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<h1>Source code for hdf5storage.lowlevel</h1><div class="highlight"><pre>
<span></span><span class="c1"># Copyright (c) 2013-2016, Freja Nordsiek</span>
<span class="c1"># All rights reserved.</span>
<span class="c1">#</span>
<span class="c1"># Redistribution and use in source and binary forms, with or without</span>
<span class="c1"># modification, are permitted provided that the following conditions are</span>
<span class="c1"># met:</span>
<span class="c1">#</span>
<span class="c1"># 1. Redistributions of source code must retain the above copyright</span>
<span class="c1"># notice, this list of conditions and the following disclaimer.</span>
<span class="c1">#</span>
<span class="c1"># 2. Redistributions in binary form must reproduce the above copyright</span>
<span class="c1"># notice, this list of conditions and the following disclaimer in the</span>
<span class="c1"># documentation and/or other materials provided with the distribution.</span>
<span class="c1">#</span>
<span class="c1"># THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS</span>
<span class="c1"># "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT</span>
<span class="c1"># LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR</span>
<span class="c1"># A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT</span>
<span class="c1"># HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,</span>
<span class="c1"># SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT</span>
<span class="c1"># LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,</span>
<span class="c1"># DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY</span>
<span class="c1"># THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</span>
<span class="c1"># (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</span>
<span class="c1"># OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span>
<span class="sd">""" Module of Exceptions and low level read and write functions.</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">posixpath</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">h5py</span>
<span class="kn">from</span> <span class="nn">hdf5storage.utilities</span> <span class="k">import</span> <span class="o">*</span>
<div class="viewcode-block" id="Hdf5storageError"><a class="viewcode-back" href="../../hdf5storage.lowlevel.html#hdf5storage.lowlevel.Hdf5storageError">[docs]</a><span class="k">class</span> <span class="nc">Hdf5storageError</span><span class="p">(</span><span class="ne">IOError</span><span class="p">):</span>
<span class="sd">""" Base class of hdf5storage package exceptions."""</span>
<span class="k">pass</span></div>
<div class="viewcode-block" id="CantReadError"><a class="viewcode-back" href="../../hdf5storage.lowlevel.html#hdf5storage.lowlevel.CantReadError">[docs]</a><span class="k">class</span> <span class="nc">CantReadError</span><span class="p">(</span><span class="n">Hdf5storageError</span><span class="p">):</span>
<span class="sd">""" Exception for a failure to read the desired data."""</span>
<span class="k">pass</span></div>
<div class="viewcode-block" id="TypeNotMatlabCompatibleError"><a class="viewcode-back" href="../../hdf5storage.lowlevel.html#hdf5storage.lowlevel.TypeNotMatlabCompatibleError">[docs]</a><span class="k">class</span> <span class="nc">TypeNotMatlabCompatibleError</span><span class="p">(</span><span class="n">Hdf5storageError</span><span class="p">):</span>
<span class="sd">""" Exception for trying to write non-MATLAB compatible data.</span>
<span class="sd"> In the event that MATLAB compatibility is being done</span>
<span class="sd"> (``Options.matlab_compatible``) and a Python type is not importable</span>
<span class="sd"> by MATLAB, the data is either not written or this exception is</span>
<span class="sd"> thrown depending on the value of</span>
<span class="sd"> ``Options.action_for_matlab_incompatible``.</span>
<span class="sd"> See Also</span>
<span class="sd"> --------</span>
<span class="sd"> hdf5storage.Options.matlab_compatible</span>
<span class="sd"> hdf5storage.Options.action_for_matlab_incompatible</span>
<span class="sd"> """</span>
<span class="k">pass</span></div>
<div class="viewcode-block" id="write_data"><a class="viewcode-back" href="../../hdf5storage.lowlevel.html#hdf5storage.lowlevel.write_data">[docs]</a><span class="k">def</span> <span class="nf">write_data</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">grp</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">type_string</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="sd">""" Writes a piece of data into an open HDF5 file.</span>
<span class="sd"> Low level function to store a Python type (`data`) into the</span>
<span class="sd"> specified Group.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> f : h5py.File</span>
<span class="sd"> The open HDF5 file.</span>
<span class="sd"> grp : h5py.Group or h5py.File</span>
<span class="sd"> The Group to place the data in.</span>
<span class="sd"> name : str</span>
<span class="sd"> The name to write the data to.</span>
<span class="sd"> data : any</span>
<span class="sd"> The data to write.</span>
<span class="sd"> type_string : str or None</span>
<span class="sd"> The type string of the data, or ``None`` to deduce</span>
<span class="sd"> automatically.</span>
<span class="sd"> options : hdf5storage.core.Options</span>
<span class="sd"> The options to use when writing.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> NotImplementedError</span>
<span class="sd"> If writing `data` is not supported.</span>
<span class="sd"> TypeNotMatlabCompatibleError</span>
<span class="sd"> If writing a type not compatible with MATLAB and</span>
<span class="sd"> `options.action_for_matlab_incompatible` is set to ``'error'``.</span>
<span class="sd"> See Also</span>
<span class="sd"> --------</span>
<span class="sd"> hdf5storage.core.write : Higher level version.</span>
<span class="sd"> read_data</span>
<span class="sd"> hdf5storage.core.Options</span>
<span class="sd"> """</span>
<span class="c1"># Get the marshaller for type(data).</span>
<span class="n">tp</span> <span class="o">=</span> <span class="nb">type</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">marshaller_collection</span><span class="o">.</span><span class="n">get_marshaller_for_type</span><span class="p">(</span><span class="n">tp</span><span class="p">)</span>
<span class="c1"># If a marshaller was found, use it to write the data. Otherwise,</span>
<span class="c1"># return an error. If we get something other than None back, then we</span>
<span class="c1"># must recurse through the entries. Also, we must set the H5PATH</span>
<span class="c1"># attribute to be the path to the containing group.</span>
<span class="k">if</span> <span class="n">m</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">m</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">grp</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">type_string</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s1">'Can''t write data type: '</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">tp</span><span class="p">))</span></div>
<div class="viewcode-block" id="read_data"><a class="viewcode-back" href="../../hdf5storage.lowlevel.html#hdf5storage.lowlevel.read_data">[docs]</a><span class="k">def</span> <span class="nf">read_data</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">grp</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">options</span><span class="p">):</span>
<span class="sd">""" Writes a piece of data into an open HDF5 file.</span>
<span class="sd"> Low level function to read a Python type of the specified name from</span>
<span class="sd"> specified Group.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> f : h5py.File</span>
<span class="sd"> The open HDF5 file.</span>
<span class="sd"> grp : h5py.Group or h5py.File</span>
<span class="sd"> The Group to read the data from.</span>
<span class="sd"> name : str</span>
<span class="sd"> The name of the data to read.</span>
<span class="sd"> options : hdf5storage.core.Options</span>
<span class="sd"> The options to use when reading.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> data</span>
<span class="sd"> The data named `name` in Group `grp`.</span>
<span class="sd"> Raises</span>
<span class="sd"> ------</span>
<span class="sd"> CantReadError</span>
<span class="sd"> If the data cannot be read successfully.</span>
<span class="sd"> See Also</span>
<span class="sd"> --------</span>
<span class="sd"> hdf5storage.core.read : Higher level version.</span>
<span class="sd"> write_data</span>
<span class="sd"> hdf5storage.core.Options</span>
<span class="sd"> """</span>
<span class="c1"># If name isn't found, return error.</span>
<span class="k">if</span> <span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">grp</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">CantReadError</span><span class="p">(</span><span class="s1">'Could not find '</span>
<span class="o">+</span> <span class="n">posixpath</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">grp</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
<span class="c1"># Get the different attributes that can be used to identify they</span>
<span class="c1"># type, which are the type string and the MATLAB class.</span>
<span class="n">type_string</span> <span class="o">=</span> <span class="n">get_attribute_string</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="s1">'Python.Type'</span><span class="p">)</span>
<span class="n">matlab_class</span> <span class="o">=</span> <span class="n">get_attribute_string</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="n">name</span><span class="p">],</span> <span class="s1">'MATLAB_class'</span><span class="p">)</span>
<span class="c1"># If the type_string is present, get the marshaller for it. If it is</span>
<span class="c1"># not, use the one for the matlab class if it is given. Otherwise,</span>
<span class="c1"># use the fallback (NumpyScalarArrayMarshaller for both Datasets and</span>
<span class="c1"># Groups). If calls to the marshaller collection to get the right</span>
<span class="c1"># marshaller don't return one (return None), we also go to the</span>
<span class="c1"># default).</span>
<span class="n">m</span> <span class="o">=</span> <span class="kc">None</span>
<span class="n">mc</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">marshaller_collection</span>
<span class="k">if</span> <span class="n">type_string</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">mc</span><span class="o">.</span><span class="n">get_marshaller_for_type_string</span><span class="p">(</span><span class="n">type_string</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">matlab_class</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">mc</span><span class="o">.</span><span class="n">get_marshaller_for_matlab_class</span><span class="p">(</span><span class="n">matlab_class</span><span class="p">)</span>
<span class="k">if</span> <span class="n">m</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">mc</span><span class="o">.</span><span class="n">get_marshaller_for_type</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">uint8</span><span class="p">)</span>
<span class="c1"># If a marshaller was found, use it to write the data. Otherwise,</span>
<span class="c1"># return an error.</span>
<span class="k">if</span> <span class="n">m</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">grp</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">options</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">CantReadError</span><span class="p">(</span><span class="s1">'Could not read '</span> <span class="o">+</span> <span class="n">grp</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">)</span></div>
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