def showDialogR(R, val):
""" Create dialog for input and save R values in settings
"""
gui = GenericDialog("Heterogeneous Z Correction")
msg = "Heterogeneous Z Correction calculates an optical model\n"\
"based on rational fluorescence intensity attenuation\n"\
"over depth, in the form of (ax+b)/(x+c). Please specify\n"\
"(a,b,c) for each region. You should provide a z-stack with\n"\
"unique pixel values for each region.\n"
gui.addMessage(msg)
for ii in range(len(val)):
gui.addNumericField(
"Region " + str(ii) + " (" + str(val[ii]) + "): a", R[ii][0], 2)
gui.addToSameRow()
gui.addNumericField("b", R[ii][1], 2)
gui.addToSameRow()
gui.addNumericField("c", R[ii][2], 2)
gui.addHelp(
r"https://github.com/alexandrebastien/heterogeneous-z-correction")
gui.showDialog()
if gui.wasOKed():
R = []
for ii in range(len(val)):
R = R + [
(gui.getNextNumber(), gui.getNextNumber(), gui.getNextNumber())
]
Prefs.set("HetZCorr.R", str(R))
return R
else:
return
def getOptions():
gd = GenericDialog("Option")
gd.addNumericField("Sliding Z Projection Slices", 5, 0) # show 0 decimals
gd.addHelp("http://www.robertcudmore.org/software/bSliding_Z_Projection.html")
gd.showDialog()
if gd.wasCanceled():
print "User cancelled dialog."
return
#read out options
userSlices = gd.getNextNumber()
return int(userSlices)
def getOptions():
global numberOfChannels
global replaceExisting
gd = GenericDialog("Options")
gd.addNumericField("Number of channel", 2, 0) # show 0 decimals
gd.addCheckbox("Replace Destination .tif files", 0)
gd.addHelp("http://robertcudmore.org/software_index.html")
gd.showDialog()
if gd.wasCanceled():
print "User cancelled dialog."
return -1
#read out options
numberOfChannels = gd.getNextNumber()
replaceExisting = gd.getNextBoolean()
return 1 #int(numberOfChannels)
def showTable(self):
"""
Add the main panel to a GenericDialog and show it
"""
gd = GenericDialog("Roi-group table")
gd.addPanel(self) # Add current table instance to panel
gd.addMessage("""If you use this plugin, please cite:
Laurent Thomas. (2020, November 18).
LauLauThom/RoiGroupTable: ImageJ/Fiji RoiGroup Table (Version 1.0)
Zenodo. http://doi.org/10.5281/zenodo.4279049""")
gd.addHelp(r"https://github.com/LauLauThom/RoiGroupTable")
gd.showDialog()
if gd.wasOKed():
# Update ImageJ Roi group names mapping
stringGroup = self.tableModel.getGroupString()
Roi.setGroupNames(stringGroup)
def getOptions():
global numberOfChannels
global replaceExisting
gd = GenericDialog("Options")
gd.addNumericField("Number of channel", 2, 0) # show 0 decimals
gd.addCheckbox("Replace Destination .tif files", 0)
gd.addHelp("http://robertcudmore.org/software_index.html")
gd.showDialog()
if gd.wasCanceled():
print "User cancelled dialog."
return -1
#read out options
numberOfChannels = gd.getNextNumber()
replaceExisting = gd.getNextBoolean()
return 1 #int(numberOfChannels)
else:
# List column headers
table = tableWindow.getResultsTable()
headers = table.getHeadings()
# Generate dialog with dropdown for column selection
dialog = GenericDialog("PieChart from table column")
dialog.addChoice("Data column", headers, headers[0])
dialog.addMessage(
"""Hover the mouse over the plot to view absolute and relative (%) values\n
Right-click to set colors, export to PNG...\n
Note: BarCharts usually provide better distinction than PieCharts for sectors with similar sizes (see Help)."""
)
dialog.addHelp(r"https://www.data-to-viz.com/caveat/pie.html")
dialog.showDialog()
# Generate PieChart with data column
if dialog.wasOKed():
# Get the data column as string
selectedHeader = dialog.getNextChoice()
column = table.getColumnAsVariables(selectedHeader)
columnString = [str(item)[1:-1]
for item in column] # [1:-1] to remove the ""
# Make the PieChart for this data column
if columnString:
chart = PieChart(selectedHeader, columnString)
chart.showFrame("PieChart")
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()
