Steve Pieper pieper

Let me fetch the forum post to understand Mike's question.

Web Fetchhttps://discourse.slicer.org/t/bug-in-importlabelmaptosegmentationnode-if-multiple-parent-transforms/46524

Fetched from https://discourse.slicer.org/t/bug-in-importlabelmaptosegmentationnode-if-multiple-parent-transforms/46524

Let me look more carefully at the forum post to understand the details, and also look at the relevant source code in the Slicer repositories to understand the bug better.

Web Fetchhttps://discourse.slicer.org/t/bug-in-importlabelmaptosegmentationnode-if-multiple-parent-transforms/46524

	#!/usr/bin/env python3
	"""Export a Project's approved Annotations as an nnU-Net v2 dataset directory.

	For every case_id in the project's CohortResolution where the head Annotation
	matches --status (default approved) and has a seg_ref, this writes:

	<output_root>/Dataset<NNN>_<task>/imagesTr/<case_id>_0000.nrrd -> CT (from cohort)
	<output_root>/Dataset<NNN>_<task>/labelsTr/<case_id>.nrrd -> seg (from annotation)
	<output_root>/Dataset<NNN>_<task>/dataset.json -> nnU-Net manifest

	import warp as wp
	import numpy as np

	"""
	This is a demo of OpenCL code ported automatically to Warp using Google Gemini.

	Given this input file, the code below was generated and worked the first time.

	https://github.com/pieper/SlicerCL/blob/master/GrowCutCL/GrowCutCL.cl.in

	import json
	import random
	import sys

	try:
	import idc_index
	import pandas
	except ModuleNotFoundError:
	import pip
	pip.main("install idc_index".split())

	import numpy

	dataDir = "/opt/data/SlicerMorph/20231003-ColorizedVR"
	segName = "Segmentation"
	ctFullName = "deep_snail_2_14.9um_2k__rec1100"
	ctName = "deep_snail_2_14"
	try:
	slicer.util.getNode(segName)
	except slicer.util.MRMLNodeNotFoundException:
	slicer.util.loadVolume(f"{dataDir}/{ctFullName}.nrrd")

	import glob
	import numpy
	import os
	import random

	includeEdema = True

	exec(open("/opt/data/nac/neurosurgicalatlas/MONAI/labels.py").read())

	tureSynthSegGlob = "/opt/data/nac/neurosurgicalatlas/MONAI/Ture-subset-2022-12-03-nii-seg/Ture--.nrrd_synthseg.nii.gz"

	"""

	exec(open("/opt/data/nac/neurosurgicalatlas/ss2-Ture-028-registration.py").read())

	"""

	import glob
	from math import floor, ceil
	import numpy


	"""
	p = "/Volumes/GoogleDrive/My Drive/hacks/sardana.py"
	exec(open(p).read())

	Screencapture of result posted here (slide 7): https://docs.google.com/presentation/d/12cDI-HHQ4OhNTN4oqx-yFiyPAqvDB5sxKrimrWgdAOY/edit?usp=sharing

	"""

	#

	"""

	filePath = "/Users/pieper/slicer/latest/SlicerMorph/loadPointCloud.py"
	modelPath = "/opt/tmp/georeferenced_model.vtk"
	exec(open(filePath).read())


	"""

	modelNode = slicer.util.loadModel(modelPath)

	"""

	Display zarr from s3 buckets for example data from here:
	https://www.openmicroscopy.org/2020/11/04/zarr-data.html

	exec(open("/Users/pieper/idc/ngff.py").read())

	see also: /Volumes/GoogleDrive/My\ Drive/hacks/sardana.py
	https://gist.github.com/pieper/10ee6add544633f4c75dbb293ef087bc