def runPoreDetection():
'''roiManager=RoiManager(False)
roiManager.runCommand("open", roiname)
roiHash=roiManager.getROIs()
roi=roiHash.get("Right")
print roi'''
imageList = Utility.GetOpenImageList()
nbgd = NonBlockingGenericDialog(Messages.AddRoi)
nbgd.addMessage(Messages.ChooseImage)
if (imageList == None):
IJ.showMessage(Messages.noOpenImages)
return
nbgd.addChoice("Image1:", imageList, imageList[0])
nbgd.showDialog()
name = nbgd.getNextChoice()
inputImp = WindowManager.getImage(name)
inputDataset = Utility.getDatasetByName(data, name)
detectionParameters = DetectionParameters(10, 200, 0.5, 1.0, 0.3)
#inputImp.setRoi(roi)
nbgd2 = NonBlockingGenericDialog(Messages.PositionRoi)
nbgd2.addMessage(Messages.PositionRoiAndPressOK)
nbgd2.showDialog()
poreDetectionUV(inputImp, inputDataset,
inputImp.getRoi().clone(), ops, data, display,
detectionParameters)
def runPoreDetection():
'''roiManager=RoiManager(False)
roiManager.runCommand("open", roiname)
roiHash=roiManager.getROIs()
roi=roiHash.get("Right")
print roi'''
imageList=Utility.GetOpenImageList()
nbgd=NonBlockingGenericDialog(Messages.AddRoi)
nbgd.addMessage(Messages.ChooseImage)
if (imageList==None):
IJ.showMessage(Messages.noOpenImages)
return;
nbgd.addChoice("Image1:", imageList, imageList[0]);
nbgd.showDialog()
name = nbgd.getNextChoice()
inputImp = WindowManager.getImage(name)
inputDataset=Utility.getDatasetByName(data, name)
detectionParameters=DetectionParameters(10, 200, 0.5, 1.0, 0.3)
#inputImp.setRoi(roi)
nbgd2=NonBlockingGenericDialog(Messages.PositionRoi)
nbgd2.addMessage(Messages.PositionRoiAndPressOK)
nbgd2.showDialog()
poreDetectionUV(inputImp, inputDataset, inputImp.getRoi().clone(), ops, data, display, detectionParameters)
def getOptions(dest):
###function that allows the user to choose their next course of action###
# colorscale()
gd = NonBlockingGenericDialog("Continue?")
gd.setCancelLabel("Quit")
gd.enableYesNoCancel("Remain on Image", "Open Next")
gd.showDialog()
if gd.wasCanceled(): # quits
imp = IJ.getImage()
current_title = imp.getTitle()
imp.close()
renamer(dest, current_title, extension)
exit()
elif gd.wasOKed(): # remains on image
count_options = 0
return
else: # opens the next image in a directory.
count_options = 1
imp = IJ.getImage()
current_title = imp.getTitle()
imp.close()
renamer(dest, current_title, extension)
file_opener(current_title, extension)
imp = IJ.getImage()
imp.setDisplayMode(IJ.GRAYSCALE)
colorscale()
imp = IJ.getImage()
win = imp.getWindow()
win.maximize()
win.setLocation(int(xpos_def), int(ypos_def))
getOptions(dest)
def ER_points(all_x, all_y, overlay, ER_measurements):
imp = IJ.getImage()
overlay = Overlay()
overlay = imp.getOverlay()
## gets points added to overlay, and extracts a list of x & y values. list length must be three ###
try:
roi_points = overlay.toArray()
except AttributeError as error:
nbgd = NonBlockingGenericDialog("Select three Roi's")
nbgd.hideCancelButton()
nbgd.showDialog()
overlay = imp.getOverlay()
roi_points = overlay.toArray()
pass
for i in range(overlay.size()):
roi = overlay.get(i)
p = roi_points[i].getPolygon()
all_x.append(p.xpoints[0])
all_y.append(p.ypoints[0])
while len(all_x) != 3:
if len(all_x) < 3:
nbgd = NonBlockingGenericDialog("Must Select three Roi's")
nbgd.setCancelLabel("Roi Reset")
nbgd.showDialog()
if nbgd.wasCanceled():
IJ.run("Remove Overlay", "")
ER_points(all_x, all_y, overlay, ER_measurements)
if len(all_x) > 3:
all_x.pop(0)
all_y.pop(0)
overlay.clear()
def pick_roi_and_crop(self):
self.show()
self.display_roi()
wait = NonBlockingGenericDialog("Move the ROI around the cell of interest")
wait.addMessage(
"Click ok to crop and process ROI\n" "Cancel to skip this image\n" "Check 'Quit' to terminate script"
)
wait.addCheckbox("Quit", False)
wait.showDialog()
kill_switch = wait.getCheckboxes()[0].state
# print kill_switch
if wait.wasOKed():
self.crop_project_and_montage()
while True:
proceed = NonBlockingGenericDialog("Process another ROI?")
proceed.addMessage("Click ok to repeat this image\n" "Click cancel to move onto next image")
proceed.showDialog()
if proceed.wasOKed():
print "Repeat this image"
self.crop_project_and_montage()
else:
print "Lets move on"
for i in self.stack_imps.values():
i.close()
break
return kill_switch
else:
print "User canceled this image before doing anything"
for i in self.stack_imps.values():
i.close()
return kill_switch
def showGui(par, title):
"""Updated version discriminates between string and numeric outputs to treat them accordingly"""
numflags = {}
gd = NonBlockingGenericDialog(title)
s_keys = sorted(par.keys())
for nm in s_keys:
if isinstance(par[nm], (int, float, long)):
gd.addNumericField(nm, par[nm], 1)
numflags[nm] = True
else:
gd.addStringField(nm, par[nm])
numflags[nm] = False
gd.setOKLabel("Go on!")
gd.setCancelLabel("Recompute..")
gd.centerDialog(False)
gd.setLocation(50, 100)
gd.showDialog()
if gd.wasCanceled():
rep = True
else:
rep = False
for nm in s_keys:
if numflags[nm]:
par[nm] = gd.getNextNumber()
else:
par[nm] = gd.getNextString().encode("ascii", "replace")
return par, rep
def MakeSubset(directory_load, directory_save, chl, frames, z_planes, loops,
total, pat, title, imp2):
subd = NonBlockingGenericDialog("Make subset")
subd.addCheckbox("Duplicate only the current frames", False)
subd.addCheckbox("Export XYTC of a subset of loops", False)
subd.addSlider("Subset from loop number", 0, loops - 1, 0)
subd.addSlider("Subset to loop number", 0, loops - 1, 0)
subd.showDialog()
slider_subd1 = subd.getSliders().get(0).getValue()
slider_subd2 = subd.getSliders().get(1).getValue()
checkbox_subd1 = subd.getNextBoolean()
checkbox_subd2 = subd.getNextBoolean()
if checkbox_subd1 == True:
SliceNum = imp2.getCurrentSlice()
FloorSlice50 = float(SliceNum) / frames
S50 = (math.floor(FloorSlice50) * frames) + 1
S100 = S50 + (frames - 1)
print("Slice" + str(SliceNum) + "_FloorSlice_" + str(FloorSlice50) +
"_frames_" + str(S50) + "-" + str(S100) + "")
IJ.run(
"Duplicate...", "title=Image_DUP duplicate range=" + str(S50) +
"-" + str(S100) + "")
impDup = WM.getImage("Image_DUP")
if checkbox_subd2 == True:
SubsetL(directory_load, directory_save, chl, frames, z_planes, loops,
total, pat, title, slider_subd1, slider_subd2)
def createListfiles() :
IJ.showMessage("Select a folder with the .tif files")
selectdir=IJ.getDirectory("image")
selectdir=IJ.getDirectory("")
listfiles=glob.glob(selectdir+"*.tif")
#fullprefix = str.rsplit(str(listfiles[0]), "/", 1)
fullprefix = os.path.split(listfiles[0])
root = fullprefix[0]
lastprefix = str.split(fullprefix[1], "_")
del(listfiles)
gdselectfiles = NonBlockingGenericDialog("List files Choice")
gdselectfiles.addMessage("")
gdselectfiles.addStringField("Prefix ?", lastprefix[0], 32)
gdselectfiles.addStringField("Filter (w00001DIA) ?", "1DIA")
gdselectfiles.addStringField("Positions (s0001) ?", "1-2")
gdselectfiles.addStringField("Temps (t0001) ?", "1-11")
#gdselectfiles.addStringField("Files pattern", "*DIA_s*1_t*.tif", 32)
gdselectfiles.showDialog()
prefix = str(gdselectfiles.getNextString())
channel = str(gdselectfiles.getNextString())
temppositions = str(gdselectfiles.getNextString())
positions = str.split(temppositions, "-")
temptimes = str(gdselectfiles.getNextString())
times = str.split(temptimes, "-")
if channel != "" : channel = "_w000"+channel
positionslist=[]
if positions[0] != "" :
for p in range(int(positions[0]), int(positions[1])+1, 1) :
positionslist.append("_s"+"%04i"%(p))
else : positionslist.append("")
timeslist=[]
if times[0] != "" :
for t in range(int(times[0]), int(times[1])+1, 1) :
timeslist.append("_t"+"%04i"%(t))
else : timeslist.append("")
patterns=[]
listfiles = []
for p in positionslist :
files = []
for t in timeslist :
patterns.append(channel+p+t+".tif")
tempfilename = os.path.join(root, prefix+patterns[-1])
files.append(tempfilename)
#files.append(root+"/"+prefix+patterns[-1])
listfiles.append(files)
if len(listfiles)>1 : return (prefix, patterns, listfiles, positionslist)
else : return (prefix, patterns, files, "_s0001")
def repeat_measure():
IJ.run("Select None")
gd = NonBlockingGenericDialog("Redraw ROI?")
gd.showDialog()
if gd.wasOKed():
selection(region)
if gd.wasCanceled():
exit_assay()
def runGUI(defaultTargetChannel=2,
defaultdt=1.0,
defaultRadius=0.3,
defaultThreshold=16,
defaultFrameGap=0.01,
defaultLinkingMax=0.01,
defaultClosingMax=0.01):
gd = NonBlockingGenericDialog("ZedMate - v0.18 beta")
gd.addMessage(
"\tZedMate is a TrackMate-based 3D prticle analyzer \n\t\t\t\t\t\t\t\t\t\t\t(copyright Artur Yakimovich 2018-19)\n\n"
)
gd.addStringField("File_extension", ".tif")
gd.addStringField("File_name_contains", "")
gd.addNumericField("Target_Channel", defaultTargetChannel, 0)
gd.addNumericField("dt", defaultdt, 2)
gd.addNumericField("Radius", defaultRadius, 2)
gd.addNumericField("Threshold", defaultThreshold, 2)
gd.addNumericField("Frame_Gap", defaultFrameGap, 0)
gd.addNumericField("Linking_Max", defaultLinkingMax, 2)
gd.addNumericField("Closing_Max", defaultClosingMax, 2)
gd.addMessage("\t\t\t\t\t\t_______________________________________")
gd.addCheckbox("Preview Parameters on the First Image Only", 0)
gd.addMessage("\t\t\t\t\t(Doesn't save results. Re-opens this Dialog).")
gd.addMessage("\t\t\t\t\t\t_______________________________________")
gd.addCheckbox("Save MNIST mimicry embedding (beta)", 0)
gd.showDialog()
if gd.wasCanceled():
return
extension = gd.getNextString()
containString = gd.getNextString()
targetChannel = int(gd.getNextNumber())
dt = gd.getNextNumber()
radius = gd.getNextNumber()
threshold = gd.getNextNumber()
frameGap = int(gd.getNextNumber())
linkingMax = gd.getNextNumber()
closingMax = gd.getNextNumber()
testMode = gd.getNextBoolean()
mimicryEmbd = gd.getNextBoolean()
inputDir = IJ.getDirectory("Input_directory")
if not inputDir:
return
if not testMode:
outputDir = IJ.getDirectory("Output_directory")
if not outputDir:
return
else:
outputDir = inputDir # for the case of test
#if not os.path.exists(outputDir):
# os.makedirs(outputDir)
runBatch(inputDir, outputDir, extension, containString, targetChannel, dt, radius, threshold, frameGap,\
linkingMax, closingMax, testMode, mimicryEmbd)
def __mainsettings(self) :
# options :
#We ask if the user wants to import cells from .cell files
# we track the cells in a stack that the user has to choose.
def outputpath(event) :
self.__pathdir=IJ.getDirectory("image")
self.__pathdir=IJ.getDirectory("")
self.__text.setText(self.__pathdir)
panel0=Panel()
pathbutton=Button("Select output path", actionPerformed = outputpath)
#pathbutton.actionPerformed = outputpath
self.__text = TextField(self.__pathdir)
panel0.add(pathbutton)
panel0.add(self.__text)
firstgd=NonBlockingGenericDialog("First choices")
firstgd.addMessage("------------------ WELCOME ----------------------")
firstgd.addMessage("")
firstgd.addMessage("Please fill the following options")
firstgd.addMessage("")
choices=["Already opened images", "Files from hard disk"]
firstgd.addChoice("Images source : ", choices, choices[0]) # 1 choice
firstgd.addCheckbox("Run in batch mode ?", False) # 2 batch
firstgd.addMessage("")
firstgd.addCheckbox("Import a set of cells from hardisk ?", self.__optionImport) # 3 import
firstgd.addMessage("")
firstgd.addNumericField("Size factor (binning)", 2, 0) # 4 number
firstgd.addPanel(panel0)
firstgd.showDialog()
#self.__optionImages=firstgd.getNextBoolean()
choice=firstgd.getNextChoiceIndex() # 1 choice
self.__batch = firstgd.getNextBoolean() # 2 batch
self.__optionImport=firstgd.getNextBoolean() # 3 import
self.__binning = firstgd.getNextNumber() # 4 number
if choice==0 : self.__optionImages=True
else : self.__optionImages=False
if firstgd.wasCanceled() : return False
#IJ.showMessage("Select a working directory to save results")
#self.__pathdir=IJ.getDirectory("image")
#self.__pathdir=IJ.getDirectory("")
#self.__pathdir=self.__pathdir+imp.getShortTitle()+os.path.sep+time.strftime('%d-%m-%y_%Hh%Mm%Ss',time.localtime())+os.path.sep
if self.__pathdir is not None : return True
else : return False
def perform_manual_qc(imp, rois, important_channel=1):
"""given cell rois generated by automatic methods, allow user to delete/add/redraw as appropriate"""
for ch in range(imp.getNChannels()):
imp.setC(ch + 1)
sat_frac = 0.99 if (ch + 1) == important_channel else 0.01
IJ.run(imp, "Enhance Contrast", "saturated={}".format(sat_frac))
imp.setC(important_channel)
IJ.setTool("freehand")
proceed = False
roim = RoiManager()
roim.runCommand("Show all with labels")
for roi in rois:
roim.addRoi(roi)
auto_rois_only = rois
while not proceed:
dialog = NonBlockingGenericDialog("Perform manual segmentation")
dialog.setOKLabel("Proceed to next image...")
dialog.addMessage("Perform manual correction of segmentation: ")
dialog.addMessage(
"Draw around cells and add to the region of interest manager (Ctrl+T). "
)
dialog.addMessage("Delete and redraw cells as appropriate. ")
dialog.addMessage(
"Then press \"proceed to next image\" when all cells have been added. "
)
dialog.showDialog()
if dialog.wasCanceled():
print("Manual segmentation canceled")
return auto_rois_only
elif dialog.wasOKed():
if roim.getCount() == 0:
rois = []
confirm_dialog = GenericDialog("Continue?")
confirm_dialog.addMessage(
"No rois selected in this FOV. Are you sure you want to proceed?"
)
confirm_dialog.setOKLabel("Yes, proceed")
confirm_dialog.setCancelLabel("No, not yet")
confirm_dialog.showDialog()
if confirm_dialog.wasOKed():
proceed = True
else:
rois = roim.getRoisAsArray()
proceed = True
roim.reset()
roim.close()
for ch in range(imp.getNChannels()):
imp.setC(ch + 1)
IJ.run(imp, "Enhance Contrast", "saturated={}".format(0.35))
imp.setC(important_channel)
return rois
def choose_segmentation_and_projection_channels(info):
dialog = NonBlockingGenericDialog("Select channels...")
channels = [info.ch1_label, info.ch2_label]
dialog.addRadioButtonGroup("Segmentation channel: ", channels, 1,
len(channels), channels[0])
dialog.addRadioButtonGroup("Projection channel: ", channels, 1,
len(channels), channels[1])
dialog.showDialog()
if dialog.wasCanceled():
return None
seg_ch = dialog.getNextRadioButton()
proj_ch = dialog.getNextRadioButton()
return channels.index(seg_ch), channels.index(proj_ch)
def makeSelections(x, y, rm, imp, circRad):
rm.reset()
for j in range(len(x)):
for i in range(len(x[-1])):
imp.setRoi(IJ.OvalRoi(x[j][i], y[j][i], circRad * 2, circRad * 2))
rm.addRoi(imp.getRoi())
rm.runCommand(imp, "Show All with labels")
gd = NonBlockingGenericDialog('Confirm ROI positions')
gd.addMessage('Are the ROIs positioned correctly? Move them if necessary')
gd.showDialog()
if gd.wasCanceled():
return None
return imp, rm
def getEdgeCoord(x, y, circRad, imp, msg):
IJ.run(imp, "Select None", "")
imp.setRoi(IJ.OvalRoi(x, y, circRad * 2, circRad * 2))
gd = NonBlockingGenericDialog(msg)
gd.addMessage('Select ' + msg + ' coordinates')
gd.showDialog()
if gd.wasCanceled():
return None
# wait for user input
coord = imp.getRoi().getContourCentroid()
IJ.run(imp, "Select None", "")
return coord[0] - circRad, coord[1] - circRad
def MyWaitForUser(title, message):
"""non-modal dialog with option to cancel the analysis"""
dialog = NonBlockingGenericDialog(title)
dialog.setCancelLabel("Cancel analysis")
if type(message) is list:
for line in message:
dialog.addMessage(line)
else:
dialog.addMessage(message)
dialog.showDialog()
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled")
return
def exit_assay():
gd = NonBlockingGenericDialog("Exit Assay")
gd.setCancelLabel("Quit & Save")
gd.setOKLabel("Quit")
gd.showDialog()
if gd.wasCanceled(): # quits
imp = IJ.getImage()
current_title = imp.getTitle()
imp.close()
renamer(dest, current_title, extension)
exit()
elif gd.wasOKed():
exit()
def selection(region):
nbgd = NonBlockingGenericDialog(region)
nbgd.setCancelLabel('Return')
nbgd.enableYesNoCancel('ROI OK', 'Redraw')
nbgd.showDialog()
if nbgd.wasOKed():
imp = IJ.getImage()
roi = imp.getRoi()
roi_check(roi)
return
if nbgd.wasCanceled():
exit_assay()
else:
repeat_measure()
def apply_thresh_overlay(overlay):
''' Clear outside rois in overlay '''
# --- Dialog -----------------------------------
wlist = WindowManager.getImageTitles()
gd = NonBlockingGenericDialog('Apply Mask to')
gd.setCancelLabel('Exit')
gd.addChoice('Select Movie', wlist, wlist[0])
gd.addCheckbox('Duplicate', True)
gd.showDialog() # dialog is open
if gd.wasCanceled():
return False
sel_win = gd.getNextChoice()
do_duplicate = gd.getNextBoolean()
# --- Dialog End ------------------------------
win_name = IJ.selectWindow(sel_win)
movie = IJ.getImage()
movie = slices_to_frames(movie)
C = movie.getC()
S = movie.getSlice()
if do_duplicate:
IJ.log('duplicating ' + movie.shortTitle)
movie = movie.duplicate()
NFrames = movie.getNFrames()
if overlay.size() != NFrames: # one roi for each frame!
display_msg(
'Mask count mismatch!', 'Mask count mismatch!\nGot ' + str(Nrois) +
' masks and ' + str(NFrames) + ' frames.. !')
for frame in range(1, NFrames + 1):
movie.setPosition(C, S, frame)
mask_roi = overlay.get(frame - 1)
ip = movie.getProcessor()
ip.setValue(0)
ip.setRoi(mask_roi)
ip.fillOutside(mask_roi)
movie.show()
return True
def measure_gd(src_folder,file_names):
from javax.swing import JButton
gd = NonBlockingGenericDialog("Loci to compartment")
gd.setResizable(True)
gd.pack()
gd.addMessage("Draw a freehand ROI aound loci and closest \n compartment(e.g. speckle) and press 0 on keyboard.")
gd.addMessage("To load next image press Next Image button.")
next_imp_bt = JButton('Next Image', actionPerformed=load_next_image)
gd.add(next_imp_bt)
gd.setLocation(10,10)
gd.setAlwaysOnTop(True)
gd.hideCancelButton()
gd.showDialog()
#
if gd.wasOKed():
IJ.log( "Measurement done! You're welcome!")
def crop_review():
"""handle UI for reviewing cropping"""
print("doing crop review...");
dialog = NonBlockingGenericDialog("Review cropping")
dialog.enableYesNoCancel("Keep this crop", "Revert to uncropped image");
dialog.setCancelLabel("Cancel analysis");
dialog.addMessage("Please check whether this cropping is as expected, \n" +
"and choose whether to press on or revert to using the \n" +
"full, uncropped image. ");
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
elif dialog.wasOKed():
keep_cropping = True;
else:
keep_cropping = False;
return keep_cropping;
def measure_gd():
# Dialouge box for measurements.
# It
from javax.swing import JButton
gd = NonBlockingGenericDialog("Loci to compartment")
gd.setResizable(True)
gd.pack()
gd.addMessage(
"Draw a freehand ROI around the loci and closest \ncompartment(e.g. speckle) and press 0 on keyboard."
)
next_imp_bt = JButton('Analyze active image',
actionPerformed=analyze_image)
gd.add(next_imp_bt)
gd.setLocation(10, 10)
gd.setAlwaysOnTop(True)
gd.hideCancelButton()
gd.showDialog()
#
if gd.wasOKed():
IJ.log("Measurement done! Happy FISHing")
def __selectMeasureStack(self) :
# We allow the user to choose what to measure in the stack, and on which stack.
gd1=NonBlockingGenericDialog("Stack Choice for measures")
idimages=WindowManager.getIDList()
images=[WindowManager.getImage(imgID) for imgID in idimages if WindowManager.getImage(imgID).getImageStackSize()>1 ]
imagesnames=[img.getTitle() for img in images]
activindex=0
for i in range(len(imagesnames)) :
if imagesnames[i] == self.__activeTitle :
activindex=i
gd1.addChoice("Select a stack in the list : ",imagesnames,imagesnames[activindex])
gd1.showDialog()
chosenstack=gd1.getNextChoice()
self.__img=WindowManager.getImage(chosenstack)
IJ.selectWindow(self.__img.getID())
if gd1.wasOKed() : return True
else : return False
def manual_analysis(imp, file_name, output_folder):
"""perform analysis based on manually drawn cells"""
cal = imp.getCalibration()
channel_imps = ChannelSplitter.split(imp)
gfp_imp = channel_imps[0]
IJ.setTool("freehand")
proceed = False
roim = RoiManager()
roim.runCommand("Show all with labels")
dialog = NonBlockingGenericDialog("Perform manual segmentation")
dialog.setOKLabel("Proceed to next image...")
dialog.addMessage("Perform manual segmentation: ")
dialog.addMessage(
"Draw around cells and add to the region of interest manager (Ctrl+T)")
dialog.addMessage(
"You can see what you've added so far if you check \"show all\" on the ROI manager"
)
dialog.addMessage(
"Then press \"proceed to next image\" when all cells have been added")
dialog.showDialog()
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled")
elif dialog.wasOKed():
rois = roim.getRoisAsArray()
roim.reset()
roim.close()
out_stats = generate_cell_shape_results(rois, gfp_imp, cal, file_name)
print("Number of cells identified = {}".format(len(out_stats)))
# save output
save_qc_image(
imp, rois, "{}_plus_overlay.tiff".format(
os.path.join(output_folder,
os.path.splitext(file_name)[0])))
save_cell_rois(rois, output_folder, os.path.splitext(file_name)[0])
imp.changes = False
imp.close()
save_output_csv(out_stats, output_folder)
return out_stats
return None
def qc_background_regions(intensity_imp, bg_rois):
"""allow the user to view and correct automatically-determined background regions"""
imp = Duplicator().run(intensity_imp);
imp.setTitle("Background region QC");
imp.show();
imp.setPosition(1);
autoset_zoom(imp);
imp.setRoi(bg_rois[0]);
IJ.setTool("freehand");
notOK = True;
while notOK:
listener = UpdateRoiImageListener(bg_rois, is_area=True);
imp.addImageListener(listener);
dialog = NonBlockingGenericDialog("Background region quality control");
dialog.enableYesNoCancel("Continue", "Use this region for all t");
dialog.setCancelLabel("Cancel analysis");
dialog.addMessage("Please redraw background regions as necessary...")
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
elif not(dialog.wasOKed()):
this_roi = imp.getRoi();
bg_rois = [this_roi for _ in listener.getRoiList()];
imp.removeImageListener(listener);
else:
last_roi = imp.getRoi();
qcd_bg_rois = listener.getRoiList();
if imp.getNFrames() > imp.getNSlices():
qcd_bg_rois[imp.getT() - 1] = last_roi;
else:
qcd_bg_rois[imp.getZ() - 1] = last_roi;
notOK = False;
imp.removeImageListener(listener);
imp.changes = False;
imp.close();
return qcd_bg_rois;
def __selectTrackStack(self) :
gd0=NonBlockingGenericDialog("Stack Choice")
idimages=WindowManager.getIDList()
#images=[WindowManager.getImage(imgID) for imgID in idimages if WindowManager.getImage(imgID).getImageStackSize()>1 ]
images=[WindowManager.getImage(imgID) for imgID in idimages]
imagesnames=[img.getTitle() for img in images]
for i in range(len(imagesnames)) :
if imagesnames[i] == self.__activeTitle : activindex=i
gd0.addChoice("Select a stack in the list : ",imagesnames,imagesnames[activindex])
gd0.showDialog()
chosenstack=gd0.getNextChoice()
self.__img = WindowManager.getImage(chosenstack)
self.__maxLife = self.__img.getImageStackSize()
IJ.selectWindow(self.__img.getID())
self.__activeTitle=self.__img.getTitle()
self.__imagesnames[:]=[]
#self.__imagesnames.append("image1")
self.__imagesnames.append(self.__activeTitle)
if gd0.wasOKed() : return True
else : return False
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
def main():
# define here which membrane indices will be used in the analysis, with last index the "control" index
membrane_indices = [-1, 0, 1, 3]
# for now, work with frontmost open image...
imp = IJ.getImage()
im_title = imp.getTitle()
settings = MembraneEvolutionAnalysisSettings(
membrane_indices=membrane_indices)
settings.loadPersistedSettings()
timestamp = datetime.strftime(datetime.now(), '%Y-%m-%d %H-%M-%S')
DirectoryChooser.setDefaultDirectory((settings.output_path))
dc = DirectoryChooser('Select the root folder for saving output')
output_root = dc.getDirectory()
if output_root is None:
raise IOError('no output path chosen')
settings.output_path = output_root
# get calibration
cal = imp.getCalibration()
if cal.getTimeUnit() == "sec":
cal.setTimeUnit('s')
# pop up a dialog prompting for selection of zero time point, frame interval, and time step for analysis
time_steps_not_ok = True
while time_steps_not_ok:
dialog = NonBlockingGenericDialog("Determine time parameters...")
dialog.addNumericField("0 timepoint frame (1-index): ",
settings.zero_timepoint_frame, 0)
dialog.addNumericField("Acquisition time step (s): ",
cal.frameInterval,
2) # assume stored in seconds
dialog.addNumericField(
"Time step for analysis (s): ",
cal.frameInterval * settings.analysis_frame_step, 2)
dialog.showDialog()
if dialog.wasCanceled():
return
zero_f = dialog.getNextNumber()
acq_t_step = dialog.getNextNumber()
analysis_t_step = dialog.getNextNumber()
if acq_t_step != 0 and analysis_t_step != 0:
analysis_frame_step = analysis_t_step / acq_t_step
if round(analysis_frame_step) == analysis_frame_step:
time_steps_not_ok = False
settings.zero_timepoint_frame = zero_f
settings.analysis_frame_step = analysis_frame_step
if time_steps_not_ok:
warning_dlg = GenericDialog("Error!")
warning_dlg.addMessage(
"Analysis time step must be an integer multiple of acquisition time steps, and neither should be zero!!"
)
warning_dlg.setOKLabel("Try again...")
warning_dlg.showDialog()
if warning_dlg.wasCanceled():
return
start_frame = int(((zero_f - 1) % analysis_frame_step) + 1)
end_frame = int(imp.getNFrames() -
(imp.getNFrames() - zero_f) % analysis_frame_step)
frames = [
f + 1
for f in range(start_frame - 1, end_frame, int(analysis_frame_step))
]
print("frames = " + str(frames))
imp.killRoi()
analysis_imp = SubstackMaker().makeSubstack(
imp,
str(start_frame) + "-" + str(end_frame) + "-" +
str(int(analysis_frame_step)))
imp.changes = False
imp.close()
analysis_imp.show()
drawn_membranes = [
TimepointsMembranes(input_image_title=im_title,
time_point_s=(t - 1) * acq_t_step) for t in frames
]
membranes_listener = UpdateRoiImageListener(drawn_membranes)
analysis_imp.addImageListener(membranes_listener)
# now attach roi listener to store all 0th membranes after showing a waitforuserdialog to prompt continuation
IJ.setTool("freeline")
for membrane_idx in membrane_indices:
# if membrane_idx>50:
# IJ.setTool("line");
analysis_imp.killRoi()
membranes_listener.resetLastFrame()
membranes_listener.setCurrentMembraneIndex(membrane_idx)
analysis_imp.setZ(1)
continue_dlg = WaitForUserDialog(
"Continue?", "Click OK once all the " + str(membrane_idx) +
"-index membranes have been drawn")
continue_dlg.show()
membranes_listener.imageUpdated(analysis_imp)
drawn_membranes = membranes_listener.getDrawnMembraneTimepointsList()
json_path = os.path.join(output_root,
"Membranes " + timestamp + ".json")
f = open(json_path, 'w+')
try:
json.dump(drawn_membranes, f, default=encode_membrane)
finally:
f.close()
# save csv containing mebrane measurements for current membrane index
csv_path = os.path.join(
output_root, ("Membrane measurements " + timestamp + ".csv"))
if membrane_idx == membrane_indices[0]:
try:
f = open(csv_path, 'wb')
writer = csv.writer(f)
writer.writerow([
"Membrane index", ("Time point, " + cal.getTimeUnit()),
("Membrane length, " + cal.getUnit()),
("Euclidean length, " + cal.getUnit()),
"Membrane sinuoisty"
])
finally:
f.close()
try:
f = open(csv_path, 'ab')
writer = csv.writer(f)
for mems in drawn_membranes:
mem = mems.getMembrane(membrane_idx)
if mem is not None:
writer.writerow([
membrane_idx, mems.time_point_s,
mem.getPathLength() * cal.pixelWidth,
mem.getEuclidean() * cal.pixelWidth,
mem.getSinuosity()
])
finally:
f.close()
settings.persistSettings()
settings.save_settings()
print("Finished getting all membranes with indices " +
str(membrane_indices))
analysis_imp.close()
def __settings(self, imgName, flag) :
"""
Allows the user to choose several parameters for the tracking.
"""
#fenetre=JFrame("Import")
#optionpane=JOptionPane("Do you want to import previous preferences ?",JOptionPane.QUESTION_MESSAGE ,JOptionPane.YES_NO_OPTION )
#optionpane.setVisible(True)
#dialog = optionpane.createDialog(fenetre, "Import")
#dialog.show()
#choice = optionpane.getValue()
#if choice==JOptionPane.YES_OPTION : self.__ImportPref()
image=self.__dictImages[imgName]
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
#self.__macropath=IJ.getDirectory("macros")
#self.__macropath=IJ.getDirectory("")
#self.__text.setText(self.__macropath)
panel0=Panel()
pathbutton=Button("Select macro file", actionPerformed = outputpath)
#pathbutton.actionPerformed = outputpath
self.__text = TextField(self.__macropath)
panel0.add(pathbutton)
panel0.add(self.__text)
# -------- start batch mode --------- #
if self.__batch :
pass
#self.__ImportPref(flag)
image.hide()
else :
image.show()
IJ.selectWindow(image.getID())
gd0=NonBlockingGenericDialog("Settings")
gd0.setFont(Font("Courrier", 1, 10))
gd0.addMessage("---------------- PRE-PROCESSING OPTIONS -------------------")
gd0.addCheckbox("Substract Background",self.__subback) #box 1 subback
gd0.addNumericField("Radius",self.__radius,0)
gd0.addCheckbox("Run a macro for pre processing",self.__runmacro) #box 2 runmacro
gd0.addPanel(panel0)
gd0.addMessage("-------------------------------------------")
gd0.addMessage("Tracking parameters")
gd0.addMessage("Coeffs modulate de weight of each parameter")
gd0.addMessage("Max delta set the maximum allowed change in absolute units")
gd0.addMessage(" ")
gd0.addNumericField("Coeff Area : ",self.__distparam[0],0)
gd0.addNumericField("Max deltaArea : ",self.__distparam[1],self.__nbdigits,6,"x times")
gd0.addNumericField("Coeff Angle : ",self.__distparam[2],0)
gd0.addNumericField("Max deltaAngle : ",self.__distparam[3],self.__nbdigits,6,"degrees")
gd0.addNumericField("Coeff Feret : ",self.__distparam[4],0)
gd0.addNumericField("Max deltaFeret : ",self.__distparam[5],self.__nbdigits,6,"x times")
gd0.addNumericField("Coeff PositionX : ",self.__distparam[6],0)
gd0.addNumericField("Max deltaPositionX : ",self.__distparam[7],self.__nbdigits,6,"pixels")
gd0.addNumericField("Coeff PositionY : ",self.__distparam[8],0)
gd0.addNumericField("Max deltaPositionY : ",self.__distparam[9],self.__nbdigits,6,"pixels")
gd0.addMessage("-------------------------------------------")
automethods=AutoThresholder.getMethods()
gd0.addCheckbox("Manual Threshold",self.__manthresh) #box 3 manthresh
gd0.addChoice("Threshol Method : ",automethods,self.__thresMethod)
gd0.addMessage("-------------------------------------------")
#gd0.addCheckbox("Symmetry Around 0-180",self.__optionAngle)
#gd0.addMessage("-------------------------------------------")
#gd0.addCheckbox("Save cell files", self.__optionSave)
#gd0.addMessage("-------------------------------------------")
gd0.addCheckbox("Track new cells", self.__optionNewCells) #box 4 newcells
gd0.addMessage("-------------------------------------------")
gd0.addCheckbox("Generate time list with follow time lapse interval ?", self.__optionTimelapse) #box 5 timelapse
gd0.addNumericField("Estimated time lapse : ",self.__timelapse,self.__nbdigits,6,"seconds")
#gd0.hideCancelButton()
gd0.showDialog()
if gd0.wasCanceled() : return False
#chosenstack=gd0.getNextChoice()
#self.__img=WindowManager.getImage(chosenstack)
self.__subback=gd0.getNextBoolean() #box 1 subback
self.__radius=gd0.getNextNumber()
self.__runmacro=gd0.getNextBoolean() #box 2 runmacro
for i in range(10) : self.__distparam[i]=gd0.getNextNumber()
#self.__distmethod=gd0.getNextChoice()
self.__manthresh=gd0.getNextBoolean() #box 3 manthresh
self.__thresMethod=gd0.getNextChoice()
#self.__optionAngle=gd0.getNextBoolean()
#self.__optionSave=gd0.getNextBoolean()
self.__optionNewCells=gd0.getNextBoolean() #box 4 newcells
self.__optionTimelapse=gd0.getNextBoolean() #box 5 timelapse
self.__timelapse=int(gd0.getNextNumber())
# -------- start end batch mode --------- #
if self.__optionTimelapse :
self.__dictTimeStack[imgName]=range(0,image.getImageStackSize()*self.__timelapse, self.__timelapse)
if not self.__optionTimelapse and self.__source=="image" :
self.__dictTimeStack[imgName]=range(0,image.getImageStackSize())
#if option_import==True :
# temparray=
#else : temparray=self.__calRois("image1", 1)
#imp=self.__dictImages["image1"]
if self.__manthresh :
ip=image.getProcessor()
self.__maxthr=ip.getMaxThreshold()
self.__minthr=ip.getMinThreshold()
temparray=self.__calRois(image, 1)
self.__rr=RangeRois(temparray, image)
if (not self.__batch) :
image.show()
self.__params=self.__rr.showSettingsDialog().values()
if self.__batch : image.hide()
return True
## Sets up main GUI interface for examining found objects
ngd = NonBlockingGenericDialog("Control box")
ngd.addCheckbox("Contained_objects",False)
ngd.addCheckbox("Duplicated_objects",False)
ngd.addCheckbox("Restitched_objects",False)
ngd.addCheckbox("Unique_objects",False)
boxes = ngd.getCheckboxes()
checkboxObjects = []
for i in range(boxes.size()):
checkboxObjects.append(boxes.elementAt(i))
for i in range(len(checkboxObjects)):
checkboxObjects[i].addItemListener(CustomCheckboxListener(objectDB,virginImage,boxImages,boxes))
ngd.setCancelLabel("Exit")
ngd.setOKLabel("Inspect")
ngd.showDialog()
if (ngd.wasCanceled()):
titles = WindowManager.getImageTitles()
p = re.compile(r'^Result')
for title in titles:
m = p.search(title)
if m is not None:
theImage = WindowManager.getImage(title)
theImage.close()
virginImage.show()
for img in boxImages:
img.close()
else:
titles = WindowManager.getImageTitles()
p = re.compile(r'^Result')
from array import zeros
from ij import IJ
from ij.gui import NonBlockingGenericDialog
from ij.process import ByteProcessor
from ij import ImageStack
from ij import ImagePlus
theImage = IJ.getImage()
gd = NonBlockingGenericDialog("Set slice params...")
gd.addNumericField("Slice start:",1,0)
gd.addNumericField("Slice end:",theImage.getNSlices(),0)
gd.showDialog()
if (gd.wasOKed()):
startSlice = gd.getNextNumber()
endSlice = gd.getNextNumber()
width = theImage.getWidth()
height = theImage.getHeight()
newStack = ImageStack(width,height)
for i in range(startSlice,endSlice+1):
theImage.setSlice(i)
theImage.killRoi()
pixels = zeros('b',width*height)
bp = ByteProcessor(width,height,pixels)
bp.setColor(127)
doStaySlice = True
while doStaySlice:
waiter = NonBlockingGenericDialog("Set cast")
from ij.io import DirectoryChooser
from ij.measure import Measurements
from ij.gui import NonBlockingGenericDialog
from ij.gui import WaitForUserDialog
# Get input and output directories
dc = DirectoryChooser("Choose an input directory")
inputDirectory = dc.getDirectory()
dc = DirectoryChooser("Choose an output directory")
outputDirectory = dc.getDirectory()
gd = NonBlockingGenericDialog("Channel Options")
gd.addStringField("Enter your name: ", "")
gd.showDialog()
name = gd.getNextString()
if gd.wasCanceled():
print "User canceled dialog!"
# Finds all the subfolders in the main directory
with open(outputDirectory + "annotations_" + name + ".csv", "w") as log:
subfolders = []
# for subfolder in os.listdir(inputDirectory):
# if os.path.isdir(inputDirectory + subfolder):
# subfolders.append(subfolder)
gw.resetok()
gw.setLabel("...")
gw.hide()
rm.runCommand("reset")
if imp.getOverlay() is not None : imp.getOverlay().clear()
overlay=Overlay()
imp.setOverlay(overlay)
gd0=NonBlockingGenericDialog("settings")
gd0.addCheckbox("Show the overlay during the process ? (slow option)", False)
gd0.addNumericField("Minimal Lifetime : ",10,0)
gd0.addNumericField("Minimal distance to reversion : ",4,0)
gd0.addNumericField("Sub sampling ? : ",1,0)
gd0.addNumericField("Radius for fluo tracking ? : ",8,0)
gd0.showDialog()
isShow = gd0.getNextBoolean()
minLife = gd0.getNextNumber()
mind = gd0.getNextNumber()
subs = gd0.getNextNumber()
rayon = gd0.getNextNumber()
if gd0.wasCanceled() :
isShow = True
imp.show()
else :
if isShow : imp.show()
else : imp.hide()
dicSens, dicSpeed, dicAngle, dicCumuld, dicPos, dicFluoA, dicFluoB ={},{},{},{},{},{},{}
def perform_user_qc(in_imp, edges, alt_edges, fixed_anchors_list, params):
"""allow the user to intervene to fix erroneously identified membrane edges"""
n_frames = in_imp.getNFrames();
n_channels = in_imp.getNChannels();
output_folder = params.output_path;
current_edges = edges;
rgbstack = ImageStack(in_imp.getWidth(), in_imp.getHeight());
if n_frames > 1:
for tidx in range(n_frames):
in_imp.setT(tidx+1);
ip = in_imp.getProcessor();
rgbip = ip.convertToRGB();
rgbstack.addSlice(rgbip);
else:
for cidx in range(n_channels):
in_imp.setC(cidx+1);
ip = in_imp.getProcessor();
rgbip = ip.convertToRGB();
rgbstack.addSlice(rgbip);
imp = ImagePlus(("RGB " + in_imp.getTitle()), rgbstack);
IJ.run("Colors...", "foreground=red background=white selection=yellow");
for tidx in range(imp.getNSlices()):
imp.setSlice(tidx+1);
for anchor in params.manual_anchor_positions:
imp.setRoi(PointRoi(anchor[0], anchor[1]));
IJ.run(imp, "Draw", "slice");
imp.show();
autoset_zoom(imp);
imp.setPosition(1);
imp.setRoi(current_edges[0]);
if n_frames > 1:
listener = UpdateRoiImageListener(current_edges);
imp.addImageListener(listener);
IJ.setTool("freeline");
do_flip = True;
while do_flip:
dialog = NonBlockingGenericDialog("User quality control");
dialog.enableYesNoCancel("Continue", "Flip all edges");
dialog.setCancelLabel("Cancel analysis");
dialog.addMessage("Please redraw the membrane edges as necessary, \n" +
"making sure to draw beyond anchor points at either end...\n" +
"Click OK when done. ");
p = Panel();
but = Button("Flip this edge");
al = Listener(edges, alt_edges, imp);
but.addActionListener(al);
p.add(but);
dialog.addPanel(p);
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
elif dialog.wasOKed():
do_flip = False;
else:
print("flip edges");
do_flip = True;
if n_frames > 1:
imp.removeImageListener(listener);
current_edges = alt_edges if (current_edges == edges) else edges;
imp.setPosition(1);
imp.setRoi(current_edges[0]);
if n_frames > 1:
listener = UpdateRoiImageListener(current_edges);
imp.addImageListener(listener);
last_roi = imp.getRoi();
if n_frames > 1:
qcd_edges = listener.getRoiList();
if imp.getNFrames() > imp.getNSlices():
qcd_edges[imp.getT() - 1] = last_roi;
else:
qcd_edges[imp.getZ() - 1] = last_roi;
imp.removeImageListener(listener);
else:
qcd_edges = [last_roi];
mbio.save_qcd_edges2(qcd_edges, output_folder);
# next four lines are a quick and dirty hack...
if n_frames > 1:
nframes = imp.getNFrames() if imp.getNFrames()>imp.getNSlices() else imp.getNSlices();
else:
nframes = n_frames;
for fridx in range(0, nframes):
if (qcd_edges[fridx].getType()==Roi.FREELINE) or (qcd_edges[fridx].getType()==Roi.POLYLINE):
if (fridx == 0) or params.constrain_anchors:
anchors = params.manual_anchor_positions;
else:
anchors = fixed_anchors_list[fridx - 1];
fixed_anchors = mb.fix_anchors_to_membrane(anchors, qcd_edges[fridx], params);
fixed_anchors = mb.order_anchors(fixed_anchors, params.manual_anchor_midpoint);
fixed_anchors_list[fridx] = fixed_anchors;
poly = qcd_edges[fridx].getInterpolatedPolygon(0.25, False);
polypoints = [(x,y) for x,y in zip(poly.xpoints, poly.ypoints)];
idx = [polypoints.index(fixed_anchors[0]), polypoints.index(fixed_anchors[1])];
idx.sort();
polypoints = polypoints[idx[0]:idx[1]];
newedge = PolygonRoi([x for (x,y) in polypoints],
[y for (x,y) in polypoints],
Roi.POLYLINE);
newedge = mb.check_edge_order(anchors, newedge);
imp.setPosition(fridx + 1);
imp.setRoi(newedge);
IJ.run(imp, "Interpolate", "interval=1.0 smooth adjust");
IJ.run(imp, "Fit Spline", "");
qcd_edges[fridx] = imp.getRoi();
mbio.save_qcd_edges2(qcd_edges, output_folder);
imp.changes = False;
imp.close();
return qcd_edges, fixed_anchors_list;
background_c2.append(float(row[1]))
# ok we can now access these variables.
# resets image
imp = IJ.getImage()
imp.setT(1)
imp.setC(1)
# sets the tools to be used
IJ.run("Point Tool...",
"type=Cross color=Yellow size=Tiny label counter=0 add_to")
IJ.setTool("point")
# Asks you to select cells, hitting cancel if you made a mistake
nbgd = NonBlockingGenericDialog("Select Cells")
nbgd.showDialog()
if nbgd.wasCanceled():
IJ.run("Remove Overlay")
# turns the overlay into an object.
imp = IJ.getImage()
overlay = Overlay()
overlay = imp.getOverlay()
# asks if you have selected anything
try:
roi_points = overlay.toArray()
except AttributeError as error:
nbgd = NonBlockingGenericDialog("Select some cells boi")
nbgd.showDialog()
if blur_state == True:
set_sigma = "sigma=" + str(blur_val) + " stack"
IJ.run("Gaussian Blur...", set_sigma)
params = Parameters()
title = "Membrane Blebbing version " + Parameters._version_string
try:
f = open(readme_fpath, "rb")
text = f.readlines()
except:
raise IOError("Error reading README.txt")
finally:
f.close()
sb = StringBuilder()
for line in text:
sb.append(line)
panel = Panel()
txtArea = JTextArea(sb.toString())
txtArea.setEditable(False)
txtArea.setLineWrap(True)
txtArea.setWrapStyleWord(True)
scrollpane = JScrollPane(txtArea)
scrollpane.setPreferredSize(Dimension(500, 200))
panel.add(scrollpane)
dialog = NonBlockingGenericDialog(title)
#for line in text:
# dialog.addMessage(line);
dialog.addPanel(panel)
dialog.showDialog()
from ij import WindowManager as WM
import os
from os import path
import re
from re import sub
from ij.plugin import Concatenator
from ij.io import OpenDialog, DirectoryChooser
from ij.gui import GenericDialog, NonBlockingGenericDialog
from ij.text import TextPanel as TP
from ij.measure import ResultsTable as RT
# Create a non-blocking dialog to enter the metadata
psgd = NonBlockingGenericDialog(
"Choose the frame that shows the right conformation of the heart?")
psgd.addNumericField("Which frame to choose?", 1, 0)
psgd.addCheckbox("Use table of selected frames?", False)
psgd.showDialog()
choose = psgd.getNextNumber()
choice = psgd.getCheckboxes().get(0).getState()
#open a tab separated txt file with one column Frame selected
if choice == 1:
choose = 0
IJ.run("Table... ", "open=")
frametable = WM.getWindow("selected_frames.txt")
meta = frametable.getTextPanel()
metaRT = TP.getResultsTable(meta)
# Choose a directory
directory_load = DirectoryChooser(
"Select the directory of your files").getDirectory()
directory_load = directory_load.replace("\\", "/")
"line",
(icalibration.getX(retval[2] + 1), icalibration.getX(retval[1] + 1)),
(retval[4], retval[4]))
valplot.add(
"line",
(icalibration.getX(retval[1] + 1), icalibration.getX(retval[1] + 1)),
(retval[3], retval[4]))
valplot.add(
"line",
(icalibration.getX(retval[2] + 1), icalibration.getX(retval[2] + 1)),
(retval[3], retval[4]))
valplot.show()
valplot.update()
proceed = NonBlockingGenericDialog("Accept Or Reject?")
proceed.addCheckbox("Uncheck To Reject", True)
proceed.showDialog()
proceed = proceed.getNextBoolean()
WindowManager.getWindow("Angle-Distance Correlation Values").close()
WindowManager.getImage("pixarr").close()
WindowManager.getImage("DUP_" + title).close()
if proceed:
roi = analyte.getRoi()
roiStats = roi.getStatistics()
ferets = roi.getFeretValues()
rt = WindowManager.getWindow(
"Cardiomyocyte Results").getTextPanel().getOrCreateResultsTable()
a = rt.getCounter()
rt.setValue("Correlation Score", a, retval[0])
rt.setValue("Sarcomere Length", a, icalibration.getX(retval[1] + 1))
rt.setValue("Area", a, roiStats.area)
rt.setValue("MaxFeret", a, ferets[0])
def __settings(self, imgName) :
"""
Lets the user to choose different measures to make, and displays it following the choice of the user.
"""
try : dico=self.__dictCells[imgName]
except KeyError :
try : dico=self.__dictCells[imgName[:-4]]
except KeyError : return False
else : imgName=imgName[:-4]
dico=self.__dictCells[imgName]
for cellname in dico.keys() :
self.__dictMeasures[dico[cellname]]={}
# Represents the datas on a diagram
def diagrambuttonPressed(event) :
IJ.showMessage("Push 'Auto' button each time you want to see the diagram")
x1=10
y1=20
x2=100
y2=50
x3=60
y3=30
xr=10
yr=20
wr=20
hr=20
rect=Rectangle(xr,yr,wr,hr)
#img=IJ.getImage()
#nbslices=self.__img.getImageStackSize()
nbslices=self.__maxLife
IJ.run("Hyperstack...", "title=Diagram type=32-bit display=Color width="+str(x2+(nbslices+1)*x3)+" height="+str(y2+y3*len(dico))+" channels=1 slices="+str(len(self.__measures))+" frames=1")
im=IJ.getImage()
ip=im.getProcessor()
for i in range(len(self.__measures)) :
indiceligne=0
maxvalue=0
minvalue=1000000
im.setPosition(1,i+1,1)
for cellname in self.__listcellname :
indiceligne+=1
for indicecolonne in range(1,nbslices+1):
rect.setLocation(x2+indicecolonne*x3+int(x3/6),(y1+indiceligne*y3-int(y3/2)))
# we create at the first iteration a dictionary with the rectangles (for a future use)
if i==0 :
self.__gridrectangle[(indiceligne,indicecolonne)]=Rectangle(rect)
im.setRoi(rect)
ipr=im.getProcessor()
# we find the min and max values of the datas for a measure given.
if self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1]>maxvalue :
maxvalue=self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1]
if self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1]<minvalue :
minvalue=self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1]
# we fill the rectangle with the value of the measure
ipr.setValue(self.__dictMeasures[dico[cellname]][self.__measures[i]][indicecolonne-1])
ipr.fill()
# we write the names and the n of slices on the image with the maxvalue.
ip.setValue(maxvalue)
ip.moveTo(x1,y1)
ip.drawString(self.__measures[i])
for j in range(1,nbslices+1) :
ip.moveTo(x2+j*x3,y1)
ip.drawString("Slice "+str(j))
j=0
for cellname in self.__listcellname :
ip.moveTo(x1,y2+j*y3)
ip.drawString(cellname)
j+=1
im.killRoi()
im=IJ.run(im,"Fire","")
IJ.run("Brightness/Contrast...", "")
#im.setMinAndMax(minvalue,maxvalue)
#im.updateImage()
#we add a mouse listener in order to be able to show the roi corresponding to a rectangle when the user clicks on it.
listener = ML()
listener.name=imgName
for imp in map(WindowManager.getImage, WindowManager.getIDList()):
if imp.getTitle().startswith("Diagram") :
win = imp.getWindow()
if win is None:
continue
win.getCanvas().addMouseListener(listener)
# Represents the datas on a series of graphs.
def graphbuttonPressed(event) :
colors=[]
#img=IJ.getImage()
#nbslices=self.__img.getImageStackSize()
nbslices=self.__maxLife
acell=dico.values()[0]
if self.__useTime :
x = acell.getListTimes()
namex="Time sec"
else :
x = range(1,nbslices+1)
namex = "Frame"
maxx=max(x)
minx=min(x)
#x=[i for i in range(1,nbslices+1)]
font=Font("new", Font.BOLD, 14)
tempname = WindowManager.getUniqueName(self.__img.getShortTitle())
for i in range(len(self.__measures)) :
#print "i", i, self.__measures[i]
yarray=[]
flag=True
miny=10000000000
maxy=-1000000000
#we find the min and max values in order to set the scale.
for cellname in self.__listcellname :
colors.append(dico[cellname].getColor())
yarray.append(self.__dictMeasures[dico[cellname]][self.__measures[i]])
#for meas in self.__dictMeasures[dico[cellname]][self.__measures[i]] :
for meas in yarray[-1] :
if (meas<miny) and (Double.isNaN(meas)==False) :
miny=meas
if max(yarray[-1])>maxy : maxy=max(yarray[-1])
miny-=0.1*miny
maxy+=0.1*maxy
count=0.05
for j in range(len(yarray)) :
if j==0 :
if len(self.__measures)>1 :
plot=Plot("Plots-"+str(self.__measures[i]),namex,str(self.__measures[i]),x,yarray[j])
else :
plot=Plot("Plot-"+tempname,namex,str(self.__measures[i]),x,yarray[j])
plot.setLimits(minx,maxx,miny,maxy)
plot.setColor(colors[j])
plot.changeFont(font)
plot.addLabel(0.05, count, self.__listcellname[j])
else :
plot.setColor(colors[j])
plot.setLineWidth(3)
plot.addPoints(x,yarray[j],Plot.LINE)
plot.addLabel(0.05, count, self.__listcellname[j])
count+=0.05
plot.setColor(colors[0])
plot.show()
if len(self.__measures)>1 :
IJ.run("Images to Stack", "name="+tempname+"-plots title=Plots- use")
#def histbuttonPressed(event) :
#
# pass
# Represents the values in a tab.
def tabbuttonPressed(event) :
tab="\t"
headings=[]
measures=[]
#img=IJ.getImage()
#for i in range(self.__img.getImageStackSize()+1) :
for i in range(self.__maxLife+1) :
headings.append("Slice "+str(i))
headings[0]=WindowManager.getUniqueName(self.__img.getShortTitle())
#for m in self.__measurescompl :
for m in self.__dictMeasures[dico[self.__listcellname[0]]].keys() :
headstring=""
for head in headings:
headstring+=head+tab
tw=TextWindow(self.__listfiles[0]+"-"+m,headstring,"",800,600)
tp=tw.getTextPanel()
#for cellname in dico.keys() :
for cellname in self.__listcellname :
line=[]
line=[str(meas)+tab for meas in self.__dictMeasures[dico[cellname]][m]]
line.insert(0, cellname+tab)
linestr=""
for s in line: linestr+=s
tp.appendLine(linestr)
tp.updateDisplay()
if self.__measuresparambool_global[0] :
tw=TextWindow("Latency","cell\tLatency", "",800,600)
tp=tw.getTextPanel()
for i in range(len(self.__listcellname)) :
#if latencies[i][0] : line=self.__listcellname[i]+"\t"+str(latencies[i][1])
#else : line=self.__listcellname[i]+"\t"+"NaN"
line=self.__listcellname[i]+"\t"+str(latencies[i][1])
tp.appendLine(line)
tp.updateDisplay()
def helpbuttonPressed(event) :
IJ.showMessage("TO DO")
def newsetPressed(event) :
gd0.dispose()
self.__settings()
def alignbuttonPressed(event) :
IJ.showMessage("TO DO")
def mergebuttonPressed(event) :
IJ.showMessage("TO DO")
def saveResults() :
#if len(self.__listcellname) == 0 :
nbslices=self.__maxLife
acell=dico.values()[0]
if self.__useTime :
x = acell.getListTimes()
namex="Time_sec"
else :
x = range(1,nbslices+1)
namex = "Frame"
if not path.exists(self.__rootpath+"Results"+os.path.sep) : os.makedirs(self.__rootpath+os.path.sep+"Results"+os.path.sep, mode=0777)
tab="\t"
nl="\n"
measures=[]
headstring=""
#if self.__savemode : mode = "a"
#else : mode ="w"
mode = "a"
#for i in range(1, self.__maxLife+1) :headstring += "Slice_"+str(i)+tab
for i in range(self.__maxLife) :headstring += str(x[i])+tab
#for m in self.__measurescompl :
for m in self.__dictMeasures[dico[self.__listcellname[0]]].keys() :
f = open(self.__rootpath+"Results"+os.path.sep+m+".txt", mode)
#f.write(m+nl)
f.write(imgName+"-"+self.__time+"-"+m+"-"+namex+tab+headstring+nl)
if len(self.__listcellname) == 0 : f.write("no cells")
else :
for cellname in self.__listcellname :
linestr=cellname+tab
for measure in self.__dictMeasures[dico[cellname]][m] :
#print m, cellname, measure
linestr += str(measure)+tab
linestr+=nl
f.write(linestr)
f.close()
if self.__measuresparambool_global[0] :
m = "Latency"
f = open(self.__rootpath+"Results"+os.path.sep+m+".txt", mode)
f.write(imgName+"-"+self.__time+"-"+m+nl)
for i in range(len(self.__listcellname)) :
#if latencies[i][0] : line=self.__listcellname[i]+"\t"+str(latencies[i][1])
#else : line=self.__listcellname[i]+"\t"+"NaN"
line=self.__listcellname[i]+"\t"+str(latencies[i][1])
line+=nl
f.write(line)
f.close()
#
# ----------- main measures dialog -------------------------
#
# Allows the user to choose the measures to make, etc..
measureslabels_indep=["MaxFeret","MinFeret","AngleFeret","XFeret","YFeret","Area","Angle","Major","Minor","Solidity","AR","Round","Circ","XC","YC","FerCoord","FerAxis","MidAxis"]
measureslabels_dep=["Mean","StdDev","IntDen","Kurt","Skew","XM","YM","Fprofil","MidProfil","NFoci","ListFoci","ListAreaFoci","ListPeaksFoci","ListMeanFoci"]
measureslabels_global=["Latency", "velocity", "cumulatedDist"]
measureslabels_dep_tabonly=set(["MidAxis","FerCoord","FerAxis","Fprofil","MidProfil","ListFoci","ListAreaFoci","ListPeaksFoci","ListMeanFoci"])
ens_measures_global=set(measureslabels_global)
ens_measures_indep=set(measureslabels_indep)
ens_measures_dep=set(measureslabels_dep)
measureslabels=[]
for label in measureslabels_indep :
measureslabels.append(label)
for label in measureslabels_dep :
measureslabels.append(label)
#self.__defaultmeasures=[False for i in range(len(measureslabels))]
#self.__defaultmeasures_global=[False for i in range(len(measureslabels_global))]
gdmeasures=NonBlockingGenericDialog("MeasuresChoice")
gdmeasures.setFont(Font("Courrier", 1, 10))
gdmeasures.addMessage("******* TIME SETTINGS *******")
gdmeasures.addCheckbox("Only starting at begining :", self.__onlystart) # 1 only start
gdmeasures.addNumericField("Minimal Lifetime : ",self.__minLife,0)
gdmeasures.addNumericField("Maximal Lifetime : ",self.__maxLife,0)
#gdmeasures.addNumericField("Maximal Lifetime : ",self.__img.getImageStackSize(),0)
gdmeasures.addCheckbox("x axis in seconds", self.__useTime) # 2 use time
gdmeasures.addMessage("")
gdmeasures.addMessage("")
gdmeasures.addMessage("Choose the measures to make on the cells : ")
gdmeasures.addMessage("******* TIME MEASURES *******")
gdmeasures.addCheckboxGroup(4,8,measureslabels,self.__defaultmeasures)
gdmeasures.addMessage("")
gdmeasures.addMessage("******* GLOBAL MEASURES *******")
gdmeasures.addMessage("PLEASE : If you have selected movement parameters you MUST to select XC and YC !")
gdmeasures.addCheckboxGroup(3,1,measureslabels_global,self.__defaultmeasures_global)
gdmeasures.addNumericField("Noise value for maxima finder: ",self.__noise,0)
gdmeasures.addMessage("")
gdmeasures.addMessage("******* OPTIONS *******")
gdmeasures.addCheckbox("Select the cells in next dialog ?", self.__onlyselect) # 3 only select
gdmeasures.addCheckbox("Save results to text files ?", self.__savetables) # 4 save files
#gdmeasures.addCheckbox("Append mode ?", self.__savemode) # 5 append mode
gdmeasures.addCheckbox("Analyse in batch mode ?", self.__batchanalyse) # 6 analysis batch mode
gdmeasures.addCheckbox("Update overlay ?", self.__updateoverlay) # 7 update overlay
gdmeasures.addMessage("")
gdmeasures.addMessage("")
help_panel=Panel()
helpbutton=Button("HELP")
helpbutton.actionPerformed = helpbuttonPressed
help_panel.add(helpbutton)
gdmeasures.addPanel(help_panel)
gdmeasures.hideCancelButton()
if not self.__batchanalyse :
gdmeasures.showDialog()
self.__onlystart=gdmeasures.getNextBoolean() # 1 only start
self.__minLife=gdmeasures.getNextNumber()
self.__maxLife=gdmeasures.getNextNumber()
self.__useTime=gdmeasures.getNextBoolean() # 2 use time
self.__measuresparambool=[]
self.__measuresparambool_global=[]
for i in range(len(measureslabels)) :
self.__measuresparambool.append(gdmeasures.getNextBoolean())
self.__defaultmeasures[i]=self.__measuresparambool[-1]
for i in range(len(measureslabels_global)) :
self.__measuresparambool_global.append(gdmeasures.getNextBoolean())
self.__defaultmeasures_global[i] = self.__measuresparambool_global[i]
self.__noise=gdmeasures.getNextNumber()
self.__onlyselect=gdmeasures.getNextBoolean() # 3 only select
self.__savetables = gdmeasures.getNextBoolean() # 4 save files
#self.__savemode = gdmeasures.getNextBoolean() # 5 append mode
self.__batchanalyse = gdmeasures.getNextBoolean() # 6 analyse mode
self.__updateoverlay = gdmeasures.getNextBoolean() # 7 update overlay
# we update a list of all cells that have a lifetime corresponding to what the user chose.
if len (self.__allcells) == 0 :
for cellname in dico.keys() :
if dico[cellname].getLifeTime()>=self.__minLife : #and dico[cellname].getLifeTime()<=self.__maxLife :
if self.__onlystart :
if dico[cellname].getSlideInit()<2 : self.__allcells.append(cellname)
else : self.__allcells.append(cellname)
if self.__noise == 0 : self.__noise = None
if self.__batchanalyse : self.__onlyselect = False
if self.__onlyselect :
try :
self.__gw
except AttributeError :
if not path.exists(self.__pathdir+"Selected-Cells"+os.path.sep) : os.makedirs(self.__pathdir+os.path.sep+"Selected-Cells"+os.path.sep, mode=0777)
self.__gw = CellsSelection()
self.__gw.setTitle(imgName)
self.__gw.run(self.__allcells, self.__pathdir+"ROIs"+os.path.sep)
self.__gw.show()
self.__gw.setSelected(self.__allcells)
while not self.__gw.oked and self.__gw.isShowing() :
self.__gw.setLabel("Validate selection with OK !!")
self.__listcellname = list(self.__gw.getSelected())
self.__gw.resetok()
self.__gw.setLabel("...")
self.__gw.hide()
else :
if self.__gw.getTitle() == imgName :
self.__gw.show()
self.__gw.setSelected(self.__listcellname)
self.__listcellname[:]=[]
while not self.__gw.oked and self.__gw.isShowing() :
self.__gw.setLabel("Validate selection with OK !!")
self.__listcellname = list(self.__gw.getSelected())
self.__gw.resetok()
self.__gw.setLabel("...")
self.__gw.hide()
else :
self.__gw.dispose()
if not path.exists(self.__pathdir+"Selected-Cells"+os.path.sep) : os.makedirs(self.__pathdir+os.path.sep+"Selected-Cells"+os.path.sep, mode=0777)
self.__gw = CellsSelection()
self.__gw.setTitle(imgName)
self.__gw.run(self.__allcells, self.__pathdir+"ROIs"+os.path.sep)
self.__gw.show()
self.__gw.setSelected(self.__allcells)
self.__listcellname[:]=[]
while not self.__gw.oked and self.__gw.isShowing() :
self.__gw.setLabel("Validate selection with OK !!")
self.__listcellname = list(self.__gw.getSelected())
self.__gw.resetok()
self.__gw.setLabel("...")
self.__gw.hide()
filestodelet=glob.glob(self.__pathdir+"Selected-Cells"+os.path.sep+"*.cell")
for f in filestodelet : os.remove(f)
for cell in self.__listcellname :
sourcestr = self.__pathdir+"Cells"+os.path.sep+cell+".cell"
deststr = self.__pathdir+"Selected-Cells"+os.path.sep+cell+".cell"
#os.system("copy "+sourcestr+", "+deststr)
#shutil.copy(self.__pathdir+"Cells"+os.path.sep+cell+".cell",self.__pathdir+"Selected-Cells"+os.path.sep+cell+".cell")
shutil.copy(sourcestr,deststr)
self.__dictNcells[imgName] = len(self.__listcellname)
else :
self.__listcellname = list(self.__allcells)
self.__dictNcells[imgName] = len(self.__listcellname)
if len(self.__listcellname) == 0 :
self.__dictNcells[imgName] = 0
return False
self.__img.hide()
# we make the measures.
for i in range(len(measureslabels)) :
IJ.showProgress(i, len(measureslabels))
if self.__measuresparambool[i]==True :
self.__measurescompl.append(measureslabels[i])
if (measureslabels[i] in measureslabels_dep_tabonly)==False :
self.__measures.append(measureslabels[i])
if (i<18) and (measureslabels[i] in ens_measures_indep) :
self.__measureAll(self.__img,measureslabels[i],False, imgName, self.__noise)
ens_measures_indep.discard(measureslabels[i])
if i>=18 :
self.__measureAll(self.__img,measureslabels[i],True, imgName, self.__noise)
if self.__measuresparambool_global[0] : # calculate latency
latencies=[]
for i in range(len(self.__listcellname)) :
IJ.showProgress(i, len(self.__listcellname))
latencies.append(self.latencie(self.__listcellname[i], self.__img, imgName, self.__useTime))
if self.__measuresparambool_global[1] : # calculate velocity
self.__measures.append("velocity")
#velocities=[]
for i in range(len(self.__listcellname)) :
IJ.showProgress(i, len(self.__listcellname))
self.__measureVelocity(self.__img,imgName)
if self.__measuresparambool_global[2] : # calculate cumulatedDistance
self.__measures.append("cumulatedDist")
#velocities=[]
for i in range(len(self.__listcellname)) :
IJ.showProgress(i, len(self.__listcellname))
self.__measurecumulDist(self.__img,imgName)
self.__img.show()
self.__img.getProcessor().resetThreshold()
if self.__updateoverlay :
if self.__img.getOverlay() is not None : self.__img.getOverlay().clear()
outputrois=[]
cellnames=[]
self.__img.hide()
for cellname in self.__listcellname :
for r in dico[cellname].getListRoi():
if isinstance(r,Roi) :
pos=r.getPosition()
#print "MC overlay", cellname, r.getName(), pos
#r.setPosition(0)
#overlay.add(r)
outputrois.append(r)
if "cell" in r.getName() : cellnames.append(r.getName())
else : cellnames.append(str(pos)+"-"+cellname)
#print cellnames[-1]
rm = RoiManager.getInstance()
if (rm==None): rm = RoiManager()
rm.show()
self.__img.show()
IJ.selectWindow(self.__img.getTitle())
rm.runCommand("reset")
for i in range(len(outputrois)) :
outputrois[i].setName(cellnames[i])
rm.addRoi(outputrois[i])
rm.select(rm.getCount()-1)
rm.runCommand("Rename", cellnames[i])
IJ.run("Show Overlay", "")
rm.runCommand("UseNames", "true")
rm.runCommand("Associate", "true")
IJ.run(self.__img, "Labels...", "color=red font=12 show use")
IJ.run(self.__img, "From ROI Manager", "")
rm.runCommand("Show None")
rm.runCommand("Show All")
# ----------- batch analyse ------------------------
if self.__batchanalyse :
if self.__savetables : saveResults()
self.__dictMeasures.clear()
self.__allcells[:]=[]
self.__measurescompl[:]=[]
self.__measures[:]=[]
return False
# ---------- display methodes dialog ----------------
# Allows the user to choose how to see the results of the measures.
gd0=NonBlockingGenericDialog("Display")
gd0.addMessage("How do you want to see the results ?")
panel0=Panel()
diagrambutton=Button("Diagram")
diagrambutton.actionPerformed = diagrambuttonPressed
panel0.add(diagrambutton)
graphbutton=Button("Graph")
graphbutton.actionPerformed = graphbuttonPressed
panel0.add(graphbutton)
tabbutton=Button("Tab")
tabbutton.actionPerformed = tabbuttonPressed
panel0.add(tabbutton)
gd0.addPanel(panel0)
gd0.addCheckbox("Analyse next stack ?", self.__nextstack)
gd0.hideCancelButton()
gd0.showDialog()
self.__nextstack = gd0.getNextBoolean()
# ---------- save tables ---------------------------
if self.__savetables : saveResults()
# --------- re-start analysis -------------------
self.__dictMeasures.clear()
#self.__listcellname[:]=[]
self.__allcells[:]=[]
self.__measurescompl[:]=[]
self.__measures[:]=[]
if self.__nextstack : return False
else : return True
activeImage = draw_roi_on_full_res_tile(containing_tiles_dict,subupcoords_dict)
if (hadStitched):
activeImage.copyScale(calibImage)
calib = calibImage.getCalibration()
calibImage.close()
activeImage.updateAndRepaintWindow()
else:
calib = activeImage.getCalibration()
## Runs interface that allows to correct for bleedthrough and refraction
if activeImage is not None:
gd = NonBlockingGenericDialog("Select channel to operate on...")
gd.addChoice("Select_channel:",["Channel "+str(i) for i in range(1,activeImage.getNChannels()+1)],"Channel 1")
gd.addChoice("Bleeding_channel:",["None"] + ["Channel "+str(i) for i in range(1,activeImage.getNChannels()+1)],"None")
gd.addChoice("Refraction_reference_channel:",["None"] + ["Channel "+str(i) for i in range(1,activeImage.getNChannels()+1)],"None")
gd.showDialog()
if (gd.wasOKed()):
channelImages = ChannelSplitter.split(activeImage)
channel = gd.getNextChoiceIndex()+1
bleedingC = gd.getNextChoiceIndex()
refractRefC = gd.getNextChoiceIndex()
if (bleedingC > 0):
params = ("bleeding_channel=" + str(bleedingC) + " bloodied_channel=" + str(channel) + " " +
"allowable_saturation_percent=1.0 rsquare_threshold=0.50")
IJ.run("Remove Bleedthrough (automatic)", params)
dataImage = WindowManager.getImage("Corrected_ch" + str(channel))
if (refractRefC > 0):
refractCImage = channelImages[refractRefC-1].duplicate()
refractCImage.show()
IJ.run("Merge Channels...", "c1=" + dataImage.getTitle() + " c2=" + refractCImage.getTitle() + " create ignore")
mergedImage = WindowManager.getImage("Composite")
from ij import IJ
from ij.gui import NonBlockingGenericDialog
from ij import ImageStack
from ij.gui import WaitForUserDialog
from ij import ImagePlus
from ij.process import ImageProcessor
theImage = IJ.getImage()
gd = NonBlockingGenericDialog("Set slice params...")
gd.addNumericField("Slice start:",1,0)
gd.addNumericField("Slice end:",theImage.getNSlices(),0)
gd.showDialog()
if (gd.wasOKed()):
startSlice = gd.getNextNumber()
endSlice = gd.getNextNumber()
width = theImage.getWidth()
height = theImage.getHeight()
newStack = ImageStack(width,height)
t_line = 240
for i in range(startSlice,endSlice+1):
theImage.setSlice(i)
waiter = WaitForUserDialog("Set ROI","Set ROI for thresholding region")
waiter.show()
roi = theImage.getRoi()
newip = theImage.getProcessor().duplicate()
newip.setColor(0)
newip.fillOutside(roi)
newip.snapshot()
ytiles = 0
else:
ytiles = int(m.group(1))
nTiles = xtiles*ytiles
## Opens the options dialog box
gd = NonBlockingGenericDialog("Select channel...")
gd.addChoice("Analysis_channel",["Channel "+str(i) for i in range(1,nChannels+1)],"Channel 1")
gd.addChoice("Bleeding_channel",["Channel "+str(i) for i in range(nChannels+1)],"Channel 0")
gd.addChoice("Refractive_reference_channel",["Channel "+str(i) for i in range(nChannels+1)],"Channel 0")
gd.addNumericField("Intensity_threshold",128,0)
gd.addNumericField("Size_threshold",100,0)
gd.addChoice("Process_filter",["None","Min","Median"],"None")
gd.addCheckbox("Operate_on_tile_subset",False)
gd.addStringField("Which_tile_subset","1-4,9,11",12)
gd.showDialog()
## Parses the information from the dialog box
if (gd.wasOKed()):
analysisChannel = gd.getNextChoiceIndex()+1
bleedingChannel = gd.getNextChoiceIndex()
refChannel = gd.getNextChoiceIndex()
intThreshold = gd.getNextNumber()
sizeThreshold = gd.getNextNumber()
processFilter = gd.getNextChoiceIndex()
doSubset = gd.getNextBoolean()
whichTiles = gd.getNextString()
tileList = []
parsingFailed = False
if doSubset:
try:
LUTarray = [LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 2:
LUTarray = [LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 3:
LUTarray = [LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 4:
LUTarray = [LUT.createLutFromColor(Color.BLUE),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.WHITE)]
elif im.getNChannels() == 5:
LUTarray = [LUT.createLutFromColor(Color.BLUE),LUT.createLutFromColor(Color.RED),LUT.createLutFromColor(Color.GREEN),LUT.createLutFromColor(Color.YELLOW),LUT.createLutFromColor(Color.WHITE)]
else:
LUTarray = []
nbgd = NonBlockingGenericDialog("Pick freehand ROI")
nbgd.setLocation(0,0)
nbgd.addMessage("OK to run, cancel to exit")
nbgd.showDialog()
isContinue = nbgd.wasOKed()
while isContinue:
roi = im.getRoi()
if (roi is not None):
float_poly = roi.getFloatPolygon()
containing_tiles_superlist = []
for i in range(float_poly.npoints):
containing_tiles_superlist.append(find_containing_tiles([float_poly.xpoints[i],float_poly.ypoints[i],0],coords_vals,scale_info[1],scale_info[2]))
upscaled_coords = upscale_coords(coords,scale_info[0])
containing_tiles_dict = rearrange_tile_list(containing_tiles_superlist)
copy_fullsize_tiles(["tile_"+key for key in containing_tiles_dict.keys()],parentLSMFilePath+"_tiles/",parentLSMFilePath+"_tiles/subtiles/",".ome.tif")
subupcoords_vals = normalize_coords_in_list(get_list_from_dict(["tile_"+key for key in containing_tiles_dict.keys()],upscaled_coords))
hadStitched = False
if len(containing_tiles_dict.keys())>1:
for i in containing_tiles_dict.keys():
