View Issue Details
| ID | Project | Category | View Status | Date Submitted | Last Update |
|---|---|---|---|---|---|
| 0003233 | Slicer4 | Module ModelToLabelMap | public | 2013-07-18 12:03 | 2017-06-10 08:51 |
| Reporter | marianna | Assigned To | nicole | ||
| Priority | high | Severity | feature | Reproducibility | always |
| Status | closed | Resolution | fixed | ||
| Platform | x86_64 | OS | Linux | OS Version | Fedora 18 |
| Product Version | Slicer 4.2.0 | ||||
| Target Version | Slicer 4.3.0 | Fixed in Version | Slicer 4.3.0 | ||
| Summary | 0003233: Model to Label Map label value hard coded to 255 | ||||
| Description | asking for the label value to be exposed as an argument to the CLI | ||||
| Tags | No tags attached. | ||||
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svn 22211 exposes the label value. |
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Closing resolved issues that have not been updated in more than 3 months |
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Bug reported that the user selected label map values weren't working properly, patch pull request is here: |
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Patch in svn 25062: |
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Slicer: 2145-support-for-installing-extension-from-file 34d9af1f 2013-07-18 16:46:51 naucoin Details Diff |
ENH: expose the label value for the model to label map CLI Updated the documentation link and updated the wiki pages to include the new parameter. Resolves issue 0003233 git-svn-id: http://svn.slicer.org/Slicer4/trunk@22211 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/CLI/ModelToLabelMap/ModelToLabelMap.cxx | Diff File | ||
| mod - Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml | Diff File | ||
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Slicer: 2145-support-for-installing-extension-from-file 5592f229 2013-07-19 17:54:00 naucoin Details Diff |
STYLE: update Model to Label Map xml file docs More testing showed that the output volume will always be cast to unsigned char, so limit the label value to 0-255 and give the user some hints about good models to use. Issue 0003233 git-svn-id: http://svn.slicer.org/Slicer4/trunk@22218 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml | Diff File | ||
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Import 2017-06-07 23:51:09: master 8707bb9e 2016-05-13 13:47:09 naucoin Details Diff |
BUG: Enable use of labelValue for output label map A bug was introduced in svn 22211 [1] when the labelValue parameter in the ModelToLabelMap CLI was exposed to the interface. The erosion and dilation filters used in the code are binary ones and by default use the maximum of the data type of the label map, in this case hard coded to 255 for unsigned char. In order to do the full pipeline with the user selected label value, the code would need to be updated to use: erodeFilter->SetErodeValue(labelValue); dilateFilter->SetDilateValue(labelValue); A quicker fix is to adjust the output label map in the last step to set the desired label value, implemented in this patch. Investigating this issue, the hard coded kernel size was set into a variable, in anticipation of exposing it via the XML (quick tests showed no visible difference). Added a test and output using the label value 128. When run from the GUI, the model and volume were offset, so a transformed model was generated that overlaps the input volume and was used to generate the new baseline comparison volume. Removed unused baseline image. [1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22211 Issue 0003233 git-svn-id: http://svn.slicer.org/Slicer4/trunk@25062 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - Modules/CLI/ModelToLabelMap/Data/Baseline/OAS10001-128.mha | Diff File | ||
| rm - Modules/CLI/ModelToLabelMap/Data/Baseline/OAS10001.1.mha | Diff File | ||
| add - Modules/CLI/ModelToLabelMap/Data/Input/OAS10001-Transformed.vtp | Diff File | ||
| mod - Modules/CLI/ModelToLabelMap/ModelToLabelMap.cxx | Diff File | ||
| mod - Modules/CLI/ModelToLabelMap/Testing/CMakeLists.txt | Diff File | ||
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Import 2017-06-07 23:51:09: master e3637ad5 2016-05-19 10:41:35 naucoin Details Diff |
BUG: fix failing ModelToLabelMapTest When putting in a fix for using the passed in label value, the baseline file OAS10001.1.mha was removed as it didn't seem to be in use any more. A closer examination of the ctest output showed that that file was being picked up as the baseline image when the test was passing as of May 11/16: http://slicer.cdash.org/testDetails.php?test=7318110&build=825978 BaselineImageName OAS10001.1.mha With the last change[1], the test is failing: http://slicer.cdash.org/testDetails.php?test=7329855&build=828864 BaselineImageName OAS10001.mha Local testing shows that the test would pass if the file OAS10001.1.mha was reinstated, but to avoid confusion going forward as to how ctest globs the baseline image files, I decided to go with testing the CLI with the same input model (transformed to overlap the input image volume when both are loaded in Slicer) for both the 255 and 128 output label cases, and to generate a new output baseline image. I removed the untransformed model file and the now unused baseline image and, locally, ctest is comparing the outputs of both tests against teh correct baselines. [1] https://github.com/Slicer/Slicer/commit/8707bb9ed2503f67ac0af29782c16db97adeab40 Reported-by: Andras Lasso <lasso@queensu.ca> Issue 0003233 git-svn-id: http://svn.slicer.org/Slicer4/trunk@25091 3bd1e089-480b-0410-8dfb-8563597acbee |
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| add - Modules/CLI/ModelToLabelMap/Data/Baseline/OAS10001-255.mha | Diff File | ||
| rm - Modules/CLI/ModelToLabelMap/Data/Baseline/OAS10001.mha | Diff File | ||
| rm - Modules/CLI/ModelToLabelMap/Data/Input/OAS10001.vtp | Diff File | ||
| mod - Modules/CLI/ModelToLabelMap/Testing/CMakeLists.txt | Diff File | ||
| Date Modified | Username | Field | Change |
|---|---|---|---|
| 2013-07-18 12:03 | marianna | New Issue | |
| 2013-07-18 12:16 | nicole | Status | new => assigned |
| 2013-07-18 12:16 | nicole | Assigned To | => nicole |
| 2013-07-18 12:17 | nicole | Summary | label value hard coded to 255 => Model to Label Map label value hard coded to 255 |
| 2013-07-18 12:45 | nicole | Priority | normal => high |
| 2013-07-18 12:45 | nicole | Target Version | => Slicer 4.3.0 |
| 2013-07-18 12:47 | nicole | Note Added: 0009132 | |
| 2013-07-18 12:47 | nicole | Status | assigned => resolved |
| 2013-07-18 12:47 | nicole | Fixed in Version | => Slicer 4.3.0 |
| 2013-07-18 12:47 | nicole | Resolution | open => fixed |
| 2014-03-06 04:56 | jcfr | Note Added: 0010809 | |
| 2014-03-06 04:58 | jcfr | Status | resolved => closed |
| 2016-05-11 16:37 | nicole | Note Added: 0013873 | |
| 2016-05-13 13:48 | nicole | Note Added: 0013874 | |
| 2017-06-07 23:27 | Changeset attached | => Slicer 2145-support-for-installing-extension-from-file 5592f229 | |
| 2017-06-07 23:27 | Changeset attached | => Slicer 2145-support-for-installing-extension-from-file 34d9af1f | |
| 2017-06-10 08:51 | Changeset attached | => Slicer master e3637ad5 | |
| 2017-06-10 08:51 | Changeset attached | => Slicer master 8707bb9e |
