def load_using_bioformats(path,
c=None,
z=0,
t=0,
series=None,
index=None,
rescale=True,
wants_max_intensity=False,
channel_names=None):
'''Load the given image file using the Bioformats library
path: path to the file
z: the frame index in the z (depth) dimension.
t: the frame index in the time dimension.
channel_names: None if you don't want them, a list which will be filled if you do
Returns either a 2-d (grayscale) or 3-d (2-d + 3 RGB planes) image
'''
#
# We loop as long as the user is willing to try logging
# in after timeout.
#
while True:
try:
return __load_using_bioformats(path, c, z, t, series, index,
rescale, wants_max_intensity,
channel_names)
except jutil.JavaException, e:
je = e.throwable
if jutil.is_instance_of(je, "loci/formats/FormatException"):
je = jutil.call(je, "getCause", "()Ljava/lang/Throwable;")
if jutil.is_instance_of(je, "Glacier2/PermissionDeniedException"):
omero_logout()
omero_login()
else:
import errno
import exceptions
import traceback
logger.warn(e.message)
for line in traceback.format_exc().split("\n"):
logger.warn(line)
if jutil.is_instance_of(je, "java/io/FileNotFoundException"):
raise exceptions.IOError(
errno.ENOENT,
"The file, \"%s\", does not exist." % path, path)
e2 = exceptions.IOError(
errno.EINVAL,
"Could not load the file as an image (see log for details)",
path.encode('utf-8'))
raise e2
def evaluate_url(filtr, url):
'''Evaluate a URL using a setting's filter
'''
global filter_class, filter_method_id
env = J.get_env()
if filter_class is None:
filter_class = env.find_class("org/cellprofiler/imageset/filter/Filter")
if filter_class is None:
jexception = get_env.exception_occurred()
raise J.JavaException(jexception)
filter_method_id = env.get_static_method_id(
filter_class,
"filter",
"(Ljava/lang/String;Ljava/lang/String;)Z")
if filter_method_id is None:
raise JavaError("Could not find static method, org.cellprofiler.imageset.filter.Filter.filter(String, String)")
try:
expression = filtr.value_text
if isinstance(expression, unicode):
expression = expression.encode("utf-8")
if isinstance(url, unicode):
url = url.encode("utf-8")
return env.call_static_method(
filter_class, filter_method_id,
env.new_string_utf(expression), env.new_string_utf(url))
except J.JavaException as e:
if J.is_instance_of(
e.throwable, "org/cellprofiler/imageset/filter/Filter$BadFilterExpressionException"):
raise
return False
def evaluate_url(filtr, url):
'''Evaluate a URL using a setting's filter
'''
global filter_class, filter_method_id
env = J.get_env()
if filter_class is None:
filter_class = env.find_class(
"org/cellprofiler/imageset/filter/Filter")
if filter_class is None:
jexception = get_env.exception_occurred()
raise J.JavaException(jexception)
filter_method_id = env.get_static_method_id(
filter_class, "filter", "(Ljava/lang/String;Ljava/lang/String;)Z")
if filter_method_id is None:
raise JavaError(
"Could not find static method, org.cellprofiler.imageset.filter.Filter.filter(String, String)"
)
try:
expression = filtr.value_text
if isinstance(expression, unicode):
expression = expression.encode("utf-8")
if isinstance(url, unicode):
url = url.encode("utf-8")
return env.call_static_method(filter_class, filter_method_id,
env.new_string_utf(expression),
env.new_string_utf(url))
except J.JavaException as e:
if J.is_instance_of(
e.throwable,
"org/cellprofiler/imageset/filter/Filter$BadFilterExpressionException"
):
raise
return False
def load_using_bioformats(path, c=None, z=0, t=0, series=None, index=None,
rescale = True,
wants_max_intensity = False,
channel_names = None):
'''Load the given image file using the Bioformats library
path: path to the file
z: the frame index in the z (depth) dimension.
t: the frame index in the time dimension.
channel_names: None if you don't want them, a list which will be filled if you do
Returns either a 2-d (grayscale) or 3-d (2-d + 3 RGB planes) image
'''
#
# We loop as long as the user is willing to try logging
# in after timeout.
#
while True:
try:
return __load_using_bioformats(
path, c, z, t, series, index, rescale, wants_max_intensity,
channel_names)
except jutil.JavaException, e:
je = e.throwable
if jutil.is_instance_of(
je, "loci/formats/FormatException"):
je = jutil.call(je, "getCause",
"()Ljava/lang/Throwable;")
if jutil.is_instance_of(
je, "Glacier2/PermissionDeniedException"):
omero_logout()
omero_login()
else:
import errno
import exceptions
import traceback
logger.warn(e.message)
for line in traceback.format_exc().split("\n"):
logger.warn(line)
if jutil.is_instance_of(je, "java/io/FileNotFoundException"):
raise exceptions.IOError(
errno.ENOENT,
"The file, \"%s\", does not exist." % path,
path)
e2 = exceptions.IOError(
errno.EINVAL, "Could not load the file as an image (see log for details)", path.encode('utf-8'))
raise e2
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
logger.info("Could not find command %s" % key)
return []
result = []
inputs = module_info.getInputs()
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
if label is None:
label = module_item.getName()
if module_item.isOutput():
# if both, qualify which is for input and which for output
label = "%s (Input)" % label
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
default = module_item.loadValue()
description = module_item.getDescription()
if field_type == ij2.FT_BOOL:
value = (J.is_instance_of(default, 'java/lang/Boolean') and
J.call(default, "booleanValue", "()Z"))
setting = cps.Binary(
label,
value = value,
doc = description)
elif field_type == ij2.FT_INTEGER:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "intValue", "()I")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Integer(
label,
value = value,
doc = description)
elif field_type == ij2.FT_FLOAT:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "doubleValue", "()D")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Float(
label,
value=value,
doc = description)
elif field_type == ij2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(default)
if choices is not None:
choices = J.get_collection_wrapper(choices)
setting = cps.Choice(
label, choices, value, doc = description)
else:
setting = cps.Text(
label, value, doc = description)
elif field_type == ij2.FT_COLOR:
value = "#ffffff"
setting = cps.Color(label, value, doc = description)
elif field_type == ij2.FT_IMAGE:
setting = cps.ImageNameSubscriber(
label, "InputImage",
doc = description)
elif field_type == ij2.FT_TABLE:
setting = IJTableSubscriber(label, "InputTable",
doc=description)
elif field_type == ij2.FT_FILE:
setting = cps.FilenameText(
label, None, doc = description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
label = output.getLabel()
if label is None:
label = output.getName()
if output.isInput():
# if both, qualify which is for input and which for output
label = "%s (Output)" % label
if field_type == ij2.FT_IMAGE:
result.append((cps.ImageNameProvider(
label, "ImageJImage",
doc = description), output))
elif field_type == ij2.FT_TABLE:
result.append((IJTableProvider(
label, "ImageJTable", doc=description), output))
d[key] = result
else:
result = d[key]
return [setting for setting, module_info in result]
def test_02_02_01_get_modules(self):
svc = ij2.get_module_service(self.context)
module_infos = svc.getModules()
self.assertTrue(J.is_instance_of(module_infos[0].o,
"imagej/module/ModuleInfo"))
def get_command_settings(self, command, d):
'''Get the settings associated with the current command
d - the dictionary that persists the setting. None = regular
'''
key = command.get_unicode_value()
if not d.has_key(key):
try:
module_info = command.get_selected_leaf()[2]
except cps.ValidationError:
logger.info("Could not find command %s" % key)
return []
result = []
inputs = module_info.getInputs()
for module_item in inputs:
field_type = module_item.getType()
label = module_item.getLabel()
if label is None:
label = module_item.getName()
if module_item.isOutput():
# if both, qualify which is for input and which for output
label = "%s (Input)" % label
minimum = module_item.getMinimumValue()
maximum = module_item.getMaximumValue()
default = module_item.loadValue()
description = module_item.getDescription()
if field_type == ij2.FT_BOOL:
value = (J.is_instance_of(default, 'java/lang/Boolean')
and J.call(default, "booleanValue", "()Z"))
setting = cps.Binary(label, value=value, doc=description)
elif field_type == ij2.FT_INTEGER:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "intValue", "()I")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Integer(label, value=value, doc=description)
elif field_type == ij2.FT_FLOAT:
if J.is_instance_of(default, 'java/lang/Number'):
value = J.call(default, "doubleValue", "()D")
elif minimum is not None:
value = minimum
elif maximum is not None:
value = maximum
else:
value = 0
setting = cps.Float(label, value=value, doc=description)
elif field_type == ij2.FT_STRING:
choices = module_item.getChoices()
value = J.to_string(default)
if choices is not None:
choices = J.get_collection_wrapper(choices)
setting = cps.Choice(label,
choices,
value,
doc=description)
else:
setting = cps.Text(label, value, doc=description)
elif field_type == ij2.FT_COLOR:
value = "#ffffff"
setting = cps.Color(label, value, doc=description)
elif field_type == ij2.FT_IMAGE:
setting = cps.ImageNameSubscriber(label,
"InputImage",
doc=description)
elif field_type == ij2.FT_TABLE:
setting = IJTableSubscriber(label,
"InputTable",
doc=description)
elif field_type == ij2.FT_FILE:
setting = cps.FilenameText(label, None, doc=description)
else:
continue
result.append((setting, module_item))
for output in module_info.getOutputs():
field_type = output.getType()
label = output.getLabel()
if label is None:
label = output.getName()
if output.isInput():
# if both, qualify which is for input and which for output
label = "%s (Output)" % label
if field_type == ij2.FT_IMAGE:
result.append(
(cps.ImageNameProvider(label,
"ImageJImage",
doc=description), output))
elif field_type == ij2.FT_TABLE:
result.append((IJTableProvider(label,
"ImageJTable",
doc=description), output))
d[key] = result
else:
result = d[key]
return [setting for setting, module_info in result]
