def run():
# ensure no other windows are open and clear resultstable
IJ.run("Close All")
IJ.run("Clear Results", "")
#Ask user for file to be converted
srcDir = IJ.getFilePath("Select file to analyse")
if not srcDir:
return
#open file
IJ.open(srcDir)
dstDir = os.path.dirname(srcDir)
print("dstDir = " + dstDir)
#open ROI manager, save ROI names as labels in measurements
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
rm.runCommand("UseNames", "true")
# set parameters to be measured
IJ.run("Set Measurements...",
"area mean integrated limit display redirect=None decimal=3")
FOVlist = WindowManager.getIDList()
chnls = IJ.getString(
"Please enter which channels you would like to analyse. Example: 123 analyses channels 1, 2 and 3",
'123')
for FOV in FOVlist:
imp = WindowManager.getImage(FOV)
IJ.run(imp, "Arrange Channels...", "new=" + chnls)
imp.close()
imp2 = WindowManager.getCurrentImage()
imageTitle = WindowManager.getImage(FOV).getTitle()
newDir = imageTitle + ' ROIs'
dirPath = os.path.join(dstDir, newDir)
if not os.path.exists(dirPath):
try:
os.makedirs(dirPath)
except OSError as e:
if e.errno != errno.EEXIST:
raise
# clear ROI list before analysis
rm.runCommand(imp2, "Deselect")
rm.runCommand(imp2, "Delete")
TMdata, nFrames = runTrackMate(imp2)
if TMdata:
iterateCoords(TMdata, nFrames, dirPath, imp2)
imp2.changes = 0
imp2.close()
#relabel()
resultsDir = os.path.splitext(srcDir)[0] + ".csv"
#while os.path.exists(resultsDir):
#resultsDir = resultsDir+"_1"+".csv"
IJ.saveAs("Results", resultsDir)
def run():
sId = IJ.getString("Filenames contain:", "T0000")
srcDir = DirectoryChooser("Choose!").getDirectory()
if not srcDir:
# user canceled dialog
return
# Assumes all files have the same size
stack = None
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-TIFF files
if not (sId in filename):
continue
print(filename)
path = os.path.join(root, filename)
# Upon finding the first image, initialize the VirtualStack
imp = IJ.openImage(path)
if stack is None:
# stack = VirtualStack(imp.width, imp.height, None, srcDir)
stack = ImageStack(imp.width, imp.height)
# Add a slice to the virtual stack, relative to the srcDir
#
#stack.addSlice(path[len(srcDir):])
# Add a slice to the real stack
#
stack.addSlice(filename, imp.getProcessor())
# Make a ImagePlus from the stack
ImagePlus("Stack from subdirectories", stack).show()
def run():
sId = IJ.getString("Filenames contain:", "T0000");
srcDir = DirectoryChooser("Choose!").getDirectory()
if not srcDir:
# user canceled dialog
return
# Assumes all files have the same size
stack = None
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-TIFF files
if not (sId in filename):
continue
print(filename)
path = os.path.join(root, filename)
# Upon finding the first image, initialize the VirtualStack
imp = IJ.openImage(path)
if stack is None:
# stack = VirtualStack(imp.width, imp.height, None, srcDir)
stack = ImageStack(imp.width, imp.height)
# Add a slice to the virtual stack, relative to the srcDir
#
#stack.addSlice(path[len(srcDir):])
# Add a slice to the real stack
#
stack.addSlice(filename, imp.getProcessor())
# Make a ImagePlus from the stack
ImagePlus("Stack from subdirectories", stack).show()
def actionPerformed(self, event):
outDir = IJ.getDirectory("Save category file in directory...")
if not outDir: return # when cancelled
filename = IJ.getString("Filename", "categories.txt")
if not filename: return # when cancelled
outPath = os.path.join(outDir, filename)
listButtons = winButton.getPanel().getComponents()
with open(outPath, "w") as catFile:
for button in listButtons:
catFile.write(button.getLabel().encode("utf-8") + "\n") # important to use UTF-8 otherwise troubles
def addCategoryComponent(self):
"""
Request a new category name, create the associated category component via the makeCategory method and update the dialog
"""
newCategory = IJ.getString("Enter new category name", "new category")
if not newCategory:
return # if Cancelled (ie newCat=="") or empty field just dont go further
# Add new component to the gui for this category and repaint GUI
newComponent = self.makeCategoryComponent(newCategory)
if newComponent is None: return
if not isinstance(newComponent, Component):
raise TypeError("Expect a component to be added to the dialog")
self.getPanel().add(newComponent) # component 1 is the panel
self.pack() # recompute the layout and update the display
def actionPerformed(self, event):
source = event.getSource() # test here if it is a button
if isinstance(source, Button): # if type is a button get label, and check command, otherwise pass to GenericDialogPlus.actionPeformed
sourceLabel = source.getLabel()
if sourceLabel == CategoryDialog.ADD_CATEGORY:
newCategory = IJ.getString("Enter new category name", "new category")
if not newCategory: return # if Cancelled (ie newCat=="") or empty field just dont go further
self.panel.add(TextField(newCategory)) # Add new text field with the new category
self.pack() # recompute the layout and update the display
# Anyway do the mother class usual action handling
GenericDialogPlus.actionPerformed(self, event)
from sys import argv
if len(argv) > 1:
file = argv[1]
else:
file = "Stitching-overview.jpg"
if len(argv) > 2:
label = argv[2]
else:
label = ''
ImageJ()
screenshot = IJ.openImage(file)
print "Opened", file, screenshot
else:
screenshot = IJ.getImage()
label = IJ.getString('Label:', '')
# make a gradient image
ip = screenshot.getProcessor()
w = ip.getWidth()
h = ip.getHeight()
u = int(0.99 * 255)
l = int(0.5 * 255)
def gray2rgb(value):
return (value << 16) | (value << 8) | value
# This is a trick: make a 1xh image (because calculation is slow in Python) and resize it to wxh
from jarray import array
#IJ.run("Multiply...", "value=2.2")
IJ.beep()
gd = GenericDialog("Clockwise Rotation?")
gd.addChoice("How Many Degrees",["0","90","180",'270'],"0")
gd.showDialog()
rotation = gd.getChoices().get(0).getSelectedItem()
#in while loop
while True:
IJ.run("Stack to Images")
IJ.run("Images to Stack", "name=Stack title=[] use")
imp = IJ.getImage()
myWait = ij.gui.WaitForUserDialog('Select Region to Load Full Res')
myWait.show()
region=IJ.getString("What to call region?", "")
print(region)
width=imp.getWidth()
height=imp.getHeight()
roi=imp.getRoi()
xmin=roi.bounds.getMinX()/width
xmax=roi.bounds.getMaxX()/width
ymin=roi.bounds.getMinY()/height
ymax=roi.bounds.getMaxY()/height
print(dir(imp))
IJ.run("Make Composite", "display=Composite")
IJ.run("Select All")
#IJ.run("Multiply...", "value=2.0")
IJ.run("Stack to RGB")
def getString(mssg, default):
return IJ.getString(mssg, default)
from ij import IJ
imp = IJ.getImage()
title = imp.getTitle()
title = title[:-4]
interval_units = IJ.getString("Collection interval units: ", 'hrs')
start_time = IJ.getString("Start time: ", '0')
interval_by_units = IJ.getNumber("Collection interval in {}:".format(interval_units), 0.17)
fontsize = IJ.getNumber("Fontsize:", 14)
#get the directory containing the active image
path = IJ.getDirectory("image")
# If the active image is a duplicate of another image open, its path will be False and
# will print as 'None'. If this is the case, have the user choose a directory to put the
# timestamped tif
if not path:
IJ.log("Image has no source directory")
path = IJ.getDirectory("Choose the directory to save the timestamped tif")
else:
pass
height = imp.getHeight()
width = imp.getWidth()
size = imp.getImageStackSize()
IJ.log("Image title: {}".format(title))
IJ.log("Save path: {}".format(path))
IJ.log("Height: {}".format(height))
IJ.log("Width: {}".format(width))
IJ.log("Size: {}".format(size))
#!/bin/sh
"""'exec "$(dirname "$0")"/ImageJ.sh --jython "$0" "$@" # (call again with fiji)"""
from ij import IJ, ImageJ
label = "Fiji Is Just ImageJ"
if IJ.getInstance() == None:
# called from the command line
from sys import argv
if len(argv) > 1:
file = argv[1]
else:
file = "Stitching-overview.jpg"
if len(argv) > 2:
label = argv[2]
ImageJ()
screenshot = IJ.openImage(file)
print "Opened", file, screenshot
else:
screenshot = IJ.getImage()
label = IJ.getString("Label:", label)
from fiji import Prettify_Wiki_Screenshot
plugin = Prettify_Wiki_Screenshot()
plugin.label = label
plugin.run(screenshot.getProcessor())
#!/bin/sh
''''exec "$(dirname "$0")"/ImageJ.sh --jython "$0" "$@" # (call again with fiji)'''
from ij import IJ, ImageJ
label = 'Fiji Is Just ImageJ'
if IJ.getInstance() == None:
# called from the command line
from sys import argv
if len(argv) > 1:
file = argv[1]
else:
file = "Stitching-overview.jpg"
if len(argv) > 2:
label = argv[2]
ImageJ()
screenshot = IJ.openImage(file)
print "Opened", file, screenshot
else:
screenshot = IJ.getImage()
label = IJ.getString('Label:', label)
from fiji import Prettify_Wiki_Screenshot
plugin = Prettify_Wiki_Screenshot()
plugin.label = label
plugin.run(screenshot.getProcessor())
