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LAMeasure.py
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LAMeasure.py
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from __future__ import with_statement
import sys
import os.path
import fnmatch
import datetime
import codecs
import java.lang.Float as JFloat
from ij import IJ, ImagePlus, Prefs
from ij.process import ImageProcessor, AutoThresholder, ImageConverter
from ij.plugin.filter import ThresholdToSelection
from ij.plugin.filter import ParticleAnalyzer as PA
from ij.measure import ResultsTable, Calibration
from fiji.util.gui import GenericDialogPlus
from fiji.threshold import Auto_Threshold
class ScanedImage(object):
def __init__(self, filename):
self.filename = filename
def set_auto_threshold_options(self, myMethod, noWhite, noBlack, doIwhite, doIset, doIlog, doIstackHistogram):
self.myMethod = myMethod
self.noWhite = noWhite
self.noBlack = noBlack
self.doIwhite = doIwhite
self.doIset = doIset
self.doIlog = doIlog
self.doIstackHistogram = doIstackHistogram
def set_pa_options(self, options, MINSIZE, MAXSIZE):
self.options = options
self.MINSIZE = MINSIZE
self.MAXSIZE = MAXSIZE
def measure(self):
imp = IJ.openImage(self.filename)
IJ.log("Input file: %s" % self.filename)
ImageConverter(imp).convertToGray8()
res = Auto_Threshold().exec(imp, self.myMethod, self.noWhite, self.noBlack, self.doIwhite, self.doIset, self.doIlog, self.doIstackHistogram)
rt = ResultsTable()
rt.showRowNumbers(False)
pa = PA(self.options, PA.AREA + PA.PERIMETER + PA.CIRCULARITY, rt, self.MINSIZE, self.MAXSIZE)
pa.analyze(imp)
self.result = self.rtToResult(rt)
self.mask = imp
def rtToResult(self, rt):
result = []
nrow = rt.size()
for i in range(nrow):
area = rt.getValue("Area", i)
perim = rt.getValue("Perim.", i)
circ = rt.getValue("Circ.", i)
ar = rt.getValue("AR", i)
round = rt.getValue("Round", i)
solidity = rt.getValue("Solidity", i)
result.append(PAResult((area, perim, circ, ar, round, solidity)))
return result
def saveMask(self, maskdir):
imp = self.mask
imp.getProcessor().invert()
filebasename = os.path.basename(self.filename)
maskfilename = os.path.join(maskdir, "mask_%s" % filebasename)
IJ.save(imp, maskfilename)
IJ.log("Mask image: %s\n" % maskfilename)
def saveResult(self, resdir, header):
filebasename = os.path.basename(self.filename)
resfilename = os.path.join(resdir, "res_%s.csv" % os.path.splitext(filebasename)[0])
with codecs.open(resfilename, "w", "utf-8") as f:
table = [",".join(header) + "\n"]
table += ["%s, %s\n" % (filebasename, row.asRow()) for row in self.result]
f.writelines(table)
IJ.log("Result: %s" % resfilename)
class PAResult(object):
def __init__(self, paResult):
self.area, self.perim, self.circ, self.ar, self.round, self.solidity = paResult
def asRow(self):
return "%f, %f, %f, %f, %f, %f" % (self.area, self.perim, self.circ, self.ar, self.round, self.solidity)
class LeafNumbers(object):
def __init__(self):
self.leafnumbers = []
def add(self, filebasename, leafnumber):
self.leafnumbers.append((filebasename, leafnumber))
def save(self, dir):
with codecs.open(os.path.join(dir, "leafnumbers.csv"), "w", "utf-8") as f:
f.writelines(["%s, %d\n" % fn for fn in self.leafnumbers])
class LAMeasure(object):
def __init__(self):
# Save current background value
bb = Prefs.blackBackground
Prefs.blackBackground = False
# PA args and options
distPixel, distCm, MINSIZE, dir, ext = self.getSettings()
MAXSIZE = JFloat.POSITIVE_INFINITY
options = PA.SHOW_NONE
# Auto_Threshold args
myMethod = "Minimum"
noWhite = False
noBlack = False
doIwhite = False
doIset = False
doIlog = True
doIstackHistogram = False
header = ["Filename", "Area", "Perim.", "Circ", "AR", "Round", "Solidity"]
self.setScale(distCm, distPixel)
maskdir = os.path.join(dir, "mask")
resdir = os.path.join(dir, "res")
for p in [maskdir, resdir]:
if not os.path.exists(p):
os.makedirs(p)
filenames = [os.path.join(dir, file) for file in os.listdir(dir) if fnmatch.fnmatch(file, ext)]
leafnumbers = LeafNumbers()
for filename in filenames:
filebasename = os.path.basename(filename)
scanedImage = ScanedImage(filename)
scanedImage.set_auto_threshold_options(myMethod, noWhite, noBlack, doIwhite, doIset, doIlog, doIstackHistogram)
scanedImage.set_pa_options(options, MINSIZE, MAXSIZE)
scanedImage.measure()
leafnumbers.add(filebasename, len(scanedImage.result))
scanedImage.saveMask(maskdir)
scanedImage.saveResult(resdir, header)
leafnumbers.save(dir)
# Reset background value
Prefs.blackBackground = bb
def getSettings(self):
gd = GenericDialogPlus("Settings")
gd.addNumericField("Distance in pixel", 600, 0)
gd.addNumericField("Distance in cm", 2.54, 2)
gd.addNumericField("Min. size (cm^2)", 0.5, 2)
gd.addDirectoryField("Directory", IJ.getDirectory("home"))
gd.addStringField("File extension", "*.jpg", 8)
gd.showDialog()
if gd.wasCanceled():
sys.exit()
else:
distPixel = gd.getNextNumber()
distCm = gd.getNextNumber()
minSize = gd.getNextNumber() * (distPixel / distCm) ** 2
imageDir = gd.getNextString()
ext = gd.getNextString()
return (distPixel, distCm, minSize, imageDir, ext)
def setScale(self, distCm, distPixel):
cal = Calibration()
cal.setUnit("cm")
cal.pixelWidth = distCm / distPixel
cal.pixelHeight = distCm / distPixel
ImagePlus().setGlobalCalibration(cal)
if __name__ == '__main__':
LAMeasure()