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])
# Ratio images
# 0 corresponds to the first mass image (e.g. mass 12.0)
# 1 corresponds to the second mass image (e.g. mass 13.0)
ratioProps1 = RatioProps(1, 0)
mp1 = MimsPlus(ui, ratioProps1)
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])
# Ratio images
# 0 corresponds to the first mass image (e.g. mass 12.0)
# 1 corresponds to the second mass image (e.g. mass 13.0)
ratioProps1 = RatioProps(1, 0)
