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parseColony.py
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parseColony.py
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"""Cell Universe Post-Processor 2
Converts colony.csv from Cell Universe to input
for radialtree.py and Cell Viewer"""
from config import *
def parseColony(pathname):
# read result from Cell Universe
f = open(pathname+"/"+lineageFilename, 'r')
data = [line.strip().split(',') for line in f]
f.close()
headers = {data[0][k]:k for k in range(len(data[0]))}
out = []
data.pop(0)
colony=[]
cells = {}
frame = [0,""]
# processing file
for cell in data:
line = {}
# ImageNumber, frameName
if frame[1]!=cell[headers["file"]]:
frame[0]+=1
frame[1]=cell[headers["file"]]
colony.append({
"frame": frame[1],
"cells": []
})
line["ImageNumber"]=str(frame[0])
# ObjectID
name = cell[headers["name"]]
line["ObjectID"]=name[1:]
# ParentObjectID
if frame[0]>1: line["ParentObjectID"]=name[1:-1]
else: line["ParentObjectID"]=''
if name not in cells: cells[name] = 1
else: line["ParentObjectID"]+=name[-1]
out.append(line)
# Colony
colony[-1]["cells"].append([
"\""+cell[headers["name"]]+"\"",
cell[headers["x"]],
cell[headers["y"]]
])
# output colony json file
fout = open(pathname+"/"+colonyFilename, 'w')
fout.write(
"{\n\t"+
"\"frames\": "+str(frame[0])+",\n\t"
"\"frameNumber\": {\n\t\t"+
"\"frame\": \"frameName\",\n\t\t"+
"\"cells\": [\n\t\t\t"+
"[\"name\",\"x\",\"y\"]\n\t\t"+
"]\n\t"
"}")
for i in range(frame[0]):
outframe = (",\n\t"+
"\""+str(i)+"\": {\n\t\t"+
"\"frame\": \""+colony[i]["frame"]+"\",\n\t\t"+
"\"cells\": [")
for cell in colony[i]["cells"]:
outframe += "\n\t\t\t["+cell[0]+","+cell[1]+","+cell[2]+"],"
fout.write(outframe[:-1]+"\n\t\t]\n\t}")
fout.write("\n}")
fout.close()
return out
if __name__ == '__main__':
# write to output file
f = open("processedColony.csv", 'w')
f.write("ImageNumber,ObjectID,ParentObjectID\n")
for line in parseColony("."):
f.write(line["ImageNumber"]+","+line["ObjectID"]+","+line["ParentObjectID"]+"\n")
f.close()