SIZE ? 0 : (isize) + ((isize)/255) + 16)
+
+/*! LZ4_compressBound() :
+    Provides the maximum size that LZ4 compression may output in a "worst case" scenario (input data not compressible)
+    This function is primarily useful for memory allocation purposes (destination buffer size).
+    Macro LZ4_COMPRESSBOUND() is also provided for compilation-time evaluation (stack memory allocation for example).
+    Note that LZ4_compress_default() compresses faster when dstCapacity is >= LZ4_compressBound(srcSize)
+        inputSize  : max supported value is LZ4_MAX_INPUT_SIZE
+        return : maximum output size in a "worst case" scenario
+              or 0, if input size is incorrect (too large or negative)
+*/
+LZ4LIB_API int LZ4_compressBound(int inputSize);
+
+/*! LZ4_compress_fast() :
+    Same as LZ4_compress_default(), but allows selection of "acceleration" factor.
+    The larger the acceleration value, the faster the algorithm, but also the lesser the compression.
+    It's a trade-off. It can be fine tuned, with each successive value providing roughly +~3% to speed.
+    An acceleration value of "1" is the same as regular LZ4_compress_default()
+    Values <= 0 will be replaced by LZ4_ACCELERATION_DEFAULT (currently == 1, see lz4.c).
+    Values > LZ4_ACCELERATION_MAX will be replaced by LZ4_ACCELERATION_MAX (currently == 65537, see lz4.c).
+*/
+LZ4LIB_API int LZ4_compress_fast (const char* src, char* dst, int srcSize, int dstCapacity, int acceleration);
+
+
+/*! LZ4_compress_fast_extState() :
+ *  Same as LZ4_compress_fast(), using an externally allocated memory space for its state.
+ *  Use LZ4_sizeofState() to know how much memory must be allocated,
+ *  and allocate it on 8-bytes boundaries (using `malloc()` typically).
+ *  Then, provide this buffer as `void* state` to compression function.
+ */
+LZ4LIB_API int LZ4_sizeofState(void);
+LZ4LIB_API int LZ4_compress_fast_extState (void* state, const char* src, char* dst, int srcSize, int dstCapacity, int acceleration);
+
+
+/*! LZ4_compress_destSize() :
+ *  Reverse the logic : compresses as much data as possible from 'src' buffer
+ *  into already allocated buffer 'dst', of size >= 'targetDestSize'.
+ *  This function either compresses the entire 'src' content into 'dst' if it's large enough,
+ *  or fill 'dst' buffer completely with as much data as possible from 'src'.
+ *  note: acceleration parameter is fixed to "default".
+ *
+ * *srcSizePtr : will be modified to indicate how many bytes where read from 'src' to fill 'dst'.
+ *               New value is necessarily <= input value.
+ * @return : Nb bytes written into 'dst' (necessarily <= targetDestSize)
+ *           or 0 if compression fails.
+ *
+ * Note : from v1.8.2 to v1.9.1, this function had a bug (fixed un v1.9.2+):
+ *        the produced compressed content could, in specific circumstances,
+ *        require to be decompressed into a destination buffer larger
+ *        by at least 1 byte than the content to decompress.
+ *        If an application uses `LZ4_compress_destSize()`,
+ *        it's highly recommended to update liblz4 to v1.9.2 or better.
+ *        If this can't be done or ensured,
+ *        the receiving decompression function should provide
+ *        a dstCapacity which is > decompressedSize, by at least 1 byte.
+ *        See https://github.com/lz4/lz4/issues/859 for details
+ */
+LZ4LIB_API int LZ4_compress_destSize (const char* src, char* dst, int* srcSizePtr, int targetDstSize);
+
+
+/*! LZ4_decompress_safe_partial() :
+ *  Decompress an LZ4 compressed block, of size 'srcSize' at position 'src',
+ *  into destination buffer 'dst' of size 'dstCapacity'.
+ *  Up to 'targetOutputSize' bytes will be decoded.
+ *  The function stops decoding on reaching this objective.
+ *  This can be useful to boost performance
+ *  whenever only the beginning of a block is required.
+ *
+ * @return : the number of bytes decoded in `dst` (necessarily <= targetOutputSize)
+ *           If source stream is detected malformed, function returns a negative result.
+ *
+ *  Note 1 : @return can be < targetOutputSize, if compressed block contains less data.
+ *
+ *  Note 2 : targetOutputSize must be <= dstCapacity
+ *
+ *  Note 3 : this function effectively stops decoding on reaching targetOutputSize,
+ *           so dstCapacity is kind of redundant.
+ *           This is because in older versions of this function,
+ *           decoding operation would still write complete sequences.
+ *           Therefore, there was no guarantee that it would stop writing at exactly targetOutputSize,
+ *           it could write more bytes, though only up to dstCapacity.
+ *           Some "margin" used to be required for this operation to work properly.
+ *           Thankfully, this is no longer necessary.
+ *           The function nonetheless keeps the same signature, in an effort to preserve API compatibility.
+ *
+ *  Note 4 : If srcSize is the exact size of the block,
+ *           then targetOutputSize can be any value,
+ *           including larger than the block's decompressed size.
+ *           The function will, at most, generate block's decompressed size.
+ *
+ *  Note 5 : If srcSize is _larger_ than block's compressed size,
+ *           then targetOutputSize **MUST** be <= block's decompressed size.
+ *           Otherwise, *silent corruption will occur*.
+ */
+LZ4LIB_API int LZ4_decompress_safe_partial (const char* src, char* dst, int srcSize, int targetOutputSize, int dstCapacity);
+
+
+/*-*********************************************
+*  Streaming Compression Functions
+***********************************************/
+typedef union LZ4_stream_u LZ4_stream_t;  /* incomplete type (defined later) */
+
+LZ4LIB_API LZ4_stream_t* LZ4_createStream(void);
+LZ4LIB_API int           LZ4_freeStream (LZ4_stream_t* streamPtr);
+
+/*! LZ4_resetStream_fast() : v1.9.0+
+ *  Use this to prepare an LZ4_stream_t for a new chain of dependent blocks
+ *  (e.g., LZ4_compress_fast_continue()).
+ *
+ *  An LZ4_stream_t must be initialized once before usage.
+ *  This is automatically done when created by LZ4_createStream().
+ *  However, should the LZ4_stream_t be simply declared on stack (for example),
+ *  it's necessary to initialize it first, using LZ4_initStream().
+ *
+ *  After init, start any new stream with LZ4_resetStream_fast().
+ *  A same LZ4_stream_t can be re-used multiple times consecutively
+ *  and compress multiple streams,
+ *  provided that it starts each new stream with LZ4_resetStream_fast().
+ *
+ *  LZ4_resetStream_fast() is much faster than LZ4_initStream(),
+ *  but is not compatible with memory regions containing garbage data.
+ *
+ *  Note: it's only useful to call LZ4_resetStream_fast()
+ *        in the context of streaming compression.
+ *        The *extState* functions perform their own resets.
+ *        Invoking LZ4_resetStream_fast() before is redundant, and even counterproductive.
+ */
+LZ4LIB_API void LZ4_resetStream_fast (LZ4_stream_t* streamPtr);
+
+/*! LZ4_loadDict() :
+ *  Use this function to reference a static dictionary into LZ4_stream_t.
+ *  The dictionary must remain available during compression.
+ *  LZ4_loadDict() triggers a reset, so any previous data will be forgotten.
+ *  The same dictionary will have to be loaded on decompression side for successful decoding.
+ *  Dictionary are useful for better compression of small data (KB range).
+ *  While LZ4 accept any input as dictionary,
+ *  results are generally better when using Zstandard's Dictionary Builder.
+ *  Loading a size of 0 is allowed, and is the same as reset.
+ * @return : loaded dictionary size, in bytes (necessarily <= 64 KB)
+ */
+LZ4LIB_API int LZ4_loadDict (LZ4_stream_t* streamPtr, const char* dictionary, int dictSize);
+
+/*! LZ4_compress_fast_continue() :
+ *  Compress 'src' content using data from previously compressed blocks, for better compression ratio.
+ * 'dst' buffer must be already allocated.
+ *  If dstCapacity >= LZ4_compressBound(srcSize), compression is guaranteed to succeed, and runs faster.
+ *
+ * @return : size of compressed block
+ *           or 0 if there is an error (typically, cannot fit into 'dst').
+ *
+ *  Note 1 : Each invocation to LZ4_compress_fast_continue() generates a new block.
+ *           Each block has precise boundaries.
+ *           Each block must be decompressed separately, calling LZ4_decompress_*() with relevant metadata.
+ *           It's not possible to append blocks together and expect a single invocation of LZ4_decompress_*() to decompress them together.
+ *
+ *  Note 2 : The previous 64KB of source data is __assumed__ to remain present, unmodified, at same address in memory !
+ *
+ *  Note 3 : When input is structured as a double-buffer, each buffer can have any size, including < 64 KB.
+ *           Make sure that buffers are separated, by at least one byte.
+ *           This construction ensures that each block only depends on previous block.
+ *
+ *  Note 4 : If input buffer is a ring-buffer, it can have any size, including < 64 KB.
+ *
+ *  Note 5 : After an error, the stream status is undefined (invalid), it can only be reset or freed.
+ */
+LZ4LIB_API int LZ4_compress_fast_continue (LZ4_stream_t* streamPtr, const char* src, char* dst, int srcSize, int dstCapacity, int acceleration);
+
+/*! LZ4_saveDict() :
+ *  If last 64KB data cannot be guaranteed to remain available at its current memory location,
+ *  save it into a safer place (char* safeBuffer).
+ *  This is schematically equivalent to a memcpy() followed by LZ4_loadDict(),
+ *  but is much faster, because LZ4_saveDict() doesn't need to rebuild tables.
+ * @return : saved dictionary size in bytes (necessarily <= maxDictSize), or 0 if error.
+ */
+LZ4LIB_API int LZ4_saveDict (LZ4_stream_t* streamPtr, char* safeBuffer, int maxDictSize);
+
+
+/*-**********************************************
+*  Streaming Decompression Functions
+*  Bufferless synchronous API
+************************************************/
+typedef union LZ4_streamDecode_u LZ4_streamDecode_t;   /* tracking context */
+
+/*! LZ4_createStreamDecode() and LZ4_freeStreamDecode() :
+ *  creation / destruction of streaming decompression tracking context.
+ *  A tracking context can be re-used multiple times.
+ */
+LZ4LIB_API LZ4_streamDecode_t* LZ4_createStreamDecode(void);
+LZ4LIB_API int                 LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream);
+
+/*! LZ4_setStreamDecode() :
+ *  An LZ4_streamDecode_t context can be allocated once and re-used multiple times.
+ *  Use this function to start decompression of a new stream of blocks.
+ *  A dictionary can optionally be set. Use NULL or size 0 for a reset order.
+ *  Dictionary is presumed stable : it must remain accessible and unmodified during next decompression.
+ * @return : 1 if OK, 0 if error
+ */
+LZ4LIB_API int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize);
+
+/*! LZ4_decoderRingBufferSize() : v1.8.2+
+ *  Note : in a ring buffer scenario (optional),
+ *  blocks are presumed decompressed next to each other
+ *  up to the moment there is not enough remaining space for next block (remainingSize < maxBlockSize),
+ *  at which stage it resumes from beginning of ring buffer.
+ *  When setting such a ring buffer for streaming decompression,
+ *  provides the minimum size of this ring buffer
+ *  to be compatible with any source respecting maxBlockSize condition.
+ * @return : minimum ring buffer size,
+ *           or 0 if there is an error (invalid maxBlockSize).
+ */
+LZ4LIB_API int LZ4_decoderRingBufferSize(int maxBlockSize);
+#define LZ4_DECODER_RING_BUFFER_SIZE(maxBlockSize) (65536 + 14 + (maxBlockSize))  /* for static allocation; maxBlockSize presumed valid */
+
+/*! LZ4_decompress_*_continue() :
+ *  These decoding functions allow decompression of consecutive blocks in "streaming" mode.
+ *  A block is an unsplittable entity, it must be presented entirely to a decompression function.
+ *  Decompression functions only accepts one block at a time.
+ *  The last 64KB of previously decoded data *must* remain available and unmodified at the memory position where they were decoded.
+ *  If less than 64KB of data has been decoded, all the data must be present.
+ *
+ *  Special : if decompression side sets a ring buffer, it must respect one of the following conditions :
+ *  - Decompression buffer size is _at least_ LZ4_decoderRingBufferSize(maxBlockSize).
+ *    maxBlockSize is the maximum size of any single block. It can have any value > 16 bytes.
+ *    In which case, encoding and decoding buffers do not need to be synchronized.
+ *    Actually, data can be produced by any source compliant with LZ4 format specification, and respecting maxBlockSize.
+ *  - Synchronized mode :
+ *    Decompression buffer size is _exactly_ the same as compression buffer size,
+ *    and follows exactly same update rule (block boundaries at same positions),
+ *    and decoding function is provided with exact decompressed size of each block (exception for last block of the stream),
+ *    _then_ decoding & encoding ring buffer can have any size, including small ones ( < 64 KB).
+ *  - Decompression buffer is larger than encoding buffer, by a minimum of maxBlockSize more bytes.
+ *    In which case, encoding and decoding buffers do not need to be synchronized,
+ *    and encoding ring buffer can have any size, including small ones ( < 64 KB).
+ *
+ *  Whenever these conditions are not possible,
+ *  save the last 64KB of decoded data into a safe buffer where it can't be modified during decompression,
+ *  then indicate where this data is saved using LZ4_setStreamDecode(), before decompressing next block.
+*/
+LZ4LIB_API int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* src, char* dst, int srcSize, int dstCapacity);
+
+
+/*! LZ4_decompress_*_usingDict() :
+ *  These decoding functions work the same as
+ *  a combination of LZ4_setStreamDecode() followed by LZ4_decompress_*_continue()
+ *  They are stand-alone, and don't need an LZ4_streamDecode_t structure.
+ *  Dictionary is presumed stable : it must remain accessible and unmodified during decompression.
+ *  Performance tip : Decompression speed can be substantially increased
+ *                    when dst == dictStart + dictSize.
+ */
+LZ4LIB_API int LZ4_decompress_safe_usingDict (const char* src, char* dst, int srcSize, int dstCapcity, const char* dictStart, int dictSize);
+
+#endif /* LZ4_H_2983827168210 */
+
+
+/*^*************************************
+ * !!!!!!   STATIC LINKING ONLY   !!!!!!
+ ***************************************/
+
+/*-****************************************************************************
+ * Experimental section
+ *
+ * Symbols declared in this section must be considered unstable. Their
+ * signatures or semantics may change, or they may be removed altogether in the
+ * future. They are therefore only safe to depend on when the caller is
+ * statically linked against the library.
+ *
+ * To protect against unsafe usage, not only are the declarations guarded,
+ * the definitions are hidden by default
+ * when building LZ4 as a shared/dynamic library.
+ *
+ * In order to access these declarations,
+ * define LZ4_STATIC_LINKING_ONLY in your application
+ * before including LZ4's headers.
+ *
+ * In order to make their implementations accessible dynamically, you must
+ * define LZ4_PUBLISH_STATIC_FUNCTIONS when building the LZ4 library.
+ ******************************************************************************/
+
+#ifdef LZ4_STATIC_LINKING_ONLY
+
+#ifndef LZ4_STATIC_3504398509
+#define LZ4_STATIC_3504398509
+
+#ifdef LZ4_PUBLISH_STATIC_FUNCTIONS
+#define LZ4LIB_STATIC_API LZ4LIB_API
+#else
+#define LZ4LIB_STATIC_API
+#endif
+
+
+/*! LZ4_compress_fast_extState_fastReset() :
+ *  A variant of LZ4_compress_fast_extState().
+ *
+ *  Using this variant avoids an expensive initialization step.
+ *  It is only safe to call if the state buffer is known to be correctly initialized already
+ *  (see above comment on LZ4_resetStream_fast() for a definition of "correctly initialized").
+ *  From a high level, the difference is that
+ *  this function initializes the provided state with a call to something like LZ4_resetStream_fast()
+ *  while LZ4_compress_fast_extState() starts with a call to LZ4_resetStream().
+ */
+LZ4LIB_STATIC_API int LZ4_compress_fast_extState_fastReset (void* state, const char* src, char* dst, int srcSize, int dstCapacity, int acceleration);
+
+/*! LZ4_attach_dictionary() :
+ *  This is an experimental API that allows
+ *  efficient use of a static dictionary many times.
+ *
+ *  Rather than re-loading the dictionary buffer into a working context before
+ *  each compression, or copying a pre-loaded dictionary's LZ4_stream_t into a
+ *  working LZ4_stream_t, this function introduces a no-copy setup mechanism,
+ *  in which the working stream references the dictionary stream in-place.
+ *
+ *  Several assumptions are made about the state of the dictionary stream.
+ *  Currently, only streams which have been prepared by LZ4_loadDict() should
+ *  be expected to work.
+ *
+ *  Alternatively, the provided dictionaryStream may be NULL,
+ *  in which case any existing dictionary stream is unset.
+ *
+ *  If a dictionary is provided, it replaces any pre-existing stream history.
+ *  The dictionary contents are the only history that can be referenced and
+ *  logically immediately precede the data compressed in the first subsequent
+ *  compression call.
+ *
+ *  The dictionary will only remain attached to the working stream through the
+ *  first compression call, at the end of which it is cleared. The dictionary
+ *  stream (and source buffer) must remain in-place / accessible / unchanged
+ *  through the completion of the first compression call on the stream.
+ */
+LZ4LIB_STATIC_API void LZ4_attach_dictionary(LZ4_stream_t* workingStream, const LZ4_stream_t* dictionaryStream);
+
+
+/*! In-place compression and decompression
+ *
+ * It's possible to have input and output sharing the same buffer,
+ * for highly contrained memory environments.
+ * In both cases, it requires input to lay at the end of the buffer,
+ * and decompression to start at beginning of the buffer.
+ * Buffer size must feature some margin, hence be larger than final size.
+ *
+ * |<------------------------buffer--------------------------------->|
+ *                             |<-----------compressed data--------->|
+ * |<-----------decompressed size------------------>|
+ *                                                  |<----margin---->|
+ *
+ * This technique is more useful for decompression,
+ * since decompressed size is typically larger,
+ * and margin is short.
+ *
+ * In-place decompression will work inside any buffer
+ * which size is >= LZ4_DECOMPRESS_INPLACE_BUFFER_SIZE(decompressedSize).
+ * This presumes that decompressedSize > compressedSize.
+ * Otherwise, it means compression actually expanded data,
+ * and it would be more efficient to store such data with a flag indicating it's not compressed.
+ * This can happen when data is not compressible (already compressed, or encrypted).
+ *
+ * For in-place compression, margin is larger, as it must be able to cope with both
+ * history preservation, requiring input data to remain unmodified up to LZ4_DISTANCE_MAX,
+ * and data expansion, which can happen when input is not compressible.
+ * As a consequence, buffer size requirements are much higher,
+ * and memory savings offered by in-place compression are more limited.
+ *
+ * There are ways to limit this cost for compression :
+ * - Reduce history size, by modifying LZ4_DISTANCE_MAX.
+ *   Note that it is a compile-time constant, so all compressions will apply this limit.
+ *   Lower values will reduce compression ratio, except when input_size < LZ4_DISTANCE_MAX,
+ *   so it's a reasonable trick when inputs are known to be small.
+ * - Require the compressor to deliver a "maximum compressed size".
+ *   This is the `dstCapacity` parameter in `LZ4_compress*()`.
+ *   When this size is < LZ4_COMPRESSBOUND(inputSize), then compression can fail,
+ *   in which case, the return code will be 0 (zero).
+ *   The caller must be ready for these cases to happen,
+ *   and typically design a backup scheme to send data uncompressed.
+ * The combination of both techniques can significantly reduce
+ * the amount of margin required for in-place compression.
+ *
+ * In-place compression can work in any buffer
+ * which size is >= (maxCompressedSize)
+ * with maxCompressedSize == LZ4_COMPRESSBOUND(srcSize) for guaranteed compression success.
+ * LZ4_COMPRESS_INPLACE_BUFFER_SIZE() depends on both maxCompressedSize and LZ4_DISTANCE_MAX,
+ * so it's possible to reduce memory requirements by playing with them.
+ */
+
+#define LZ4_DECOMPRESS_INPLACE_MARGIN(compressedSize)          (((compressedSize) >> 8) + 32)
+#define LZ4_DECOMPRESS_INPLACE_BUFFER_SIZE(decompressedSize)   ((decompressedSize) + LZ4_DECOMPRESS_INPLACE_MARGIN(decompressedSize))  /**< note: presumes that compressedSize < decompressedSize. note2: margin is overestimated a bit, since it could use compressedSize instead */
+
+#ifndef LZ4_DISTANCE_MAX   /* history window size; can be user-defined at compile time */
+#  define LZ4_DISTANCE_MAX 65535   /* set to maximum value by default */
+#endif
+
+#define LZ4_COMPRESS_INPLACE_MARGIN                           (LZ4_DISTANCE_MAX + 32)   /* LZ4_DISTANCE_MAX can be safely replaced by srcSize when it's smaller */
+#define LZ4_COMPRESS_INPLACE_BUFFER_SIZE(maxCompressedSize)   ((maxCompressedSize) + LZ4_COMPRESS_INPLACE_MARGIN)  /**< maxCompressedSize is generally LZ4_COMPRESSBOUND(inputSize), but can be set to any lower value, with the risk that compression can fail (return code 0(zero)) */
+
+#endif   /* LZ4_STATIC_3504398509 */
+#endif   /* LZ4_STATIC_LINKING_ONLY */
+
+
+
+#ifndef LZ4_H_98237428734687
+#define LZ4_H_98237428734687
+
+/*-************************************************************
+ *  Private Definitions
+ **************************************************************
+ * Do not use these definitions directly.
+ * They are only exposed to allow static allocation of `LZ4_stream_t` and `LZ4_streamDecode_t`.
+ * Accessing members will expose user code to API and/or ABI break in future versions of the library.
+ **************************************************************/
+#define LZ4_HASHLOG   (LZ4_MEMORY_USAGE-2)
+#define LZ4_HASHTABLESIZE (1 << LZ4_MEMORY_USAGE)
+#define LZ4_HASH_SIZE_U32 (1 << LZ4_HASHLOG)       /* required as macro for static allocation */
+
+#if defined(__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */)
+# include <stdint.h>
+  typedef  int8_t  LZ4_i8;
+  typedef uint8_t  LZ4_byte;
+  typedef uint16_t LZ4_u16;
+  typedef uint32_t LZ4_u32;
+#else
+  typedef   signed char  LZ4_i8;
+  typedef unsigned char  LZ4_byte;
+  typedef unsigned short LZ4_u16;
+  typedef unsigned int   LZ4_u32;
+#endif
+
+typedef struct LZ4_stream_t_internal LZ4_stream_t_internal;
+struct LZ4_stream_t_internal {
+    LZ4_u32 hashTable[LZ4_HASH_SIZE_U32];
+    LZ4_u32 currentOffset;
+    LZ4_u32 tableType;
+    const LZ4_byte* dictionary;
+    const LZ4_stream_t_internal* dictCtx;
+    LZ4_u32 dictSize;
+};
+
+typedef struct {
+    const LZ4_byte* externalDict;
+    size_t extDictSize;
+    const LZ4_byte* prefixEnd;
+    size_t prefixSize;
+} LZ4_streamDecode_t_internal;
+
+
+/*! LZ4_stream_t :
+ *  Do not use below internal definitions directly !
+ *  Declare or allocate an LZ4_stream_t instead.
+ *  LZ4_stream_t can also be created using LZ4_createStream(), which is recommended.
+ *  The structure definition can be convenient for static allocation
+ *  (on stack, or as part of larger structure).
+ *  Init this structure with LZ4_initStream() before first use.
+ *  note : only use this definition in association with static linking !
+ *  this definition is not API/ABI safe, and may change in future versions.
+ */
+#define LZ4_STREAMSIZE       16416  /* static size, for inter-version compatibility */
+#define LZ4_STREAMSIZE_VOIDP (LZ4_STREAMSIZE / sizeof(void*))
+union LZ4_stream_u {
+    void* table[LZ4_STREAMSIZE_VOIDP];
+    LZ4_stream_t_internal internal_donotuse;
+}; /* previously typedef'd to LZ4_stream_t */
+
+
+/*! LZ4_initStream() : v1.9.0+
+ *  An LZ4_stream_t structure must be initialized at least once.
+ *  This is automatically done when invoking LZ4_createStream(),
+ *  but it's not when the structure is simply declared on stack (for example).
+ *
+ *  Use LZ4_initStream() to properly initialize a newly declared LZ4_stream_t.
+ *  It can also initialize any arbitrary buffer of sufficient size,
+ *  and will @return a pointer of proper type upon initialization.
+ *
+ *  Note : initialization fails if size and alignment conditions are not respected.
+ *         In which case, the function will @return NULL.
+ *  Note2: An LZ4_stream_t structure guarantees correct alignment and size.
+ *  Note3: Before v1.9.0, use LZ4_resetStream() instead
+ */
+LZ4LIB_API LZ4_stream_t* LZ4_initStream (void* buffer, size_t size);
+
+
+/*! LZ4_streamDecode_t :
+ *  information structure to track an LZ4 stream during decompression.
+ *  init this structure  using LZ4_setStreamDecode() before first use.
+ *  note : only use in association with static linking !
+ *         this definition is not API/ABI safe,
+ *         and may change in a future version !
+ */
+#define LZ4_STREAMDECODESIZE_U64 (4 + ((sizeof(void*)==16) ? 2 : 0) /*AS-400*/ )
+#define LZ4_STREAMDECODESIZE     (LZ4_STREAMDECODESIZE_U64 * sizeof(unsigned long long))
+union LZ4_streamDecode_u {
+    unsigned long long table[LZ4_STREAMDECODESIZE_U64];
+    LZ4_streamDecode_t_internal internal_donotuse;
+} ;   /* previously typedef'd to LZ4_streamDecode_t */
+
+
+
+/*-************************************
+*  Obsolete Functions
+**************************************/
+
+/*! Deprecation warnings
+ *
+ *  Deprecated functions make the compiler generate a warning when invoked.
+ *  This is meant to invite users to update their source code.
+ *  Should deprecation warnings be a problem, it is generally possible to disable them,
+ *  typically with -Wno-deprecated-declarations for gcc
+ *  or _CRT_SECURE_NO_WARNINGS in Visual.
+ *
+ *  Another method is to define LZ4_DISABLE_DEPRECATE_WARNINGS
+ *  before including the header file.
+ */
+#ifdef LZ4_DISABLE_DEPRECATE_WARNINGS
+#  define LZ4_DEPRECATED(message)   /* disable deprecation warnings */
+#else
+#  if defined (__cplusplus) && (__cplusplus >= 201402) /* C++14 or greater */
+#    define LZ4_DEPRECATED(message) [[deprecated(message)]]
+#  elif defined(_MSC_VER)
+#    define LZ4_DEPRECATED(message) __declspec(deprecated(message))
+#  elif defined(__clang__) || (defined(__GNUC__) && (__GNUC__ * 10 + __GNUC_MINOR__ >= 45))
+#    define LZ4_DEPRECATED(message) __attribute__((deprecated(message)))
+#  elif defined(__GNUC__) && (__GNUC__ * 10 + __GNUC_MINOR__ >= 31)
+#    define LZ4_DEPRECATED(message) __attribute__((deprecated))
+#  else
+#    pragma message("WARNING: LZ4_DEPRECATED needs custom implementation for this compiler")
+#    define LZ4_DEPRECATED(message)   /* disabled */
+#  endif
+#endif /* LZ4_DISABLE_DEPRECATE_WARNINGS */
+
+/*! Obsolete compression functions (since v1.7.3) */
+LZ4_DEPRECATED("use LZ4_compress_default() instead")       LZ4LIB_API int LZ4_compress               (const char* src, char* dest, int srcSize);
+LZ4_DEPRECATED("use LZ4_compress_default() instead")       LZ4LIB_API int LZ4_compress_limitedOutput (const char* src, char* dest, int srcSize, int maxOutputSize);
+LZ4_DEPRECATED("use LZ4_compress_fast_extState() instead") LZ4LIB_API int LZ4_compress_withState               (void* state, const char* source, char* dest, int inputSize);
+LZ4_DEPRECATED("use LZ4_compress_fast_extState() instead") LZ4LIB_API int LZ4_compress_limitedOutput_withState (void* state, const char* source, char* dest, int inputSize, int maxOutputSize);
+LZ4_DEPRECATED("use LZ4_compress_fast_continue() instead") LZ4LIB_API int LZ4_compress_continue                (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize);
+LZ4_DEPRECATED("use LZ4_compress_fast_continue() instead") LZ4LIB_API int LZ4_compress_limitedOutput_continue  (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize, int maxOutputSize);
+
+/*! Obsolete decompression functions (since v1.8.0) */
+LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize);
+LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize);
+
+/* Obsolete streaming functions (since v1.7.0)
+ * degraded functionality; do not use!
+ *
+ * In order to perform streaming compression, these functions depended on data
+ * that is no longer tracked in the state. They have been preserved as well as
+ * possible: using them will still produce a correct output. However, they don't
+ * actually retain any history between compression calls. The compression ratio
+ * achieved will therefore be no better than compressing each chunk
+ * independently.
+ */
+LZ4_DEPRECATED("Use LZ4_createStream() instead") LZ4LIB_API void* LZ4_create (char* inputBuffer);
+LZ4_DEPRECATED("Use LZ4_createStream() instead") LZ4LIB_API int   LZ4_sizeofStreamState(void);
+LZ4_DEPRECATED("Use LZ4_resetStream() instead")  LZ4LIB_API int   LZ4_resetStreamState(void* state, char* inputBuffer);
+LZ4_DEPRECATED("Use LZ4_saveDict() instead")     LZ4LIB_API char* LZ4_slideInputBuffer (void* state);
+
+/*! Obsolete streaming decoding functions (since v1.7.0) */
+LZ4_DEPRECATED("use LZ4_decompress_safe_usingDict() instead") LZ4LIB_API int LZ4_decompress_safe_withPrefix64k (const char* src, char* dst, int compressedSize, int maxDstSize);
+LZ4_DEPRECATED("use LZ4_decompress_fast_usingDict() instead") LZ4LIB_API int LZ4_decompress_fast_withPrefix64k (const char* src, char* dst, int originalSize);
+
+/*! Obsolete LZ4_decompress_fast variants (since v1.9.0) :
+ *  These functions used to be faster than LZ4_decompress_safe(),
+ *  but this is no longer the case. They are now slower.
+ *  This is because LZ4_decompress_fast() doesn't know the input size,
+ *  and therefore must progress more cautiously into the input buffer to not read beyond the end of block.
+ *  On top of that `LZ4_decompress_fast()` is not protected vs malformed or malicious inputs, making it a security liability.
+ *  As a consequence, LZ4_decompress_fast() is strongly discouraged, and deprecated.
+ *
+ *  The last remaining LZ4_decompress_fast() specificity is that
+ *  it can decompress a block without knowing its compressed size.
+ *  Such functionality can be achieved in a more secure manner
+ *  by employing LZ4_decompress_safe_partial().
+ *
+ *  Parameters:
+ *  originalSize : is the uncompressed size to regenerate.
+ *                 `dst` must be already allocated, its size must be >= 'originalSize' bytes.
+ * @return : number of bytes read from source buffer (== compressed size).
+ *           The function expects to finish at block's end exactly.
+ *           If the source stream is detected malformed, the function stops decoding and returns a negative result.
+ *  note : LZ4_decompress_fast*() requires originalSize. Thanks to this information, it never writes past the output buffer.
+ *         However, since it doesn't know its 'src' size, it may read an unknown amount of input, past input buffer bounds.
+ *         Also, since match offsets are not validated, match reads from 'src' may underflow too.
+ *         These issues never happen if input (compressed) data is correct.
+ *         But they may happen if input data is invalid (error or intentional tampering).
+ *         As a consequence, use these functions in trusted environments with trusted data **only**.
+ */
+LZ4_DEPRECATED("This function is deprecated and unsafe. Consider using LZ4_decompress_safe() instead")
+LZ4LIB_API int LZ4_decompress_fast (const char* src, char* dst, int originalSize);
+LZ4_DEPRECATED("This function is deprecated and unsafe. Consider using LZ4_decompress_safe_continue() instead")
+LZ4LIB_API int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* src, char* dst, int originalSize);
+LZ4_DEPRECATED("This function is deprecated and unsafe. Consider using LZ4_decompress_safe_usingDict() instead")
+LZ4LIB_API int LZ4_decompress_fast_usingDict (const char* src, char* dst, int originalSize, const char* dictStart, int dictSize);
+
+/*! LZ4_resetStream() :
+ *  An LZ4_stream_t structure must be initialized at least once.
+ *  This is done with LZ4_initStream(), or LZ4_resetStream().
+ *  Consider switching to LZ4_initStream(),
+ *  invoking LZ4_resetStream() will trigger deprecation warnings in the future.
+ */
+LZ4LIB_API void LZ4_resetStream (LZ4_stream_t* streamPtr);
+
+
+#endif /* LZ4_H_98237428734687 */
+
+
+#if defined (__cplusplus)
+}
+#endif

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

@@ -3,49 +3,49 @@
  * 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 dataset_properties_t {
-	int data_width;
-	hsize_t dims[3];
+struct ds_desc_t {
+  hid_t det_g_id;
+  hid_t data_g_id;
+  hsize_t dims[3];
+  int data_width;
+  int image_number_offset;
+  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 *);
+  int i2i[]; // array to hold a translation from the image number requested by XDS and the actual position in the HDF5 file
 };
 
-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*);
+struct nxs_ds_desc_t {
+  struct ds_desc_t base;
 };
 
-void free_nxs_data_description(struct data_description_t *desc);
-
-struct eiger_data_description_t {
-	int n_data_blocks;
-	int *block_sizes;
+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 *);
 };
 
-void free_eiger_data_description(struct data_description_t *desc);
+struct opt_eiger_ds_desc_t {
+  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;
 };
 
-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 */

src/filters.c

@@ -0,0 +1,58 @@
+/*
+ * Copyright (c) 2018 Diamond Light Source Ltd.
+ * Author: Charles Mita
+ */
+
+#include <stdio.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)
+ */
+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;
+
+  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);
+  }
+
+  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");
+    }
+  }
+
+done:
+  return retval;
+}

src/filters.h

@@ -0,0 +1,16 @@
+/*
+ * Copyright (c) 2018 Diamond Light Source Ltd.
+ * Author: Charles Mita
+ */
+
+#ifndef NXS_XDS_FILTER_H
+#define NXS_XDS_FILTER_H
+
+#define BS_H5_N_PARAMS 5
+#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);
+
+#endif /* NXS_XDS_FILTER_H */

src/plugin.c

@@ -3,175 +3,462 @@
  * Author: Charles Mita
  */
 
-
 #include <hdf5.h>
 #include <stdlib.h>
+#include <string.h>
+
 #include "file.h"
+#include "filters.h"
 #include "plugin.h"
 
+#ifdef USE_BITSHUFFLE
+#include "bshuf_h5filter.h"
+#endif
 
-/* 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 */
+/* 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 (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 {                                                                   \
+      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 data_description_t data_desc = {0};
-static struct dataset_properties_t ds_prop = {0};
+static struct ds_desc_t *data_desc = NULL;
 static int *mask_buffer = NULL;
 
+// CV-20240605: potentially provide a mapping from frame number (as
+//              requested by caller) to actual 2D slice within 3D data
+//              array.
+//
+//              This is defined by the environment variable
+//              DURIN_IMAGE2ORDINAL (see below).
+int *image2ordinal = NULL;
+int image2ordinal_debug = 0;
+int image2ordinal_imin = 0;
+int image2ordinal_imax = 0;
 
 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;
+  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);
+  }
+
+  cenv = getenv("DURIN_IMAGE2ORDINAL");
+  if (cenv!=NULL&&(!image2ordinal)) {
+
+    char *denv = getenv("DURIN_IMAGE2ORDINAL_DEBUG");
+    if (denv!=NULL) {
+      image2ordinal_debug=1;
+    }
+
+    // <ordinal_start>,<image_1_start>-<image_1_end>,<image_2_start>-<image_2_end>,..,<image_N_start>-<image_N_end>
+    if (image2ordinal_debug) printf("DURIN_IMAGE2ORDINAL = \"%s\"\n",cenv);
+
+    const char outer_delimiters[] = ",";
+    const char inner_delimiters[] = "-";
+
+    char *found;
+
+    char *outer_saveptr;
+    char *inner_saveptr;
+
+    int ordinal_start = 0;
+    int ordinal = 0;
+    int ntt = -1;
+    found = strtok_r(cenv,outer_delimiters, &outer_saveptr);
+    if (found!=NULL) {
+      int tt[1000][2];
+      while(found) {
+        if (ordinal_start==0) {
+          ordinal_start = atoi(found);
+          ordinal = ordinal_start - 1;
+        }
+        else {
+          char* s = strtok_r(found, inner_delimiters, &inner_saveptr);
+          if (s!=NULL) {
+            int i1 = atoi(s);
+            s = strtok_r(NULL,inner_delimiters, &inner_saveptr);
+            if (s!=NULL) {
+              int i2 = atoi(s);
+              ntt++;
+              if (ntt<=1000) {
+                tt[ntt][0] = i1;
+                tt[ntt][1] = i2;
+                for(int i=i1; i<=i2; ++i) {
+                  ordinal++;
+                  if (ordinal==1) {
+                    image2ordinal_imin=i;
+                    image2ordinal_imax=i;
+                  }
+                  else {
+                    if (i<image2ordinal_imin) image2ordinal_imin=i;
+                    if (i>image2ordinal_imax) image2ordinal_imax=i;
+                  }
+                }
+              }
+            }
+          }
+        }
+        found = strtok_r(NULL,outer_delimiters,&outer_saveptr);
+      }
+
+      if (ordinal_start>0) {
+        if (image2ordinal_debug) {
+          printf("ordinal_start, end = %d %d\n",ordinal_start, ordinal);
+          printf("imin, imax         = %d %d\n",image2ordinal_imin,image2ordinal_imax);
+        }
+
+        // allocate array to go from image number/id to ordinal:
+        image2ordinal = malloc((image2ordinal_imax-image2ordinal_imin+1) * sizeof(image2ordinal_imin));
+        int ordinal = ordinal_start - 1;
+        for(int i=0; i<=ntt; i++) {
+          for(int j=tt[i][0];j<=tt[i][1];j++) {
+            ordinal++;
+            //printf(" %d -> %d\n",ordinal,j);
+            image2ordinal[j] = ordinal;
+          }
+        }
+        if (image2ordinal&&image2ordinal_debug) {
+          for(int i=image2ordinal_imin; i<=image2ordinal_imax; i++) {
+            if (image2ordinal[i]>0) {
+              printf(" %d -> %d\n",i,image2ordinal[i]);
+            }
+          }
+        }
+      }
+    }
+  }
+
 }
 
-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++;
-	}
-}
+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 */
 
+  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;
+}
 
 #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);
-	}
+#ifdef USE_BITSHUFFLE
+  if (bshuf_register_h5filter() < 0 ) {
+    ERROR_JUMP(-2, done, "Failed to register bitshuffle filter");
+  }
+#endif
 
-	reset_error_stack();
-	retval = extract_detector_info(file_id, &data_desc, &ds_prop);
-	if (retval < 0) {
-		ERROR_JUMP(-4, done, "");
-	}
+  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);
+  }
 
-	mask_buffer = malloc(ds_prop.dims[1] * ds_prop.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;
+  reset_error_stack();
+  retval = get_detector_info(file_id, &data_desc);
+  if (retval < 0) {
+    ERROR_JUMP(-4, done, "");
+  }
+
+  data_desc->image_number_offset = info[5];
+
+  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;
+
+#ifdef GPHL_COMPILE_DATE
+  fprintf(ERROR_OUTPUT, "\n XDS HDF5/Durin plugin %d.%d.%d (DLS, 2018-2023; GPhL, 2020-2024 - built %d)\n", info[1], info[2], info[3], GPHL_COMPILE_DATE);
+#endif
 
 done:
-	*error_flag = retval;
-	if (retval < 0) {
-		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 = 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;
+  *nx = data_desc->dims[2];
+  *ny = data_desc->dims[1];
+  *nbytes = abs(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;
-	reset_error_stack();
-	fill_info_array(info);
-	if (data_desc.get_data_frame(&data_desc, &ds_prop, (*frame_number) - 1, sizeof(int), data_array) < 0) {
-		char message[64] = {0};
-		sprintf(message, "Failed to retrieve data for frame %d", *frame_number);
-		ERROR_JUMP(-2, done, message);
-	}
-	if (mask_buffer) {
-		apply_mask(data_array, mask_buffer, ds_prop.dims[1] * ds_prop.dims[2]);
-	}
+  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) == abs(data_desc->data_width)) {
+    buffer = data_array;
+  } else {
+    buffer = malloc(abs(data_desc->data_width) * frame_size_px);
+    if (!buffer) {
+      ERROR_JUMP(-1, done, "Unable to allocate data buffer");
+    }
+  }
+
+  int ordinal = *frame_number;
+  if (image2ordinal) {
+    if (ordinal < image2ordinal_imin || ordinal>image2ordinal_imax) {
+      char message[64] = {0};
+      sprintf(message, "Failed to map frame %d to ordinals since outside of range %d - %d", ordinal,image2ordinal_imin,image2ordinal_imax);
+      ERROR_JUMP(-2, done, message);
+    }
+    ordinal = image2ordinal[ordinal];
+    if (ordinal!=*frame_number) {
+      if (image2ordinal_debug) printf("fetching data from ordinal %d for frame %d\n",ordinal,*frame_number);
+    }
+  }
+
+  if (data_desc->get_data_frame(data_desc, ordinal - 1, buffer) < 0) {
+    char message[64] = {0};
+    if (image2ordinal) {
+      sprintf(message, "Failed to retrieve data for frame %d (ordinal %d)", *frame_number, ordinal);
+    } else {
+      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, info[6], data_array,
+                                frame_size_px, mask_buffer) < 0) {
+      char message[64];
+      if (image2ordinal) {
+        sprintf(message, "Error converting data for frame %d (ordinal %d)", *frame_number, ordinal);
+      } else {
+        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);
-	}
+  *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_extra) data_desc.free_extra(&data_desc);
-	if (H5close() < 0) {
-		*error_flag = -1;
-	}
+  if (image2ordinal) {
+    free(image2ordinal);
+    image2ordinal = NULL;
+  }
+
+  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

@@ -1,107 +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"
-
-
-void apply_mask(int *data, int *mask, int size) {
-	int *dptr, *mptr;
-	dptr = data;
-	mptr = mask;
-	while (dptr < data + size && mptr < mask + size) {
-		if (*mptr & 0x01) *dptr = -1;
-		if (*mptr & 0xFE) *dptr = -2;
-		dptr++;
-		mptr++;
-	}
-}
 
+#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 data_description_t desc = {0};
-	struct dataset_properties_t prop = {0};
-	int dims[3] = {0};
-	hid_t fid = 0;
-	int frame_idx = 0;
-	int *mask = NULL;
-	int *data = 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 = extract_detector_info(fid, &desc, &prop);
-	if (err < 0) {
-		ERROR_JUMP(err, done, "");
-	}
-	dims[0] = prop.dims[0];
-	dims[1] = prop.dims[1];
-	dims[2] = prop.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));
-	err = desc.get_data_frame(&desc, &prop, frame_idx, sizeof(*data), data);
-	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;
+  }
 
-	apply_mask(data, mask, dims[1] * dims[2]);
-	{
-		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");
-		}
-	}
+  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);
+    }
+  }
+
+  {
+    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 (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;
 }

tools/gitea_release_upload.py

@@ -0,0 +1,195 @@
+#!/usr/bin/env python2
+# -*- coding: utf-8 -*-
+
+import json
+import mimetools
+import mimetypes
+import os
+import sys
+import urllib2
+
+
+def fail(msg, code=1):
+    sys.stderr.write("ERROR: %s\n" % msg)
+    sys.exit(code)
+
+
+def api_request(url, token, method="GET", json_data=None, content_type=None):
+    data = None
+    headers = {
+        "Authorization": "token %s" % token,
+    }
+
+    if json_data is not None:
+        data = json.dumps(json_data)
+        headers["Content-Type"] = "application/json"
+    elif content_type is not None:
+        headers["Content-Type"] = content_type
+
+    request = urllib2.Request(url, data=data, headers=headers)
+    request.get_method = lambda: method
+
+    try:
+        response = urllib2.urlopen(request)
+        body = response.read()
+        status = response.getcode()
+        return status, body
+    except urllib2.HTTPError as e:
+        return e.code, e.read()
+
+
+def encode_multipart_formdata(fields, files):
+    boundary = mimetools.choose_boundary()
+    crlf = "\r\n"
+    lines = []
+
+    for key, value in fields:
+        lines.append("--" + boundary)
+        lines.append('Content-Disposition: form-data; name="%s"' % key)
+        lines.append("")
+        lines.append(value)
+
+    for key, filename, content, content_type in files:
+        lines.append("--" + boundary)
+        lines.append(
+            'Content-Disposition: form-data; name="%s"; filename="%s"' % (key, filename)
+        )
+        lines.append("Content-Type: %s" % content_type)
+        lines.append("")
+        lines.append(content)
+
+    lines.append("--" + boundary + "--")
+    lines.append("")
+    body = crlf.join(lines)
+    content_type = "multipart/form-data; boundary=%s" % boundary
+    return content_type, body
+
+
+def multipart_request(url, token, fields, files):
+    content_type, body = encode_multipart_formdata(fields, files)
+    headers = {
+        "Authorization": "token %s" % token,
+        "Content-Type": content_type,
+    }
+
+    request = urllib2.Request(url, data=body, headers=headers)
+    request.get_method = lambda: "POST"
+
+    try:
+        response = urllib2.urlopen(request)
+        return response.getcode(), response.read()
+    except urllib2.HTTPError as e:
+        return e.code, e.read()
+
+
+def get_release_by_tag(api_base, token, tag):
+    url = "%s/releases/tags/%s" % (api_base, tag)
+    status, body = api_request(url, token, method="GET")
+    if status == 200:
+        return json.loads(body)
+    if status == 404:
+        return None
+    fail("failed to fetch release for tag %s: HTTP %s\n%s" % (tag, status, body))
+
+
+def create_release(api_base, token, tag):
+    url = "%s/releases" % api_base
+    payload = {
+        "tag_name": tag,
+        "name": tag,
+        "draft": False,
+        "prerelease": False,
+    }
+    status, body = api_request(url, token, method="POST", json_data=payload)
+    if status not in (200, 201):
+        fail("failed to create release for tag %s: HTTP %s\n%s" % (tag, status, body))
+    return json.loads(body)
+
+
+def ensure_release(api_base, token, tag):
+    release = get_release_by_tag(api_base, token, tag)
+    if release is not None:
+        print("Release for tag %s already exists (id=%s)" % (tag, release.get("id")))
+        return release
+
+    print("Release for tag %s does not exist, creating it" % tag)
+    release = create_release(api_base, token, tag)
+    print("Created release id=%s" % release.get("id"))
+    return release
+
+
+def upload_asset(api_base, token, release_id, file_path):
+    if not os.path.isfile(file_path):
+        fail("file not found: %s" % file_path)
+
+    asset_name = os.path.basename(file_path)
+    mime_type = mimetypes.guess_type(asset_name)[0] or "application/octet-stream"
+
+    with open(file_path, "rb") as f:
+        content = f.read()
+
+    url = "%s/releases/%s/assets" % (api_base, release_id)
+    status, body = multipart_request(
+        url,
+        token,
+        fields=[("name", asset_name)],
+        files=[("attachment", asset_name, content, mime_type)],
+    )
+
+    if status not in (200, 201):
+        fail("failed to upload asset %s: HTTP %s\n%s" % (asset_name, status, body))
+
+    print("Uploaded asset: %s" % asset_name)
+
+
+def find_assets(build_dir):
+    names = []
+    for name in sorted(os.listdir(build_dir)):
+        if name.startswith("libdurin-plugin.so"):
+            full = os.path.join(build_dir, name)
+            if os.path.isfile(full):
+                names.append(full)
+    return names
+
+
+def main():
+    if len(sys.argv) != 4:
+        sys.stderr.write(
+            "Usage: %s <gitea-server> <owner/repo> <tag>\n" % sys.argv[0]
+        )
+        sys.stderr.write(
+            "Example: %s https://gitea.psi.ch mx/durin 1.0.0\n" % sys.argv[0]
+        )
+        sys.exit(1)
+
+    server = sys.argv[1].rstrip("/")
+    repo = sys.argv[2]
+    tag = sys.argv[3]
+
+    token = os.environ.get("GITEA_TOKEN")
+    if not token:
+        fail("GITEA_TOKEN environment variable is not set")
+
+    build_dir = "build"
+    if not os.path.isdir(build_dir):
+        fail("build directory not found: %s" % build_dir)
+
+    assets = find_assets(build_dir)
+    if not assets:
+        fail("no libdurin-plugin.so* files found in %s" % build_dir)
+
+    api_base = "%s/api/v1/repos/%s" % (server, repo)
+
+    release = ensure_release(api_base, token, tag)
+    release_id = release.get("id")
+    if not release_id:
+        fail("release id missing in API response")
+
+    for asset in assets:
+        upload_asset(api_base, token, release_id, asset)
+
+    print("Done.")
+
+
+if __name__ == "__main__":
+    main()