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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">I’m trying to extract an ROI from a large binary file. Whenever I run nibabel.fileslice.fileslice, I’m getting the following error:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<pre style="line-height:12.75pt;background:white;vertical-align:baseline;word-break:break-all"><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">C:\Anaconda2\lib\site-packages\nibabel\fileslice.pyc in </span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue">optimize_read_slicers</span></span><span class="ansiblue"><span style="font-size:10.5pt;color:darkblue">(sliceobj, in_shape, itemsize, heuristic)</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"><o:p></o:p></span></span></pre>
<pre style="line-height:12.75pt;background:white;vertical-align:baseline;word-break:break-all"><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen"> 560</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"> </span></span><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">if</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"> </span></span><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">not</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"> isinstance</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">(</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue">read_slicer</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">,</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"> Integral</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">):</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"><o:p></o:p></span></span></pre>
<pre style="line-height:12.75pt;background:white;vertical-align:baseline;word-break:break-all"><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen"> 561</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"> post_slicers</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">.</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue">append</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">(</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue">post_slicer</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">)</span></span><span class="ansicyan"><span style="font-size:10.5pt;color:steelblue"><o:p></o:p></span></span></pre>
<pre style="line-height:12.75pt;background:white;vertical-align:baseline;word-break:break-all"><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">--> 562</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000"> </span></span><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">stride</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">*=</span></span><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">dim_len<o:p></o:p></span></span></pre>
<pre style="line-height:12.75pt;background:white;vertical-align:baseline;word-break:break-all"><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen"> 563 <o:p></o:p></span></span></pre>
<pre style="line-height:12.75pt;background:white;vertical-align:baseline;word-break:break-all"><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen"> 564 return tuple</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">(</span></span><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">read_slicers</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">),</span></span><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen"> tuple</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">(</span></span><span class="ansigreen"><span style="font-size:10.5pt;color:darkgreen">post_slicers</span></span><span class="ansiyellow"><span style="font-size:10.5pt;color:#C4A000">)</span></span><span style="font-size:10.5pt;color:black"><o:p></o:p></span></pre>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal" style="line-height:12.75pt;background:white;vertical-align:baseline;word-break:break-all">
<span style="font-size:10.5pt;font-family:"Courier New";color:darkred">TypeError</span><span style="font-size:10.5pt;font-family:"Courier New";color:darkgreen">: unsupported operand type(s) for *=: 'getset_descriptor' and 'int'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">I’m calling this function with the following:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">filepath = filepath<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">dtype = 'uint16'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">chunksize = int((npix*nframes))<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">sliceobj=slice((0,20,None),(0,20,None))<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">f = open(filepath, 'r')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">dat=nibabel.fileslice.fileslice(f, sliceobj=sliceobj, shape=(2048,2048,100), dtype=np.uint16)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">The binary file I’m trying to analyze is imaging data, and thus the final shape of the array is 3D. The slice object I’m inputting is a 20 by 20 pixel ROI.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Thanks!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Natalia
<o:p></o:p></span></p>
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