orig = ImagePlus(fi)
strName = os.path.basename(fi)
strName = strName.split('.')[0]
lStr = strName.split('-')
l = len(lStr)
strNum = lStr[l-1]
iNum = int(strNum)
orig.setTitle(strNum)
if i == 1:
# a hack to get the scale bars to work reliably
foo = orig.duplicate()
IJ.run(foo, "RGB Color", "")
IJ.run(foo, "Add Scale Bar", strBar)
iZero = jmg.findI0(orig, maxSearchFrac=0.5, chAvg=5)
# print(iZero)
rt = jmg.anaParticlesWatershed(orig, minPx=30)
nMeas = rt.getCounter()
nCols = rt.getLastColumn()
lArea = rt.getColumn(rt.getColumnIndex("Area"))
lMode = rt.getColumn(rt.getColumnIndex("Mode"))
# lPeri = rt.getColumn(rt.getColumnIndex("Perim."))
# lMaj = rt.getColumn(rt.getColumnIndex("Major"))
# lMin = rt.getColumn(rt.getColumnIndex("Minor"))
lCirc = rt.getColumn(rt.getColumnIndex("Circ."))
# lFeretX = rt.getColumn(rt.getColumnIndex("FeretX"))
# lFeretY = rt.getColumn(rt.getColumnIndex("FeretY"))
lAspRat = rt.getColumn(rt.getColumnIndex("AR"))
lRound = rt.getColumn(rt.getColumnIndex("Round"))
lSolid = rt.getColumn(rt.getColumnIndex("Solidity"))
for j in range(len(lArea)):
jmg.ensureDir(sRptPath)
sRptCsvPath = sRptPath + sampID + ".csv"
sRptImgPath = sRptPath + "png/"
jmg.ensureDir(sRptImgPath)
orig = ImagePlus(sImgPath)
strName = os.path.basename(sImgPath)
strName = strName.split('.')[0]
orig.setTitle(strName)
# orig.show()
iZero = jmg.findI0(orig, maxSearchFrac=0.5, chAvg=5)
print(iZero)
# [ana, rt] = anaParticles(orig, minSize, maxSize, minCirc, bHeadless=bHeadless)
rt = jmg.anaParticlesWatershed(orig)
orig.show()
nMeas = rt.getCounter()
print("%d particles detected in image %d" % (nMeas,1) )
nCols = rt.getLastColumn()
if bVerbose == True:
for j in range(nCols+1):
print(rt.getColumnHeading(j))
print("Area = %d" % rt.getColumnIndex("Area"))
print("Mean = %d" % rt.getColumnIndex("Mean"))
print("Mode = %d" % rt.getColumnIndex("Mode"))
print("Perim. = %d" % rt.getColumnIndex("Perim."))
print("Major = %d" % rt.getColumnIndex("Major"))
i += 1
orig = ImagePlus(fi)
orig = jmg.calibImageDirect(orig, umPerPx, units=-6)
strName = orig.getShortTitle()
strNum = strName.split('IMAGE')[1]
iNum = int(strNum)
strName = "%s-%02d" % (sampID, iNum )
orig.setTitle(strName)
orig.show()
if i == 1:
# a hack to get the scale bars to work reliably
foo = orig.duplicate()
IJ.run(foo, "RGB Color", "")
IJ.run(foo, "Add Scale Bar", strBar)
rt = jmg.anaParticlesWatershed(orig, strThrMeth="method=Otsu white", bFillHoles=True, minPx=minArea, maxPx=maxArea, minCirc=minCirc, maxAR=maxAR)
nMeas = rt.getCounter()
nCols = rt.getLastColumn()
lArea = rt.getColumn(rt.getColumnIndex("Area"))
lMode = rt.getColumn(rt.getColumnIndex("Mode"))
# lPeri = rt.getColumn(rt.getColumnIndex("Perim."))
# lMaj = rt.getColumn(rt.getColumnIndex("Major"))
# lMin = rt.getColumn(rt.getColumnIndex("Minor"))
lCirc = rt.getColumn(rt.getColumnIndex("Circ."))
# lFeretX = rt.getColumn(rt.getColumnIndex("FeretX"))
# lFeretY = rt.getColumn(rt.getColumnIndex("FeretY"))
lAspRat = rt.getColumn(rt.getColumnIndex("AR"))
lRound = rt.getColumn(rt.getColumnIndex("Round"))
lSolid = rt.getColumn(rt.getColumnIndex("Solidity"))
k = 0
for r in ra:
i += 1
rLab = "%d" % i
r.setName(rLab)
imp = addRoiToOverlay(imp, r, labCol=labCol, linCol=linCol)
# let's put a PointRoi outside the image to get the overlays all the same color
r = PointRoi(-10, -10)
imp = addRoiToOverlay(imp, r, labCol=labCol, linCol=linCol)
# clear the roi manager and return the results table
rm.reset()
rm.close()
if bDebug == False:
wrk.changes = False
wrk.close()
imp.setTitle(title)
return rt
closeRW = False
IJ.run("Blobs (25K)")
ori = IJ.getImage()
myRT = jmg.anaParticlesWatershed(ori)
myRT.show("Results")
if closeRW:
myRT.getResultsWindow().close(False)
else:
myRT.show("Results")
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
import glob
import time
from math import sqrt
from ij import IJ
from ij import ImagePlus
import jmFijiGen as jmg
orig = IJ.getImage()
orig.setTitle("orig")
print(orig.getShortTitle())
iZero = jmg.findI0(orig, maxSearchFrac=0.5, chAvg=5)
print(iZero)
rt = jmg.anaParticlesWatershed(orig, strThrMeth="method=Otsu white", bFillHoles=True, minPx=7, maxPx=150)
nMeas = rt.getCounter()
print(nMeas)
