Initial commit to github (Version 1.0.0)

.gitignore

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

README.txt

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

autohandle.h

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