reading multichannel tiff

sardana.py

"""
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

"""

#
# make RGBA of three
#

referenceNode = getNode("1_post_uint8")
redArray = array(getNode("1_post_uint8").GetID())
greenArray = array(getNode("16_post_uint8").GetID())
blueArray = array(getNode("30_post_uint8").GetID())

try:
    rgbaNode = getNode("RGBAVolume")
except slicer.util.MRMLNodeNotFoundException:
    rgbaNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLVectorVolumeNode")
    rgbaNode.SetName("RGBAVolume")

referenceImage = referenceNode.GetImageData()
rgbaImage = vtk.vtkImageData()
rgbaImage.SetDimensions(referenceImage.GetDimensions())
rgbaImage.AllocateScalars(referenceImage.GetScalarType(), 4)
rgbaNode.SetAndObserveImageData(rgbaImage)

rgbaArray = slicer.util.array(rgbaNode.GetID())
rgbaArray[:,:,:,0] = redArray
rgbaArray[:,:,:,1] = greenArray
rgbaArray[:,:,:,2] = blueArray
rgbaArray[:,:,:,3] = (redArray + blueArray + greenArray) / 3

slicer.util.arrayFromVolumeModified(rgbaNode)

"""
volumeRenderingLogic = slicer.modules.volumerendering.logic()
displayNode = volumeRenderingLogic.CreateDefaultVolumeRenderingNodes(rgbaNode)
displayNode.SetVisibility(True)
# Enable direct RGBA color mapping
displayNode.GetVolumePropertyNode().GetVolumeProperty().SetIndependentComponents(False)
"""

#
# make RGB of three
#

referenceNode = getNode("1_post_uint8")
redArray = array(getNode("1_post_uint8").GetID())
greenArray = array(getNode("16_post_uint8").GetID())
blueArray = array(getNode("30_post_uint8").GetID())

try:
    rbgNode = getNode("RGBVolume")
except slicer.util.MRMLNodeNotFoundException:
    rbgNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLVectorVolumeNode")
    rbgNode.SetName("RGBVolume")

referenceImage = referenceNode.GetImageData()
rbgImage = vtk.vtkImageData()
rbgImage.SetDimensions(referenceImage.GetDimensions())
rbgImage.AllocateScalars(referenceImage.GetScalarType(), 3)
rbgNode.SetAndObserveImageData(rbgImage)

rbgArray = slicer.util.array(rbgNode.GetID())
rbgArray[:,:,:,0] = redArray
rbgArray[:,:,:,1] = greenArray
rbgArray[:,:,:,2] = blueArray

slicer.util.arrayFromVolumeModified(rbgNode)


#
# make RGB of all
#

referenceNode = getNode("1_post_uint8")
referenceImage = referenceNode.GetImageData()

nodes = getNodes('*_post_uint8')
nodeKeyList = list(nodes.keys())

nodeIndex = 0
nodeCount = len(nodeKeyList)

for iteration in range(int(nodeCount/3)):
    rbgNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLVectorVolumeNode")
    rbgNode.SetName("RGBVolume" + str(iteration))
    rbgImage = vtk.vtkImageData()
    rbgImage.SetDimensions(referenceImage.GetDimensions())
    rbgImage.AllocateScalars(referenceImage.GetScalarType(), 3)
    rbgNode.SetAndObserveImageData(rbgImage)
    redArray = slicer.util.array(nodes[nodeKeyList[nodeIndex+0]].GetID())
    greenArray = slicer.util.array(nodes[nodeKeyList[nodeIndex+1]].GetID())
    blueArray = slicer.util.array(nodes[nodeKeyList[nodeIndex+2]].GetID())
    nodeIndex += 3
    rbgArray = slicer.util.array(rbgNode.GetID())
    rbgArray[:,:,:,0] = redArray
    rbgArray[:,:,:,1] = greenArray
    rbgArray[:,:,:,2] = blueArray
    slicer.util.arrayFromVolumeModified(rbgNode)
    print("finished iteration " + str(iteration))



# rename files based on marker names

import csv
import shutil

markerNames = []
with open("/opt/data/idc/htan/Sardana/markers_SARDANA_csv.csv") as fp:
    reader = csv.reader(fp)
    for row in reader:
        markerNames.append(row[2])

rgbPath = "/opt/data/idc/htan/Sardana/RGB"

markerIndex = 1
for iteration in range(int(len(markerNames)/3)):
    destFileName = f"{rgbPath}/{markerNames[markerIndex]}+{markerNames[markerIndex+1]}+{markerNames[markerIndex+2]}.nrrd"
    srcFileName = f"{rgbPath}/RGBVolume{iteration}.nrrd"
    print(f"copy {srcFileName} {destFileName}")
    shutil.copyfile(srcFileName, destFileName)
    markerIndex += 3