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dynamicSPECT
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pythonScripts
Andrej Studen@Labkey-KNM 7f7c5fe190 Clearing merge conflicts 1 rok temu
..
LambdaOptimization.png 5cb119b5ff Optimization hyperparameter lambda setting illustration for regularizing on IVF parameter A 1 rok temu
README.md bbe9982a4c Adding test.py slicer script 1 rok temu
analysis.py 8d8c79e32b Updating analysis.py to work with modified version of segmentation.py 1 rok temu
analyze.ipynb 345e0bdcec Minor updates to scripts, config file is also used in vangogh mode 1 rok temu
assignOrthancStudy.ipynb ad99d7cd50 Recent updates 1 rok temu
calculateCenters.py e556aa5b32 Adding update status function to report progress 1 rok temu
calculateK1.ipynb 1440d682a0 Adding scripts 3 lat temu
clusterAnalysis.ipynb 87d8bfd583 validating summaryIVF 1 rok temu
clusterAnalysisLeftovers.ipynb c317e06d8d Version that produced results sent in email to Luka, Oct 28th 2022. 2 lat temu
config.py 012848dc66 Adding regularization to compartment fits 1 rok temu
doAnalysis.py a4028e9849 Minor corrections to doAnalysis 1 rok temu
doPixelAnalysis.py 985248eb9f Changing loops in doPixelAnalysis 1 rok temu
doSummary.py 6f536a609c operable doSummary.py 1 rok temu
downloadPatient.py 1440d682a0 Adding scripts 3 lat temu
fitData.py 012848dc66 Adding regularization to compartment fits 1 rok temu
fitModel.py 012848dc66 Adding regularization to compartment fits 1 rok temu
generateCenters.ipynb fde4aa8d47 Up to generate centers, including matlab files 2 lat temu
geometry.py 504c2ae9db Adding port from matlab fitting to python fitting, new python code based on global optimization with lambda adjusted regularizer 1 rok temu
getData.py 5bffcfe431 Cleared error from getData updateStatus, making sure that status is also checked for entries with converted images 1 rok temu
loadData.py 012848dc66 Adding regularization to compartment fits 1 rok temu
parseDicom.py 9941f28c57 Adding convertToNRRD.py script 2 lat temu
pixelAnalysis.ipynb c317e06d8d Version that produced results sent in email to Luka, Oct 28th 2022. 2 lat temu
plotData.py a0af1ed42c Moving plotSegmentation from segmentation.py to plotData to avoid matplotlib dependency in Slicer, through convertToNRRD.py which depends on segmentation.py 1 rok temu
plotK1.ipynb 9941f28c57 Adding convertToNRRD.py script 2 lat temu
plotPolar.ipynb c317e06d8d Version that produced results sent in email to Luka, Oct 28th 2022. 2 lat temu
plotViews.ipynb 1440d682a0 Adding scripts 3 lat temu
segmentation.ipynb 15edb29494 Update to jupyter 1 rok temu
segmentation.py a0af1ed42c Moving plotSegmentation from segmentation.py to plotData to avoid matplotlib dependency in Slicer, through convertToNRRD.py which depends on segmentation.py 1 rok temu
selectCenters.ipynb 1440d682a0 Adding scripts 3 lat temu
statAnalysis.ipynb 1440d682a0 Adding scripts 3 lat temu
table.ipynb 1440d682a0 Adding scripts 3 lat temu
test.ipynb 8b606a3b56 Cleaning up listCreatedFiles in workflow 1 rok temu
vtkInterface.py 9941f28c57 Adding convertToNRRD.py script 2 lat temu
workflow.py 7f7c5fe190 Clearing merge conflicts 1 rok temu

README.md

Instructions

Look at `clusterAnalysis.ipynb' for a step by step algorithm.

The only required files for analysis are:

  • ../slicerScripts/convertToNRRD.py
  • analysis.py
  • segmentation.py
  • getData.py
  • config.py
  • segmentation.ipynb
  • clusterAnalysis.ipynb

The rest are for backup only.