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dvc.yaml
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dvc.yaml
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stages:
cachecodec:
foreach: ${videos}
do:
cmd: julia -t auto --project=. src/reducevideo.jl cachecodec ${item.mouseid} ${key}
deps:
- ${item.mouseid}/${key}.avi
- ${item.mouseid}/${key}-synchronizedtimestamps.csv
outs:
- ${item.mouseid}/pca/${key}-cropped-raw.dat: {persist: true}
pca:
foreach: ${sessions}
do:
cmd: julia -t auto --project=. src/reducevideo.jl pca ${key}
deps:
- ${key}/pca/${item.videos[0]}-cropped-raw.dat
- ${key}/pca/${item.videos[1]}-cropped-raw.dat
params:
- maxpc
- chunksize
- chunkdim
- backgroundrate
- diffimagerate
outs:
- ${key}/pca/${key}-pc-latent.dat: {persist: true}
- ${key}/pca/${key}-pc-latent.csv: {persist: true}
dpca:
foreach: ${sessions}
do:
cmd: julia -t auto --project=. src/reducevideo.jl dpca ${key}
deps:
- ${key}/pca/${item.videos[0]}-cropped-raw.dat
- ${key}/pca/${item.videos[1]}-cropped-raw.dat
params:
- maxpc
- chunksize
- chunkdim
- backgroundrate
- diffimagerate
outs:
- ${key}/pca/${key}-dpc-latent.dat: {persist: true}
- ${key}/pca/${key}-dpc-latent.csv: {persist: true}
display:
foreach: ${sessions}
do:
cmd: julia -t auto --project=. src/reducevideo.jl display ${key}
deps:
- ${key}/pca/${key}-pc-latent.dat
- ${key}/pca/${key}-dpc-latent.dat
outs:
- ${key}/pca/${key}-pc-latent-short.png: {persist: true}
- ${key}/pca/${key}-pc-latent-long.png: {persist: true}
- ${key}/pca/${key}-dpc-latent-short.png: {persist: true}
- ${key}/pca/${key}-dpc-latent-long.png: {persist: true}
threshold:
foreach: ${sessions}
do:
cmd:
- julia -t auto --project=. src/reducevideo.jl threshold ${key}
- cp ${key}/pca/${key}-pc-latent-motionenergy,threshold.csv ${rawbehaviourrootpath}/${key}/${key}-motionenergy,threshold.csv
- chmod u+w ${rawbehaviourrootpath}/${key}/${key}-motionenergy,threshold.csv
deps:
- ${key}/pca/${key}-dpc-latent.dat
params:
- kernelhalfwidth
- motionthresholds
- proportiontrialmotionthresholds
outs:
- ${key}/pca/${key}-dpc-latent-motionenergy,threshold.csv: {persist: true}
- ${key}/pca/${key}-dpc-latent-motionenergy,threshold.png: {persist: true}
- ${key}/pca/${key}-motionenergy,threshold-view.avi: {persist: true}
- ${key}/pca/${key}-dpc-latent-motionenergy,levels.csv: {persist: true}
- ${key}/pca/${key}-dpc-latent-motionenergy,levelstrials.csv: {persist: true}
bodyparts:
foreach: ${sessions}
do:
cmd:
- julia -t auto --project=. src/reducevideo.jl bodyparts ${key}
deps:
- ${key}/pca/${item.videos[0]}-cropped-raw.dat
- ${key}/pca/${item.videos[1]}-cropped-raw.dat
params:
- bodypartnames
- bodypartboundaries.${key}
outs:
- ${key}/pca/${key}-bodyparts,rois.png: {persist: true}
- ${key}/pca/${key}-absolutemotion,bodyparts.csv: {persist: true}
- ${key}/pca/${key}-bodyparts-motionenergy,levels.csv: {persist: true}
- ${key}/pca/${key}-bodyparts,nose-motionenergy,levelstrials.csv: {persist: true}
- ${key}/pca/${key}-bodyparts,mouth-motionenergy,levelstrials.csv: {persist: true}
- ${key}/pca/${key}-bodyparts,eye-motionenergy,levelstrials.csv: {persist: true}
- ${key}/pca/${key}-bodyparts,ear-motionenergy,levelstrials.csv: {persist: true}
- ${key}/pca/${key}-bodyparts,forepaw-motionenergy,levelstrials.csv: {persist: true}
- ${key}/pca/${key}-bodyparts,back-motionenergy,levelstrials.csv: {persist: true}
reconstruct:
foreach: ${sessions}
do:
cmd: julia -t auto --project=. src/reducevideo.jl reconstruct ${key}
deps:
- ${key}/pca/${item.videos[0]}-cropped-raw.dat
- ${key}/pca/${item.videos[1]}-cropped-raw.dat
- ${key}/pca/${key}-dpc-latent.dat
params:
- maxpc
- reconstructpc
- downsample
- chunksize
- chunkdim
- backgroundrate
- diffimagerate
- exportframestart
- exportframeduration
outs:
- ${key}/pca/${key}-dpc-reconstruction.avi: {persist: true}
- ${key}/pca/${key}-reconstructionframes-dpcs.csv: {persist: true}