https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&feed=atom&action=history2017 Winter Project Week/SubjectHierarchyRefactoring - Revision history2024-03-29T11:52:35ZRevision history for this page on the wikiMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=95015&oldid=prevPinter: /* Project Description */2017-01-13T14:54:07Z<p><span dir="auto"><span class="autocomment">Project Description</span></span></p>
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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><!-- Progress and Next steps bullet points (fill out at the end of project week) --></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><!-- Progress and Next steps bullet points (fill out at the end of project week) --></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>*</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>* <ins class="diffchange diffchange-inline">Rewrote all subject hierarchy classes (node, logic, model, tree view, plugin handler, plugin logic, abstract plugin) and updating classes using subject hierarchy</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 class="diffchange diffchange-inline">* It compiles, but need to work on making it really work</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 class="diffchange diffchange-inline">* Need to make sure all components, all plugins work well. Also need to check all extensions and update them if they use subject hierarchy directly</ins></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;"></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>==Background and References==</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>==Background and References==</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 this space for information that may help people better understand your project, like links to papers, source code, or data --></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 this space for information that may help people better understand your project, like links to papers, source code, or data --></div></td></tr>
</table>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=94703&oldid=prevPinter at 19:12, 9 January 20172017-01-09T19:12:43Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:12, 9 January 2017</td>
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<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;">* Jorge Onieva</ins></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>==Project Description==</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>==Project Description==</div></td></tr>
</table>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=94702&oldid=prevPinter at 19:12, 9 January 20172017-01-09T19:12:03Z<p></p>
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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>Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]</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>Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]</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;">Image:20170109_SubjectHierarchy.png|Subject hierarchy tree</ins></div></td></tr>
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</table>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=94150&oldid=prevPinter: /* Project Description */2017-01-02T18:59:51Z<p><span dir="auto"><span class="autocomment">Project Description</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:59, 2 January 2017</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>** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)</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>** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)</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>** Postfixes of the SH nodes to differentiate them from the associated data nodes</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>** Postfixes of the SH nodes to differentiate them from the associated data nodes</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>This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors <del class="diffchange diffchange-inline">to show the information</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>This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors.</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>|</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>|</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><!-- Approach and Plan bullet points --></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><!-- Approach and Plan bullet points --></div></td></tr>
</table>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=94149&oldid=prevPinter at 18:58, 2 January 20172017-01-02T18:58:44Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:58, 2 January 2017</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>* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes</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>* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes</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>These issues are due to</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>These issues are due to</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>* The <del class="diffchange diffchange-inline">extremely </del>complex Qt MRML scene model infrastructure, which is <del class="diffchange diffchange-inline">quite </del>rigid in <del class="diffchange diffchange-inline">various </del>ways, and <del class="diffchange diffchange-inline">has unstable </del>features</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>* The <ins class="diffchange diffchange-inline">overly </ins>complex Qt MRML scene model infrastructure, which is rigid in <ins class="diffchange diffchange-inline">some </ins>ways, and <ins class="diffchange diffchange-inline">bloated in others</ins></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>* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases<del class="diffchange diffchange-inline">, e.g.</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><ins class="diffchange diffchange-inline">** Can only show nodes, so if an item is needed to be shown, a new node needs to be created (thus the lot of SH nodes and the virtual branches, see below). Also pointer tracking of nodes complicates things.</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 class="diffchange diffchange-inline">** Index calculation is very complex and gets even more complex in the sub classes.</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 class="diffchange diffchange-inline">** The </ins>features <ins class="diffchange diffchange-inline">that are needed for specific models but are implemented in the base model overcomplicate the implementation (e.g. pre- and post items)</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>* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases</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>** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies</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>** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies</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>** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)</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>** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)</div></td></tr>
</table>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=93962&oldid=prevPinter: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."2016-12-12T20:13:52Z<p>Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|<a href="/wiki/2017_Winter_Project_Week#Projects" title="2017 Winter Project Week">Projects List</a> <!-- Use the "Upload file" link on the l..."</p>
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<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* ? (JC, Steve, Andras)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
Although the subject hierarchy mechanism is in place and is already used, there are several issues and limitations that cannot be addressed in its current form:<br />
* Subject hierarchy needs to be disabled by default, because<br />
** A second node is created for each data node and the scene can grow very large in case of many data nodes<br />
** Model hierarchies and subject hierarchies are not fully compatible, so problems may arise in case of complex model hierarchies (such as atlases)<br />
** Because of this, a popup is shown to the user, which is confusing for users. It prevents some from using SH, and is annoying for the others<br />
* Expanded state is reset to all extended when switching to another module and back. This can be very frustrating when there are many subjects or folders, because the user sees it very differently after returning to SH<br />
* Manual re-ordering of nodes is not possible<br />
* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes<br />
These issues are due to<br />
* The extremely complex Qt MRML scene model infrastructure, which is quite rigid in various ways, and has unstable features<br />
* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases, e.g.<br />
** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies<br />
** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)<br />
** Postfixes of the SH nodes to differentiate them from the associated data nodes<br />
This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors to show the information.<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Store the whole tree in one vtkMRMLSubjectHierarchy node<br />
** Items have unique identifier numbers that is strictly incremental<br />
** Item information can be accessed using accessors, the item class itself is private<br />
* Automatically populate from added nodes (as before), observe modified and removed events<br />
* Implement new Qt item model that is synchronized with the subject hierarchy node instead of the scene<br />
* Import model hierarchies to SH node on entering SH module if new detected (thus model hierarchies can be fully used from <br />
* Subject hierarchy logic makes sure there is only one SH node and it is valid (at import, deletion, potential undo, etc.)<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinter