def enter_thread(self):
J.attach()
if not cpprefs.get_awt_headless():
J.activate_awt()
self.notify_socket = the_zmq_context.socket(zmq.SUB)
self.notify_socket.setsockopt(zmq.SUBSCRIBE, "")
self.notify_socket.connect(NOTIFY_ADDR)
def enter_thread(self):
J.attach()
if not cpprefs.get_awt_headless():
J.activate_awt()
self.notify_socket = the_zmq_context.socket(zmq.SUB)
self.notify_socket.setsockopt(zmq.SUBSCRIBE, "")
self.notify_socket.connect(NOTIFY_ADDR)
def OnInit(self):
# The wx.StandardPaths aren't available until this is set.
from cellprofiler.utilities.version import dotted_version
self.SetAppName('CellProfiler%s' % dotted_version)
wx.InitAllImageHandlers()
if self.show_splashbox:
# If the splash image has alpha, it shows up transparently on
# windows, so we blend it into a white background.
splashbitmap = wx.EmptyBitmapRGBA(
CellProfilerSplash.GetWidth(),
CellProfilerSplash.GetHeight(), 255, 255, 255, 255)
dc = wx.MemoryDC()
dc.SelectObject(splashbitmap)
dc.DrawBitmap(wx.BitmapFromImage(CellProfilerSplash), 0, 0)
dc.SelectObject(wx.NullBitmap)
dc.Destroy() # necessary to avoid a crash in splashscreen
self.splash = wx.SplashScreen(
splashbitmap,
wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_NO_TIMEOUT,
2000, None, -1)
self.splash_timer = wx.Timer()
self.splash_timer.Bind(wx.EVT_TIMER, self.destroy_splash_screen)
self.splash_timer.Start(milliseconds = 2000, oneShot=True)
else:
self.splash = None
if self.check_for_new_version:
self.new_version_check()
from javabridge import activate_awt
activate_awt()
from cellprofiler.gui.cpframe import CPFrame
self.frame = CPFrame(None, -1, "Cell Profiler")
self.destroy_splash_screen()
try:
self.frame.start(self.workspace_path, self.pipeline_path)
except:
return 0
if self.abort_initialization:
return 0
# set up error dialog for uncaught exceptions
def show_errordialog(type, exc, tb):
def doit():
cpp.cancel_progress()
display_error_dialog(self.frame, exc, None, tb=tb, continue_only=True,
message="Exception in CellProfiler core processing")
# continue is really the only choice
wx.CallAfter(doit)
# replace default hook with error dialog
self.orig_excepthook = sys.excepthook
sys.excepthook = show_errordialog
self.SetTopWindow(self.frame)
self.frame.Show()
if self.frame.startup_blurb_frame.IsShownOnScreen():
self.frame.startup_blurb_frame.Raise()
return 1
def OnInit(self):
"""Initialize CPA
"""
"""List of tables created by the user during this session"""
self.user_tables = []
# splashscreen
splashimage = cpa.icons.cpa_splash.ConvertToBitmap()
# If the splash image has alpha, it shows up transparently on
# windows, so we blend it into a white background.
splashbitmap = wx.EmptyBitmapRGBA(splashimage.GetWidth(), splashimage.GetHeight(), 255, 255, 255, 255)
dc = wx.MemoryDC()
dc.SelectObject(splashbitmap)
dc.DrawBitmap(splashimage, 0, 0)
dc.Destroy() # necessary to avoid a crash in splashscreen
splash = wx.SplashScreen(splashbitmap, wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_TIMEOUT, 2000, None, -1)
self.splash = splash
p = Properties.getInstance()
if not p.is_initialized():
from cpa.guiutils import show_load_dialog
splash.Destroy()
if not show_load_dialog():
logging.error("CellProfiler Analyst requires a properties file. Exiting.")
return False
self.frame = MainGUI(p, None, size=(860, -1))
self.frame.Show(True)
db = cpa.dbconnect.DBConnect.getInstance()
# Black magic: Bus errors occur on Mac OS X if we wait until
# the JVM or the wx event look has started to connect. But it
# has to be done after we have read the properties file. So we
# do it here.
db.connect()
db.register_gui_parent(self.frame)
# The JVM has to be started after db.connect(), otherwise bus errors
# occur on Mac OS X.
javabridge.start_vm(class_path=bioformats.JARS, run_headless=False)
javabridge.attach()
javabridge.activate_awt()
try:
if __version__ != -1:
import cellprofiler.utilities.check_for_updates as cfu
cfu.check_for_updates(
"http://cellprofiler.org/CPAupdate.html",
max(__version__, cpaprefs.get_skip_version()),
new_version_cb,
user_agent="CPAnalyst/2.0.%d" % (__version__),
)
except ImportError:
logging.warn(
"CPA was unable to check for updates. Could not import cellprofiler.utilities.check_for_updates."
)
return True
def begin(self):
import javabridge
javabridge.start_vm(self.extra_jvm_args,
class_path=self.class_path.split(os.pathsep),
run_headless=self.headless,
max_heap_size=self.max_heap_size)
if not self.headless:
javabridge.activate_awt()
def begin(self):
import javabridge
javabridge.start_vm(self.extra_jvm_args,
class_path=self.class_path.split(os.pathsep),
run_headless=self.headless,
max_heap_size=self.max_heap_size)
if not self.headless:
javabridge.activate_awt()
def get(self):
total = dm.get_total_object_count()
objKeys = dm.GetRandomObjects(total)
# Start the virtual machine
javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
javabridge.attach()
javabridge.activate_awt()
return calculateAllJSON(objKeys, base64=True)
def get(self):
if cached_json["base64"] == False:
# Start the virtual machine
javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
javabridge.attach()
javabridge.activate_awt()
# Calculate the Training DataSet and store it
cached_json["json"] = calculateTrainingSetJSON(base64=True)
cached_json["base64"] = True
return cached_json["json"]
def OnInit(self):
'''Initialize CPA
'''
'''List of tables created by the user during this session'''
self.user_tables = []
# splashscreen
splashimage = cpa.icons.cpa_splash.ConvertToBitmap()
# If the splash image has alpha, it shows up transparently on
# windows, so we blend it into a white background.
splashbitmap = wx.EmptyBitmapRGBA(splashimage.GetWidth(),
splashimage.GetHeight(), 255, 255,
255, 255)
dc = wx.MemoryDC()
dc.SelectObject(splashbitmap)
dc.DrawBitmap(splashimage, 0, 0)
dc.Destroy() # necessary to avoid a crash in splashscreen
splash = wx.SplashScreen(
splashbitmap, wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_TIMEOUT, 2000,
None, -1)
self.splash = splash
p = Properties.getInstance()
if not p.is_initialized():
from cpa.guiutils import show_load_dialog
splash.Destroy()
if not show_load_dialog():
logging.error(
'CellProfiler Analyst requires a properties file. Exiting.'
)
return False
self.frame = MainGUI(p, None, size=(860, -1))
self.frame.Show(True)
db = cpa.dbconnect.DBConnect.getInstance()
# Black magic: Bus errors occur on Mac OS X if we wait until
# the JVM or the wx event look has started to connect. But it
# has to be done after we have read the properties file. So we
# do it here.
db.connect()
db.register_gui_parent(self.frame)
# The JVM has to be started after db.connect(), otherwise bus errors
# occur on Mac OS X.
javabridge.start_vm(class_path=bioformats.JARS, run_headless=False)
javabridge.attach()
javabridge.activate_awt()
try:
if __version__ != -1:
import cellprofiler.utilities.check_for_updates as cfu
cfu.check_for_updates('http://cellprofiler.org/CPAupdate.html',
max(__version__,
cpaprefs.get_skip_version()),
new_version_cb,
user_agent='CPAnalyst/2.0.%d' %
(__version__))
except ImportError:
logging.warn(
"CPA was unable to check for updates. Could not import cellprofiler.utilities.check_for_updates."
)
return True
def run_pipeline_headless(options, args):
'''Run a CellProfiler pipeline in headless mode'''
if sys.platform == 'darwin':
if options.start_awt:
import bioformats
from javabridge import activate_awt
activate_awt()
if not options.first_image_set is None:
if not options.first_image_set.isdigit():
raise ValueError("The --first-image-set option takes a numeric argument")
else:
image_set_start = int(options.first_image_set)
else:
image_set_start = None
image_set_numbers = None
if not options.last_image_set is None:
if not options.last_image_set.isdigit():
raise ValueError("The --last-image-set option takes a numeric argument")
else:
image_set_end = int(options.last_image_set)
if image_set_start is None:
image_set_numbers = np.arange(1, image_set_end+1)
else:
image_set_numbers = np.arange(image_set_start, image_set_end+1)
else:
image_set_end = None
if ((options.pipeline_filename is not None) and
(not options.pipeline_filename.lower().startswith('http'))):
options.pipeline_filename = os.path.expanduser(options.pipeline_filename)
from cellprofiler.pipeline import Pipeline, EXIT_STATUS, M_PIPELINE
import cellprofiler.measurements as cpmeas
pipeline = Pipeline()
initial_measurements = None
try:
if h5py.is_hdf5(options.pipeline_filename):
initial_measurements = cpmeas.load_measurements(
options.pipeline_filename,
image_numbers=image_set_numbers)
except:
logging.root.info("Failed to load measurements from pipeline")
if initial_measurements is not None:
pipeline_text = \
initial_measurements.get_experiment_measurement(
M_PIPELINE)
pipeline_text = pipeline_text.encode('us-ascii')
pipeline.load(StringIO(pipeline_text))
if not pipeline.in_batch_mode():
#
# Need file list in order to call prepare_run
#
from cellprofiler.utilities.hdf5_dict import HDF5FileList
with h5py.File(options.pipeline_filename, "r") as src:
if HDF5FileList.has_file_list(src):
HDF5FileList.copy(
src, initial_measurements.hdf5_dict.hdf5_file)
else:
pipeline.load(options.pipeline_filename)
if options.groups is not None:
kvs = [x.split('=') for x in options.groups.split(',')]
groups = dict(kvs)
else:
groups = None
use_hdf5 = len(args) > 0 and not args[0].lower().endswith(".mat")
measurements = pipeline.run(
image_set_start=image_set_start,
image_set_end=image_set_end,
grouping=groups,
measurements_filename = None if not use_hdf5 else args[0],
initial_measurements = initial_measurements)
if len(args) > 0 and not use_hdf5:
pipeline.save_measurements(args[0], measurements)
if options.done_file is not None:
if (measurements is not None and
measurements.has_feature(cpmeas.EXPERIMENT, EXIT_STATUS)):
done_text = measurements.get_experiment_measurement(EXIT_STATUS)
else:
done_text = "Failure"
fd = open(options.done_file, "wt")
fd.write("%s\n"%done_text)
fd.close()
if measurements is not None:
measurements.close()
def main(args):
javabridge.activate_awt()
script = """
//--------------------------------------
//
// The anonymous callable runs on the thread
// that started Java - that's the rule with AWT.
//
// The callable returns a Java Map whose keys
// have the labels of objects like "qUp" for
// the upward queue. Python can then fetch
// whichever ones it wants and do Java stuff
// with them.
//
//--------------------------------------
new java.util.concurrent.Callable() {
call: function() {
importClass(javax.swing.SpringLayout);
importClass(javax.swing.JFrame);
importClass(javax.swing.JTextField);
importClass(javax.swing.JButton);
importClass(javax.swing.JScrollPane);
importClass(javax.swing.JTextArea);
importClass(java.util.Hashtable);
importClass(java.awt.event.ActionListener);
importClass(java.awt.event.WindowAdapter);
importClass(java.util.concurrent.SynchronousQueue);
d = new Hashtable();
frame = new JFrame("Callbacks in Java");
d.put("frame", frame);
contentPane = frame.getContentPane();
layout = new SpringLayout();
contentPane.setLayout(layout);
textField = new JTextField("'Hello, world.'", 60);
d.put("textField", textField);
contentPane.add(textField);
execButton = new JButton("Exec");
contentPane.add(execButton);
evalButton = new JButton("Eval");
contentPane.add(evalButton);
result = new JTextArea("None");
scrollPane = new JScrollPane(result)
contentPane.add(scrollPane);
d.put("result", result);
//-----------------------------------------------------
//
// The layout is:
//
// [ textField] [execButton] [evalButton]
// [ scrollPane ]
//
//-----------------------------------------------------
layout.putConstraint(SpringLayout.WEST, textField,
5, SpringLayout.WEST, contentPane);
layout.putConstraint(SpringLayout.NORTH, textField,
5, SpringLayout.NORTH, contentPane);
layout.putConstraint(SpringLayout.WEST, execButton,
5, SpringLayout.EAST, textField);
layout.putConstraint(SpringLayout.NORTH, execButton,
0, SpringLayout.NORTH, textField);
layout.putConstraint(SpringLayout.WEST, evalButton,
5, SpringLayout.EAST, execButton);
layout.putConstraint(SpringLayout.NORTH, evalButton,
0, SpringLayout.NORTH, textField);
layout.putConstraint(SpringLayout.NORTH, scrollPane,
5, SpringLayout.SOUTH, textField);
layout.putConstraint(SpringLayout.WEST, scrollPane,
0, SpringLayout.WEST, textField);
layout.putConstraint(SpringLayout.EAST, scrollPane,
0, SpringLayout.EAST, evalButton);
layout.putConstraint(SpringLayout.EAST, contentPane,
5, SpringLayout.EAST, evalButton);
layout.putConstraint(SpringLayout.SOUTH, contentPane,
20, SpringLayout.SOUTH, scrollPane);
//------------------------------------------------
//
// qUp sends messages from Java to Python
// qDown sends messages from Python to Java
//
// The communications protocol is that qUp sends
// a command. For Exec and Eval commands, qUp sends
// text and qDown must send a reply to continue.
// For the Exit command, qUp sends the command and
// Python must dispose of Java
//
//-------------------------------------------------
qUp = new SynchronousQueue();
qDown = new SynchronousQueue();
d.put("qUp", qUp);
d.put("qDown", qDown);
//-----------------------------------------------
//
// Create an action listener that binds the execButton
// action to a function that instructs Python to
// execute the contents of the text field.
//
//-----------------------------------------------
alExec = new ActionListener() {
actionPerformed: function(e) {
qUp.put("Exec");
qUp.put(textField.getText());
result.setText(qDown.take());
}
};
execButton.addActionListener(alExec);
//-----------------------------------------------
//
// Create an action listener that binds the evalButton
// action to a function that instructs Python to
// evaluate the contents of the text field.
//
//-----------------------------------------------
alEval = new ActionListener() {
actionPerformed: function(e) {
qUp.put("Eval");
qUp.put(textField.getText());
result.setText(qDown.take());
}
};
evalButton.addActionListener(alEval);
//-----------------------------------------------
//
// Create a window listener that binds the frame's
// windowClosing action to a function that instructs
// Python to exit.
//
//-----------------------------------------------
wl = new WindowAdapter() {
windowClosing: function(e) {
qUp.put("Exit");
}
};
frame.addWindowListener(wl);
frame.pack();
frame.setVisible(true);
return d;
}
};"""
c = javabridge.run_script(script)
f = javabridge.make_future_task(c)
d = javabridge.execute_future_in_main_thread(f)
d = javabridge.get_map_wrapper(d)
qUp = d["qUp"]
qDown = d["qDown"]
frame = d["frame"]
while True:
cmd = javabridge.run_script("qUp.take();", dict(qUp=qUp))
if cmd == "Exit":
break
text = javabridge.run_script("qUp.take();", dict(qUp=qUp))
if cmd == "Eval":
try:
result = eval(text, globals(), locals())
except Exception as e:
result = "%s\n%s" % (str(e), traceback.format_exc())
except:
result = "What happened?"
else:
try:
exec(text, globals(), locals())
result = "Operation succeeded"
except Exception as e:
result = "%s\n%s" % (str(e), traceback.format_exc())
except:
result = "What happened?"
javabridge.run_script("qDown.put(result);",
dict(qDown=qDown, result=str(result)))
javabridge.run_script("frame.dispose();", dict(frame=frame))
def run_ui():
figure = plt.figure()
ax = figure.add_axes([.05, .05, .9, .9])
x = np.linspace(0, np.pi * 8)
ax.plot(x, np.sin(x))
canvas = figure.canvas
frame = canvas.component.getTopLevelAncestor()
toolbar = plt.get_current_fig_manager().frame.toolbar
toolbar.add_button(lambda event: popup_script_dlg(canvas), "hand")
plt.show()
return frame, canvas, toolbar
javabridge.start_vm()
javabridge.activate_awt()
event = threading.Event()
event_ref_id, event_ref = javabridge.create_jref(event)
cpython = javabridge.JClassWrapper('org.cellprofiler.javabridge.CPython')()
set_event_script = ('import javabridge\n'
'event = javabridge.redeem_jref("%s")\n'
'event.set()') % event_ref_id
adapter = javabridge.run_script(
"""
new java.awt.event.WindowAdapter() {
windowClosed: function(e) {
cpython.exec(script);
}
}
""", dict(cpython=cpython, script=set_event_script))
frame, canvas, toolbar = run_ui()
def main(args):
javabridge.activate_awt()
script = """
//--------------------------------------
//
// The anonymous callable runs on the thread
// that started Java - that's the rule with AWT.
//
// The callable returns a Java Map whose keys
// have the labels of objects like "qUp" for
// the upward queue. Python can then fetch
// whichever ones it wants and do Java stuff
// with them.
//
//--------------------------------------
new java.util.concurrent.Callable() {
call: function() {
importClass(javax.swing.SpringLayout);
importClass(javax.swing.JFrame);
importClass(javax.swing.JTextField);
importClass(javax.swing.JButton);
importClass(javax.swing.JScrollPane);
importClass(javax.swing.JTextArea);
importClass(java.util.Hashtable);
importClass(java.awt.event.ActionListener);
importClass(java.awt.event.WindowAdapter);
importClass(java.util.concurrent.SynchronousQueue);
d = new Hashtable();
frame = new JFrame("Callbacks in Java");
d.put("frame", frame);
contentPane = frame.getContentPane();
layout = new SpringLayout();
contentPane.setLayout(layout);
textField = new JTextField("'Hello, world.'", 60);
d.put("textField", textField);
contentPane.add(textField);
execButton = new JButton("Exec");
contentPane.add(execButton);
evalButton = new JButton("Eval");
contentPane.add(evalButton);
result = new JTextArea("None");
scrollPane = new JScrollPane(result)
contentPane.add(scrollPane);
d.put("result", result);
//-----------------------------------------------------
//
// The layout is:
//
// [ textField] [execButton] [evalButton]
// [ scrollPane ]
//
//-----------------------------------------------------
layout.putConstraint(SpringLayout.WEST, textField,
5, SpringLayout.WEST, contentPane);
layout.putConstraint(SpringLayout.NORTH, textField,
5, SpringLayout.NORTH, contentPane);
layout.putConstraint(SpringLayout.WEST, execButton,
5, SpringLayout.EAST, textField);
layout.putConstraint(SpringLayout.NORTH, execButton,
0, SpringLayout.NORTH, textField);
layout.putConstraint(SpringLayout.WEST, evalButton,
5, SpringLayout.EAST, execButton);
layout.putConstraint(SpringLayout.NORTH, evalButton,
0, SpringLayout.NORTH, textField);
layout.putConstraint(SpringLayout.NORTH, scrollPane,
5, SpringLayout.SOUTH, textField);
layout.putConstraint(SpringLayout.WEST, scrollPane,
0, SpringLayout.WEST, textField);
layout.putConstraint(SpringLayout.EAST, scrollPane,
0, SpringLayout.EAST, evalButton);
layout.putConstraint(SpringLayout.EAST, contentPane,
5, SpringLayout.EAST, evalButton);
layout.putConstraint(SpringLayout.SOUTH, contentPane,
20, SpringLayout.SOUTH, scrollPane);
//------------------------------------------------
//
// qUp sends messages from Java to Python
// qDown sends messages from Python to Java
//
// The communications protocol is that qUp sends
// a command. For Exec and Eval commands, qUp sends
// text and qDown must send a reply to continue.
// For the Exit command, qUp sends the command and
// Python must dispose of Java
//
//-------------------------------------------------
qUp = new SynchronousQueue();
qDown = new SynchronousQueue();
d.put("qUp", qUp);
d.put("qDown", qDown);
//-----------------------------------------------
//
// Create an action listener that binds the execButton
// action to a function that instructs Python to
// execute the contents of the text field.
//
//-----------------------------------------------
alExec = new ActionListener() {
actionPerformed: function(e) {
qUp.put("Exec");
qUp.put(textField.getText());
result.setText(qDown.take());
}
};
execButton.addActionListener(alExec);
//-----------------------------------------------
//
// Create an action listener that binds the evalButton
// action to a function that instructs Python to
// evaluate the contents of the text field.
//
//-----------------------------------------------
alEval = new ActionListener() {
actionPerformed: function(e) {
qUp.put("Eval");
qUp.put(textField.getText());
result.setText(qDown.take());
}
};
evalButton.addActionListener(alEval);
//-----------------------------------------------
//
// Create a window listener that binds the frame's
// windowClosing action to a function that instructs
// Python to exit.
//
//-----------------------------------------------
wl = new WindowAdapter() {
windowClosing: function(e) {
qUp.put("Exit");
}
};
frame.addWindowListener(wl);
frame.pack();
frame.setVisible(true);
return d;
}
};"""
c = javabridge.run_script(script);
f = javabridge.make_future_task(c)
d = javabridge.execute_future_in_main_thread(f);
d = javabridge.get_map_wrapper(d)
qUp = d["qUp"]
qDown = d["qDown"]
frame = d["frame"]
while True:
cmd = javabridge.run_script("qUp.take();", dict(qUp=qUp))
if cmd == "Exit":
break
text = javabridge.run_script("qUp.take();", dict(qUp=qUp))
if cmd == "Eval":
try:
result = eval(text, globals(), locals())
except Exception as e:
result = "%s\n%s" % (str(e), traceback.format_exc())
except:
result = "What happened?"
else:
try:
exec(text, globals(), locals())
result = "Operation succeeded"
except Exception as e:
result = "%s\n%s" % (str(e), traceback.format_exc())
except:
result = "What happened?"
javabridge.run_script("qDown.put(result);",
dict(qDown=qDown, result = str(result)))
javabridge.run_script("frame.dispose();", dict(frame=frame))
def OnInit(self):
javabridge.activate_awt()
return True
def main(args):
javabridge.activate_awt()
cpython = javabridge.make_instance(
"org/cellprofiler/javabridge/CPython", "()V")
script = """
//--------------------------------------
//
// The anonymous callable runs on the thread
// that started Java - that's the rule with AWT.
//
// The callable returns a Java Map whose keys
// have the labels of objects like "qUp" for
// the upward queue. Python can then fetch
// whichever ones it wants and do Java stuff
// with them.
//
//--------------------------------------
new java.util.concurrent.Callable() {
call: function() {
importClass(javax.swing.SpringLayout);
importClass(javax.swing.JFrame);
importClass(javax.swing.JTextField);
importClass(javax.swing.JButton);
importClass(javax.swing.JScrollPane);
importClass(javax.swing.JTextArea);
importClass(java.util.Hashtable);
importClass(java.util.ArrayList);
importClass(java.util.concurrent.CountDownLatch);
importClass(java.awt.event.ActionListener);
importClass(java.awt.event.WindowAdapter);
d = new Hashtable();
signal = new CountDownLatch(1);
d.put("signal", signal);
frame = new JFrame("Callbacks in Java");
d.put("frame", frame);
contentPane = frame.getContentPane();
layout = new SpringLayout();
contentPane.setLayout(layout);
textField = new JTextField("'Hello, world.'", 60);
d.put("textField", textField);
contentPane.add(textField);
execButton = new JButton("Exec");
contentPane.add(execButton);
evalButton = new JButton("Eval");
contentPane.add(evalButton);
result = new JTextArea("None");
scrollPane = new JScrollPane(result)
contentPane.add(scrollPane);
d.put("result", result);
//-----------------------------------------------------
//
// The layout is:
//
// [ textField] [execButton] [evalButton]
// [ scrollPane ]
//
//-----------------------------------------------------
layout.putConstraint(SpringLayout.WEST, textField,
5, SpringLayout.WEST, contentPane);
layout.putConstraint(SpringLayout.NORTH, textField,
5, SpringLayout.NORTH, contentPane);
layout.putConstraint(SpringLayout.WEST, execButton,
5, SpringLayout.EAST, textField);
layout.putConstraint(SpringLayout.NORTH, execButton,
0, SpringLayout.NORTH, textField);
layout.putConstraint(SpringLayout.WEST, evalButton,
5, SpringLayout.EAST, execButton);
layout.putConstraint(SpringLayout.NORTH, evalButton,
0, SpringLayout.NORTH, textField);
layout.putConstraint(SpringLayout.NORTH, scrollPane,
5, SpringLayout.SOUTH, textField);
layout.putConstraint(SpringLayout.WEST, scrollPane,
0, SpringLayout.WEST, textField);
layout.putConstraint(SpringLayout.EAST, scrollPane,
0, SpringLayout.EAST, evalButton);
layout.putConstraint(SpringLayout.EAST, contentPane,
5, SpringLayout.EAST, evalButton);
layout.putConstraint(SpringLayout.SOUTH, contentPane,
20, SpringLayout.SOUTH, scrollPane);
//-----------------------------------------------
//
// Create an action listener that binds the execButton
// action to a function that instructs Python to
// execute the contents of the text field.
//
//-----------------------------------------------
alExec = new ActionListener() {
actionPerformed: function(e) {
try {
cpython.exec(textField.getText());
result.setText("OK");
} catch(err) {
result.setText(err.message);
}
}
};
execButton.addActionListener(alExec);
//-----------------------------------------------
//
// Create an action listener that binds the evalButton
// action to a function that instructs Python to
// evaluate the contents of the text field.
//
//-----------------------------------------------
alEval = new ActionListener() {
actionPerformed: function(e) {
try {
locals = new Hashtable();
jresult = new ArrayList();
locals.put("script", textField.getText());
locals.put("jresult", jresult);
script = "import javabridge\\n" +
"result=eval(javabridge.to_string(script))\\n" +
"jwresult=javabridge.JWrapper(jresult)\\n" +
"jwresult.add(str(result))"
cpython.exec(script, locals, null);
result.setText(jresult.get(0));
} catch(err) {
result.setText(err.message);
}
}
};
evalButton.addActionListener(alEval);
//-----------------------------------------------
//
// Create a window listener that binds the frame's
// windowClosing action to a function that instructs
// Python to exit.
//
//-----------------------------------------------
wl = new WindowAdapter() {
windowClosing: function(e) {
signal.countDown();
}
};
frame.addWindowListener(wl);
frame.pack();
frame.setVisible(true);
return d;
}
};"""
c = javabridge.run_script(script, dict(cpython=cpython));
f = javabridge.make_future_task(c)
d = javabridge.execute_future_in_main_thread(f);
d = javabridge.get_map_wrapper(d)
frame = javabridge.JWrapper(d["frame"])
signal = javabridge.JWrapper(d["signal"]);
signal.await();
frame.dispose();
def OnInit(self):
# The wx.StandardPaths aren't available until this is set.
from cellprofiler.utilities.version import dotted_version
self.SetAppName('CellProfiler%s' % dotted_version)
wx.InitAllImageHandlers()
if self.show_splashbox:
# If the splash image has alpha, it shows up transparently on
# windows, so we blend it into a white background.
splashbitmap = wx.EmptyBitmapRGBA(CellProfilerSplash.GetWidth(),
CellProfilerSplash.GetHeight(),
255, 255, 255, 255)
dc = wx.MemoryDC()
dc.SelectObject(splashbitmap)
dc.DrawBitmap(wx.BitmapFromImage(CellProfilerSplash), 0, 0)
dc.SelectObject(wx.NullBitmap)
dc.Destroy() # necessary to avoid a crash in splashscreen
self.splash = wx.SplashScreen(
splashbitmap,
wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_NO_TIMEOUT, 2000, None,
-1)
self.splash_timer = wx.Timer()
self.splash_timer.Bind(wx.EVT_TIMER, self.destroy_splash_screen)
self.splash_timer.Start(milliseconds=2000, oneShot=True)
else:
self.splash = None
if self.check_for_new_version:
self.new_version_check()
from javabridge import activate_awt
activate_awt()
from cellprofiler.gui.cpframe import CPFrame
self.frame = CPFrame(None, -1, "Cell Profiler")
self.destroy_splash_screen()
try:
self.frame.start(self.workspace_path, self.pipeline_path)
except:
return 0
if self.abort_initialization:
return 0
# set up error dialog for uncaught exceptions
def show_errordialog(type, exc, tb):
def doit():
cpp.cancel_progress()
display_error_dialog(
self.frame,
exc,
None,
tb=tb,
continue_only=True,
message="Exception in CellProfiler core processing")
# continue is really the only choice
wx.CallAfter(doit)
# replace default hook with error dialog
self.orig_excepthook = sys.excepthook
sys.excepthook = show_errordialog
self.SetTopWindow(self.frame)
self.frame.Show()
if self.frame.startup_blurb_frame.IsShownOnScreen():
self.frame.startup_blurb_frame.Raise()
return 1
def run_pipeline_headless(options, args):
'''Run a CellProfiler pipeline in headless mode'''
#
# Start Ilastik's workers
#
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.set_thread_count(1)
except:
logging.root.warn("Failed to stop Ilastik")
if sys.platform == 'darwin':
if options.start_awt:
import bioformats
from javabridge import activate_awt
activate_awt()
if not options.first_image_set is None:
if not options.first_image_set.isdigit():
raise ValueError("The --first-image-set option takes a numeric argument")
else:
image_set_start = int(options.first_image_set)
else:
image_set_start = None
image_set_numbers = None
if not options.last_image_set is None:
if not options.last_image_set.isdigit():
raise ValueError("The --last-image-set option takes a numeric argument")
else:
image_set_end = int(options.last_image_set)
if image_set_start is None:
image_set_numbers = np.arange(1, image_set_end+1)
else:
image_set_numbers = np.arange(image_set_start, image_set_end+1)
else:
image_set_end = None
if ((options.pipeline_filename is not None) and
(not options.pipeline_filename.lower().startswith('http'))):
options.pipeline_filename = os.path.expanduser(options.pipeline_filename)
from cellprofiler.pipeline import Pipeline, EXIT_STATUS, M_PIPELINE
import cellprofiler.measurements as cpmeas
import cellprofiler.preferences as cpprefs
pipeline = Pipeline()
initial_measurements = None
try:
if h5py.is_hdf5(options.pipeline_filename):
initial_measurements = cpmeas.load_measurements(
options.pipeline_filename,
image_numbers=image_set_numbers)
except:
logging.root.info("Failed to load measurements from pipeline")
if initial_measurements is not None:
pipeline_text = \
initial_measurements.get_experiment_measurement(
M_PIPELINE)
pipeline_text = pipeline_text.encode('us-ascii')
pipeline.load(StringIO(pipeline_text))
if not pipeline.in_batch_mode():
#
# Need file list in order to call prepare_run
#
from cellprofiler.utilities.hdf5_dict import HDF5FileList
with h5py.File(options.pipeline_filename, "r") as src:
if HDF5FileList.has_file_list(src):
HDF5FileList.copy(
src, initial_measurements.hdf5_dict.hdf5_file)
else:
pipeline.load(options.pipeline_filename)
if options.groups is not None:
kvs = [x.split('=') for x in options.groups.split(',')]
groups = dict(kvs)
else:
groups = None
file_list = cpprefs.get_image_set_file()
if file_list is not None:
pipeline.read_file_list(file_list)
#
# Fixup CreateBatchFiles with any command-line input or output directories
#
if pipeline.in_batch_mode():
create_batch_files = [
m for m in pipeline.modules()
if m.is_create_batch_module()]
if len(create_batch_files) > 0:
create_batch_files = create_batch_files[0]
if options.output_directory is not None:
create_batch_files.custom_output_directory.value = \
options.output_directory
if options.image_directory is not None:
create_batch_files.default_image_directory.value = \
options.image_directory
use_hdf5 = len(args) > 0 and not args[0].lower().endswith(".mat")
measurements = pipeline.run(
image_set_start=image_set_start,
image_set_end=image_set_end,
grouping=groups,
measurements_filename = None if not use_hdf5 else args[0],
initial_measurements = initial_measurements)
if len(args) > 0 and not use_hdf5:
pipeline.save_measurements(args[0], measurements)
if options.done_file is not None:
if (measurements is not None and
measurements.has_feature(cpmeas.EXPERIMENT, EXIT_STATUS)):
done_text = measurements.get_experiment_measurement(EXIT_STATUS)
else:
done_text = "Failure"
fd = open(options.done_file, "wt")
fd.write("%s\n"%done_text)
fd.close()
if measurements is not None:
measurements.close()
@app.route("/start", methods=["GET"])
def init():
start()
return "starting CPA"
##
## Actually setup the Api resource routing here
##
api.add_resource(helloworld, "/")
# api.add_resource(TrainingSet, '/')
api.add_resource(getImagePaths, "/images")
api.add_resource(getBase64, "/base64")
api.add_resource(getAll, "/all")
# Server Main Function
if __name__ == "__main__":
# app.debug = True
# app.run(host='0.0.0.0', port=5000) #Public IP
start()
# Start the virtual machine
javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
javabridge.attach()
javabridge.activate_awt()
# Calculate the Training DataSet and store it
calculateTrainingSetJSON(base64=True)
def run_pipeline_headless(options, args):
'''Run a CellProfiler pipeline in headless mode'''
if sys.platform == 'darwin':
if options.start_awt:
from javabridge import activate_awt
activate_awt()
if not options.first_image_set is None:
if not options.first_image_set.isdigit():
raise ValueError(
"The --first-image-set option takes a numeric argument")
else:
image_set_start = int(options.first_image_set)
else:
image_set_start = None
image_set_numbers = None
if not options.last_image_set is None:
if not options.last_image_set.isdigit():
raise ValueError(
"The --last-image-set option takes a numeric argument")
else:
image_set_end = int(options.last_image_set)
if image_set_start is None:
image_set_numbers = np.arange(1, image_set_end + 1)
else:
image_set_numbers = np.arange(image_set_start,
image_set_end + 1)
else:
image_set_end = None
if ((options.pipeline_filename is not None)
and (not options.pipeline_filename.lower().startswith('http'))):
options.pipeline_filename = os.path.expanduser(
options.pipeline_filename)
from cellprofiler.pipeline import Pipeline, EXIT_STATUS, M_PIPELINE
import cellprofiler.measurement as cpmeas
import cellprofiler.preferences as cpprefs
pipeline = Pipeline()
initial_measurements = None
try:
if h5py.is_hdf5(options.pipeline_filename):
initial_measurements = cpmeas.load_measurements(
options.pipeline_filename, image_numbers=image_set_numbers)
except:
logging.root.info("Failed to load measurements from pipeline")
if initial_measurements is not None:
pipeline_text = \
initial_measurements.get_experiment_measurement(
M_PIPELINE)
pipeline_text = pipeline_text.encode('us-ascii')
pipeline.load(StringIO(pipeline_text))
if not pipeline.in_batch_mode():
#
# Need file list in order to call prepare_run
#
from cellprofiler.utilities.hdf5_dict import HDF5FileList
with h5py.File(options.pipeline_filename, "r") as src:
if HDF5FileList.has_file_list(src):
HDF5FileList.copy(src,
initial_measurements.hdf5_dict.hdf5_file)
else:
pipeline.load(options.pipeline_filename)
if options.groups is not None:
kvs = [x.split('=') for x in options.groups.split(',')]
groups = dict(kvs)
else:
groups = None
file_list = cpprefs.get_image_set_file()
if file_list is not None:
pipeline.read_file_list(file_list)
#
# Fixup CreateBatchFiles with any command-line input or output directories
#
if pipeline.in_batch_mode():
create_batch_files = [
m for m in pipeline.modules() if m.is_create_batch_module()
]
if len(create_batch_files) > 0:
create_batch_files = create_batch_files[0]
if options.output_directory is not None:
create_batch_files.custom_output_directory.value = \
options.output_directory
if options.image_directory is not None:
create_batch_files.default_image_directory.value = \
options.image_directory
use_hdf5 = len(args) > 0 and not args[0].lower().endswith(".mat")
measurements = pipeline.run(
image_set_start=image_set_start,
image_set_end=image_set_end,
grouping=groups,
measurements_filename=None if not use_hdf5 else args[0],
initial_measurements=initial_measurements)
if len(args) > 0 and not use_hdf5:
pipeline.save_measurements(args[0], measurements)
if options.done_file is not None:
if (measurements is not None
and measurements.has_feature(cpmeas.EXPERIMENT, EXIT_STATUS)):
done_text = measurements.get_experiment_measurement(EXIT_STATUS)
exit_code = (0 if done_text == "Complete" else -1)
else:
done_text = "Failure"
exit_code = -1
fd = open(options.done_file, "wt")
fd.write("%s\n" % done_text)
fd.close()
if measurements is not None:
measurements.close()
return exit_code
def OnInit(self):
javabridge.activate_awt()
return True
