def Dialog(imp):
dpi = 300
# a4 width in inches
defaultWidth = 11.69
defaultHeight = defaultWidth / ratio
defaultAspectRatio = 1.41
if imp:
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Input Options")
gd.addFileField("Select image database", "", 20)
gd.addMessage("Cover Maker Options")
gd.addNumericField("tile width", 12, 0)
gd.addNumericField("tile height", 9, 0)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
databasepath = gd.getNextString()
tilewidth = gd.getNextNumber()
tileheight = gd.getNextNumber()
return databasepath, imp.getWidth(), imp.getHeight(), int(
tilewidth), int(tileheight)
else:
IJ.showMessage("You should have at least one image open.")
def Dialog(imp):
dpi = 300
# a4 width in inches
defaultWidth = 11.69
defaultHeight = defaultWidth/ratio
defaultAspectRatio = 1.41
if imp:
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Input Options")
gd.addFileField("Select image database", "", 20)
gd.addMessage("Cover Maker Options")
gd.addNumericField("tile width", 12, 0)
gd.addNumericField("tile height", 9, 0)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
databasepath = gd.getNextString()
tilewidth = gd.getNextNumber()
tileheight = gd.getNextNumber()
print 'path:', databasepath
return databasepath, imp.getWidth(), imp.getHeight(), int(tilewidth), int(tileheight)
else:
IJ.showMessage( "You should have at least one image open." )
def run():
gd = GenericDialogPlus("ND2 Conversion Tool")
gd.addMessage("This plugin uses BioFormats to convert ND2 images to JPEG for further processing in ImageJ.")
gd.addDirectoryOrFileField("Input: ", "G:\\Subdir testing\\") #srcDir
gd.addDirectoryOrFileField("Output: ", "G:\\Subdir testing\\") #dstDir
gd.addStringField("File name contains: ", "") #nameContains
gd.addCheckbox("Preserve directory structure?", True) #keepDirs
gd.addCheckbox("Run in headless mode?", True) #anneBoleyn
gd.addCheckbox("Overwrite existing output files?", True)
gd.showDialog()
if gd.wasCanceled():
return
srcDir = gd.getNextString()
dstDir = gd.getNextString()
nameContains = gd.getNextString()
keepDirectories = gd.getNextBoolean()
anneBoleyn = gd.getNextBoolean()
overOut = gd.getNextBoolean()
IJ.run("Input/Output...", "jpeg=100")
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Check for file extension
if not filename.endswith(".nd2"):
continue
# Check for file name pattern
if nameContains not in filename:
continue
process(srcDir, dstDir, nameContains, root, filename, keepDirectories, anneBoleyn, overOut)
def dialog(imp2, labelColorBarImp):
gd = GenericDialogPlus("ROI labeller")
categories=11
#placeholder slider variables so the class can be initiated
slider1=0
slider2=0
slider3=0
slider4=0
test=previewLabelerAndListeners(imp2, slider1,slider2,slider3,slider4, gd)
for i in range(1,categories):
gd.addButton("label "+str(i), test)
gd.addImage(labelColorBarImp)
#imp7.close() - causes an error as image needed for the dialog
gd.addButton("Set top",test)
gd.addButton("Whole stack",test)
gd.addButton("Set bottom", test)
gd.addSlider("Top",1, imp2.getStackSize(), 1)
gd.addSlider("Bottom",1, imp2.getStackSize(),imp2.getStackSize())
gd.addSlider("Minimum ROI size", 0, 9999, 0, 1)
gd.addSlider("Maximum ROI size", 1, 10000, 10000, 1)
slider1=gd.getSliders().get(0)
slider2=gd.getSliders().get(1)
test.slider1=slider1
test.slider2=slider2
slider3=gd.getSliders().get(2)
slider4=gd.getSliders().get(3)
test.slider3=slider3
test.slider4=slider4
slider1.addAdjustmentListener(test)
slider2.addAdjustmentListener(test)
slider3.addAdjustmentListener(test)
slider4.addAdjustmentListener(test)
gd.addChoice("Apply labeling to:", ["(Sub)stack", "Slice"], "(Sub)stack")
gd.setLayout(GridLayout(0,2))
gd.setModal(False)
buttons=gd.getButtons()
gd.showDialog()
while ((not gd.wasCanceled()) and not (gd.wasOKed())):
Thread.sleep(50)
return test
def DialogGenerate(imageBaseDir, summary):
dpi = 300
defaultAspectRatio = 1.33
defaultTileWidth = 15
defaultOriginalWidth = 150
defaultOriginalHeight = 113
defaultTileHeight = round(defaultTileWidth / defaultAspectRatio)
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Prepare Image database")
gd.addDirectoryField("Select base directory containing images",
imageBaseDir, 20)
gd.addMessage(summary)
gd.addNumericField("Aspect ratio", defaultAspectRatio, 2)
gd.addNumericField("Original width", defaultOriginalWidth, 0)
gd.addNumericField("Original height", defaultOriginalHeight, 0)
gd.addNumericField("minimal tile width", defaultTileWidth, 0)
gd.addNumericField("maximal tile width", defaultTileWidth, 0)
gd.addNumericField("minimal tile height", defaultTileHeight, 0)
gd.addNumericField("maximal tile height", defaultTileHeight, 0)
fields = gd.getNumericFields()
aspRatio = fields.get(0)
minw = fields.get(3)
maxw = fields.get(4)
minh = fields.get(5)
maxh = fields.get(6)
# resolution and size listener
textListener = RatioToDim(aspRatio, minw, maxw, minh, maxh)
aspRatio.addTextListener(textListener)
minw.addTextListener(textListener)
maxw.addTextListener(textListener)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
imageBaseDir = gd.getNextString()
aspectRatio = gd.getNextNumber()
majorWidth = gd.getNextNumber()
majorHeight = gd.getNextNumber()
mintilewidth = gd.getNextNumber()
maxtilewidth = gd.getNextNumber()
return int(mintilewidth), int(maxtilewidth), imageBaseDir, float(
aspectRatio), int(majorWidth), int(majorHeight)
def optionsDialog():
dialog = GenericDialogPlus("Automated Weka Percentages")
dialog.addDirectoryField("Image Directory", "")
dialog.addFileField("Training Model", "")
dialog.addStringField("Output Subdirectory", "output", 20)
dialog.addStringField("Probability Threshold", "0.75", 20)
dialog.showDialog()
# Check if canceled
if dialog.wasCanceled(): return None
textVals = [x.text for x in dialog.getStringFields()]
#boolVals = [x.getState() for x in dialog.getCheckboxes()]
return textVals
def optionsDialog():
dialog = GenericDialogPlus("Fluorescent Cell Counting")
dialog.addDirectoryField("Image Directory", "")
dialog.addFileField("Training Model", "")
dialog.addStringField("Output Subdirectory", "output", 20)
dialog.addStringField("Probability Threshold", "0.67", 20)
dialog.addStringField("Minimum Pixel Size", "2", 20)
dialog.showDialog()
# Check if canceled
if dialog.wasCanceled(): return None
textVals = [x.text for x in dialog.getStringFields()]
return textVals
def openMainDialogBox():
#od = OpenDialog("Selectionner un fichier")
#folder = od.getDirectory()
#IJ.log(folder);
#filename = od.getFileName() #intérêt de récupérer le nom du fichier -> récupérer l'extension
#extension = od.getFileName().split('.').pop() #Array.pop(). Pratique pour faire une fonction getExtension()
#IJ.log(folder+filename)
# Create an instance of GenericDialogPlus
mainDialogBox = GenericDialogPlus("Restack Tiff deconvolved images from Huygens")
mainDialogBox.addMessage("Ne fonctionnera correctement que si les noms des fichiers images de sortie de Huygens ont ete laisses intacts. Ne pas les modifier.")
#mainDialogBox.addButton("Ouvrir image", imageSelectionListener())
mainDialogBox.addMessage("------------------------------------------")
mainDialogBox.addDirectoryField("Choisir un repertoire-cible", "None")
mainDialogBox.addMessage("------------------------------------------")
mainDialogBox.addDirectoryField("Choisir un repertoire pour deposer les piles d'images", "None")
mainDialogBox.addMessage("------------------------------------------")
#Select File Type
choixType = ["1 fichier par canal (NOM_FICHIER_chXX.tif)", "1 fichier par canal + temps (NOM_FICHIER_tXX_chXX.tif)", "1 fichier par canal et par profondeur (NOM_FICHIER_zXX_chXX.tif)", "1 fichier par canal et par profondeur + temps (NOM_FICHIER_tXX_zXX_chXX.tif)"]
selectionType = choixType[0]
mainDialogBox.addChoice("Selectionner type de fichiers",choixType,selectionType)
mainDialogBox.addMessage("------------------------------------------")
choixDisplayMode = ["Color", "Greyscale", "Composite"]
selectionDisplayModeDefaut = choixDisplayMode[0]
mainDialogBox.addChoice("Color Display Mode",choixDisplayMode,selectionDisplayModeDefaut)
mainDialogBox.addMessage("------------------------------------------")
#Affichage de la boîte de dialogue
mainDialogBox.showDialog();
#Récupération choix
folder = mainDialogBox.getNextString()
save_folder = mainDialogBox.getNextString()
vecteurChoix=mainDialogBox.getChoices()
selectionTypeFichier = vecteurChoix[0]
valeurSelectionTypeFichier = str(selectionTypeFichier.getSelectedItem())
selectionDisplayMode = vecteurChoix[1]
valeurSelectionDisplayMode = str(selectionDisplayMode.getSelectedItem())
if mainDialogBox.wasCanceled() == True:
print("Canceled, Values set to None")
folder = None
save_folder = None
valeurSelectionTypeFichier = None
valeurSelectionDisplayMode = None
return folder, save_folder, valeurSelectionTypeFichier, valeurSelectionDisplayMode
def optionsDialog():
dialog = GenericDialogPlus("Cilia Sizes")
dialog.addDirectoryField("Image Directory", DEFAULT_DIR)
dialog.addFileField("Training Model", DEFAULT_TRAIN)
dialog.addStringField("Output Subdirectory", "output", 20)
dialog.addStringField("Confocal Channel", "1", 20)
dialog.addStringField("Probability Threshold", "0.67", 20)
dialog.addStringField("Minimum Pixel Size", "2", 20)
dialog.showDialog()
# Check if canceled
if dialog.wasCanceled(): return None
textVals = [x.text for x in dialog.getStringFields()]
return textVals
def DialogAnalyze():
dpi = 300
defaultAspectRatio = 1.41
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Prepare Image database")
gd.addDirectoryField("Select base directory containing images", "", 20)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
imageBaseDir = gd.getNextString()
return imageBaseDir
def DialogAnalyze():
dpi = 300
defaultAspectRatio = 1.41
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Prepare Image database")
gd.addDirectoryField("Select base directory containing images", "", 20)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
imageBaseDir = gd.getNextString()
return imageBaseDir
def DialogGenerate(imageBaseDir, summary):
dpi = 300
defaultAspectRatio = 1.33
defaultTileWidth = 15
defaultOriginalWidth = 150
defaultOriginalHeight = 113
defaultTileHeight = round(defaultTileWidth/defaultAspectRatio)
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Prepare Image database")
gd.addDirectoryField("Select base directory containing images", imageBaseDir, 20)
gd.addMessage(summary)
gd.addNumericField("Aspect ratio", defaultAspectRatio, 2)
gd.addNumericField("Original width", defaultOriginalWidth, 0)
gd.addNumericField("Original height", defaultOriginalHeight, 0)
gd.addNumericField("minimal tile width", defaultTileWidth, 0)
gd.addNumericField("maximal tile width", defaultTileWidth, 0)
gd.addNumericField("minimal tile height", defaultTileHeight, 0)
gd.addNumericField("maximal tile height", defaultTileHeight, 0)
fields = gd.getNumericFields()
aspRatio = fields.get(0)
minw = fields.get(3)
maxw = fields.get(4)
minh = fields.get(5)
maxh = fields.get(6)
# resolution and size listener
textListener = RatioToDim(aspRatio, minw, maxw, minh, maxh)
aspRatio.addTextListener(textListener)
minw.addTextListener(textListener)
maxw.addTextListener(textListener)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
imageBaseDir = gd.getNextString()
aspectRatio = gd.getNextNumber()
majorWidth = gd.getNextNumber()
majorHeight = gd.getNextNumber()
mintilewidth = gd.getNextNumber()
maxtilewidth = gd.getNextNumber()
return int(mintilewidth), int(maxtilewidth), imageBaseDir, float(aspectRatio), int(majorWidth), int(majorHeight)
def get_parameters(p):
gd = GenericDialogPlus("Please enter parameters")
for k in p['expose_to_gui']['value']:
if p[k]['type'] == 'boolean':
gd.addCheckbox(k, p[k]['value'])
elif p[k]['type'] == 'folder':
gd.addDirectoryField(k, p[k]['value'], 100)
elif p[k]['type'] == 'file':
gd.addFileField(k, p[k]['value'], 100)
elif p[k]['type'] == 'string':
if p[k]['choices']:
gd.addChoice(k, p[k]['choices'], p[k]['value'])
else:
gd.addStringField(k, p[k]['value'])
elif p[k]['type'] == 'int':
if p[k]['choices']:
gd.addChoice(k, p[k]['choices'], p[k]['value'])
else:
gd.addNumericField(k, p[k]['value'], 0)
elif p[k]['type'] == 'float':
gd.addNumericField(k, p[k]['value'], 2)
gd.showDialog()
if gd.wasCanceled():
return
for k in p['expose_to_gui']['value']:
if p[k]['type'] == 'boolean':
p[k]['value'] = gd.getNextBoolean()
elif p[k]['type'] == 'folder' or p[k]['type'] == 'file':
p[k]['value'] = gd.getNextString()
elif p[k]['type'] == 'string':
if p[k]['choices']:
p[k]['value'] = gd.getNextChoice()
else:
p[k]['value'] = gd.getNextString()
elif p[k]['type'] == 'int':
if p[k]['choices']:
p[k]['value'] = int(gd.getNextChoice())
else:
p[k]['value'] = int(gd.getNextNumber())
elif p[k]['type'] == 'float':
p[k]['value'] = gd.getNextNumber()
return p
def SaveDialog(imp):
dpi = 300
# a4 width in inches
defaultWidth = 11.69
defaultHeight = defaultWidth / ratio
defaultAspectRatio = 1.41
if imp:
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Saving options")
gd.addNumericField("resolution (dpi)", dpi, 0)
gd.addNumericField("width (pixels)", defaultWidth * dpi, 0)
gd.addNumericField("height (pixels)", defaultHeight * dpi, 0)
gd.addNumericField("width (inches)", defaultWidth, 2)
gd.addNumericField("height (inches)", defaultHeight, 2)
gd.addFileField("Select Originals database", "", 20)
fields = gd.getNumericFields()
resField = fields.get(0)
widthPixels = fields.get(1)
heightPixels = fields.get(2)
widthInches = fields.get(3)
heightInches = fields.get(4)
# resolution and size listener
textListener = ResolutionListener(resField, widthPixels, heightPixels,
widthInches, heightInches)
resField.addTextListener(textListener)
widthInches.addTextListener(textListener)
heightInches.addTextListener(textListener)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
newres = gd.getNextNumber()
newwidth = gd.getNextNumber()
newheight = gd.getNextNumber()
originalspath = gd.getNextString()
return int(newwidth), int(newheight), newres, originalspath
else:
IJ.showMessage("You should have at least one image open.")
def SaveDialog(imp):
dpi = 300
# a4 width in inches
defaultWidth = 11.69
defaultHeight = defaultWidth/ratio
defaultAspectRatio = 1.41
if imp:
gd = GenericDialogPlus("Cover Maker")
gd.addMessage("Saving options")
gd.addNumericField("resolution (dpi)", dpi, 0)
gd.addNumericField("width (pixels)", defaultWidth*dpi, 0)
gd.addNumericField("height (pixels)", defaultHeight*dpi, 0)
gd.addNumericField("width (inches)", defaultWidth, 2)
gd.addNumericField("height (inches)", defaultHeight, 2)
gd.addFileField("Select Originals database", "", 20)
fields = gd.getNumericFields()
resField = fields.get(0)
widthPixels = fields.get(1)
heightPixels = fields.get(2)
widthInches = fields.get(3)
heightInches = fields.get(4)
# resolution and size listener
textListener = ResolutionListener(resField, widthPixels, heightPixels, widthInches, heightInches)
resField.addTextListener(textListener)
widthInches.addTextListener(textListener)
heightInches.addTextListener(textListener)
gd.showDialog()
if gd.wasCanceled():
print "User canceled dialog!"
return
newres = gd.getNextNumber()
newwidth = gd.getNextNumber()
newheight = gd.getNextNumber()
originalspath = gd.getNextString()
return int(newwidth), int(newheight), newres, originalspath
else:
IJ.showMessage( "You should have at least one image open." )
def getSettings(self):
gd = GenericDialogPlus("Settings")
gd.addNumericField("Distance in pixel", 600, 0)
gd.addNumericField("Distance in cm", 2.54, 2)
gd.addNumericField("Min. size (cm^2)", 0.5, 2)
gd.addDirectoryField("Directory", IJ.getDirectory("home"))
gd.addStringField("File extension", "*.jpg", 8)
gd.showDialog()
if gd.wasCanceled():
sys.exit()
else:
distPixel = gd.getNextNumber()
distCm = gd.getNextNumber()
minSize = gd.getNextNumber() * (distPixel / distCm) ** 2
imageDir = gd.getNextString()
ext = gd.getNextString()
return (distPixel, distCm, minSize, imageDir, ext)
def make_dialog():
parameters = {}
gd = GenericDialogPlus("Grid Stitch SDC Data")
gd.addMessage( "Warning!\n"\
"In order to display a fused image upon completion of stitching\n"\
"please disable Fiji's ImageJ2 options. When enabled an ImageJ\n"\
"exception will be displayed upon completion. This exception can\n"
"be safely ignored.")
gd.addMessage( "Information\n"\
"This plugin is a wrapper around the Fiji 'Grid Stitching' plugin.\n"\
"It allows tiles generated in SlideBook to be directly stitched by\n"\
"by first writing out the individual tiles, executing the 'Grid Stitching'\n"\
"plugin and writing the fused image to disk.")
gd.addMessage("")
gd.addNumericField("grid_size_x", 3, 0)
gd.addNumericField("grid_size_y", 3, 0)
gd.addCheckbox("Select channel",False)
gd.addNumericField("", 0, 0)
gd.addCheckbox("Are the Z slices separate files?",False)
gd.addDirectoryField("directory", "", 50)
gd.showDialog()
if (gd.wasCanceled()): return
parameters['gridX'] = int(math.ceil(gd.getNextNumber()))
parameters['gridY'] = int(math.ceil(gd.getNextNumber()))
parameters['select_channel'] = gd.getNextBoolean()
parameters['channel'] = None
if parameters['select_channel']:
parameters['channel'] = int(gd.getNextNumber())
parameters['separate_z'] = gd.getNextBoolean()
directory = str(gd.getNextString())
if directory is None:
# User canceled the dialog
return None
else:
directory = os.path.abspath(directory)
parameters['directory'] = directory + os.path.sep
return parameters
def get_parameters(p):
gd = GenericDialogPlus("Please enter parameters")
for k in p['expose_to_gui']['value']:
if p[k]['type'] == 'folder':
gd.addDirectoryField(k, p[k]['value'], 100)
if p[k]['type'] == 'file':
gd.addFileField(k, p[k]['value'], 100)
elif p[k]['type'] == 'string':
if p[k]['choices']:
gd.addChoice(k, p[k]['choices'], p[k]['value'])
else:
gd.addStringField(k, p[k]['value'], 50)
elif p[k]['type'] == 'int':
if p[k]['choices']:
gd.addChoice(k, p[k]['choices'], p[k]['value'])
else:
gd.addNumericField(k, p[k]['value'], 0)
elif p[k]['type'] == 'float':
gd.addNumericField(k, p[k]['value'], 2)
gd.showDialog()
if gd.wasCanceled():
return(0)
for k in p['expose_to_gui']['value']:
if p[k]['type'] == 'folder' or p[k]['type'] == 'file':
p[k]['value'] = gd.getNextString()
elif p[k]['type'] == 'string':
if p[k]['choices']:
p[k]['value'] = gd.getNextChoice()
else:
p[k]['value'] = gd.getNextString()
elif p[k]['type'] == 'int':
if p[k]['choices']:
p[k]['value'] = int(gd.getNextChoice())
else:
p[k]['value'] = int(gd.getNextNumber())
elif p[k]['type'] == 'float':
p[k]['value'] = gd.getNextNumber()
return(p)
def optionsDialog():
dialog = GenericDialogPlus("Automated Size Analysis")
dialog.addDirectoryField("Image Directory", "")
dialog.addStringField("Output Subdirectory", "output", 20)
dialog.addStringField("Minimum Pixel Size", "50000", 20)
dialog.addStringField("Minimum Roundness", "0.4", 20)
dialog.addStringField("Gaussian Blur", "6", 20)
dialog.addStringField("Rotation Steps", "3", 20)
dialog.addStringField("Thresholds", ",".join(THRESHOLDS), 20)
dialog.addCheckbox("Rotate Images", True)
dialog.addCheckbox("Multiple Thresholds", True)
dialog.showDialog()
# Check if canceled
if dialog.wasCanceled(): return None
textVals = [x.text for x in dialog.getStringFields()]
boolVals = [x.getState() for x in dialog.getCheckboxes()]
return textVals + boolVals
def selectionDialog(categories,labelColorBarImp):
gd = GenericDialogPlus("ROI labeller -image picking")
imps = WM.getImageTitles()
nonimages=WM.getNonImageTitles()
gd.addChoice("Image to quantify", imps, imps[0])
try:
gd.addChoice("FRETENTATOR results table", nonimages, nonimages[0])
fail=0
except:
gd.addMessage("No results table open")
fail=1
gd.addImage(labelColorBarImp)
for i in range(categories):
gd.addStringField("Label "+str(i) +" name:", "Label "+str(i))
gd.addChoice("Quantify an open image or add labels to open results table?", ["Image", "Results table"], "Results table")
#quantImp= IJ.getImage(gd.getNextChoice())
gd.setModal(False)
gd.showDialog()
while ((not gd.wasCanceled()) and not (gd.wasOKed())):
Thread.sleep(50)
names=dict()
for i in range(categories):
names[i]=str(gd.getNextString())
imageName=gd.getNextChoice()
if fail==0:
resultsName=gd.getNextChoice()
imageOrTable=gd.getNextChoice()
else:
imageOrTable="Image"
resultsName=0
return names, imageName, resultsName, imageOrTable
outsuffixf = gd.getStringFields().get(3)
gd.addStringField("(Further) Registration Params", "", 50)
regparamf = gd.getStringFields().get(4)
gd.addStringField("Additional Arguments to munger.pl", "", 50)
regrootf.addTextListener(RegRootListener())
imgdirf.addTextListener(ImageDirListener())
outsuffixf.addTextListener(OuputSuffixListener())
choicef.addItemListener(RegParamListener())
# used for errors etc
gd.addMessage(
"Start by choosing a registration directory or images directory!")
statusf = gd.getMessage()
gd.showDialog()
if gd.wasCanceled():
sys.exit("User cancelled!")
# Process Dialog Choices
rootDir = gd.getNextString()
os.chdir(rootDir)
refBrain = gd.getNextString()
image = gd.getNextString()
image = relpath(image, rootDir)
print refBrain
refBrain = relpath(refBrain, rootDir)
print refBrain
affine = gd.getNextBoolean()
ch01 = gd.getNextBoolean()
warp = gd.getNextBoolean()
ch02 = gd.getNextBoolean()
def previewDialog(imp):
gd = GenericDialogPlus("Nuclear segmentation and quantification v1.01")
#create a list of the channels in the provided imagePlus
types = []
for i in xrange(1, imp.getNChannels() + 1):
types.append(str(i))
#user can pick which channel to base the segmentation on
gd.addChoice("Channel number to use for segmentation", types, types[0])
gd.addChoice("Channel to quantify", types, types[0])
methods = [
"Otsu", "Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData",
"Li", "MaxEntropy", "Mean", "MinError", "Minimum", "Moments",
"Percentile", "RenyiEntropy", "Shanbhag", "Triangle", "Yen"
]
gd.addChoice("Autosegmentation method", methods, methods[0])
intensities = ["254", "4094", "65534"]
gd.addChoice("Max Intensity", intensities, intensities[-1])
gd.addSlider("Small DoG sigma", 0.5, 10, 1, 0.1)
gd.addSlider("Large DoG sigma", 0.5, 20, 5, 0.1)
gd.addCheckbox("TopHat background subtraction? (Slower, but better) ",
True)
gd.addSlider("TopHat sigma", 5, 20, 8, 0.1)
gd.setModal(False)
gd.addCheckbox("Manually set threshold? ", False)
gd.addSlider("Manual threshold", 10, 65534, 2000, 1)
gd.hideCancelButton()
gd.showDialog()
cal = imp.getCalibration()
pixelAspect = (cal.pixelDepth / cal.pixelWidth)
originalTitle = imp1.getTitle()
choices = gd.getChoices()
print choices
sliders = gd.getSliders()
checkboxes = gd.getCheckboxes()
segmentChannel = int(choices.get(0).getSelectedItem())
quantChannel = int(choices.get(1).getSelectedItem())
thresholdMethod = choices.get(2).getSelectedItem()
maxIntensity = int(choices.get(3).getSelectedItem())
gaussianSigma = sliders.get(0).getValue() / 10.0
largeDoGSigma = gd.sliders.get(1).getValue() / 10.0
topHat = gd.checkboxes.get(0).getState()
topHatSigma = gd.sliders.get(2).getValue() / 10.0
manualSegment = gd.checkboxes.get(1).getState()
manualThreshold = gd.sliders.get(3).getValue()
segmentChannelOld = segmentChannel
thresholdMethodOld = thresholdMethod
maxIntensityOld = maxIntensity
gaussianSigmaOld = gaussianSigma
largeDoGSigmaOld = largeDoGSigma
topHatOld = topHat
topHatSigmaOld = topHatSigma
manualSegmentOld = manualSegment
manualThresholdOld = manualThreshold
clij2.clear()
segmentImp = extractChannel(imp1, segmentChannel, 0)
try:
gfx1 = clij2.push(segmentImp)
gfx2 = clij2.create(gfx1)
gfx3 = clij2.create(gfx1)
gfx4 = clij2.create(gfx1)
gfx5 = clij2.create(gfx1)
gfx7 = clij2.create([imp.getWidth(), imp.getHeight()])
except:
try:
Thread.sleep(500)
IJ.log(
"Succeeded to sending to graphics card on the second time...")
gfx1 = clij2.push(segmentImp)
gfx2 = clij2.create(gfx1)
gfx3 = clij2.create(gfx1)
gfx4 = clij2.create(gfx1)
gfx5 = clij2.create(gfx1)
gfx7 = clij2.create([imp.getWidth(), imp.getHeight()])
except:
errorDialog(
"""Could not send image to graphics card, it may be too large!
Easy solutions: Try processing as 8-bit, cropping or scaling the image, or
select a different CLIJ2 GPU.
This issue is often intermittent, so trying again may also work!
See the "Big Images on x graphics cards' notes at:
https://clij2.github.io/clij2-docs/troubleshooting for more solutions
""" + str(clij2.reportMemory()))
gfx1, gfx2, gfx3, gfx4, gfx5 = segment(gfx1, gfx2, gfx3, gfx4, gfx5,
gaussianSigma, thresholdMethod,
maxIntensity, largeDoGSigma,
pixelAspect, originalTitle, topHat,
topHatSigma, manualSegment,
manualThreshold)
clij2.maximumZProjection(gfx5, gfx7)
labelPrevImp = clij2.pull(gfx7)
IJ.setMinAndMax(labelPrevImp, 0, clij2.getMaximumOfAllPixels(gfx7))
labelPrevImp.setTitle("Preview segmentation")
labelPrevImp.show()
IJ.run("glasbey_inverted")
while ((not gd.wasCanceled()) and not (gd.wasOKed())):
segmentChannel = int(choices.get(0).getSelectedItem())
quantChannel = int(choices.get(1).getSelectedItem())
thresholdMethod = choices.get(2).getSelectedItem()
maxIntensity = int(choices.get(3).getSelectedItem())
gaussianSigma = sliders.get(0).getValue() / 10.0
largeDoGSigma = gd.sliders.get(1).getValue() / 10.0
topHat = gd.checkboxes.get(0).getState()
topHatSigma = gd.sliders.get(2).getValue() / 10.0
manualSegment = gd.checkboxes.get(1).getState()
manualThreshold = gd.sliders.get(3).getValue()
if (segmentChannelOld != segmentChannel
or thresholdMethodOld != thresholdMethod
or maxIntensityOld != maxIntensity
or gaussianSigmaOld != gaussianSigma
or largeDoGSigmaOld != largeDoGSigma or topHatOld != topHat
or topHatSigmaOld != topHatSigma
or manualSegmentOld != manualSegment
or manualThresholdOld != manualThreshold):
if segmentChannelOld != segmentChannel:
clij2.clear()
segmentImp = extractChannel(imp1, segmentChannel, 0)
gfx1 = clij2.push(segmentImp)
gfx2 = clij2.create(gfx1)
gfx3 = clij2.create(gfx1)
gfx4 = clij2.create(gfx1)
gfx5 = clij2.create(gfx1)
gfx7 = clij2.create([imp.getWidth(), imp.getHeight()])
gfx1, gfx2, gfx3, gfx4, gfx5 = segment(
gfx1, gfx2, gfx3, gfx4, gfx5, gaussianSigma, thresholdMethod,
maxIntensity, largeDoGSigma, pixelAspect, originalTitle,
topHat, topHatSigma, manualSegment, manualThreshold)
clij2.maximumZProjection(gfx5, gfx7)
labelPrevImp.close()
labelPrevImp = clij2.pull(gfx7)
IJ.setMinAndMax(labelPrevImp, 0, clij2.getMaximumOfAllPixels(gfx7))
labelPrevImp.setTitle("Preview segmentation")
labelPrevImp.show()
IJ.run("glasbey_inverted")
segmentChannelOld = segmentChannel
thresholdMethodOld = thresholdMethod
maxIntensityOld = maxIntensity
gaussianSigmaOld = gaussianSigma
largeDoGSigmaOld = largeDoGSigma
topHatOld = topHat
topHatSigmaOld = topHatSigma
manualSegmentOld = manualSegment
manualThresholdOld = manualThreshold
Thread.sleep(200)
labelPrevImp.close()
return segmentChannel, quantChannel, thresholdMethod, maxIntensity, gaussianSigma, largeDoGSigma, topHat, topHatSigma, manualSegment, manualThreshold
def previewDialog(imp):
gd = GenericDialogPlus("FRETENATOR")
#create a list of the channels in the provided imagePlus
types = []
for i in xrange(1, imp.getNChannels()+1):
types.append(str(i))
gd.addMessage("""Rowe, J. H, Rizza, A., Jones A. M. (2022) Quantifying phytohormones
in vivo with FRET biosensors and the FRETENATOR analysis toolset
Methods in Molecular Biology
Rowe, JH., Grangé-Guermente, M., Exposito-Rodriguez, M.,Wimalasekera, R., Lenz, M.,
Shetty, K., Cutler, S., Jones, AM., Next-generation ABACUS biosensors reveal cellular
ABA dynamics driving root growth at low aerial humidity
""")
#user can pick which channel to base the segmentation on
if len(types)>2:
gd.addChoice("Channel number to use for segmentation", types, types[2])
gd.addChoice("Channel number to use for donor", types, types[0])
gd.addChoice("Channel number to use for acceptor (FRET)", types, types[1])
gd.addChoice("Channel number to use for acceptor", types, types[2])
#print('YAY')
else:
gd.addChoice("Channel number to use for segmentation", types, types[-1])
gd.addChoice("Channel number to use for donor", types, types[0])
gd.addChoice("Channel number to use for acceptor (FRET)", types, types[-2])
gd.addChoice("Channel number to use for acceptor", types, types[-1])
methods=["Otsu","Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData", "Li", "MaxEntropy", "Mean", "MinError", "Minimum", "Moments", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle", "Yen"]
gd.addChoice("Autosegmentation method", methods, methods[0])
intensities=["254", "4094", "65534"]
gd.addChoice("Max Intensity", intensities, intensities[-1])
gd.addSlider("Small DoG sigma", 0.5, 10, 0.8, 0.1)
gd.addSlider("Large DoG sigma", 0.5, 20, 4 ,0.1)
gd.addCheckbox("TopHat background subtraction? (Slower, but better) ", False)
gd.addSlider("TopHat sigma", 5, 20, 8 ,0.1)
gd.setModal(False)
gd.addCheckbox("Manually set threshold? ", False)
gd.addSlider("Manual threshold", 10, 65534, 2000, 1)
dilationOptions=["0", "1", "2","3", "4", "5", "6"]
gd.addChoice("Dilation?", dilationOptions, "0")
gd.addCheckbox("Size exclusion of ROI? ", False)
gd.addSlider("Minimum ROI size", 0, 9999, 20, 1)
gd.addSlider("Maximum ROI size", 1, 10000, 10000, 1)
gd.addCheckbox("Create nearest point projection with outlines (SLOW)? ", True)
gd.addCheckbox("Watershed object splitting? ", True)
gd.showDialog()
cal = imp.getCalibration()
pixelAspect=(cal.pixelDepth/cal.pixelWidth)
originalTitle=imp1.getTitle()
choices=gd.getChoices()
sliders=gd.getSliders()
checkboxes=gd.getCheckboxes()
segmentChannel=int(choices.get(0).getSelectedItem())
donorChannel=int(choices.get(1).getSelectedItem())
acceptorChannel=int(choices.get(2).getSelectedItem())
acceptorChannel2=int(choices.get(3).getSelectedItem())
thresholdMethod=choices.get(4).getSelectedItem()
maxIntensity=int(choices.get(5).getSelectedItem())
gaussianSigma=sliders.get(0).getValue()/10.0
largeDoGSigma = gd.sliders.get(1).getValue()/10.0
topHat=gd.checkboxes.get(0).getState()
topHatSigma=gd.sliders.get(2).getValue()/10.0
manualSegment = gd.checkboxes.get(1).getState()
manualThreshold=gd.sliders.get(3).getValue()
dilation=int(choices.get(6).getSelectedItem())
sizeExclude=gd.checkboxes.get(2).getState()
minSize = gd.sliders.get(4).getValue()
maxSize = gd.sliders.get(5).getValue()
watershed = gd.checkboxes.get(4).getState()
#print dir(gd.sliders.get(5))
#print maxSize
segmentChannelOld=segmentChannel
thresholdMethodOld=thresholdMethod
maxIntensityOld=maxIntensity
gaussianSigmaOld=gaussianSigma
largeDoGSigmaOld= largeDoGSigma
topHatOld=topHat
topHatSigmaOld=topHatSigma
manualSegmentOld= manualSegment
manualThresholdOld=manualThreshold
dilationOld=dilation
sizeExcludeOld=sizeExclude
minSizeOld=minSize
maxSizeOld=maxSize
watershedOld=watershed
clij2.clear()
segmentImp=extractChannel(imp1, segmentChannel, 0)
try:
gfx1=clij2.push(segmentImp)
gfx2=clij2.create(gfx1)
gfx3=clij2.create(gfx1)
gfx4=clij2.create(gfx1)
gfx5=clij2.create(gfx1)
gfx7=clij2.create([imp.getWidth(), imp.getHeight()])
except:
try:
Thread.sleep(500)
print("Succeeded to sending to graphics card on the second time...")
gfx1=clij2.push(segmentImp)
gfx2=clij2.create(gfx1)
gfx3=clij2.create(gfx1)
gfx4=clij2.create(gfx1)
gfx5=clij2.create(gfx1)
gfx7=clij2.create([imp.getWidth(), imp.getHeight()])
except:
errorDialog("""Could not send image to graphics card, it may be too large!
Easy solutions: Try processing as 8-bit, cropping or scaling the image, or
select a different CLIJ2 GPU.
This issue is often intermittent, so trying again may also work!
See the "Big Images on x graphics cards' notes at:
https://clij2.github.io/clij2-docs/troubleshooting for more solutions
""" + str(clij2.reportMemory()) )
gfx1,gfx2,gfx3,gfx4,gfx5 = segment(gfx1,gfx2,gfx3,gfx4,gfx5, gaussianSigma, thresholdMethod,maxIntensity, largeDoGSigma, pixelAspect, originalTitle, topHat, topHatSigma , manualSegment, manualThreshold, dilation,sizeExclude, minSize, maxSize, watershed)
clij2.maximumZProjection(gfx5, gfx7)
labelPrevImp= clij2.pull(gfx7)
IJ.setMinAndMax(labelPrevImp, 0,clij2.getMaximumOfAllPixels(gfx7))
labelPrevImp.setTitle("Preview segmentation")
labelPrevImp.show()
IJ.run("glasbey_inverted")
while ((not gd.wasCanceled()) and not (gd.wasOKed())):
segmentChannel=int(choices.get(0).getSelectedItem())
donorChannel=int(choices.get(1).getSelectedItem())
acceptorChannel=int(choices.get(2).getSelectedItem())
acceptorChannel2=int(choices.get(3).getSelectedItem())
thresholdMethod=choices.get(4).getSelectedItem()
maxIntensity=int(choices.get(5).getSelectedItem())
gaussianSigma=sliders.get(0).getValue()/10.0
largeDoGSigma = gd.sliders.get(1).getValue()/10.0
topHat=gd.checkboxes.get(0).getState()
topHatSigma=gd.sliders.get(2).getValue()/10.0
manualSegment = gd.checkboxes.get(1).getState()
manualThreshold = gd.sliders.get(3).getValue()
dilation=int(choices.get(6).getSelectedItem())
sizeExclude=gd.checkboxes.get(2).getState()
minSize = gd.sliders.get(4).getValue()
maxSize = gd.sliders.get(5).getValue()
watershed = gd.checkboxes.get(4).getState()
if (segmentChannelOld !=segmentChannel or
thresholdMethodOld !=thresholdMethod or
maxIntensityOld !=maxIntensity or
gaussianSigmaOld !=gaussianSigma or
largeDoGSigmaOld != largeDoGSigma or
topHatOld !=topHat or
topHatSigmaOld !=topHatSigma or
manualSegmentOld != manualSegment or
manualThresholdOld !=manualThreshold or
dilation != dilationOld or
sizeExcludeOld!=sizeExclude or
minSizeOld!=minSize or
maxSizeOld!=maxSize or
watershedOld!=watershed
):
if minSizeOld!=minSize:
if minSize>=maxSize:
maxSize=minSize+1
gd.sliders.get(5).setValue(maxSize)
if maxSizeOld!=maxSize:
if minSize>=maxSize:
minSize=maxSize-1
gd.sliders.get(4).setValue(minSize)
if segmentChannelOld!=segmentChannel:
clij2.clear()
segmentImp=extractChannel(imp1, segmentChannel, 0)
gfx1=clij2.push(segmentImp)
gfx2=clij2.create(gfx1)
gfx3=clij2.create(gfx1)
gfx4=clij2.create(gfx1)
gfx5=clij2.create(gfx1)
gfx7=clij2.create([imp.getWidth(), imp.getHeight()])
gfx1,gfx2,gfx3,gfx4,gfx5 = segment(gfx1,gfx2,gfx3,gfx4,gfx5, gaussianSigma, thresholdMethod,maxIntensity, largeDoGSigma, pixelAspect, originalTitle, topHat,topHatSigma, manualSegment, manualThreshold, dilation,sizeExclude, minSize, maxSize, watershed)
clij2.maximumZProjection(gfx5, gfx7)
labelPrevImp.close()
labelPrevImp= clij2.pull(gfx7)
IJ.setMinAndMax(labelPrevImp, 0,clij2.getMaximumOfAllPixels(gfx7))
labelPrevImp.setTitle("Preview segmentation")
labelPrevImp.show()
IJ.run("glasbey_inverted")
segmentChannelOld=segmentChannel
thresholdMethodOld=thresholdMethod
maxIntensityOld=maxIntensity
gaussianSigmaOld=gaussianSigma
largeDoGSigmaOld = largeDoGSigma
topHatOld=topHat
topHatSigmaOld=topHatSigma
manualSegmentOld= manualSegment
manualThresholdOld=manualThreshold
dilationOld=dilation
sizeExcludeOld=sizeExclude
minSizeOld=minSize
maxSizeOld=maxSize
watershedOld=watershed
Thread.sleep(200)
labelPrevImp.close()
makeNearProj = gd.checkboxes.get(3).getState()
return segmentChannel, donorChannel, acceptorChannel, acceptorChannel2, thresholdMethod, maxIntensity, gaussianSigma, largeDoGSigma, topHat, topHatSigma, manualSegment, manualThreshold, makeNearProj, dilation, sizeExclude, minSize, maxSize, watershed
gd.addStringField("Output folder suffix","",20)
outsuffixf = gd.getStringFields().get(3)
gd.addStringField("(Further) Registration Params","",50);
regparamf = gd.getStringFields().get(4)
gd.addStringField("Additional Arguments to munger.pl","",50);
regrootf.addTextListener(RegRootListener())
imgdirf.addTextListener(ImageDirListener())
outsuffixf.addTextListener(OuputSuffixListener())
choicef.addItemListener(RegParamListener())
# used for errors etc
gd.addMessage("Start by choosing a registration directory or images directory!")
statusf=gd.getMessage()
gd.showDialog()
if gd.wasCanceled():
sys.exit("User cancelled!")
# Process Dialog Choices
rootDir=gd.getNextString()
os.chdir(rootDir)
refBrain=gd.getNextString()
image=gd.getNextString()
image=relpath(image,rootDir)
print refBrain
refBrain=relpath(refBrain,rootDir)
print refBrain
affine=gd.getNextBoolean()
ch01=gd.getNextBoolean()
warp=gd.getNextBoolean()
ch02=gd.getNextBoolean()
doRigidTransformCheckbox = gdp.getCheckboxes().get(1); translationXSlider = gdp.getSliders().get(2); translationYSlider = gdp.getSliders().get(3); translationZSlider = gdp.getSliders().get(4); rotationXSlider = gdp.getSliders().get(5); rotationYSlider = gdp.getSliders().get(6); rotationZSlider = gdp.getSliders().get(7); doSpotDetectionCheckbox = gdp.getCheckboxes().get(2); toleranceSlider = gdp.getSliders().get(8); thresholdSlider = gdp.getSliders().get(9); # loop until user closed the dialog stillValid = False; while ((not gdp.wasCanceled()) and not (gdp.wasOKed())): # reserve memory for input and output images if (input is None): input = clijx.create([ (long)(imp.getWidth() * scaleX), (long)(imp.getHeight() * scaleY), (long)(imp.getNSlices() * scaleZ)], clijx.Float); temp1 = clijx.create(input); temp2 = clijx.create(input); dog = clijx.create(input); transformed = clijx.create(input); reslicedFromTop = clijx.create([input.getWidth(), input.getDepth(), input.getHeight()], input.getNativeType()); cylinderProjection = clijx.create([(long)(input.getWidth() * 0.75), input.getHeight(), 540], input.getNativeType());
