kitwaremedical / shaperegressionextension

Computation and visualization of time-regressed shapes in a collection of 3D shape inputs associated to a linear variable

ShapeRegressionExtension

Description

Computation and visualization of time-regressed shapes in a collection of 3D shape inputs associated to a linear variable thanks to two modules: RegressionComputation and RegressionVisualization.

ShapeRegressionExtension is now available as a 3D Slicer and as a SlicerSALT extension.

Prerequisites

• RegressionComputation module uses Shape4D CLI to compute time-regressed shapes.
• RegressionVisualization module uses Sequences module to visualize the time-regressed shapes over time.

shaperegressionextension's Issues

Changes to RegressionVisualization 3D view and volume plot

I would like to request some small changes to the 3D view and volume plot:

• When the sequence is created and first displayed, center and zoom in on the shape
• Plot the regression volume as a solid line
• Change the default location of the legend, top-middle or bottom-middle preferably so as not to obstruct data
• Optional: Have the legend be draggable to any location in the plot

Comparison tests in RegComputation

@jamesfishbaugh, in the test that compare files, are the comparison files up-to-date with the output of the RegressionComputation module?

The first test runs green, but the comparison fails with all the files except _000.vtk

Is this test passing on your machine? Do you think the test has been exercised often enough with the changes, or we should upload new comparison files?

I have a PR #14, but the comparison test is failing, just want to make sure the failure is not related to the minor changes introduced in the PR.

IO failing in RegressionVisualization

With Qt5

Traceback (most recent call last):
  File "/home/user/Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/ShapeRegressionExtension-build/lib/SlicerSALT-4.9/qt-scripted-modules/RegressionVisualization.py", line 370, in onSequenceCreation
    self.loadModels()
  File "/home/user/Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/ShapeRegressionExtension-build/lib/SlicerSALT-4.9/qt-scripted-modules/RegressionVisualization.py", line 396, in loadModels
    model = MRMLUtility.loadMRMLNode(shapeRootname, inputDirectory, shapeBasename, 'ModelFile')
  File "/home/user/Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/ShapeRegressionExtension-build/lib/SlicerSALT-4.9/qt-scripted-modules/ShapeRegressionUtilities/utility.py", line 16, in loadMRMLNode
    node = slicer.util.getNode(node_name)
  File "/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build/bin/Python/slicer/util.py", line 656, in getNode
    raise MRMLNodeNotFoundException("could not find nodes in the scene by name or id '%s'" % (pattern if (type(pattern) == str) else ""))
slicer.util.MRMLNodeNotFoundException: could not find nodes in the scene by name or id 'Regression_output_final_time_000'

BUG: RegressionVisualization model rotation and color change during sequence loading

When the 'Create Sequence' button is clicked, the model first appears grey in the upper right corner and rotates briefly back and forth before abruptly changing color to yellow and moving to the center of the window.

Warnings

Dumping the warnings for future reference.

Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tmplandmark.cpp: In copy constructor ‘tmpLandmarks::tmpLandmarks(const tmpLandmarks&)’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tmplandmark.cpp:36:1: warning: base class ‘class ShapeObject’ should be explicitly initialized in the copy constructor [-Wextra]
 tmpLandmarks::tmpLandmarks(const tmpLandmarks& shape)
 ^~~~~~~~~~~~
[12/33] Building CXX object CMakeFiles/shape4DLib.dir/src/regressionacceleration.cpp.o
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tmpsurfacecurrent.cpp: In copy constructor ‘tmpSurfaceCurrent::tmpSurfaceCurrent(const tmpSurfaceCurrent&)’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tmpsurfacecurrent.cpp:36:1: warning: base class ‘class ShapeObject’ should be explicitly initialized in the copy constructor [-Wextra]
 tmpSurfaceCurrent::tmpSurfaceCurrent(const tmpSurfaceCurrent& shape)
 ^~~~~~~~~~~~~~~~~
[14/33] Building CXX object CMakeFiles/shape4DLib.dir/src/regressionacceleration.cpp.o
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionvelocity.cpp: In member function ‘virtual Array3D<double> RegressionVelocity::Run()’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionvelocity.cpp:257:12: warning: deleting object of abstract class type ‘Optimizer’ which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete optimizer;
            ^~~~~~~~~
[26/33] Building CXX object CMakeFiles/shape4DLib.dir/src/regressionacceleration.cpp.o
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tinyxmlparser.cpp: In static member function ‘static void TiXmlBase::ConvertUTF32ToUTF8(long unsigned int, char*, int*)’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tinyxmlparser.cpp:113:10: warning: this statement may fall through [-Wimplicit-fallthrough=]
    input >>= 6;
    ~~~~~~^~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tinyxmlparser.cpp:114:3: note: here
   case 3:
   ^~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tinyxmlparser.cpp:117:10: warning: this statement may fall through [-Wimplicit-fallthrough=]
    input >>= 6;
    ~~~~~~^~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tinyxmlparser.cpp:118:3: note: here
   case 2:
   ^~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tinyxmlparser.cpp:121:10: warning: this statement may fall through [-Wimplicit-fallthrough=]
    input >>= 6;
    ~~~~~~^~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/tinyxmlparser.cpp:122:3: note: here
   case 1:
   ^~~~
[28/33] Building CXX object CMakeFiles/shape4DLib.dir/src/polydatareader.cpp.o
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp: In member function ‘void RegressionAcceleration::FISTA(Array3D<double>&, Array2D<double>&, Array2D<double>&)’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1175:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
         for (; lineIter < maxLineIters; lineIter++)
                ~~~~~~~~~^~~~~~~~~~~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp: In member function ‘void RegressionAcceleration::GradientDescent(Array3D<double>&, Array2D<double>&, Array2D<double>&)’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1528:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
         for (; lineIter < maxLineIters; lineIter++)
                ~~~~~~~~~^~~~~~~~~~~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp: In member function ‘void RegressionAcceleration::FISTA(Array3D<double>&, Array2D<double>&, Array2D<double>&)’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1360:50: warning: ‘regularity4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         regularityValues[iter+1] = regularity4;
                         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1359:52: warning: ‘dataMatching4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         dataMatchingValues[iter+1] = dataMatching4;
                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1340:50: warning: ‘regularity3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         regularityValues[iter+1] = regularity3;
                         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1339:52: warning: ‘dataMatching3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         dataMatchingValues[iter+1] = dataMatching3;
                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1358:49: warning: ‘functCase4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         criterionValues[iter+1] = functCase4;
                         ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/regressionacceleration.cpp:1338:49: warning: ‘functCase3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         criterionValues[iter+1] = functCase3;
                         ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[30/33] Building CXX object CMakeFiles/shape4DLib.dir/src/main.cpp.o
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/polydatawriter.cpp: In member function ‘bool VTKPolyDataWriter::WritePointsAndTris(const Array2D<double>&, const Array2D<int>&)’:
Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/shape4D/src/polydatawriter.cpp:133:36: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
         for (unsigned int j = 0; j <field.GetWidth(); j++)

RegressionVisualization 3D rendering issue

When viewing a surface in the 3D scene view at certain angles the shape will be not be rendered properly. Instead, there is a strange transparency and portions of the shape that should be occluded are shown through the surface. I attach a sequence of images to illustrate the issue (3rd image).

BUG: Make sure the root name textbox in RegressionVisualization is not requiring a certain name structure

It should not need to use "_final_time", just have a numeric sufix that can be used to build the sequence.

It is certainly true that if you use RegressionComputation that will be the filename, but if you happen to compile the code and run the regression commanline and then want to visualize in SALT, this will not work.

Check minimum required Slicer version

xref #3

BUG: RegressionVisualization shows only "Solid Color" option for some vtk sequences

I attach a sequence which has several attributes, such as velocity, acceleration, and expansion. However, when loaded with RegressionVisualization, the only option for "Color Map" is "Solid Color".

The sequence loads with the all the color map choices correctly in Paraview.

vtk_sequence.zip

Update PlotData to PlotSeries

Following changes in Slicer/Slicer@082edc40c

PlotData was renamed to PlotSeries

Homepage, icon, and screenshot URLs are missing

Extension installation fails because these required fields are missing from the extension description. We'll relax these requirements but adding this information to the extension is still essential.

ENH: Add Pablo and James as contributors to both modules

In the acknowledgement part

Cmake error during building

I encounter the following error, for various versions of cmake:

...
-- SuperBuild - First pass
-- SuperBuild - First pass - done
-- SuperBuild - shape4D => Requires FFTW, 
-- SuperBuild -   FFTW[OK]
-- SuperBuild - shape4D[OK]
CMake Error at SuperBuild.cmake:85 (ExternalProject_AlwaysConfigure):
  Unknown CMake command "ExternalProject_AlwaysConfigure".
Call Stack (most recent call first):
  CMakeLists.txt:69 (include)

I didn't change anything during configuration, I left everything on default settings.

@phcerdan @jcfr