def getOptions():
pixels = zeros('f', 4) # 4 elements
# First Dialog Box
item = [
"coralline", "tunicate", "red", "macro", "background", "more than one"
]
gd = GenericDialog("Options")
gd.addRadioButtonGroup("options", item, 3, 2, "coralline")
gd.showDialog()
button = gd.getNextRadioButton()
# Second Dialog Box
gd2 = GenericDialog("Multiple Options")
items = ["coralline", "tunicate", "red", "macro", "garbage"]
defaultVal = [False] * 5
gd2.addCheckboxGroup(2, 3, items, defaultVal)
gd2.addNumericField("coralline %", 0, 0)
gd2.addNumericField("tunicate %", 0, 0)
gd2.addNumericField("red %", 0, 0)
gd2.addNumericField("macro %", 0, 0)
gd2.addNumericField("background %", 0, 0)
if gd.wasCanceled():
return 0
if button == "coralline":
pixels[0] = 1
elif button == "tunicate":
pixels[1] = 1
elif button == "red":
pixels[2] = 1
elif button == "macro":
pixels[3] = 1
elif button == "more than one":
gd2.showDialog()
checklist = gd2.getCheckboxes()
pixels[0] = int(
checklist[0].state) * (float(gd2.getNextNumber()) / 100)
pixels[1] = int(
checklist[1].state) * (float(gd2.getNextNumber()) / 100)
pixels[2] = int(
checklist[2].state) * (float(gd2.getNextNumber()) / 100)
pixels[3] = int(
checklist[3].state) * (float(gd2.getNextNumber()) / 100)
return pixels
def uScopeCalDialog(cal):
''' Pop up a dialog asking user to edit line settings etc.
CalIdx, SetGlobalScale, AddScaleBar = uScopeCalDialog(cal)
`cal` should be the object containing `names`, `cals`, `units` attributes
as set in the "user_settings.py" file.
`CalIdx` is the list index to the chosen calibration.
Eg., if the options were
['5x', '10x', '20x']
and the user chose '10x', then
CalIdx = 1
Returns `None` if the user cancelled the dialog.
`SetGlobalScale` is a boolean (True/False) from a checkbox option, if the user wants this calibration set 'globally' to all open images.
`AddScaleBar` is also a boolean (True/False), for a checkbox option, if user would like to run "Scale Bar..." afterwards.
'''
# The following inspired heavily by Correct_3D_drift.py:
#print "uScopeCalDialog():"
#print cal.names, [str(x) for x in cal.cals]
gd = GenericDialog("Microscope Calibrations")
gd.addMessage("Choose the calibration to load:")
# generate text to display in list:
# Radio Buttons:
CalStr = []
CalType_IsFunc = []
for ii, name in enumerate(cal.names):
if MC_DEBUG:
print("item #%i: name=" % (ii), name, "\n\t type=", type(name))
if isinstance(name, basestring):
'''It's just a regular calibration setting'''
CalStr.append(name + " (%s" % cal.cals[ii] +
" pixels/%s)" % cal.units[ii])
else:
''' Assume we'll be loading a custom function/class '''
CalStr.append(
name.name) # get the name from the Class' .name attribute
#end if(str)
#end for(cal.names)
'''if > 20 cals, use dropdown list, otherwise use radio buttons'''
if len(cal.names) > 20:
Radio = False
# Drop-Down list:
gd.addChoice(" Calibration:", CalStr,
CalStr[0]) # default = 1st (#0)
else:
Radio = True
gd.addRadioButtonGroup(" Calibration:", CalStr, len(CalStr), 1,
CalStr[0])
#addRadioButtonGroup(label, [String items], rows, columns, String:defaultItem)
#end if(cal>20)
gd.addCheckbox("Apply Scale to all open images?", False)
gd.addCheckbox("Add Scale Bar to this image?", False)
gd.addMessage(
"These calibrations can be altered by editing the file: \nFiji.app/plugins/Scripts/Plugins/Analyze/...\n\tMicroscope Measurement Tools/...\n\tMicroscope_Calibrations_user_settings.py"
)
gd.showDialog()
if gd.wasCanceled():
return None, None, None # return None's if user cancels
if Radio:
ChosenCal = gd.getNextRadioButton()
# Find the index to the chosen radio button w/ [list].index():
CalIdx = CalStr.index(ChosenCal)
else:
ChosenCal = gd.getNextChoiceIndex()
CalIdx = ChosenCal # the index to the choice
SetGlobalScale = gd.getNextBoolean()
AddScaleBar = gd.getNextBoolean()
#if MC_DEBUG: print( ChosenCal,CalIdx, SetGlobalScale )
#if MC_DEBUG: print( "end uScopeCalDialog()." )
return CalIdx, SetGlobalScale, AddScaleBar
imageCount = 0
voxel_info = str()
gd = GenericDialog("Set ToTiff Options")
gd.addStringField("File extension to be processed", ".nd2")
gd.addRadioButtonGroup("Output", outDirChoices, 3, 1, outDirChoices[0])
gd.addRadioButtonGroup("Overwrite", overwriteChoices, 2, 1, overwriteChoices[0])
gd.addRadioButtonGroup("Save channels in different subfolders", channelSubfolderChoices, 1, 1,
channelSubfolderChoices[0])
gd.addCheckboxGroup(2, 1, mipChoices, [False, False], ["Do you want maximum intensity projections of your images?"])
gd.showDialog()
if gd.wasCanceled():
exit()
fileExt = gd.getNextString()
outDirPref = gd.getNextRadioButton()
overwritePref = gd.getNextRadioButton()
channelSubfolderPref = gd.getNextRadioButton()
mipPrefTIFF = gd.getNextBoolean()
mipPrefJPG = gd.getNextBoolean()
if not fileExt.startswith('.'):
fileExt = '.' + fileExt
inDir = IJ.getDirectory("Choose Directory Containing Input Files")
if inDir is None:
exit('No input directory selected!')
if outDirPref == outDirChoices[2]:
outDir = inDir
else:
overwriteList = []
startTime = time.time()
imageCount = 0
gd = GenericDialog("Set binarization.py Options")
gd.addStringField("String to identify your input images", "_deconv")
gd.addRadioButtonGroup("Output", outDirChoices, 3, 1, outDirChoices[0])
gd.addRadioButtonGroup("Threshold Settings", thresholdChoices, 3, 1, thresholdChoices[0])
gd.addRadioButtonGroup("Overwrite", overwriteChoices, 2, 1, overwriteChoices[0])
gd.addCheckboxGroup(2, 1, mipChoices, [False, False], ["Do you want maximum intensity projections of your images?"])
gd.showDialog()
if gd.wasCanceled():
exit()
fileID = gd.getNextString()
outDirPref = gd.getNextRadioButton()
thresholdPref = gd.getNextRadioButton()
overwritePref = gd.getNextRadioButton()
mipPrefTIFF = gd.getNextBoolean()
mipPrefJPG = gd.getNextBoolean()
IJ.redirectErrorMessages(True)
inDir = IJ.getDirectory("Choose Directory Containing Input Files")
if inDir is None:
exit('No input directory selected!')
if outDirPref == outDirChoices[2]:
outDir = inDir
else:
outDir = IJ.getDirectory("Choose Directory For Output")
if outDir is None:
imTitles = WindowManager.getImageTitles()
nTitles = len(imTitles)
## DIALOG
d = GenericDialog("Measure")
d.addChoice("Mask", imTitles, "-")
d.addChoice("470 image", imTitles, "-")
d.addChoice("410 image", imTitles, "-")
d.addRadioButtonGroup("Binning", ["4x4", "2x2"], 1, 2, "4x4")
d.showDialog()
imgMask = WindowManager.getImage(d.getNextChoice())
img470 = WindowManager.getImage(d.getNextChoice())
img410 = WindowManager.getImage(d.getNextChoice())
binning = d.getNextRadioButton()
PARENT_DIR = img410.getOriginalFileInfo().directory
# setup data collection object
dataTable = ResultsTable()
##################################################
# INITIAL MEASUREMENTS
table = ResultsTable()
roiManager = RoiManager(True) # Boolean => Don't Display
PA.setRoiManager(roiManager)
# Measure Median 410 and 470
addValues(dataTable, 'Median 410', getMedians(img410))
addValues(dataTable, 'Median 470', getMedians(img470))
def uScopeCalDialog(cal):
''' Pop up a dialog asking user to choose from the calibration names etc.
CalIdx, SetGlobalScale, AddScaleBar = uScopeCalDialog(cal)
`cal` should be the object containing `names`, `cals`, `units` attributes
as set in the "user_settings.py" file.
`CalIdx` is the list index to the chosen calibration.
Eg., if the options were
['5x', '10x', '20x']
and the user chose '10x', then
CalIdx = 1
Returns `None` if the user cancelled the dialog.
`SetGlobalScale` is a boolean (True/False) from a checkbox option, if the user wants this calibration set 'globally' to all open images.
`AddScaleBar` is also a boolean (True/False), for a checkbox option, if user would like to run "Scale Bar..." afterwards.
'''
# The following inspired heavily by Correct_3D_drift.py:
#print "uScopeCalDialog():"
#print cal.names, [str(x) for x in cal.cals]
gd = GenericDialog("Microscope Calibrations")
gd.addMessage("Choose the calibration to load:")
# generate text to display in list:
# Radio Buttons:
CalStr = []
CalType_IsFunc = []
for ii, name in enumerate(cal.names):
if mc_DEBUG: print( "item #%i: name=" % (ii), name, "\n\t type=", type(name) )
if isinstance(name, basestring):
'''It's just a regular calibration setting'''
CalStr.append( name + " (%s"%cal.cals[ii] + " pixels/%s)"%cal.units[ii] )
else:
''' Assume we'll be loading a custom function/class '''
CalStr.append( name.name ) # get the name from the Class' .name attribute
#end if(str)
#end for(cal.names)
'''if > 20 cals, use dropdown list, otherwise use radio buttons'''
if len(cal.names) > 20:
Radio=False
# Drop-Down list:
gd.addChoice(" Calibration:", CalStr, CalStr[0] ) # default = 1st (#0)
else:
Radio=True
gd.addRadioButtonGroup(" Calibration:", CalStr, len(CalStr), 1, CalStr[0])
#addRadioButtonGroup(label, [String items], rows, columns, String:defaultItem)
#end if(cal>20)
gd.addCheckbox("Apply Scale to all open images?", False)
gd.addCheckbox("Add Scale Bar to this image?", False)
gd.addMessage("These calibrations can be altered by editing the file: \nFiji.app/plugins/Scripts/Plugins/Analyze/...\n\tMicroscope Measurement Tools/...\n\tMicroscope_Calibrations_user_settings.py")
gd.showDialog()
if gd.wasCanceled():
return None, None, None # return None's if user cancels
if Radio:
ChosenCal = gd.getNextRadioButton()
# Find the index to the chosen radio button w/ [list].index():
CalIdx = CalStr.index( ChosenCal )
else:
ChosenCal = gd.getNextChoiceIndex()
CalIdx = ChosenCal # the index to the choice
SetGlobalScale = gd.getNextBoolean()
AddScaleBar = gd.getNextBoolean()
#if mc_DEBUG: print( ChosenCal,CalIdx, SetGlobalScale )
#if mc_DEBUG: print( "end uScopeCalDialog()." )
return CalIdx, SetGlobalScale, AddScaleBar
