Script to plot 3d coordinate from a text file over a 3D stack.

plot3DPoints.py

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+import os
+import string
+from javax.vecmath import Color3f, Point3f
+from ij.io import OpenDialog
+from loci.plugins import BF
+from ij import IJ, ImagePlus, ImageStack
+from ij.process import ImageConverter
+from ij3d import Image3DUniverse
+from script.imglib import ImgLib
+
+#Static parameters
+USE_POINT=1
+USE_ICOSPHERE=2
+USE_ICOSPHERE_WITH_LIMIT=3 #Plot all points, may be slow over 3495
+LIMIT_SPHERE_PER_MESH=3495 #Limit of number of icospheres per Mesh
+
+
+#Use point(1), icosphere(2), or icosphere but limited to the first 3495 points in X (3)
+plotType=USE_POINT
+# diameter Cell visualization
+cellIcosophere=3.0
+
+#Open the image and duplicate it to get an 8 Bits version use to plot
+od = OpenDialog("Open coordinate file", None)
+srcFile = od.getPath()
+fp = open(srcFile)
+
+points=[]
+try:
+  for line in fp:
+  	result=string.split(line,",")
+  	for coor in result:
+  	  point = Point3f(float(result[0]),float(result[1]),float(result[2]))
+  	  #print "add point  : %f %f  %f" % (float(result[0]),float(result[1]),float(result[2]))
+  	  points.append(point)
+  	  #print result[0],
+finally:
+  fp.close()
+
+
+
+
+#Open the image and duplicate it to get an 8 Bits version use to plot
+od = OpenDialog("Open image file", None)
+srcFile = od.getPath()
+srcDir = od.getDirectory()
+imp = BF.openImagePlus(srcFile)[0]
+#imp8Bits = imp.duplicate()
+ImageConverter(imp).convertToGray8()
+
+#Create the Image3D	
+univ=Image3DUniverse(512,512)
+
+#Plot all points as Point , Icosphere or if too many points (>3495), only the first 3495
+if plotType == USE_POINT:
+	univ.addPointMesh(points[0:len(points)-1],Color3f(1,0,0),cellIcosophere, 'Cells').setLocked(True)
+elif plotType == USE_ICOSPHERE:
+	#Plot all points, splitted if needed in multiple mesh containing each a maximum of 3495 Icosphere
+	a, b= divmod(len(peaks), LIMIT_SPHERE_PER_MESH)
+	start=0
+	for i in range(0,a):
+		univ.addIcospheres(points[start:start+LIMIT_SPHERE_PER_MESH],Color3f(1,0,0),2,cellIcosophere/2, 'Cells'+str(i)).setLocked(True)
+		print "Plot point %f to %f" % (start, start+LIMIT_SPHERE_PER_MESH)
+		start=start+LIMIT_SPHERE_PER_MESH
+	univ.addIcospheres(points[start:len(points)-1],Color3f(1,0,0),2,cellIcosophere/2, 'Cells'+str(a)).setLocked(True)  
+	print "Plot point %f to %f" % (start+1, len(points))
+elif plotType == USE_ICOSPHERE_WITH_LIMIT:
+	if len(points) < LIMIT_SPHERE_PER_MESH:
+		univ.addIcospheres(points[0:len(points)-1],Color3f(1,0,0),2,cellIcosophere/2, 'Cells').setLocked(True)
+	else:
+		univ.addIcospheres(points[0:LIMIT_SPHERE_PER_MESH-1],Color3f(1,0,0),2,cellIcosophere/2, 'Cells').setLocked(True)
+		print "Plot only the first", LIMIT_SPHERE_PER_MESH, "points"
+else: #Default is plot points
+	univ.addPointMesh(points[0:len(points)-1],Color3f(1,0,0),6, 'Cells').setLocked(True)
+
+#Add the orthoslice of the stack
+#Orhoslices can be manipulated using the context menu (right click once the orthoslice has been selected then >Adjust Slices
+#univ.addOrthoslice(imp).setLocked(True)
+
+#Add the stack and display it in 3D
+univ.addVoltex(imp).setLocked(True)
+
+#Display the 3D View
+univ.show()
+print "Done"  
+#List<Object>