berkels / match-series Goto Github PK
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Hi Berkels,
I tried to use your code to simply process my experimental data, it seems the code fails.
log:
Created directory results/stage1/0/
The par file content:
templateNamePattern D:/sampledata/sample%04d.dm4
templateNumOffset 0
templateNumStep 1
numTemplates 15
deformationModel 0
#templateSkipNums { 1 9 10 173 }
cropInput 0
cropStartX 512
cropStartY 512
dontResizeOrCropReference 0
preSmoothSigma 1
saveRefAndTempl 0
numExtraStages 2
saveDirectory results/
dontNormalizeInputImages 0
enhanceContrastSaturationPercentage 0.15
normalizeMinToZero 1
lambda 200
lambdaFactor 1
maxGDIterations 500
stopEpsilon 1e-6
startLevel 6
stopLevel 10
precisionLevel 10
refineStartLevel 10
refineStopLevel 10
checkboxWidth 16
resizeInput 0
dontAccumulateDeformation 0
reuseStage1Results 1
extraStagesLambdaFactor 0.1
useMedianAsNewTarget 1
calcInverseDeformation 0
skipStage1 0
saveNamedDeformedTemplates 1
saveNamedDeformedTemplatesUsingNearestNeighborInterpolation 1
saveNamedDeformedTemplatesExtendedWithMean 1
saveDeformedTemplates 1
saveNamedDeformedDMXTemplatesAsDMX 1
Hi Dr. Berkels, Thanks for sharing your work. I am wondering if there is any plan to support multithreaded CPU implementation or GPU implementation? Thanks.
Here is an example of a C++/CUDA code with python bindings:
https://github.com/prism-em/prismatic
Everything is in the same repository.
I have no idea how it is done.
I currently try to create a conda package:
conda-forge/staged-recipes#11956
To be able to install match-series
with all the required dependencies as easy as:
conda install -c conda-forge match-series
So to be able to fix one version of match-series
for future reference and to increase the reproducibility it would be great if you could create a Github release.
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