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<h1>Source code for PIL.SpiderImagePlugin</h1><div class="highlight"><pre>
<span></span><span class="c1">#</span>
<span class="c1"># The Python Imaging Library.</span>
<span class="c1">#</span>
<span class="c1"># SPIDER image file handling</span>
<span class="c1">#</span>
<span class="c1"># History:</span>
<span class="c1"># 2004-08-02 Created BB</span>
<span class="c1"># 2006-03-02 added save method</span>
<span class="c1"># 2006-03-13 added support for stack images</span>
<span class="c1">#</span>
<span class="c1"># Copyright (c) 2004 by Health Research Inc. (HRI) RENSSELAER, NY 12144.</span>
<span class="c1"># Copyright (c) 2004 by William Baxter.</span>
<span class="c1"># Copyright (c) 2004 by Secret Labs AB.</span>
<span class="c1"># Copyright (c) 2004 by Fredrik Lundh.</span>
<span class="c1">#</span>
<span class="c1">##</span>
<span class="c1"># Image plugin for the Spider image format. This format is is used</span>
<span class="c1"># by the SPIDER software, in processing image data from electron</span>
<span class="c1"># microscopy and tomography.</span>
<span class="c1">##</span>
<span class="c1">#</span>
<span class="c1"># SpiderImagePlugin.py</span>
<span class="c1">#</span>
<span class="c1"># The Spider image format is used by SPIDER software, in processing</span>
<span class="c1"># image data from electron microscopy and tomography.</span>
<span class="c1">#</span>
<span class="c1"># Spider home page:</span>
<span class="c1"># https://spider.wadsworth.org/spider_doc/spider/docs/spider.html</span>
<span class="c1">#</span>
<span class="c1"># Details about the Spider image format:</span>
<span class="c1"># https://spider.wadsworth.org/spider_doc/spider/docs/image_doc.html</span>
<span class="c1">#</span>
<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">print_function</span>
<span class="kn">from</span> <span class="nn">PIL</span> <span class="k">import</span> <span class="n">Image</span><span class="p">,</span> <span class="n">ImageFile</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">struct</span>
<span class="kn">import</span> <span class="nn">sys</span>
<div class="viewcode-block" id="isInt"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.isInt">[docs]</a><span class="k">def</span> <span class="nf">isInt</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">i</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
<span class="k">if</span> <span class="n">f</span><span class="o">-</span><span class="n">i</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="mi">0</span>
<span class="k">except</span> <span class="p">(</span><span class="ne">ValueError</span><span class="p">,</span> <span class="ne">OverflowError</span><span class="p">):</span>
<span class="k">return</span> <span class="mi">0</span></div>
<span class="n">iforms</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="o">-</span><span class="mi">11</span><span class="p">,</span> <span class="o">-</span><span class="mi">12</span><span class="p">,</span> <span class="o">-</span><span class="mi">21</span><span class="p">,</span> <span class="o">-</span><span class="mi">22</span><span class="p">]</span>
<span class="c1"># There is no magic number to identify Spider files, so just check a</span>
<span class="c1"># series of header locations to see if they have reasonable values.</span>
<span class="c1"># Returns no. of bytes in the header, if it is a valid Spider header,</span>
<span class="c1"># otherwise returns 0</span>
<div class="viewcode-block" id="isSpiderHeader"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.isSpiderHeader">[docs]</a><span class="k">def</span> <span class="nf">isSpiderHeader</span><span class="p">(</span><span class="n">t</span><span class="p">):</span>
<span class="n">h</span> <span class="o">=</span> <span class="p">(</span><span class="mi">99</span><span class="p">,)</span> <span class="o">+</span> <span class="n">t</span> <span class="c1"># add 1 value so can use spider header index start=1</span>
<span class="c1"># header values 1,2,5,12,13,22,23 should be integers</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">12</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="mi">22</span><span class="p">,</span> <span class="mi">23</span><span class="p">]:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">isInt</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="n">i</span><span class="p">]):</span>
<span class="k">return</span> <span class="mi">0</span>
<span class="c1"># check iform</span>
<span class="n">iform</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span>
<span class="k">if</span> <span class="n">iform</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">iforms</span><span class="p">:</span>
<span class="k">return</span> <span class="mi">0</span>
<span class="c1"># check other header values</span>
<span class="n">labrec</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">13</span><span class="p">])</span> <span class="c1"># no. records in file header</span>
<span class="n">labbyt</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">22</span><span class="p">])</span> <span class="c1"># total no. of bytes in header</span>
<span class="n">lenbyt</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">23</span><span class="p">])</span> <span class="c1"># record length in bytes</span>
<span class="k">if</span> <span class="n">labbyt</span> <span class="o">!=</span> <span class="p">(</span><span class="n">labrec</span> <span class="o">*</span> <span class="n">lenbyt</span><span class="p">):</span>
<span class="k">return</span> <span class="mi">0</span>
<span class="c1"># looks like a valid header</span>
<span class="k">return</span> <span class="n">labbyt</span></div>
<div class="viewcode-block" id="isSpiderImage"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.isSpiderImage">[docs]</a><span class="k">def</span> <span class="nf">isSpiderImage</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">'rb'</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
<span class="n">f</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">92</span><span class="p">)</span> <span class="c1"># read 23 * 4 bytes</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">'>23f'</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span> <span class="c1"># try big-endian first</span>
<span class="n">hdrlen</span> <span class="o">=</span> <span class="n">isSpiderHeader</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
<span class="k">if</span> <span class="n">hdrlen</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">'<23f'</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span> <span class="c1"># little-endian</span>
<span class="n">hdrlen</span> <span class="o">=</span> <span class="n">isSpiderHeader</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
<span class="k">return</span> <span class="n">hdrlen</span></div>
<div class="viewcode-block" id="SpiderImageFile"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.SpiderImageFile">[docs]</a><span class="k">class</span> <span class="nc">SpiderImageFile</span><span class="p">(</span><span class="n">ImageFile</span><span class="o">.</span><span class="n">ImageFile</span><span class="p">):</span>
<span class="nb">format</span> <span class="o">=</span> <span class="s2">"SPIDER"</span>
<span class="n">format_description</span> <span class="o">=</span> <span class="s2">"Spider 2D image"</span>
<span class="n">_close_exclusive_fp_after_loading</span> <span class="o">=</span> <span class="kc">False</span>
<span class="k">def</span> <span class="nf">_open</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="c1"># check header</span>
<span class="n">n</span> <span class="o">=</span> <span class="mi">27</span> <span class="o">*</span> <span class="mi">4</span> <span class="c1"># read 27 float values</span>
<span class="n">f</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">n</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bigendian</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">'>27f'</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span> <span class="c1"># try big-endian first</span>
<span class="n">hdrlen</span> <span class="o">=</span> <span class="n">isSpiderHeader</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
<span class="k">if</span> <span class="n">hdrlen</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">bigendian</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">struct</span><span class="o">.</span><span class="n">unpack</span><span class="p">(</span><span class="s1">'<27f'</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span> <span class="c1"># little-endian</span>
<span class="n">hdrlen</span> <span class="o">=</span> <span class="n">isSpiderHeader</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
<span class="k">if</span> <span class="n">hdrlen</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s2">"not a valid Spider file"</span><span class="p">)</span>
<span class="k">except</span> <span class="n">struct</span><span class="o">.</span><span class="n">error</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s2">"not a valid Spider file"</span><span class="p">)</span>
<span class="n">h</span> <span class="o">=</span> <span class="p">(</span><span class="mi">99</span><span class="p">,)</span> <span class="o">+</span> <span class="n">t</span> <span class="c1"># add 1 value : spider header index starts at 1</span>
<span class="n">iform</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span>
<span class="k">if</span> <span class="n">iform</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s2">"not a Spider 2D image"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_size</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">12</span><span class="p">]),</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="c1"># size in pixels (width, height)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">istack</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">24</span><span class="p">])</span>
<span class="bp">self</span><span class="o">.</span><span class="n">imgnumber</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">27</span><span class="p">])</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">istack</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">imgnumber</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># stk=0, img=0: a regular 2D image</span>
<span class="n">offset</span> <span class="o">=</span> <span class="n">hdrlen</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_nimages</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">istack</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">imgnumber</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># stk>0, img=0: Opening the stack for the first time</span>
<span class="bp">self</span><span class="o">.</span><span class="n">imgbytes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">12</span><span class="p">])</span> <span class="o">*</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> <span class="o">*</span> <span class="mi">4</span>
<span class="bp">self</span><span class="o">.</span><span class="n">hdrlen</span> <span class="o">=</span> <span class="n">hdrlen</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_nimages</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">h</span><span class="p">[</span><span class="mi">26</span><span class="p">])</span>
<span class="c1"># Point to the first image in the stack</span>
<span class="n">offset</span> <span class="o">=</span> <span class="n">hdrlen</span> <span class="o">*</span> <span class="mi">2</span>
<span class="bp">self</span><span class="o">.</span><span class="n">imgnumber</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">istack</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">imgnumber</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="c1"># stk=0, img>0: an image within the stack</span>
<span class="n">offset</span> <span class="o">=</span> <span class="n">hdrlen</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">stkoffset</span>
<span class="bp">self</span><span class="o">.</span><span class="n">istack</span> <span class="o">=</span> <span class="mi">2</span> <span class="c1"># So Image knows it's still a stack</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">SyntaxError</span><span class="p">(</span><span class="s2">"inconsistent stack header values"</span><span class="p">)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bigendian</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">rawmode</span> <span class="o">=</span> <span class="s2">"F;32BF"</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">rawmode</span> <span class="o">=</span> <span class="s2">"F;32F"</span>
<span class="bp">self</span><span class="o">.</span><span class="n">mode</span> <span class="o">=</span> <span class="s2">"F"</span>
<span class="bp">self</span><span class="o">.</span><span class="n">tile</span> <span class="o">=</span> <span class="p">[</span>
<span class="p">(</span><span class="s2">"raw"</span><span class="p">,</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="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="n">offset</span><span class="p">,</span>
<span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rawmode</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="bp">self</span><span class="o">.</span><span class="n">__fp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">fp</span> <span class="c1"># FIXME: hack</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">n_frames</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nimages</span>
<span class="nd">@property</span>
<span class="k">def</span> <span class="nf">is_animated</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nimages</span> <span class="o">></span> <span class="mi">1</span>
<span class="c1"># 1st image index is zero (although SPIDER imgnumber starts at 1)</span>
<div class="viewcode-block" id="SpiderImageFile.tell"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.SpiderImageFile.tell">[docs]</a> <span class="k">def</span> <span class="nf">tell</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">imgnumber</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">return</span> <span class="mi">0</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">imgnumber</span> <span class="o">-</span> <span class="mi">1</span></div>
<div class="viewcode-block" id="SpiderImageFile.seek"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.SpiderImageFile.seek">[docs]</a> <span class="k">def</span> <span class="nf">seek</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frame</span><span class="p">):</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">istack</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">EOFError</span><span class="p">(</span><span class="s2">"attempt to seek in a non-stack file"</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_seek_check</span><span class="p">(</span><span class="n">frame</span><span class="p">):</span>
<span class="k">return</span>
<span class="bp">self</span><span class="o">.</span><span class="n">stkoffset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">hdrlen</span> <span class="o">+</span> <span class="n">frame</span> <span class="o">*</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">hdrlen</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">imgbytes</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__fp</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fp</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stkoffset</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_open</span><span class="p">()</span></div>
<span class="c1"># returns a byte image after rescaling to 0..255</span>
<div class="viewcode-block" id="SpiderImageFile.convert2byte"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.SpiderImageFile.convert2byte">[docs]</a> <span class="k">def</span> <span class="nf">convert2byte</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">depth</span><span class="o">=</span><span class="mi">255</span><span class="p">):</span>
<span class="p">(</span><span class="n">minimum</span><span class="p">,</span> <span class="n">maximum</span><span class="p">)</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getextrema</span><span class="p">()</span>
<span class="n">m</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="n">maximum</span> <span class="o">!=</span> <span class="n">minimum</span><span class="p">:</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">depth</span> <span class="o">/</span> <span class="p">(</span><span class="n">maximum</span><span class="o">-</span><span class="n">minimum</span><span class="p">)</span>
<span class="n">b</span> <span class="o">=</span> <span class="o">-</span><span class="n">m</span> <span class="o">*</span> <span class="n">minimum</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">point</span><span class="p">(</span><span class="k">lambda</span> <span class="n">i</span><span class="p">,</span> <span class="n">m</span><span class="o">=</span><span class="n">m</span><span class="p">,</span> <span class="n">b</span><span class="o">=</span><span class="n">b</span><span class="p">:</span> <span class="n">i</span> <span class="o">*</span> <span class="n">m</span> <span class="o">+</span> <span class="n">b</span><span class="p">)</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="s2">"L"</span><span class="p">)</span></div>
<span class="c1"># returns a ImageTk.PhotoImage object, after rescaling to 0..255</span>
<div class="viewcode-block" id="SpiderImageFile.tkPhotoImage"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.SpiderImageFile.tkPhotoImage">[docs]</a> <span class="k">def</span> <span class="nf">tkPhotoImage</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">PIL</span> <span class="k">import</span> <span class="n">ImageTk</span>
<span class="k">return</span> <span class="n">ImageTk</span><span class="o">.</span><span class="n">PhotoImage</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">convert2byte</span><span class="p">(),</span> <span class="n">palette</span><span class="o">=</span><span class="mi">256</span><span class="p">)</span></div>
<span class="k">def</span> <span class="nf">_close__fp</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">__fp</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">fp</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__fp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">pass</span>
<span class="k">finally</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__fp</span> <span class="o">=</span> <span class="kc">None</span></div>
<span class="c1"># --------------------------------------------------------------------</span>
<span class="c1"># Image series</span>
<span class="c1"># given a list of filenames, return a list of images</span>
<div class="viewcode-block" id="loadImageSeries"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.loadImageSeries">[docs]</a><span class="k">def</span> <span class="nf">loadImageSeries</span><span class="p">(</span><span class="n">filelist</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">"""create a list of Image.images for use in montage"""</span>
<span class="k">if</span> <span class="n">filelist</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">filelist</span><span class="p">)</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">return</span>
<span class="n">imglist</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">img</span> <span class="ow">in</span> <span class="n">filelist</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">img</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"unable to find </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">img</span><span class="p">)</span>
<span class="k">continue</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">im</span> <span class="o">=</span> <span class="n">Image</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">img</span><span class="p">)</span><span class="o">.</span><span class="n">convert2byte</span><span class="p">()</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">isSpiderImage</span><span class="p">(</span><span class="n">img</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="n">img</span> <span class="o">+</span> <span class="s2">" is not a Spider image file"</span><span class="p">)</span>
<span class="k">continue</span>
<span class="n">im</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">'filename'</span><span class="p">]</span> <span class="o">=</span> <span class="n">img</span>
<span class="n">imglist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">im</span><span class="p">)</span>
<span class="k">return</span> <span class="n">imglist</span></div>
<span class="c1"># --------------------------------------------------------------------</span>
<span class="c1"># For saving images in Spider format</span>
<div class="viewcode-block" id="makeSpiderHeader"><a class="viewcode-back" href="../../reference/plugins.html#PIL.SpiderImagePlugin.makeSpiderHeader">[docs]</a><span class="k">def</span> <span class="nf">makeSpiderHeader</span><span class="p">(</span><span class="n">im</span><span class="p">):</span>
<span class="n">nsam</span><span class="p">,</span> <span class="n">nrow</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">size</span>
<span class="n">lenbyt</span> <span class="o">=</span> <span class="n">nsam</span> <span class="o">*</span> <span class="mi">4</span> <span class="c1"># There are labrec records in the header</span>
<span class="n">labrec</span> <span class="o">=</span> <span class="mi">1024</span> <span class="o">/</span> <span class="n">lenbyt</span>
<span class="k">if</span> <span class="mi">1024</span> <span class="o">%</span> <span class="n">lenbyt</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">labrec</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">labbyt</span> <span class="o">=</span> <span class="n">labrec</span> <span class="o">*</span> <span class="n">lenbyt</span>
<span class="n">hdr</span> <span class="o">=</span> <span class="p">[]</span>
<span class="n">nvalues</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">labbyt</span> <span class="o">/</span> <span class="mi">4</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="n">nvalues</span><span class="p">):</span>
<span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mf">0.0</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">hdr</span><span class="p">)</span> <span class="o"><</span> <span class="mi">23</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[]</span>
<span class="c1"># NB these are Fortran indices</span>
<span class="n">hdr</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="c1"># nslice (=1 for an image)</span>
<span class="n">hdr</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">nrow</span><span class="p">)</span> <span class="c1"># number of rows per slice</span>
<span class="n">hdr</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="c1"># iform for 2D image</span>
<span class="n">hdr</span><span class="p">[</span><span class="mi">12</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">nsam</span><span class="p">)</span> <span class="c1"># number of pixels per line</span>
<span class="n">hdr</span><span class="p">[</span><span class="mi">13</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">labrec</span><span class="p">)</span> <span class="c1"># number of records in file header</span>
<span class="n">hdr</span><span class="p">[</span><span class="mi">22</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">labbyt</span><span class="p">)</span> <span class="c1"># total number of bytes in header</span>
<span class="n">hdr</span><span class="p">[</span><span class="mi">23</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">lenbyt</span><span class="p">)</span> <span class="c1"># record length in bytes</span>
<span class="c1"># adjust for Fortran indexing</span>
<span class="n">hdr</span> <span class="o">=</span> <span class="n">hdr</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
<span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mf">0.0</span><span class="p">)</span>
<span class="c1"># pack binary data into a string</span>
<span class="n">hdrstr</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
<span class="n">hdrstr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">struct</span><span class="o">.</span><span class="n">pack</span><span class="p">(</span><span class="s1">'f'</span><span class="p">,</span> <span class="n">v</span><span class="p">))</span>
<span class="k">return</span> <span class="n">hdrstr</span></div>
<span class="k">def</span> <span class="nf">_save</span><span class="p">(</span><span class="n">im</span><span class="p">,</span> <span class="n">fp</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
<span class="k">if</span> <span class="n">im</span><span class="o">.</span><span class="n">mode</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s2">"F"</span><span class="p">:</span>
<span class="n">im</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="s1">'F'</span><span class="p">)</span>
<span class="n">hdr</span> <span class="o">=</span> <span class="n">makeSpiderHeader</span><span class="p">(</span><span class="n">im</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">hdr</span><span class="p">)</span> <span class="o"><</span> <span class="mi">256</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="s2">"Error creating Spider header"</span><span class="p">)</span>
<span class="c1"># write the SPIDER header</span>
<span class="n">fp</span><span class="o">.</span><span class="n">writelines</span><span class="p">(</span><span class="n">hdr</span><span class="p">)</span>
<span class="n">rawmode</span> <span class="o">=</span> <span class="s2">"F;32NF"</span> <span class="c1"># 32-bit native floating point</span>
<span class="n">ImageFile</span><span class="o">.</span><span class="n">_save</span><span class="p">(</span><span class="n">im</span><span class="p">,</span> <span class="n">fp</span><span class="p">,</span> <span class="p">[(</span><span class="s2">"raw"</span><span class="p">,</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="o">+</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="p">(</span><span class="n">rawmode</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="k">def</span> <span class="nf">_save_spider</span><span class="p">(</span><span class="n">im</span><span class="p">,</span> <span class="n">fp</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
<span class="c1"># get the filename extension and register it with Image</span>
<span class="n">ext</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">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">Image</span><span class="o">.</span><span class="n">register_extension</span><span class="p">(</span><span class="n">SpiderImageFile</span><span class="o">.</span><span class="n">format</span><span class="p">,</span> <span class="n">ext</span><span class="p">)</span>
<span class="n">_save</span><span class="p">(</span><span class="n">im</span><span class="p">,</span> <span class="n">fp</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
<span class="c1"># --------------------------------------------------------------------</span>
<span class="n">Image</span><span class="o">.</span><span class="n">register_open</span><span class="p">(</span><span class="n">SpiderImageFile</span><span class="o">.</span><span class="n">format</span><span class="p">,</span> <span class="n">SpiderImageFile</span><span class="p">)</span>
<span class="n">Image</span><span class="o">.</span><span class="n">register_save</span><span class="p">(</span><span class="n">SpiderImageFile</span><span class="o">.</span><span class="n">format</span><span class="p">,</span> <span class="n">_save_spider</span><span class="p">)</span>
<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"Syntax: python SpiderImagePlugin.py [infile] [outfile]"</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">isSpiderImage</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"input image must be in Spider format"</span><span class="p">)</span>
<span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
<span class="n">im</span> <span class="o">=</span> <span class="n">Image</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"image: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">im</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"format: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">im</span><span class="o">.</span><span class="n">format</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"size: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">im</span><span class="o">.</span><span class="n">size</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"mode: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">im</span><span class="o">.</span><span class="n">mode</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"max, min: "</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="s1">' '</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">im</span><span class="o">.</span><span class="n">getextrema</span><span class="p">())</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">></span> <span class="mi">2</span><span class="p">:</span>
<span class="n">outfile</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="c1"># perform some image operation</span>
<span class="n">im</span> <span class="o">=</span> <span class="n">im</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">Image</span><span class="o">.</span><span class="n">FLIP_LEFT_RIGHT</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span>
<span class="s2">"saving a flipped version of </span><span class="si">%s</span><span class="s2"> as </span><span class="si">%s</span><span class="s2"> "</span> <span class="o">%</span>
<span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">),</span> <span class="n">outfile</span><span class="p">))</span>
<span class="n">im</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">SpiderImageFile</span><span class="o">.</span><span class="n">format</span><span class="p">)</span>
</pre></div>
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