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Tore Niermann
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Initial commit to github (Version 1.0.0)
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‎.gitignore

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/3rdparty/utfcpp*
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/3rdparty/zlib*
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/3rdparty/hdf5*
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/3rdparty/szip*

‎3rdparty/README.txt

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See INSTALL.txt for required contents of this directory

‎INSTALL.txt

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1. Introduction
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======================================================================
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Their are two versions of the plugin.
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* the GMS-2.X version, which is build using Visual Studio 2008
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and obviously requires the DMSDK for GMS 2.X
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* the GMS-1.X version, which is build using Visual Studio 2003
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and obviously requires the DMSDK for GMS 1.X (aka DMSDK382)
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For the DMSDKs contact Gatan or look on their website www.gatan.com.
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2. Prerequisites
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======================================================================
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The DMSDK must running work (examples will compile), so any prerequisites
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for the DMSDK (e.g. boost) must be properly installed.
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The plugin depends on some 3rdparty libraries (for example the HDF5 library...).
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These must be separately downloaded and unpacked or linked to the directory
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names mentioned below
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Required libraries:
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utfcpp
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* see http://utfcpp.sourceforge.net
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* version 2.3.1A was used for building the plugin
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* unpack to 3rdparty/utfcpp
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zlib
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* see http://zlib.org
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* version 1.2.8 was used for building the plugin
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* unpack to 3rdparty/zlib
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szip
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* see http://www.hdfgroup.org/HDF5
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* version version 2.1 was used for building the plugin
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* unpack to 3rdparty/szip
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* As there are special licensing issues with this library, the
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compression is disabled by the build instructions below. The
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decompression has no licensing problems.
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hdf5
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* see http//www.hdfgroup.org/HDF5
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* Version 1.8.8 was used for the GMS-2.X plugin
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* Version 1.8.3 was used for the GMS-1.X plugin, due to the needed
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VS2003 support)
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* unpack to 3rdparty/hdf5
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3. Building
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======================================================================
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3.1 Build zlib
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--------------------------------------------------------------
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This can be done from the Visual Studio command prompt. Go to the
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3rdparty/zlib directory and execute either
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nmake -f win32/Makefile.msc LOC="-DASMV -DASMINF" OBJA="inffas32.obj match686.obj"
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or
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nmake -f win32/Makefile.msc
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3.2 Build szip
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--------------------------------------------------------------
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For GMS-1.X:
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* Copy the vc2003/szip_static_vs2003.vcproj file to 3rdparty/szip/window/static
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* Open the 3rdparty/szip/windows/static/szip_static_vs2003.vcproj in Visual Studio 2003.
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For GMS-2.X:
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* Open the 3rdparty/szip/windows/static/szip_static.vcproj in Visual Studio 2008.
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The following steps are for both versions:
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* Remove line "#define HAVE_ENCODING" in SZconfig.h
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* Build the Release build
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3.3 Build hdf5
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--------------------------------------------------------------
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* Set up environment variables
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HDF5_EXT_ZLIB=YOURDIR\3rdparty\zlib\zlib.lib
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HDF5_EXT_SZIB=YOURDIR\3rdparty\szib\windows\static\lib\Win32\Release\libszip.lib
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* Call windows\copy_hdf.bat
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* For GMS-1.X: Open windows_vnet\proj\all\all.sln with Visual Studio 2003
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For GMS-2.X: Open windows\proj\all\all.sln with Visual Studio 2008
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* In Visual Studio add to the include directories (in Tools/Options/Projects and Solutions/VC++ Directories)
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3rdparty\zlib
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3rdparty\szib\src
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* IMPORTANT: In the "Release" configuration of the projects hdf5 set the Runtime Library (under
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C/C++/Code Generation) to Multi-threaded DLL (/MD).
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* Build the hdf5 project (Release build).
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3.4 Build the plugin
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--------------------------------------------------------------
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GMS-2.X:
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* Open vc2008/hdf5_plugin.vcproj with Visual Studio 2008
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* Add your DMSDK include and library directories to the VC++ Directories
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in Visual Studio (in Tools/Options/Projects and Solutions/VC++ Directories). The
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DMSDK is usally installed to C:\ProgramData\Gatan\DMSDK
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* Build the Release build
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* You should find your plugin as vc2008/Release/hdf5_plugin.dll
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GMS-1.X:
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* Open vc2003/hdf5_plugin.vcproj with Visual Studio 2003
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* Add your DMSDK include and library directories to the VC++ Directories
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in Visual Studio (in Tools/Options/Projects/VC++ Directories).
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* Build the Release build
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* You should find your plugin as vc2003/Release/hdf5_GMS1X_x86.dll
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3.5 Building the documentation
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--------------------------------------------------------------
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The documentation requires the Sphinx Python tool (www.sphinx-doc.org).
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With Sphinx/Python properly installed, simply change into the doc
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directory and execute
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make WHATEVER
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to produce the documentation in the desired format. Call make
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without an argument to see a list of possible formats.
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Tested with Sphinx version 1.3
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4. Testing
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======================================================================
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To run the tests, the unittest.s (in tests/unittest) script must be installed in DigitalMicrograph.
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Follow the instruction accompanied with the script for installation.
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The tests access some test data files, which are also in the tests directory. In order to
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know that directory under DigitalMicrograph the tests must be immediately run after loading
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them into DigitalMicrograph. Otherwise the directory may not be discoverable anymore.
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The tests are designed to succeed under GMS-2.X. Under GMS-1.X some magic numbers and functionality
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is different. To run change the arguments of the following calls
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# Current directory
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GMS-2.X: GetApplicationDirectory(0, 0)
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GMS-1.X: GetApplicationDirectory(2, 0)
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# Temporary directory
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GMS-2.X: GetApplicationDirectory(6, 0)
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GMS-1.X: GetApplicationDirectory(3, 0)
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A known issue is that the handling of packed complex data is different and currently only works under GMS 2.X.
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5. Install
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======================================================================
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The Visual Studio project files are designed to produce different outputs, depending on the
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combination of target GMS version and platform. The plugins produced are:
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GMS-1.X (32 bit): vc2008\Release\hdf5_GMS1X_x86.dll
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GMS-2.X (32 bit): vc2008\Release\hdf5_GMS2X_x86.dll
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GMS-2.X (64 bit): vc2008\x64\Release\hdf5_GMS2X_amd64.dll
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For installation simply copy the correct DLL file into the plugin directory of your Digital
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Micrograph installation. By default these are:
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GMS-2.X: c:\ProgramData\Gatan\Plugins
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GMS-1.X: c:\Program Files\Gatan\DigitalMicrograph\Plugins

‎README.txt

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HDF5 Plugin for DigitalMicrograph
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=================================
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This is a plugin allowing to read and write HDF5 files under
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DigitalMicrograph by Gatan Inc.
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Tested on
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DigitalMicrograph Version 1.8.X (32 Bit)
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DigitalMicrograph Version 2.3.X (32 Bit)
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Usage
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=====
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The plugin provides functions to be called from the DigitalMicrograph
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scripting language. An example script which can be installed into the
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menu for importing HDF5 files is provided under
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tests/CMD_import_hdf5.s
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For details of the functions the plugin provides,
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see documentation in the doc/ directory.
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Building and Installation
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=========================
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For building instruction see INSTALL.txt file.
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Copyright
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=========
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The plugin itself is licensed under GPL v3+ (see below). Other parts of
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this software have different licenses. See the license information
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in the documentation for details.
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HDF5 Plugin for DigitalMicrograph
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Copyright (C) 2012-2016 Tore Niermann
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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* For copyright / license information see doc/license.rst file.
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Disclaimer
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==========
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All product and company names are trademarks or registered trademarks of
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their respective holders. Use of them does not imply any affiliation
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with or endorsement by them.
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Author & Contact
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================
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The plugin was written by Tore Niermann.
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Email: niermann at physik.tu-berlin.de

‎autohandle.h

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#ifndef HDF5_AUTOHANDLE_INC
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#define HDF5_AUTOHANDLE_INC
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#include <hdf5.h>
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#include <algorithm>
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// Forwards
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void debug(const char* fmt, ...);
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typedef herr_t (*auto_handle_closer_t)(hid_t);
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/**
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* A wrapper class for HDF5 handles (hid_t), that provides RAII semantics.
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* The class interface is designed like auto_ptr.
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* No method throws an exception.
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*/
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template <auto_handle_closer_t closer> class auto_handle
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{
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private:
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hid_t hid;
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public:
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/** Default CTOR: Creates invalid handle. */
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auto_handle() throw (): hid(-1) {}
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/** Copy CTOR: Transfers handle ownership to the newly created handle. */
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auto_handle(auto_handle<closer>& h) throw () : hid(h.hid) { h.hid = -1; }
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/** Create handle from hid_t. */
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explicit auto_handle(hid_t id) throw () : hid(id)
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{
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// if (valid())
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// debug("CREATE %s hid=%x\n", typeid(*this).name(), hid);
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}
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// DTOR
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~auto_handle() throw ()
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{
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if (valid()) {
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// debug("DESTROY %s hid=%x\n", typeid(*this).name(), hid);
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closer(hid);
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}
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}
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/** Assign handle. Ownership is transferred to this class. */
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auto_handle& operator=(auto_handle<closer>& h) throw ()
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{
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reset(h.release());
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return *this;
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}
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/** Returns true, if this is a valid handle */
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bool valid() const throw () { return hid >= 0; }
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/** Swaps to handles. */
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void swap(auto_handle<closer>& h) throw () { std::swap(hid, h.hid); }
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/** Resets this handle to a new value. */
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void reset(hid_t id = -1) throw ()
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{
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auto_handle<closer> tmp(id);
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swap(tmp);
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}
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/** Returns handle id */
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hid_t get() const throw () { return hid; }
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/** Releases handle id. This is an invalid handle afterwards. */
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hid_t release() throw ()
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{
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hid_t id = hid;
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hid = -1;
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return id;
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}
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};
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template <auto_handle_closer_t closer>
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inline void swap(auto_handle<closer>& h1, auto_handle<closer>&h2)
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{
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h1.swap(h2);
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}
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typedef auto_handle<H5Oclose> object_handle_t;
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typedef auto_handle<H5Tclose> type_handle_t;
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typedef auto_handle<H5Sclose> space_handle_t;
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typedef auto_handle<H5Aclose> attr_handle_t;
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typedef auto_handle<H5Fclose> file_handle_t;
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typedef auto_handle<H5Dclose> dataset_handle_t;
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typedef auto_handle<H5Pclose> plist_handle_t;
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typedef auto_handle<H5Gclose> group_handle_t;
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#endif // HDF5_AUTOHANDLE_INC

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