[med-svn] [Git][med-team/libxdf][master] 10 commits: New upstream version 0.99.6+dfsg
Andreas Tille
gitlab at salsa.debian.org
Fri Dec 18 18:02:17 GMT 2020
Andreas Tille pushed to branch master at Debian Med / libxdf
Commits:
debd3a43 by Andreas Tille at 2020-12-18T16:56:00+01:00
New upstream version 0.99.6+dfsg
- - - - -
20377b95 by Andreas Tille at 2020-12-18T16:56:00+01:00
routine-update: New upstream version
- - - - -
325d2e3b by Andreas Tille at 2020-12-18T16:56:01+01:00
Update upstream source from tag 'upstream/0.99.6+dfsg'
Update to upstream version '0.99.6+dfsg'
with Debian dir ab8e2e26b3ee6a8405ff9a4246fb05b9d1e9be4d
- - - - -
5c389328 by Andreas Tille at 2020-12-18T16:56:01+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
a8204b6f by Andreas Tille at 2020-12-18T16:56:01+01:00
routine-update: debhelper-compat 13
- - - - -
470f0d78 by Andreas Tille at 2020-12-18T16:56:05+01:00
routine-update: Add salsa-ci file
- - - - -
329041ed by Andreas Tille at 2020-12-18T16:56:05+01:00
routine-update: Rules-Requires-Root: no
- - - - -
c6101fd9 by Andreas Tille at 2020-12-18T16:56:11+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
8e5a4cfe by Andreas Tille at 2020-12-18T18:06:51+01:00
Deactivate patches
- - - - -
7825557c by Andreas Tille at 2020-12-18T18:58:51+01:00
Create shared and static library
- - - - -
18 changed files:
- + .github/workflows/cppcmake.yml
- + CHANGELOG.txt
- CMakeLists.txt
- LICENSE.txt
- README.md
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/shared_and_static.patch
- + debian/salsa-ci.yml
- + debian/upstream/metadata
- smarc/filtering.c
- smarc/filtering.h
- smarc/polyfilt.c
- smarc/polyfilt.h
- xdf.cpp
- xdf.h
- xdf.pro
Changes:
=====================================
.github/workflows/cppcmake.yml
=====================================
@@ -0,0 +1,76 @@
+name: C/C++ CI
+
+on:
+ push:
+ tags:
+ - v*.*
+ pull_request:
+ branches:
+ - master
+
+jobs:
+ build:
+ name: ${{ matrix.config.name }}
+ runs-on: ${{ matrix.config.os }}
+ strategy:
+ matrix:
+ config:
+ - {name: "ubuntu-latest", os: ubuntu-latest, cmake_extra: ""}
+ - {name: "windows-x64", os: windows-latest, cmake_extra: "-T v140"}
+ - {name: "windows-32", os: windows-latest, cmake_extra: "-T v140 -A Win32"}
+ - {name: "macOS-latest", os: macOS-latest, cmake_extra: ""}
+ fail-fast: false
+
+ steps:
+ - uses: actions/checkout at v2
+
+ - name: CMake version
+ run: cmake --version
+
+ - name: Configure CMake
+ shell: bash
+ run: |
+ cmake -S . -B build ${{ matrix.config.cmake_extra }} -DCMAKE_INSTALL_PREFIX=${PWD}/build/install -DCPACK_PACKAGE_DIRECTORY=${PWD}/build/package -DCPACK_DEBIAN_PACKAGE_SHLIBDEPS=ON
+
+ - name: Make
+ run: cmake --build build --config Release -j
+
+ - name: Install
+ run: cmake --build build --config Release -j --target install
+
+ - name: Package
+ run: cmake --build build --config Release -j --target package
+
+ - name: Upload Artifact
+ uses: actions/upload-artifact at master
+ # if: "!startsWith(github.ref, 'refs/heads')"
+ with:
+ name: pkg-${{ matrix.config.name }}
+ path: |
+ build/package/*.deb
+ build/package/*.tar.bz2
+ build/package/*.zip
+
+
+ release:
+ needs: build
+ runs-on: ubuntu-latest
+ steps:
+
+ - name: Download Artifacts
+ if: startsWith(github.ref, 'refs/tags/')
+ uses: actions/download-artifact at v2
+
+ - name: Create Release
+ if: startsWith(github.ref, 'refs/tags/')
+ id: create_release
+ uses: softprops/action-gh-release at v1
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ with:
+ # tag_name: ${{ github.ref }} # ${{ github.ref }} is default
+ name: Release ${{ github.ref }}
+ draft: false
+ prerelease: false
+ # body_path: CHANGELOG.txt
+ files: 'pkg-*/*'
=====================================
CHANGELOG.txt
=====================================
@@ -0,0 +1,5 @@
+# Changelog
+
+## [0.992] - 2020-11-11
+### Added
+- GitHub Actions for automatic build on pull requests to master and automatic build and release on tags.
=====================================
CMakeLists.txt
=====================================
@@ -1,14 +1,16 @@
cmake_minimum_required(VERSION 3.7)
set(CMAKE_OSX_DEPLOYMENT_TARGET 10.9)
-project(libxdf)
+project(libxdf
+ VERSION 0.99.6
+ DESCRIPTION "C++ library for loading multimodal, multi-rate signals stored in XDF files."
+ HOMEPAGE_URL https://xdf-modules.github.io/libxdf/)
+
+option(XDF_NO_SYSTEM_PUGIXML "Force use of bundled pugixml" OFF)
set(SOURCES
xdf.h
xdf.cpp
- pugixml/pugiconfig.hpp
- pugixml/pugixml.hpp
- pugixml/pugixml.cpp
smarc/filtering.h
smarc/filtering.c
smarc/multi_stage.h
@@ -23,10 +25,48 @@ set(SOURCES
smarc/stage_impl.c
)
-add_library(xdf-static STATIC ${SOURCES})
-add_library(xdf-shared SHARED ${SOURCES})
+add_library(xdf ${SOURCES})
+
+find_package(pugixml 1.9 QUIET)
+if(TARGET pugixml AND NOT XDF_NO_SYSTEM_PUGIXML)
+ message(STATUS "Using system pugixml")
+ target_link_libraries(xdf PRIVATE pugixml)
+else()
+ message(STATUS "Using bundled pugixml")
+ target_sources(xdf PRIVATE pugixml/pugixml.cpp)
+ target_include_directories(xdf PRIVATE pugixml)
+endif()
+
+target_compile_features(xdf PUBLIC cxx_std_11)
+set_target_properties(xdf PROPERTIES OUTPUT_NAME xdf PUBLIC_HEADER xdf.h)
+target_include_directories(xdf PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>
+ $<INSTALL_INTERFACE:include>
+)
+include(GNUInstallDirs)
+install(TARGETS xdf
+ EXPORT "${PROJECT_NAME}Config"
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+)
+install(EXPORT "${PROJECT_NAME}Config"
+ COMPONENT ${PROJECT_NAME}
+ NAMESPACE "XDF::"
+ DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}
+)
+
+# set(CPACK_STRIP_FILES ON)
+# set(CPACK_ARCHIVE_COMPONENT_INSTALL ON)
+set(CPACK_PACKAGE_CONTACT "yl3842 at columbia.edu")
+if(APPLE)
+ set(CPACK_GENERATOR TBZ2)
+elseif(WIN32)
+ set(CPACK_GENERATOR ZIP)
+elseif(UNIX)
+ set(CPACK_GENERATOR DEB)
+ set(CPACK_DEBIAN_LIBLSL_PACKAGE_SHLIBDEPS ON)
+ set(CPACK_DEBIAN_PACKAGE_GENERATE_SHLIBS ON)
+endif()
+include(CPack)
-set_property(TARGET xdf-static xdf-shared PROPERTY CXX_STANDARD 11)
-set_property(TARGET xdf-static xdf-shared PROPERTY C_STANDARD 99)
-set_target_properties(xdf-static PROPERTIES OUTPUT_NAME xdf)
-set_target_properties(xdf-shared PROPERTIES OUTPUT_NAME xdf)
=====================================
LICENSE.txt
=====================================
@@ -1,674 +1,27 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
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-might be different; for a GUI interface, you would use an "about box".
-
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-if any, to sign a "copyright disclaimer" for the program, if necessary.
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-
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-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
\ No newline at end of file
+BSD 2-Clause License
+
+Copyright (c) 2017-2020, Yida Lin
+Copyright (c) 2017-2020, Clemens Brunner
+Copyright (c) 2017-2020, Paul Sajda
+Copyright (c) 2017-2020, Josef Faller
+
+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 HOLDER 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.
=====================================
README.md
=====================================
@@ -1,33 +1,49 @@
# Libxdf - a C++ library for loading [XDF](https://github.com/sccn/xdf/wiki/Specifications "Extensible Data Format") files
+[](http://www.repostatus.org/#active)
+[](https://opensource.org/licenses/BSD-2-Clause)
* [Introduction](#intro)
-* [Download](#download)
* [Quick-Start Guide](#quick)
+ * [Download](#download)
* [Documentation](#doc)
+* [Reference](#reference)
* [Support](#support)
## <a name="intro"></a>Introduction
Libxdf is a cross-platform C++ library for loading multimodal, multi-rate signals stored in [XDF](https://github.com/sccn/xdf/wiki/Specifications "Extensible Data Format") files.
-Libxdf is used in the biosignal viewing application [SigViewer](https://github.com/cbrnr/sigviewer). It can also be integrated into other
-C++ applications.
+Libxdf is used in the biosignal viewing application [SigViewer](https://github.com/cbrnr/sigviewer) and the LSL application [XDFStreamer](https://github.com/labstreaminglayer/App-XDFStreamer/). It can also be integrated into other C++ applications.
Libxdf is open-source, free, and actively maintained.
+## <a name="quick"></a>Quick-Start Guide
-## <a name="download"></a>Download
-
-* [Source code (zip)](https://github.com/Yida-Lin/libxdf/archive/0.94.zip)
-* [Source code (tar.gz)](https://github.com/Yida-Lin/libxdf/archive/0.94.tar.gz)
-* [Pre-built binaries](https://github.com/Yida-Lin/libxdf/releases)
+### <a name="download"></a>Download
-## <a name="quick"></a>Quick-Start Guide
+* Find Source and Prebuilt Binaries on the [releases page](https://github.com/Yida-Lin/libxdf/releases).
+ * You may need to expand the list of Assets to find the downloads.
+* For Linux Debian (Ubuntu) users: `sudo dpkg -i libxdf-{version}-Linux.deb`
+* For Windows and Mac users: simply extract the archive somewhere convenient.
### Building libxdf
+
+If the release does not have assets for your platform or they do not work for you for some other reason, then
Libxdf can be conveniently built either using `qmake` or `cmake`. Configuration files for both build tools are included with the source.
+To build with cmake from command prompt / terminal:
+
+```sh
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX=${PWD}/build/install
+cmake --build build --config Release -j --target install
+```
+
+`cmake` builds a static library by default, but you can build a shared library
+by setting the
+[`BUILD_SHARED_LIBS`](https://cmake.org/cmake/help/latest/variable/BUILD_SHARED_LIBS.html)
+variable (e.g. add `-DBUILD_SHARED_LIBS=ON` to the first cmake command above).
+
### Use in conjunction with [SigViewer](https://github.com/cbrnr/sigviewer)
Libxdf is a built-in component of [SigViewer](https://github.com/cbrnr/sigviewer). If you wish to build SigViewer from source, follow these steps:
@@ -44,8 +60,22 @@ Example: SigViewer using _libxdf_ to display signals in an XDF file.
### Use in other C++ applications
-1. Build libxdf from source or use a pre-built binary release
-2. Instantiate an object of the `Xdf` class and call the `load_xdf` method.
+1. Install a prebuilt binary release or build from source as above.
+2. For CMake users:
+ * In your project's CMakeLists.txt, use the following snippet:
+ ```CMake
+ find_package(libxdf REQUIRED
+ HINTS ${XDF_INSTALL_ROOT}
+ PATH_SUFFIXES share
+ )
+ target_link_libraries(${PROJECT_NAME}
+ PRIVATE
+ # ... other dependencies
+ XDF::xdf
+ )
+ ```
+ * If the libxdf package was installed or extracted into a folder other than a standard system library folder, you will have to pass a cmake command line argument to indicate where to find it: `-DXDF_INSTALL_ROOT=path/to/libxdf`
+3. In your source code, `#include "xdf.h"`, instantiate an object of the `Xdf` class and call the `load_xdf` method.
Example:
@@ -82,6 +112,23 @@ Detailed documentation was generated via [Doxygen](http://www.stack.nl/~dimitri/
## <a name="SigViewer"></a> SigViewer Online Repo
SigViewer Online Repository is [here](repository/Updates.xml).
-## <a name="support"></a>Support
+## <a name="reference"></a> Reference
+If you use this code in your project, please cite:
+```
+Yida Lin, Clemens Brunner, Paul Sajda and Josef Faller. SigViewer: Visualizing Multimodal Signals Stored in XDF (Extensible Data Format) Files. The 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.
+```
+Direct link: https://arxiv.org/abs/1708.06333
+Bibtex format:
+```
+ at article{lin2017sigviewer,
+ title={SigViewer: visualizing multimodal signals stored in XDF (Extensible Data Format) files},
+ author={Lin, Yida and Brunner, Clemens and Sajda, Paul and Faller, Josef},
+ journal={arXiv},
+ pages={arXiv--1708},
+ year={2017}
+}
+```
+
+## <a name="support"></a>Support
[Email author](mailto:yl3842 at columbia.edu) or report a new [issue](https://github.com/Yida-Lin/libxdf/issues).
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+libxdf (0.99.6+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.5.1 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org> Fri, 18 Dec 2020 16:56:00 +0100
+
libxdf (0.99+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -3,14 +3,15 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
cmake,
d-shlibs,
libpugixml-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/libxdf
Vcs-Git: https://salsa.debian.org/med-team/libxdf.git
Homepage: https://github.com/Yida-Lin/libxdf
+Rules-Requires-Root: no
Package: libxdf0
Architecture: any
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
-soversion.patch
-use_debian_packaged_pugixml.patch
+#soversion.patch
+#use_debian_packaged_pugixml.patch
+shared_and_static.patch
=====================================
debian/patches/shared_and_static.patch
=====================================
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 18 Dec 2020 16:56:00 +0100
+Description: Create shared and static library
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -26,6 +26,7 @@ set(SOURCES
+ )
+
+ add_library(xdf ${SOURCES})
++add_library(xdf_shared SHARED ${SOURCES})
+
+ find_package(pugixml 1.9 QUIET)
+ if(TARGET pugixml AND NOT XDF_NO_SYSTEM_PUGIXML)
+@@ -39,6 +40,7 @@ endif()
+
+ target_compile_features(xdf PUBLIC cxx_std_11)
+ set_target_properties(xdf PROPERTIES OUTPUT_NAME xdf PUBLIC_HEADER xdf.h)
++set_target_properties(xdf_shared PROPERTIES OUTPUT_NAME xdf PUBLIC_HEADER xdf.h)
+ target_include_directories(xdf PUBLIC
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}>
+ $<INSTALL_INTERFACE:include>
+@@ -50,6 +52,12 @@ install(TARGETS xdf
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+ )
++install(TARGETS xdf_shared
++ EXPORT "${PROJECT_NAME}Config"
++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
++ PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
++)
+ install(EXPORT "${PROJECT_NAME}Config"
+ COMPONENT ${PROJECT_NAME}
+ NAMESPACE "XDF::"
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,5 @@
+---
+Bug-Database: https://github.com/Yida-Lin/libxdf/issues
+Bug-Submit: https://github.com/Yida-Lin/libxdf/issues/new
+Repository: https://github.com/Yida-Lin/libxdf.git
+Repository-Browse: https://github.com/Yida-Lin/libxdf
=====================================
smarc/filtering.c
=====================================
@@ -26,7 +26,7 @@
#ifndef __SSE2__
-double filter(const double* restrict filt, const double* restrict signal, const int K)
+double filter(const double* SMARC_RESTRICT filt, const double* SMARC_RESTRICT signal, const int K)
{
register double v = 0.0;
for (int k=0;k<K;++k)
@@ -38,7 +38,7 @@ double filter(const double* restrict filt, const double* restrict signal, const
#include <emmintrin.h>
-double basic_filter(const double* restrict filt, const double* restrict signal, const int K)
+double basic_filter(const double* SMARC_RESTRICT filt, const double* SMARC_RESTRICT signal, const int K)
{
// printf("basic filter for K=%i\n",K);
register double v = 0.0;
@@ -47,7 +47,7 @@ double basic_filter(const double* restrict filt, const double* restrict signal,
return v;
}
-double sse_filtering_aligned(const double* restrict filt, const double* restrict signal, const int K) {
+double sse_filtering_aligned(const double* SMARC_RESTRICT filt, const double* SMARC_RESTRICT signal, const int K) {
// printf("sse_filtering filt=%p signal=%p K=%i\n",filt,signal,K);
// filt and signal are 16 byte aligned, K % 2 = 0
__m128d v = _mm_setzero_pd();
@@ -65,7 +65,7 @@ double sse_filtering_aligned(const double* restrict filt, const double* restrict
return tmp[0] + tmp[1] + filt[k]*signal[k];
}
-double sse_filtering_misaligned(const double* restrict filt, const double* restrict signal, const int K) {
+double sse_filtering_misaligned(const double* SMARC_RESTRICT filt, const double* SMARC_RESTRICT signal, const int K) {
// printf("sse_filtering_misaligned filt=%p signal=%p K=%i\n",filt,signal,K);
__m128d v = _mm_setzero_pd();
__m128d s = _mm_load1_pd(signal);
@@ -87,7 +87,7 @@ double sse_filtering_misaligned(const double* restrict filt, const double* restr
return tmp[0] + tmp[1];
}
-double filter(const double* restrict filt, const double* restrict signal, int K)
+double filter(const double* SMARC_RESTRICT filt, const double* SMARC_RESTRICT signal, int K)
{
if (K<8)
return basic_filter(filt,signal,K);
=====================================
smarc/filtering.h
=====================================
@@ -25,6 +25,12 @@
#ifndef FILTER_H_
#define FILTER_H_
-double filter(const double* restrict filt, const double* restrict signal, const int K);
+#ifdef _MSC_VER
+#define SMARC_RESTRICT __restrict
+#else
+#define SMARC_RESTRICT restrict
+#endif
+
+double filter(const double* SMARC_RESTRICT filt, const double* SMARC_RESTRICT signal, const int K);
#endif /* FILTER_H_ */
=====================================
smarc/polyfilt.c
=====================================
@@ -71,8 +71,8 @@ void polyfiltLM(struct PSFilter* pfilt, struct PSState* pstate,
void polyfiltM(struct PSFilter* pfilt, struct PSState* pstate,
- const double* restrict signal, const int signalLen, int* restrict nbConsume,
- double* restrict output, const int outputLen, int* restrict nbWritten) {
+ const double* SMARC_RESTRICT signal, const int signalLen, int* SMARC_RESTRICT nbConsume,
+ double* SMARC_RESTRICT output, const int outputLen, int* SMARC_RESTRICT nbWritten) {
const int M = pfilt->M;
const int K = pfilt->K;
const double* filt = pfilt->filters;
=====================================
smarc/polyfilt.h
=====================================
@@ -41,8 +41,8 @@
* - w [IN]: workspace to use for temporary results.
*/
void polyfiltLM(struct PSFilter* pfilt, struct PSState* pstate,
- const double* restrict signal, const int signalLen, int* nbConsume,
- double* restrict output, const int outputLen, int* nbWritten);
+ const double* SMARC_RESTRICT signal, const int signalLen, int* nbConsume,
+ double* SMARC_RESTRICT output, const int outputLen, int* nbWritten);
/**
* Filter signal with a decimation filter (interpolation factor L is 1)
@@ -57,8 +57,8 @@ void polyfiltLM(struct PSFilter* pfilt, struct PSState* pstate,
* - w [IN]: workspace to use for temporary results.
*/
void polyfiltM(struct PSFilter* pfilt, struct PSState* pstate,
- const double* restrict signal, const int signalLen, int* restrict nbConsume,
- double* restrict output, const int outputLen, int* restrict nbWritten);
+ const double* SMARC_RESTRICT signal, const int signalLen, int* SMARC_RESTRICT nbConsume,
+ double* SMARC_RESTRICT output, const int outputLen, int* SMARC_RESTRICT nbWritten);
/**
* Filter signal with a interpolation filter (decimation factor M is 1)
@@ -73,7 +73,7 @@ void polyfiltM(struct PSFilter* pfilt, struct PSState* pstate,
* - w [IN]: workspace to use for temporary results.
*/
void polyfiltL(struct PSFilter* pfilt, struct PSState* pstate,
- const double* restrict signal, const int signalLen, int* restrict nbConsume,
- double* restrict output, const int outputLen, int* restrict nbWritten);
+ const double* SMARC_RESTRICT signal, const int signalLen, int* SMARC_RESTRICT nbConsume,
+ double* SMARC_RESTRICT output, const int outputLen, int* SMARC_RESTRICT nbWritten);
#endif /* POLYFILTLM_H_ */
=====================================
xdf.cpp
=====================================
@@ -20,7 +20,7 @@
#include <iostream>
#include <fstream>
-#include "pugixml/pugixml.hpp" //pugi XML parser
+#include <pugixml.hpp> //pugi XML parser
#include <sstream>
#include <algorithm>
#include "smarc/smarc.h" //resampling library
@@ -85,7 +85,7 @@ int Xdf::load_xdf(std::string filename)
break;
uint16_t tag; //read tag of the chunk, 6 possibilities
- file.read(reinterpret_cast<char *>(&tag), 2);
+ readBin(file, &tag);
switch (tag)
{
@@ -109,9 +109,9 @@ int Xdf::load_xdf(std::string filename)
case 2: //read [StreamHeader] chunk
{
//read [StreamID]
- int streamID;
+ uint32_t streamID;
int index;
- file.read((char*)&streamID, 4);
+ Xdf::readBin(file, &streamID);
std::vector<int>::iterator it {std::find(idmap.begin(),idmap.end(),streamID)};
if (it == idmap.end())
{
@@ -160,9 +160,9 @@ int Xdf::load_xdf(std::string filename)
case 3: //read [Samples] chunk
{
//read [StreamID]
- int streamID;
+ uint32_t streamID;
int index;
- file.read((char*)&streamID, 4);
+ Xdf::readBin(file, &streamID);
std::vector<int>::iterator it {std::find(idmap.begin(),idmap.end(),streamID)};
if (it == idmap.end())
{
@@ -188,14 +188,13 @@ int Xdf::load_xdf(std::string filename)
for (size_t i = 0; i < numSamp; i++)
{
//read or deduce time stamp
- uint8_t tsBytes;
- file.read(reinterpret_cast<char *>(&tsBytes), 1);
+ auto tsBytes = readBin<uint8_t>(file);
double ts; //temporary time stamp
if (tsBytes == 8)
{
- file.read((char*)&ts, 8);
+ Xdf::readBin(file, &ts);
streams[index].time_stamps.emplace_back(ts);
}
else
@@ -210,7 +209,7 @@ int Xdf::load_xdf(std::string filename)
for (int v = 0; v < streams[index].info.channel_count; ++v)
{
float data;
- file.read((char*)&data, 4);
+ Xdf::readBin(file, &data);
streams[index].time_series[v].emplace_back(data);
}
}
@@ -225,14 +224,13 @@ int Xdf::load_xdf(std::string filename)
for (size_t i = 0; i < numSamp; i++)
{
//read or deduce time stamp
- uint8_t tsBytes;
- file.read(reinterpret_cast<char *>(&tsBytes), 1);
+ auto tsBytes = readBin<uint8_t>(file);
double ts; //temporary time stamp
if (tsBytes == 8)
{
- file.read((char*)&ts, 8);
+ Xdf::readBin(file, &ts);
streams[index].time_stamps.emplace_back(ts);
}
else
@@ -247,7 +245,7 @@ int Xdf::load_xdf(std::string filename)
for (int v = 0; v < streams[index].info.channel_count; ++v)
{
double data;
- file.read((char*)&data, 8);
+ Xdf::readBin(file, &data);
streams[index].time_series[v].emplace_back(data);
}
}
@@ -262,14 +260,13 @@ int Xdf::load_xdf(std::string filename)
for (size_t i = 0; i < numSamp; i++)
{
//read or deduce time stamp
- uint8_t tsBytes;
- file.read(reinterpret_cast<char *>(&tsBytes), 1);
+ auto tsBytes = readBin<uint8_t>(file);
double ts; //temporary time stamp
if (tsBytes == 8)
{
- file.read((char*)&ts, 8);
+ Xdf::readBin(file, &ts);
streams[index].time_stamps.emplace_back(ts);
}
else
@@ -284,7 +281,7 @@ int Xdf::load_xdf(std::string filename)
for (int v = 0; v < streams[index].info.channel_count; ++v)
{
int8_t data;
- file.read((char*)&data, 1);
+ Xdf::readBin(file, &data);
streams[index].time_series[v].emplace_back(data);
}
}
@@ -299,14 +296,13 @@ int Xdf::load_xdf(std::string filename)
for (size_t i = 0; i < numSamp; i++)
{
//read or deduce time stamp
- uint8_t tsBytes;
- file.read(reinterpret_cast<char *>(&tsBytes), 1);
+ auto tsBytes = readBin<uint8_t>(file);
double ts; //temporary time stamp
if (tsBytes == 8)
{
- file.read((char*)&ts, 8);
+ Xdf::readBin(file, &ts);
streams[index].time_stamps.emplace_back(ts);
}
else
@@ -321,7 +317,7 @@ int Xdf::load_xdf(std::string filename)
for (int v = 0; v < streams[index].info.channel_count; ++v)
{
int16_t data;
- file.read((char*)&data, 2);
+ Xdf::readBin(file, &data);
streams[index].time_series[v].emplace_back(data);
}
}
@@ -336,14 +332,13 @@ int Xdf::load_xdf(std::string filename)
for (size_t i = 0; i < numSamp; i++)
{
//read or deduce time stamp
- uint8_t tsBytes;
- file.read(reinterpret_cast<char *>(&tsBytes), 1);
+ auto tsBytes = readBin<uint8_t>(file);
double ts; //temporary time stamp
if (tsBytes == 8)
{
- file.read((char*)&ts, 8);
+ Xdf::readBin(file, &ts);
streams[index].time_stamps.emplace_back(ts);
}
else
@@ -358,7 +353,7 @@ int Xdf::load_xdf(std::string filename)
for (int v = 0; v < streams[index].info.channel_count; ++v)
{
int32_t data;
- file.read((char*)&data, 4);
+ Xdf::readBin(file, &data);
streams[index].time_series[v].emplace_back(data);
}
}
@@ -373,14 +368,13 @@ int Xdf::load_xdf(std::string filename)
for (size_t i = 0; i < numSamp; i++)
{
//read or deduce time stamp
- uint8_t tsBytes;
- file.read(reinterpret_cast<char *>(&tsBytes), 1);
+ auto tsBytes = readBin<uint8_t>(file);
double ts; //temporary time stamp
if (tsBytes == 8)
{
- file.read((char*)&ts, 8);
+ Xdf::readBin(file, &ts);
streams[index].time_stamps.emplace_back(ts);
}
else
@@ -395,7 +389,7 @@ int Xdf::load_xdf(std::string filename)
for (int v = 0; v < streams[index].info.channel_count; ++v)
{
int64_t data;
- file.read((char*)&data, 8);
+ Xdf::readBin(file, &data);
streams[index].time_series[v].emplace_back(data);
}
}
@@ -406,50 +400,23 @@ int Xdf::load_xdf(std::string filename)
for (size_t i = 0; i < numSamp; i++)
{
//read or deduce time stamp
- uint8_t tsBytes;
- file.read(reinterpret_cast<char *>(&tsBytes), 1);
+ auto tsBytes = readBin<uint8_t>(file);
double ts; //temporary time stamp
if (tsBytes == 8)
- file.read((char*)&ts, 8);
+ Xdf::readBin(file, &ts);
else
ts = streams[index].last_timestamp + streams[index].sampling_interval;
//read the event
- int8_t bytes;
- file.read((char*)&bytes, 1);
- if (bytes == 1)
- {
- uint8_t length;
- file.read((char*)&length, 1);
- char* buffer = new char[length + 1];
- file.read(buffer, length);
- buffer[length] = '\0';
- eventMap.emplace_back(std::make_pair(buffer, ts), index);
- delete[] buffer;
- }
- else if (bytes == 4)
- {
- uint32_t length;
- file.read((char*)&length, 4);
- char* buffer = new char[length + 1];
- file.read(buffer, length);
- buffer[length] = '\0';
- eventMap.emplace_back(std::make_pair(buffer, ts), index);
- delete[] buffer;
- }
- else if (bytes == 8)
- {
- uint64_t length;
- file.read((char*)&length, 8);
- char* buffer = new char[length + 1];
- file.read(buffer, length);
- buffer[length] = '\0';
- eventMap.emplace_back(std::make_pair(buffer, ts), index);
- delete[] buffer;
- }
+ auto length = Xdf::readLength(file);
+ char* buffer = new char[length + 1];
+ file.read(buffer, length);
+ buffer[length] = '\0';
+ eventMap.emplace_back(std::make_pair(buffer, ts), index);
+ delete[] buffer;
streams[index].last_timestamp = ts;
}
}
@@ -457,9 +424,9 @@ int Xdf::load_xdf(std::string filename)
break;
case 4: //read [ClockOffset] chunk
{
- int streamID;
+ uint32_t streamID;
int index;
- file.read((char*)&streamID, 4);
+ Xdf::readBin(file, &streamID);
std::vector<int>::iterator it {std::find(idmap.begin(),idmap.end(),streamID)};
if (it == idmap.end())
{
@@ -474,8 +441,8 @@ int Xdf::load_xdf(std::string filename)
double collectionTime;
double offsetValue;
- file.read((char*)&collectionTime, 8);
- file.read((char*)&offsetValue, 8);
+ Xdf::readBin(file, &collectionTime);
+ Xdf::readBin(file, &offsetValue);
streams[index].clock_times.emplace_back(collectionTime);
streams[index].clock_values.emplace_back(offsetValue);
@@ -486,9 +453,9 @@ int Xdf::load_xdf(std::string filename)
pugi::xml_document doc;
//read [StreamID]
- int streamID;
+ uint32_t streamID;
int index;
- file.read((char*)&streamID, 4);
+ Xdf::readBin(file, &streamID);
std::vector<int>::iterator it {std::find(idmap.begin(),idmap.end(),streamID)};
if (it == idmap.end())
{
@@ -746,34 +713,27 @@ void Xdf::resample(int userSrate)
uint64_t Xdf::readLength(std::ifstream &file)
{
uint8_t bytes;
- file.read((char*)&bytes, 1);
+ Xdf::readBin(file, &bytes);
uint64_t length = 0;
switch (bytes)
{
case 1:
- {
- uint8_t buffer = 0;
- file.read(reinterpret_cast<char *>(&buffer), 1);
- length = buffer;
- return length;
- }
+ length = readBin<uint8_t>(file);
+ break;
case 4:
- {
- uint32_t buffer = 0;
- file.read(reinterpret_cast<char *>(&buffer), 4);
- length = buffer;
- return length;
- }
+ length = readBin<uint32_t>(file);
+ break;
case 8:
- {
- file.read(reinterpret_cast<char *>(&length), 8);
- return length;
- }
+ length = readBin<uint64_t>(file);
+ break;
default:
- std::cout << "Invalid variable-length integer encountered.\n";
+ std::cout << "Invalid variable-length integer length ("
+ << static_cast<int>(bytes) << ") encountered.\n";
return 0;
}
+
+ return length;
}
void Xdf::findMinMax()
@@ -781,7 +741,7 @@ void Xdf::findMinMax()
//find the smallest timestamp of all streams
for (auto const &stream : streams)
{
- if (stream.info.first_timestamp != -1)
+ if (!std::isnan(stream.info.first_timestamp))
{
minTS = stream.info.first_timestamp;
break;
@@ -789,14 +749,14 @@ void Xdf::findMinMax()
}
for (auto const &stream : streams)
{
- if (stream.info.first_timestamp != -1 && stream.info.first_timestamp < minTS)
+ if (!std::isnan(stream.info.first_timestamp) && stream.info.first_timestamp < minTS)
minTS = stream.info.first_timestamp;
}
//find the max timestamp of all streams
for (auto const &stream : streams)
{
- if (stream.info.last_timestamp != 0 && stream.info.last_timestamp > maxTS)
+ if (!std::isnan(stream.info.last_timestamp) && stream.info.last_timestamp > maxTS)
maxTS = stream.info.last_timestamp;
}
}
@@ -915,7 +875,7 @@ void Xdf::detrend()
{
long double init = 0.0;
long double mean = std::accumulate(row.begin(), row.end(), init) / row.size();
- std::transform(row.begin(), row.end(), row.begin(), bind2nd(std::minus<double>(), mean));
+ for(auto &val: row) val -= mean;
offsets.emplace_back(mean);
}
}
@@ -1126,3 +1086,10 @@ void Xdf::loadDictionary()
eventType.emplace_back(std::distance(dictionary.begin(), it));
}
}
+
+template<typename T> T Xdf::readBin(std::istream& is, T* obj) {
+ T dummy;
+ if(!obj) obj = &dummy;
+ is.read(reinterpret_cast<char*>(obj), sizeof(T));
+ return *obj;
+}
=====================================
xdf.h
=====================================
@@ -297,6 +297,20 @@ private:
* \return The length of the upcoming chunk (in bytes).
*/
uint64_t readLength(std::ifstream &file);
+
+ /*!
+ * \brief Read a binary scalar variable from an input stream.
+ *
+ * readBin is a convenience wrapper for the common
+ * file.read((char*) var, sizeof(var))
+ * operation. Examples:
+ * double foo = readBin<double>(file); // use return value
+ * readBin(file, &foo); // read directly into foo
+ * \param is an input stream to read from
+ * \param obj pointer to a variable to load the data into or nullptr
+ * \return the read data
+ */
+ template<typename T> T readBin(std::istream& is, T* obj = nullptr);
};
#endif // XDF_H
=====================================
xdf.pro
=====================================
@@ -3,6 +3,7 @@ QT -= gui
TARGET = xdf
TEMPLATE = lib
CONFIG += c++11 shared_and_static build_all
+INCLUDEPATH += pugixml
QMAKE_CFLAGS += -std=c99
View it on GitLab: https://salsa.debian.org/med-team/libxdf/-/compare/d9e21947c9050b1377a0ff7acdc55cc1fa401e63...7825557ce7457596c840540a9737fa442436d836
--
View it on GitLab: https://salsa.debian.org/med-team/libxdf/-/compare/d9e21947c9050b1377a0ff7acdc55cc1fa401e63...7825557ce7457596c840540a9737fa442436d836
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