def getOK(text):
gd = GenericDialog('User prompt')
gd.addMessage(text)
gd.hideCancelButton()
gd.enableYesNoCancel()
gd.showDialog()
return gd.wasOKed()
def get_metadata_table_filepath():
"""Get a the metadata template filename"""
d = GenericDialog("Metadata Template")
d.addMessage("Please choose a metadata template")
d.enableYesNoCancel("OK", "Cancel")
d.hideCancelButton()
d.showDialog()
if d.wasOKed():
od = OpenDialog("Metadata File")
return os.path.join(od.getDirectory(), od.getFileName())
else:
return
from ij.gui import GenericDialog
gd = GenericDialog("How to cite the plugins")
gd.addMessage("""If you use these plugins, please cite :
Thomas LSV, Schaefer F and Gehrig J.
Fiji plugins for qualitative image annotations: routine analysis and application to image classification
[version 2; peer review: 2 approved, 1 approved with reservations].
F1000Research 2021, 9:1248
doi : 10.12688/f1000research.26872.2""")
#URL = r"https://doi.org/10.12688/f1000research.26872.1/" # mind the last slash at the end of URL, otherwise not working
URL = r"https://f1000research.com/articles/9-1248"
gd.addHelp(URL)
gd.setHelpLabel("Article page")
gd.hideCancelButton()
gd.showDialog()
def display_msg(title, message):
gd = GenericDialog(title)
gd.addMessage(message)
gd.hideCancelButton()
gd.showDialog()
uThres = gdp.getNextNumber()
uGsize = gdp.getNextNumber()
uGshape = gdp.getNextNumber()
uGshapemax = gdp.getNextNumber()
uOverlap = gdp.getNextNumber()
uExclude = gdp.getNextChoice()
# Files will automatically be output to a new Fiji_Analysis directory. If this directory already exists, files will be overwritten. This checks to make sure the directory does not yet exist.
if path.exists(outdir + File.separatorChar +
"Fiji_Analysis") and path.isdir(outdir + File.separatorChar +
"Fiji_Analysis"):
gdchk = GenericDialog("WARNING")
gdchk.addMessage(
"Analysis folder already exists. Choose a different directory to avoid overwritng your current data"
)
gdchk.hideCancelButton()
gdchk.showDialog()
print "Analysis folder already exists. Choose a new directory to avoid overwriting your current analysis"
uknow = gdchk.wasOKed()
if uknow == True:
IJ.getImage()
#Creates Fiji_Analysis directory.
File(outdir + File.separatorChar + "Fiji_Analysis").mkdir()
analysisOut = outdir + File.separatorChar + "Fiji_Analysis"
print analysisOut
inputPaths = [path_wt, path_dic, path_mut, path_bg]
# Since the script is critically depedent on file input order, files are duplicated and saved with easily referenced names in the new Directory. 0 = WT, 1 = DIC, 2 = MUT, 3 = BG. ALWAYS.
newPaths = []
