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RangeRois.py
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RangeRois.py
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import sys
import os
import os.path
import math
from sets import Set
from java.awt import TextField, Panel, GridLayout, ComponentOrientation, Label, Checkbox, BorderLayout, Button, Color
from java.awt.event import ActionListener, AdjustmentListener, WindowEvent
from java.awt import Font
from ij.plugin.frame import RoiManager
from ij import ImageStack, ImagePlus, WindowManager, IJ
from ij.gui import Roi, NonBlockingGenericDialog, Overlay, ImageRoi, Line, OvalRoi, PolygonRoi, ShapeRoi, TextRoi
from ij.plugin.frame import RoiManager
from ij.plugin.filter import MaximumFinder, Analyzer
from ij.text import TextWindow
from ij.plugin import Straightener, Duplicator, ZProjector, MontageMaker, ImageCalculator
from ij.process import ShortProcessor, ByteProcessor
from ij.measure import ResultsTable
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
from ij import IJ, ImagePlus
from ij.measure import Calibration, Measurements
from ij.gui import Overlay, NonBlockingGenericDialog, Roi
from ij.plugin.filter import ParticleAnalyzer
#mypath=os.path.expanduser(IJ.getDirectory("plugins")+"MeasureCells")
mypath=os.path.expanduser(os.path.join("~","Dropbox","MacrosDropBox","py","MorphoBactProject"))
#mypath=os.path.expanduser("~/Dropbox/MacrosDropBox/py/MeasureCells_7")
#mypath=os.path.expanduser(os.path.join("~","Dropbox","MacrosDropBox","py","MeasureCells_7"))
sys.path.append(mypath)
from MorphoBact import Morph
class RangeRois(object):
"""This class allows to sort an array of ROI according to a range of measures
in a range between min and max values
"""
__rawRanges={}
__image=None
__test=""
def __init__(self, rois, img): #constructor initialize a private rois array
self.__roisArray=[]
self.__roisArray+=rois
self.__image=img
self.__firstslice=img.getSlice()
self.__ranges={}
self.__test="ok"
Roi.setColor(Color.BLUE)
self.__setMaxValues()
def setRoisarray(self, rois, img) :
self.__roisArray=[]
self.__roisArray+=rois
self.__image=img
self.__firstslice=img.getSlice()
self.__ranges={}
self.__test="ok"
Roi.setColor(Color.BLUE)
def __setMaxValues(self) :
areas, means, majors, minors=[],[],[],[]
for roi in self.__roisArray:
m=Morph(self.__image, roi)
areas.append(m.Area)
means.append(m.Mean)
majors.append(m.Major)
minors.append(m.Minor)
maxarea=max(areas)*1000
maxint=max(means)*10
maxline=max(majors)*100
maxminline=max(minors)*100
minline=min(minors)
self.__namemeasures=["Area", "Mean", "Angle", "Major", "Minor", "Solidity", "AR", "Round", "Circ"]
self.__maxmeasures=[maxarea, maxint, 180*10, maxline, maxminline, 1*1000, (maxline/minline), 1*1000, 1*1000]
self.__set1000=Set(["Solidity", "Round", "Circ"])
self.__set10=Set(["Angle"])
self.__dictMaxList={}
for i in range(len(self.__namemeasures)) :
self.__dictMaxList[self.__namemeasures[i]]=self.__maxmeasures[i]
def setRange(self, stackposition, *params):
"""
This method expect a list of tuples composed by:
(measure_name, min_value, max_value, boolean flag to apply or not)
"""
test=isinstance(params[0][0],str)
#self.__ranges.clear()
if test:
self.__ranges[params[0][0]]=(params[0][0], params[0][1], params[0][2], params[0][3])
else :
for p in params:
#print "p", p
for i in range(len(p)):
#self.__ranges[p[i][0]]=(p[i][0], p[i][1], p[i][2])
if stackposition==1 : self.__ranges[p[i][0]]=(p[i][0], p[i][1], p[i][2], p[i][3])
elif stackposition>1 and p[i][3] : self.__ranges[p[i][0]]=(p[i][0], p[i][1], p[i][2], p[i][3])
else : self.__ranges[p[i][0]]=(p[i][0], 0, self.__dictMaxList[p[i][0]], p[i][3])
def getIncludeRois(self):
self.__yieldRois=[]
self.__yieldRois[:]=[]
for roi in self.__roisArray:
m=Morph(self.__image, roi)
state=0
for r in self.__ranges.values():
if r[1]<=m.__getattribute__(r[0])<=r[2]: state=state+0
else: state=state+1
if state<1 : self.__yieldRois.append(roi)
return self.__yieldRois
def showSettingsDialog(self):
if self.__image.getOverlay() is not None : self.__image.getOverlay().clear()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
#rm.runCommand("Deselect")
#for i in range(rm.getCount()) :
# rm.select(i)
# rm.runCommand("Set Color", "0000FF", 2)
IJ.resetThreshold(self.__image)
rm.runCommand("Show All")
self.__ranges.clear()
#areas, means, majors, minors=[],[],[],[]
#for roi in self.__roisArray:
# m=Morph(self.__image, roi)
# areas.append(m.Area)
# means.append(m.Mean)
# majors.append(m.Major)
# minors.append(m.Minor)
#maxarea=max(areas)*1000
#maxint=max(means)*10
#maxline=max(majors)*100
#maxminline=max(minors)*100
#minline=min(minors)
#namemeasures=["Area", "Mean", "Angle", "Major", "Minor", "Solidity", "AR", "Round", "Circ"]
#maxmeasures=[maxarea, maxint, 180*10, maxline, maxminline, 1*1000, (maxline/minline), 1*1000, 1*1000]
#set1000=Set(["Solidity", "Round", "Circ"])
#set10=Set(["Angle"])
def buttonPressed(event):
temprois=self.getIncludeRois()
for roi in temprois:
m=Morph(self.__image, roi)
IJ.log("----------------------------------")
IJ.log(roi.getName())
for r in self.__ranges.values():
IJ.log(r[0]+" min= "+str(r[1])+" < val="+str(m.__getattribute__(r[0]))+" < max= "+str(r[2]))
IJ.run(self.__image, "Remove Overlay", "")
o=Overlay()
for roi in temprois:
o.addElement(roi)
self.__image.killRoi()
self.__image.setOverlay(o)
self.__image.updateAndDraw()
def updatepressed(event):
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.run("Threshold...")
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#for i in range(rm.getCount()) :
# rm.select(i)
# rm.runCommand("Set Color", "0000FF", 2)
IJ.resetThreshold(self.__image)
rt.show("tempRT")
areas=rt.getColumn(ResultsTable.AREA)
means=rt.getColumn(ResultsTable.MEAN)
majors=rt.getColumn(ResultsTable.MAJOR)
minors=rt.getColumn(ResultsTable.MINOR)
#print 0
if self.__slidersDict["Area_max"].getMaximum() < int(max(areas)+1):
# print 1
self.__slidersDict["Area_max"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Area_min"].getMaximum() < int(max(areas)+1):
# print 2
self.__slidersDict["Area_min"].setMaximum(int(max(areas))+1)
if self.__slidersDict["Mean_max"].getMaximum() < int(max(means)+1):
# print 3
self.__slidersDict["Mean_max"].setMaximum(int(max(means))+1)
if self.__slidersDict["Mean_min"].getMaximum() < int(max(means)+1):
# print 4
self.__slidersDict["Mean_min"].setMaximum(int(max(means))+1)
if self.__slidersDict["Major_max"].getMaximum() < int(max(majors)):
# print 5
self.__slidersDict["Major_max"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Major_min"].getMaximum() < int(max(majors)+1):
# print 6
self.__slidersDict["Major_min"].setMaximum(int(max(majors))+1)
if self.__slidersDict["Minor_max"].getMaximum() < int(max(minors)+1):
# print 7
self.__slidersDict["Minor_max"].setMaximum(int(max(minors))+1)
if self.__slidersDict["Minor_min"].getMaximum() < int(max(minors)+1):
# print 8
self.__slidersDict["Minor_min"].setMaximum(int(max(minors))+1)
if self.__slidersDict["AR_max"].getMaximum() < int((max(majors)+1)/min(minors)+1):
# print 9
self.__slidersDict["AR_max"].setMaximum(int((max(majors)+1)/(min(minors))))
if self.__slidersDict["AR_min"].getMaximum() < int((max(majors)+1)/min(minors)):
# print 10
self.__slidersDict["AR_min"].setMaximum(int((max(majors)+1)/(min(minors))))
#print 11
for sb in self.__slidersDict.values():
sb.repaint()
#rm.runCommand("reset")
#temprois=self.getIncludeRois()
#IJ.run(self.__image, "Remove Overlay", "")
#o=Overlay()
#for roi in temprois:
# o.addElement(roi)
#self.__image.killRoi()
#self.__image.setOverlay(o)
self.__image.updateAndDraw()
def resetpressed(event):
self.__ranges.clear()
self.__image=IJ.getImage()
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
self.__image.killRoi()
IJ.setAutoThreshold(self.__image, "MaxEntropy")
rt=ResultsTable()
pa=ParticleAnalyzer(ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.CLEAR_WORKSHEET , Measurements.AREA+Measurements.ELLIPSE+Measurements.MEAN, rt, 0.00, 10000.00, 0.00, 1.00)
pa.analyze(self.__image)
self.__roisArray=[]
self.__roisArray=rm.getRoisAsArray()
#rm.runCommand("Show All")
#rm.runCommand("Select All")
#rm.runCommand("Set Color", "blue")
IJ.resetThreshold(self.__image)
keys=self.__slidersDict.keys()
for k in keys:
if k.endswith("min"):
self.__slidersDict[k].setValue(0)
self.__slidersDict[k].repaint()
else:
self.__slidersDict[k].setValue(self.__slidersDict[k].getMaximum())
self.__slidersDict[k].repaint()
def valueChanged(event):
name=event.getSource().getName()
names=name.split("_")
factor=1
if names[0] in self.__set1000: factor=0.001
if names[0] in self.__set10:factor=0.1
value=event.getSource().getValue()*factor
if names[1]=="min":
self.__ranges[names[0]]=(names[0], value, self.__slidersDict[names[0]+"_max"].getValue()*factor, self.__boxesDict[names[0]].getState())
#self.__ranges[names[0]]=(names[0], value, self.__slidersDict[names[0]+"_max"].getValue()*factor)
else: self.__ranges[names[0]]=(names[0], self.__slidersDict[names[0]+"_min"].getValue()*factor, value, self.__boxesDict[names[0]].getState())
#self.__ranges[names[0]]=(names[0], self.__slidersDict[names[0]+"_min"].getValue()*factor, value)
temprois=self.getIncludeRois()
IJ.run(self.__image, "Remove Overlay", "")
o=Overlay()
for roi in temprois:
o.addElement(roi)
self.__image.killRoi()
self.__image.setOverlay(o)
self.__image.updateAndDraw()
def selectAll(event):
name=event.getSource().getLabel()
names=name.split("_")
factor=1
if names[0] in self.__set1000: factor=0.001
if names[0] in self.__set10:factor=0.1
name=event.getSource().getLabel()
names=name.split("_")
value=event.getSource().getState()
self.__ranges[names[0]]=(names[0], self.__slidersDict[names[0]+"_min"].getValue()*factor, self.__slidersDict[names[0]+"_max"].getValue()*factor, value)
gd0=NonBlockingGenericDialog("settings")
gd0.setResizable(True)
gd0.setFont(Font("Courrier", 1, 8))
count=0
self.__slidersDict={}
self.__boxesDict={}
self.__boxesDict.clear()
self.__slidersDict.clear()
for i in range(len(self.__namemeasures)):
gd0.setInsets(-10,0,0)
gd0.addSlider("Min"+self.__namemeasures[i], 0, self.__maxmeasures[i], 0)
gd0.getSliders().get(count).adjustmentValueChanged = valueChanged
gd0.getSliders().get(count).setName(self.__namemeasures[i]+"_min")
self.__slidersDict[self.__namemeasures[i]+"_min"]=gd0.getSliders().get(count)
gd0.addSlider("Max"+self.__namemeasures[i], 0, self.__maxmeasures[i], self.__maxmeasures[i])
gd0.getSliders().get(count+1).adjustmentValueChanged = valueChanged
gd0.getSliders().get(count+1).setName(self.__namemeasures[i]+"_max")
self.__slidersDict[self.__namemeasures[i]+"_max"]=gd0.getSliders().get(count+1)
gd0.addCheckbox("all", True)
gd0.getCheckboxes().get(i).itemStateChanged = selectAll
gd0.getCheckboxes().get(i).setLabel(self.__namemeasures[i]+"_all")
self.__boxesDict[self.__namemeasures[i]]=gd0.getCheckboxes().get(i)
gd0.setInsets(-10,0,0)
#gd0.addMessage("...........................................................................")
count=count+2
panel0=Panel()
#trybutton=Button("Try")
#trybutton.setActionCommand("DrawOverlay")
#trybutton.actionPerformed = buttonPressed
#updatebutton=Button("Update")
#updatebutton.setActionCommand("Update")
#updatebutton.actionPerformed = updatepressed
#resetbutton=Button("Reset")
#resetbutton.setActionCommand("Reset")
#resetbutton.actionPerformed = resetpressed
#panel0.add(trybutton)
#panel0.add(updatebutton)
#panel0.add(resetbutton)
#gd0.addPanel(panel0)
gd0.setResizable(True)
gd0.showDialog()
#self.__image.setSlice(self.__firstslice)
#self.__image.updateAndDraw()
if gd0.wasOKed():
#for key in self.__ranges.keys(): IJ.log("Measure : "+str(self.__ranges[key][0])+" min = "+str(self.__ranges[key][1])+" max = "+str(self.__ranges[key][2]))
return self.__ranges
includeRois=property(getIncludeRois, doc="rois include in the measures ranges")
#----- end class ----------
if __name__ == "__main__":
rm=RoiManager.getInstance()
rois=rm.getRoisAsArray()
img=IJ.getImage()
r=RangeRois(rois, img)
r.showSettingsDialog()
for roi in r.includeRois : print roi.getName()