def measureChannels(ROIset, imp, frameNumber):
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
nChannels = imp.getNChannels()
for channel in range(nChannels):
target_imp = extractChannel(imp, channel + 1, frameNumber)
target_imp.show()
for roi in ROIset:
rm.setSelectedIndexes([roi])
IJ.setAutoThreshold(target_imp, "Huang dark")
rm.runCommand(target_imp, "Measure")
target_imp.close()
# except OSError as e:
# if e.errno != errno.EEXIST:
# raise
Nuclei = Segment_Nuclei(imp1, nucleus_channel)
IJ.run(
Nuclei, "Analyze Particles...",
"size=5000-Infinity pixel circularity=0.3-1.00 add exclude stack")
IJ.run("Tile", "")
time.sleep(0.2)
name1 = imp1.getTitle()
nuclei_count = rm.getCount()
if rm.getCount() != 0:
rois = rm.getIndexes()
rm.setSelectedIndexes(rois)
if rm.getCount() > 1:
rm.runCommand("Combine")
rm.runCommand("Delete")
rm.runCommand("Add")
rois1 = rm.getIndexes()
for roi in rois1:
rm.select(imp1, roi)
imp1.setC(1)
IJ.run(imp1, "Draw", "slice")
IJ.selectWindow(name1)
IJ.run("Select None")
print nuclei_count
nuclei_count_sum = nuclei_count_sum + nuclei_count
from java.util import Random
import random
fields = random.sample(range(0, gridSquares), fieldsNeeded)
# print fields
# convert the list to an array that is usable by ROI Manager
from array import array
aFields = array('i', [0] * fieldsNeeded)
aFields = fields
# select the rois and save as temp
rm.setSelectedIndexes(aFields)
rm.runCommand("save selected", os.path.join(folder, "selected.zip"))
# reset ROI mgr, open the temp
rm.reset()
rm.runCommand("Open", os.path.join(folder, "selected.zip"))
# rename the remaining ROIs so that VSI can deal with them
# i is the index within ROI Mgr. i+1 is the number given by VSI Reader
# get base name of ROIs
# searching the last 5 characters for the hashmark because there are usually 2 in the ROI name
oldname = rm.getName(0)
hashPos = oldname.find("#",-5) + 1
def adjustRoiAndMeasure(imp, frameNumber, dstDir):
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
nROIs = rm.getCount()
indexlist = range(nROIs)
if nROIs > 2:
for roi in indexlist:
indexlist_copy = list(indexlist)
del indexlist_copy[roi]
rm.setSelectedIndexes(indexlist_copy)
rm.runCommand(imp, "Combine")
IJ.run(imp, "Make Inverse", "")
rm.addRoi(imp.getRoi())
new_nROI = rm.getCount()
rm.setSelectedIndexes([roi, new_nROI - 1])
rm.runCommand(imp, "AND")
if imp.getRoi():
rm.addRoi(imp.getRoi())
rm.setSelectedIndexes([new_nROI])
rm.runCommand("Rename", "Cell" + str(roi))
else:
rm.setSelectedIndexes([roi])
rm.addRoi(imp.getRoi())
rm.setSelectedIndexes([new_nROI - 1])
rm.runCommand(imp, "Delete")
elif nROIs == 2:
for roi in indexlist:
indexlist_copy = list(indexlist)
del indexlist_copy[roi]
rm.setSelectedIndexes(indexlist_copy)
IJ.run(imp, "Make Inverse", "")
rm.addRoi(imp.getRoi())
new_nROI = rm.getCount()
rm.setSelectedIndexes([roi, new_nROI - 1])
rm.runCommand(imp, "AND")
rm.addRoi(imp.getRoi())
rm.setSelectedIndexes([new_nROI])
rm.runCommand("Rename", "Cell" + str(roi))
rm.setSelectedIndexes([new_nROI - 1])
rm.runCommand(imp, "Delete")
elif nROIs == 1:
nROIs = 0
new_nROI = 1
rm.setSelectedIndexes([new_nROI])
rm.runCommand("Rename", "Cell0")
else:
return
adjustedROIs = range(nROIs, new_nROI, 1)
rm.setSelectedIndexes(adjustedROIs)
measureChannels(adjustedROIs, imp, frameNumber)
rm.setSelectedIndexes(adjustedROIs)
rm.runCommand("Save selected",
dstDir + "\\Frame " + str(frameNumber + 1) + " roi set.zip")
rm.runCommand(imp, "Deselect")
rm.runCommand(imp, "Delete")
rm.runCommand(
"Save",
analysisOut + File.separatorChar + "ROIindividual_wt" + ".zip")
if image == newPaths[1]:
rm.runCommand(
"Save",
analysisOut + File.separatorChar + "ROIindividual_dic" + ".zip")
if image == newPaths[2]:
rm.runCommand(
"Save",
analysisOut + File.separatorChar + "ROIindividual_mut" + ".zip")
if image == newPaths[3]:
rm.runCommand(
"Save",
analysisOut + File.separatorChar + "ROIindividual_bg" + ".zip")
rm.setSelectedIndexes(range(0, rct - 1))
x = rm.getSelectedIndexes()
rm.runCommand("Deselect")
rm.setSelectedIndexes(x)
rm.runCommand("Delete")
rm.select(0)
if image == newPaths[0]:
rm.runCommand(
"Save", analysisOut + File.separatorChar + "ROIcombo_wt" + ".zip")
if image == newPaths[1]:
rm.runCommand(
"Save", analysisOut + File.separatorChar + "ROIcombo_dic" + ".zip")
if image == newPaths[2]:
rm.runCommand(
"Save", analysisOut + File.separatorChar + "ROIcombo_mut" + ".zip")
if image == newPaths[3]:
