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 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 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 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
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
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)),
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
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(" ")
gdp.addMessage("Set R0 range (timepoint position x1 to x2):", boldFont)
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 )
gd.addStringField("Image filename pattern", formatString, 70)
gd.addStringField("Group By", groupBy, 70)
gd.addStringField("Nuclear Stain Channel Name", nucChannel, 70)
gd.addStringField("Cardiomyocyte Image Channel Name", cmChannel, 70)
gd.addCheckbox("Are images stitched by well", stitched)
gd.addChoice("Nuclear thresholding method", methodsList, nucMethod)
gd.addCheckbox("Threshold nuclei by stack?", analyzeNucStack)
gd.addCheckbox("Are the cardiomyocyte images brightfield?", brightfield)
gd.addChoice("Cardiomyocyte thresholding method", methodsList, cmMethod)
gd.addCheckbox("Threshold cardiomyocyes by stack?", analyzeCmStack)
gd.addNumericField("Rows per well", rowNo, 0)
gd.addNumericField("Columns per well", colNo, 0)
gd.addNumericField("Nuclear minimum size (pixels)", nucMinSize, 0)
gd.addNumericField("Cardiomyocyte minimum size (pixels)", cmMinSize, 0)
gd.showDialog()
folderPath = gd.getNextString() + "/"
def getOptions():
gui = GenericDialogPlus("Options for Moving TIFF files")
gui.addMessage("Select the number of imput files to be used per stitched image")
gui.addSlider("", 2, 10, 2)
gui.addFileField("Select csv file", "")
gui.addMessage("Add key values and corresponding genotype, when finished, leave fields empty")
gui.addStringField("Key :", prefs.get(None, "key1", "p"))
gui.addToSameRow()
gui.addStringField("Genotype :", prefs.get(None, "genotype1", "PROM-1_HA"))
gui.addStringField("Key :", prefs.get(None, "key2", "p"))
gui.addToSameRow()
gui.addStringField("Genotype :", prefs.get(None, "genotype2", "PROM-1_HA"))
gui.addStringField("Key :", prefs.get(None, "key3", "p"))
gui.addToSameRow()
gui.addStringField("Genotype :", prefs.get(None, "genotype3", "PROM-1_HA"))
gui.addStringField("Key :", prefs.get(None, "key4", "p"))
gui.addToSameRow()
gui.addStringField("Genotype :", prefs.get(None, "genotype4", "PROM-1_HA"))
gui.addStringField("Key :", prefs.get(None, "key5", "p"))
gui.addToSameRow()
gui.addStringField("Genotype :", prefs.get(None, "genotype5", "PROM-1_HA"))
gui.showDialog()
if gui.wasOKed():
tiffs_per_image = int(gui.getNextNumber())
csv_file = str(gui.getNextString())
genotypes = {}
for i in range(5):
key = str(gui.getNextString())
value = str(gui.getNextString())
if key != "":
genotypes[key] = value
else:
return
if len(genotypes) > 0:
a = list(genotypes.items())[0]
prefs.put(None, "key1", a[0])
prefs.put(None, "genotype1", a[1])
if len(genotypes) > 1:
a = list(genotypes.items())[1]
prefs.put(None, "key2", a[0])
prefs.put(None, "genotype2", a[1])
if len(genotypes) > 2:
a = list(genotypes.items())[2]
prefs.put(None, "key3", a[0])
prefs.put(None, "genotype3", a[1])
if len(genotypes) > 3:
a = list(genotypes.items())[3]
prefs.put(None, "key4", a[0])
prefs.put(None, "genotype4", a[1])
if len(genotypes) > 4:
a = list(genotypes.items())[4]
prefs.put(None, "key5", a[0])
prefs.put(None, "genotype5", a[1])
return tiffs_per_image, csv_file, genotypes
# 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()
gdp.addStringField("ER Selection Radius: ", radius_def, 5)
gd.setInsets(25,100,10)
gd.addMessage("Advanced Options:",font)
advancedoptionsf=gd.getMessage()
ncores=Runtime.getRuntime().availableProcessors()
defaultCores=1
if ncores >=8:
defaultCores=4
elif ncores>=4:
defaultCores=2
gd.addSlider("Number of cpu cores to use",1,ncores,defaultCores)
gd.setInsets(0,230,10)
gd.addCheckbox("Verbose log messages",False)
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():
The search region can be limited to a rectangular ROI, that is drawn on the image/stack before execution of the plugin.
Requirements:
- IJ-OpenCV update site
'''
#import time
#@PrefService prefs
from fiji.util.gui import GenericDialogPlus
## Create GUI
Win = GenericDialogPlus("Multiple Template Matching")
Win.addImageChoice("Template", prefs.get("Template", "Choice"))
Win.addImageChoice("Image", prefs.get("Image", "Choice"))
Win.addCheckbox("Flip_template_vertically", prefs.getInt("FlipV", False))
Win.addCheckbox("Flip_template_horizontally", prefs.getInt("FlipH", False))
Win.addStringField("Rotate template by ..(comma-separated)",
prefs.get("Angles", ""))
Win.addChoice("Matching_method", [
"Normalised Square Difference", "Normalised cross-correlation",
"Normalised 0-mean cross-correlation"
], prefs.get("Method", "Normalised 0-mean cross-correlation"))
Win.addNumericField("Number_of_templates expected", prefs.getInt("N_hit", 1),
0)
Win.addMessage("If more than 1 template expected :")
Win.addNumericField("Score_Threshold [0-1]",
prefs.getFloat("Score_Threshold", 0.5), 2)
#Win.addNumericField("Min_peak_height relative to neighborhood ([0-1], decrease to get more hits)", prefs.getFloat("Tolerance",0.1), 2)
Win.addNumericField("Maximal_overlap between Bounding boxes [0-1]",
prefs.getFloat("MaxOverlap", 0.4), 2)
Win.addMessage("Outputs")
Win.addCheckbox("Add_ROI detected to ROI manager",
prefs.getInt("AddRoi", True))
gd.setInsets(25, 100, 10)
gd.addMessage("Advanced Options:", font)
advancedoptionsf = gd.getMessage()
ncores = Runtime.getRuntime().availableProcessors()
defaultCores = 1
if ncores >= 8:
defaultCores = 4
elif ncores >= 4:
defaultCores = 2
gd.addSlider("Number of cpu cores to use", 1, ncores, defaultCores)
gd.setInsets(0, 230, 10)
gd.addCheckbox("Verbose log messages", False)
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()
