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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>ClearMap.IO.Imaris — ClearMap 0.9.2 documentation</title>
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<h1>Source code for ClearMap.IO.Imaris</h1><div class="highlight"><pre>
<span class="c"># -*- coding: utf-8 -*-</span>
<span class="sd">"""</span>
<span class="sd">Interface to Imaris Files </span>
<span class="sd">Module to read data and write points to `Imaris <http://www.bitplane.com/imaris/imaris>`_</span>
<span class="sd">files.</span>
<span class="sd">Note: </span>
<span class="sd"> To write points without errors make sure the original file has at least one spot object! You can create a fake point in Imaris, then save the file. The point will be overwritten by ClearMap.</span>
<span class="sd">Example:</span>
<span class="sd"> >>> import os, numpy</span>
<span class="sd"> >>> import ClearMap.IO.Imaris as ims</span>
<span class="sd"> >>> from ClearMap.Settings import ClearMapPath</span>
<span class="sd"> >>> filename = os.path.join(ClearMapPath,'Test/Data/Imaris/test for spots added spot.ims') </span>
<span class="sd"> >>> ims.dataSize(filename);</span>
<span class="sd"> (256, 320, 256)</span>
<span class="sd">"""</span>
<span class="c">#:copyright: Copyright 2015 by Christoph Kirst, The Rockefeller University, New York City</span>
<span class="c">#:license: GNU, see LICENSE.txt for details.</span>
<span class="c">#Todo: </span>
<span class="c"># * Fix writing new spots to imaris file</span>
<span class="c"># * Get settings to directly render points as 'pixel' and not as spheres</span>
<span class="kn">import</span> <span class="nn">h5py</span>
<span class="kn">import</span> <span class="nn">numpy</span>
<span class="kn">import</span> <span class="nn">ClearMap.IO</span> <span class="kn">as</span> <span class="nn">io</span>
<div class="viewcode-block" id="openFile"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.openFile">[docs]</a><span class="k">def</span> <span class="nf">openFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">mode</span> <span class="o">=</span> <span class="s">"a"</span><span class="p">):</span>
<span class="sd">"""Open Imaris file as hdf5 object</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> filename (str): file name</span>
<span class="sd"> mode (str): argument to h5py.File</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> object: h5py object</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">mode</span><span class="p">);</span></div>
<div class="viewcode-block" id="closeFile"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.closeFile">[docs]</a><span class="k">def</span> <span class="nf">closeFile</span><span class="p">(</span><span class="n">h5file</span><span class="p">):</span>
<span class="sd">"""Close Imaris hdf5 file object</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> h5file (object): h5py opject</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> bool: success</span>
<span class="sd"> """</span>
<span class="k">return</span> <span class="n">h5file</span><span class="o">.</span><span class="n">close</span><span class="p">();</span></div>
<div class="viewcode-block" id="readDataSet"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.readDataSet">[docs]</a><span class="k">def</span> <span class="nf">readDataSet</span><span class="p">(</span><span class="n">h5file</span><span class="p">,</span> <span class="n">resolution</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">channel</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">timepoint</span> <span class="o">=</span> <span class="mi">0</span><span class="p">):</span>
<span class="sd">"""Open Imaris file and returns hdf5 image data</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> h5file (object): h5py object</span>
<span class="sd"> resolution (int): resolution level</span>
<span class="sd"> channel (int): color channel</span>
<span class="sd"> timepoint (int): time point</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> array: image data</span>
<span class="sd"> """</span>
<span class="n">dsname</span> <span class="o">=</span> <span class="s">"/DataSet/ResolutionLevel "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">resolution</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/TimePoint "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">timepoint</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/Channel "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">channel</span><span class="p">)</span> <span class="o">+</span> <span class="s">"/Data"</span><span class="p">;</span>
<span class="k">return</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">dsname</span><span class="p">);</span></div>
<div class="viewcode-block" id="dataSize"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.dataSize">[docs]</a><span class="k">def</span> <span class="nf">dataSize</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">resolution</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">channel</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">timepoint</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="o">**</span><span class="n">args</span><span class="p">):</span>
<span class="sd">"""Read data size of the imaris image data set</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> filename (str): imaris file name</span>
<span class="sd"> resolution (int): resolution level</span>
<span class="sd"> channel (int): color channel</span>
<span class="sd"> timepoint (int): time point</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> tuple: image data size</span>
<span class="sd"> """</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">openFile</span><span class="p">(</span><span class="n">filename</span><span class="p">);</span>
<span class="n">ds</span> <span class="o">=</span> <span class="n">readDataSet</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">resolution</span> <span class="o">=</span> <span class="n">resolution</span><span class="p">,</span> <span class="n">channel</span> <span class="o">=</span> <span class="n">channel</span><span class="p">,</span> <span class="n">timepoint</span> <span class="o">=</span> <span class="n">timepoint</span><span class="p">);</span>
<span class="n">dims</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">ds</span><span class="o">.</span><span class="n">shape</span><span class="p">);</span>
<span class="n">dims</span> <span class="o">=</span> <span class="p">(</span><span class="n">dims</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">dims</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">dims</span><span class="p">[</span><span class="mi">0</span><span class="p">]);</span>
<span class="k">return</span> <span class="n">io</span><span class="o">.</span><span class="n">dataSizeFromDataRange</span><span class="p">(</span><span class="n">dims</span><span class="p">,</span> <span class="o">**</span><span class="n">args</span><span class="p">);</span></div>
<div class="viewcode-block" id="dataZSize"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.dataZSize">[docs]</a><span class="k">def</span> <span class="nf">dataZSize</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">args</span><span class="p">):</span>
<span class="sd">"""Read z data size of the imaris image data set</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> filename (str): imaris file name</span>
<span class="sd"> resolution (int): resolution level</span>
<span class="sd"> channel (int): color channel</span>
<span class="sd"> timepoint (int): time point</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> int: image z data size</span>
<span class="sd"> """</span>
<span class="n">dsize</span> <span class="o">=</span> <span class="n">dataSize</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">args</span><span class="p">);</span>
<span class="k">return</span> <span class="n">dsize</span><span class="p">[</span><span class="mi">2</span><span class="p">];</span></div>
<div class="viewcode-block" id="readData"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.readData">[docs]</a><span class="k">def</span> <span class="nf">readData</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">x</span> <span class="o">=</span> <span class="nb">all</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="nb">all</span><span class="p">,</span> <span class="n">z</span> <span class="o">=</span> <span class="nb">all</span><span class="p">,</span> <span class="n">resolution</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">channel</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">timepoint</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="o">**</span><span class="n">args</span><span class="p">):</span>
<span class="sd">"""Read data from imaris file</span>
<span class="sd"> Arguments:</span>
<span class="sd"> filename (str): file name as regular expression</span>
<span class="sd"> x,y,z (tuple): data range specifications</span>
<span class="sd"> resolution (int): resolution level</span>
<span class="sd"> channel (int): color channel</span>
<span class="sd"> timepoint (int): time point</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> array: image data</span>
<span class="sd"> """</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">"r"</span><span class="p">);</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">readDataSet</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">resolution</span> <span class="o">=</span> <span class="n">resolution</span><span class="p">,</span> <span class="n">channel</span> <span class="o">=</span> <span class="n">channel</span><span class="p">,</span> <span class="n">timepoint</span> <span class="o">=</span> <span class="n">timepoint</span><span class="p">);</span>
<span class="n">dsize</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">shape</span><span class="p">;</span>
<span class="n">rz</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">toDataRange</span><span class="p">(</span><span class="n">dsize</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">r</span> <span class="o">=</span> <span class="n">z</span><span class="p">);</span>
<span class="n">ry</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">toDataRange</span><span class="p">(</span><span class="n">dsize</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">r</span> <span class="o">=</span> <span class="n">y</span><span class="p">);</span>
<span class="n">rx</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">toDataRange</span><span class="p">(</span><span class="n">dsize</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">r</span> <span class="o">=</span> <span class="n">x</span><span class="p">);</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">dataset</span><span class="p">[</span><span class="n">rz</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">rz</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="n">ry</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">ry</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="n">rx</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span><span class="n">rx</span><span class="p">[</span><span class="mi">1</span><span class="p">]];</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">transpose</span><span class="p">((</span><span class="mi">2</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">));</span> <span class="c"># imaris stores files in reverse x,y,z ordering</span>
<span class="c">#data = dataset[x[0]:x[1],y[0]:y[1],z[0]:z[1]];</span>
<span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">();</span>
<span class="k">return</span> <span class="n">data</span><span class="p">;</span></div>
<div class="viewcode-block" id="getDataSize"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.getDataSize">[docs]</a><span class="k">def</span> <span class="nf">getDataSize</span><span class="p">(</span><span class="n">h5file</span><span class="p">):</span>
<span class="sd">"""Get the full data size in pixel from h5py imaris object</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> h5file (object): h5py object</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> tuple: image data size</span>
<span class="sd"> """</span>
<span class="n">pn</span> <span class="o">=</span> <span class="s">'/DataSetInfo/Image'</span><span class="p">;</span>
<span class="n">ia</span> <span class="o">=</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">pn</span><span class="p">)</span><span class="o">.</span><span class="n">attrs</span><span class="p">;</span>
<span class="n">x</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"X"</span><span class="p">]));</span>
<span class="n">y</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"Y"</span><span class="p">]));</span>
<span class="n">z</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"Z"</span><span class="p">]));</span>
<span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">]);</span></div>
<div class="viewcode-block" id="getDataExtent"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.getDataExtent">[docs]</a><span class="k">def</span> <span class="nf">getDataExtent</span><span class="p">(</span><span class="n">h5file</span><span class="p">):</span>
<span class="sd">"""Get the spatial extent of data from h5py imaris object</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> h5file (object): h5py object</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> array: spatial extend of image</span>
<span class="sd"> """</span>
<span class="n">pn</span> <span class="o">=</span> <span class="s">'/DataSetInfo/Image'</span><span class="p">;</span>
<span class="n">ia</span> <span class="o">=</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">pn</span><span class="p">)</span><span class="o">.</span><span class="n">attrs</span><span class="p">;</span>
<span class="n">x1</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"ExtMin0"</span><span class="p">]));</span>
<span class="n">y1</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"ExtMin1"</span><span class="p">]));</span>
<span class="n">z1</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"ExtMin2"</span><span class="p">]));</span>
<span class="n">x2</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"ExtMax0"</span><span class="p">]));</span>
<span class="n">y2</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"ExtMax1"</span><span class="p">]));</span>
<span class="n">z2</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">ia</span><span class="p">[</span><span class="s">"ExtMax2"</span><span class="p">]));</span>
<span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="n">x1</span><span class="p">,</span><span class="n">y1</span><span class="p">,</span><span class="n">z1</span><span class="p">],</span> <span class="p">[</span><span class="n">x2</span><span class="p">,</span><span class="n">y2</span><span class="p">,</span><span class="n">z2</span><span class="p">]]);</span></div>
<div class="viewcode-block" id="getScaleAndOffset"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.getScaleAndOffset">[docs]</a><span class="k">def</span> <span class="nf">getScaleAndOffset</span><span class="p">(</span><span class="n">h5file</span><span class="p">):</span>
<span class="sd">"""Determine scale and offset to transform pixel to spatial coordinates as used by imaris</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> h5file (object): h5py object</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> tuple: image scale (length / pixel) and offset (from origin)</span>
<span class="sd"> """</span>
<span class="n">ds</span> <span class="o">=</span> <span class="n">getDataSize</span><span class="p">(</span><span class="n">h5file</span><span class="p">);</span>
<span class="n">de</span> <span class="o">=</span> <span class="n">getDataExtent</span><span class="p">(</span><span class="n">h5file</span><span class="p">);</span>
<span class="n">sc</span> <span class="o">=</span> <span class="n">de</span><span class="p">[</span><span class="mi">1</span><span class="p">,:]</span> <span class="o">-</span> <span class="n">de</span><span class="p">[</span><span class="mi">0</span><span class="p">,:];</span>
<span class="n">sc</span> <span class="o">=</span> <span class="n">sc</span> <span class="o">/</span> <span class="n">ds</span><span class="p">;</span>
<span class="k">return</span> <span class="p">(</span><span class="n">sc</span><span class="p">,</span> <span class="n">de</span><span class="p">[</span><span class="mi">0</span><span class="p">,:]);</span></div>
<div class="viewcode-block" id="transformPointsToImaris"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.transformPointsToImaris">[docs]</a><span class="k">def</span> <span class="nf">transformPointsToImaris</span><span class="p">(</span><span class="n">points</span><span class="p">,</span> <span class="n">scale</span> <span class="o">=</span> <span class="p">(</span><span class="mf">4.0625</span><span class="p">,</span> <span class="mf">4.0625</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">offset</span> <span class="o">=</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)):</span>
<span class="sd">"""Transform pixel coordinates of cell centers to work in Imaris</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> points (array): point coordinate array</span>
<span class="sd"> scale (tuple): spatial scale of the image data</span>
<span class="sd"> offset (tuple): spatial offset of the image data</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> array: scaled points</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">scale</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">scale</span> <span class="o">=</span> <span class="p">(</span><span class="n">scale</span><span class="p">,</span> <span class="n">scale</span><span class="p">,</span> <span class="n">scale</span><span class="p">);</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">):</span>
<span class="n">points</span><span class="p">[:,</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">points</span><span class="p">[:,</span><span class="n">i</span><span class="p">]</span> <span class="o">*</span> <span class="n">scale</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">offset</span><span class="p">[</span><span class="n">i</span><span class="p">];</span>
<span class="k">return</span> <span class="n">points</span></div>
<div class="viewcode-block" id="writePoints"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.writePoints">[docs]</a><span class="k">def</span> <span class="nf">writePoints</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">points</span><span class="p">,</span> <span class="n">mode</span> <span class="o">=</span> <span class="s">"o"</span><span class="p">,</span> <span class="n">radius</span> <span class="o">=</span> <span class="mf">0.5</span><span class="p">,</span> <span class="n">scale</span> <span class="o">=</span> <span class="nb">all</span><span class="p">,</span> <span class="n">offset</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""Write points to Imaris file </span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> filename (str): imaris file name </span>
<span class="sd"> points (array): point data</span>
<span class="sd"> mode (str): 'o'= override, 'a'=add</span>
<span class="sd"> radius (float): size of each point</span>
<span class="sd"> scale (tuple or all): spatial scaling of points</span>
<span class="sd"> offset (tuple or None): spatial offset of points</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> str: file name of imaris file</span>
<span class="sd"> </span>
<span class="sd"> Note:</span>
<span class="sd"> This routine is still experimental !</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">h5file</span> <span class="o">=</span> <span class="n">openFile</span><span class="p">(</span><span class="n">filename</span><span class="p">);</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">h5file</span> <span class="o">=</span> <span class="n">filename</span><span class="p">;</span>
<span class="c">#delete Scene8 info so do not need to write it</span>
<span class="n">s8</span> <span class="o">=</span> <span class="s">"/Scene8"</span><span class="p">;</span>
<span class="k">if</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">s8</span><span class="p">)</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">del</span> <span class="n">h5file</span><span class="p">[</span><span class="n">s8</span><span class="p">];</span>
<span class="c">#get number of point sets</span>
<span class="n">ct</span> <span class="o">=</span> <span class="s">"Scene/Content"</span><span class="p">;</span>
<span class="n">ca</span> <span class="o">=</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ct</span><span class="p">)</span><span class="o">.</span><span class="n">attrs</span>
<span class="n">np</span> <span class="o">=</span> <span class="n">ca</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">"NumberOfPoints"</span><span class="p">);</span>
<span class="k">if</span> <span class="n">np</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">ca</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">"NumberOfPoints"</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dtype</span> <span class="o">=</span> <span class="s">"uint64"</span><span class="p">)</span>
<span class="n">np</span> <span class="o">=</span> <span class="mi">0</span><span class="p">;</span>
<span class="n">mode</span> <span class="o">=</span> <span class="s">"a"</span><span class="p">;</span>
<span class="c">#write points</span>
<span class="k">if</span> <span class="n">mode</span> <span class="o">==</span> <span class="s">"a"</span><span class="p">:</span> <span class="c"># add points -> need to test further</span>
<span class="c">#update number of points(4.0625, 4.0625, 3)</span>
<span class="n">np</span> <span class="o">=</span> <span class="n">np</span> <span class="o">+</span> <span class="mi">1</span><span class="p">;</span>
<span class="n">ca</span><span class="p">[</span><span class="s">"NumberOfPoints"</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="p">;</span>
<span class="c"># Create Pointset and attributes</span>
<span class="n">pn</span> <span class="o">=</span> <span class="n">ct</span> <span class="o">+</span> <span class="s">"/Points"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="o">-</span><span class="mi">1</span><span class="p">));</span>
<span class="n">histlog</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="s">''</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'|S1'</span><span class="p">);</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="s">'Spots '</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="p">))],</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'|S'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="mi">6</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="p">)))));</span>
<span class="n">material</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span> <span class="s">'<bpMaterial mDiffusion="0.8 0.8 0.8" mSpecular="0.2 0.2 0.2" mEmission="0 0 0" mAmbient="0 0 0" mTransparency="0" mShinyness="0.1"/></span><span class="se">\n</span><span class="s">'</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'|S133'</span><span class="p">);</span>
<span class="n">iid</span> <span class="o">=</span> <span class="mi">200000</span> <span class="o">+</span> <span class="n">np</span> <span class="c"># int64</span>
<span class="n">unit</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="s">'um'</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'|S2'</span><span class="p">);</span>
<span class="n">descrp</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="s">''</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'|S1'</span><span class="p">);</span>
<span class="n">pg</span> <span class="o">=</span> <span class="n">h5file</span><span class="o">.</span><span class="n">create_group</span><span class="p">(</span><span class="n">pn</span><span class="p">);</span>
<span class="n">pa</span> <span class="o">=</span> <span class="n">pg</span><span class="o">.</span><span class="n">attrs</span><span class="p">;</span>
<span class="n">pa</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">"HistoryLog"</span><span class="p">,</span> <span class="n">histlog</span><span class="p">);</span>
<span class="n">pa</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">"Name"</span><span class="p">,</span> <span class="n">name</span><span class="p">);</span>
<span class="n">pa</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">"Material"</span><span class="p">,</span> <span class="n">material</span><span class="p">);</span>
<span class="n">pa</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">"Id"</span><span class="p">,</span> <span class="n">iid</span><span class="p">,</span> <span class="n">dtype</span> <span class="o">=</span> <span class="s">'uint64'</span><span class="p">);</span>
<span class="n">pa</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">"Unit"</span><span class="p">,</span> <span class="n">unit</span><span class="p">);</span>
<span class="n">pa</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">"Description"</span><span class="p">,</span> <span class="n">descrp</span><span class="p">);</span>
<span class="c">#add TimeInfos</span>
<span class="n">tb</span> <span class="o">=</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'DataSetTimes/TimeBegin'</span><span class="p">);</span>
<span class="n">tb</span> <span class="o">=</span> <span class="n">tb</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">];</span>
<span class="c">#del h5file[pn + "/TimeInfos"]</span>
<span class="n">h5file</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="n">pn</span> <span class="o">+</span> <span class="s">"/TimeInfos"</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">tb</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">23</span><span class="p">]],</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'|S23'</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">pn</span> <span class="o">=</span> <span class="n">ct</span> <span class="o">+</span> <span class="s">"/Points"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">np</span><span class="o">-</span><span class="mi">1</span><span class="p">));</span>
<span class="c"># make points</span>
<span class="n">npts</span> <span class="o">=</span> <span class="n">points</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">];</span>
<span class="k">if</span> <span class="n">points</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="mi">3</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">StandardError</span><span class="p">(</span><span class="s">"Points shape is not (n,3)!"</span><span class="p">);</span>
<span class="c">#points = points[:,[0,1,2]]; # todo: check exchange of coordinates</span>
<span class="c">#scale points frfom pixel to </span>
<span class="k">if</span> <span class="n">scale</span> <span class="ow">is</span> <span class="nb">all</span><span class="p">:</span> <span class="c"># automatically determine scaling for points </span>
<span class="p">(</span><span class="n">scale</span><span class="p">,</span> <span class="n">offset</span><span class="p">)</span> <span class="o">=</span> <span class="n">getScaleAndOffset</span><span class="p">(</span><span class="n">h5file</span><span class="p">);</span>
<span class="k">if</span> <span class="n">offset</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">offset</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">]);</span>
<span class="n">pointsS</span> <span class="o">=</span> <span class="n">points</span><span class="o">.</span><span class="n">copy</span><span class="p">();</span>
<span class="n">pointsS</span> <span class="o">=</span> <span class="n">transformPointsToImaris</span><span class="p">(</span><span class="n">pointsS</span><span class="p">,</span> <span class="n">scale</span> <span class="o">=</span> <span class="n">scale</span><span class="p">,</span> <span class="n">offset</span> <span class="o">=</span> <span class="n">offset</span><span class="p">);</span>
<span class="k">print</span> <span class="n">pointsS</span>
<span class="n">pts</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">c_</span><span class="p">[</span><span class="n">pointsS</span><span class="p">,</span> <span class="n">radius</span> <span class="o">*</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="n">npts</span><span class="p">)];</span>
<span class="n">ts</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">npts</span><span class="p">);</span>
<span class="c"># write points</span>
<span class="n">pnt</span> <span class="o">=</span> <span class="n">pn</span> <span class="o">+</span> <span class="s">'/Time'</span><span class="p">;</span>
<span class="n">pnc</span> <span class="o">=</span> <span class="n">pn</span> <span class="o">+</span> <span class="s">'/CoordsXYZR'</span><span class="p">;</span>
<span class="k">if</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">pnt</span><span class="p">)</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">del</span> <span class="n">h5file</span><span class="p">[</span><span class="n">pnt</span><span class="p">];</span>
<span class="n">h5file</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="n">pnt</span><span class="p">,</span> <span class="n">shape</span><span class="o">=</span><span class="p">(</span><span class="n">npts</span><span class="p">,</span><span class="mi">1</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'i64'</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">ts</span><span class="p">);</span>
<span class="k">if</span> <span class="n">h5file</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">pnc</span><span class="p">)</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">del</span> <span class="n">h5file</span><span class="p">[</span><span class="n">pnc</span><span class="p">];</span>
<span class="n">h5file</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span><span class="n">pnc</span><span class="p">,</span> <span class="n">shape</span><span class="o">=</span><span class="n">pts</span><span class="o">.</span><span class="n">shape</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="s">'f32'</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">pts</span><span class="p">);</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">h5file</span><span class="o">.</span><span class="n">close</span><span class="p">();</span>
<span class="k">return</span> <span class="n">filename</span><span class="p">;</span></div>
<div class="viewcode-block" id="writeData"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.writeData">[docs]</a><span class="k">def</span> <span class="nf">writeData</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">args</span><span class="p">):</span>
<span class="sd">"""Write image data to imaris file</span>
<span class="sd"> </span>
<span class="sd"> Note:</span>
<span class="sd"> Not implemented yet !</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Writing data to imaris file not implemented yet"""</span><span class="p">)</span></div>
<div class="viewcode-block" id="readPoints"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.readPoints">[docs]</a><span class="k">def</span> <span class="nf">readPoints</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="sd">"""Read points from imaris file</span>
<span class="sd"> </span>
<span class="sd"> Note:</span>
<span class="sd"> Not implemented yet !</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Reading points form imaris file not implemented yet"""</span><span class="p">)</span></div>
<div class="viewcode-block" id="copyData"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.copyData">[docs]</a><span class="k">def</span> <span class="nf">copyData</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">sink</span><span class="p">):</span>
<span class="sd">"""Copy a imaris file from source to sink</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> source (str): file name pattern of source</span>
<span class="sd"> sink (str): file name pattern of sink</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> str: file name patttern of the copy</span>
<span class="sd"> """</span>
<span class="n">io</span><span class="o">.</span><span class="n">copyFile</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">sink</span><span class="p">);</span></div>
<div class="viewcode-block" id="test"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.Imaris.test">[docs]</a><span class="k">def</span> <span class="nf">test</span><span class="p">():</span>
<span class="sd">"""Test Imaris module"""</span>
<span class="kn">import</span> <span class="nn">ClearMap.IO.Imaris</span> <span class="kn">as</span> <span class="nn">self</span>
<span class="nb">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">ClearMap.Settings</span> <span class="kn">import</span> <span class="n">ClearMapPath</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">numpy</span>
<span class="n">basedir</span> <span class="o">=</span> <span class="n">ClearMapPath</span><span class="p">;</span>
<span class="n">fn</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basedir</span><span class="p">,</span><span class="s">'Test/Data/Imaris/test for spots with spot.ims'</span><span class="p">)</span>
<span class="n">fn</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basedir</span><span class="p">,</span><span class="s">'Test/Data/Imaris/test for spots added spot.ims'</span><span class="p">)</span>
<span class="kn">import</span> <span class="nn">h5py</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="n">fn</span><span class="p">,</span> <span class="s">"a"</span><span class="p">);</span>
<span class="n">dsname</span> <span class="o">=</span> <span class="s">"/DataSet/ResolutionLevel 0/TimePoint 0/Channel 0/Data"</span>
<span class="n">ds</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">dsname</span><span class="p">)</span>
<span class="k">print</span> <span class="n">ds</span><span class="o">.</span><span class="n">shape</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">rand</span><span class="p">(</span><span class="mi">20</span><span class="p">,</span><span class="mi">50</span><span class="p">,</span><span class="mi">10</span><span class="p">);</span>
<span class="n">data</span><span class="p">[</span><span class="mi">5</span><span class="p">:</span><span class="mi">15</span><span class="p">,</span> <span class="mi">20</span><span class="p">:</span><span class="mi">45</span><span class="p">,</span> <span class="mi">2</span><span class="p">:</span><span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span><span class="p">;</span>
<span class="n">data</span> <span class="o">=</span> <span class="mi">20</span> <span class="o">*</span> <span class="n">data</span><span class="p">;</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s">'int32'</span><span class="p">);</span>
<span class="c">#reload(self)</span>
<span class="k">print</span> <span class="s">"writing raw image to: "</span> <span class="o">+</span> <span class="n">fn</span><span class="p">;</span>
<span class="bp">self</span><span class="o">.</span><span class="n">writeData</span><span class="p">(</span><span class="n">fn</span><span class="p">,</span> <span class="n">data</span><span class="p">);</span></div>
<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span>
<span class="n">test</span><span class="p">();</span>
<span class="c">##Misc Code</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c"># import h5py </span>
<span class="c"># </span>
<span class="c"># fn = "/home/ckirst/Data/Science/Projects/BrainActivityMap/iDISCO_2015_06/Adult cfos all shaved 20HF 150523.ims";</span>
<span class="c"># </span>
<span class="c"># dsname = "/DataSet/ResolutionLevel 4/TimePoint 0/Channel 0/Data"</span>
<span class="c">#</span>
<span class="c"># </span>
<span class="c"># f = h5py.File(fn, "a");</span>
<span class="c"># ds = f.get(dsname)</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c"># fn = "/home/ckirst/Data/Science/Projects/BrainActivityMap/ImarisTest/test for spots added spot.ims";</span>
<span class="c"># f = h5py.File(fn, "a");</span>
<span class="c">#</span>
<span class="c">#### write spots to file with spots</span>
<span class="c">#</span>
<span class="c">##Scene</span>
<span class="c">#pn = '/Scene/Content/Points0'</span>
<span class="c">#</span>
<span class="c">#pnt = pn + '/Time';</span>
<span class="c">#pnc = pn + '/CoordsXYZR';</span>
<span class="c">#</span>
<span class="c">#pts = numpy.arange(1, 10);</span>
<span class="c">#npts = pts.size;</span>
<span class="c">#</span>
<span class="c">#pts = numpy.array([1900 + 50 * numpy.sin(2 * numpy.pi * pts / npts), 2000 + 50 * numpy.cos(2 * numpy.pi * pts / npts), 1700 + numpy.zeros(npts), 2.5 + numpy.zeros(npts)])</span>
<span class="c">#pts = numpy.transpose(pts);</span>
<span class="c">#t = numpy.zeros(npts);</span>
<span class="c">#</span>
<span class="c">#del f[pnt]</span>
<span class="c">#dt = f.create_dataset(pnt, shape=(npts,1), dtype='i64', data=t)</span>
<span class="c">#</span>
<span class="c">#del f[pnc]</span>
<span class="c">#dc = f.create_dataset(pnc, shape=pts.shape, dtype='f32', data=pts)</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c">#fn = '/home/nicolas/Windows/Nico/cfosRegistrations/Adult cfos C row 20HF 150524.ims';</span>
<span class="c">#</span>
<span class="c">##</span>
<span class="c">#pts = np.arange(1, 10);</span>
<span class="c">#npts = pts.size;</span>
<span class="c">#</span>
<span class="c">#pts2 = np.array([1900 + 50 * np.sin(2 * np.pi * pts / npts), 2000 + 50 * np.cos(2 * np.pi * pts / npts), 1700 + np.zeros(npts), 2.5 + np.zeros(npts)])</span>
<span class="c">#pts2 = np.transpose(pts2);</span>
<span class="c">#t = np.zeros(npts);</span>
<span class="c">#</span>
<span class="c">#ti = '2015-03-13 21:16:16.000';</span>
<span class="c">#ti = np.array([ti.encode("ascii", "ignore")])</span>
<span class="c">#</span>
<span class="c">## open hdf5 file</span>
<span class="c">#f = h5py.File(fn, "a")</span>
<span class="c">#dt = f.create_dataset(pnt, shape=(npts,1), dtype='i64', data=t)</span>
<span class="c">#dc = f.create_dataset(pnc, shape=pts2.shape, dtype='f32', data=pts2)</span>
<span class="c">#di = f.create_dataset(pni, data = ti)</span>
<span class="c">#</span>
<span class="c">##attributes</span>
<span class="c">#</span>
<span class="c">#f.close()</span>
</pre></div>
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