#////////////////////////////
# Loop over files.
#////////////////////////////
for i in range(len(imFileNames)):
imFile = File(imFileNames[i])
roiFile = File(roiFileNames[i])
#IJ.log("Opening: "+imFileNames[i])
ui.openFile(imFile)
#IJ.log("Opening: "+roiFileNames[i])
ui.openFile(roiFile)
#////////////////////////////
# Get the planes.
#////////////////////////////
planes = ui.getmimsTomography().getPlanes()
#////////////////////////////
# Get the rois.
#////////////////////////////
rois = ui.getRoiManager().getAllROIs()
#////////////////////////////
# Get images.
#////////////////////////////
imageArray = ArrayList()
massimages = ui.getOpenMassImages()
for j in range(len(massimages)):
imageArray.add(massimages[j])
#////////////////////////////
for i in range(len(imFileName)):
#where is this going?
#print "Opening: " #+ imFileName[i] + ", " roiFileName[i]
imFile = File(imDirName, imFileName[i])
roiFile = File(imDirName, roiFileName[i])
IJ.log("Opening: "+imFileName[i])
ui.openFile(imFile)
IJ.log("Opening: "+roiFileName[i])
ui.openFile(roiFile)
#////////////////////////////
# Get the planes.
#////////////////////////////
planes = ui.getmimsTomography().getPlanes()
#////////////////////////////
# Get the rois.
#////////////////////////////
rois = ui.getRoiManager().getAllROIs()
#////////////////////////////
# Get images.
#////////////////////////////
imageArray = ArrayList()
massimages = ui.getOpenMassImages()
for j in range(len(massimages)):
imageArray.add(massimages[j])
