from ij import IJ
from ij.gui import GenericDialog
gd = GenericDialog("Change Estimated Sarcomere Length")
gd.addNumericField("Estimated Sarcomere Length", 1.5, 0)
gd.showDialog()
ll = gd.getNextNumber()
IJ.setProperty("sarcomereLength", ll)
from ij import IJ
import sys
sys.path.append(
IJ.getDirectory("imagej") + "/jars/HaralickFeaturesInteractive/")
from Haralick_Features import Haralick_Features as hf
cmChan = int(IJ.getProperty("cmChan"))
analyte = WindowManager.getCurrentImage()
analyte.setC(cmChan)
title = analyte.getTitle()
cmNumber = IJ.getProperty("cmNumber")
if cmNumber is None:
cmNumber = 1
IJ.setProperty("cmNumber", cmNumber)
cmNumber += 1
sarcomereLength = IJ.getProperty("sarcomereLength")
if sarcomereLength is None:
sarcomereLength = 1.5
icalibration = analyte.getCalibration()
pixelDistance = round(icalibration.getRawX(sarcomereLength))
pixelDistance = round(icalibration.getRawX(sarcomereLength))
retval = findMaximaSeqs([
list(hfi) for hfi in hf().calculate(analyte, "Sarcomeres", 45,
sarcomereLength, 10, 8)
], pixelDistance)
print(list(retval))
valplot = WindowManager.getWindow(
"Angle-Distance Correlation Values").getPlot()
valplot.setColor("black")
histsum = sum(hist)
ii = 0
for jj in range(0, 65536):
ii += hist[jj]
if ii > histsum / 2:
break
return jj
gd = GenericDialog("Image Information")
gd.addNumericField("Cardiomyocye Stain Channel Number", 1, 0, 10, "")
gd.addNumericField("Nuclear Stain Channel Number", 2, 0, 10, "")
gd.showDialog()
cmChan = int(gd.getNextNumber())
nucChan = int(gd.getNextNumber())
IJ.setProperty("cmChan", cmChan)
IJ.setProperty("nucChan", nucChan)
analyte = WindowManager.getCurrentImage()
title = analyte.getTitle()
IJ.run("Split Channels")
nucTitle = "C{}-{}".format(nucChan, title)
nucIp = WindowManager.getImage(nucTitle)
nucIpMedian = calcMedian(nucIp)
IJ.run(nucIp, "Subtract...", "value=" + str(nucIpMedian) + " stack")
IJ.run("Merge Channels...",
"c1=[C1-{}] c2=[C2-{}] create".format(title, title))
cmt = ResultsTable()
cmt.show("Cardiomyocyte Results")
IJ.renameResults("Cardiomyocyte Results")
nuct = ResultsTable()