def addDefaultOptions(self):
'''
Add default GUI items
- checkbox runMeasurement
- add to Manager, nextSlice, runMeasurement
- resource message
- help button
'''
# Checkbox next slice and run Measure
self.addCheckbox("Auto next slice/image file",
bool(Prefs.get("annot.doNext", True)))
if self.browseMode == "stack":
self.addToSameRow()
self.addChoice("- dimension (for hyperstack)", hyperstackDim,
Prefs.get("annot.dimension", hyperstackDim[0]))
elif self.browseMode == "directory":
# Add button previous/next
self.addButton(BrowseButton.LABEL_PREVIOUS, BrowseButton())
self.addToSameRow()
self.addButton(BrowseButton.LABEL_NEXT, BrowseButton())
self.addMessage(
"Documentation and generic analysis workflows available on the GitHub repo (click Help)"
)
# Add Help button pointing to the github
self.addHelp(
r"https://github.com/LauLauThom/Fiji-QualiAnnotations#readme")
self.hideCancelButton()
def main(*R):
""" Main function
"""
# Show intial progress bar
IJ.showProgress(0, 50)
IJ.showStatus("Heterogeneous Z Correction")
# Retrieve the values R (with default values) from previous attempts
Rstr = "[(-0.05977, 83.3, 78.73),(-0.05976, 41.65, 39.36)]"
R = eval(Prefs.get("HetZCorr.R", Rstr))
# Load current image and get infos
imp = IJ.getImage()
stk = imp.getStack()
(sx, sy, sz) = stackSize(stk)
cal = imp.getCalibration()
# Get unique values
val = getUniqueValues(stk)
# Get R from dialog
R = showDialogR(R, val)
# Generate optical model
correction = generateModel(stk, R, val)
imp.setCalibration(cal)
#Show model image
correction.show()
correction.setSlice(sz)
IJ.run(correction, "Enhance Contrast", "saturated=0.35")
IJ.run(correction, "Fire", "")
def actionPerformed(self, event):
"""Delete the last row"""
# Generate a save dialog
dialog = JFileChooser(Prefs.get("roiGroup.importDir", ""))
dialog.setSelectedFile(File("roiGroups.txt"))
dialog.setFileFilter(FileNameExtensionFilter("Text file", ["txt"]))
output = dialog.showOpenDialog(
self.groupTable) # could be None argument too
if output in [JFileChooser.CANCEL_OPTION, JFileChooser.ERROR_OPTION]:
return
selectedFile = dialog.getSelectedFile()
directory = selectedFile.getParent()
Prefs.set("roiGroup.importDir", directory)
if not selectedFile.isFile(): return
filePath = selectedFile.getPath()
# Read comma-separated group from file
with open(filePath, "r") as textFile:
stringGroup = textFile.readline().rstrip()
# Update table with content of file
tableModel = self.groupTable.tableModel
tableModel.setGroupColumn(stringGroup)
def GetLastMeasureCount():
myCount = Prefs.get("JRM.meas.counter", int(-1))
if myCount < 0:
# it was not set, so set it to zero
resetLastMeasureCount()
return 0
else:
myCount = int(myCount)
return myCount
def makeCategoryComponent(self, category):
"""
Generates a checkbox with the new category name, to add to the GUI
Overwrite the original method
"""
stringCat = Prefs.get("annot.listCat", "")
newStringCat = stringCat + "," + category if stringCat else category
Prefs.set("annot.listCat", newStringCat)
# Make a new checkbox with the category name
checkbox = Checkbox(category, False)
checkbox.setFocusable(
False) # important to have the keybard shortcut working
return checkbox
def debug_mode():
"""Wrapper to check if 'imcf.debugging' is enabled.
This is a workaround for a Jython issue in ImageJ with values that are
stored in the "IJ_Prefs.txt" file being cast to the wrong types and / or
values in Python. Callling Prefs.get() using a (Python) boolean as the
second parameter always leads to the return value '0.0' (Python type float),
no matter what is actually stored in the preferences. Doing the same in e.g.
Groovy behaves correctly.
Calling Prefs.get() as below with the second parameter being a string and
subsequently checking the string value leads to the expected result.
"""
debug = Prefs.get("imcf.debugging", "false")
return debug == "true"
def actionPerformed(self, event):
"""Delete the last row"""
# Generate a save dialog
dialog = JFileChooser(Prefs.get("roiGroup.exportDir", ""))
dialog.setSelectedFile(File("roiGroups.txt"))
dialog.setFileFilter(FileNameExtensionFilter("Text file", ["txt"]))
output = dialog.showSaveDialog(
self.groupTable) # could be argument None too
if output in [JFileChooser.CANCEL_OPTION, JFileChooser.ERROR_OPTION]:
return
selectedFile = dialog.getSelectedFile()
directory = selectedFile.getParent()
Prefs.set("roiGroup.exportDir", directory)
filePath = selectedFile.getPath()
if not ("." in filePath):
filePath += ".txt" # Add extension if missing
# Write the groupString to the file
groupString = self.groupTable.tableModel.getGroupString()
with open(filePath, "w") as textFile:
textFile.write(groupString)
# for Ambro 2016-05-16
# gLo = 500
# gHi = 3800
# for Kang LM 2016-05-24
gLo = 730
gHi = 2850
bDoTiltCorrect = False
mu = IJ.micronSymbol
scaUm = mu + "m"
lastPath = Prefs.get("Last.Image.Dir", "None")
if os.path.exists(lastPath):
os.chdir(lastPath)
dc = DirectoryChooser("Choose directory")
basePath = dc.getDirectory()
print(basePath)
Prefs.set("Last.Image.Dir", basePath)
names = []
for file in os.listdir(basePath):
if file.endswith(".tif"):
name = os.path.splitext(file)[0]
names.append(name)
def getCategoriesFromPersistence():
"""Return categories saved in memory as a list."""
stringCat = Prefs.get(
"annot.listCat", "Category1"
) # Retrieve the list of categories as a comma separated list, if not defined default to Category1
return stringCat.split(",") if stringCat else []
