def printAllMenus(): mbar = Menus.getMenuBar() n = mbar.getMenuCount() for i in range(0, n): menu = mbar.getMenu(i) print menu.getLabel() printMenu(menu, ' ') print 'Help' printMenu(mbar.getHelpMenu(), ' ')
def check_dependencies():
installed_plugins = os.listdir(Menus.getPlugInsPath())
for dependency, site in _dependencies.iteritems():
if not any(dependency in x for x in installed_plugins):
msg = GenericDialog("Missing dependency")
msg.addMessage(
"Missing dependency {}, \n go to {} for installation instructions. "
.format(dependency, site))
msg.showDialog()
raise RuntimeError(
"Missing dependency {}, \n go to {} for installation instructions. "
.format(dependency, site))
def getMenuEntry(path):
if isinstance(path, str):
path = path.split('>')
try:
menu = None
mbar = Menus.getMenuBar()
for i in range(0, mbar.getMenuCount()):
if path[0] == mbar.getMenu(i).getLabel():
menu = mbar.getMenu(i)
break
for j in range(1, len(path)):
entry = None
for i in range(0, menu.getItemCount()):
if path[j] == menu.getItem(i).getLabel():
entry = menu.getItem(i)
break
menu = entry
return menu
except:
return None
''''exec "$(dirname "$0")"/../ImageJ --jython "$0" "$@" # (call again with fiji)''' # Test whether any menu items contain pointers to non-existent classes which # likely indicate a missconfiguration of a plugins.config file in a .jar plugin. from ij import IJ, ImageJ, Menus from java.lang import Class, ClassNotFoundException, NoClassDefFoundError import sys # Launch ImageJ ImageJ() if len(sys.argv) > 1 and sys.argv[1] == '-v': for key in Menus.getCommands(): command = Menus.getCommands().get(key) print key, '->', command sys.exit() ok = 1 def doesClassExist(name): try: IJ.getClassLoader().loadClass(name) return True except ClassNotFoundException: return False except NoClassDefFoundError: return False
from os import makedirs, rename, stat
from os.path import exists, isdir
from sys import stderr
from time import sleep
import urllib
# force initialization
IJ.runMacro("", "")
menu = User_Plugins.getMenuItem('File>Open Samples')
commands = Menus.getCommands()
plugin = 'ij.plugin.URLOpener("'
samples = System.getProperty('fiji.dir') + '/samples'
class FileSizeReporter(Thread):
def __init__(self, name, path):
self.name = name
self.path = path
self.canceled = False
def run(self):
while self.canceled == False:
if exists(self.path):
stderr.write('\rDownload ' + self.name \
+ ': ' + str(stat(self.path).st_size) \
+ ' bytes')
''''exec "$(dirname "$0")"/../ImageJ --jython "$0" "$@" # (call again with fiji)'''
# Test whether any menu items contain pointers to non-existent classes which
# likely indicate a missconfiguration of a plugins.config file in a .jar plugin.
from ij import IJ, ImageJ, Menus
from java.lang import Class, ClassNotFoundException, NoClassDefFoundError
import sys
# Launch ImageJ
ImageJ()
if len(sys.argv) > 1 and sys.argv[1] == '-v':
for key in Menus.getCommands():
command = Menus.getCommands().get(key)
print key, '->', command
sys.exit()
ok = 1
def doesClassExist(name):
try:
IJ.getClassLoader().loadClass(name)
return True
except ClassNotFoundException:
return False
except NoClassDefFoundError:
return False
z = [0]*len(x)
# Calculate distances for all positions. Retrieve NNs distances
for i in range(len(x)):
minDx = sys.maxint
nearest = 0
for j in range(len(x)):
if i==j: continue
dx = (x[i]-x[j])**2
dy = (y[i]-y[j])**2
dz = (z[i]-z[j])**2
dst = math.sqrt(dx+dy+dz)
if dst>0 and dst<minDx:
minDx = dst
nearest = j+1
rt.setValue("NN pair", i, nearest)
rt.setValue("NN distance", i, minDx);
# Display appended results
rt.showRowNumbers(True)
rt.show("Results")
# Display distributions
dp = "Distribution Plotter"
if dp in Menus.getCommands().keySet().toArray():
IJ.run(dp, "parameter=[NN distance] automatic=Freedman-Diaconis");
else:
IJ.error("File missing", dp+" not found.\nPlease check your BAR installation.")
else:
IJ.error("Invalid Results Table","Data for X,Y positions not found.")
from os import makedirs, rename, stat
from os.path import exists, isdir
from sys import stderr
from time import sleep
import urllib
# force initialization
IJ.runMacro("", "")
menu = User_Plugins.getMenuItem('File>Open Samples')
commands = Menus.getCommands()
plugin = 'ij.plugin.URLOpener("'
samples = System.getProperty('ij.dir') + '/samples'
class FileSizeReporter(Thread):
def __init__(self, name, path):
self.name = name
self.path = path
self.canceled = False
def run(self):
while self.canceled == False:
if exists(self.path):
stderr.write('\rDownload ' + self.name \
+ ': ' + str(stat(self.path).st_size) \
from java.awt import Color
from java.awt.event import TextListener
from ij import IJ
from ij import Menus
from ij.gui import GenericDialog
#commands = [c for c in ij.Menus.getCommands().keySet()]
# Above, equivalent list as below:
commands = Menus.getCommands().keySet().toArray()
gd = GenericDialog('Command Launcher')
gd.addStringField('Command: ', '');
prompt = gd.getStringFields().get(0)
prompt.setForeground(Color.red)
class TypeListener(TextListener):
def textValueChanged(self, tvc):
if prompt.getText() in commands:
prompt.setForeground(Color.black)
return
prompt.setForeground(Color.red)
# or loop:
#for c in commands:
# if c == text:
# prompt.setForeground(Color.black)
# return
#
#prompt.setForeground(Color.red)
prompt.addTextListener(TypeListener())
gd.showDialog()
if not gd.wasCanceled(): IJ.doCommand(gd.getNextString())
