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 drawLines(imp, points=None):
if points and (len(points)%2 == 0):
# points is numeric list of even length
pRoi = PointRoi(points[0::2], points[1::2], len(points)/2)
pRoi.setShowLabels(True)
pRoi.setSize(3)
imp.setRoi(pRoi)
roi = imp.getRoi()
pp = roi.getFloatPolygon()
# print "Added", pp.npoints
if pp.npoints <= 1:
# don't draw if only one point
return
xys = []
for i in xrange(pp.npoints):
xys.append([pp.xpoints[i], pp.ypoints[i]])
ol = Overlay()
x0 = xys[0][0]
y0 = xys[0][1]
cal = imp.getCalibration()
for i in xrange(1, pp.npoints):
xi = xys[i][0]
yi = xys[i][1]
# prepare text label
d = math.sqrt((xi - x0)**2 + (yi - y0)**2) * cal.pixelWidth
dText = String.format("%.2f ", d) + cal.getUnits()
textOffset = 30
xt = xi
yt = yi
# if xi > x0:
# xt += textOffset
if xi < x0:
xt -= textOffset
# if yi > y0:
# yt += textOffset
if yi < y0:
yt -= textOffset
dTextRoi = TextRoi(xt, yt, dText)
ol.add(dTextRoi)
lineRoi = Line(x0, y0, xi, yi)
lineRoi.setStrokeWidth(1)
lineRoi.setStrokeColor(Color(255,255,0))
ol.add(lineRoi)
imp.setOverlay(ol)
imp.updateAndDraw()
def draw_scale(image, ticks):
cal = image.getCalibration()
overlay = Overlay()
image.setOverlay(overlay)
TextRoi.setGlobalJustification(TextRoi.CENTER)
offset = image.getHeight() - extend
for tick in ticks:
tick_pos = cal.getRawX(tick)
line = Line(tick_pos, offset, tick_pos, offset + font_size)
line.setWidth(font_size // 8)
line.setStrokeColor(Color(1.00, 1.00, 1.00))
overlay.add(line)
text = TextRoi(tick_pos, offset + font_size, str(tick), font)
text_width = text.getFloatWidth()
text_y = text.getYBase()
text.setLocation(tick_pos - text_width/2, text_y)
text.setStrokeColor(Color(1.00, 1.00, 1.00))
overlay.add(text)
def generateOverlayRoi(self):
"""Generate the overlay ROI"""
if (abs(self.p1[0] - self.p2[0])
) > 800: # assume for now that lines run full length of image
factor = 1024.0 / 800
loresp1x = int(round(
self.p1[0] / factor)) - self.referenceRoiOffsetXY[0]
loresp1y = int(round(
self.p1[1] / factor)) - self.referenceRoiOffsetXY[1]
loresp2x = int(round(
self.p2[0] / factor)) - self.referenceRoiOffsetXY[0]
loresp2y = int(round(
self.p2[1] / factor)) - self.referenceRoiOffsetXY[1]
#print([(loresp1x, loresp1y), (loresp2x,loresp2y)]);
return Line(loresp1x, loresp1y, loresp2x, loresp2y)
else:
return Line(self.p1[0] - self.referenceRoiOffsetXY[0],
self.p1[1] - self.referenceRoiOffsetXY[1],
self.p2[0] - self.referenceRoiOffsetXY[0],
self.p2[1] - self.referenceRoiOffsetXY[1])
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 __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 drawLines(imp, points=None):
if points and (len(points) % 2 == 0):
# points is numeric list of even length
pRoi = PointRoi(points[0::2], points[1::2], len(points) / 2)
pRoi.setShowLabels(True)
pRoi.setSize(3)
imp.setRoi(pRoi)
roi = imp.getRoi()
pp = roi.getFloatPolygon()
# print "Added", pp.npoints
if pp.npoints <= 1:
# don't draw if only one point
return
xys = []
for i in xrange(pp.npoints):
xys.append([pp.xpoints[i], pp.ypoints[i]])
ol = Overlay()
x0 = xys[0][0]
y0 = xys[0][1]
cal = imp.getCalibration()
for i in xrange(1, pp.npoints):
xi = xys[i][0]
yi = xys[i][1]
# prepare text label
d = math.sqrt((xi - x0)**2 + (yi - y0)**2) * cal.pixelWidth
dText = String.format("%.2f ", d) + cal.getUnits()
textOffset = 30
xt = xi
yt = yi
# if xi > x0:
# xt += textOffset
if xi < x0:
xt -= textOffset
# if yi > y0:
# yt += textOffset
if yi < y0:
yt -= textOffset
dTextRoi = TextRoi(xt, yt, dText)
ol.add(dTextRoi)
lineRoi = Line(x0, y0, xi, yi)
lineRoi.setStrokeWidth(1)
lineRoi.setStrokeColor(Color(255, 255, 0))
ol.add(lineRoi)
imp.setOverlay(ol)
imp.updateAndDraw()
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")
def getEuclidean(self):
"""return the length of the straight line joining start and end points of the membrane"""
poly = self.roi.getInterpolatedPolygon(1, True)
line = Line(poly.xpoints[0], poly.ypoints[0], poly.xpoints[-1],
poly.ypoints[-1])
return line.getLength()
# using a default generic RealType converter via t.setReal(t.getRealDouble())
compute(op).into(blurred, None, FloatType(), None)
# Show the blurred image with the same LUT as the original
imp2 = IL.wrap(blurred, "integral image radius 5 blur")
imp2.getProcessor().setLut(imp.getProcessor().getLut())
imp2.show()
# Compare with Gaussian blur
from ij import ImagePlus
from ij.plugin.filter import GaussianBlur
from ij.gui import Line, ProfilePlot
# Gaussian of the original image
imp_gauss = ImagePlus(imp.getTitle() + " Gauss",
imp.getProcessor().duplicate())
GaussianBlur().blurGaussian(imp_gauss.getProcessor(), radius)
imp_gauss.show()
# Plot values from a diagonal from bottom left to top right
line = Line(imp.getWidth() - 1, 0, 0, imp.getHeight() - 1)
imp_gauss.setRoi(line)
pp1 = ProfilePlot(imp_gauss)
plot = pp1.getPlot()
imp2.setRoi(line)
pp2 = ProfilePlot(imp2)
profile2 = pp2.getProfile() # double[]
plot.setColor("red")
plot.add("line", range(len(profile2)), profile2)
plot.show()
def getCells(dicStack):
outStack = ImageStack(W,H)
cells = [None for t in range(T+1)]
for t in range(1,T+1):
mapp = dicStack.getProcessor(t).convertToFloatProcessor()
mapp.subtract( mapp.getStatistics().mean )
mapp.abs()
RankFilters().rank(mapp, 1.0, RankFilters.VARIANCE)
mapp.sqrt()
mapp.blurGaussian(5)
hist = mapp.getHistogram(256)
stats = mapp.getStatistics()
thresh = AutoThresholder().getThreshold( AutoThresholder.Method.Otsu, hist )
thresh = (thresh/float(255)) * (stats.max-stats.min) + stats.min
mask = ByteProcessor(W,H)
for i in range(W*H):
value = mapp.getf(i)
bite = 255 if value>=thresh else 0
mask.set(i, bite)
fillHoles(mask)
ed = 3
for e in range(ed): mask.erode(1, 0)
for d in range(ed): mask.dilate(1, 0)
watershed(mask)
minA = 5000 #px²
mask.setThreshold(255,255, ImageProcessor.NO_LUT_UPDATE)
composite = ThresholdToSelection().convert(mask)
rois = ShapeRoi(composite).getRois()
keep = []
for roi in rois:
if roi.getStatistics().area >= minA:
if not onEdge(roi):
keep.append(roi)
else:
edgeRoi = ShapeRoi(roi)
edgeRoi.setPosition(0,0,t)
edgeRoi.setStrokeColor(Color.YELLOW)
ol.add(edgeRoi)
print("T"+str(t)+" using "+str(len(keep))+"/"+str(len(rois))+" ROIs")
rois = keep
#rois = [ roi for roi in rois if roi.getStatistics().area >= minA and not onEdge(roi) ] #keep big enough and not on edges
# if there is only one Roi, cut it along the fitted ellipse minor axis
if len(rois)==1:
el = EllipseFitter()
mask.setRoi(rois[0])
el.fit(mask, None)
el.makeRoi(mask)
theta = el.angle * (maths.pi/180.0)
length = el.major/2.0
dy = maths.sin(theta)* length
dx = maths.cos(theta)* length
#major axis
lineX0 = el.xCenter - dx
lineY0 = el.yCenter + dy
lineX1 = el.xCenter + dx
lineY1 = el.yCenter - dy
line = Line(lineX0, lineY0, lineX1, lineY1)
line.setStrokeColor(Color.BLUE)
line.setStrokeWidth(1)
line.setPosition(0,0,t)
ol.add(line)
#minor axis scaled length to make sure cut ends are outside Roi
cutX0 = el.xCenter + dy*100
cutY0 = el.xCenter + dx*100
cutX1 = el.yCenter - dy*100
cutY1 = el.yCenter - dx*100
cut = Line(cutX0,cutY0, cutX1, cutY1)
cut.setStrokeWidth(2)
cut = PolygonRoi( cut.getFloatPolygon(), PolygonRoi.POLYGON )
mask.setColor(0)
mask.fill(cut)
composite = ThresholdToSelection().convert(mask)
rois = ShapeRoi(composite).getRois()
rois = [ roi for roi in rois if roi.getStatistics().area >= minA ]
print(str(t) + ":" + str(len(rois)))
rois = [ PolygonRoi(roi.getInterpolatedPolygon(20, True), PolygonRoi.POLYGON) for roi in rois ]
rois = [ PolygonRoi(roi.getConvexHull(), PolygonRoi.POLYGON) for roi in rois ]
rois = sorted(list(rois), key=lambda roi:roi.getLength() ) #size order
rois = rois[-2:] #keep 2 biggest
rois = sorted(list(rois), key=lambda roi:roi.getStatistics().xCentroid+roi.getStatistics().yCentroid ) #top left to bottom right order
if len(rois)>0:
rois[0].setStrokeColor(Color.RED)
rois[0].setPosition(0, 0, t)
ol.add(rois[0])
if len(rois)>1:
rois[1].setStrokeColor(Color.GREEN)
rois[1].setPosition(0, 0, t)
ol.add(rois[1])
cells[t] = (rois[0], rois[1])
return cells
def makeArrow(x1, y1, x2, y2):
IJ.setTool("arrow")
imp = IJ.getImage()
imp.setRoi(Line(x1, y1, x2, y2))
def do_angular_projection(imp,
max_r_pix=60,
min_r_pix=10,
generate_roi_stack=True):
"""perform ray-based projection of vessel wall, c.f. ICY TubeSkinner (Lancino 2018)"""
Prefs.blackBackground = True
print("do angular projection input imp = " + str(imp))
split_chs = ChannelSplitter().split(imp)
mch_imp = split_chs[0]
IJ.setAutoThreshold(mch_imp, "IsoData dark stack")
egfp_imp = split_chs[1]
proj_imp = Duplicator().run(egfp_imp)
cl_imp = split_chs[2]
if generate_roi_stack:
egfp_imp_disp = Duplicator().run(egfp_imp)
roi_stack = IJ.createImage("rois", egfp_imp.getWidth(),
egfp_imp.getHeight(), egfp_imp.getNSlices(),
16)
centres = []
projected_im_pix = []
ring_rois = []
for zidx in range(cl_imp.getNSlices()):
if ((zidx + 1) % 100) == 0:
print("Progress = " +
str(round(100 * (float(zidx + 1) / cl_imp.getNSlices()))))
projected_im_row = []
proj_imp.setZ(zidx + 1)
mch_imp.setZ(zidx + 1)
bp = mch_imp.createThresholdMask()
bp.dilate()
bp.erode()
bp.erode()
bp.erode()
mask_imp = ImagePlus("mask", bp)
IJ.run(mask_imp, "Create Selection", "")
roi = mask_imp.getRoi()
proj_imp.setRoi(roi)
IJ.run(proj_imp, "Set...", "value=0 slice")
IJ.run(proj_imp, "Make Inverse", "")
roi = proj_imp.getRoi()
centre = (roi.getStatistics().xCentroid, roi.getStatistics().yCentroid)
centres.append(centre)
ring_roi_xs = []
ring_roi_ys = []
for theta in range(360):
pt1 = (centre[0] + min_r_pix * math.cos(math.radians(theta)),
centre[1] + min_r_pix * math.sin(math.radians(theta)))
pt2 = (centre[0] + max_r_pix * math.cos(math.radians(theta)),
centre[1] + max_r_pix * math.sin(math.radians(theta)))
roi = Line(pt1[0], pt1[1], pt2[0], pt2[1])
proj_imp.setRoi(roi)
profile = roi.getPixels()
projected_im_row.append(max(profile))
try:
ring_roi_xs.append(roi.getContainedPoints()[profile.index(
max(profile))].x)
except IndexError:
ring_roi_xs.append(pt2[0])
try:
ring_roi_ys.append(roi.getContainedPoints()[profile.index(
max(profile))].y)
except IndexError:
ring_roi_ys.append(pt2[1])
proj_imp.killRoi()
ring_roi = PolygonRoi(ring_roi_xs, ring_roi_ys, Roi.FREELINE)
ring_rois.append(ring_roi)
if generate_roi_stack:
roi_stack.setZ(zidx + 1)
roi_stack.setRoi(ring_roi)
IJ.run(roi_stack, "Line to Area", "")
IJ.run(
roi_stack, "Set...",
"value=" + str(roi_stack.getProcessor().maxValue()) + " slice")
#egfp_imp.setRoi(ring_roi);
projected_im_pix.append(projected_im_row)
# for ch in split_chs:
# ch.close();
out_imp = ImagePlus(
"projected", FloatProcessor([list(x) for x in zip(*projected_im_pix)]))
if generate_roi_stack:
roi_stack.show()
egfp_imp_disp.show()
# merge?
else:
roi_stack = None
return out_imp, roi_stack, ring_rois, centres
for bp in brightestpixellist:
x = bp%imp.width
y = bp/imp.width
#print "max. brightness coordinates:", x, y
# note that the following chooses for x, y the last element in the brightestpixelist which is OK if there is only one element
# TODO: would be nicer to loop over this list or specify which element to pick
length = 400/2
angular_accuracy = 5 # degrees
for alpha in range(0, 180, angular_accuracy):
myimp = ImagePlus("Profile_"+str(alpha), ip)
vecx, vecy = length * cos(alpha * pi/180), length * sin(alpha * pi/180)
roi = Line(x-vecx, y-vecy, x+vecx, y+vecy)
myimp.setRoi(roi)
#ip.draw(roi) # enabling this creates artifacts - careful!
# create ProfilePlot
profplot = ProfilePlot(myimp)
#profplot.createWindow() # enabling this creates a nice animation
#print alpha, sum(profplot.getProfile())/len(profplot.getProfile()) # test: average of profile values as proxy for brightness
# get the data
profarray = profplot.getProfile()
# smooth the data by calculating moving average
win = 12 # window size for moving average, must be even
movavg = moving_average(profarray, win)
medi = median(movavg)
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)
from ij import IJ, WindowManager
from ij.gui import Line
IJ.run("Close All")
imp = IJ.openImage("/Users/jrminter/Downloads/three_phase.jpeg")
IJ.run(imp, "RGB to CIELAB", "")
IJ.run("Stack to Images", "")
imp_L = WindowManager.getImage("L")
imp_a = WindowManager.getImage("a")
imp_b = WindowManager.getImage("b")
the_line = Line(0,178,690,178)
the_line.setWidth(20)
imp_L.setRoi(the_line)
imp_L.show()
IJ.run(imp_L, "Plot Profile", "")
imp_a.setRoi(Line(0,231,690,220))
IJ.run(imp_a, "Plot Profile", "")
imp_a.show()
def main(imp, tolerance, window_radius, pixel_size_nm, out_dir):
# set output dir
out_dir = str(out_dir)
# Find maxima
excludeOnEdge = True
polygon = MaximumFinder().getMaxima(imp.getProcessor(), tolerance, excludeOnEdge)
roi = PointRoi(polygon)
# get RoiManager
rm = RoiManager.getInstance();
if rm is None:
rm = RoiManager()
# Check if output table is writable
out_table_fn = os.path.join(out_dir, "fwhm_values.txt")
try:
file_handle = open(out_table_fn, 'w')
except IOError:
IJ.showMessage("Output file '' not writeable. Check if file is open in Excel...")
sys.exit(0)
# iterate and write output
with file_handle as csvfile:
writer = csv.DictWriter(csvfile,
fieldnames=["id", "peak_id", "x_pos", "y_pos",
"type", "fwhm", "fwhm_nm", "r2_GoF",
"avg_fwhm", "area_profile", "area_gauss"], delimiter="\t", lineterminator='\n')
writer.writeheader()
id_ = 0
# over all peaks
for i, p in list(enumerate(roi)):
IJ.showProgress(i, roi.getNCounters() +1)
# Horizontal
lroi = Line(p.x+0.5-window_radius, p.y+0.5,
p.x+0.5+window_radius, p.y+0.5)
output = fit_gauss(lroi, imp, p, i, id_, "H", rm)
writer.writerow(output)
id_+=1
# Vertical
lroi = Line(p.x+0.5, p.y+0.5-window_radius,
p.x+0.5, p.y+0.5+window_radius)
output = fit_gauss(lroi, imp, p, i, id_, "V", rm)
writer.writerow(output)
id_+=1
# Diagonal 1
lroi = Line(p.x+0.5-MN*window_radius, p.y+0.5+MN*window_radius,
p.x+0.5+MN*window_radius, p.y+0.5-MN*window_radius)
output = fit_gauss(lroi, imp, p, i, id_, "D1", rm)
writer.writerow(output)
id_+=1
# Diagonal 2
lroi = Line(p.x+0.5-MN*window_radius, p.y+0.5-MN*window_radius,
p.x+0.5+MN*window_radius, p.y+0.5+MN*window_radius)
output = fit_gauss(lroi, imp, p, i, id_, "D2", rm)
writer.writerow(output)
id_+=1
IJ.showProgress(1)
rm.runCommand("Deselect"); # deselect ROIs to save them all
rm.runCommand("Save", os.path.join(out_dir, "fwhm_fiji_rois.zip"))
IJ.showMessage("FWHM on Spots: Done")
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 __addroi(self, event) :
if ( not self.__init) :
IJ.showMessage("", "please start a new stack")
return
if ( not self.__initDIA) :
IJ.showMessage("", "please select an image for DIA")
return
if ( not self.__initFLUO) :
IJ.showMessage("", "please select an image for FLUO")
return
twres = TextWindow("measures-"+self.__name, "label\tname\tsol\tarea\tcirc\tAR\tFeret\taxis\traf\tdMajor\tdFeret\tdArea", "", 300, 450)
tab="\t"
self.__widthl = self.__display2.getText()
IJ.selectWindow(self.__impF.getTitle())
self.__rm = RoiManager.getInstance()
if (self.__rm==None): self.__rm = RoiManager()
if self.__impF.getImageStackSize() > 1 :
roisarray =[(roi, self.__rm.getSliceNumber(roi.getName())) for roi in self.__rm.getRoisAsArray()]
else :
roisarray =[(roi, 1) for roi in self.__rm.getRoisAsArray()]
self.__rm.runCommand("reset")
#self.__rm.runCommand("Delete")
IJ.selectWindow(self.__impF.getTitle())
self.__maxraf=float(self.__display19.text)
self.__minraf=float(self.__display20.text)
count=1
for roielement in roisarray :
roi = roielement[0]
pos = roielement[1]
lab = self.__impF.getImageStack().getShortSliceLabel(pos)
if lab==None : lab=str(pos)
if self.__conEllipses :
IJ.selectWindow(self.__impF.getTitle())
self.__impF.setSlice(pos)
self.__impF.setRoi(roi)
self.__rm.runCommand("Add")
IJ.run(self.__impF, "Fit Ellipse", "")
ellipse=self.__impF.getRoi()
params = ellipse.getParams()
ferets = ellipse.getFeretValues()
imp2 = Duplicator().run(self.__impF,pos,pos)
IJ.run(imp2, "Rotate... ", "angle="+str(ferets[1])+" grid=0 interpolation=Bilinear enlarge slice")
temproi=Roi((imp2.getWidth()-ferets[0])/2.0,(imp2.getHeight()-ferets[2])/2.0,ferets[0],ferets[2])
imp2.setRoi(temproi)
imp3 = Duplicator().run(imp2,1,1)
ip3=imp3.getProcessor()
if int(self.__display5.text) < ip3.getWidth() < int(self.__display6.text) :
self.__iplist.append(ip3)
self.__display.text = self.__name + " cell " + str(len(self.__iplist))
fer=Line(params[0],params[1],params[2],params[3])
self.__cellsrois.append((fer, pos))
self.__labels.append(self.__isF.getShortSliceLabel(pos))
m=Morph(self.__impF, roi)
twres.append(lab+tab+str(roi.getName())+tab+str(m.Solidity)+tab+str(m.Area)+tab+str(m.Circ)+tab+str(m.AR)+tab+str(m.MaxFeret)+tab+str(fer.getLength())+tab+str(1)+tab+str(0)+tab+str(0)+tab+str(0))
self.__dictCells[count]=(str(roi.getName()), lab, roi)
count=count+1
continue
if roi.getType() in [6,7] :
self.__impF.setSlice(pos)
self.__impF.setRoi(roi)
self.__rm.runCommand("Add")
elif roi.getType() in [2,4] :
self.__impF.setSlice(pos)
self.__impF.setRoi(roi)
m=Morph(self.__impF, roi)
m.setMidParams(10, 2)
midroi=m.MidAxis
if midroi == None : continue
raf = m.MaxFeret/midroi.getLength()
if (self.__maxraf < raf) or (raf < self.__minraf) : continue
maxsol = float(self.__display7.text)
minsol = float(self.__display8.text)
maxarea = float(self.__display9.text)
minarea = float(self.__display10.text)
maxcirc = float(self.__display11.text)
mincirc = float(self.__display12.text)
maxar = float(self.__display13.text)
minar = float(self.__display14.text)
maxfer = float(self.__display15.text)
minfer = float(self.__display16.text)
maxmean = float(self.__display17.text)
minmean = float(self.__display18.text)
maxmferet = float(self.__display21.text)
minmferet = float(self.__display22.text)
testsol = (minsol<= m.Solidity <= maxsol)
testarea = (minarea<= m.Area <= maxarea)
testcirc = (mincirc<= m.Circ <= maxcirc)
testar = (minar<= m.AR <= maxar)
testfer = (minfer<= m.MaxFeret <= maxfer)
testmean = (minmean <= m.Mean <= maxmean)
testmferet = (minmferet <= m.MinFeret <= maxmferet)
#print minmferet , m.MinFeret , maxmferet
test = (testsol+testarea+testcirc+testar+testfer+testmean+testmferet)/7
if test :
fmaj, ffmx, fa =[],[],[]
for r in m.getMidSegments(10, 40, 0)[0] :
if r == None : continue
m2=Morph(self.__impF, r)
fmaj.append(m2.Major)
ffmx.append(m2.MaxFeret)
fa.append(m2.Area)
diffmajor, diffferet, diffarea = 0,0,0
if len(fa) > 4 :
medfmaj = self.listmean(fmaj[1:-1])
medffmx = self.listmean(ffmx[1:-1])
medfa = self.listmean(fa[1:-1])
diffmajor = (max(fmaj[1:-1])-medfmaj)/medfmaj
diffferet = (max(ffmx[1:-1])-medffmx)/medffmx
diffarea = (max(fa[1:-1])-medfa)/medfa
twres.append(lab+tab+str(roi.getName())+tab+str(m.Solidity)+tab+str(m.Area)+tab+str(m.Circ)+tab+str(m.AR)+tab+str(m.MaxFeret)+tab+str(midroi.getLength())+tab+str(m.MaxFeret/midroi.getLength())+tab+str(diffmajor)+tab+str(diffferet)+tab+str(diffarea))
#print lab+tab+str(roi.getName())+tab+str(m.Solidity)+tab+str(m.Area)+tab+str(m.Circ)+tab+str(m.AR)+tab+str(m.MaxFeret)+tab+str(midroi.getLength())+tab+str(m.MaxFeret/midroi.getLength())+tab+str(diffmajor)+tab+str(diffferet)+tab+str(diffarea)
self.__impF.setRoi(roi)
self.__rm.runCommand("Add")
self.__impF.killRoi()
self.__impF.setRoi(midroi)
#self.__dictCells[str(roi.getName())]=(str(roi.getName()), lab, roi)
self.__dictCells[count]=(str(roi.getName()), lab, roi)
count=count+1
else :
#print "test falls"
continue
else :
print "out loop"
continue
straightener = Straightener()
new_ip = straightener.straighten(self.__impF, midroi, int(self.__widthl))
if int(self.__display5.text) < new_ip.getWidth() < int(self.__display6.text) :
self.__iplist.append(new_ip.convertToShort(False))
self.__display.text = self.__name + " cell " + str(len(self.__iplist))
#print "add", roi.getName(), roi.getType()
self.__cellsrois.append((midroi, pos))
self.__labels.append(self.__isF.getShortSliceLabel(pos))
#roisarray=self.__rm.getRoisAsArray()
#self.__rm.runCommand("reset")
#self.__rm.runCommand("Delete")
self.__impD.killRoi()
self.__impF.killRoi()
IJ.selectWindow(self.__impD.getTitle())
def batch_open_images(pathImage, file_typeImage, name_filterImage=None):
if isinstance(pathImage, File):
pathImage = pathImage.getAbsolutePath()
def check_filter(string):
'''This function is used to check for a given filter.
It is possible to use a single string or a list/tuple of strings as filter.
This function can access the variables of the surrounding function.
:param string: The filename to perform the filtering on.
'''
if name_filterImage:
# The first branch is used if name_filter is a list or a tuple.
if isinstance(name_filterImage, (list, tuple)):
for name_filter_ in name_filterImage:
if name_filter_ in string:
# Exit the function with True.
return True
else:
# Next iteration of the for loop.
continue
# The second branch is used if name_filter is a string.
elif isinstance(name_filterImage, string):
if name_filterImage in string:
return True
else:
return False
return False
else:
# Accept all files if name_filter is None.
return True
def check_type(string):
'''This function is used to check the file type.
It is possible to use a single string or a list/tuple of strings as filter.
This function can access the variables of the surrounding function.
:param string: The filename to perform the check on.
'''
if file_typeImage:
# The first branch is used if file_type is a list or a tuple.
if isinstance(file_typeImage, (list, tuple)):
for file_type_ in file_typeImage:
if string.endswith(file_type_):
# Exit the function with True.
return True
else:
# Next iteration of the for loop.
continue
# The second branch is used if file_type is a string.
elif isinstance(file_typeImage, string):
if string.endswith(file_typeImage):
return True
else:
return False
return False
# Accept all files if file_type is None.
else:
return True
# We collect all files to open in a list.
path_to_Image = []
# Replacing some abbreviations (e.g. $HOME on Linux).
path = os.path.expanduser(pathImage)
path = os.path.expandvars(pathImage)
# If we don't want a recursive search, we can use os.listdir().
for directory, dir_names, file_names in os.walk(pathImage):
# We are only interested in files.
for file_name in file_names:
# The list contains only the file names.
# The full path needs to be reconstructed.
full_path = os.path.join(directory, file_name)
# Both checks are performed to filter the files.
if check_type(file_name):
if check_filter(file_name) is False:
# Add the file to the list of images to open.
path_to_Image.append([
full_path,
os.path.basename(os.path.splitext(full_path)[0])
])
Images = []
for img_path, file_name in path_to_Image:
imp = IJ.openImage(img_path)
maskimage = ops.run("create.img", imp)
cursor = maskimage.localizingCursor()
imp.show()
IJ.run("Select None")
overlay = imp.getOverlay()
if overlay == None:
overlay = Overlay()
imp.setOverlay(overlay)
else:
overlay.clear()
imp.updateAndDraw()
impY = imp.getHeight()
impX = imp.getWidth()
print(impY, impX)
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
rm.runCommand("reset")
WaitForUserDialog("Select the landmark and the second point").show()
rm.runCommand("Add")
roi_points = rm.getRoisAsArray()
for Roi in roi_points:
xpoints = Roi.getPolygon().xpoints
ypoints = Roi.getPolygon().ypoints
print(xpoints, ypoints)
print('Start Landmark', xpoints[0], ypoints[0])
fixedpointX = xpoints[0]
fixedpointY = ypoints[0]
print('End Landmark', xpoints[1], ypoints[1])
IJ.makeLine(xpoints[0], ypoints[0], xpoints[1], ypoints[1])
gui = GenericDialog("Rotation Angle")
gui.addNumericField("Choose Angle", 15, 0)
gui.showDialog()
if gui.wasOKed():
rotateangle = gui.getNextNumber()
IJ.run("Rotate...", "angle=" + str(int(float(rotateangle))))
rm.runCommand("reset")
overlay = imp.getOverlay()
rm.runCommand("Add")
roi_points = rm.getRoisAsArray()
for Roi in roi_points:
xpoints = Roi.getPolygon().xpoints
ypoints = Roi.getPolygon().ypoints
print(xpoints, ypoints)
print('Rotated Start Landmark', xpoints[0], ypoints[0])
print('Rotated End Landmark', xpoints[1], ypoints[1])
slope = (ypoints[1] - ypoints[0]) / (xpoints[1] - xpoints[0] + 1.0E-20)
intercept = fixedpointY - slope * fixedpointX
print(fixedpointX, fixedpointY)
print('Slope', slope, 'Intercept', intercept)
XwY0 = -intercept / slope
YxwY0 = slope * XwY0 + intercept
XwYmax = (impY - intercept) / slope
YxwYmax = slope * XwYmax + intercept
YwX0 = intercept
XywX0 = (YwX0 - intercept) / slope
YwXmax = impX * slope + intercept
XxwXmax = (YwXmax - intercept) / slope
rm.runCommand("reset")
if XwY0 > 0:
lineROIA = Line(fixedpointX, fixedpointY, XwY0, YxwY0)
lineROIB = Line(fixedpointX, fixedpointY, XwYmax, YxwYmax)
overlay.add(lineROIA)
overlay.add(lineROIB)
if XwY0 < 0:
lineROIA = Line(fixedpointX, fixedpointY, XywX0, YwX0)
lineROIB = Line(fixedpointX, fixedpointY, XxwXmax, YwXmax)
overlay.add(lineROIA)
overlay.add(lineROIB)
while cursor.hasNext():
cursor.fwd()
X = cursor.getDoublePosition(0)
Y = cursor.getDoublePosition(1)
if abs(Y - slope * X - intercept) <= 4:
cursor.get().set(0)
else:
cursor.get().set(1)
labeling = ops.labeling().cca(maskimage,
StructuringElement.EIGHT_CONNECTED)
# get the index image (each object will have a unique gray level)
labelingIndex = labeling.getIndexImg()
dataImg = ds.create(labelingIndex)
location = ls.resolve(
str(savedir) + '/' + file_name + '.' + file_type_image)
dio.save(dataImg, location)
imp.close()
for l in range(0, height):
for c in range(l + 1, width):
p1 = pointList[l]
p2 = pointList[c]
delta_x = p1.x - p2.x
delta_y = p1.y - p2.y
value = math.sqrt((delta_x * delta_x) + (delta_y * delta_y))
matrix[l][c] = value
matrix[c][l] = value
nearestNeighborsDist = []
nearestNeighborsInd = []
for l in range(0, width):
minimum = min(matrix[l])
index = matrix[l].index(minimum)
nearestNeighborsDist.append(minimum)
nearestNeighborsInd.append(index)
RoiManager()
roiManager = RoiManager.getRoiManager()
for i in range(0, width):
nnI = nearestNeighborsInd[i]
if (nnI < i and nearestNeighborsInd[nnI] == i):
continue
p1 = pointList[i]
p2 = pointList[nnI]
roi = Line(p1.x, p1.y, p2.x, p2.y)
roiManager.addRoi(roi)
def main(imp,options):
from ij.plugin import ChannelSplitter
from ij.gui import Roi,PointRoi, PolygonRoi, Overlay, Line
from java.awt import Color
from ij import WindowManager
from ij.measure import ResultsTable
from ij.text import TextWindow
active_z=imp.getZ()
imps = ChannelSplitter.split(imp)
imp.setZ(active_z)
roi_int = imp.getRoi()
comp_imp=Zproj(imps[options["comp_ch"]],
"SUM",
active_z,
options["z_range"])
comp_imp=mode_subtract(comp_imp,roi_int)
loci_imp=Zproj(imps[options["loci_ch"]],
"SUM",
imp.getZ(),
options["z_range"])
loci_imp=mode_subtract(loci_imp,roi_int)
#Finding the boundaries of compartment and loci
comp_roi=thresh(sum_prj=comp_imp,thresh=options["comp_T"],roi=roi_int,method="boundary")
print "ok"
if (options["loci_method"]== "locus center"):
loci_roi=thresh(sum_prj=loci_imp,
thresh=options["loci_T"],
roi=roi_int,
method="point")
elif options["loci_method"]== "locus boundary":
loci_roi=thresh(sum_prj=loci_imp,
thresh=options["loci_T"],
roi=roi_int,
method="boundary")
if options["loci_method"]== "locus center":
dist,xc,yc,xl,yl=get_center_edge_dist(imp,comp_roi, loci_roi)
elif options["loci_method"]== "locus boundary":
dist,xc,yc,xl,yl=get_closest_points(imp,comp_roi,loci_roi)
rt_exist = WindowManager.getWindow("Loci distance to compartment")
if rt_exist==None or not isinstance(rt_exist, TextWindow):
table= ResultsTable()
else:
table = rt_exist.getTextPanel().getOrCreateResultsTable()
table.incrementCounter()
table.addValue("Label", imp.title)
table.addValue("Distance(micron)", dist)
if options['measure_feret']:
feret_roi,loci_feret,loci_area= feret(sum_prj=loci_imp,thresh=options["loci_T"],
roi=roi_int,pixel_size=imp.getCalibration().pixelWidth)
table.addValue("Loci feret", loci_feret)
table.addValue("Loci area", loci_area)
table.show("Loci distance to compartment")
## Adding loci overlay
ov=imp.getOverlay()
if ov==None:
ov=Overlay()
line = Line(xc,yc, xl,yl)
line.setStrokeWidth(0.2)
line.setStrokeColor(Color.PINK)
ov.add(line)
if options["loci_method"]== "locus center":
ov.add(PointRoi(loci_roi["x"],loci_roi["y"]))
elif options["loci_method"]== "locus boundary":
ov.add(loci_roi)
if options['measure_feret']:
ov.add(feret_roi)
ov.add(comp_roi)
imp.setOverlay(ov)
egfp_imp.setZ(zidx + 1)
cl_imp.setZ(zidx + 1)
ip = cl_imp.getProcessor()
out = MaximumFinder().getMaxima(ip, 10, True)
centres.append((out.xpoints[0], out.ypoints[0]))
centre = (out.xpoints[0], out.ypoints[0])
ring_roi_xs = []
ring_roi_ys = []
for theta in range(359):
# for theta_idx in range(6):
# theta = theta_idx * 60 - 90;
pt1 = (centre[0] + min_r_pix * math.cos(math.radians(theta)),
centre[1] + min_r_pix * math.sin(math.radians(theta)))
pt2 = (centre[0] + max_r_pix * math.cos(math.radians(theta)),
centre[1] + max_r_pix * math.sin(math.radians(theta)))
roi = Line(pt1[0], pt1[1], pt2[0], pt2[1])
egfp_imp.setRoi(roi)
profile = roi.getPixels()
projected_im_row.append(max(profile))
try:
ring_roi_xs.append(roi.getContainedPoints()[profile.index(
max(profile))].x)
except IndexError:
ring_roi_xs.append(pt2[0])
try:
ring_roi_ys.append(roi.getContainedPoints()[profile.index(
max(profile))].y)
except IndexError:
ring_roi_ys.append(pt2[1])
#print("Max val = " + str(max(profile)));
egfp_imp.killRoi()
def angle(xy1, xy2):
diffx = xy2[0] - xy1[0]
diffy = xy2[1] - xy1[1]
return math.atan2(diffy, diffx)
def calculate_point(x_orig, y_orig, distance, angle):
x_new = distance * math.cos(math.radians(angle)) + x_orig
y_new = (distance * math.sin(math.radians(angle)) - y_orig) * -1
return (x_new, y_new)
# Defining the boxes
roi1 = Line(point1[0], point1[1], point2[0], point2[1])
upangle = roi1.getAngle() + 90
downangle = roi1.getAngle() - 90
distance = roi1.getLength() / pixelsize
# calculating the coordinates of the box ROIs
starting_upper_point = (calculate_point(point1[0], point1[1], roi_width,
upangle))
starting_lower_point = (calculate_point(point1[0], point1[1], roi_width,
downangle))
end_upper_point = (calculate_point(point2[0], point2[1], roi_width,
roi1.getAngle() + 90))
end_lower_point = (calculate_point(point2[0], point2[1], roi_width,
