Steve Pieper pieper

pieper / fish.py

Last active October 4, 2023 22:48

RGBA volume rendering in 3D Slicer from segmentation

	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")

pieper / segment-names.py

Created June 13, 2023 16:02

Example of assigning segment names from table

	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"

pieper / ss2-Ture-028-registration.py

Created December 8, 2022 18:49

example slicer transforms

	"""

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

	"""

	import glob
	from math import floor, ceil
	import numpy

pieper / sardana.py

Created June 27, 2022 16:21

reading multichannel tiff


	"""
	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

	"""

	#

pieper / loadPointCloud.py

Created June 3, 2022 20:57

Load a ply point cloud in Slicer

	"""

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


	"""

	modelNode = slicer.util.loadModel(modelPath)

pieper / ngff.py

Last active July 6, 2022 13:14

Display NGFF volume data in 3D Slicer

	"""

	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

pieper / slicer-compute.py

Created May 21, 2022 20:57

Slicer with python WebGPU compute shader

	"""

	Install wgpu as described here: https://github.com/pygfx/wgpu-py

	Tested with Slicer 5.0.2 and wgpu 537c3eab68e9eef77681fc5545532380df26d8cc (basically 0.8.1)

	exec(open("./slicer-compute.py").read())

	"""

pieper / vr-depthpeel-crop.py

Last active June 21, 2021 17:03

Example script related to this discussion: https://discourse.slicer.org/t/trying-to-diagnose-an-issue-with-virtualgl-and-slicer/17685/14

	#!/usr/bin/env python

	comment = """
	You can use this script with either Slicer's python wrapped VTK or with pip installed VTK like this:

	~/Downloads/Slicer-4.13.0-2021-06-18-linux-amd64/bin/PythonSlicer vr-depth-crop.py

	python vr-depth-crop.py

	"""

pieper / make.log

Created August 1, 2020 19:49

make package output on mac

	pieper@hive Slicer-build % time make package
	[ 0%] Built target ExtensionWizard-Resources
	[ 0%] Built target SlicerPythonResources
	[ 3%] Built target CopySlicerPythonScriptFiles
	[ 3%] Built target CompileSlicerPythonFiles
	[ 9%] Built target CopySlicerPythonResourceFiles
	[ 12%] Built target SlicerData
	[ 12%] Configuring vtkSlicerVersionConfigure.h
	-- Configuring Slicer release type [Experimental]
	-- Found Git: /usr/local/bin/git

pieper / InstallSlicerModuleFromGit.py

Created June 27, 2020 16:37

	import os
	import shutil

	archiveFilePath = os.path.join(slicer.app.temporaryPath, "master.zip")
	outputDir = os.path.join(slicer.app.temporaryPath, "SlicerImageStacks")

	try:
	os.remove(archiveFilePath)
	except FileNotFoundError:
	pass