https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&feed=atom&action=history
Documentation/Labs/ImageStacks - Revision history
2024-03-29T09:33:04Z
Revision history for this page on the wiki
MediaWiki 1.33.0
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61509&oldid=prev
Pieper: /* Options */
2019-10-28T20:31:38Z
<p><span dir="auto"><span class="autocomment">Options</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:31, 28 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l60" >Line 60:</td>
<td colspan="2" class="diff-lineno">Line 60:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: put dicom files in database for reuse</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: put dicom files in database for reuse</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: use low-res as visualization proxy but use fill res for processing</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: use low-res as visualization proxy but use fill res for processing</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* option: displays available computer memory before trying to load (maybe use https://psutil.readthedocs.io/en/latest/#memory)</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Work in Progress ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Work in Progress ==</div></td></tr>
</table>
Pieper
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61497&oldid=prev
Pieper: /* Work in Progress */
2019-10-21T14:22:00Z
<p><span dir="auto"><span class="autocomment">Work in Progress</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 14:22, 21 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l62" >Line 62:</td>
<td colspan="2" class="diff-lineno">Line 62:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Work in Progress ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Work in Progress ==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">As of October 2019, the repo below has an implementation that works for slice files ready by SimpleITK (png, tiff, etc) extracting one component and options for 50% downsampling.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* https://github.com/pieper/SlicerImageStacks</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* https://github.com/pieper/SlicerImageStacks</div></td></tr>
</table>
Pieper
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61496&oldid=prev
Pieper: /* Work in Progres */
2019-10-17T20:23:12Z
<p><span dir="auto"><span class="autocomment">Work in Progres</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:23, 17 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l61" >Line 61:</td>
<td colspan="2" class="diff-lineno">Line 61:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: use low-res as visualization proxy but use fill res for processing</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: use low-res as visualization proxy but use fill res for processing</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>== Work in <del class="diffchange diffchange-inline">Progres </del>==</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>== Work in <ins class="diffchange diffchange-inline">Progress </ins>==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* https://github.com/pieper/SlicerImageStacks</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* https://github.com/pieper/SlicerImageStacks</div></td></tr>
</table>
Pieper
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61495&oldid=prev
Pieper: /* Options */
2019-10-16T20:05:07Z
<p><span dir="auto"><span class="autocomment">Options</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:05, 16 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l52" >Line 52:</td>
<td colspan="2" class="diff-lineno">Line 52:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Implementation</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Implementation</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* stand-<del class="diffchange diffchange-inline">along </del>processing script with command line options -- too difficult for users in general, no interactive feedback</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* stand-<ins class="diffchange diffchange-inline">alone </ins>processing script with command line options -- too difficult for users in general, no interactive feedback</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* plugin for Add Data module that exposes some options -- not enough room for gui, not interactive</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* plugin for Add Data module that exposes some options -- not enough room for gui, not interactive</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Independent importer module -- probably the best option with reusable logic</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Independent importer module -- probably the best option with reusable logic</div></td></tr>
</table>
Pieper
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61494&oldid=prev
Pieper: /* Options */
2019-10-16T20:03:07Z
<p><span dir="auto"><span class="autocomment">Options</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:03, 16 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l60" >Line 60:</td>
<td colspan="2" class="diff-lineno">Line 60:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: put dicom files in database for reuse</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: put dicom files in database for reuse</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: use low-res as visualization proxy but use fill res for processing</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* option: use low-res as visualization proxy but use fill res for processing</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">== Work in Progres ==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* https://github.com/pieper/SlicerImageStacks</ins></div></td></tr>
</table>
Pieper
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61486&oldid=prev
Pieper: /* Desired properties */
2019-10-01T17:34:02Z
<p><span dir="auto"><span class="autocomment">Desired properties</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:34, 1 October 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l47" >Line 47:</td>
<td colspan="2" class="diff-lineno">Line 47:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* allow scripted use outside slicer</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* allow scripted use outside slicer</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* use reference volume or ROI to define desired geometry (e.g. reuse crop volume logic)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* use reference volume or ROI to define desired geometry (e.g. reuse crop volume logic)</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* handle greater than 8 bits per pixel if the source format supports it</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Options ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Options ==</div></td></tr>
</table>
Pieper
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61485&oldid=prev
Pieper: /* Options */
2019-10-01T17:18:41Z
<p><span dir="auto"><span class="autocomment">Options</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 17:18, 1 October 2019</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* stand-along processing script with command line options -- too difficult for users in general, no interactive feedback</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* stand-along processing script with command line options -- too difficult for users in general, no interactive feedback</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Features</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Features</div></td></tr>
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Pieper
https://www.slicer.org/w/index.php?title=Documentation/Labs/ImageStacks&diff=61484&oldid=prev
Pieper: Created page with "== Background == Image stacks are generated in a lot of scenarios, like microscopes, microCT, and other non-medical sources. Examples are like: <pre> directoryPath = '/V..."
2019-10-01T17:17:48Z
<p>Created page with "== Background == Image stacks are generated in a lot of scenarios, like microscopes, microCT, and other non-medical sources. Examples are like: <pre> directoryPath = '/V..."</p>
<p><b>New page</b></p><div>== Background ==<br />
<br />
Image stacks are generated in a lot of scenarios, like microscopes, microCT, and other non-medical sources.<br />
<br />
Examples are like:<br />
<pre><br />
directoryPath = '/Volumes/SSD2T/data/SlicerMorph/Sample_for_steve/1326_Rec'<br />
pathFormat = '%s/1326__rec%04d.png'<br />
</pre><br />
<br />
== Common issues ==<br />
* Data is really grayscale, but encoded using jpg or other color format<br />
* Data may be large and needs to be cropped or resampled for use<br />
* Data will not have any consistent metadata<br />
** pixel / slice spacing<br />
** orientation (e.g. mapping to anatomical coordinates)<br />
** acquisition time, equipment, operator, etc<br />
* Only a subset of data may actually be wanted (ROI or subsampled volume)<br />
<br />
== Current reader ==<br />
<br />
Delegates to ITK via vtkITKArchetype mechanism. Lots of hidden logic to guess possible mapping from image files to volumes.<br />
* Guesses filename pattern, which can easily fail<br />
* Creates vector volume for RGB and user must manually convert to scalar<br />
* Reads full volume and then must crop or resample<br />
* Can be slow to read / decompress large files<br />
<br />
== Available readers ==<br />
<br />
* vtkPNGReader<br />
* itk image IO<br />
* Qt Image<br />
* PIL / PILLOW python packages (not currently bundled in Slicer, but pip installable)<br />
* QWebEngine<br />
<br />
== Desired properties ==<br />
<br />
* fast, ideally multithreaded<br />
* compatible with multiple file formats (at least jpg, tiff, bmp, png)<br />
* clean slicer integration<br />
* support arbitrary file naming conventions with different ways of mapping names to volumes or other structures<br />
* ability to map anatomical coordinates (e.g. click on nose, right ear, and top of head)<br />
* ability to convert to scalar and/or crop/resample while reading<br />
* store pyramid encoded volumes for later reuse<br />
* use a single-file format for simplicity (avoid creating even more single slice image files)<br />
* store metadata for later reuse<br />
* allow scripted use outside slicer<br />
* use reference volume or ROI to define desired geometry (e.g. reuse crop volume logic)<br />
<br />
== Options ==<br />
<br />
Implementation<br />
* stand-along processing script with command line options -- too difficult for users in general, no interactive feedback<br />
* plugin for Add Data module that exposes some options -- not enough room for gui, not interactive<br />
* Independent importer module -- probably the best option<br />
<br />
Features<br />
* store pyramid files in nrrd or some minimal dicom<br />
* option: put dicom files in database for reuse<br />
* option: use low-res as visualization proxy but use fill res for processing</div>
Pieper