def getFlipArray(maskPAImgPlus):
"""Given the PA-aligned mask image, return a list of booleans, indicating whether or not we should flip the corresponding index"""
maskPAImgPlus.show()
# IJ.run(maskPAImgPlus, "Shape Smoothing", "relative_proportion_fds=15 absolute_number_fds=2 keep=[Relative_proportion of FDs] stack");
IJ.run("Set Measurements...", "shape")
IJ.setThreshold(maskPAImgPlus, 1, 1000, "No Update")
stk = maskPAImgPlus.getStack()
tableLeft = ResultsTable()
PA.setResultsTable(tableLeft)
IJ.makeRectangle(0, 0,
maskPAImgPlus.getWidth() / 2 - 5,
maskPAImgPlus.getHeight())
IJ.run(maskPAImgPlus, "Analyze Particles...", "stack")
tableRight = ResultsTable()
PA.setResultsTable(tableRight)
IJ.makeRectangle(maskPAImgPlus.getWidth() / 2 - 5, 0,
maskPAImgPlus.getWidth() / 2 + 5,
maskPAImgPlus.getHeight())
IJ.run(maskPAImgPlus, "Analyze Particles...", "stack")
maskPAImgPlus.hide()
IJ.resetThreshold(maskPAImgPlus)
leftCirc = [tableLeft.getValue("Circ.", i) for i in range(stk.getSize())]
rightCirc = [tableRight.getValue("Circ.", i) for i in range(stk.getSize())]
return [leftCirc[i] < rightCirc[i] for i in range(len(leftCirc))]
def run_straighten(roiWindowsize=4):
""" Original straightening function based on Nick's macro. Used in final version.
Returns coordinate string used to make centerline. """
IJ.run("Set Measurements...", "mean min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80")
numPoints = 512 / roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
for i in range(0, 512, roiWindowsize):
IJ.run("Clear Results")
IJ.makeRectangle(i, 0, roiWindowsize, 512)
IJ.run("Measure")
table = RT.getResultsTable()
xvals.append(i + roiWindowsize / 2)
yvals.append(RT.getValue(table, "YM", 0))
maxvals.append((RT.getValue(table, "Max", 0)))
if maxvals[counter] == 0 and counter > 0:
yvals[counter] = yvals[counter - 1]
counter += 1
coords = ""
for i in range(numPoints - 1):
coords += str(xvals[i]) + ", " + str(yvals[i]) + ", "
coords += str(xvals[numPoints - 1]) + ", " + str(yvals[numPoints - 1])
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")
return coords
def run_straighten(roiWindowsize = 4):
""" Original straightening function based on Nick's macro. Used in final version.
Returns coordinate string used to make centerline. """
IJ.run("Set Measurements...", "mean min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80");
numPoints = 512/roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
for i in range(0, 512, roiWindowsize):
IJ.run("Clear Results")
IJ.makeRectangle(i, 0, roiWindowsize, 512)
IJ.run("Measure")
table = RT.getResultsTable()
xvals.append(i + roiWindowsize/2)
yvals.append(RT.getValue(table, "YM", 0))
maxvals.append((RT.getValue(table, "Max", 0)))
if maxvals[counter] == 0 and counter > 0:
yvals[counter] = yvals[counter - 1]
counter += 1
coords = ""
for i in range(numPoints - 1):
coords += str(xvals[i]) + ", " + str(yvals[i]) +", "
coords += str(xvals[numPoints-1]) + ", " + str(yvals[numPoints-1])
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
return coords
def straighten_roi_rotation(roiWindowsize = 8):
""" Root straightening function that rotates ROI to follow root slope.
Does not work properly.
"""
IJ.run("Set Measurements...", "mean standard min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80");
#numPoints = 512/roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
maxIters = 800/roiWindowsize
minIters = 10
imp = IJ.getImage().getProcessor()
rm = RoiManager()
if find_first_pixel(0,imp) == None or find_last_pixel(0,imp)[1] == None:
return
y = (find_first_pixel(0,imp)[1]+find_last_pixel(0,imp)[1])/2
roi = roiWindow_(imp, center = (roiWindowsize/2,y), width = roiWindowsize, height = 512)
xvals.append(roiWindowsize/2)
yvals.append(y)
maxvals.append(0)
roi.findTilt_()
i = 0
while i < maxIters and roi.containsRoot_():
roi.advance_(roiWindowsize)
IJ.run("Clear Results")
IJ.run("Measure")
table = RT.getResultsTable()
x = RT.getValue(table, "XM", 0)
y = RT.getValue(table, "YM", 0)
if imp.getPixel(int(x),int(y)) != 0:
xvals.append(x)
yvals.append(y)
maxvals.append((RT.getValue(table, "Max", 0)))
#roi.advance_(roiWindowsize)
print "here"
roi.unrotateRoot_()
IJ.run("Clear Results")
IJ.run("Measure")
roi.restoreCenter_(RT.getValue(table, "XM", 0), RT.getValue(table, "YM", 0))
#exit(1)
sleep(.5)
roi.findTilt_()
i += 1
coords = ""
for i in range(len(xvals)-1):
coords += str(xvals[i]) + ", " + str(yvals[i]) +", "
coords += str(xvals[len(xvals)-1]) + ", " + str(yvals[len(xvals)-1])
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
def containsRoot_(self):
IJ.run("Clear Results")
IJ.run("Measure")
table = RT.getResultsTable()
if RT.getValue(table, "Max", 0) == 0:
return False
return True
def measure_growth(imgDir, filename = "Fiji_Growth.txt"):
""" Collects measurement data in pixels and writes to a file. Uses straightened binary images"""
f = open(imgDir + filename, 'w')
f.write("Img number\tEnd point (pixels)\n")
IJ.run("Set Measurements...", "area mean min center redirect=None decimal=3")
index = "000000000"
filename = imgDir + "/binary" + "/img_" + index + "__000-padded.tif"
while path.exists(filename):
imp = IJ.openImage(filename)
imp.show()
IJ.run("Clear Results")
for i in xrange(800): #hard coded to target length for now
IJ.makeRectangle(i, 0, 1, 80)
IJ.run("Measure")
table = RT.getResultsTable()
#print "i:", i, "counter:", table.getCounter()
maxi = RT.getValue(table, "Max", i)
if maxi == 0:
f.write(str(int(index)) + "\t" + str(i) + "\n")
break
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index)+1))
filename = imgDir + "/padded" + "/img_" + index + "__000-padded.tif"
f.close()
def containsRoot_(self):
IJ.run("Clear Results")
IJ.run("Measure")
table = RT.getResultsTable()
if RT.getValue(table, "Max", 0) == 0:
return False
return True
def measure_growth(imgDir, filename="Fiji_Growth.txt"):
""" Collects measurement data in pixels and writes to a file. Uses straightened binary images"""
f = open(imgDir + filename, 'w')
f.write("Img number\tEnd point (pixels)\n")
IJ.run("Set Measurements...",
"area mean min center redirect=None decimal=3")
index = "000000000"
filename = imgDir + "/binary" + "/img_" + index + "__000-padded.tif"
while path.exists(filename):
imp = IJ.openImage(filename)
imp.show()
IJ.run("Clear Results")
for i in xrange(800): #hard coded to target length for now
IJ.makeRectangle(i, 0, 1, 80)
IJ.run("Measure")
table = RT.getResultsTable()
#print "i:", i, "counter:", table.getCounter()
maxi = RT.getValue(table, "Max", i)
if maxi == 0:
f.write(str(int(index)) + "\t" + str(i) + "\n")
break
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index) + 1))
filename = imgDir + "/padded" + "/img_" + index + "__000-padded.tif"
f.close()
def quantify(quantgfx, labelgfx, table, nFrame, originalTitle):
results = ResultsTable()
clij2.statisticsOfBackgroundAndLabelledPixels(gfx4, gfx5, results)
for i in range(results.size()):
table.incrementCounter()
table.addValue("Frame (Time)", nFrame)
table.addValue("Label", i)
table.addValue("MEAN_INTENSITY", results.getValue("MEAN_INTENSITY", i))
table.addValue("SUM_INTENSITY", results.getValue("SUM_INTENSITY", i))
table.addValue("MINIMUM_INTENSITY",
results.getValue("MINIMUM_INTENSITY", i))
table.addValue("MAXIMUM_INTENSITY",
results.getValue("MAXIMUM_INTENSITY", i))
table.addValue("STANDARD_DEVIATION_INTENSITY",
results.getValue("STANDARD_DEVIATION_INTENSITY", i))
table.addValue("PIXEL_COUNT", results.getValue("PIXEL_COUNT", i))
table.addValue("CENTROID_X", results.getValue("CENTROID_X", i))
table.addValue("CENTROID_Y", results.getValue("CENTROID_Y", i))
table.addValue("CENTROID_Z", results.getValue("CENTROID_Z", i))
table.addValue("File name", originalTitle)
return table
if ".ome" in dL:
#open the images as virtual stack
imp = IJ.run(
"Bio-Formats", "open=[" + dL +
"] color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT use_virtual_stack"
)
imp = IJ.getImage()
#get right name for duplication of the desired frame
if n < 10:
numstr = "000" + str(n)
elif n < 100:
numstr = "00" + str(n)
elif n > 99:
numstr = "0" + str(n)
if choice == 1:
choose = RT.getValue(metaRT, "Frame selected", n - 1)
#duplicate the right frame and give it the right title
impDup = IJ.run(
"Duplicate...", "title=Image_R" + str(numstr) +
" duplicate frames=" + str(choose) + "")
imp.close()
# add 1 to the counter
n = n + 1
#get list imageplus objects of all open images
impl = [WM.getImage(id) for id in WM.getIDList()]
end = len(impl)
imp2 = impl[0]
ti = 0
#concatenate all the frames to a time lapse
flipIfNecessary(getFlipArray(maskPA), [img410PA, img470PA, maskPA])
img410PA.show()
img470PA.show()
# MORPHOLOGICAL MEASUREMENTS
# These are done on the rotated image mask
scales = {
"4x4": 2.58,
"2x2": 1.29
}
morphTable = ResultsTable()
PA.setResultsTable(morphTable)
maskPA.show()
IJ.run(maskPA, "Select None", "")
IJ.run(maskPA, "Set Scale...", "distance=1 known=" + str(scales[binning]) + " pixel=1 unit=μm"); #TODO scale?
IJ.run(maskPA, "Set Measurements...", "area centroid center perimeter bounding fit shape feret's median skewness kurtosis scientific redirect=None decimal=7");
IJ.run(maskPA, "Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing stack");
morph_headings = morphTable.getColumnHeadings().strip(' ').split('\t')
for m_heading in morph_headings[1:]: # because of formatting, the first is empty
addValues(dataTable, m_heading, [morphTable.getValue(m_heading, i) for i in range(morphTable.size())])
for imPlus in [img410PA, img470PA, maskPA]:
cropStack(imPlus)
IJ.saveAsTiff(imPlus, os.path.join(PARENT_DIR, imPlus.getTitle()))
dataTable.show("Measurements")
dataTable.save(os.path.join(PARENT_DIR, 'measurements.csv'))
def fretCalculations(imp1, nFrame, donorChannel, acceptorChannel,
acceptorChannel2, table, gfx1, gfx2, gfx3, gfx4, gfx5,
originalTitle):
donorImp = extractChannel(imp1, donorChannel, nFrame)
acceptorImp = extractChannel(imp1, acceptorChannel, nFrame)
acceptorImp2 = extractChannel(imp1, acceptorChannel2, nFrame)
#push donor and acceptor channels to gpu and threshold them both to remove saturated pixels
gfx4 = clij2.push(donorImp)
gfx5 = clij2.push(acceptorImp)
gfx6 = clij2.create(gfx5)
clij2.threshold(gfx4, gfx2, maxIntensity)
clij2.binarySubtract(gfx3, gfx2, gfx6)
clij2.threshold(gfx5, gfx2, maxIntensity)
clij2.binarySubtract(gfx6, gfx2, gfx3)
clij2.threshold(gfx3, gfx6, 0.5)
clij2.multiplyImages(gfx6, gfx4, gfx2)
clij2.multiplyImages(gfx6, gfx5, gfx4)
gfx6 = clij2.push(acceptorImp2)
#donor is gfx2, acceptor FRET is gfx4, segment channel (acceptor normal) is gfx6
results = ResultsTable()
clij2.statisticsOfBackgroundAndLabelledPixels(gfx2, gfx1, results)
donorChIntensity = results.getColumn(13)
results2 = ResultsTable()
clij2.statisticsOfBackgroundAndLabelledPixels(gfx4, gfx1, results2)
acceptorChIntensity = results2.getColumn(13)
results3 = ResultsTable()
clij2.statisticsOfBackgroundAndLabelledPixels(gfx6, gfx1, results3)
#calculate the fret ratios, removing any ROI with intensity of zero
FRET = []
for i in xrange(len(acceptorChIntensity)):
if (acceptorChIntensity[i] > 0) and (donorChIntensity[i] > 0):
#don't write in the zeros to the results
FRET.append((1000 * acceptorChIntensity[i] / donorChIntensity[i]))
table.incrementCounter()
table.addValue("Frame (Time)", nFrame)
table.addValue("Label", i)
table.addValue("Emission ratio",
acceptorChIntensity[i] / donorChIntensity[i])
table.addValue("Mean donor emission",
results.getValue("MEAN_INTENSITY", i))
table.addValue("Mean acceptor emission (FRET)",
results2.getValue("MEAN_INTENSITY", i))
table.addValue("Mean acceptor emission",
results3.getValue("MEAN_INTENSITY", i))
table.addValue("Sum donor emission", donorChIntensity[i])
table.addValue("Sum acceptor emission (FRET)",
acceptorChIntensity[i])
table.addValue("Sum acceptor emission",
results3.getValue("SUM_INTENSITY", i))
table.addValue(
"Volume",
cal.pixelWidth * cal.pixelHeight * cal.pixelDepth *
results.getValue("PIXEL_COUNT", i))
table.addValue("Pixel count", results.getValue("PIXEL_COUNT", i))
table.addValue("x",
cal.pixelWidth * results.getValue("CENTROID_X", i))
table.addValue("y",
cal.pixelHeight * results.getValue("CENTROID_Y", i))
table.addValue("z",
cal.pixelDepth * results.getValue("CENTROID_Z", i))
table.addValue("File name", originalTitle)
else:
#must write in the zeros as this array is used to generate the map of emission ratios
FRET.append(0)
table.show("Results of " + originalTitle)
FRET[0] = 0
FRETarray = array("f", FRET)
fp = FloatProcessor(len(FRET), 1, FRETarray, None)
FRETImp = ImagePlus("FRETImp", fp)
gfx4 = clij2.push(FRETImp)
clij2.replaceIntensities(gfx1, gfx4, gfx5)
maxProj = clij2.create(gfx5.getWidth(), gfx5.getHeight(), 1)
clij2.maximumZProjection(gfx5, maxProj)
#pull the images
FRETimp2 = clij2.pull(gfx5)
FRETProjImp = clij2.pull(maxProj)
labelImp = clij2.pull(gfx1)
clij2.clear()
donorImp.close()
acceptorImp.close()
acceptorImp2.close()
return table, FRETimp2, FRETProjImp, labelImp
def process(self,imp):
# extract nucleus channel, 8-bit and twice binned
imp.setC(self.nucleusChannel)
ip = imp.getChannelProcessor().duplicate()
ip = ip.convertToByteProcessor()
ip = ip.bin(4)
nucleus = ImagePlus("nucleus_channel", ip)
# threshold image and separate clumped nuclei
IJ.run(nucleus, "Auto Threshold", "method=Otsu white setthreshold show");
IJ.run(nucleus, "Make Binary", "thresholded remaining black");
IJ.run(nucleus, "Watershed", "");
directory = imp.getTitle()
directory = directory.replace(" ", "_")\
.replace(",", "_")\
.replace("#", "_series")\
.replace("...", "")\
.replace(".","_")
directory = os.path.join(self.exportDir, directory)
sliceDirectory = os.path.join(directory, "slices")
print directory
print sliceDirectory
if not os.path.exists(sliceDirectory):
os.makedirs(sliceDirectory)
# Create a table to store the results
table = ResultsTable()
# Create a hidden ROI manager, to store a ROI for each blob or cell
#roim = RoiManager(True)
# remove small particles and border particles
pa = ParticleAnalyzer(\
ParticleAnalyzer.ADD_TO_MANAGER | ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES,\
Measurements.CENTER_OF_MASS,\
table,\
self.minArea, self.maxArea,\
0.0,1.0)
if pa.analyze(nucleus):
print "All ok, number of particles: ", table.size()
else:
print "There was a problem in analyzing", imp, nucleus
table.save(os.path.join(directory, "rt.csv"))
# read the center of mass coordinates
cmx = table.getColumn(0)
cmy = table.getColumn(1)
if self.debug:
imp.show()
i=0
for i in range(0, min(self.nCells,table.size())):
# ROI around the cell
cmx = table.getValue("XM",i)
cmy = table.getValue("YM",i)
x = 4 * cmx - (self.boxSize - 1) / 2
y = 4 * cmy - (self.boxSize - 1) / 2
if (x < self.edge or y < self.edge or x > imp.getWidth() - self.edge or y > imp.getHeight() - self.edge):
continue
roi = Roi(x,y,self.boxSize,self.boxSize)
imp.setRoi(roi, False)
cellStack = ImageStack(self.boxSize, self.boxSize)
for z in range(1, imp.getNSlices() + 1):
imp.setSlice(z)
for c in range(1, imp.getNChannels() + 1):
imp.setC(c)
# copy ROI to stack
imp.copy()
impSlice = imp.getClipboard()
cellStack.addSlice(impSlice.getProcessor())
if self.slices:
sliceTitle = "cell_%s_z%s_c%s" % (str(i).zfill(4), str(z).zfill(3), str(c))
print sliceTitle
IJ.saveAsTiff(impSlice, os.path.join(sliceDirectory, sliceTitle))
impSlice.close()
title = "cell_" + str(i).zfill(4)
cell = ImagePlus(title, cellStack)
# save ROI image
IJ.saveAsTiff(cell, os.path.join(directory, title))
cell.close()
if self.debug:
imp.updateAndDraw()
wait = Wait("particle done")
wait.show()
# Check if Column even exists (in case it didn't measure anything)
if table.getColumnIndex("Area") != -1:
# Find the ROI with the largest area
for i, area in enumerate(table.getColumn(table.getColumnIndex("Area"))):
if area > maxArea:
index = i
# Writes everything in the output file
if index != -1:
diameter = 2* math.sqrt( float(table.getValue("Area", index)) / (2* math.pi))
isOrganoid = table.getValue("Area", index) > area_threshold and table.getValue("Area", index) > round_threshold
output.write(str(subfolder) + ',' + filename + ',' + str(table.getValue("Feret", index)) + ',' + str(table.getValue("MinFeret", index)) + ',' + str((table.getValue("MinFeret", index)+table.getValue("Feret", index))/2) + ',' + str(table.getValue("Area", index)) + ',' + str(diameter) + ',' + str(table.getValue("Major", index)) + ','+ str(table.getValue("Minor", index)) + ','+ str(table.getValue("Circ.", index)) + ',' +str(table.getValue("Round", index)) + ',' + str(table.getValue("Solidity", index)) + ',' + str(isOrganoid))
else:
output.write(str(subfolder) + ',' + filename + ",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA")
output.write('\n')
imp.changes = False
imp.close()
roim.reset()
roim.close()
# End of macro
cat = """
class Morph(object):
"""
Fourni les mesures principales pour l'analyse des cellules bacteriennes:
proprietes:
1-MaxFeret
2-MinFeret
3-AngleFeret
4-XFeret
5-YFeret
6-Area
7-Mean
8-StdDev
9-IntDen
10-Kurt
11-Skew
12-Angle
13-Major
14-Minor
15-Solidity
16-AR
17-Round
18-Circ.
19-XM
20-YM
21-X
22-Y
23-FerCoord: tuple contenant x1, y1, x2, y2 du MaxFeret
24-Fprofil: list contenant les valeurs du profil le long de MaxFeret
25-FerAxis: Line ROI
26-MidAxis: Polyline ROI de l'axe median par skeletonize
27-MidProfil: list contenant les valeurs du profil le long de MidAxis
28-nb Foci
29-ListFoci: liste des positions des foci par cellule
30-ListAreaFoci: liste des area des foci
31-ListPeaksFoci: liste des int max des foci
32-ListMeanFoci liste des int mean des foci
toute les proprietes mettent a jour l'image cible par: object.propriete=imp
Methodes:
getFeretSegments(n segments)
getMidSegments(n segments, radius, tool 0= ligne perpendiculaire, 1= cercle, 2= ligne tangente)
selectInitRoi: active la ROI initiale
Statics:
distMorph(liste de coordonees a mesurer= (coefficient, valeur initiale, valeur finale))
setteurs:
setImage(ImagePlus)
setImageMeasures(imagePlus) met a jours les mesures avec imagePlus
setImageMidprofil(imagePlus) met a jours le profil avec imagePlus
setLineWidth(width) afecte la largeur de ligne pour le profil pour Fprofile et MidProfil defaut = 0
setshowFprof(True) affiche le graphique de profil Fprofil defaut = False
setMidParams(longueur mesurer l'angle de l'extremite en pixels defaut=10, coefficient pour prolonger et trouver l'intersection avec le contour defaut=1.3
"""
def __Measures(self):
self.__boolmeasures=True
if (self.__contour is not None) and (self.__contour.getType() not in [9,10]):
self.__image.killRoi()
self.__image.setRoi(self.__contour)
self.__ip=self.__image.getProcessor()
self.__rt= ResultsTable()
analyser= Analyzer(self.__image, Analyzer.AREA+Analyzer.CENTER_OF_MASS+Analyzer.CENTROID+Analyzer.ELLIPSE+Analyzer.FERET+Analyzer.INTEGRATED_DENSITY+Analyzer.MEAN+Analyzer.KURTOSIS+Analyzer.SKEWNESS+Analyzer.MEDIAN+Analyzer.MIN_MAX+Analyzer.MODE+Analyzer.RECT+Analyzer.SHAPE_DESCRIPTORS+Analyzer.SLICE+Analyzer.STACK_POSITION+Analyzer.STD_DEV, self.__rt)
analyser.measure()
#self.__rt.show("myRT")
else:
self.__rt = ResultsTable()
analyser = Analyzer(self.__image, Analyzer.AREA+Analyzer.CENTER_OF_MASS+Analyzer.CENTROID+Analyzer.ELLIPSE+Analyzer.FERET+Analyzer.INTEGRATED_DENSITY+Analyzer.MEAN+Analyzer.KURTOSIS+Analyzer.SKEWNESS+Analyzer.MEDIAN+Analyzer.MIN_MAX+Analyzer.MODE+Analyzer.RECT+Analyzer.SHAPE_DESCRIPTORS+Analyzer.SLICE+Analyzer.STACK_POSITION+Analyzer.STD_DEV, self.__rt)
analyser.measure()
#self.__rt.show("myRT")
maxValues=self.__rt.getRowAsString(0).split("\t")
heads=self.__rt.getColumnHeadings().split("\t")
for val in heads: self.__rt.setValue(val, 0, Float.NaN)
#self.__rt.show("myRT")
# calculate the 1/2 , 1/4 ... 1/n positions for a liste while 1/n >= 1 returns a dict = 0: (0, [0, 0, pos(1/2)]) 1: (1, [-1, -0.5, -pos(1/4)], [0, 0, pos(1/2)], [1, 0.5, pos(1/2)])
def __Centers(self, line) :
L=len(line)
l2=L//2
l=L
pos={}
for i in range(self.log2(L)) :
l = l//2
pos[i]=l
l=L
dicPos={}
jtot=1
for i in range(self.log2(L)) :
s=[]
j=1
while (l2-j*pos[i])>0 or (l2+j*pos[i])<L :
s.append((-j,(l2-j*pos[i])))
s.append((j,(l2+j*pos[i])))
j=j+1
s.append((0,l2))
s.sort()
if ((len(s)+1)*pos[i]-L)//pos[i] > 0 :
del s[0]
del s[-1]
else : pass
if len(s) - 1 != 0 : jtot= (( len(s) - 1 ) / 2.00)+1
else : jtot=1
centers=[[v[0], v[0]/jtot, v[1]] for v in s]
dicPos[i]=(i, centers)
del(s)
return dicPos
#calculate angle from the center of the midline to ends
def __flexAngle(self) :
try :
p1 = self.__midLine[0]
p3 = self.__midLine[-1]
except AttributeError :
self.__midline()
p1 = self.__midLine[0]
p3 = self.__midLine[-1]
icenter = self.__midCenters[0][1][0][2]
p2 = self.__midLine[icenter]
#xpoints = (429,472,466)
#ypoints = (114,133,99)
xpoints = [int(p1[0]), int(p2[0]), int(p3[0])]
ypoints = [int(p1[1]), int(p2[1]), int(p3[1])]
#print ypoints
#return ""
r = PolygonRoi(xpoints, ypoints, 3, Roi.ANGLE)
return r.getAngle()
def __NbFoci(self):
self.__boolFoci=True
self.__image.killRoi()
self.__image.setRoi(self.__contour)
self.__ip=self.__image.getProcessor()
rt=ResultsTable.getResultsTable()
rt.reset()
mf=MaximumFinder()
mf.findMaxima(self.__ip, self.__noise, 0, MaximumFinder.LIST, True, False)
self.__listMax[:]=[]
#feret=self.getFercoord()
#xc=feret[0]-((feret[0]-feret[2])/2.0)
#yc=feret[1]-((feret[1]-feret[3])/2.0)
#print xc, yc
xc=self.getXC()
yc=self.getYC()
#print xc, yc
for i in range(rt.getCounter()):
x=int(rt.getValue("X", i))
y=int(rt.getValue("Y", i))
size=self.__localwand(x, y, self.__ip, self.__seuilPeaks, self.__peaksMethod, self.__light)
coord=[(1, xc, x), (1, yc, y)]
d=self.distMorph(coord,"Euclidean distance")
d=( d / (self.getMaxF()/2) )*100
self.__listMax.append((x, y, size[0], size[1], size[2], size[3], size[4], d))
rt.reset()
def __FeretAxis(self):
__boolFL=True
if (self.__contour is not None) and (self.__contour.getType() in range(1,11)):
self.__image.killRoi()
self.__image.setRoi(self.__contour)
if self.__contour.getType() in [1,5,9,10]:
self.__polygon=self.__contour.getPolygon()
else:
self.__polygon=self.__contour.getFloatPolygon()
points = self.__polygon.npoints
self.__polx = self.__polygon.xpoints
self.__poly = self.__polygon.ypoints
diameter=0.0
for i in range(points):
for j in range(i, points):
dx=self.__polx[i]-self.__polx[j]
dy=self.__poly[i]-self.__poly[j]
d=math.sqrt(dx*dx+dy*dy)
if d>diameter:
diameter=d
i1=i
i2=j
tempDictY={ self.__poly[i1]:(self.__polx[i1],self.__poly[i1],self.__polx[i2],self.__poly[i2]), self.__poly[i2]:(self.__polx[i2],self.__poly[i2],self.__polx[i1],self.__poly[i1]) }
minY=min((self.__poly[i1],self.__poly[i2]))
maxY=max((self.__poly[i1],self.__poly[i2]))
lineTuple=tempDictY[maxY]
self.__x1=lineTuple[0]
self.__y1=lineTuple[1]
self.__x2=lineTuple[2]
self.__y2=lineTuple[3]
self.__line= Line(self.__x1,self.__y1,self.__x2,self.__y2)
elif (self.__contour is not None) and (self.__contour.getType()==0):
self.__x2=self.__contour.getBounds().x
self.__y2=self.__contour.getBounds().y
self.__x1=self.__contour.getBounds().x+self.__contour.getBounds().width
self.__y1=self.__contour.getBounds().y+self.__contour.getBounds().height
self.__line= Line(self.__x1,self.__y1,self.__x2,self.__y2)
else:
self.__x1="NaN"
self.__y1="NaN"
self.__x2="NaN"
self.__y2="NaN"
self.__fprofArray="NaN"
def __FeretProfile(self):
"""
genere le profile le long du diametre de Feret
"""
self.__line.setWidth(self.__lw)
self.__image.setRoi(self.__line, True)
self.__fprof= ProfilePlot(self.__image)
self.__fprofArray=self.__fprof.getProfile()
if self.__showFpro: self.__fprof.createWindow()
self.__image.killRoi()
self.__line.setWidth(0)
self.__image.setRoi(self.__contour)
return self.__fprofArray
def __midline(self):
debug=False
#print "line 251", self.__boolML
if self.__boolML :
ordpoints=self.__midLine[:]
npoints=len(ordpoints)
xpoints=[point[0] for point in ordpoints]
ypoints=[point[1] for point in ordpoints]
polyOrd=PolygonRoi(xpoints, ypoints, npoints, PolygonRoi.POLYLINE)
return polyOrd
#if self.getMaxF()<15 : return None
#self.__FeretAxis()
#return self.__line
self.__boolML=True
self.__image.killRoi()
self.__image.setRoi(self.__contour)
boundRect=self.__contour.getBounds()
boundRoi=Roi(boundRect)
xori=boundRect.x
yori=boundRect.y
wori=boundRect.width
hori=boundRect.height
ip2 = ByteProcessor(self.__image.getWidth(), self.__image.getHeight())
ip2.setColor(255)
ip2.setRoi(self.__contour)
ip2.fill(self.__contour)
skmp=ImagePlus("ip2", ip2)
skmp.setRoi(xori-1,yori-1,wori+1,hori+1)
ip3=ip2.crop()
skmp3=ImagePlus("ip3", ip3)
skmp3.killRoi()
#-------------------------------------------------------------
if debug :
skmp3.show()
IJ.showMessage("imp3 l287")
#-------------------------------------------------------------
IJ.run(skmp3, "Skeletonize (2D/3D)", "")
#IJ.run(skmp3, "Skeletonize", "")
#-------------------------------------------------------------
if debug :
skmp3.show()
IJ.showMessage("imp3 l294")
#-------------------------------------------------------------
IJ.run(skmp3, "BinaryConnectivity ", "white")
ip3.setThreshold(3,4, ImageProcessor.BLACK_AND_WHITE_LUT)
IJ.run(skmp3, "Convert to Mask", "")
#-------------------------------------------------------------
if debug :
skmp3.show()
IJ.showMessage("imp3 l302")
#-------------------------------------------------------------
#IJ.run(skmp3, "Skeletonize", "")
#-------------------------------------------------------------
if debug :
skmp3.updateAndDraw()
skmp3.show()
IJ.showMessage("imp3 l308")
#-------------------------------------------------------------
rawPoints=[]
w=ip3.getWidth()
h=ip3.getHeight()
rawPoints=[(x+xori,y+yori,self.__sommeVals(x,y,ip3)) for x in range(w) for y in range(h) if ip3.getPixel(x,y)==255]
tempbouts=[val for val in rawPoints if val[2]==2]
if len(tempbouts)!=2 : return None
# test
#if len(tempbouts)!=2 :
#
# IJ.run(skmp3, "BinaryConnectivity ", "white")
# ip3.setThreshold(3,3, ImageProcessor.BLACK_AND_WHITE_LUT)
# IJ.run(skmp3, "Convert to Mask", "")
# #-------------------------------------------------------------
# if debug==debug :
# skmp3.updateAndDraw()
# skmp3.show()
# IJ.showMessage("if test l 328")
##-------------------------------------------------------------
# rawPoints=[(x+xori,y+yori,self.__sommeVals(x,y,ip3)) for x in range(w) for y in range(h) if ip3.getPixel(x,y)==255]
# tempbouts=[val for val in rawPoints if val[2]==2]
ip3.setRoi(boundRect)
if rawPoints==[]: return None
npoints=len(rawPoints)
xpoints=[point[0] for point in rawPoints]
ypoints=[point[1] for point in rawPoints]
valpoints=[point[2] for point in rawPoints]
bouts={}
if tempbouts==[]: return None
if tempbouts[0][1]>tempbouts[1][1]:
bouts["A"]=tempbouts[0]
bouts["B"]=tempbouts[1]
else:
bouts["A"]=tempbouts[1]
bouts["B"]=tempbouts[0]
rawPoints.remove(bouts["A"])
rawPoints.remove(bouts["B"])
rawPoints.append(bouts["B"])
tempList=[val for val in rawPoints]
p=bouts["A"]
Dist={}
ordPoints=[]
for j in range(len(rawPoints)):
Dist.clear()
for i in range(len(tempList)):
dx=p[0]-tempList[i][0]
dy=p[1]-tempList[i][1]
d=math.sqrt(dx*dx+dy*dy)
Dist[d]=tempList[i]
distList=Dist.keys()
mind=min(distList)
nextpoint=Dist[mind]
ordPoints.append(nextpoint)
tempList.remove(nextpoint)
p=nextpoint
ordPoints.insert(0, bouts["A"])
npoints=len(ordPoints)
if npoints < 4 : return None
xpoints=[point[0] for point in ordPoints]
ypoints=[point[1] for point in ordPoints]
polyOrd1=PolygonRoi(xpoints, ypoints, npoints, PolygonRoi.POLYLINE)
f=min(self.__midParams[0], len(xpoints)//2)
angleA1=polyOrd1.getAngle(xpoints[0],ypoints[0], xpoints[1],ypoints[1])
angleA2=polyOrd1.getAngle(xpoints[1],ypoints[1], xpoints[2],ypoints[3])
angleA = (angleA1+angleA2)/2.00
angleA=polyOrd1.getAngle(xpoints[0],ypoints[0], xpoints[f],ypoints[f])
angleA=angleA*(math.pi/180)
angleB1=polyOrd1.getAngle(xpoints[-2],ypoints[-2], xpoints[-1],ypoints[-1])
angleB2=polyOrd1.getAngle(xpoints[-3],ypoints[-3], xpoints[-2],ypoints[-2])
angleB = (angleB1+angleB2)/2.00
angleB=polyOrd1.getAngle(xpoints[-f],ypoints[-f], xpoints[-1],ypoints[-1])
angleB=angleB*(math.pi/180)
coef=self.__midParams[1]
xa = xpoints[0]-coef*f*math.cos(angleA)
ya = ypoints[0]+coef*f*math.sin(angleA)
xb = xpoints[-1]+coef*f*math.cos(angleB)
yb = ypoints[-1]-coef*f*math.sin(angleB)
lineA=Line(xpoints[0],ypoints[0], xa, ya)
lineB=Line(xpoints[-1],ypoints[-1], xb, yb)
lineA.setWidth(0)
lineB.setWidth(0)
lineA.setStrokeWidth(0)
lineB.setStrokeWidth(0)
ip2.setColor(0)
ip2.fill()
ip2.setColor(255)
ip2.setRoi(lineA)
lineA.drawPixels(ip2)
ip2.setRoi(lineB)
lineB.drawPixels(ip2)
ip2.setRoi(self.__contour)
ip2.setColor(0)
ip2.fillOutside(self.__contour)
ip2=ip2.crop()
imb=ImagePlus("new-ip2", ip2)
#-------------------------------------------------------------
if debug :
imb.show()
IJ.showMessage("imb l416")
#-------------------------------------------------------------
w2=ip2.getWidth()
h2=ip2.getHeight()
ip4 = ByteProcessor(w2+2, h2+2)
im4=ImagePlus("im4", ip4)
for i in range(w2):
for j in range(h2):
ip4.set(i+1,j+1,max([ip2.getPixel(i,j),ip3.getPixel(i,j)]))
#im4.show()
#-------------------------------------------------------------
if debug :
im4.show()
IJ.showMessage("im4 l430")
#-------------------------------------------------------------
im4.killRoi()
#IJ.run(im4, "Skeletonize (2D/3D)", "")
#IJ.run(skmp3, "Skeletonize", "")
#-------------------------------------------------------------
if debug :
imb.show()
IJ.showMessage("imb l300")
#-------------------------------------------------------------
#IJ.run(skmp3, "Skeletonize", "")
ip4=im4.getProcessor()
rawPoints2=[]
w4=ip4.getWidth()
h4=ip4.getHeight()
rawPoints2=[(x+xori-2,y+yori-2,self.__sommeVals(x,y,ip4)) for x in range(w4) for y in range(h4) if ip4.getPixel(x,y)==255]
self.__MidBouts=[val for val in rawPoints2 if val[2]==2]
# test
if len(self.__MidBouts)!=2 :
IJ.run(im4, "BinaryConnectivity ", "white")
ip4.setThreshold(3,3, ImageProcessor.BLACK_AND_WHITE_LUT)
IJ.run(im4, "Convert to Mask", "")
rawPoints2=[(x+xori-2,y+yori-2,self.__sommeVals(x,y,ip4)) for x in range(w4) for y in range(h4) if ip4.getPixel(x,y)==255]
self.__MidBouts=[val for val in rawPoints2 if val[2]==2]
ordpoints=[]
p0=self.__MidBouts[0]
rawPoints2.remove(p0)
c=0
while p0!=self.__MidBouts[1]:
if c<len(rawPoints2):
point=rawPoints2[c]
else: break
if abs(point[0]-p0[0])<2 and abs(point[1]-p0[1])<2:
p0=point
ordpoints.append(point)
rawPoints2.remove(point)
c=0
else: c=c+1
ordpoints.insert(0, self.__MidBouts[0])
self.__midLine=ordpoints[:]
self.__midCenters = self.__Centers(self.__midLine)
npoints=len(ordpoints)
xpoints=[point[0] for point in ordpoints]
ypoints=[point[1] for point in ordpoints]
polyOrd=PolygonRoi(xpoints, ypoints, npoints, PolygonRoi.POLYLINE)
#print self.__midLine
#print self.__MidBouts
#print xpoints
#print ypoints
return polyOrd
def __sommeVals(self, x, y, ip):
return (ip.getPixel(x,y)+ip.getPixel(x-1,y-1)+ip.getPixel(x,y-1)+ip.getPixel(x+1,y-1)+ip.getPixel(x-1,y)+ip.getPixel(x+1,y)+ip.getPixel(x-1,y+1)+ip.getPixel(x,y+1)+ip.getPixel(x+1,y+1))/255
def __localwand(self, x, y, ip, seuil, method, light):
self.__image.killRoi()
ip.snapshot()
if method == "mean" :
peak=ip.getPixel(x,y)
tol = (peak - self.getMean())*seuil
w = Wand(ip)
w.autoOutline(x, y, tol, Wand.EIGHT_CONNECTED)
#print "method=", method, tol, peak
elif method == "background" :
radius = self.getMinF()/4
bs = BackgroundSubtracter()
#rollingBallBackground(ImageProcessor ip, double radius, boolean createBackground, boolean lightBackground, boolean useParaboloid, boolean doPresmooth, boolean correctCorners)
bs.rollingBallBackground(ip, radius, False, light, False, True, False)
peak=ip.getPixel(x,y)
tol = peak*seuil
w = Wand(ip)
w.autoOutline(x, y, tol, Wand.EIGHT_CONNECTED)
ip.reset()
#print "method=", method, tol, radius, peak
else :
peak=ip.getPixel(x,y)
tol = peak*seuil
w = Wand(ip)
w.autoOutline(x, y, tol, Wand.EIGHT_CONNECTED)
#print "method=", method, tol
peak=ip.getPixel(x,y)
temproi=PolygonRoi(w.xpoints, w.ypoints, w.npoints, PolygonRoi.POLYGON)
self.__image.setRoi(temproi)
#self.__image.show()
#time.sleep(1)
#peakip=self.__image.getProcessor()
#stats=peakip.getStatistics()
temprt = ResultsTable()
analyser = Analyzer(self.__image, Analyzer.AREA+Analyzer.INTEGRATED_DENSITY+Analyzer.FERET, temprt)
analyser.measure()
#temprt.show("temprt")
rtValues=temprt.getRowAsString(0).split("\t")
area=float(rtValues[1])
intDen=float(rtValues[4])
feret=float(rtValues[2])
mean=intDen/area
#time.sleep(2)
temprt.reset()
self.__image.killRoi()
return [peak, area, mean, intDen, feret]
def __MidProfil(self):
if not self.__boolML : self.__midline()
ip=self.__image.getProcessor()
line=Line(self.__midLine[0][0],self.__midLine[0][1],self.__midLine[-1][0],self.__midLine[-1][1])
line.setWidth(self.__lw)
self.__MprofArray=[]
self.__MprofArray[:]=[]
for i in range(0,len(self.__midLine)-1):
templine=Line(self.__midLine[i][0],self.__midLine[i][1],self.__midLine[i+1][0],self.__midLine[i+1][1])
templine.setWidth(self.__lw)
self.__image.setRoi(templine)
#time.sleep(0.5)
temprof= ProfilePlot(self.__image)
temparray=temprof.getProfile()
self.__MprofArray+=temparray
templine.setWidth(0)
#if self.__showMidpro: self.__fprof.createWindow()
return
def getFeretSegments(self, n):
self.__boolFS=True
if(not self.__boolFL):
self.__FeretAxis()
radius=self.getMinF()
lsegment=self.__line.getLength()/((n-1)*2)
xo=self.__x1
yo=self.__y1
xf=self.__x2
yf=self.__y2
angle1=self.getAngF()*(math.pi/180)
angle2=self.getAngF()*(math.pi/180)+(math.pi/2)
avancex=(lsegment*2)*math.cos(angle1)
avancey=(lsegment*2)*math.sin(angle1)
delta90x=(radius)*math.cos(angle2)
delta90y=(radius)*math.sin(angle2)
self.__line.setWidth(int(lsegment*2))
#self.__image.setRoi(self.__line)
tempcontour=self.__contour.clone()
shapeContour=ShapeRoi(tempcontour)
segsRoi=[]
for i in range(n):
tempLine=Line(xo-delta90x, yo+delta90y, xo+delta90x, yo-delta90y)
tempLine.setWidth(int(lsegment*2))
poly=tempLine.getPolygon()
roipol=PolygonRoi(poly, Roi.POLYGON)
shapePoly= ShapeRoi(roipol)
interShape=shapePoly.and(shapeContour)
segsRoi.append(interShape.shapeToRoi())
xo=xo+avancex
yo=yo-avancey
#self.__image.setRoi(self.__contour, True)
#time.sleep(0)
self.__line.setWidth(0)
#self.__image.setRoi(tempcontour)
#self.__image.updateAndDraw()
return segsRoi # return Roi array
def getMidSegments(self, n=10, r=5, tool=0):
self.__boolMS=True
if(not self.__boolML):
self.__midline()
lsegment=int(len(self.__midLine)/n)
if lsegment<2:lsegment=2
ls2=int(len(self.__midLine)/(2*n))
if ls2<1: ls2=1
ip=self.__image.getProcessor()
#print(len(self.__midLine), lsegment, ls2)
xo=self.__MidBouts[0][0]
yo=self.__MidBouts[0][1]
xf=self.__MidBouts[1][0]
yf=self.__MidBouts[1][1]
line1=Line(xo,yo,xf,yf)
line1.setWidth(0)
angles=[line1.getAngle(self.__midLine[i][0], self.__midLine[i][1], self.__midLine[i+lsegment][0], self.__midLine[i+lsegment][1]) for i in range(0,len(self.__midLine)-lsegment,lsegment)]
points=[self.__midLine[i] for i in range(0,len(self.__midLine),lsegment)]
lastangle=line1.getAngle(self.__midLine[-ls2][0],self.__midLine[-ls2][1],self.__midLine[-1][0],self.__midLine[-1][1])
angles.append(lastangle)
tempcontour=self.__contour.clone()
shapeContour=ShapeRoi(tempcontour)
angles=[angle*(math.pi/180)+(math.pi/2) for angle in angles]
line1.setWidth((ls2+1)*2)
segsRoi=[]
linesRois=[]
cRois=[]
for i in range(len(angles)):
x=points[i][0]
y=points[i][1]
cRois.append(PointRoi(x,y))
if tool==0: # ligne perpendiculaire d'epaiseur (ls2+1)*2
line1.setWidth((ls2+1)*2)
x1=x+r*math.cos(angles[i])
y1=y-r*math.sin(angles[i])
x2=x-r*math.cos(angles[i])
y2=y+r*math.sin(angles[i])
#print(x, y, x1, y1, x2, y2)
tempLine=Line(x1,y1,x2,y2)
linesRois.append(tempLine)
tempLine.setWidth((ls2+1)*2)
#self.__image.setRoi(tempLine, True)
#time.sleep(0.3)
poly=tempLine.getPolygon()
roipol=PolygonRoi(poly, Roi.POLYGON)
shapePoly= ShapeRoi(roipol)
elif tool==1:
#r1=r*0.7
x1=x+r
y1=y-r
x2=x-r
y2=y+r
ellipse=EllipseRoi(x1, y1, x2, y2, 1)
linesRois.append(ellipse)
#print(x, y, x1, y1, x2, y2)
#self.__image.setRoi(ellipse, True)
shapePoly= ShapeRoi(ellipse)
#time.sleep(0.3)
else:
x1=x
y1=y
line1.setWidth(r)
if (i+1)<len(points):
x2=points[i+1][0]
y2=points[i+1][1]
else:
#x1=x+lsegment*math.cos(angles[i]-(math.pi/2))
#y1=y-lsegment*math.sin(angles[i]-(math.pi/2))
x2=x+lsegment*math.cos(angles[i]-(math.pi/2))
y2=y-lsegment*math.sin(angles[i]-(math.pi/2))
#x2=xf
#y2=yf
tempLine=Line(x1,y1,x2,y2)
linesRois.append(tempLine)
tempLine.setWidth(r)
#self.__image.setRoi(tempLine, True)
#time.sleep(0.5)
poly=tempLine.getPolygon()
roipol=PolygonRoi(poly, Roi.POLYGON)
shapePoly= ShapeRoi(roipol)
interShape=shapePoly.and(shapeContour)
interRoi=interShape.shapeToRoi()
segsRoi.append(interShape.shapeToRoi())
line1.setWidth(0)
return (segsRoi, linesRois, cRois)
def selectInitRoi(self):
self.__image.killRoi()
self.__image.setRoi(self.__contour)
time.sleep(0)
@staticmethod
def distMorph(coord,distmethod="Euclidean distance"):
if distmethod == "Euclidean distance" :
s=[val[0]*(val[2]-val[1])*(val[2]-val[1]) for val in coord]
#print s
#print sum(s)
return math.sqrt(sum(s))
if distmethod == "Logarithm distance" :
s=[val[0]*abs(math.log(val[2]/val[1])) for val in coord]
return sum(s)
@staticmethod
def log2(n) : return math.log(n)/math.log(2)
def Out(self): print("out")
#------ end methodes---------------
#------ constructeur -------------
def __init__(self, imp, roi):
self.__lw=0
self.__showFpro=False
self.__Feret=[]
self.__image=imp
self.__cal=imp.getCalibration()
self.__contour=roi.clone()
self.__boolmeasures=False
self.__boolFP=False
self.__boolFL=False
self.__boolML=False
self.__boolMP=False
self.__boolFS=False
self.__boolMS=False
self.__boolFoci=False
self.__midParams=[10, 1.3]
self.__listMax=[]
self.__noise=150
self.__seuilPeaks=0.75
self.__peaksMethod="mean"
self.__light=False
self.__distot=0.00
self.__flexangle=0.00
#print "dropbox MorphoBactProject"
#---------- end constructor---------
#---------- getteurs----------------
def getMaxF(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Feret", 0)
def getMinF(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("MinFeret", 0)
def getXF(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("FeretX", 0)
def getYF(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("FeretY", 0)
def getAngF(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("FeretAngle", 0)
def getArea(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Area", 0)
def getMean(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Mean", 0)
def getKurt(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Kurt", 0)
def getSkew(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Skew", 0)
def getIntDen(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("IntDen", 0)
def getStdDev(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("StdDev", 0)
def getAngle(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Angle", 0)
def getMajor(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Major", 0)
def getMinor(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Minor", 0)
def getSolidity(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Solidity", 0)
def getAR(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("AR", 0)
def getRound(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Round", 0)
def getCirc(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Circ.", 0)
def getXM(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("XM",0)
def getYM(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("YM",0)
def getXC(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("X",0)
def getYC(self):
if(not self.__boolmeasures): self.__Measures()
return self.__rt.getValue("Y",0)
def getNfoci(self):
if(not self.__boolFoci):self.__NbFoci()
return len(self.__listMax)
def getListFoci(self):
if(not self.__boolFoci):self.__NbFoci()
xy=[]
for val in self.__listMax:
xy.append((val[0], val[1]))
return xy
def getListPeaksFoci(self):
if(not self.__boolFoci):self.__NbFoci()
peaks=[]
for val in self.__listMax:
peaks.append(val[2])
return peaks
def getListAreaFoci(self):
if(not self.__boolFoci):self.__NbFoci()
areas=[]
for val in self.__listMax:
areas.append(val[3])
return areas
def getListMeanFoci(self):
if(not self.__boolFoci):self.__NbFoci()
means=[]
for val in self.__listMax:
means.append(val[4])
return means
def getListIntDenFoci(self):
if(not self.__boolFoci):self.__NbFoci()
ints=[]
for val in self.__listMax:
ints.append(val[5])
return ints
def getListFeretFoci(self):
if(not self.__boolFoci):self.__NbFoci()
ferets=[]
for val in self.__listMax:
ferets.append(val[6])
return ferets
def getListDistsFoci(self):
if(not self.__boolFoci):self.__NbFoci()
dists=[]
for val in self.__listMax:
dists.append(val[7])
return dists
def getFercoord(self):
"""
FerCoord: tuple contenant x1, y1, x2, y2 du MaxFeret
"""
if (not self.__boolFL): self.__FeretAxis()
return (self.__x1,self.__y1,self.__x2,self.__y2)
def getFprofil(self):
"""
Fprofil: list contenant les valeurs du profil le long de MaxFeret
"""
if (not self.__boolFL): self.__FeretAxis()
self.__FeretProfile()
return self.__fprofArray
def getFerAxis(self):
"""
FerAxis: Line ROI
"""
if(not self.__boolFL): self.__FeretAxis()
return self.__line
def getMidAxis(self):
"""
MidAxis: Polyline ROI de l'axe median par skeletonize
"""
if(not self.__boolML): return self.__midline()
def getMidSegs(self, n, r, tool):
"""
Rois des segments 0 = rois , 1 = points, 2 = lines ou ellipses
"""
if(not self.__boolMS): return self.getMidSegments(n, r, tool)
def getMidProfil(self):
"""
MidProfil: list contenant les valeurs du profil le long de MidAxis
"""
self.__MidProfil()
return self.__MprofArray
def getMidPoints(self) :
"""
MidPoints : list of two extreme points of mid Axis
"""
if(not self.__boolML): self.__midline()
return self.__MidBouts
def getCenters(self) :
if(not self.__boolML): self.__midline()
return self.__midCenters
def getFlexAngle(self) :
return self.__flexAngle()
#------ setteurs --------
def setImage(self, imp):
self.__image=imp
def setImageMeasures(self, imp):
self.__image=imp
self.__Measures()
def setImageFprofil(self, imp):
self.__image=imp
self.__FeretProfile()
def setImageMidprofil(self, imp):
self.__image=imp
self.__MidProfil()
def setLineWidth(self, lw):
self.__lw=lw
def setshowFpro(self, fpshow):
self.__showFpro=fpshow
def setMidParams(self, lseg, coeff):
self.__midParams[:]=[]
self.__midParams.append(lseg)
self.__midParams.append(coeff)
def setNoise(self, noise):
self.__noise=noise
def setSeuilPeaks(self, seuil):
self.__seuilPeaks=seuil
def setpeaksMethod(self, method):
self.__peaksMethod=method
def setlight(self, light):
self.__light=light
#------- properties -----------------------
MaxFeret=property(getMaxF, setImageMeasures, doc="caliper max Feret=")
MinFeret=property(getMinF, setImageMeasures, doc="caliper min Feret=")
AngleFeret=property(getAngF, setImageMeasures, doc="angle Feret=")
XFeret=property(getXF, setImageMeasures, doc="X Feret=")
YFeret=property(getYF, setImageMeasures, doc="Y Feret=")
Area=property(getArea, setImageMeasures, doc="Area=")
Mean=property(getMean, setImageMeasures, doc="Mean=")
Kurt=property(getKurt, setImageMeasures, doc="Kurtosis=")
Skew=property(getSkew, setImageMeasures, doc="Skewness=")
IntDen=property(getIntDen, setImageMeasures, doc="Integrated Intensity=")
StdDev=property(getStdDev, setImageMeasures, doc="Standard Deviation=")
Angle=property(getAngle, setImageMeasures, doc="Angle=")
Major=property(getMajor, setImageMeasures, doc="Major ellipse axis=")
Minor=property(getMinor, setImageMeasures, doc="Minor ellipse axis=")
Solidity=property(getSolidity, setImageMeasures, doc="Solidity area/convexHull=")
AR=property(getAR, setImageMeasures, doc="Major axis/Minor axis=")
Round=property(getRound, setImageMeasures, doc="Area/(pi*Major*Major)=1/AR=")
Circ=property(getCirc, setImageMeasures, doc="(4*pi*Area)/(perimeter*perimeter)=")
XM=property(getXM, setImageMeasures, doc="X center of Mass=")
YM=property(getYM, setImageMeasures, doc="Y center of Mass=")
XC=property(getXC, setImageMeasures, doc="X of centroid=")
YC=property(getYC, setImageMeasures, doc="Y of centroid=")
NFoci=property(getNfoci, setImageMeasures, doc="nb foci in the roi=")
ListFoci=property(getListFoci, setImageMeasures, doc="list of foci coordinates=")
ListPeaksFoci=property(getListPeaksFoci, setImageMeasures, doc="list of foci peaks=")
ListAreaFoci=property(getListAreaFoci, setImageMeasures, doc="list of foci areas=")
ListMeanFoci=property(getListMeanFoci, setImageMeasures, doc="list of foci means=")
ListIntDenFoci=property(getListIntDenFoci, setImageMeasures, doc="list of foci IntDen=")
ListFeretFoci=property(getListFeretFoci, setImageMeasures, doc="list of foci Ferets=")
ListDistsFoci=property(getListDistsFoci, setImageMeasures, doc="list of foci distances=")
FerCoord=property(getFercoord, doc="x1, y1, x2, y2 of Feret diameter =")
Fprofil=property(getFprofil, setImageFprofil, doc="Profil along Feret diameter") # return array values
FerAxis=property(getFerAxis, doc="ROI along Feret diameter") # return Roi
MidAxis=property(getMidAxis, doc="ROI along the median axis") # return Roi
MidProfil=property(getMidProfil, setImageMidprofil, doc="profile values of mid axis") # return array values
MidPoints=property(getMidPoints, doc= "extreme points of mid line")
Centers=property(getCenters, doc= "list of positions (tuples) of 1/2 of the midaxis, 1/4, 1/8 ...") # return a list of tuples
FlexAngle=property(getFlexAngle, doc="angle of the center of midline to ends")
class previewLabelerAndListeners(ActionListener, AdjustmentListener):
'''Class which unique function is to handle the button clics'''
def __init__(self, imp1, slider1, slider2, gd):
self.height = imp1.getHeight()
self.width = imp1.getWidth()
self.depth = imp1.getStackSize()
self.stats = StackStatistics(imp1)
self.src = clij2.push(imp1)
self.cal = imp1.getCalibration()
self.size = int(self.stats.max)
self.labelValues = [1] * int(self.size + 1)
self.labelValues[0] = 0
self.nucleiLabels = range(self.size + 1)
self.results = ResultsTable()
self.renderPreview(1)
#self.results.show("results")
self.labelDict = {
0: [0],
1: sorted(self.nucleiLabels[1:]),
2: [],
3: [],
4: [],
5: [],
6: [],
7: [],
8: [],
9: [],
10: []
}
self.identifiers = []
self.xs = []
self.ys = []
self.zs = []
self.bbz = []
self.bbze = []
for i in range(int(self.size + 1)):
try:
self.xs.append(int(self.results.getValue("CENTROID_X", i)))
self.ys.append(int(self.results.getValue("CENTROID_Y", i)))
self.zs.append(int(self.results.getValue("CENTROID_Z", i)))
self.bbz.append(self.results.getValue("BOUNDING_BOX_Z", i) + 1)
self.bbze.append(
self.results.getValue("BOUNDING_BOX_END_Z", i) + 1)
self.identifiers.append(self.results.getValue("IDENTIFIER", i))
except:
print i
self.identifiers.append(self.results.getValue("IDENTIFIER", i))
self.xs.append(int(width / 2))
self.ys.append(int(height / 2))
self.zs.append(int(depth / 2))
self.bbz.append(1)
self.bbze.append(1)
self.nucLoc = map(lambda i: self.ys[i] * width + self.xs[i],
range(len(self.xs)))
"""labelPreviewImp - label image preview; maxZPreviewImp - maxZ label preview; maxYPreviewImp - maxY label preview"""
self.slider1 = slider1
self.slider2 = slider2
self.gd = gd
self.current = self.labelPreviewImp.getCurrentSlice()
def renderPreview(self, runStats):
try:
self.labelPreviewImp.close()
self.maxZPreviewImp.close()
self.maxYPreviewImp.close()
except:
print "imps already closed"
fp = ShortProcessor(len(self.labelValues), 1, self.labelValues, None)
labelerImp = ImagePlus("labeler", fp)
src2 = clij2.push(labelerImp)
dst = clij2.create(self.src)
labelerImp.close()
clij2.replaceIntensities(self.src, src2, dst)
self.labelPreviewImp = clij2.pull(dst)
previewDisplaySettings(self.labelPreviewImp, "label preview", 100,
self.cal)
try:
self.labelPreviewImp.setSlice(self.current)
except:
pass
if runStats:
clij2.statisticsOfBackgroundAndLabelledPixels(
dst, self.src, self.results)
dst2 = clij2.create(width, height, 1)
clij2.maximumZProjection(dst, dst2)
self.maxZPreviewImp = clij2.pull(dst2)
previewDisplaySettings(self.maxZPreviewImp, "maxZ label preview", 50,
self.cal)
dst3 = clij2.create(width, depth, 1)
clij2.maximumYProjection(dst, dst3)
self.maxYPreviewImp = clij2.pull(dst3)
previewDisplaySettings(self.maxYPreviewImp, "maxY label preview", 50,
self.cal)
dst3.close()
dst.close()
dst2.close()
src2.close()
labelWindow = self.labelPreviewImp.getWindow()
x = labelWindow.getLocation().x
y = labelWindow.getLocation().y
maxZPreviewWindow = self.maxZPreviewImp.getWindow()
maxZPreviewWindow.setLocation(x, y + height + 50)
maxYPreviewWindow = self.maxYPreviewImp.getWindow()
maxYPreviewWindow.setLocation(x + width / 2, y + height + 50)
print labelWindow
def actionPerformed(self, event):
"""event: actionlistener does stuff on buttonpress"""
Source = event.getSource() # returns the Button object
self.current = self.labelPreviewImp.getCurrentSlice()
if Source.label == "Set top":
self.top = self.labelPreviewImp.getCurrentSlice()
self.bottom = self.slider2.getValue()
self.slider1.setValue(int(self.top))
if (self.bottom < self.top):
self.bottom = self.top
self.slider2.setValue(int(self.top))
return
if Source.label == "Set bottom":
self.top = self.slider1.getValue()
self.bottom = self.labelPreviewImp.getCurrentSlice()
self.slider2.setValue(int(self.bottom))
if self.bottom < self.top:
self.slider1.setValue(int(self.bottom))
self.top = self.bottom
print "B"
return
if Source.label == "Whole stack":
self.top = 1
self.bottom = depth
self.slider1.setValue(int(self.top))
self.slider2.setValue(int(self.bottom))
return
if Source.label == "Just slice":
print "current slice"
self.top = self.labelPreviewImp.getCurrentSlice()
self.bottom = self.labelPreviewImp.getCurrentSlice()
self.slider2.setValue(int(self.top))
self.slider1.setValue(int(self.bottom))
return
if Source.label[:5] == "label":
[int(s) for s in Source.label.split() if s.isdigit()]
s = int(s)
print "s " + str(s)
#try:
roi1 = self.labelPreviewImp.getRoi()
selectedPixels = roi1.getContainedPoints()
roiPixelLoc = map(lambda i: i.y * width + i.x, selectedPixels)
pixels2 = filter(lambda i: self.nucLoc[i] in roiPixelLoc,
xrange(len(self.nucLoc)))
#on first run set self.top and self.bottom to top and bottom of the stack
try:
print self.top
except:
self.top = 1
try:
print self.bottom
except:
self.bottom = self.labelPreviewImp.getNSlices()
choice = self.gd.getChoices().get(0)
if choice.getSelectedItem() == "Slice":
top = self.current
bottom = self.current
else:
top = self.top
bottom = self.bottom
pixels2 = filter(
lambda i: max(self.bbze[i], bottom) - min(top, self.bbz[i]) <=
(self.bbze[i] - self.bbz[i]) + (bottom - top), pixels2)
self.nucleiLabels = map(lambda i: i, pixels2)
#print(map(lambda i:self.zs[i], pixels2))
#print len(pixels2)
self.labelDict[s] = self.nucleiLabels + self.labelDict[s]
self.labelDict[s] = sorted(list(set(self.labelDict[s])))
for key in self.labelDict:
if key != s:
self.labelDict[key] = filter(
lambda x: x not in self.labelDict[s],
self.labelDict[key])
#print labelDict
for key in self.labelDict:
for value in self.labelDict[int(key)]:
self.labelValues[value] = int(key)
self.labelValues[0] = 0
self.labelDict[0] = [0]
for key in self.labelDict.keys()[1:]:
self.labelDict[key] = filter(lambda x: x != 0, self.labelDict[key])
self.renderPreview(0)
#except:
# print "No roi"
return
# Do an action depending on the button clicked
def adjustmentValueChanged(self, event):
""" event: an AdjustmentEvent with data on the state of the scroll bar. """
#return if the user is still dragging
if event.getValueIsAdjusting():
return
Source = event.getSource()
try:
self.slider1 = self.gd.getSliders().get(0)
except:
print "huh?"
try:
self.slider2 = self.gd.getSliders().get(1)
except:
print "huh?2"
self.top = self.slider1.getValue()
self.bottom = self.slider2.getValue()
#make top and bottom sliders autocorrect for each other
if Source == self.slider1:
if self.top > self.bottom:
self.slider2.setValue(int(self.top))
self.bottom = self.top
print "A"
if Source == self.slider2:
if self.bottom < self.top:
self.slider1.setValue(int(self.bottom))
self.top = self.bottom
print "B"
def import_and_straighten(imgDir):
"""
Core function. Opens images in given directory in series and calls a straightening function.
Thresholds using weka if stddev of pixel intensities is too high (bright field), otherwise uses
histogram based segmentation.
"""
targetWidth = 800 #adjustable
make_directory(imgDir)
index = "000000000"
filename = imgDir + "/img_" + index + "__000.tif"
if path.exists(filename):
weka = Weka_segmentor(IJ.openImage(filename))
while path.exists(filename):
IJ.run("Set Measurements...", "mean standard min center redirect=None decimal=3")
IJ.run("Clear Results")
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("Measure")
table = RT.getResultsTable()
stddev = RT.getValue(table, "StdDev", 0)
if stddev < 20:
segmented = weka.getThreshold(imp)
segmented.show()
IJ.run("8-bit")
IJ.run("Invert")
imp.close()
imp = segmented
else:
IJ.run(imp, "Auto Threshold", "method=Li white") #threshold
imp = preProcess_(imp)
#straighten_roi_rotation()
coords = run_straighten()
newImp = IJ.getImage()
"""
fs = FileSaver(newImp)
fs.saveAsTiff(imgDir + "/straightened" + "/img_" + index + "__000-straight.tif")
"""
IJ.run("Image Padder", "pad_right="+str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/binary" + "/img_" + index + "__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
#use same centerline for original greyscale image
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("8-bit")
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
newImp = IJ.getImage()
IJ.run("Image Padder", "pad_right="+str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
IJ.run("8-bit")
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/greyscale" + "/img_" + index + "__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index)+1))
filename = filename = imgDir + "/img_" + index + "__000.tif"
consol.addValue("foci_count", 0)
rowcount = 1
# loop over all cells, add cell number to the "cell" column
for count in range(cell):
consol.setValue("cell", count, count)
# loop over all foci
for count in range(rt.size()):
# get in which cell that foci is and increase the
# counter on the summary results table
currcell = int(rt.getValue("cell", count))
consol.setValue(
"foci_count", currcell,
int(consol.getValue("foci_count", currcell)) + 1)
for count in range(1, cell):
foci = consol.getValue("foci_count", count)
if foci <= 3:
cellsperfoci[foci] = cellsperfoci[foci] + 1
else:
cellsperfoci["more"] = cellsperfoci["more"] + 1
print(cellsperfoci)
# close the results window
IJ.selectWindow("Results")
IJ.run("Close")
# this segment only runs if a mCherry channel is present
if (linechannel > 0):
# generate image with mCherry channel
ImagePlus("stack", linefoci_stack).show()
# Find the ROI with the largest area
for i, area in enumerate(
table.getColumn(table.getColumnIndex("Area"))):
if area > maxArea:
index = i
if thresholdMode:
imp.show()
# Writes everything in the output file
if index != -1:
diameter = 2 * math.sqrt(
float(table.getValue("Area", index)) / (2 * math.pi))
isOrganoid = table.getValue(
"Area", index) > area_threshold and table.getValue(
"Area", index) > round_threshold
output.write(
str(subfolder) + ',' + filename + ',' +
str(table.getValue("Feret", index)) + ',' +
str(table.getValue("MinFeret", index)) + ',' +
str((table.getValue("MinFeret", index) +
table.getValue("Feret", index)) / 2) + ',' +
str(table.getValue("Area", index)) + ',' +
str(diameter) + ',' +
str(table.getValue("Major", index)) + ',' +
str(table.getValue("Minor", index)) + ',' +
str(table.getValue("Circ.", index)) + ',' +
str(table.getValue("Round", index)) + ',' +
for value in test.labelDict[key]:
listOfNames[value] = names[key]
if imageOrTable == "Results table":
rt = ResultsTable.getResultsTable(resultsName)
else:
measureImp = WM.getImage(imageName)
src2 = clij2.push(measureImp)
rt = ResultsTable()
clij2.statisticsOfBackgroundAndLabelledPixels(src2, test.src, rt)
src2.close()
resultsName = "Results table"
collumnNumber = rt.getLastColumn() + 1
for i in range(len(listOfNames)):
try:
j = rt.getValue("Identifier", i)
except:
try:
j = rt.getValue("Label", i)
except:
j = i
rt.setValue("Label name", i, listOfNames[int(j)])
rt.setValue("Label value", i, test.labelValues[int(j)])
rt.show(resultsName + " with labels")
clij2.clear()
labelColorBarImp.close()
def import_and_straighten(imgDir):
"""
Core function. Opens images in given directory in series and calls a straightening function.
Thresholds using weka if stddev of pixel intensities is too high (bright field), otherwise uses
histogram based segmentation.
"""
targetWidth = 800 #adjustable
make_directory(imgDir)
index = "000000000"
filename = imgDir + "/img_" + index + "__000.tif"
if path.exists(filename):
weka = Weka_segmentor(IJ.openImage(filename))
while path.exists(filename):
IJ.run("Set Measurements...",
"mean standard min center redirect=None decimal=3")
IJ.run("Clear Results")
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("Measure")
table = RT.getResultsTable()
stddev = RT.getValue(table, "StdDev", 0)
if stddev < 20:
segmented = weka.getThreshold(imp)
segmented.show()
IJ.run("8-bit")
IJ.run("Invert")
imp.close()
imp = segmented
else:
IJ.run(imp, "Auto Threshold", "method=Li white") #threshold
imp = preProcess_(imp)
#straighten_roi_rotation()
coords = run_straighten()
newImp = IJ.getImage()
"""
fs = FileSaver(newImp)
fs.saveAsTiff(imgDir + "/straightened" + "/img_" + index + "__000-straight.tif")
"""
IJ.run("Image Padder",
"pad_right=" + str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/binary" + "/img_" + index +
"__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
#use same centerline for original greyscale image
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("8-bit")
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")
newImp = IJ.getImage()
IJ.run("Image Padder",
"pad_right=" + str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
IJ.run("8-bit")
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/greyscale" + "/img_" + index +
"__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index) + 1))
filename = filename = imgDir + "/img_" + index + "__000.tif"
def straighten_roi_rotation(roiWindowsize=8):
""" Root straightening function that rotates ROI to follow root slope.
Does not work properly.
"""
IJ.run("Set Measurements...",
"mean standard min center redirect=None decimal=3")
IJ.runMacro("//setTool(\"freeline\");")
IJ.run("Line Width...", "line=80")
#numPoints = 512/roiWindowsize
xvals = []
yvals = []
maxvals = []
counter = 0
maxIters = 800 / roiWindowsize
minIters = 10
imp = IJ.getImage().getProcessor()
rm = RoiManager()
if find_first_pixel(0, imp) == None or find_last_pixel(0, imp)[1] == None:
return
y = (find_first_pixel(0, imp)[1] + find_last_pixel(0, imp)[1]) / 2
roi = roiWindow_(imp,
center=(roiWindowsize / 2, y),
width=roiWindowsize,
height=512)
xvals.append(roiWindowsize / 2)
yvals.append(y)
maxvals.append(0)
roi.findTilt_()
i = 0
while i < maxIters and roi.containsRoot_():
roi.advance_(roiWindowsize)
IJ.run("Clear Results")
IJ.run("Measure")
table = RT.getResultsTable()
x = RT.getValue(table, "XM", 0)
y = RT.getValue(table, "YM", 0)
if imp.getPixel(int(x), int(y)) != 0:
xvals.append(x)
yvals.append(y)
maxvals.append((RT.getValue(table, "Max", 0)))
#roi.advance_(roiWindowsize)
print "here"
roi.unrotateRoot_()
IJ.run("Clear Results")
IJ.run("Measure")
roi.restoreCenter_(RT.getValue(table, "XM", 0),
RT.getValue(table, "YM", 0))
#exit(1)
sleep(.5)
roi.findTilt_()
i += 1
coords = ""
for i in range(len(xvals) - 1):
coords += str(xvals[i]) + ", " + str(yvals[i]) + ", "
coords += str(xvals[len(xvals) - 1]) + ", " + str(yvals[len(xvals) - 1])
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")