Ebrahim Ebrahim ebrahimebrahim

## vtkMRMLMarkupsStorageNodeTest2-fix.md

      
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                ebrahimebrahim
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              March 11, 2026 21:43
            
              
                Analysis of vtkMRMLMarkupsStorageNodeTest2 failure with VTK 9.6 (rapidjson ODR violation)
              
          
    (Generated by Claude Code)
vtkMRMLMarkupsStorageNodeTest2 failure analysis

Symptom

The test writes a markups JSON file containing NaN (for an undefined control point position),
then reads it back. The read fails:


## slicer_bridge.py
"""Slicer integration for abcdmicro resources.

This module provides resources that wrap 3D Slicer MRML scene objects,
allowing seamless integration between abcdmicro's Resource abstraction
and Slicer's visualization and analysis capabilities.

SlicerVolumeResource is considered "loaded" (is_loaded=True) because the
data lives in memory (Slicer's VTK structures). This is analogous to
InMemoryVolumeResource, just with VTK as the backing storage instead of
numpy arrays.

## slicer-curved-planar-reformat-demo.py
slicer.mrmlScene.Clear(0)

# Check that registration of "ResampleScalarVectorDWIVolume" worked.
resamplerName = "ResampleScalarVectorDWIVolume"
generalizedReformatLogic = slicer.modules.generalizedreformat.logic()
generalizedReformatLogic.SetMRMLApplicationLogic(slicer.app.applicationLogic())
found = generalizedReformatLogic.IsVolumeResamplerRegistered(resamplerName)
print(f"{resamplerName!r} was{'' if found else ' NOT'} found in module logic")

# Check that we can find an existing vtkMRMLSliceLogic.

## Snake code with wasd.html
<!DOCTYPE html>
<html>
<head>
  <title>Snake Game</title>
  <script src="https://code.jquery.com/jquery-1.11.3.js"></script>
  <style>
  html, body {
    height: 100%;
    margin: 0;
  }

## running_mean.py
import numpy as np
from numpy.typing import NDArray

class RunningMean:
    """Like numpy.mean but aggregates data in chunks at a time."""

    def __init__(self, axis=None, keepdims=False):
        """For axis and keepdims, see the documentation of these arg names in numpy.mean"""
        self.axis=axis
        self.keepdims=keepdims

## cambria_math_install.sh
# some annoying document formatting requirements made me to this in tex:
# \setmathfont{Cambria Math}
# \setmainfont{Times New Roman}
# and of course these microsoft fonts are not found when compiling with xelatex on ubuntu
# this gist helps set up  the texlive environment in ubuntu to find the fonts

# thanks to maxwelleite: https://gist.github.com/maxwelleite/10774746
# their script is way better and more automated, but I didn't want to sudo an entire script,
# so below I have extracted the commands I want and made it clear where sudo is needed
# I recommend running the below one by one to check that each step works

## slicer_plot_data.py
# To try this example, save this to a file slicer_plot_data.py, then execute Slicer from the command line
# with the arguments `--python-script slicer_plot_data.py`.

import slicer, qt, vtk

PLOT_TYPES = {
  "line" : slicer.vtkMRMLPlotSeriesNode.PlotTypeLine,
  "bar" : slicer.vtkMRMLPlotSeriesNode.PlotTypeBar,
  "scatter" : slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter,
  "scatterbar" : slicer.vtkMRMLPlotSeriesNode.PlotTypeScatterBar,
	"""Slicer integration for abcdmicro resources.

	This module provides resources that wrap 3D Slicer MRML scene objects,
	allowing seamless integration between abcdmicro's Resource abstraction
	and Slicer's visualization and analysis capabilities.

	SlicerVolumeResource is considered "loaded" (is_loaded=True) because the
	data lives in memory (Slicer's VTK structures). This is analogous to
	InMemoryVolumeResource, just with VTK as the backing storage instead of
	numpy arrays.
	slicer.mrmlScene.Clear(0)

	# Check that registration of "ResampleScalarVectorDWIVolume" worked.
	resamplerName = "ResampleScalarVectorDWIVolume"
	generalizedReformatLogic = slicer.modules.generalizedreformat.logic()
	generalizedReformatLogic.SetMRMLApplicationLogic(slicer.app.applicationLogic())
	found = generalizedReformatLogic.IsVolumeResamplerRegistered(resamplerName)
	print(f"{resamplerName!r} was{'' if found else ' NOT'} found in module logic")

	# Check that we can find an existing vtkMRMLSliceLogic.
	<!DOCTYPE html>
	<html>
	<head>
	<title>Snake Game</title>
	<script src="https://code.jquery.com/jquery-1.11.3.js"></script>
	<style>
	html, body {
	height: 100%;
	margin: 0;
	}
	import numpy as np
	from numpy.typing import NDArray

	class RunningMean:
	"""Like numpy.mean but aggregates data in chunks at a time."""

	def __init__(self, axis=None, keepdims=False):
	"""For axis and keepdims, see the documentation of these arg names in numpy.mean"""
	self.axis=axis
	self.keepdims=keepdims
	# some annoying document formatting requirements made me to this in tex:
	# \setmathfont{Cambria Math}
	# \setmainfont{Times New Roman}
	# and of course these microsoft fonts are not found when compiling with xelatex on ubuntu
	# this gist helps set up the texlive environment in ubuntu to find the fonts

	# thanks to maxwelleite: https://gist.github.com/maxwelleite/10774746
	# their script is way better and more automated, but I didn't want to sudo an entire script,
	# so below I have extracted the commands I want and made it clear where sudo is needed
	# I recommend running the below one by one to check that each step works
	# To try this example, save this to a file slicer_plot_data.py, then execute Slicer from the command line
	# with the arguments `--python-script slicer_plot_data.py`.

	import slicer, qt, vtk

	PLOT_TYPES = {
	"line" : slicer.vtkMRMLPlotSeriesNode.PlotTypeLine,
	"bar" : slicer.vtkMRMLPlotSeriesNode.PlotTypeBar,
	"scatter" : slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter,
	"scatterbar" : slicer.vtkMRMLPlotSeriesNode.PlotTypeScatterBar,