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UI updates to Segment Mesher #7

Merged

lassoan merged 7 commits into lassoan:master from sjh26:ui-updates

Nov 5, 2020

Contributor

sjh26 commented Aug 26, 2020

breaks out useful command line options to GUI options
Separate advanced parameters into tabs
Allows TetGen to mesh directly from a surface
Instead of selecting segments to mesh based on visibility, a check-able drop down is now provided

lassoan approved these changes

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Owner

lassoan left a comment

Thank you, very nice improvements. If you plan to make future GUI changes, it would be better to upgrade this module to genereate GUI using .ui file instead of Python code.

Owner

lassoan commented Aug 26, 2020

It would be great if you could make a small GUI adjustment: make "General" tab the first, and only show the tab that belongs to the selected meshing method. If you don't plan to make these changes then fine, just let me know and I merge this as is.

Contributor Author

sjh26 commented Aug 27, 2020

Sure, I can do those changes. I agree, we should update this to use a UI file. I can do that in this PR, there will likely be more updates to SegmentMesher from this project.

sjh26 force-pushed the ui-updates branch from 44e3890 to 4dbbe76 Compare

November 4, 2020 15:31

sjh26 requested a review from lassoan

November 4, 2020 15:32

Contributor Author

sjh26 commented Nov 4, 2020

Converted to ui file interface, and reordered/hide tabs.

lassoan reviewed

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Owner

lassoan left a comment

Thank you. There are a few regressions (mostly related to changed parametrization in Cleaver) that must be fixed, and a few small improvements got removed that should be restored, but otherwise it looks good.

SegmentMesher/SegmentMesher.py Outdated

+                    self.ui.advancedTabWidget.setTabEnabled( self.ui.advancedTabWidget.indexOf(self.ui.tetgenTab), False)
+                    self.ui.advancedTabWidget.setTabEnabled( self.ui.advancedTabWidget.indexOf(self.ui.cleaverTab), True)
+                    self.ui.advancedTabWidget.setStyleSheet("QTabBar::tab::disabled {width: 0; height: 0; margin: 0; padding: 0; border: none;} ")
                   enabled = True

Owner

lassoan Nov 4, 2020

is this used anywhere?

Contributor Author

sjh26 Nov 4, 2020

typo, will remove

SegmentMesher/SegmentMesher.py Outdated

@@ @@ -403,13 +331,13 @@ def getTetGenPath(self): @@
                 def getCustomCleaverPath(self):
                   settings = qt.QSettings()
                   if settings.contains(self.customCleaverPathSettingsKey):
-                    return settings.value(self.customCleaverPathSettingsKey)
+                    return slicer.util.toVTKString(settings.value(self.customCleaverPathSettingsKey))

Owner

lassoan Nov 4, 2020

This reverts an intentional change. toVTKString is not needed anymore.

SegmentMesher/SegmentMesher.py Outdated

                   return ''
                 def getCustomTetGenPath(self):
                   settings = qt.QSettings()
                   if settings.contains(self.customTetGenPathSettingsKey):
-                    return settings.value(self.customTetGenPathSettingsKey)
+                    return slicer.util.toVTKString(settings.value(self.customTetGenPathSettingsKey))

Owner

lassoan Nov 4, 2020

This reverts an intentional change. toVTKString is not needed anymore.

SegmentMesher/SegmentMesher.py Outdated

                   logging.info("Generate mesh using: "+executableFilePath+": "+repr(cmdLineArguments))
                   return subprocess.Popen([executableFilePath] + cmdLineArguments,
-                                          stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True, startupinfo=info)

Owner

lassoan Nov 4, 2020

This reverts an intentional change.

SegmentMesher/SegmentMesher.py Outdated

@@ @@ -489,10 +417,11 @@ def createTempDirectory(self): @@
                   qt.QDir().mkpath(dirPath)
                   return dirPath
-                def createMeshFromSegmentationCleaver(self, inputSegmentation, outputMeshNode, additionalParameters = None, removeBackgroundMesh = False, paddingRatio = 0.10):
+                def createMeshFromSegmentationCleaver(self, inputSegmentation, outputMeshNode, segments = [], additionalParameters = None, removeBackgroundMesh = False, paddingRatio = 0.10, scale = 0.2, multiplier=0.5, grading=1.0):

Owner

lassoan Nov 4, 2020

Parametrization has changed in Cleaver. Parameters are now: feature scaling, sampling rate, and maximum rate of change

SegmentMesher/SegmentMesher.py Outdated

                   inputLabelmapVolumeFilePath = os.path.join(tempDir, "inputLabelmap.nrrd")
                   slicer.util.saveNode(labelmapVolumeNode, inputLabelmapVolumeFilePath, {"useCompression": False})
                   inputParamsCleaver.extend(["--input_files", inputLabelmapVolumeFilePath])
+                  inputParamsCleaver.append("--segmentation")

Owner

lassoan Nov 4, 2020

This reverts an intentional change.

SegmentMesher/SegmentMesher.py Outdated

                   slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
                   slicer.mrmlScene.RemoveNode(colorTableNode)
+                  #User set parameters
+                  inputParamsCleaver.extend(["--scale", "{:.2f}".format(scale)])

Owner

lassoan Nov 4, 2020

These parameter values are not valid anymore.

SegmentMesher/SegmentMesher.py Outdated

                   inputParamsCleaver.append("--verbose")
                   # Quality
-                  inputParamsCleaver.extend(additionalParameters.split(' '))
+                  inputParamsCleaver.extend(slicer.util.toVTKString(additionalParameters).split(' '))

Owner

lassoan Nov 4, 2020

This reverts an intentional change.

SegmentMesher/SegmentMesher.py

                 def cleanup(self):
                   pass
                 def updateMRMLFromGUI(self):

Owner

lassoan Nov 4, 2020

It would be nice to save widgets state into a parameter node (see how it is done in the module template)

Contributor Author

sjh26 commented Nov 4, 2020

Ah, it looks like i screwed up the rebase.

sjh26 added 6 commits

November 4, 2020 12:15


          ENH: Improve UI and options

84c9da8

 - Allow TetGen to use surface mesh as input
 - Expose useful Cleaver options
 - Expose useful TetGen options


          ENH: Allow meshing of arbitrary label sets in segmentation nodes

db7fd8e

Adds a checkable combobox for selecting segment(s) to mesh


          ENH: Define interface with .ui file

fdd4bb9


          ENH: Reorder advanced parameters tabs, and hide unused tabs

a3de5ca


          ENH: Format float parameter values to 2 decimal places

f035b35

Previously they were un-formatted at full machine precision.


          BUG: Use updated cleaver parameters

92ae4fb

sjh26 force-pushed the ui-updates branch from 4dbbe76 to 92ae4fb Compare

November 4, 2020 18:03

Contributor Author

sjh26 commented Nov 4, 2020

Fixed the unintended reverts, and the Cleaver parameters. Working on parameter node saving


          ENH: Save UI parameters in parameter node

2d8eb7d

sjh26 requested a review from lassoan

November 5, 2020 22:31

lassoan approved these changes

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Owner

lassoan left a comment

Thanks a lot for the thorough update. There are so many changes that I cannot review them in detail, but overall everything looks good and we can fix things up later if we find problems.

lassoan merged commit ea925a6 into lassoan:master

sjh26 deleted the ui-updates branch

November 12, 2020 18:02

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