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 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(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 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
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 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 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 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 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
# rest of imports below on purpose (otherwise searchRoi lost)
## 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_objects expected", prefs.getInt("N_hit", 1), 0)
Win.addMessage("If more than 1 object expected :")
Win.addSlider("Score_Threshold", 0, 1, prefs.getFloat("Score_Threshold", 0.5),
0.1)
#Win.addNumericField("Min_peak_height relative to neighborhood ([0-1], decrease to get more hits)", prefs.getFloat("Tolerance",0.1), 2)
Win.addSlider("Maximal_overlap between Bounding boxes", 0, 1,
prefs.getFloat("MaxOverlap", 0.4), 0.1)
Win.addMessage("Outputs")
Win.addCheckbox("Add_ROI detected to ROI manager",
prefs.getInt("AddRoi", True))
Win.addCheckbox("Show_result table", prefs.getInt("ShowTable", False))
Win.addMessage("Version 1.1.2")
Win.addMessage("""If you use this plugin please cite :
Thomas, L.S.V., Gehrig, J.
Multi-template matching: a versatile tool for object-localization in microscopy images.
BMC Bioinformatics 21, 44 (2020). https://doi.org/10.1186/s12859-020-3363-7""")
Win.addHelp(
Requirements:
- IJ-OpenCV update site
'''
#import time
#from timeit import default_timer as timer
#@PrefService prefs
from Template_Matching.Version import version
from fiji.util.gui import GenericDialogPlus
# rest of imports below on purpose (otherwise searchRoi lost)
## Create GUI
Win = GenericDialogPlus("Multiple Template Matching")
Win.addImageChoice("Template", prefs.get("Template", "Choice"))
Win.addImageChoice("Image", prefs.get("Image", "Choice"))
Win.addMessage("# Template pre-processing")
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.addMessage("# Detection parameters")
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_objects expected", prefs.getInt("N_hit", 1), 0)
Win.addMessage("# Non-Maxima Suppression (if N_object > 1)")
Win.addSlider("Score_Threshold", 0, 1, prefs.getFloat("Score_Threshold", 0.5),
0.1)
#Win.addNumericField("Min_peak_height relative to neighborhood ([0-1], decrease to get more hits)", prefs.getFloat("Tolerance",0.1), 2)
Win.addSlider("Maximal_overlap between Bounding boxes", 0, 1,
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"])
# Registration options
# Jefferis,Potter 2007, Cachero,Ostrovsky 2010, Manual
gd.addChoice("Registration Params",["Jefferis, Potter 2007","Cachero, Ostrovsky 2010"],"Jefferis, Potter 2007")
choicef=gd.getChoices().get(0)
print choicef.getSelectedItem()
# final Action (Test, Run, Write Script)
gd.addChoice("Action",["Test","Write Script","Run"],"Write Script")
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)
gdp.addStringField("x1:", '2', 3)
gdp.addToSameRow()
gdp.addStringField(" x2:", '8', 3)
gdp.addMessage("Set output file headers:", boldFont)
gdp.addStringField("Channel 1:", 'A', 8)
gdp.addToSameRow()
gdp.addStringField("Channel 2:", 'B', 8)
gdp.addStringField("Channel Z/Channel W:", 'C', 8)
gdp.addToSameRow()
gdp.addStringField("R/R0:", 'D', 8)
gdp.showDialog()
if gdp.wasOKed():
dest = gdp.getNextString().strip()
ProFolder = gdp.getNextString().strip()
cmtkgui.movefile(frompath,target_dir)
print("Cleaning up!")
try:
shutil.rmtree(td)
except OSError:
print("Failed to remove temporary directory: "+td+"\n")
pass
download_urls=cmtkgui.downloads()
# download_urls=['http://www.nitrc.org/frs/download.php/4814/CMTK-2.2.3-CYGWIN-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4812/CMTK-2.2.3-Linux-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4820/CMTK-2.2.3-MacOSX-10.4-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4822/CMTK-2.2.3-MacOSX-10.5-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4824/CMTK-2.2.3-MacOSX-10.6-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4604/CMTK-2.2.1-CYGWIN-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4596/CMTK-2.2.1-Linux-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4608/CMTK-2.2.1-MacOSX-10.4-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4610/CMTK-2.2.1-MacOSX-10.5-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4611/CMTK-2.2.1-MacOSX-10.6-x86_64.tar.gz']
download_files=map(os.path.basename,download_urls)
download_dict=dict(zip(download_files,download_urls))
print cmtkgui.install_dir()
gd = GenericDialogPlus('Install CMTK')
gd.addMessage('Currently installed CMTK version: '+cmtkgui.installed_version())
recommended_file=cmtkgui.recommended_file(download_files)
if recommended_file is None:
recommended_file = download_files[0]
gd.addChoice("Download file",download_files,recommended_file)
gd.addMessage('By downloading this file you agree to the following (if you '+
'do not agree to this, please press "Cancel" below):')
gd.addMessage('Core CMTK code is licensed under the GPLv3.\nBundled software'+
' may be licensed under different terms - see licences/ directory for details')
gd.showDialog()
if gd.wasOKed():
download_file=gd.getNextChoice()
# nb url has a suffix to indicate that user agreed to license
download_url=download_dict[download_file]+'/?i_agree=1&download_now=1'
print "Downloading "+download_file+' from url '+download_url+' to '+cmtkgui.install_dir()
cmtkgui.download_and_untar_url(download_url,cmtkgui.install_dir(),untar_binaries,download_file)
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
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)
gdp.addChoice("View Mode:", color_options, color_def)
gdp.addMessage("------------------------------------------------------------", italicFont)
gdp.addMessage(" Advanced Options: ", italicFont)
print("Cleaning up!")
try:
shutil.rmtree(td)
except OSError:
print("Failed to remove temporary directory: " + td + "\n")
pass
download_urls = cmtkgui.downloads()
# download_urls=['http://www.nitrc.org/frs/download.php/4814/CMTK-2.2.3-CYGWIN-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4812/CMTK-2.2.3-Linux-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4820/CMTK-2.2.3-MacOSX-10.4-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4822/CMTK-2.2.3-MacOSX-10.5-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4824/CMTK-2.2.3-MacOSX-10.6-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4604/CMTK-2.2.1-CYGWIN-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4596/CMTK-2.2.1-Linux-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4608/CMTK-2.2.1-MacOSX-10.4-i686.tar.gz', 'http://www.nitrc.org/frs/download.php/4610/CMTK-2.2.1-MacOSX-10.5-x86_64.tar.gz', 'http://www.nitrc.org/frs/download.php/4611/CMTK-2.2.1-MacOSX-10.6-x86_64.tar.gz']
download_files = map(os.path.basename, download_urls)
download_dict = dict(zip(download_files, download_urls))
print cmtkgui.install_dir()
gd = GenericDialogPlus('Install CMTK')
gd.addMessage('Currently installed CMTK version: ' +
cmtkgui.installed_version())
recommended_file = cmtkgui.recommended_file(download_files)
if recommended_file is None:
recommended_file = download_files[0]
gd.addChoice("Download file", download_files, recommended_file)
gd.addMessage('By downloading this file you agree to the following (if you ' +
'do not agree to this, please press "Cancel" below):')
gd.addMessage(
'Core CMTK code is licensed under the GPLv3.\nBundled software' +
' may be licensed under different terms - see licences/ directory for details'
)
gd.showDialog()
if gd.wasOKed():
download_file = gd.getNextChoice()
# nb url has a suffix to indicate that user agreed to license
download_url = download_dict[download_file] + '/?i_agree=1&download_now=1'
rm = RoiManager().getInstance()
#Set some defaults
IJ.run(
"Set Measurements...",
"area integrated area_fraction limit display scientific redirect=None decimal=3"
)
IJ.setForegroundColor(0, 0, 0)
IJ.setBackgroundColor(255, 255, 255)
#User Input Dialoge
analyses = ["Counts", "ATP"]
yn = ["YES", "NO"]
gdp = GenericDialogPlus("Ex Vivo Granule Analysis")
gdp.addMessage("Choose a UNIQUE directory to save analysis files")
gdp.addDirectoryOrFileField("Output Directory", "D:/Samantha/")
gdp.addMessage("IMPORTANT: Files are tracked based on input order")
gdp.addMessage("Select input files (.tiff)...")
gdp.addFileField("Wildtype", "D:/Samantha/test/VLEwt.tif")
gdp.addFileField("DIC", "D:/Samantha/test/dic.tif")
gdp.addFileField("Mutant", "D:/Samantha/test/ddmut.tif")
gdp.addFileField("Background (DAPI)", "D:/Samantha/test/bg.tif")
gdp.addChoice("Select analysis type", analyses, "Counts")
gdp.addMessage("Choose variable conditions:")
gdp.addNumericField(
"Minimum Threshold. Choose value (0-1) as a percent of maximum threshold",
0.20, 2)
gdp.addNumericField("Minimum granule size (pixel^2)", 20, 0)
gdp.addNumericField(
"Minimum granule circularity/shape. 1.0 = perfect cirlce, 0.5 = ellipse, 0.0 = rod",
shutil.move(os.path.join(td,subdir),target_dir)
try:
download_url='https://github.com/jefferis/fiji-cmtk-gui/tarball/master'
# check date
installed_version='NA'
local_version_info=cmtkgui.gui_local_versioninfo()
if local_version_info.has_key('date'):
installed_version=local_version_info['date']
github_version_info=cmtkgui.gui_github_versioninfo()
update_available=cmtkgui.gui_update_available(github_version_info)
gd = GenericDialogPlus('Update CMTK GUI')
if update_available:
gd.addMessage('CMTK GUI update available')
gd.setOKLabel("Download")
else:
gd.addMessage('CMTK GUI is up to date')
gd.addMessage('Currently installed CMTK GUI version: '+installed_version)
gd.showDialog()
if gd.wasOKed() and update_available:
# nb url has a suffix to indicate that user agreed to license
from ij import IJ
IJ.showStatus('Downloading CMTK GUI')
cmtkgui.download_and_untar_url(download_url,cmtkgui.gui_install_dir(),untar_github_archive)
cmtkgui.gui_write_local_versioninfo(github_version_info)
except SystemExit, e:
from ij import IJ
"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"])
# Registration options
# Jefferis,Potter 2007, Cachero,Ostrovsky 2010, Manual
gd.addChoice("Registration Params",
["Jefferis, Potter 2007", "Cachero, Ostrovsky 2010"],
"Jefferis, Potter 2007")
choicef = gd.getChoices().get(0)
calib = imp.getCalibration();
scaleX = calib.pixelWidth / calib.pixelDepth * zoom;
scaleY = calib.pixelHeight / calib.pixelDepth * zoom;
scaleZ = 1.0 * zoom;
# initialize state
input = None;
formerT = None;
resultCylinderMaxProjection = None;
resultMaxProjection = None;
spots = None;
circles = None;
blobs = None;
# build up user interface
gdp = GenericDialogPlus("Spot detection workflow");
gdp.addMessage("Noise and background subtraction (DoG)");
gdp.addCheckbox("Do noise and background subtraction ", formerDoNoiseAndBackgroundRemoval);
gdp.addSlider("Sigma 1 (in 0.1 pixel)", 0, 100, formerSigma1);
gdp.addSlider("Sigma 2 (in 0.1 pixel)", 0, 100, formerSigma2);
gdp.addMessage("Rigid transform");
gdp.addCheckbox("Do rigid transformation", formerDoRigidTransform);
gdp.addSlider("Translation X (in pixel)", -100, 100, formerTranslationX);
gdp.addSlider("Translation Y (in pixel)", -100, 100, formerTranslationY);
gdp.addSlider("Translation Z (in pixel)", -100, 100, formerTranslationZ);
gdp.addSlider("Rotation X (in degrees)", -180, 180, formerRotationX);
gdp.addSlider("Rotation Y (in degrees)", -180, 180, formerRotationY);
gdp.addSlider("Rotation Z (in degrees)", -180, 180, formerRotationZ);
gdp.addMessage("Spot detection")
gdp.addCheckbox("Do spot detection", formerDoSpotDetection);
gdp.addSlider("Tolerance", 0, 100, formerTolerance);
# define some variables
# EM = electron microscopic image
# rLM = real light microscopic image (ground truth) with chromatin channel
# pLM = predictet light microscopic image
# c1LM, c2LM, c3LM ... = channels of interest (COI)
# define input (java.io.File to string)
EMfilepath = EMfilepath.toString()
rLMfilepath = rLMfilepath.toString()
workdir = workdir.toString()
# check if workdir is empty
if len(os.listdir(workdir)) != 0:
gd = GenericDialogPlus("Options")
gd.addMessage("Working directory must be empty!")
gd.addMessage(
"Please delete all files in the working directory, or choose another working directory and restart the Deep CLEM Plugin."
)
gd.showDialog()
if len(os.listdir(workdir)) != 0:
sys.exit()
# create a couple of folder in workdir
# for registration
registration_inputdir = os.path.join(workdir, "registration_input")
os.mkdir(registration_inputdir)
registration_outputdir = os.path.join(workdir, "registration_output")
os.mkdir(registration_outputdir)
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 errorDialog(message):
gd = GenericDialogPlus("Error")
gd.addMessage(message)
gd.showDialog()
return
## 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))
Win.addCheckbox("Show_result table", prefs.getInt("ShowTable", False))
Win.addMessage("""If you use this plugin please cite :
Laurent SV Thomas, Jochen Gehrig
bioRxiv 619338; doi: https://doi.org/10.1101/619338""")
Win.addHelp(
"https://github.com/multi-template-matching/MultiTemplateMatching-Fiji/wiki"
)
shutil.move(os.path.join(td, subdir), target_dir)
try:
download_url = 'https://github.com/jefferis/fiji-cmtk-gui/tarball/master'
# check date
installed_version = 'NA'
local_version_info = cmtkgui.gui_local_versioninfo()
if local_version_info.has_key('date'):
installed_version = local_version_info['date']
github_version_info = cmtkgui.gui_github_versioninfo()
update_available = cmtkgui.gui_update_available(github_version_info)
gd = GenericDialogPlus('Update CMTK GUI')
if update_available:
gd.addMessage('CMTK GUI update available')
gd.setOKLabel("Download")
else:
gd.addMessage('CMTK GUI is up to date')
gd.addMessage('Currently installed CMTK GUI version: ' + installed_version)
gd.showDialog()
if gd.wasOKed() and update_available:
# nb url has a suffix to indicate that user agreed to license
from ij import IJ
IJ.showStatus('Downloading CMTK GUI')
cmtkgui.download_and_untar_url(download_url, cmtkgui.gui_install_dir(),
untar_github_archive)
cmtkgui.gui_write_local_versioninfo(github_version_info)
except SystemExit, e:
