def run():
global pmWin
global imgData
helpText = "This is Point Marker, " + \
"a program for marking points in images.\n\n" + \
">> Press OK to Select a file for storing points infomation.\n"+\
">> TIF-Images within the same directory will be auto-loaded."
MessageDialog(IJ.getInstance(),"Point Marker Guide", helpText)
fileChooser = OpenDialog("Point Marker: Choose working directory and file")
outfilePath = fileChooser.getPath()
imgDir = fileChooser.getDirectory()
if not imgDir: return
imgPaths = []
if imgDir:
for root, directories, filenames in os.walk(imgDir):
for filename in filenames:
if not filename.endswith(".tif"):
continue
imgPaths.append(os.path.join(root, filename))
pointsTable1 = readPoints(outfilePath)
imgData = PointMarkerData(imgPaths, outfilePath, pointsTable1)
IJ.setTool("multipoint")
PointRoi.setDefaultSize(3)
pmWin = PointMarkerWin(imgData)
pmWin.win.setLocation(IJ.getInstance().getLocation())
prepareNewImage(imgData)
def run():
global pmWin
global imgData
helpText = "This is Point Marker, " + \
"a program for marking points in images.\n\n" + \
">> Press OK to Select a file for storing points infomation.\n"+\
">> TIF-Images within the same directory will be auto-loaded."
MessageDialog(IJ.getInstance(), "Point Marker Guide", helpText)
fileChooser = OpenDialog("Point Marker: Choose working directory and file")
outfilePath = fileChooser.getPath()
imgDir = fileChooser.getDirectory()
if not imgDir: return
imgPaths = []
if imgDir:
for root, directories, filenames in os.walk(imgDir):
for filename in filenames:
if not filename.endswith(".tif"):
continue
imgPaths.append(os.path.join(root, filename))
pointsTable1 = readPoints(outfilePath)
imgData = PointMarkerData(imgPaths, outfilePath, pointsTable1)
IJ.setTool("multipoint")
PointRoi.setDefaultSize(3)
pmWin = PointMarkerWin(imgData)
pmWin.win.setLocation(IJ.getInstance().getLocation())
prepareNewImage(imgData)
def MultiFileDialog(title):
#hide/show debug prints
verbose = 0
# Choose image file(s) to open
fc = JFileChooser()
fc.setMultiSelectionEnabled(True)
fc.setDialogTitle(title)
sdir = OpenDialog.getDefaultDirectory()
if sdir!=None:
fdir = File(sdir)
if fdir!=None:
fc.setCurrentDirectory(fdir)
returnVal = fc.showOpenDialog(IJ.getInstance())
if returnVal!=JFileChooser.APPROVE_OPTION:
return
files = fc.getSelectedFiles()
paths = []
for i in range(len(files)):
paths.append(os.path.join(files[i].getParent(), files[i].getName()))
if verbose > 0:
for i in range(len(files)):
path = os.path.join(files[i].getParent(), files[i].getName())
print "Path: " + path
return paths
def run():
projects = Project.getProjects()
if projects is None or projects.isEmpty():
IJ.log('No project open!')
return
ls = projects.get(0).getRootLayerSet()
trees = ls.getZDisplayables(Treeline)
trees.addAll(ls.getZDisplayables(AreaTree))
if trees.isEmpty():
IJ.log('No trees to process!')
return
dc = DirectoryChooser('Target folder')
targetFolder = dc.getDirectory()
if targetFolder is None:
return # user canceled
if targetFolder[len(targetFolder) -1] != '/':
targetFolder += '/'
fdir = File(targetFolder)
for f in fdir.listFiles():
if f.isHidden():
continue
yn = YesNoCancelDialog(IJ.getInstance(), "WARNING", "Folder not empty! Continue?")
if yn.yesPressed():
break
else:
return
process(trees, targetFolder)
def MultiFileDialog(title):
#hide/show debug prints
verbose = 0
# Choose image file(s) to open
fc = JFileChooser()
fc.setMultiSelectionEnabled(True)
fc.setDialogTitle(title)
sdir = OpenDialog.getDefaultDirectory()
if sdir != None:
fdir = File(sdir)
if fdir != None:
fc.setCurrentDirectory(fdir)
returnVal = fc.showOpenDialog(IJ.getInstance())
if returnVal != JFileChooser.APPROVE_OPTION:
return
files = fc.getSelectedFiles()
paths = []
for i in range(len(files)):
paths.append(os.path.join(files[i].getParent(), files[i].getName()))
if verbose > 0:
for i in range(len(files)):
path = os.path.join(files[i].getParent(), files[i].getName())
print "Path: " + path
return paths
def run():
helpText = "This program will batch convert any tif image to 8-bit greyscale, " + \
"and empty calibration infomation.\n\n" + \
">> Press OK to Select a directory of TIFF images."
MessageDialog(IJ.getInstance(), "Empty Calibration Guide", helpText)
srcDir = DirectoryChooser("Chose Source Dir").getDirectory()
if srcDir is None:
IJ.log("Choose Dir Canceled!")
return
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
if not filename.endswith(".tif"):
continue
imgPath = os.path.join(root, filename)
outPath = os.path.join(root, "decal-" + filename)
imp = IJ.openImage(imgPath)
imp.setCalibration(Calibration())
ic = ImageConverter(imp)
ic.convertToGray8()
IJ.saveAsTiff(imp, outPath)
print "removed calibration and saved to ", os.path.basename(
outPath)
def validate(target_folder):
f = File(target_folder)
if len(File(target_folder).list(Filter())) > 0:
yn = YesNoCancelDialog(IJ.getInstance(), "Warning!", "Target folder is not empty! May overwrite files! Continue?")
if yn.yesPressed():
return True
else:
return False
return True
def run():
helpText = "This program will batch convert .swc files to " + \
"SVG vector graphs.\n\n" + \
">> Press OK to Select a directory of .swc traces."
MessageDialog(IJ.getInstance(),"Batch SWC to SVG Guide", helpText)
d = DirectoryChooser("Chose Traces Dir").getDirectory()
if d is None:
IJ.log("Choose Dir Canceled!")
return
swc_files = [ os.path.join(d,x) for x in os.listdir(d) if re.search('(?i)\.swc$',x) ]
pafm = PathAndFillManager(10240, # width
10240, # height
1, # depth
1, # x spacing
1, # y spacing
1, # z spacing
"pixel")
for swc_file in swc_files:
out_file = swc_file + ".svg"
if not pafm.importSWC(swc_file,False): # second parameter is ignoreCalibration
IJ.error("Failed to load: "+swc_file)
for i in range(pafm.size()):
path = pafm.getPath(i)
f = open(out_file, "wb")
f.write(toSvgString_polyline(path))
f.close()
f = open(swc_file + "-path.svg", "wb")
f.write(toSvgString_path(path))
f.close()
f = open(swc_file + "-points.csv",'wb')
writer = csv.writer(f)
writer.writerow(["x", "y"])
writer.writerows(toListOfPoints(path))
f.close()
def FolderDialog(title, folder):
fc = JFileChooser()
fc.setMultiSelectionEnabled(False)
fc.setDialogTitle(title)
fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
fc.setAcceptAllFileFilterUsed(False);
if folder ==None:
sdir = OpenDialog.getDefaultDirectory()
else:
sdir = folder
if sdir!=None:
fdir = File(sdir)
if fdir!=None:
fc.setCurrentDirectory(fdir)
returnVal = fc.showOpenDialog(IJ.getInstance())
if returnVal!=JFileChooser.APPROVE_OPTION:
return
folder = fc.getSelectedFile();
path = os.path.join(folder.getParent(), folder.getName())
return path
def arrange():
# Fiji JFrame Instance and Measurements
IJ_FRAME = IJ.getInstance()
IJ_WIDTH = IJ_FRAME.getWidth()
IJ_HEIGHT = IJ_FRAME.getHeight()
#
# Display Screen Measurements
SCREEN_DIMS = IJ_FRAME.getGraphicsConfiguration().getBounds()
SCREEN_WIDTH = int(SCREEN_DIMS.getWidth())
SCREEN_HEIGHT = int(SCREEN_DIMS.getHeight())
print SCREEN_WIDTH, SCREEN_HEIGHT
#
SPECS = {
# Format:
# WINDOW : [x, y, w, h]
#
ImageJ : [SCREEN_WIDTH - IJ_WIDTH, 0, None, None],
TextEditor : [SCREEN_WIDTH-640, SCREEN_HEIGHT-540, 640, 540],
RoiManager : [0, 0, None, None],
TextWindow : [0, SCREEN_HEIGHT-320, 480, 320],
Recorder : [0, SCREEN_HEIGHT-320-120, 480, 320],
}
# the window is Fiji JFrame itself
x,y,w,h = SPECS[ type(IJ_FRAME) ]
IJ_FRAME.setLocation(x,y)
#
niws = WM.getNonImageWindows()
print "%i non-image windows are open" % (len(niws))
for win in niws:
print type(win)
x, y, w, h = SPECS[ type(win) ]
if w == None: w = win.getWidth()
if h == None: h = win.getHeight()
win.setSize(w, h)
win.setLocation(x, y)
def run():
helpText = "This program will batch convert any tif image to 8-bit greyscale, " + \
"and empty calibration infomation.\n\n" + \
">> Press OK to Select a directory of TIFF images."
MessageDialog(IJ.getInstance(),"Empty Calibration Guide", helpText)
srcDir = DirectoryChooser("Chose Source Dir").getDirectory()
if srcDir is None:
IJ.log("Choose Dir Canceled!")
return
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
if not filename.endswith(".tif"):
continue
imgPath = os.path.join(root, filename)
outPath = os.path.join(root, "decal-" + filename)
imp = IJ.openImage(imgPath)
imp.setCalibration(Calibration())
ic = ImageConverter(imp)
ic.convertToGray8()
IJ.saveAsTiff(imp, outPath)
print "removed calibration and saved to ", os.path.basename(outPath)
event_interfaces = set([])
while len(classes) > 0:
cl = classes.pop() # remove the last one
if cl.isInterface() and list(cl.getInterfaces()).count(EventListener) > 0:
event_interfaces.add(cl)
continue
# Else, search its superclass and its implemented interfaces
sup = cl.getSuperclass()
if sup:
classes.append(sup)
for interface in cl.getInterfaces():
classes.append(interface)
return event_interfaces
# ImageJ main window deals with KeyListener, so use it too to search for interfaces
obs = [canvas, IJ.getInstance()]
classes = map(lambda x: x.getClass(), obs)
# Add spying instances of each event interface to the image canvas
for i, interface in enumerate(findEventInterfaces(*classes)):
# Find the method, if it exists, like "addMouseListener" for "MouseListener"
adder = getattr(canvas, "add" + interface.getSimpleName(), None)
if adder:
# Dynamically create a class that implements the interface
# with all its methods using the spyEvent function to print the event
methods = {method.getName(): spyEvent for method in interface.getDeclaredMethods()}
event_listener_class = type('EventInterface_%i' % i, # the name of the new class
(interface,), # the tuple of interfaces that it implements
methods) # the dictionary of method names vs functions
adder(event_listener_class()) # add a new instance
#!/bin/sh
''''exec "$(dirname "$0")"/../fiji --jython "$0" "$@" # (call again with fiji)'''
from java.awt import *
from ij3d import Image3DUniverse
from javax.media.j3d import Transform3D
from ij import IJ
if IJ.getInstance() == None:
# called from the command line
from ij import ImageJ, ImagePlus
from ij.process import Blitter, ColorProcessor
from java.lang import Math
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:', '')
f = open(home + '/.netrc')
for line in f.readlines():
line = line.strip()
if line == 'machine ' + host:
found = True
elif found == False:
continue
elif line.startswith('login '):
user = line[6:]
elif line.startswith('password '):
password = line[9:]
elif line.startswith('machine '):
break
f.close()
if not client.isLoggedIn():
if user != None and password != None:
client.logIn(user, password)
response = client.uploadPage(PAGE, result, 'Updated by plugin-list-parser')
if client.isLoggedIn():
client.logOut()
if not response:
print 'There was a problem with uploading', PAGE
if IJ.getInstance() == None:
sys.exit(1)
else:
print 'No .netrc entry for', URL
if IJ.getInstance() == None:
sys.exit(1)
else:
print result
def quitIJ(): global currentWindow IJ.getInstance().quit() currentWindow = None
# Python05-4.py
# IJ BAR: https://github.com/tferr/Scripts#scripts
####################################################
# 5.4 Scripting ImageJ: Creating an empty image (IV)
####################################################
# What about changing the ROI properties (color, name
# name, dimensions, etc.) of the Rectangle created in
# the previous exercise? Lets ask ourselves about it:
from ij import IJ
import ij.gui.YesNoCancelDialog as dialog
# Let's prompt us for the question:
question_prompt = dialog(
IJ.getInstance(), # 1st argument: Parent frame
"What about ROI properties?", # 2nd argument: Dialog title
"Can you change the ROI color, its name, etc?" # 3rd argument: Dialog message
) # see http://javadoc.imagej.net/ImageJ1/index.html?ij/gui/YesNoCancelDialog.html
# Let's get the answer:
if question_prompt.cancelPressed(): # Was the dialog canceled?
IJ.showMessage("Refuse to answer? Are you tired?")
elif question_prompt.yesPressed(): # Was the answer "Yes"?
IJ.showMessage("Cool. Go ahead!")
else: # If none of the above, the remaining option was "No"
IJ.showMessage("Hmmm... Did you look into the ij.gui.Roi API?")
# Tip 1: You will find useful methods in:
# - http://javadoc.imagej.net/ImageJ1/index.html?ij/gui/Roi.html
# - http://javadoc.imagej.net/ImageJ1/index.html?ij/ImagePlus.html
#
def quitIJ(): global currentWindow IJ.getInstance().quit() currentWindow = None
from ij import IJ
from ij.plugin.frame import RoiManager
from ij.gui import PolygonRoi
from ij.gui import Roi
from java.awt import FileDialog
fd = FileDialog(IJ.getInstance(), "Open", FileDialog.LOAD)
fd.show()
file_name = fd.getDirectory() + fd.getFile()
print(file_name)
RM = RoiManager()
rm = RM.getRoiManager()
imp = IJ.getImage()
textfile = open(file_name, 'r')
for line in textfile:
xy = map(int, line.rstrip().split(','))
X = xy[::2]
Y = xy[1::2]
imp.setRoi(PolygonRoi(X, Y, Roi.POLYGON))
#IJ.run(imp, "Convex Hull", "")
roi = imp.getRoi()
print roi
rm.addRoi(roi)
rm.runCommand("Associate", "true")
rm.runCommand("Show All with labels")
1, # y spacing
1, # z spacing
"pixel")
for swc_file in swc_files:
out_file = swc_file + ".svg"
if not pafm.importSWC(swc_file,False): # second parameter is ignoreCalibration
IJ.error("Failed to load: "+swc_file)
for i in range(pafm.size()):
path = pafm.getPath(i)
f = open(out_file, "wb")
f.write(toSvgString_polyline(path))
f.close()
f = open(swc_file + "-path.svg", "wb")
f.write(toSvgString_path(path))
f.close()
f = open(swc_file + "-points.csv",'wb')
writer = csv.writer(f)
writer.writerow(["x", "y"])
writer.writerows(toListOfPoints(path))
f.close()
##############
run()
MessageDialog(IJ.getInstance(),"Batch SWC to SVG Guide", "Done")
def check_fusion_settings(czi_path):
"""Check for fusion settings and asks confirmation to user if H5/XML fusion
Parameters
----------
czi_path : str
Path to the CZI file
Returns
-------
bool
Bool for fusion
str
Method of RAM handling
bool
Bool for TIFF or H5/XML fusion
"""
# Default values
do_fusion = True
fuse_tiff = True
reader = ZeissCZIReader()
m = DynamicMetadataOptions()
m.setBoolean(ZeissCZIReader.ALLOW_AUTOSTITCHING_KEY, False)
m.setBoolean(ZeissCZIReader.RELATIVE_POSITIONS_KEY, True)
reader.setMetadataOptions(m)
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(str(czi_path))
nbr_tp = omeMeta.getTimestampAnnotationCount() + 1
nbr_chnl = omeMeta.getChannelCount(0)
# check the file size of the file to be fused and compare to the available RAM
# h5_filesize = os.path.getsize(export_path_temp + ".h5")
h5_filesize = os.path.getsize(czi_path) / 2
free_memory = get_free_memory()
print("h5 filesize " + convert_bytes(h5_filesize))
print("free memory in ij " + convert_bytes(free_memory))
# TODO: include in below calculation t_end, since only one t is fused at a time.
if free_memory > (6 * h5_filesize / downsampling):
ram_handling = "[Precompute Image]"
else:
ram_handling = "Virtual"
print("fusion mode used " + str(ram_handling))
# if autoselect_illuminations and nbr_ill > 1:
# ill_value = 2
# else:
# ill_value = 1
ram_requirement = 2 * h5_filesize / (nbr_tp * nbr_chnl * downsampling)
print(ram_requirement)
sufficient_ram = ram_requirement < free_memory / 10
if not sufficient_ram:
try:
yn = YesNoCancelDialog(
IJ.getInstance(),
"Warning!",
(
"File size is too big to use TIFF for fusion\n"
"Fusion will happen using H5/XML which might take weeks. Are you "
"sure you want to do fusion ?\n"
"All steps prior to fusion would still happen, allowing for manual "
"fusion and tile selection."
),
)
if yn.yesPressed():
fuse_tiff = False
else:
do_fusion = False
except Exception:
# when running headless the above will raise a java.awt.HeadlessException,
# so we simply fall back to the same behavior as if "No" was clicked:
do_fusion = False
return do_fusion, ram_handling, fuse_tiff
if Verbose:
IJ.log('... ' + str(xpos) + ', ' + str(ypos) + ', ' + str(zpos))
outimp.getStack().getProcessor(int(zpos)+1).putPixel(int(xpos), int(ypos), i+1)
return outimp
Verbose = False
if IJ.isMacro():
opt = getArgument()# ImageJ specific function Macro.getOptions()
if len(opt) == 0:
opt = OPT_PLACEHOLDER
IJ.log(opt)
optA = opt.split()
Number_of_Cluster = int(optA[0])
Iteration = int(optA[1])
else:
gd = GenericDialog("KMean Points Clustering", IJ.getInstance())
gd.addNumericField("Expected Number of Clusters", 4, 0)
gd.addNumericField("Iterations", 10, 0)
gd.showDialog()
Number_of_Cluster = int(gd.getNextNumber())
Iteration = int(gd.getNextNumber())
imp = IJ.getImage()
outimp = core(imp)
outimp.show()
IJ.run(outimp, "glasbey inverted", "")
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