Hi All,
I am new to programming with Groovy and was wondering if anyone had any suggestions for a modification to a script I am working on. Overall, I have it designed to be used with the Line ROI, but recently with the release of v0.2.0-m2 which has a Polyline ROI feature, I have been trying to adapt it so it can be used with the polyline ROI.
The goal of this script is to calculate the shortest distance between two lines which the user draws and then creates new lines connecting the user drawn lines. Finally, it will calculate the area between each of the interval lines and determine the largest combination of adjacent intervals and create a new polygon such that the deviation of the mean total area is no greater than 50um.
The user will draw 2 semi-parallel lines (shown below). Note although one set/pair of lines in the image, the script is designed such that the user should be able to draw several pairs/sets.
Then after running the script, an image similar to the one below should appear
I would like to modify the script such that it can be used with polylines such as in the image below
I would greatly appreciate any time or assistance from anyone as this has been something I have been struggling with for quite sometime.
Please see the script below:
import qupath.lib.roi.LineROI
import qupath.lib.roi.PolygonROI
import qupath.lib.geom.Point2
import qupath.lib.objects.classes.PathClassFactory
import qupath.lib.objects.PathAnnotationObject
import qupath.lib.objects.classes.PathClass
import qupath.lib.gui.scripting.QPEx
import qupath.lib.common.ColorTools
def imageData = QPEx.getCurrentImageData()
def server = imageData.getServer()
t=server.getAveragedPixelSizeMicrons() //echelle pixel/micron
X1=[]
X2=[]
Y1=[]
Y2=[]
slope=[]
i=0
def double inf=Double.POSITIVE_INFINITY
def double ninf=Double.NEGATIVE_INFINITY
gmSampName=[]
gmHierar=[]
polysizes=[]
//Setting such that the mean total area can deviate by 50um to be considered within the greatest GM ROI - this is equivlent to 0.2mm in HALO protocol
deviation=50
//Sets increments/layer thickness to 250um
step=250
acc=250
for (pathAnnotation in getCurrentHierarchy().getFlattenedObjectList()[1..-1]){
if (pathAnnotation.getPathClass()==null && pathAnnotation.getROI().getRoiName()=='Line'){
X1.add(pathAnnotation.getROI().getX1()*t)
X2.add(pathAnnotation.getROI().getX2()*t)
Y1.add(pathAnnotation.getROI().getY1()*t)
Y2.add(pathAnnotation.getROI().getY2()*t)
slope.add((Y2[i]-Y1[i])/(X2[i]-X1[i]))
i+=1
}
}
0.step X1.size(),2,{
x11=X1[it]
y11=Y1[it]
x21=X2[it]
y21=Y2[it]
s1=slope[it]
d1=Math.sqrt(Math.pow(x21-x11,2)+Math.pow(y21-y11,2))
x12=X1[it+1]
y12=Y1[it+1]
x22=X2[it+1]
y22=Y2[it+1]
s2=slope[it+1]
d2=Math.sqrt(Math.pow(x22-x12,2)+Math.pow(y22-y12,2))
testmax1=1e5
testmax2=1e5
if (s1==-(double)0){s1=0}
if (s2==-(double)0){s2=0}
switch(s1){
case 0:
ysop1=0
if (x11<x21){
xsop1=250
}else{
xsop1=-250
}
break
case inf:
xsop1=0
ysop1=250
break
case ninf:
xsop1=0.
ysop1=-250
break
default:
if (s1<0){
if (x11>=x21 && y11<=y21){
for (int i=1;i<step*acc;i++){
xs1=-i/acc
ys1=Math.sqrt(Math.pow(step,2)-Math.pow(xs1,2))
test1=Math.abs(ys1/(xs1*s1)-1)
if(test1<testmax1){
testmax1=test1
xsop1=xs1
ysop1=ys1
}
}
}else if (x11<=x21 && y11>=y21){
for (int i=1;i<step*acc;i++){
xs1=i/acc
ys1=-Math.sqrt(Math.pow(step,2)-Math.pow(xs1,2))
test1=Math.abs(ys1/(xs1*s1)-1)
if(test1<testmax1){
testmax1=test1
xsop1=xs1
ysop1=ys1
}
}
}
}else if (s1>0){
if (x11<=x21 && y11<=y21){
for (int i=1;i<step*acc;i++){
xs1=i/acc
ys1=Math.sqrt(Math.pow(step,2)-Math.pow(xs1,2))
test1=Math.abs(ys1/(xs1*s1)-1)
if(test1<testmax1){
testmax1=test1
xsop1=xs1
ysop1=ys1
}
}
}else if (x11>=x21 && y11>=y21){
for (int i=1;i<step*acc;i++){
xs1=-i/acc
ys1=-Math.sqrt(Math.pow(step,2)-Math.pow(xs1,2))
test1=Math.abs(ys1/(xs1*s1)-1)
if(test1<testmax1){
testmax1=test1
xsop1=xs1
ysop1=ys1
}
}
}
}
break
}
switch(s2){
case 0:
ysop2=0
if (x12<x22){
xsop2=250
}else{
xsop2=-250
}
break
case inf:
xsop2=0
ysop2=250
break
case ninf:
xsop2=0
ysop2=-250
break
default:
if (s2<0){
if (x12>=x22 && y12<=y22){
for (int i=1;i<step*acc;i++){
xs2=-i/acc
ys2=Math.sqrt(Math.pow(step,2)-Math.pow(xs2,2))
test2=Math.abs(ys2/(xs2*s2)-1)
if(test2<testmax2){
testmax2=test2
xsop2=xs2
ysop2=ys2
}
}
}else if (x12<=x22 && y12>=y22){
for (int i=1;i<step*acc;i++){
xs2=i/acc
ys2=-Math.sqrt(Math.pow(step,2)-Math.pow(xs2,2))
test2=Math.abs(ys2/(xs2*s2)-1)
if(test2<testmax2){
testmax2=test2
xsop2=xs2
ysop2=ys2
}
}
}
}else if (s2>0){
if (x12<=x22 && y12<=y22){
for (int i=1;i<step*acc;i++){
xs2=i/acc
ys2=Math.sqrt(Math.pow(step,2)-Math.pow(xs2,2))
test2=Math.abs(ys2/(xs2*s2)-1)
if(test2<testmax2){
testmax2=test2
xsop2=xs2
ysop2=ys2
}
}
}else if (x12>=x22 && y11>=y22){
for (int i=1;i<step*acc;i++){
xs2=-i/acc
ys2=-Math.sqrt(Math.pow(step,2)-Math.pow(xs2,2))
test2=Math.abs(ys2/(xs2*s2)-1)
if(test2<testmax2){
testmax2=test2
xsop2=xs2
ysop2=ys2
}
}
}
}
break
}
classname='GM sampling '+(it/2+1).toString()
def newPassClass=new PathClass(classname,ColorTools.makeRGB(18,255,87))
while (d1>=2*step && d2>=2*step){
x11+=xsop1
y11+=ysop1
x12+=xsop2
y12+=ysop2
d1=Math.sqrt(Math.pow(x21-x11,2)+Math.pow(y21-y11,2))
d2=Math.sqrt(Math.pow(x22-x12,2)+Math.pow(y22-y12,2))
def roi = new LineROI(x11/t,y11/t,x12/t,y12/t)
def newLine=new PathAnnotationObject(roi,newPassClass)
imageData.getHierarchy().addPathObject(newLine,false)
}
}
for (pathAnnotation in getCurrentHierarchy().getFlattenedObjectList()[1..-1]){
if (pathAnnotation.getPathClass()!=null && pathAnnotation.getROI().getRoiName()=='Line'){
if (!gmSampName.contains(pathAnnotation.getPathClass().getName())){
gmSampName.add(pathAnnotation.getPathClass().getName())
}
gmHierar.add(pathAnnotation)
}
}
for (lines in gmSampName){
mean=0.0
N=0
poly=[]
for (gmSample in gmHierar){
if (gmSample.getPathClass().getName()==lines){
mean+=gmSample.getROI().getLength()*t
N+=1
}
}
mean/=N
for (gmSample in gmHierar){
l=Math.abs(gmSample.getROI().getLength()*t-mean)
if (gmSample.getPathClass().getName()==lines && l<=deviation){
poly.add(gmSample)
//imageData.getHierarchy().removeObject(gmSample,false)
}
}
polysizes.add(poly.size()*step)
def point1 = new Point2(poly[0].getROI().getX1(),poly[0].getROI().getY1())
def point2 = new Point2(poly[0].getROI().getX2(),poly[0].getROI().getY2())
def point3 = new Point2(poly[-1].getROI().getX1(),poly[-1].getROI().getY1())
def point4 = new Point2(poly[-1].getROI().getX2(),poly[-1].getROI().getY2())
points=[point1,point3,point4,point2,point1]
def roi = new PolygonROI(points)
def newPoly=new PathAnnotationObject(roi)
imageData.getHierarchy().addPathObject(newPoly,false)
}
P=[]
imax=polysizes.indexOf(Collections.max(polysizes))
def maxPolyClass=new PathClass('Greatest GM Sampling zone',ColorTools.makeRGB(0,94,32))
for (pA in getCurrentHierarchy().getFlattenedObjectList()[1..-1]){
if (pA.getROI().getRoiName()=='Polygon'){
P.add(pA)
}
}
P[imax].setPathClass(maxPolyClass)
//selectAnnotations();
selectObjects { p -> p.getPathClass() == getPathClass("Greatest GM Sampling zone") };
print('Done')
Thank you so very much for your time, patience, advice, and assistance! This is a wonderful platform and I look forward as it continues to grow and improve!
