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 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 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 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 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 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 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 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 getImgRoiDir():
gui = GenericDialogPlus(
"Select directories to process images and ROI sets to apply")
default_dir = OpenDialog.getDefaultDirectory()
gui.addDirectoryField("Choose a iamge folder to be processed", default_dir)
gui.addDirectoryField("Choose a ROI set folder to apply", default_dir)
gui.showDialog()
if gui.wasOKed():
img_dir = gui.getNextString()
if not img_dir.endswith(os.sep):
img_dir = img_dir + os.sep
roi_dir = gui.getNextString()
if not roi_dir.endswith(os.sep):
roi_dir = roi_dir + os.sep
return img_dir, roi_dir
gd = GenericDialogPlus('CMTK Registration GUI')
# 0.1) Identify path to CMTK binaries
bindir = cmtkgui.install_dir()
print 'bindir is ' + bindir
# 0.1) Identify path to munger.pl script
#munger='/Users/jefferis/bin/munger.pl'
munger = cmtkgui.tool_path('munger')
print 'munger is ' + munger
gd.addHelp(
"http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui"
)
dirFieldWidth = 50
gdMargin = 130
gd.addDirectoryField("Registration Folder", None, dirFieldWidth)
regrootf = gd.getStringFields().get(0)
# reference brain
gd.addFileField("Reference Brain", "", dirFieldWidth)
# input directory/image
gd.addDirectoryOrFileField("Input Image or Image Directory", None,
dirFieldWidth)
imgdirf = gd.getStringFields().get(2)
gd.setInsets(10, gdMargin, 10)
gd.addMessage("Output folders:")
outputf = gd.getMessage()
# what to do: affine/warp/reformat
gd.setInsets(10, 200, 10)
gd.addCheckboxGroup(3, 2, ["affine", "01", "warp", "02", "reformat", "03"],
import csv
from ij.gui import Roi, PolygonRoi, GenericDialog, TextRoi, NonBlockingGenericDialog
import os
from fiji.util.gui import GenericDialogPlus
import re
gdp=GenericDialogPlus("File Derandomizer")
gdp.addFileField("'Key' path :", " ")
gdp.addFileField("Data file :", " ")
gdp.addDirectoryField("Derandomized path", "(optional)")
gdp.addDirectoryField("Processed Image Folder", " ")
gdp.addCheckbox("Derandomize Data File", True)
gdp.addCheckbox("Derandomize Image Folder", False)
gdp.showDialog()
if gdp.wasOKed():
key_path = gdp.getNextString().strip()
data_path = gdp.getNextString().strip()
deR_path = gdp.getNextString().strip()
pi_path= gdp.getNextString().strip()
ddf=gdp.getNextBoolean()
dif=gdp.getNextBoolean()
if deR_path == "(optional)":
deR_path = os.path.dirname(data_path)
else:
exit()
# function to return key for any value
def get_key(val):
for key, value in random.items():
file_def = default_values['file_def']
# Dumps values into a dictionary
json_object = json.dumps(default_values, indent=4)
dest = IJ.getDirectory("image")
os.chdir(dest)
json_selected = os.path.join(dest, json_selected)
json_selected = json_selected+'/'
# Writing to sample.json
with open(json_selected, "w") as outfile:
outfile.write(json_object)
# sets up a generic dialog box to start the script.
dest = IJ.getDirectory("image")
gdp = GenericDialogPlus("Transport Assay - "+version)
gdp.addDirectoryField("Image Folder:", dest, 40)
gdp.addStringField("Processed Image Folder:", ProFolder_def, 40)
gdp.addStringField("Transport Output:", Quant_def, 40)
gdp.addStringField("Mean_Max Output:", Quant_MM_def, 40)
gdp.addMessage("------------------------------------------------------------", italicFont)
gdp.addChoice("Transport Channel:", channels_available, tran_def)
gdp.addToSameRow()
gdp.addStringField("File Type: ", file_def, 5)
gdp.addChoice(" Golgi Channel:", channels_available, golgi_def)
gdp.addToSameRow()
gdp.addStringField("Processed File Extension: ", ext_def, 5)
gdp.addMessage(" ", italicFont)
gdp.addToSameRow()
gdp.addMessage(" ", italicFont)
gdp.addChoice(" Zoom: ", zoom, zoom_def)
gdp.addToSameRow()
from ij.gui import GenericDialog
from fiji.util.gui import GenericDialogPlus
import os, shutil
gdp = GenericDialogPlus("File Mover")
file_type = gdp.getNextString()
gdp.addStringField("File Extension ", '.tif', 5)
x = gdp.addDirectoryField("Source: ", " ")
gdp.addDirectoryField("Destination: ", " ")
gdp.showDialog()
if gdp.wasOKed():
file_type = gdp.getNextString().strip()
source_path = gdp.getNextString()
dest_path = gdp.getNextString()
print(file_type)
print("source " + source_path)
print("dest " + dest_path)
else:
exit()
moved = 'Moved Images'
path = os.path.join(dest_path, moved)
try:
dest = os.mkdir(path)
except OSError as error:
print("Error: Moved Images is already present")
exit()
def move():
for root, dirs, files in os.walk((os.path.normpath(source_path)),
delIp = cmIp
delIp.changes = False
delIp.close()
cmIp = WindowManager.getImage("CmStain-Closing")
IJ.run(cmIp,"Fill Holes", "stack")
cmIp.show()
IJ.run("Set Measurements...", "stack redirect=None decimal=3")
IJ.run(cmIp, "Analyze Particles...", "size={}-Infinity show=[Masks] exclude in_situ stack".format(cmMinSize))
cmMaskIp = cmIp.duplicate()
IJ.run(cmIp, "Analyze Particles...", "size={}-Infinity show=[Count Masks] exclude in_situ stack".format(cmMinSize))
cmMaskIp.show(), cmIp.show()
return cmIp, cmMaskIp
import re
preGd = GenericDialog("Output Folder")
preGd.addDirectoryField("Output folder", "")
preGd.showDialog()
outputFolder = preGd.getNextString()
os.chdir(outputFolder)
folderPath, formatString, groupBy, nucChannel, cmChannel, stitched, analyzeNucStack, brightfield, nucMethod, cmMethod, analyzeCmStack, rowNo, colNo, nucMinSize, cmMinSize =\
"", "", "", "DAPI", "GFP", False, True, False, "Otsu", "Triangle", True, 8, 7, 50, 500
__dict__ = globals()
try:
with open("savedSettings.json") as f:
thing = json.load(f)
for k, v in thing.iteritems():
__dict__[k] = v
print(thing)
except Exception as e: print(e)
gd = GenericDialog("Analysis parameters")
gd.addDirectoryField("Image folder location", folderPath )
## START!
gd = GenericDialogPlus('CMTK Registration GUI')
# 0.1) Identify path to CMTK binaries
bindir=cmtkgui.install_dir()
print 'bindir is ' + bindir
# 0.1) Identify path to munger.pl script
#munger='/Users/jefferis/bin/munger.pl'
munger=cmtkgui.tool_path('munger')
print 'munger is ' + munger
gd.addHelp("http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui")
dirFieldWidth=50
gdMargin=130
gd.addDirectoryField("Registration Folder",None,dirFieldWidth)
regrootf = gd.getStringFields().get(0)
# reference brain
gd.addFileField("Reference Brain", "",dirFieldWidth)
# input directory/image
gd.addDirectoryOrFileField("Input Image or Image Directory",None,dirFieldWidth)
imgdirf = gd.getStringFields().get(2)
gd.setInsets(10,gdMargin,10)
gd.addMessage("Output folders:")
outputf=gd.getMessage()
# what to do: affine/warp/reformat
gd.setInsets(10,200,10)
gd.addCheckboxGroup(3,2,["affine","01","warp","02","reformat","03"],[True,True,True,True,True,True],["Registration Actions","Reformat Channels"])
#gd.addCheckboxGroup(1,3,["01","02","03"],[True,True,True],["Reformat Channels"])
import os
import csv
from fiji.util.gui import GenericDialogPlus
from loci.formats import ChannelSeparator
from ij.io import Opener
import json
import time
boldFont = Font("SansSerif", Font.BOLD, 13)
fret_fura = []
fret_fura.append("C1/C2 (FURA)")
fret_fura.append("C2/C1 (FRET)")
dest = IJ.getDirectory("image")
bck_path = 'optional'
gdp = GenericDialogPlus("FRET Assay, Version 3.4")
gdp.addDirectoryField("Output Location:", dest, 40)
gdp.addStringField("Processed Folder:", 'Processed_FRET', 40)
gdp.addStringField("FRET Outfile:", 'FRET_Outfile.csv', 40)
gdp.addStringField("Selection Radius:", '3', 10)
gdp.addStringField("Image interval (sec):", '4', 10)
gdp.addStringField("ZeroDivisionErorVal:", 'NA', 10)
gdp.addRadioButtonGroup("", fret_fura, 1, 2, "C1/C2 (FURA)")
#gdp.addCheckbox("Set Background to value:", False)
gdp.addFileField("background file:", bck_path, 40)
gdp.addToSameRow()
gdp.addStringField("", '0', 5)
gdp.addCheckbox("Apply Gaussian blur? Input sigma value:", False)
gdp.addToSameRow()
gdp.addStringField("", '4', 5)
gdp.addMessage(" ")
