def outputpath(event) :
macrodir=IJ.getDirectory("macros")
frame = Frame("Select the macro file")
fd = FileDialog(frame)
fd.setDirectory(macrodir)
fd.show()
macrodir = fd.getDirectory()
self.__macropath = fd.getFile()
self.__text.setText(self.__macropath)
print self.__macropath
def __ImportPref(self, flag) :
indiceinterest=5
if len(self.__params) < 1 :
if flag == 1 :
IJ.showMessage("Select the text file containing the preferences you want (Track.txt file)")
self.__selectdir=IJ.getDirectory("image")
frame = Frame("Text file settings ?")
fd = FileDialog(frame)
fd.setDirectory(self.__selectdir)
fd.show()
self.__selectdir = fd.getDirectory()
self.__textfile = fd.getFile()
#self.__selectdir=IJ.getDirectory("")
#listfiles=glob.glob(selectdir+"*DIA_s0001*.tif")
#fichier = open(self.__selectdir+"Track.txt","r")
fichier = open(self.__selectdir+self.__textfile,"r")
lignes=fichier.readlines()
self.__params=[]
for i in range(indiceinterest,len(lignes)): # ATTENTION À CHANGER AVEC PARAM DE RANGEROI
params=lignes[i].split("=")
val=params[1].split("\n")
if params[0]=="SUBBACK" : self.__subback=bool(int(val[0]))
if params[0]=="SUBBACKRADIUS" : self.__radius=Double(val[0])
if params[0]=="DISTPARAM_AREA_COEFF" : self.__distparam[0]=int(val[0])
if params[0]=="DISTPARAM_AREA_MAXDELTA" : self.__distparam[1]=Double(val[0])
if params[0]=="DISTPARAM_ANGLE_COEFF" : self.__distparam[2]=int(val[0])
if params[0]=="DISTPARAM_ANGLE_MAXDELTA" : self.__distparam[3]=Double(val[0])
if params[0]=="DISTPARAM_FERETMAX_COEFF" : self.__distparam[4]=int(val[0])
if params[0]=="DISTPARAM_FERETMAX_MAXDELTA" : self.__distparam[5]=Double(val[0])
if params[0]=="DISTPARAM_POSITIONX_COEFF" : self.__distparam[6]=int(val[0])
if params[0]=="DISTPARAM_POSITIONX_MAXDELTA" : self.__distparam[7]=int(val[0])
if params[0]=="DISTPARAM_POSITIONY_COEFF" : self.__distparam[8]=int(val[0])
if params[0]=="DISTPARAM_POSITIONY_MAXDELTA" : self.__distparam[9]=int(val[0])
if params[0]=="DISTMETHOD" : self.__distmethod=str(val[0])
if params[0]=="OPTIONMANTHRESH" : self.__manthresh=bool(int(val[0]))
if params[0]=="THRESHMETHOD" : self.__thresMethod=str(val[0])
if params[0]=="OPTIONANGLE" : self.__optionAngle=bool(int(val[0]))
if params[0]=="OPTIONNEWCELLS" : self.__optionNewCells=bool(int(val[0]))
if params[0]=="OPTIONTIMELAPSE" : self.__optionTimelapse=bool(int(val[0]))
if params[0]=="TIMELAPSE" : self.__timelapse=int(val[0])
# imported booleans : self.__subback, self.__manthresh, self.__optionAngle, self.__optionNewCells, self.__optionTimelapse
minmax=val[0].split(";")
if params[0]=="Area" : self.__params.append(("Area",Double(minmax[0]),Double(minmax[1])))
if params[0]=="Mean" : self.__params.append(("Mean",Double(minmax[0]),Double(minmax[1])))
if params[0]=="Angle" : self.__params.append(("Angle",Double(minmax[0]),Double(minmax[1])))
if params[0]=="Major" : self.__params.append(("Major",Double(minmax[0]),Double(minmax[1])))
if params[0]=="Minor" : self.__params.append(("Minor",Double(minmax[0]),Double(minmax[1])))
if params[0]=="Solidity" : self.__params.append(("Solidity",Double(minmax[0]),Double(minmax[1])))
if params[0]=="AR" : self.__params.append(("AR",Double(minmax[0]),Double(minmax[1])))
if params[0]=="Round" : self.__params.append(("Round",Double(minmax[0]),Double(minmax[1])))
if params[0]=="Circ" : self.__params.append(("Circ",Double(minmax[0]),Double(minmax[1])))
from ij import IJ
from ij.plugin.frame import RoiManager
from ij.gui import PolygonRoi
from ij.gui import Roi
from java.awt import FileDialog
fd = FileDialog(IJ.getInstance(), "Open", FileDialog.LOAD)
fd.show()
file_name = fd.getDirectory() + fd.getFile()
print(file_name)
RM = RoiManager()
rm = RM.getRoiManager()
imp = IJ.getImage()
textfile = open(file_name, 'r')
for line in textfile:
xy = map(int, line.rstrip().split(','))
X = xy[::2]
Y = xy[1::2]
imp.setRoi(PolygonRoi(X, Y, Roi.POLYGON))
#IJ.run(imp, "Convex Hull", "")
roi = imp.getRoi()
print roi
rm.addRoi(roi)
rm.runCommand("Associate", "true")
rm.runCommand("Show All with labels")
def __ImportCells(self, imagesnames) :
#self.__dictCells[imgName]={}
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.runCommand("reset")
listpaths = []
listfilescells=[]
if self.__optionImages :
IJ.showMessage("Select the folder 'Cells' containing the cells to import")
selectdir=IJ.getDirectory("image")
selectdir=IJ.getDirectory("")
listfilescells.extend(glob.glob(selectdir+os.path.sep+"*"))
listpaths.append("")
else :
IJ.showMessage("Select the text file containing the list cell paths (listpaths.txt)")
selectdir=IJ.getDirectory("current")
frame = Frame("Text file settings ?")
fd = FileDialog(frame)
fd.setDirectory(selectdir)
fd.show()
selectdir = fd.getDirectory()
textfile = fd.getFile()
fichier = open(selectdir+textfile,"r")
listpaths=[ glob.glob(f.split("\n")[0]+"Selected-Cells"+os.path.sep+"*") for f in fichier.readlines()]
#for f in templist :
# listpaths.append(f.split("\n")+"Cells")
listfilescells.append("")
if listfilescells[0]=="" : importmode = True
else : importmode = False
for j in range(len(listpaths)) :
self.__dictCells[imagesnames[j]]={}
if importmode : listfilescells = listpaths[j]
pathtemp = []
for cellfile in listfilescells :
filetemp = open(cellfile,"r")
linestemp=filetemp.readlines()
for line in linestemp :
params=line.split("=")
values=params[1].split("\n")
if params[0] == "NAMECELL" :
celltemp=Bacteria_Cell(str(values[0]))
self.__dictCells[imagesnames[j]][values[0]]=celltemp
self.__dictMeasures[self.__dictCells[imagesnames[j]][values[0]]]={}
if params[0] == "PATHROIS" :
pathtemp.append(str(values[0]))
if params[0] == "NSLICES" :
for i in range(int(values[0])) :
celltemp.getListRoi().append("")
if params[0] == "SLICEINIT" :
celltemp.setSlideInit(int(values[0]))
for i in range(int(values[0])-2) :
celltemp.setRoi("NOT HERE YET",i)
if params[0] == "SLICEEND" :
celltemp.setSlideEnd(int(values[0]))
for i in range(int(values[0])) :
celltemp.setRoi("LOST",i)
if params[0] == "COLOR" :
colorstemp=values[0].split(";")
celltemp.setColor(Color(int(colorstemp[0]),int(colorstemp[1]),int(colorstemp[2])))
indiceroi=0
ind=0
tempimp = WindowManager.getImage(imagesnames[j])
if tempimp is not None :
IJ.selectWindow(imagesnames[j])
tempimp.show()
else :
if imagesnames[j][-4:]==".tif" :
IJ.selectWindow(imagesnames[j][:-4])
tempimp = IJ.getImage()
else :
IJ.selectWindow(imagesnames[j]+".tif")
tempimp = IJ.getImage()
rm.runCommand("reset")
for cellname in self.__dictCells[imagesnames[j]].keys() :
rm.runCommand("Open", pathtemp[ind])
ind+=1
nbtemp=self.__dictCells[imagesnames[j]][cellname].getLifeTime()
for i in range(nbtemp) :
rm.select(tempimp, indiceroi)
roi=rm.getSelectedRoisAsArray()[0]
self.__dictCells[imagesnames[j]][cellname].setRoi(roi,i+self.__dictCells[imagesnames[j]][cellname].getSlideInit()-1)
indiceroi+=1
IJ.run("Show Overlay", "")
rm.runCommand("UseNames", "true")
rm.runCommand("Associate", "true")
IJ.run(tempimp, "Labels...", "color=red font=12 show use")
if rm.getCount()>0 : IJ.run(tempimp, "From ROI Manager", "")
rm.runCommand("Show None")
rm.runCommand("Show All")
roipath = os.path.split(pathtemp[0])[0]+os.path.sep
rootpath = roipath.rsplit(os.path.sep, 2)[0]+os.path.sep
self.__listpaths[j] = rootpath
self.__rootpath=rootpath
homeDir = os.environ.get("HOMEPATH")
except:
pass
if not homeDir: homeDir = "?"
return homeDir
if i_want_popups or fileToImport is None or fileToImport == "":
if Platform.isOSX():
System.setProperty(
"com.apple.macos.use-file-dialog-packages", "true"
) # In theory prevents access to app file structure (but doesnt seem to work)
System.setProperty("apple.awt.fileDialogForDirectories", "false")
fDialog = FileDialog(None, "Select file for import")
fDialog.setMultipleMode(False)
fDialog.setMode(FileDialog.LOAD)
if fileToImport is None:
fDialog.setFile("select_your_file")
fDialog.setDirectory(get_home_dir())
else:
fDialog.setFile(fileToImport)
fDialog.setVisible(True)
if (fDialog.getFile() is None) or fDialog.getFile() == "":
raise Exception(
"User chose to cancel or no file selected >> So no Import will be performed... "
)
fileToImport = os.path.join(fDialog.getDirectory(), fDialog.getFile())