def askToSaveUnsavedChanges():
if note_status.getText() == "Unsaved changes.":
if IJ.showMessageWithCancel("Alert", "Save current note?"):
requestSave(None)
else:
# Stash current note in the log window
IJ.log("Discarded note for image at:")
IJ.log(path.getText())
IJ.log(textarea.getText())
IJ.log("===")
def setup() :
"""setup"""
if Exper.IN_DEV :
canceled = False
else :
canceled = not IJ.showMessageWithCancel(__program__,'To proceed program will close all open images and windows, continue?')
if not canceled :
IJ.run("Colors...", "foreground=white background=black selection=yellow");
## aspirational todo: identify current settings and return settings at the end
## set setting to save column headers
IJ.run("Input/Output...", "jpeg=85 gif=-1 file=.csv use_file save_column");
## set setting to copy column headers - not actually necessary
IJ.run("Input/Output...", "jpeg=85 gif=-1 file=.csv copy_column save_column");
futils.force_close_all_images()
rm = RoiManager.getRoiManager()
rm.reset()
rm.show()
# Process list of images
for (counter, f) in enumerate(files):
# Display progress
IJ.showStatus("Processing file "+ str(counter+1) +"/"+ str(len(files)))
# Open each image and process it
imp = IJ.openImage(f)
myRoutines(imp)
# Save processed image in out_dir (enforcing .tif extension)
newpath = os.path.splitext(out_dir + imp.getTitle())[0] +".tif"
IJ.saveAsTiff(imp, newpath)
imp.close()
# Log paths of processed files
csvWriter.writerow([f, newpath])
# Display CSV log
csvFile.close()
rt = ResultsTable.open(csvPath)
rt.show("_ProcessedFileList.csv")
# Proudly inform that processing terminated
if IJ.showMessageWithCancel("All done","Reveal output directory?"):
Utils.revealFile(out_dir);
else:
# Inform no filtered files were found
IJ.error("No matches for the selected extension(s).")
return self.__pathdir
def setPositionslist(self, positions) :
self.__positionsList=positions
def parsebool(self, val) :
if val : return str(1)
else : return str(0)
############################################## end class Bacteria_Tracking ################################################################################################
if __name__ == "__main__":
import os, glob
from os import path
bact=Bacteria_Tracking()
#def run(self, files, path, scale, batch, **settings):
if IJ.showMessageWithCancel("", "active image ? (ok) \nfiles (cancel)") :
bact.run(IJ.getImage(), "", 1, False)
else :
selectdir=IJ.getDirectory("image")
selectdir=IJ.getDirectory("")
listfiles=[]
listfiles.append(glob.glob(selectdir+"*DIA_s0001*t000[1-9].tif"))
listfiles.append(glob.glob(selectdir+"*DIA_s0002*t000[1-9].tif"))
bact.run(listfiles)
for ndId, tagNames in candidateTable.iteritems():
nd = candidateIdVsNode[ndId]
isCandidate = False
votes = []
for tagName in tagNames:
if candidateRe.match(tagName):
isCandidate = True
if voteRe.match(tagName):
votes.append(tagName)
if isCandidate:
if 1 != len(votes):
# one and only one vote should exist
print "found missing vote"
nMissingVotes = nMissingVotes + 1
nd.addTag(Tag("REVOTE-this", KeyEvent.VK_R))
print "done."
return nMissingVotes
## run checking votes with a dialogue hint
firstProject = Project.getProjects().get(0)
if IJ.showMessageWithCancel("Checking Votes For TrakEM2 Project", "Will now check for missing votes in TrakEM2 project:\n"+firstProject.getTitle()):
n = checkVotes(firstProject)
if 0 == n:
msg = "Well done! All candidates ara voted in:\n"+firstProject.getTitle()
else:
msg = str(n)+" votes missing in project:\n"+firstProject.getTitle()+"\n \nSearch REVOTE- to view missed votes.\nPlease re-check after appending missing votes."
IJ.showMessage("Checking Votes Done", msg)
# exper.hsegs.append(hseg)
# exper.cells.append(vl3)
# exper.cells.append(vl4)
return exper
## main program
if IN_DEV :
canceled = False
else :
canceled = not IJ.showMessageWithCancel(__program__,'To proceed program will close all open images and windows, continue?')
if not canceled :
setup()
if IN_DEV :
exper_path = "/Users/baylieslab/Documents/Amelia/data/patrick/2019-05-20_Dmef2-2xeGFP"
else :
dir_chooser = DirectoryChooser(__program__)
exper_path = dir_chooser.getDirectory()
if exper_path.endswith('/') :
exper_path = exper_path[:-1]
for tagName in tagNames:
if candidateRe.match(tagName):
isCandidate = True
if voteRe.match(tagName):
votes.append(tagName)
if isCandidate:
if 1 != len(votes):
# one and only one vote should exist
print "found missing vote"
nMissingVotes = nMissingVotes + 1
nd.addTag(Tag("REVOTE-this", KeyEvent.VK_R))
print "done."
return nMissingVotes
## run checking votes with a dialogue hint
firstProject = Project.getProjects().get(0)
if IJ.showMessageWithCancel(
"Checking Votes For TrakEM2 Project",
"Will now check for missing votes in TrakEM2 project:\n" +
firstProject.getTitle()):
n = checkVotes(firstProject)
if 0 == n:
msg = "Well done! All candidates ara voted in:\n" + firstProject.getTitle(
)
else:
msg = str(n) + " votes missing in project:\n" + firstProject.getTitle(
) + "\n \nSearch REVOTE- to view missed votes.\nPlease re-check after appending missing votes."
IJ.showMessage("Checking Votes Done", msg)