## Use this area to create a log file for tracking output of Trackmate
######
#####
####
###
##
#
for i in image_list:
ImageJ();
imp = [];
match_roi = [];
match_count = 1;
m = re.search('(Batch\d+_\d+_XY\d{2}).*.tif', i);
match = m.group(1);
quality_value = 0;
for j in roi_list:
if re.search(match, j):
match_roi.append(j);
if len(match_roi) >= 1:
os.mkdir(image_directory + "Results/" + file_name);
#!/bin/sh
''''exec "$(dirname "$0")"/ImageJ.sh --jython "$0" "$@" # (call again with fiji)'''
from org.jpedal import PdfDecoder
from ij import ImageJ, ImagePlus
import sys
if len(sys.argv) != 2:
print 'Usage:', sys.argv[0], 'source.pdf'
sys.exit(1)
ij = None
decoder = PdfDecoder(False)
decoder.setExtractionMode(PdfDecoder.RAWIMAGES | PdfDecoder.FINALIMAGES)
decoder.openPdfFile(sys.argv[1])
for page in range(0, decoder.getPageCount()):
decoder.decodePage(page + 1)
images = decoder.getPdfImageData()
image_count = images.getImageCount()
for i in range(0, image_count):
name = images.getImageName(i)
image = decoder.getObjectStore().loadStoredImage('R' + name)
if ij == None:
ij = ImageJ()
ij.exitWhenQuitting(True)
ImagePlus(name, image).show()
decoder.flushObjectValues(True)
decoder.closePdfFile()
#!/bin/sh
''''exec "$(dirname "$0")"/../fiji --jython "$0" "$@" # (call again with fiji)'''
import sys
from ij import IJ, ImageJ
if len(sys.argv) < 2:
print 'Need an output file'
sys.exit(1)
window = ImageJ()
window.hide()
IJ.run("Capture Screen ")
IJ.save(sys.argv[1])
sys.exit(0)
from org.jpedal import PdfDecoder
from ij import ImageJ, ImagePlus
import sys
if len(sys.argv) != 2:
print 'Usage:', sys.argv[0], 'source.pdf'
sys.exit(1)
ij = None
decoder = PdfDecoder(False)
decoder.setExtractionMode(PdfDecoder.RAWIMAGES | PdfDecoder.FINALIMAGES)
decoder.openPdfFile(sys.argv[1])
for page in range(0, decoder.getPageCount()):
decoder.decodePage(page + 1)
images = decoder.getPdfImageData()
image_count = images.getImageCount()
for i in range(0, image_count):
name = images.getImageName(i)
image = decoder.getObjectStore().loadStoredImage('R' + name)
if ij == None:
ij = ImageJ()
ij.exitWhenQuitting(True)
ImagePlus(name, image).show()
decoder.flushObjectValues(True)
decoder.closePdfFile()
def startIJ(): Main.premain() global currentWindow currentWindow = ImageJ() currentWindow.exitWhenQuitting(True) Main.postmain()
#!/bin/sh
''''exec "$(dirname "$0")"/../fiji --jython "$0" "$@" # (call again with fiji)'''
import sys
from ij import IJ, ImageJ
if len(sys.argv) < 2:
print 'Need an output file'
sys.exit(1)
window = ImageJ()
window.hide()
IJ.run("Capture Screen ")
IJ.save(sys.argv[1])
sys.exit(0)
# Fetch all the samples into a local directory
from fiji import User_Plugins
from ij import IJ, ImageJ, Menus
from java.lang import System
from os import makedirs, rename
from os.path import exists, isdir
import urllib
ij = ImageJ()
menu = User_Plugins.getMenuItem('File>Open Samples')
commands = Menus.getCommands()
plugin = 'ij.plugin.URLOpener("'
samples = System.getProperty('fiji.dir') + '/samples'
for i in range(0, menu.getItemCount()):
label = menu.getItem(i).getLabel()
if label == '-':
continue
command = commands[label]
if command != None and \
command.startswith(plugin) and command.endswith('")'):
url = command[len(plugin):-2]
slash = url.rfind('/')
def startIJ(): Main.premain() global currentWindow currentWindow = ImageJ() currentWindow.exitWhenQuitting(True) Main.postmain()
