def getTable():
''' Check if a table exists otherwise open a new one'''
## Check if we can get a table window
if IJ.getFullVersion() >= "1.53g":
# try to get any active table
tableWindow = WindowManager.getActiveTable(
) # this function requires 1.53g (or at least not working with 1.53c), return None if no table
else:
# Fallback on fetching either a window called Annotations or Annotations.csv as in previous plugin version
win = WindowManager.getWindow("Annotations")
win2 = WindowManager.getWindow(
"Annotations.csv") # upon saving it adds this extension
if win:
tableWindow = win
elif win2:
tableWindow = win2
else:
tableWindow = None
## If a table window then get its table, otherwise new table. In this case, its name is set later
return tableWindow.getResultsTable() if tableWindow else ResultsTable()
def __init__(self):
if IJ.getFullVersion() < "1.53b":
message = "ImageJ with at least version 1.53b required. Update with Help > Update ImageJ..."
IJ.error(message)
raise Exception(message)
super(TableModel, self).__init__()
self.headers = ["Group", "Name"]
groupNames = Roi.getGroupNames() # groupNames can be None !
groupNames = groupNames.split(",") if groupNames else [
"ExampleName-doubleClick to edit"
] # groupNames is a list
self.nRows = len(groupNames)
self.columns = [[], []] # 2 columns
self.columns[0] = range(1, len(groupNames) + 1)
self.columns[1] = groupNames
def actionPerformed(self, event):
if IJ.getFullVersion() < "1.53g":
IJ.error("This plugin requires ImageJ version 1.53g minimum.\n Update using Help > Update ImageJ...")
return
tableWindow = WindowManager.getActiveTable() # this function requires the 1.53g (or at least not working with 1.53c)
if not tableWindow: return
# Get column Category
table = tableWindow.getResultsTable()
column = table.getColumnAsVariables("Category")
columnString = [str(item) for item in column]
# Plot Pie Plot for this column
pieChart = PieChart("Category", columnString)
pieChart.showFrame("Data-distribution")
from QualiAnnotations.Charts import PieChart
from ij.gui import GenericDialog
from ij import IJ, WindowManager
if IJ.getFullVersion() < "1.53g":
IJ.error(
"This plugin requires ImageJ version 1.53g minimum.\n Update using Help > Update ImageJ..."
)
raise Exception("ImageJ version 1.53g minimum required")
tableWindow = WindowManager.getActiveTable(
) # this function requires the 1.53g (or at least not working with 1.53c)
#print tableWindow
if not tableWindow:
IJ.error("No open table")
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)."""
)
On my version of ImageJ (1.52n99) 2019-06-15 setting
res.showRowNumbers() as True or False made no difference
"""
from ij.measure import ResultsTable
from ij import IJ
from ij.plugin.filter import Analyzer
import jmFijiGen as jmg
# start cean
IJ.run("Close All")
jmg.close_open_non_image_window("Results")
jmg.close_open_non_image_window("ROI Manager")
# open our image
imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif")
Analyzer.setOption("BlackBackground", True)
imp.show()
IJ.run("Convert to Mask")
imp.show()
IJ.run("Set Measurements...",
"area perimeter shape display redirect=None decimal=3")
IJ.run("Analyze Particles...",
"size=20-Infinity circularity=0.2-1.00 display exclude clear add")
# Note that this showed the result numbers independent of T/F below
res = ResultsTable.getResultsTable()
res.showRowNumbers(True)
res.updateResults()
print("ImageJ version " + IJ.getFullVersion())
# has to be the first line
from __future__ import print_function
import os, sys
from ij import IJ, WindowManager
from ij.io import OpenDialog
from ij.process import ImageConverter # by default convert to 8-bit will scale, i need to turn ot off. See: https://ilovesymposia.com/2014/02/26/fiji-jython/
# see: https://imagej.nih.gov/ij/developer/api/ij/process/ImageConverter.html
# Set true to scale to 0-255 when converting short to byte or float to byte and to 0-65535 when converting float to short.
from loci.plugins import BF
# lifeline version is 1.51n99
# newer (April 2020) version is 1.52p99
fijiVersion = IJ.getFullVersion()
fijiVersion = str(fijiVersion)
print('simpleConvert() is running in ImageJ/Fiji:', fijiVersion)
goodVersion = fijiVersion.find('1.51') != -1
def myConvert(path='', imp=None):
if path == '' and imp is None:
# NOT USED
# ask user for file. I do not know how to handle when users hits cancel??? Script will just fail
notUsedBy_oxs = 'Open a two-channel deconvoluted .oir file'
path = OpenDialog(notUsedBy_oxs).getPath()
if len(path) > 0:
print(' user selected path:', path)
fileName = os.path.basename(path)
Requirements :
- IJ-OpenCV (from the updater)
TO DO :
- Images with overlay in Stack : change to the easier ij.plugin.ImagesToStack that use a list to make the stack. No need to precise the size..
'''
# Python
from __future__ import division
# ImageJ
from ij import IJ,ImagePlus, ImageStack
from ij.plugin.filter import MaximumFinder
#from ij.gui import Roi, PointRoi
if IJ.getFullVersion()<"1.52o":
IJ.error("Please update ImageJ to min v1.52o. Help>Update ImageJ...")
# OpenCV
try:
from org.bytedeco.javacpp.opencv_imgproc import matchTemplate, threshold, CV_THRESH_TOZERO
from org.bytedeco.javacpp.opencv_core import Mat, Scalar, Point, minMaxLoc, subtract # UNUSED normalize, NORM_MINMAX, CV_8UC1, CV_32FC1
from org.bytedeco.javacpp import DoublePointer
except:
IJ.error("Missing OpenCV dependencies. Make sure to activate 'IJ-OpenCV plugins' update site.")
# Java
from java.lang import Float #used to convert BytesToFloat
def defaultActionSequence(self):
"""
Central function (DO NOT OVERWRITE) called if a button is clicked or shortcut called
It trigger the following actions:
- getting the current table
- checking the GUI state (checkboxes, dropdown...)
- running measurements if measure is selected
- setting ROI attribute (if roi)
- incrementing table counter
- adding image directory and name to table
- filling columns from GUI state using custom fillTable()
- switching to next slice
- displaying the annotation GUI to the front, important to catch next keyboard shortcuts
"""
try:
imp = IJ.getImage() # get current image
except: # no image: just stop the execution then
return
# Get current table
table = getTable()
table.showRowNumbers(True)
# Check options, use getCheckboxes(), because the checkbox plugin have other checkboxes
checkboxes = self.getCheckboxes()
# Initialize Analyzer
if self.runMeasure:
analyzer = Analyzer(imp, table)
analyzer.setMeasurement(Measurements.LABELS,
False) # dont add label to table
# Check if existing roi manager
rm = RoiManager.getInstance()
indexes = rm.getSelectedIndexes() if rm else [
] # Check if roi selected
if indexes:
# Loop over selected ROI
for index in indexes: # set selected features as property of rois
roi = rm.getRoi(index)
imp.setRoi(roi)
# Run measure for the ROI
if self.runMeasure: # Automatically increment counter
analyzer.measure() # as selected in Set Measurements
else:
table.incrementCounter(
) # Automatically done if runMeasure
#table.addValue("Index", table.getCounter() )
for key, value in getImageDirAndName(imp).iteritems():
table.addValue(key, value)
# Add selected items (implementation-specific)
self.fillTable(table)
# Read comment
stringField = self.getStringFields()[0]
table.addValue("Comment", stringField.text)
# Add roi name to the table + set its property
table.addValue("Roi", roi.getName()) # Add roi name to table
setRoiProperties(roi, table)
# No roi selected in the Manager
else:
if self.runMeasure: # also automatically increment counter
analyzer.measure() # as selected in Set Measurements
else:
table.incrementCounter() # Automatically done if runMeasure
#table.addValue("Index", table.getCounter() )
for key, value in getImageDirAndName(imp).iteritems():
table.addValue(key, value)
# Add selected items (implementation-specific)
self.fillTable(table)
# Read comment
stringField = self.getStringFields()[0]
table.addValue("Comment", stringField.text)
# Check if an active Roi, not yet present in Manager
roi = imp.getRoi()
if roi is not None:
roi.setPosition(imp)
rm = getRoiManager()
rm.addRoi(roi)
# get back the roi from the manager to set properties
roiBis = rm.getRoi(rm.getCount() - 1)
roiName = roiBis.getName()
table.addValue("Roi", roiName) # Add roi name to table
setRoiProperties(roiBis, table)
title = table.getTitle() if table.getTitle(
) else "Annotations" # getTitle is None for newly generated table
table.show(title) # Update table
#table.updateResults() # only for result table but then addValue does not work !
# Go to next slice
doNext = checkboxes[-1].getState()
if doNext:
if self.browseMode == "stack":
nextSlice(imp, self.getSelectedDimension())
elif self.browseMode == "directory":
NextImageOpener().run("forward")
# Bring back the focus to the button window (otherwise the table is in the front)
if not IJ.getFullVersion().startswith("1.52p"):
WindowManager.toFront(self) # prevent some ImageJ bug with 1.52p
