Steve Pieper pieper
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| 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 |
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| import json | |
| import random | |
| import sys | |
| try: | |
| import idc_index | |
| import pandas | |
| except ModuleNotFoundError: | |
| import pip | |
| pip.main("install idc_index".split()) |
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| 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") |
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| 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" |
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| """ | |
| exec(open("/opt/data/nac/neurosurgicalatlas/ss2-Ture-028-registration.py").read()) | |
| """ | |
| import glob | |
| from math import floor, ceil | |
| import numpy |
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| """ | |
| 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 | |
| """ | |
| # |
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| """ | |
| filePath = "/Users/pieper/slicer/latest/SlicerMorph/loadPointCloud.py" | |
| modelPath = "/opt/tmp/georeferenced_model.vtk" | |
| exec(open(filePath).read()) | |
| """ | |
| modelNode = slicer.util.loadModel(modelPath) |
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| """ | |
| 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 |
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| """ | |
| 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
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| #!/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 | |
| """ |
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