def fn(self, *args):
script = """
o.%s(%s);
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
J.run_script(script, d)
def test_05_07_get_pixel_data_3d(self):
svc = ij2.get_dataset_service(self.context)
result = svc.create1(np.array([10, 7, 3]),
"MyDataset",
[ij2.Axes().Y, ij2.Axes().X, ij2.Axes().CHANNEL],
16, False, False)
imgplus = result.getImgPlus()
script = """
ra = imgplus.randomAccess();
for (x=0;x<imgplus.dimension(0);x++) {
ra.setPosition(x, 0);
for (y=0;y<imgplus.dimension(1);y++) {
ra.setPosition(y, 1);
for (c=0;c<imgplus.dimension(2);c++) {
ra.setPosition(c, 2);
ra.get().set(x + y * 10 + c * 100);
}
}
}
"""
J.run_script(script, dict(imgplus=imgplus))
pixel_data = ij2.get_pixel_data(imgplus)
self.assertSequenceEqual(pixel_data.shape, [10, 7, 3])
i, j, c = np.mgrid[0:10, 0:7, 0:3]
np.testing.assert_array_equal(pixel_data, i + j*10 + c*100)
def get_context():
'''Get the ImageJ context
This is a singleton ImageJ context. We need a singleton for now because
of http://trac.imagej.net/ticket/1413
This is an imagej.ImageJ, which at one point was the context.
Call self.getContext() to get the org.scijava.Context which may be
what you want.
'''
global the_imagej_context
if the_imagej_context is None:
the_imagej_context = create_context(None)
#
# We have to turn off the updater and tell ImageJ to never call
# System.exit. We have to tell ImageJ that we read the readme file.
#
# To Do: programatically turn off the updater and take control of
# the quitting and exit process.
#
max_value = J.run_script(
"java.lang.Long.toString(java.lang.Long.MAX_VALUE);")
prefs = [
("net.imagej.updater.UpToDate", "latestNag", max_value),
("net.imagej.options.OptionsMisc", "exitWhenQuitting", "false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("org.scijava.ui.UserInterface")
script = """
var result = java.lang.System.getProperty('ij.ui');
if (! result) {
var infos = pluginService.getPluginsOfType(ui_interface);
if (infos.size() > 0) {
result = infos.get(0).getClassName();
}
}
result;"""
ui_class = J.run_script(script, dict(pluginService=plugin_service,
ui_interface=ui_interface))
first_run = "firstRun-"+the_imagej_context.getVersion()
if ui_class:
prefs.append((ui_class, first_run, "false"))
for class_name, key, value in prefs:
c = J.class_for_name(class_name)
J.static_call(
"org/scijava/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V",
c, key, value)
return the_imagej_context
def fn_launch_frame(event):
javabridge.execute_runnable_in_main_thread(javabridge.run_script("""
new java.lang.Runnable() {
run: function() {
with(JavaImporter(java.awt.Frame)) Frame().setVisible(true);
}
};"""))
def omero_login():
global __omero_config_file
global __omero_session_id
global __omero_server
global __omero_username
global __omero_port
global __omero_password
if __omero_config_file is not None and os.path.isfile(__omero_config_file):
env = jutil.get_env()
config = env.make_object_array(1, env.find_class("java/lang/String"))
env.set_object_array_element(
config, 0, env.new_string("--Ice.Config=%s" % __omero_config_file))
script = """
var client = Packages.omero.client(config);
client.createSession();
client.getSessionId();
"""
__omero_session_id = jutil.run_script(script, dict(config=config))
elif all([
x is not None for x in (__omero_server, __omero_port,
__omero_username, __omero_password)
]):
set_omero_credentials(__omero_server, __omero_port, __omero_username,
__omero_password)
else:
__omero_login_fn()
return __omero_session_id
def get_omero_reader():
'''Return an ``loci.ome.io.OMEROReader`` instance, wrapped as a FormatReader.
'''
script = """
var rdr = new Packages.loci.ome.io.OmeroReader();
rdr.setServer(server);
rdr.setPort(port);
rdr.setUsername(username);
rdr.setSessionID(sessionID);
rdr;
"""
if __omero_session_id is None:
omero_login()
jrdr = jutil.run_script(
script,
dict(server=__omero_server,
port=__omero_port,
username=__omero_username,
sessionID=__omero_session_id))
rdr = make_iformat_reader_class()()
rdr.o = jrdr
return rdr
def get_omexml_metadata(path=None, url=None):
'''Read the OME metadata from a file using Bio-formats
:param path: path to the file
:param groupfiles: utilize the groupfiles option to take the directory structure
into account.
:returns: the metdata as XML.
'''
with ImageReader(path=path, url=url, perform_init=False) as rdr:
#
# Below, "in" is a keyword and Rhino's parser is just a little wonky I fear.
#
# It is critical that setGroupFiles be set to false, goodness knows
# why, but if you don't the series count is wrong for flex files.
#
script = """
importClass(Packages.loci.common.services.ServiceFactory,
Packages.loci.formats.services.OMEXMLService,
Packages.loci.formats['in'].DefaultMetadataOptions,
Packages.loci.formats['in'].MetadataLevel);
reader.setGroupFiles(false);
reader.setOriginalMetadataPopulated(true);
var service = new ServiceFactory().getInstance(OMEXMLService);
var metadata = service.createOMEXMLMetadata();
reader.setMetadataStore(metadata);
reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));
reader.setId(path);
var xml = service.getOMEXML(metadata);
xml;
"""
xml = jutil.run_script(script, dict(path=rdr.path, reader=rdr.rdr))
return xml
def set_omero_credentials(omero_server, omero_port, omero_username,
omero_password):
'''Set the credentials to be used to connect to the Omero server
:param omero_server: DNS name of the server
:param omero_port: use this port to connect to the server
:param omero_username: log on as this user
:param omero_password: log on using this password
The session ID is valid after this function is called. An exception is thrown
if the login fails. :func:`bioformats.omero_logout()` can be called to log out.
'''
global __omero_server
global __omero_username
global __omero_session_id
global __omero_port
__omero_server = omero_server
__omero_port = omero_port
__omero_username = omero_username
script = """
var client = Packages.omero.client(server, port);
var serverFactory = client.createSession(user, password);
client.getSessionId();
"""
__omero_session_id = jutil.run_script(
script,
dict(server=__omero_server,
port=__omero_port,
user=__omero_username,
password=omero_password))
return __omero_session_id
def set_omero_credentials(omero_server, omero_port, omero_username, omero_password):
'''Set the credentials to be used to connect to the Omero server
:param omero_server: DNS name of the server
:param omero_port: use this port to connect to the server
:param omero_username: log on as this user
:param omero_password: log on using this password
The session ID is valid after this function is called. An exception is thrown
if the login fails. :func:`bioformats.omero_logout()` can be called to log out.
'''
global __omero_server
global __omero_username
global __omero_session_id
global __omero_port
__omero_server = omero_server
__omero_port = omero_port
__omero_username = omero_username
script = """
var client = Packages.omero.client(server, port);
var serverFactory = client.createSession(user, password);
client.getSessionId();
"""
__omero_session_id = jutil.run_script(script, dict(
server = __omero_server,
port = __omero_port,
user = __omero_username,
password = omero_password))
return __omero_session_id
def omero_login():
global __omero_config_file
global __omero_session_id
global __omero_server
global __omero_username
global __omero_port
global __omero_password
if __omero_config_file is not None and os.path.isfile(__omero_config_file):
env = jutil.get_env()
config = env.make_object_array(1, env.find_class("java/lang/String"))
env.set_object_array_element(
config, 0, env.new_string("--Ice.Config=%s" % __omero_config_file))
script = """
var client = Packages.omero.client(config);
client.createSession();
client.getSessionId();
"""
__omero_session_id = jutil.run_script(script, dict(config=config))
elif all([x is not None for x in
(__omero_server, __omero_port, __omero_username, __omero_password)]):
set_omero_credentials(__omero_server, __omero_port, __omero_username,
__omero_password)
else:
__omero_login_fn()
return __omero_session_id
def get_omexml_metadata(path=None, url=None):
'''Read the OME metadata from a file using Bio-formats
:param path: path to the file
:param groupfiles: utilize the groupfiles option to take the directory structure
into account.
:returns: the metdata as XML.
'''
with ImageReader(path=path, url=url, perform_init=False) as rdr:
#
# Below, "in" is a keyword and Rhino's parser is just a little wonky I fear.
#
# It is critical that setGroupFiles be set to false, goodness knows
# why, but if you don't the series count is wrong for flex files.
#
script = """
importClass(Packages.loci.common.services.ServiceFactory,
Packages.loci.formats.services.OMEXMLService,
Packages.loci.formats['in'].DefaultMetadataOptions,
Packages.loci.formats['in'].MetadataLevel);
reader.setGroupFiles(false);
reader.setOriginalMetadataPopulated(true);
var service = new ServiceFactory().getInstance(OMEXMLService);
var metadata = service.createOMEXMLMetadata();
reader.setMetadataStore(metadata);
reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));
reader.setId(path);
var xml = service.getOMEXML(metadata);
xml;
"""
xml = jutil.run_script(script, dict(path=rdr.path, reader = rdr.rdr))
return xml
def test_06_03_future_main(self):
c = javabridge.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
result = javabridge.execute_future_in_main_thread(
javabridge.make_future_task(c, fn_post_process=javabridge.unwrap_javascript))
self.assertEqual(result, 4)
def finalize(self, result):
try:
javabridge.deactivate_awt()
import imagej.imagej2
if imagej.imagej2.the_imagej_context is not None:
script = """
new java.lang.Runnable () {
run: function() {
ctx.getContext().dispose();
}
}"""
runnable = javabridge.run_script(
script, dict(ctx=imagej.imagej2.the_imagej_context))
javabridge.execute_runnable_in_main_thread(runnable, True)
imagej.imagej2.the_imagej_context = None
javabridge.static_call("java/lang/System", "gc", "()V")
except:
pass
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary")
def _init_writer(self):
# If file already exists, delete it before initializing again.
# If this is not done, then the file will be appended.
if os.path.exists(self._file_path):
os.remove(self._file_path)
w_klass = make_ome_tiff_writer_class()
w_klass.setId = jutil.make_method('setId', '(Ljava/lang/String;)V',
'Sets the current file name.')
w_klass.saveBytesXYWH = jutil.make_method(
'saveBytes', '(I[BIIII)V',
'Saves the given byte array to the current file')
w_klass.close = jutil.make_method(
'close', '()V',
'Closes currently open file(s) and frees allocated memory.')
w_klass.setTileSizeX = jutil.make_method(
'setTileSizeX', '(I)I', 'Set tile size width in pixels.')
w_klass.setTileSizeY = jutil.make_method(
'setTileSizeY', '(I)I', 'Set tile size height in pixels.')
w_klass.getTileSizeX = jutil.make_method(
'getTileSizeX', '()I', 'Set tile size width in pixels.')
w_klass.getTileSizeY = jutil.make_method(
'getTileSizeY', '()I', 'Set tile size height in pixels.')
writer = w_klass()
script = """
importClass(Packages.loci.formats.services.OMEXMLService,
Packages.loci.common.services.ServiceFactory);
var service = new ServiceFactory().getInstance(OMEXMLService);
var metadata = service.createOMEXMLMetadata(xml);
var writer = writer
writer.setMetadataRetrieve(metadata);
"""
jutil.run_script(
script,
dict(path=self._file_path,
xml=self._metadata.to_xml(),
writer=writer))
writer.setId(self._file_path)
writer.setInterleaved(False)
writer.setCompression("LZW")
x = writer.setTileSizeX(self._TILE_SIZE)
y = writer.setTileSizeY(self._TILE_SIZE)
self._pix['chunk'] = self._MAX_BYTES / (
self._pix['spp'] * self._pix['bpp']
) # number of pixels to load at a time
self.__writer = writer
def test_06_03_future_main(self):
c = javabridge.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
result = javabridge.execute_future_in_main_thread(
javabridge.make_future_task(
c, fn_post_process=javabridge.unwrap_javascript))
self.assertEqual(result, 4)
def test_valid(self, pipeline):
try:
import javabridge as J
J.run_script(
"""
importPackage(Packages.org.cellprofiler.imageset.filter);
new Filter(expr, klass);
""",
dict(
expr=self.value_text,
klass=J.class_for_name(
"org.cellprofiler.imageset.ImagePlaneDetailsStack"),
),
)
except Exception as e:
raise ValidationError(str(e), self)
def fn_launch_frame(event):
javabridge.execute_runnable_in_main_thread(
javabridge.run_script("""
new java.lang.Runnable() {
run: function() {
with(JavaImporter(java.awt.Frame)) Frame().setVisible(true);
}
};"""))
def cast(o, klass):
'''Cast the given object to the given class
:param o: either a Python object or Java object to be cast
:param klass: a java.lang.Class indicating the target class
raises a TypeError if the object can't be cast.
'''
if J.call(klass, "getName", "()Ljava/lang/String;") == 'void':
return None
is_primitive = J.call(klass, "isPrimitive", "()Z")
csig = sig(klass)
if o is None:
if not is_primitive:
return None
else:
raise TypeError("Can't cast None to a primitive type")
if isinstance(o, J.JB_Object):
if J.call(klass, "isInstance", "(Ljava/lang/Object;)Z", o):
return o
classname = J.run_script("o.getClass().getCanonicalName()", dict(o=o))
klassname = J.run_script("klass.getCanonicalName()", dict(klass=klass))
raise TypeError("Object of class %s cannot be cast to %s", classname,
klassname)
elif hasattr(o, "o"):
return cast(o.o, klass)
elif not np.isscalar(o):
component_type = J.call(klass, "getComponentType",
"()Ljava/lang/Class;")
if component_type is None:
raise TypeError("Argument must not be a sequence")
if len(o) > 0:
# Test if an element can be cast to the array type
cast(o[0], component_type)
return J.get_nice_arg(o, csig)
elif is_primitive or csig in \
('Ljava/lang/String;', 'Ljava/lang/CharSequence;',
'Ljava/lang/Object;'):
if csig == 'Ljava/lang/CharSequence;':
csig = 'Ljava/lang/String;'
elif csig == 'C' and isinstance(o, basestring) and len(o) != 1:
raise TypeError("Failed to convert string of length %d to char" %
len(o))
return J.get_nice_arg(o, csig)
raise TypeError("Failed to convert argument to %s" % csig)
def test_07_04_make_future_task_from_callable(self):
call_able = javabridge.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
future = javabridge.make_future_task(
call_able, fn_post_process=javabridge.unwrap_javascript)
future.run()
self.assertEqual(future.get(), 4)
def test_07_04_make_future_task_from_callable(self):
call_able = javabridge.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
future = javabridge.make_future_task(
call_able, fn_post_process=javabridge.unwrap_javascript)
future.run()
self.assertEqual(future.get(), 4)
def cast(o, klass):
'''Cast the given object to the given class
:param o: either a Python object or Java object to be cast
:param klass: a java.lang.Class indicating the target class
raises a TypeError if the object can't be cast.
'''
if J.call(klass, "getName", "()Ljava/lang/String;") == 'void':
return None
is_primitive = J.call(klass, "isPrimitive", "()Z")
csig = sig(klass)
if o is None:
if not is_primitive:
return None
else:
raise TypeError("Can't cast None to a primitive type")
if isinstance(o, J.JB_Object):
if J.call(klass, "isInstance", "(Ljava/lang/Object;)Z", o):
return o
classname = J.run_script("o.getClass().getCanonicalName()", dict(o=o))
klassname = J.run_script("klass.getCanonicalName()", dict(klass=klass))
raise TypeError("Object of class %s cannot be cast to %s",
classname, klassname)
elif hasattr(o, "o"):
return cast(o.o, klass)
elif not np.isscalar(o):
component_type = J.call(klass, "getComponentType", "()Ljava/lang/Class;")
if component_type is None:
raise TypeError("Argument must not be a sequence")
if len(o) > 0:
# Test if an element can be cast to the array type
cast(o[0], component_type)
return J.get_nice_arg(o, csig)
elif is_primitive or csig in \
('Ljava/lang/String;', 'Ljava/lang/CharSequence;',
'Ljava/lang/Object;'):
if csig == 'Ljava/lang/CharSequence;':
csig = 'Ljava/lang/String;'
elif csig == 'C' and isinstance(o, basestring) and len(o) != 1:
raise TypeError("Failed to convert string of length %d to char" %
len(o))
return J.get_nice_arg(o, csig)
raise TypeError("Failed to convert argument to %s" % csig)
def setActiveDisplay(self, display):
'''Make this the active display'''
# Note: has to be run in GUI thread on mac
r = J.run_script(
"""new java.lang.Runnable() {
run:function() { displayService.setActiveDisplay(display); }
}
""", dict(displayService=self.o, display=display.o))
J.execute_runnable_in_main_thread(r, True)
def test_java_bridge():
javabridge.start_vm(run_headless=True)
try:
print(
javabridge.run_script(
'java.lang.String.format("Hello, %s!", name);',
dict(name='world')))
finally:
javabridge.kill_vm()
def do_new_engine(payload):
'''Create a new engine thread
payload: first member is request queue, second is response queue
'''
logger.info("Creating new engine")
thread = threading.Thread(target=engine,
args=list(payload[:2]),
name="Scripting-CPythonEngine")
thread.setDaemon(True)
thread.start()
J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
var payload = new java.util.ArrayList();
var response = new CPythonScriptEngine.Message(
CPythonScriptEngine.EngineCommands.NEW_ENGINE_RESULT, payload);
CPythonScriptEngine.engineResponseQueue.put(response);
""")
def setActiveDisplay(self, display):
'''Make this the active display'''
# Note: has to be run in GUI thread on mac
r = J.run_script(
"""new java.lang.Runnable() {
run:function() { displayService.setActiveDisplay(display); }
}
""", dict(displayService=self.o, display=display.o))
J.execute_runnable_in_main_thread(r, True)
def engine(q_request, q_response):
logger.info("Starting script engine thread")
J.attach()
while True:
try:
msg = J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
q_request.take();""", dict(q_request=q_request))
if logger.level <= logging.INFO:
logger.info("Received engine request: %s", J.to_string(msg))
payload = J.get_collection_wrapper(
J.run_script("msg.payload", dict(msg=msg)))
if J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.EXECUTE;
""", dict(msg=msg)):
response = do_execute(payload)
elif J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.EVALUATE;
""", dict(msg=msg)):
response = do_evaluate(payload)
elif J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
msg.command==CPythonScriptEngine.EngineCommands.CLOSE_ENGINE;
""", dict(msg=msg)):
logger.info("Exiting script engine thread after close request")
break
else:
logger.warn(
"Received unknown command: %s" %
J.run_script("msg.command.toString()", dict(msg=msg)))
response = J.run_script(
"""importPackage(Packages.org.scijava.plugins.scripting.cpython);
var exception = new java.lang.RuntimeException(
java.lang.String.format('Unknown command: %s', msg.command.toString()));
var payload = new java.util.ArrayList();
payload.add(exception);
new CPythonScriptEngine.Message(
CPythonScriptEngine.EngineCommands.EXCEPTION, payload);
""", dict(msg=msg))
J.run_script("q_response.put(response);",
dict(q_response=q_response, response=response))
except:
# To do: how to handle failure, probably from .take()
# Guessing that someone has managed to interrupt our thread
logger.warn("Exiting script engine thread", exc_info=True)
J.detach()
def hide(self):
J.execute_runnable_in_main_thread(
J.run_script(
"""
new java.lang.Runnable() {
run: function() { o.hide(); }}""",
dict(o=self.o),
),
synchronous=True,
)
def run_javabridge(java_code_to_run):
javabridge.start_vm(run_headless=True)
try:
output = javabridge.run_script(java_code_to_run)
print(output)
# need to process and return some stuff here
finally:
javabridge.kill_vm()
def test_07_02_cancel_future(self):
future = javabridge.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = javabridge.get_future_wrapper(
future, fn_post_process=javabridge.unwrap_javascript)
wfuture.cancel(True)
self.assertTrue(wfuture.isCancelled())
self.assertRaises(javabridge.JavaException, wfuture.get)
def test_07_02_cancel_future(self):
future = javabridge.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = javabridge.get_future_wrapper(
future, fn_post_process=javabridge.unwrap_javascript)
wfuture.cancel(True)
self.assertTrue(wfuture.isCancelled())
self.assertRaises(javabridge.JavaException, wfuture.get)
def execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
interp = J.make_instance("ij/macro/Interpreter","()V");
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run: function() {
interp.run(macro_text);
}}""", dict(interp=interp, macro_text=macro_text)), synchronous=True)
def set_temp_current_image(imagej_obj):
'''Set the temporary current image for the UI thread'''
script = """
new java.lang.Runnable() {
run: function() {
Packages.ij.WindowManager.setTempCurrentImage(ip);
}
};
"""
javabridge.execute_runnable_in_main_thread(
javabridge.run_script(script, dict(ip=imagej_obj.o)), True)
def get_measurements_for_good_pipeline(nimages=1, group_numbers=None):
'''Get an appropriately initialized measurements structure for the good pipeline'''
path = os.path.join(tests.modules.example_images_directory(),
"ExampleSBSImages")
m = cellprofiler.measurement.Measurements()
if group_numbers is None:
group_numbers = [1] * nimages
group_indexes = [1]
last_group_number = group_numbers[0]
group_index = 1
for group_number in group_numbers:
if group_number == last_group_number:
group_index += 1
else:
group_index = 1
group_indexes.append(group_index)
for i in range(1, nimages + 1):
filename = ("Channel2-%02d-%s-%02d.tif" % (i, "ABCDEFGH"[int(
(i - 1) / 12)], ((i - 1) % 12) + 1))
url = cellprofiler.modules.loadimages.pathname2url(
os.path.join(path, filename))
m[cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_FILE_NAME + "_DNA", i] = filename
m[cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_PATH_NAME + "_DNA", i] = path
m[cellprofiler.measurement.IMAGE,
cellprofiler.measurement.C_URL + "_DNA", i] = url
m[cellprofiler.measurement.IMAGE,
cellprofiler.measurement.GROUP_NUMBER, i] = group_numbers[i - 1]
m[cellprofiler.measurement.IMAGE, cellprofiler.measurement.GROUP_INDEX,
i] = group_indexes[i - 1]
jblob = javabridge.run_script(
"""
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
var imageFile=new ImageFile(new java.net.URI(url));
var imageFileDetails = new ImageFileDetails(imageFile);
var imageSeries=new ImageSeries(imageFile, 0);
var imageSeriesDetails = new ImageSeriesDetails(imageSeries, imageFileDetails);
var imagePlane=new ImagePlane(imageSeries, 0, ImagePlane.ALWAYS_MONOCHROME);
var ipd = new ImagePlaneDetails(imagePlane, imageSeriesDetails);
var stack = ImagePlaneDetailsStack.makeMonochromeStack(ipd);
var stacks = java.util.Collections.singletonList(stack);
var keys = java.util.Collections.singletonList(imageNumber);
var imageSet = new ImageSet(stacks, keys);
imageSet.compress(java.util.Collections.singletonList("DNA"), null);
""", dict(url=url, imageNumber=str(i)))
blob = javabridge.get_env().get_byte_array_elements(jblob)
m[cellprofiler.measurement.IMAGE,
cellprofiler.modules.namesandtypes.M_IMAGE_SET, i, blob.dtype] = blob
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.loadtxt(cStringIO.StringIO(GOOD_PIPELINE))
pipeline.write_pipeline_measurement(m)
return m
def set_temp_current_image(imagej_obj):
'''Set the temporary current image for the UI thread'''
script = """
new java.lang.Runnable() {
run: function() {
Packages.ij.WindowManager.setTempCurrentImage(ip);
}
};
"""
J.execute_runnable_in_main_thread(
J.run_script(script, dict(ip=imagej_obj.o)), True)
def close(self):
'''Close the display
This is run in the UI thread with synchronization.
'''
r = J.run_script(
"""new java.lang.Runnable() {
run: function() { display.close(); }
};
""", dict(display=self.o))
J.execute_runnable_in_main_thread(r, True)
def close(self):
'''Close the display
This is run in the UI thread with synchronization.
'''
r = J.run_script(
"""new java.lang.Runnable() {
run: function() { display.close(); }
};
""", dict(display=self.o))
J.execute_runnable_in_main_thread(r, True)
def execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
interp = javabridge.make_instance("ij/macro/Interpreter", "()V");
javabridge.execute_runnable_in_main_thread(javabridge.run_script(
"""new java.lang.Runnable() {
run: function() {
interp.run(macro_text);
}}""", dict(interp=interp, macro_text=macro_text)), synchronous=True)
def get_pixel_data(self, axes=None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
script = """
var result = java.util.ArrayList();
for (i=0;i<imgplus.numDimensions();i++)
result.add(imgplus.axis(i).type());
result"""
inv_axes = J.run_script(script, dict(imgplus=imgplus))
inv_axes = list(J.iterate_collection(inv_axes))
transpose = calculate_transpose(inv_axes, axes)
return pixel_data.transpose(transpose)
def test_07_01_wrap_future(self):
future = javabridge.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = javabridge.get_future_wrapper(
future, fn_post_process=javabridge.unwrap_javascript)
self.assertFalse(wfuture.isDone())
self.assertFalse(wfuture.isCancelled())
wfuture.run()
self.assertTrue(wfuture.isDone())
self.assertEqual(wfuture.get(), 4)
def test_07_01_wrap_future(self):
future = javabridge.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = javabridge.get_future_wrapper(
future, fn_post_process=javabridge.unwrap_javascript)
self.assertFalse(wfuture.isDone())
self.assertFalse(wfuture.isCancelled())
wfuture.run()
self.assertTrue(wfuture.isDone())
self.assertEqual(wfuture.get(), 4)
def get_temp_current_image():
'''Get the temporary ImagePlus object for the current thread'''
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getTempCurrentImage();
}
};
"""
gtci = J.make_future_task(J.run_script(script))
imageplus_obj = J.execute_future_in_main_thread(gtci)
return get_imageplus_wrapper(imageplus_obj)
def get_temp_current_image():
'''Get the temporary ImagePlus object for the current thread'''
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getTempCurrentImage();
}
};
"""
gtci = javabridge.make_future_task(javabridge.run_script(script))
imageplus_obj = javabridge.execute_future_in_main_thread(gtci)
return imagej.imageplus.get_imageplus_wrapper(imageplus_obj)
def get_pixel_data(self, axes = None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
script = """
var result = java.util.ArrayList();
for (i=0;i<imgplus.numDimensions();i++)
result.add(imgplus.axis(i).type());
result"""
inv_axes = J.run_script(script, dict(imgplus=imgplus))
inv_axes = list(J.iterate_collection(inv_axes))
transpose = calculate_transpose(inv_axes, axes)
return pixel_data.transpose(transpose)
def test_05_03_get_pixel_data(self):
svc = ij2.get_dataset_service(self.context)
result = svc.create1(np.array([10, 7]), "MyDataset",
[ij2.Axes().Y, ij2.Axes().X], 8, False, False)
imgplus = result.getImgPlus()
script = """
ra = imgplus.randomAccess();
for (x=0;x<imgplus.dimension(0);x++) {
ra.setPosition(x, 0);
for (y=0;y<imgplus.dimension(1);y++) {
ra.setPosition(y, 1);
ra.get().set(x + y * 10);
}
}
"""
J.run_script(script, dict(imgplus=imgplus))
pixel_data = ij2.get_pixel_data(imgplus)
self.assertSequenceEqual(pixel_data.shape, [10, 7])
i, j = np.mgrid[0:10, 0:7]
np.testing.assert_array_equal(pixel_data, i + j * 10)
def __init__(self, figure):
FigureCanvasAgg.__init__(self, figure)
self.__ref_id, self.__ref = javabridge.create_jref(self)
self.__cpython = javabridge.make_instance(
'org/cellprofiler/javabridge/CPython', '()V')
paint_script = (
'import javabridge\n'
'self = javabridge.redeem_jref("%s")\n'
'self.draw(javabridge.JWrapper(graphics))\n') % self.__ref_id
component = javabridge.run_script(
"""
new javax.swing.JComponent() {
paintComponent: function(graphics) {
locals = new java.util.Hashtable();
locals.put("graphics", graphics);
cpython.exec(script, locals, locals);
}
}
""", dict(cpython=self.__cpython, script=paint_script))
self.__component = javabridge.JWrapper(component)
self.__event_queue_class = None
self.__component_listener = javabridge.JProxy(
'java.awt.event.ComponentListener',
dict(componentHidden=self._on_component_hidden,
componentMoved=self._on_component_moved,
componentResized=self._on_component_resized,
componentShown=self._on_component_shown))
self.__component.addComponentListener(self.__component_listener.o)
self.__key_event_cls = javabridge.JClassWrapper(
'java.awt.event.KeyEvent')
self.__key_listener = javabridge.JProxy(
'java.awt.event.KeyListener',
dict(keyPressed=self._on_key_pressed,
keyReleased=self._on_key_released,
keyTyped=self._on_key_typed))
self.__component.addKeyListener(self.__key_listener.o)
self.__component.setFocusable(True)
self.__mouse_listener = javabridge.JProxy(
'java.awt.event.MouseListener',
dict(mouseClicked=self._on_mouse_clicked,
mouseEntered=self._on_mouse_entered,
mouseExited=self._on_mouse_exited,
mousePressed=self._on_mouse_pressed,
mouseReleased=self._on_mouse_released))
self.__component.addMouseListener(self.__mouse_listener.o)
self.__mouse_motion_listener = javabridge.JProxy(
'java.awt.event.MouseMotionListener',
dict(mouseDragged=self._on_mouse_dragged,
mouseMoved=self._on_mouse_moved))
self.__component.addMouseMotionListener(self.__mouse_motion_listener.o)
def fn(self, *args):
script = """
new java.lang.Runnable() {
run: function() {
o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return future.get()
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.call(ctxt_fn, 'call', '()Ljava/lang/Object;')
def fn(self, *args):
script = """
new java.util.concurrent.Callable() {
call: function() {
return o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return fn_post_process(future.get())
def fn(self, *args):
script = """
new java.util.concurrent.Callable() {
call: function() {
return o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return fn_post_process(future.get())
def fn(self, *args):
script = """
new java.lang.Runnable() {
run: function() {
o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return future.get()
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script("""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES
]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.net.imagej.ImageJ(classes);
}
}""", dict(classes=classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def test_05_06_create_dataset(self):
i,j = np.mgrid[:7, :9]
image = (i+j*10).astype(float)
ds = ij2.create_dataset(self.context, image, "Foo")
imgplus = ds.getImgPlus()
script = """
var ra=imgplus.randomAccess();
ra.setPosition(x, 0);
ra.setPosition(y, 1);
ra.get().get()"""
fn = np.frompyfunc(
lambda x, y: J.run_script(script,
dict(imgplus=imgplus, x=x, y=y)), 2, 1)
pixel_data = fn(j, i)
np.testing.assert_array_equal(image, pixel_data)
def select_overlay(display, overlay, select=True):
'''Select or deselect an overlay
display - the overlay's display
overlay - the overlay to select
'''
for view in J.get_collection_wrapper(display, fn_wrapper = wrap_data_view):
if J.call(overlay, "equals", "(Ljava/lang/Object;)Z", view.getData()):
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run: function() { view.setSelected(select);}
}""", dict(view = view.o, select=select)), synchronous=True)
break
else:
logger.info("Failed to select overlay")
def get_measurements_for_good_pipeline(nimages = 1,
group_numbers = None):
'''Get an appropriately initialized measurements structure for the good pipeline'''
path = os.path.join(example_images_directory(), "ExampleSBSImages")
m = cpmeas.Measurements()
if group_numbers is None:
group_numbers = [1] * nimages
group_indexes = [1]
last_group_number = group_numbers[0]
group_index = 1
for group_number in group_numbers:
if group_number == last_group_number:
group_index += 1
else:
group_index = 1
group_indexes.append(group_index)
for i in range(1, nimages+1):
filename = ("Channel2-%02d-%s-%02d.tif" %
(i, "ABCDEFGH"[int((i-1) / 12)], ((i-1) % 12) + 1))
url = pathname2url(os.path.join(path, filename))
m[cpmeas.IMAGE, cpmeas.C_FILE_NAME + "_DNA", i] = filename
m[cpmeas.IMAGE, cpmeas.C_PATH_NAME + "_DNA", i] = path
m[cpmeas.IMAGE, cpmeas.C_URL+"_DNA", i] = url
m[cpmeas.IMAGE, cpmeas.GROUP_NUMBER, i] = group_numbers[i-1]
m[cpmeas.IMAGE, cpmeas.GROUP_INDEX, i] = group_indexes[i-1]
jblob = J.run_script("""
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
var imageFile=new ImageFile(new java.net.URI(url));
var imageFileDetails = new ImageFileDetails(imageFile);
var imageSeries=new ImageSeries(imageFile, 0);
var imageSeriesDetails = new ImageSeriesDetails(imageSeries, imageFileDetails);
var imagePlane=new ImagePlane(imageSeries, 0, ImagePlane.ALWAYS_MONOCHROME);
var ipd = new ImagePlaneDetails(imagePlane, imageSeriesDetails);
var stack = ImagePlaneDetailsStack.makeMonochromeStack(ipd);
var stacks = java.util.Collections.singletonList(stack);
var keys = java.util.Collections.singletonList(imageNumber);
var imageSet = new ImageSet(stacks, keys);
imageSet.compress(java.util.Collections.singletonList("DNA"), null);
""", dict(url=url, imageNumber = str(i)))
blob = J.get_env().get_byte_array_elements(jblob)
m[cpmeas.IMAGE, M_IMAGE_SET, i, blob.dtype] = blob
pipeline = cpp.Pipeline()
pipeline.loadtxt(StringIO(GOOD_PIPELINE))
pipeline.write_pipeline_measurement(m)
return m
def set_current_image(imagej_obj):
'''Set the currently active window
imagej_obj - an ImagePlus to become the current image
'''
javabridge.execute_runnable_in_main_thread(javabridge.run_script(
"""new java.lang.Runnable() {
run:function() {
var w = imp.getWindow();
if (w == null) {
imp.show();
} else {
Packages.ij.WindowManager.setCurrentWindow(w);
}
}
}
""", dict(imp=imagej_obj.o)), synchronous=True)
def createDisplay(self, name, dataset):
'''Create a display that contains the given dataset'''
#
# Must be run on the gui thread
#
jcallable = J.run_script(
"""new java.util.concurrent.Callable() {
call:function() {
return displayService.createDisplay(name, dataset);
}
};
""", dict(displayService=self.o,
name = name,
dataset = dataset.o))
future = J.make_future_task(jcallable,
fn_post_process = wrap_display)
return J.execute_future_in_main_thread(future)
def get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
#
# Run this on the UI thread so its thread context is the same
# as the macro invocation
#
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getCurrentImage();
}
};
"""
gci = javabridge.make_future_task(javabridge.run_script(script))
imageplus_obj = javabridge.execute_future_in_main_thread(gci)
return imagej.imageplus.get_imageplus_wrapper(imageplus_obj)
