def gen_macro(mosaics, indir, outfile=None, opts=None):
"""Generate stitcher macro code and optionally save it in a file.
Parameters
----------
mosaics : micrometa.experiment.MosaicExperiment
The mosaic object of the stitching experiment.
indir : str
The path to use as input directory *INSIDE* the macro.
outfile : str (optional)
The path to a file for saving the generated macro code.
opts : dict (optional)
A dict to be passed on to micrometa.imagej.gen_stitching_macro().
Returns
-------
list(str)
The generated macro code as a list of strings (one str per line).
"""
templates = join(getProperty("fiji.dir"), "jars", "python-micrometa.jar")
log.info("Using macro templates from [%s].", templates)
log.info("Using [%s] as base directory.", indir)
# set the default stitcher options
stitcher_options = {
"export_format": '".ids"',
"split_z_slices": "false",
"rotation_angle": 0,
"stitch_regression": 0.3,
"stitch_maxavg_ratio": 2.5,
"stitch_abs_displace": 3.5,
"compute": "false",
}
# merge explicit options, overriding the defaults from above if applicable:
if opts:
stitcher_options.update(opts)
code = micrometa.imagej.gen_stitching_macro(
name=mosaics.infile["dname"],
path=indir,
tplpfx="templates/imagej-macro/stitching",
tplpath=templates,
opts=stitcher_options,
)
log.debug("============= begin of generated macro code =============")
log.debug(flatten(code))
log.debug("============= end of generated macro code =============")
if outfile is not None:
log.info("Writing stitching macro.")
micrometa.imagej.write_stitching_macro(code, outfile)
return code
def _raise_import_failed(self, name, error):
import_type = '%s ' % self._type if self._type else ''
msg = "Importing %s'%s' failed: %s" % (import_type, name, error.message)
if not error.details:
raise DataError(msg)
msg = [msg, error.details]
msg.extend(self._get_items_in('PYTHONPATH', sys.path))
if JYTHON:
classpath = getProperty('java.class.path').split(os.path.pathsep)
msg.extend(self._get_items_in('CLASSPATH', classpath))
raise DataError('\n'.join(msg))
def _raise_import_failed(self, name, error):
import_type = '%s ' % self._type if self._type else ''
msg = "Importing %s'%s' failed: %s" % (import_type, name, error.message)
if not error.details:
raise DataError(msg)
msg = [msg, error.details]
msg.extend(self._get_items_in('PYTHONPATH', sys.path))
if sys.platform.startswith('java'):
classpath = getProperty('java.class.path').split(os.path.pathsep)
msg.extend(self._get_items_in('CLASSPATH', classpath))
raise DataError('\n'.join(msg))
from __future__ import with_statement
import com.nrims as nrims
import com.nrims.data as nrimsData
import time
from datetime import timedelta, datetime, date
import java.io.File as File
import java.util.ArrayList as ArrayList
import java.lang.Integer as Integer
import java.lang.Double as Double
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/Scripts/Plugins/OpenMIMS Scripts/")
#from OMUtilities import MultiFileDialog
#from OMUtilities import CheckFileLists
import javax.swing.JFileChooser as JFileChooser
import java.io.File as File
from ij import IJ
import ij.io.OpenDialog as OpenDialog
import ij.gui.YesNoCancelDialog as YesNoCancelDialog
import csv
import os
import jarray
def FolderDialog(title, folder):
fc = JFileChooser()
fc.setMultiSelectionEnabled(False)
fc.setDialogTitle(title)
fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
fc.setAcceptAllFileFilterUsed(False);
if folder ==None:
from ij import IJ
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/NordenTools")
import NordenTools as nt
from setup import *
for timepointstring in time_points:
IJ.log("Processing " + timepointstring + "...")
project = Project.openFSProject(trakem_dir + timepointstring + ".xml", True)
Thread.sleep(2000)
# EXPORT RAW
windowName = nt.openStack()
IJ.log(">> "+windowName)
IJ.selectWindow(windowName);
IJ.run("Save", "save="+output_dir+"raw_"+timepointstring+".tif");
IJ.run("Close")
# EXPORT MASK
nt.exportMask()
IJ.selectWindow("Labels");
IJ.run("Save", "save="+output_dir+"labels_"+timepointstring+".tif");
IJ.run("Close")
# EXPORT SEGMENTATION
nt.exportSegmentation()
IJ.selectWindow("Segmentation");
IJ.run("Save", "save="+output_dir+"seg_"+timepointstring+".tif");
IJ.run("Close")
# CLOSE PROJECT
Thread.sleep(1000)
project.getLoader().setChanged(False) # avoid dialog at closing
#import os, sys
from ij import IJ, ImagePlus, ImageStack
from ij3d import Image3DUniverse, Content
from java.lang.System import getProperty
import vib.PointList
from javax.vecmath import Color3f, Point3f
from ij.plugin.frame import RoiManager
from ij.gui import PointRoi
print "===Starting bMergeChannels_"
pluginDir = getProperty("fiji.dir") + "/plugins/bob-fiji-plugins/"
#open text file that gives us a list of images (for now it will be 2)
file = open(pluginDir + "bMergeChannels.txt", "r")
do3d = 0
doComposite = 0
pointList = [] #list of spine points
cPointList = [] #list of connection points
lPointList = [] #list of backbone centerline points
doROI = 0
for line in file.readlines():
currLine = line.strip()
print currLine
token, value = currLine.split("=")
if currLine.startswith('file1'):
filepath1 = value
if currLine.startswith('file2'):
import sys
# before doing anything else check the Python version:
if not sys.version_info[:2] >= (2, 7):
raise Exception('Python 2.7 or newer is required!')
import argparse
from os.path import join, dirname, basename
# ImageJ imports
from ij import IJ
from ij.io import OpenDialog
from ij.gui import GenericDialog
# explicitly add our libs to the module search path
from java.lang.System import getProperty
imcfdir = join(getProperty('fiji.dir'), 'plugins', 'IMCF')
imcftpl = join(imcfdir, 'imcf_macros.jar')
import microscopy.fluoview as fv
from microscopy import imagej
from log import log, set_loglevel
from misc import flatten
from ijpy import IJLogHandler
import imcf
def ui_get_input_file():
"""Ask user for input file and process results."""
dialog = OpenDialog("Choose a 'MATL_Mosaic.log' file")
fname = dialog.getFileName()
if (fname is None):
#@File (label="Images folder", style="directory") imgdir
#@String (label="Images extension", value=".tif") ext
#@Boolean (label="Save the stack?") save
#@String (visibility=MESSAGE, value="Select save if you want to keep to stack containing the images to be traced on disk.") msg
# Bootstrap to extend modules search path #
from sys import path
import os.path
from java.lang.System import getProperty
jython_scripts = os.path.join(getProperty('user.home'), 'Jython_scripts')
path.append(jython_scripts)
#=========================================#
from IBPlib.ij.Utils.Files import buildList
from IBPlib.ij.Utils import ThreadedFileSaver
from ij import (IJ, ImagePlus, ImageStack)
from ij.plugin import ZProjector
def images_to_frames_stack(imgdir, savestack=False):
'''
Method for preparing a stack of frames using images inside the input folder.
When savestack is true it saves the resulting stack to the images folder while opening the stack.
'''
title = "tracing_stack.tiff" # Title of the final image stack.
imgdir = imgdir.getPath()
imglist = buildList(imgdir, ext)
if not imglist:
raise IOError("No {0} were found in {0}.".format(ext, imgdir))
method = "max"
# @File(label = "Image File", persist=True) FILENAME
# @OUTPUT String FILENAME
# @UIService uiService
# @LogService log
# required imports
import os
import json
import time
import sys
import jarray
from java.lang.System import getProperty
sys.path.append(getProperty('fiji.dir') + '/scripts')
from java.lang import Double, Integer
from ij import IJ, ImagePlus, ImageStack, Prefs
from ij.process import ImageProcessor, LUT
from ij.plugin import ChannelSplitter
from fijipytools import ExportTools, FilterTools, ImageTools, ImportTools
from fijipytools import AnalyzeTools, RoiTools, MiscTools, ThresholdTools
from org.scijava.log import LogLevel
from ij.plugin import Duplicator
def calc_normvar(ip, mean, width, height):
normvar = 0
b = 0
for x in range(0, width):
for y in range(0, height):
'''Finds the sector boundaries, giving us the
chirality of range expansions.'''
###### Import Stuff #######
import sys
import os
from java.lang.System import getProperty
from ij import IJ
# Add the path of all of my scripts
fijiDir = getProperty("fiji.dir")
myPluginsTop = os.path.join(fijiDir, 'plugins');
myPluginsTop = os.path.join(myPluginsTop, 'Bryan');
walker = os.walk(myPluginsTop)
for root, dirs, files in os.walk(myPluginsTop, topdown=False):
for name in dirs:
sys.path.append(os.path.join(root, name))
# Continue
import GlobalRangeVariables_ as globalRangeVariables
radiusToFillIncrease = 1.10
def run(original):
'''Assumes that there are 3 images. The first two are
fluorescence, the last one is brightfield.'''
# Adjust the scale of the original image so that the scale of the unit is of order 1
adjustScale(original)
fluorescence, brightfield = separateChannels(original)
edges = findRegionEdges(fluorescence)
#!/bin/sh
''''exec "$(dirname "$0")"/../fiji --jython "$0" "$@" # (call again with fiji)'''
from java.lang.System import getProperty
# Find out the checksum
dbPath = getProperty('fiji.dir') + '/db.xml.gz'
def getTimestamp(plugin, checksum):
from fiji.updater.logic import PluginCollection, XMLFileReader
if PluginCollection.getInstance().size() == 0:
from java.io import FileInputStream
from java.util.zip import GZIPInputStream
print 'Reading db.xml.gz'
XMLFileReader(GZIPInputStream(FileInputStream(dbPath)), 0)
if plugin.startswith('precompiled/'):
plugin = plugin[12:]
plugin = PluginCollection.getInstance().getPlugin(plugin)
if plugin.current != None and checksum == plugin.current.checksum:
return plugin.current.timestamp
for version in plugin.previous.keySet():
if checksum == version.checksum:
return version.timestamp
from sys import argv
if len(argv) == 2:
from fiji.updater.util import Util
print 'Checksumming', argv[1]
checksum = Util.getDigest(argv[1], argv[1])
#!/bin/sh
''''exec "$(dirname "$0")"/../fiji --jython "$0" "$@" # (call again with fiji)'''
from os import system
from sys import argv
from fiji.updater.logic import PluginCollection, XMLFileReader, XMLFileWriter
from java.io import FileInputStream
from java.lang.System import getProperty
from java.util.zip import GZIPInputStream
dbPath = getProperty('fiji.dir') + '/db.xml.gz'
XMLFileReader(GZIPInputStream(FileInputStream(dbPath)), 0)
plugins = PluginCollection.getInstance()
for plugin in plugins:
if plugin.current == None or not plugin.filename.endswith('.jar'):
continue
if len(argv) > 1:
if not plugin.filename in argv[1:]:
continue
from ij import IJ
IJ.debugMode = True
print 'Handling', plugin
dependencies = [dep.filename for dep in plugin.getDependencies()]
seen = set()
# dependencies have timestamps, so let's keep them intact when possible
result = plugins.analyzeDependencies(plugin)
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import re
try:
from java.lang.System import getProperties as get_java_properties, getProperty
get_java_property = lambda name: getProperty(name) if name else None
except ImportError:
get_java_property = lambda name: None
get_java_properties = lambda: {}
from robot.errors import DataError, VariableError
from robot.utils import (get_env_var, get_env_vars, get_error_message,
normalize, NormalizedDict)
from .evaluation import evaluate_expression
from .notfound import variable_not_found
from .search import search_variable, VariableMatch
NOT_FOUND = object()
#!/bin/sh
''''exec "$(dirname "$0")"/../fiji --jython "$0" "$@" # (call again with fiji)'''
from java.lang.System import getProperty
# Find out the checksum
dbPath = getProperty('fiji.dir') + '/db.xml.gz'
def getTimestamp(plugin, checksum):
from fiji.updater.logic import PluginCollection, XMLFileReader
plugins = PluginCollection()
from java.io import FileInputStream
from java.util.zip import GZIPInputStream
print 'Reading db.xml.gz'
XMLFileReader(plugins).read(None, GZIPInputStream(FileInputStream(dbPath)),
0)
if plugin.startswith('precompiled/'):
plugin = plugin[12:]
plugin = plugins.getPlugin(plugin)
if plugin == None:
print 'Could not find plugin', plugin, 'in db.xml.gz'
return None
if plugin.current != None and checksum == plugin.current.checksum:
return plugin.current.timestamp
for version in plugin.previous.keySet():
if checksum == version.checksum:
return version.timestamp
# Obtains submodules for Fiji and switches to the proper branch for each.
#
# Author: Curtis Rueden (ctrueden at wisc.edu)
import os, re, sys
from fiji.build import Fake
from java.lang.System import getProperty
from java.io import File, FileInputStream
# script prefix, for error messages
prefix = sys.argv[0] + ':'
# path to fiji environment
fijiPath = getProperty('fiji.dir')
# TODO - Edit Fake.java to allow access to entire ruleset. Then we can iterate
# over all rules and discover the mappings, instead of hardcoding them.
# mapping from known submodules to corresponding targets
targets = {
'AutoComplete':'jars/autocomplete.jar',
'ImageJA':'jars/ij.jar',
'RSyntaxTextArea':'jars/rsyntaxtextarea.jar',
#'Retrotranslator':'',
'TrakEM2':'plugins/TrakEM2_.jar',
'VIB':'plugins/VIB_.jar',
'batik':'jars/batik.jar',
'bio-formats':'plugins/loci_tools.jar',
'clojure':'jars/clojure.jar',
# Obtains submodules for Fiji and switches to the proper branch for each.
#
# Author: Curtis Rueden (ctrueden at wisc.edu)
import os, re, sys
from fiji.build import Fake
from java.lang.System import getProperty
from java.io import File, FileInputStream
# script prefix, for error messages
prefix = sys.argv[0] + ':'
# path to fiji environment
fijiPath = getProperty('fiji.dir')
# TODO - Edit Fake.java to allow access to entire ruleset. Then we can iterate
# over all rules and discover the mappings, instead of hardcoding them.
# mapping from known submodules to corresponding targets
targets = {
'AutoComplete': 'jars/autocomplete.jar',
'ImageJA': 'jars/ij.jar',
'RSyntaxTextArea': 'jars/rsyntaxtextarea.jar',
#'Retrotranslator':'',
'TrakEM2': 'plugins/TrakEM2_.jar',
'batik': 'jars/batik.jar',
'bio-formats': 'plugins/loci_tools.jar',
'clojure': 'jars/clojure.jar',
'ij-plugins': 'plugins/ij-ImageIO_.jar',
"""'exec "$(dirname "$0")"/../fiji --jython "$0" "$@" # (call again with fiji)"""
from os import listdir, mkdir, remove, rmdir, system
from os.path import isdir
from re import compile
from sys import argv, exit
from sys.stderr import write
from tempfile import mktemp
from fiji.updater.logic import Checksummer, PluginCollection, XMLFileReader, XMLFileWriter
from fiji.updater.util import StderrProgress, Util
from java.io import FileInputStream, FileOutputStream
from java.lang.System import getProperty
from java.util.zip import GZIPInputStream, GZIPOutputStream
dbPath = getProperty("fiji.dir") + "/db.xml.gz"
plugins = PluginCollection()
XMLFileReader(plugins).read(None, GZIPInputStream(FileInputStream(dbPath)))
def addPreviousVersion(plugin, checksum, timestamp):
p = plugins.getPlugin(plugin)
if p != None:
if not p.hasPreviousVersion(checksum):
p.addPreviousVersion(checksum, timestamp)
prefix = "/var/www/update/"
pattern = compile("^(.*)-([0-9]{14})$")
if showMessages:
print('User "%s" is not listed as a developer,' % getpass.getuser())
print("Plugin code is only reloaded when ImageJ restarts.")
developer = False
# figure out if we are inside ImageJ or in another editor
try:
from java.lang.System import getProperty # should crash your IDE
insideImageJ = True
except:
print("You're running this script OUTSIDE ImageJ's Jython")
insideImageJ = False
# if we are in imagej, allow imports from adjacent files
if insideImageJ:
fijiDir = os.path.abspath(getProperty('user.dir') + "/")
thisPath = os.path.abspath(fijiDir + THIS_FOLDER)
if not os.path.exists(thisPath):
print("CRITICAL PROBLEM! IMPORT PATH DOESNT EXIST:")
print(thisPath + "\n" + "#" * 50)
assert os.path.exists(thisPath)
if not thisPath in sys.path:
sys.path.append(thisPath)
if showMessages:
print("Running inside ImageJ, added import path:\n " + thisPath)
if developer:
sys.modules.clear() # forces unloading of all modules
for fname in [
str(x) for x in os.listdir(thisPath) if x.endswith('$py.class')
]:
print(" -- deleting compiled code: %s" % fname)
from os import listdir, mkdir, remove, rmdir, system
from os.path import isdir
from re import compile
from sys import argv, exit
from sys.stderr import write
from tempfile import mktemp
from fiji.updater.logic import Checksummer, PluginCollection, \
XMLFileReader, XMLFileWriter
from fiji.updater.util import StderrProgress, Util
from java.io import FileInputStream, FileOutputStream
from java.lang.System import getProperty
from java.util.zip import GZIPInputStream, GZIPOutputStream
dbPath = getProperty('ij.dir') + '/db.xml.gz'
plugins = PluginCollection()
XMLFileReader(plugins).read(None, GZIPInputStream(FileInputStream(dbPath)))
def addPreviousVersion(plugin, checksum, timestamp):
p = plugins.getPlugin(plugin)
if p != None:
if not p.hasPreviousVersion(checksum):
p.addPreviousVersion(checksum, timestamp)
prefix = '/var/www/update/'
pattern = compile('^(.*)-([0-9]{14})$')
def addPreviousVersions(path):
write('Adding ' + path + '...\r')
if isdir(prefix + path):
import os
from java.lang.System import getProperty
from os.path import join
import sys.path
libs = join(getProperty('fiji.dir'), join('plugins', join('IMCF', 'libs')))
sys.path.append(libs)
print(sys.path)
import fluoview
import log
print fluoview.__file__
print log.__file__
'''
Download appropriate CMTK binary archive and install to fiji bin/cmtk directory
'''
import urllib2,os,sys,tarfile,shutil,tempfile
from fiji.util.gui import GenericDialogPlus
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/CMTK_Registration")
import cmtkgui
def bin_files(members):
'''
Quick utility function to select binary files to install from CMTK Archive.
'''
for tarinfo in members:
lastdir=os.path.basename(os.path.dirname(tarinfo.name))
if lastdir == "bin":
# print 'keeping '+tarinfo.name
yield tarinfo
def license_files(members):
'''
Quick utility function to select license files to install from CMTK Archive.
Do this by copying files from doc
'''
for tarinfo in members:
if re.search(os.path.join(os.path.sep,"doc",""),tarinfo.name):
yield tarinfo
log.info('Writing tile configuration files.')
write_tile_configs = micrometa.imagej.write_all_tile_configs
write_tile_configs(mosaics, out_dir)
stitcher_options = {
'export_format': '".ids"',
'split_z_slices': 'false',
'rotation_angle': angle,
'stitch_regression': stitch_regression,
'stitch_maxavg_ratio': stitch_maxavg_ratio,
'stitch_abs_displace': stitch_abs_displace,
}
if not stitch_register:
stitcher_options['compute'] = 'false'
template_path = join(getProperty('fiji.dir'), 'jars', 'python-micrometa.jar')
log.info("Using macro templates from [%s]." % template_path)
log.info("Using [%s] as base directory." % indir)
code = micrometa.imagej.gen_stitching_macro(
name=mosaics.infile['dname'],
path=out_dir,
tplpfx='templates/imagej-macro/stitching',
tplpath=template_path,
opts=stitcher_options)
log.debug("============= generated macro code =============")
log.debug(imcflibs.strtools.flatten(code))
log.debug("============= end of generated macro code =============")
log.info('Writing stitching macro.')
timeRange = val
elif switch == "-h":
host = val
elif switch == "-p":
port = int(val)
elif switch == "-u":
userName = val
elif switch == "-c":
configFile = val
elif switch == "-z":
import offsetTime
offsetTime.setDrtOffset(val)
elif switch == "-m":
mutableModel = val
elif switch == "-V":
exec "varDict = " + val
if userName is None:
userName = getProperty("user.name")
if procName is None or configFile is None:
usage()
sys.exit(1)
runProc = RunProcedure(procName, host, port, userName,
configFile, startTime, endTime,
timeRange, editArea, mutableModel, varDict)
if __name__ == "__main__":
main()
#!/bin/sh
''''exec "$(dirname "$0")"/ImageJ.sh --jython "$0" "$@" # (call again with fiji)'''
from os import system
from sys import argv
from fiji.updater.logic import PluginCollection, XMLFileReader, XMLFileWriter
from java.io import FileInputStream, FileOutputStream
from java.lang.System import getProperty
from java.util.zip import GZIPInputStream, GZIPOutputStream
dbPath = getProperty('ij.dir') + '/db.xml.gz'
plugins = PluginCollection()
XMLFileReader(plugins).read(None, GZIPInputStream(FileInputStream(dbPath)), 0)
for plugin in plugins:
if plugin.current == None or not plugin.filename.endswith('.jar'):
continue
if len(argv) > 1:
if not plugin.filename in argv[1:]:
continue
from ij import IJ
IJ.debugMode = True
print 'Handling', plugin
dependencies = [dep.filename for dep in plugin.getDependencies()]
seen = set()
# dependencies have timestamps, so let's keep them intact when possible
result = plugins.analyzeDependencies(plugin)
for dependency in result:
# Obtains submodules for Fiji and switches to the proper branch for each.
#
# Author: Curtis Rueden (ctrueden at wisc.edu)
import os, re, sys
from fiji.build import Fake
from java.lang.System import getProperty
from java.io import File, FileInputStream
# script prefix, for error messages
prefix = sys.argv[0] + ':'
# path to ImageJ environment
ijPath = getProperty('ij.dir')
# TODO - Edit Fake.java to allow access to entire ruleset. Then we can iterate
# over all rules and discover the mappings, instead of hardcoding them.
# mapping from known submodules to corresponding targets
targets = {
'AutoComplete':'jars/autocomplete.jar',
'ImageJA':'jars/ij.jar',
'RSyntaxTextArea':'jars/rsyntaxtextarea.jar',
#'Retrotranslator':'',
'TrakEM2':'plugins/TrakEM2_.jar',
'batik':'jars/batik.jar',
'bio-formats':'plugins/loci_tools.jar',
'clojure':'jars/clojure.jar',
'ij-plugins':'plugins/ij-ImageIO_.jar',
#import os, sys
from ij import IJ, ImagePlus, ImageStack
from ij3d import Image3DUniverse, Content
from java.lang.System import getProperty
import vib.PointList
from javax.vecmath import Color3f, Point3f
from ij.plugin.frame import RoiManager
from ij.gui import PointRoi
print "===Starting bMergeChannels_"
pluginDir = getProperty("fiji.dir") + "/plugins/bob-fiji-plugins/"
#open text file that gives us a list of images (for now it will be 2)
file = open(pluginDir + "bMergeChannels.txt", "r")
do3d = 0
doComposite = 0
pointList = [] #list of spine points
cPointList = [] #list of connection points
lPointList = [] #list of backbone centerline points
doROI = 0
for line in file.readlines():
currLine = line.strip()
print currLine
token, value = currLine.split("=")
if currLine.startswith('file1'):
filepath1 = value
if currLine.startswith('file2'):
import com.nrims.UI as UI
import com.nrims.RatioProps as RatioProps
import com.nrims.MimsPlus as MimsPlus
import com.nrims.MimsJTable as MimsJTable
import java.io.File as File
import java.util.ArrayList as ArrayList
import java.lang.Integer as Integer
import sys
from java.lang.System import getProperty
sys.path.append(
getProperty("fiji.dir") + "/plugins/Scripts/Plugins/OpenMIMS Scripts/")
from OMUtilities import MultiFileDialog
from OMUtilities import CheckFileLists
import os
import jarray
#hide/show debug prints
verbose = 1
IJ.log("\n\nStarting OpenMIMSTables")
# The directory containing the .im/.nrrd files.
#imDirName = "/nrims/home3/cpoczatek/Fiji_test/test_images";
# The list of files.
imFileNames = MultiFileDialog("Open Image Files")
from ij.gui import GenericDialog
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/CMTK_Registration")
gd = GenericDialog('About CMTK')
gd.addMessage(
'CMTK Registration suite is open source software released under GPLv3', )
gd.addMessage('Currently installed CMTK version: ' +
cmtkgui.installed_version())
gd.addMessage('CMTK binary directory: ' + cmtkgui.bin_dir())
gd.setCancelLabel("CMTK Web Page")
gd.showDialog()
if gd.wasCanceled():
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher",
"http://www.nitrc.org/projects/cmtk/")
from os import listdir, mkdir, remove, rmdir, system
from os.path import isdir
from re import compile
from sys import argv, exit
from sys.stderr import write
from tempfile import mktemp
from fiji.updater.logic import Checksummer, PluginCollection, \
XMLFileReader, XMLFileWriter
from fiji.updater.util import StderrProgress, Util
from java.io import FileInputStream, FileOutputStream
from java.lang.System import getProperty
from java.util.zip import GZIPInputStream, GZIPOutputStream
dbPath = getProperty('fiji.dir') + '/db.xml.gz'
plugins = PluginCollection()
XMLFileReader(plugins).read(None, GZIPInputStream(FileInputStream(dbPath)))
def addPreviousVersion(plugin, checksum, timestamp):
p = plugins.getPlugin(plugin)
if p != None:
if not p.hasPreviousVersion(checksum):
p.addPreviousVersion(checksum, timestamp)
prefix = '/var/www/update/'
pattern = compile('^(.*)-([0-9]{14})$')
from ij import IJ
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/NordenTools")
import NordenTools as nt
filename = getProperty("fiji.dir") + "/plugins/NordenTools/setup.py"
IJ.open(filename)
