fileout = os.path.join(analyzeDir, os.path.basename(filepath))
IJ.saveAs(impOut, "Jpeg", fileout)
def createOutputImg(image, roim, centPart, metaphase):
#maximal projection
imp = image
if image.getNSlices() > 1:
zp = ZProjector()
zp.setMethod(zp.MAX_METHOD)
zp.setImage(image)
zp.doProjection()
imp = zp.getProjection()
else:
imp = image
IJ.run(imp,"Enhance Contrast", "saturated=0.35")
IJ.setForegroundColor(255,0,0)
#need to show the image to draw overlay
imp.show()
IJ.run(imp,"RGB Color", "");
for i in range(roim.getCount()):
roim.select(imp, i)
roim.runCommand("Draw")
if metaphase:
IJ.setForegroundColor(0,255,255)
else:
IJ.setForegroundColor(0,255,0)
roim.select(imp, centPart)
def do_projection(self, channel, proj_type=None):
proj = ZProjector() ## create projection class
if proj_type is None:
if self.do_z[channel] == "MAX":
proj.setMethod(ZProjector.MAX_METHOD)
elif self.do_z[channel] == "AVG":
proj.setMethod(ZProjector.AVG_METHOD)
else:
print "Dont know how to project this way"
print "Just using a single slice for images!!"
return None
else:
if proj_type == "MAX":
proj.setMethod(ZProjector.MAX_METHOD)
elif proj_type == "AVG":
proj.setMethod(ZProjector.AVG_METHOD)
else:
print "Dont know how to project this way"
print "Just using a single slice for images!!"
return None
proj.setImage(self.stack_imps[channel])
proj.doProjection()
projection = proj.getProjection()
conv = ImageConverter(projection)
conv.convertToGray16()
conv.setDoScaling(False)
self.projections[channel] = projection
self.projections_done[channel] = self.do_z[channel]
def zproj(imp): zpimp = ZP() zpimp.setImage(imp) zpimp.setMethod(zpimp.MAX_METHOD) zpimp.setStartSlice(1) zpimp.setStopSlice(imp.getNSlices()) zpimp.doHyperStackProjection(True) zpedimp = zpimp.getProjection() return zpedimp
return runCamR, runCamL, CamRScale, CamLScale, BackgroundWindowStart, BackgroundWindowEnd, GridSize, TranslateR, TranslateL # a tuple with the parameters
options = getOptions()
if options is not None:
runCamR, runCamL, CamRScale, CamLScale, BackgroundWindowStart, BackgroundWindowEnd, GridSize, TranslateR, TranslateL = options # unpack each parameter
print runCamR, runCamL, CamRScale, CamLScale, BackgroundWindowStart, BackgroundWindowEnd, GridSize, TranslateR, TranslateL
if runCamR:
impR1 = FolderOpener.open(folder, "file=CamR sort")
UID = impR1.title
filepath = folder.strip(UID + '/')
projectR = ZProjector(impR1)
projectR.setMethod(ZProjector.AVG_METHOD)
projectR.setImage(impR1)
projectR.setStartSlice(int(BackgroundWindowStart))
projectR.setStopSlice(int(BackgroundWindowEnd))
projectR.doProjection()
projectionR = projectR.getProjection()
impR2 = ImageCalculator().run("Subtract create stack", impR1, projectionR)
IJ.run(impR2, "Enhance Contrast", "saturated=0.4 process_all")
IJ.run(impR2, "Set Scale...",
"distance=" + str(CamRScale) + " known=1 unit=cm")
IJ.run(impR2, "Grid...",
"grid=Lines area=" + str(GridSize) + " color=Cyan")
IJ.run(impR2, "Translate...",
"x=" + str(TranslateR) + " y=0 interpolation=None stack")
savepath = path.join(folder, UID + "_CR.tif")
# the metadata. Stops otherwise.
# TODO : Should work fine for CZIs but could be
# improved with default values or min/max values.
emissionWL = [0]
try:
for x in xrange(1,nbrChannels+1,1):
WL = int(imp.getNumericProperty("Information|Image|Channel|EmissionWavelength #" + str(x).zfill(2)))
emissionWL.append(WL)
except ValueError:
raise Exception("Couldn't find the EmissionWavelength info in the metadata")
# Make the maximum intensity projection
# and show it for user input.
project = ZProjector()
project.setMethod(ZProjector.MAX_METHOD)
project.setImage(imp)
project.doProjection()
projection = project.getProjection()
projection.show()
# Wait for the user to draw a line
# and check if line ROI.
IJ.setTool("line");
myWait = WaitForUserDialog ("waitForUser", "Make a line with the region of interest and press OK")
myWait.show()
roi = projection.getRoi()
# Check if roi is a line
# otherwise exit
if not (roi.isLine()):
def imageprojector(channels, timelist_unsorted, dirs):
""" Projects .lif timepoints and saves in a common directory,
as well as channel separated directories. """
# Defines in path
path = str(Experiment)
# BF Importer
options = ImporterOptions()
try:
options.setId(path)
except Exception(e):
print str(e)
options.setOpenAllSeries(True)
options.setSplitTimepoints(True)
options.setSplitChannels(True)
imps = BF.openImagePlus(options)
timelist = [x for item in timelist_unsorted for x in repeat(item, channels)]
timelist, imps = zip(*sorted(zip(timelist, imps)))
counter_C0 = -1
counter_C1 = -1
counter_C2 = -1
# Opens all images, splits channels, z-projects and saves to disk
for imp in (imps):
# Projection, Sum Intensity
project = ZProjector()
project.setMethod(ZProjector.SUM_METHOD)
project.setImage(imp)
project.doProjection()
impout = project.getProjection()
projection = impout.getTitle()
try:
# Saves channels to disk,
# add more channels here if desired,
# remember to define new counters.
if "C=0" in projection:
counter_C0 += 1
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections"],
"Scan" + str(counter_C0).zfill(3) + "C0"))
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections_C0"],
"Scan" + str(counter_C0).zfill(3) + "C0"))
elif "C=1" in projection:
counter_C1 += 1
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections"],
"Scan" + str(counter_C1).zfill(3) + "C1"))
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections_C1"],
"Scan" + str(counter_C1).zfill(3) + "C1"))
elif "C=2" in projection:
counter_C2 += 1
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections"],
"Scan" + str(counter_C2).zfill(3) + "C2"))
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections_C2"],
"Scan" + str(counter_C2).zfill(3) + "C2"))
except IOException:
print "Directory does not exist"
raise
IJ.log("Images projected and saved to disk")
def CheckMoment(image):
#Perform a maximum projection on the stack
stack = image.getStack()
NSlices=image.getNSlices()
#Take a fixed number of central slices
i=float(NSlices-SimulationCharacteristics['CentralZSlices'])
i1=math.floor(i/2)
i2=math.ceil(i/2)
startSlice=int(1+i1)
stopSlice=int(NSlices-i2)
p=bool(1)
proj = ZProjector()
proj.setMethod(ZProjector.MAX_METHOD)
proj.setImage(image)
proj.setStartSlice(startSlice)
proj.setStopSlice(stopSlice)
proj.doHyperStackProjection(p)
imageMax = proj.getProjection()
imageMax.show()
stack = imageMax.getStack()
n_slices= stack.getSize()
#Get a Segmentation Mask List for every frame in the stack
RoiList=[]
RoiRatioList=[]
for index in range(1, n_slices+1):
ip = stack.getProcessor(index).convertToFloat()
boundRoi=SegmentMask(ip)
mask=boundRoi.getMask()
PixelsMask=mask.getPixels()
r=(-1)*float(sum(PixelsMask))/(ip.height*ip.width)
RoiList.append(boundRoi)
RoiRatioList.append(r)
# print(RoiRatioList)
#Optimize the Roi List. No 1.0 ratios
AllRois1=all(item == 1.0 for item in RoiRatioList)
NFrames=len(RoiRatioList)
if not AllRois1:
for i in range(NFrames):
if RoiRatioList[i]==1.0 or RoiList[i]==None:
#Find the next value that is not 1.0
NearestNot1=-1
prevIndex=i-1
nextIndex=i+1
Token=True #To run through the list alternating positions
while prevIndex>=0 or nextIndex<NFrames:
if prevIndex>0 and Token:
if RoiRatioList[prevIndex]<0.9999:
NearestNot1=prevIndex
break
else:
prevIndex-=1
if nextIndex<NFrames:Token=False
continue
if nextIndex<NFrames:
if RoiRatioList[nextIndex]<0.9999:
NearestNot1=nextIndex
break
else:
nextIndex+=1
if prevIndex>0: Token=True
continue
if NearestNot1!=-1:
#Change RoiList and RoiRationList for the NearestNot1 element
RoiList[i]=RoiList[NearestNot1]
RoiRatioList[i]=RoiRatioList[NearestNot1]
else:
AllRois1=True
print("No avaliable segmentation")
if not AllRois1:
RoiListMin=ModifyRoiList(RoiRatioList,RoiList)
else:
RoiListMin=[ None for i in range(len(RoiList))]
#Find Optimum Scale for the Wavelet
Gamma=endosomeCharacteristics['Gamma_media']
To=endosomeCharacteristics['A_media']
index=1 #Image 1
ipOrig = stack.getProcessor(index).convertToFloat()
boundRoi=RoiListMin[0]
MaxAmp,Ropt=AmplificationCurveMax(ipOrig,To,Gamma,boundRoi)
print("Choosen Scale",Ropt)
Moment3Array=[]
for index in range(1,n_slices+1):
print("time:"+str(index))
ip = stack.getProcessor(index).convertToFloat()
boundRoi=RoiListMin[index-1]
Skew=GetSigmaWavelet(ip,Ropt,boundRoi)
Moment3Array.append(Skew)
return Moment3Array