Roman Grothausmann

switches to specify vertical and horizontal char densities

1

This PR (originally based on v1.2a) offers switches to specify vertical and horizontal character densities and the options to change these during run-time.

SimpleElastix segfaults if an InitialTransformParameterFile itself contains `InitialTransformParametersFileName`

35

Following suggestion number 2 (http://lists.bigr.nl/pipermail/elastix/2016-December/002431.html), i.e. setting an InitialTransformParameterFile which itself contains `InitialTransformParametersFileName` SimpleElastix segfaults during `Execute()`. Removing/commenting `InitialTransformParametersFileName` in the InitialTransformParameterFile resovles the issue but that way no chaining...

Click'n'Join-Mode extension to ITK-SNAP incuding global, dynamic watershed segmentation

5

These extensions to _ITK-SNAP_ implement a global watershed segmentation mode (**gWS**). The extensions incorporate a Click'n'Join mode (**CnJ**) as the intended usage of **gWS** is related to the _SegmentationEditor_ (http://www.itk.org/ITK/applications/segmentationeditor.html,...

make2graph output discrepancy if file already exists

9

Considering this simple Makefile: %.a: echo "$@" > $@ %.b : %.a echo "$@" > $@ %.z : %.b echo "$@" > $@ If 1.a does not exist make2graph yields:...

"HasKey" or similar method for the wrapped ParameterObject

1

For pythonic way of checking if a key is in a list/dict like `if 'InitialTransformParametersFileName' in parameterObject:` it would be helpful to have a "HasKey" or similar method for the...

enumeration support for the wrapping of ParameterObject

1

It would be helpful to have a way of enumerating a list/dict of a ParameterObject like `for i, parameterMap in enumerate(parameterObject):`. Currently, this needs to be done as: ``` for...

Gradient sometimes zero (which prevents a gradient decent optimizer from decenting)

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I have experienced many cases where I can extract a path with the [IterateNeighborhoodOptimizer](https://itk.org/Doxygen/html/classitk_1_1IterateNeighborhoodOptimizer.html) but where the [GradientDescentOptimizer](https://itk.org/Doxygen/html/classitk_1_1GradientDescentOptimizer.html) does not start to decent even though the speed function is continuous...

Trying to solve #61 I found that the interpolator that is used to calculate the gradient is always linear https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction/blob/2ff1ab58f30842ac57d76c8bc9462fcbc7523e67/include/itkPhysicalCentralDifferenceImageFunction.h#L86 and not using the interpolator that is (possibly) set for...

Make instantiation of cost function internal

1

Why is the (special) cost function ([SingleImageCostFunction](https://github.com/InsightSoftwareConsortium/ITKMinimalPathExtraction/blob/master/include/itkSingleImageCostFunction.h)) not instantiated internally? From the publication it seems that ```c++ PathFilterType :: CostFunctionType :: Pointer cost = PathFilterType :: CostFunctionType :: New ();...

itkMorphologicalDistanceTransformImageFilter instead of itkSignedMaurerDistanceMapImageFilter

2

Is there a particular reason to use itkSignedMaurerDistanceMapImageFilter https://github.com/InsightSoftwareConsortium/ITKThickness3D/blob/2539b34e4b43fd9369a0ad961c4811f2f329c0e4/include/itkMedialThicknessImageFilter3D.h#L23 instead of e.g. [itkMorphologicalDistanceTransformImageFilter](https://itk.org/Doxygen/html/classitk_1_1MorphologicalDistanceTransformImageFilter.html) (which would be multi-threaded)? Why signed DM? Are there cases where the skeleton reaches outside of the...