def get_commands():
'''Return a list of the available command strings'''
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
#
# This is a little bogus, but works - trick IJ into initializing
#
execute_command("pleaseignorethis")
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
return []
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [
J.to_string(x) for x in J.iterate_java(
J.call(values, 'iterator', "()Ljava/util/Iterator;"))
]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def get_commands():
"""Return a list of the available command strings"""
script = """
new java.util.concurrent.Callable() {
call: function() {
importClass(Packages.ij.Menus, Packages.ij.IJ);
var hashtable=Menus.getCommands();
if (hashtable==null) {
IJ.run("pleaseignorethis");
hashtable = Menus.getCommands();
}
return hashtable;
}
};
"""
c = J.run_script(script, class_loader=get_user_loader())
hashtable = J.execute_callable_in_main_thread(c)
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [J.to_string(x) for x in J.iterate_java(J.call(values, "iterator", "()Ljava/util/Iterator;"))]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def getModules(self):
modules = J.call(o, "getModules", "()Ljava/util/List;")
if modules is None:
return []
module_iterator = J.call(modules, "iterator",
"()Ljava/util/Iterator;")
return [wrap_module_info(x) for x in J.iterate_java(module_iterator)]
def getModules(self):
modules = J.call(o, "getModules", "()Ljava/util/List;")
if modules is None:
return []
module_iterator = J.call(modules, "iterator",
"()Ljava/util/Iterator;")
return [ModuleInfo(x) for x in J.iterate_java(module_iterator)]
def get_fields_and_parameters_from_iterator(parameters):
iterator = J.call(parameters, 'iterator',
'()L%(ITERATOR_CLASS)s;' % globals())
result = []
for jfield in J.iterate_java(iterator):
field = J.get_field_wrapper(jfield)
parameter = field.getAnnotation(PARAMETER_CLASS.replace('/','.'))
if parameter is not None:
parameter = get_parameter_wrapper(parameter)
result.append((field, parameter))
return result
def get_fields_and_parameters_from_iterator(parameters):
iterator = J.call(parameters, 'iterator',
'()L%(ITERATOR_CLASS)s;' % globals())
result = []
for jfield in J.iterate_java(iterator):
field = J.get_field_wrapper(jfield)
parameter = field.getAnnotation(PARAMETER_CLASS.replace('/', '.'))
if parameter is not None:
parameter = get_parameter_wrapper(parameter)
result.append((field, parameter))
return result
def fn():
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
#
# This is a little bogus, but works - trick IJ into initializing
#
execute_command("pleaseignorethis")
hashtable = J.static_call('ij/Menus', 'getCommands',
'()Ljava/util/Hashtable;')
if hashtable is None:
return []
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [J.to_string(x) for x in J.iterate_java(
J.call(values, 'iterator', "()Ljava/util/Iterator;"))]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def prepare_run(self, workspace):
'''Initialize the pipeline's metadata'''
if workspace.pipeline.in_batch_mode():
return True
file_list = workspace.file_list
pipeline = workspace.pipeline
ipds = pipeline.get_filtered_image_plane_details(workspace)
extractor = self.build_extractor()
max_series = 0
max_index = 0
for ipd in ipds:
if ipd.series is not None:
max_series = max(max_series, ipd.series)
if ipd.index is not None:
max_index = max(max_index, ipd.index)
if max_series > 0:
series_digits = int(np.log10(max_series)) + 1
else:
series_digits = 1
if max_index > 0:
index_digits = int(np.log10(max_index)) + 1
else:
index_digits = 1
if max_series > 0 or max_index > 0:
script = """
importPackage(Packages.org.cellprofiler.imageset);
extractor.addImagePlaneExtractor(new SeriesIndexMetadataExtractor(
seriesDigits, indexDigits));
"""
J.run_script(script, dict(extractor = extractor,
seriesDigits = series_digits,
indexDigits = index_digits))
env = J.get_env()
entry_set_class = env.find_class("java/util/Map$Entry")
get_key_id = env.get_method_id(entry_set_class, "getKey", "()Ljava/lang/Object;")
get_value_id = env.get_method_id(entry_set_class, "getValue", "()Ljava/lang/Object;")
def wrap_entry_set(o):
return (env.get_string_utf(env.call_method(o, get_key_id)),
env.get_string_utf(env.call_method(o, get_value_id)))
#
# Much of what appears below is optimized to avoid the cost of
# "getting nice arguments" for the Java bridge. The IPDs should be
# in alphabetical order which means that, for stacks, we can
# save the results of OME-XML parsing in the Java ImageFile object.
#
extractor_class = env.find_class(
"org/cellprofiler/imageset/ImagePlaneMetadataExtractor")
extract_metadata_id = env.get_method_id(
extractor_class,
"extractMetadata",
"(Ljava/lang/String;IILjava/lang/String;"
"[Lorg/cellprofiler/imageset/filter/ImagePlaneDetails;"
"[Lorg/cellprofiler/imageset/ImageFile;"
")Ljava/util/Iterator;")
extract_metadata_if_id = env.get_method_id(
extractor_class,
"extractMetadata",
"(Lorg/cellprofiler/imageset/ImageFile;II"
"[Lorg/cellprofiler/imageset/filter/ImagePlaneDetails;"
")Ljava/util/Iterator;")
ipd_class = env.find_class("org/cellprofiler/imageset/filter/ImagePlaneDetails")
if_class = env.find_class("org/cellprofiler/imageset/ImageFile")
clear_xml_document_id = env.get_method_id(
if_class,
"clearXMLDocument", "()V")
pIPD = env.make_object_array(1, ipd_class)
pIF = env.make_object_array(1, if_class)
last_url = None
last_if = None
if_has_metadata = False
for ipd in ipds:
series, index = [x if x is not None else 0
for x in ipd.series, ipd.index]
if ipd.url != last_url:
if if_has_metadata:
env.call_method(last_if, clear_xml_document_id)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
if_has_metadata = False
xmlmetadata = file_list.get_metadata(ipd.url)
if xmlmetadata is not None:
xmlmetadata = env.new_string_utf(xmlmetadata)
if_has_metadata = True
metadata = env.call_method(extractor, extract_metadata_id,
env.new_string_utf(ipd.url),
int(series), int(index),
xmlmetadata, pIPD, pIF)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
last_url = ipd.url
last_if = env.get_object_array_elements(pIF)[0]
else:
metadata = env.call_method(
extractor, extract_metadata_if_id,
last_if, int(series), int(index), pIPD)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
ipd.metadata.update(J.iterate_java(metadata, wrap_entry_set))
ipd.jipd = env.get_object_array_elements(pIPD)[0]
if if_has_metadata:
env.call_method(last_if, clear_xml_document_id)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
return True
def getOutputs(self):
outputs = J.call(self.o, "outputs", "()Ljava/lang/Iterable;")
output_iterator = J.call(outputs, "iterator",
"()Ljava/util/Iterator;")
return [ModuleItem(o) for o in J.iterate_java(output_iterator)]
def getOutputs(self):
outputs = J.call(self.o, "outputs", "()Ljava/lang/Iterable;")
output_iterator = J.call(outputs, "iterator", "()Ljava/util/Iterator;")
return [ModuleItem(o) for o in J.iterate_java(output_iterator)]
def prepare_run(self, workspace):
'''Initialize the pipeline's metadata'''
if workspace.pipeline.in_batch_mode():
return True
file_list = workspace.file_list
pipeline = workspace.pipeline
ipds = pipeline.get_filtered_image_plane_details(workspace)
extractor = self.build_extractor()
max_series = 0
max_index = 0
for ipd in ipds:
if ipd.series is not None:
max_series = max(max_series, ipd.series)
if ipd.index is not None:
max_index = max(max_index, ipd.index)
if max_series > 0:
series_digits = int(np.log10(max_series)) + 1
else:
series_digits = 1
if max_index > 0:
index_digits = int(np.log10(max_index)) + 1
else:
index_digits = 1
if max_series > 0 or max_index > 0:
script = """
importPackage(Packages.org.cellprofiler.imageset);
extractor.addImagePlaneExtractor(new SeriesIndexMetadataExtractor(
seriesDigits, indexDigits));
"""
J.run_script(
script,
dict(extractor=extractor,
seriesDigits=series_digits,
indexDigits=index_digits))
env = J.get_env()
entry_set_class = env.find_class("java/util/Map$Entry")
get_key_id = env.get_method_id(entry_set_class, "getKey",
"()Ljava/lang/Object;")
get_value_id = env.get_method_id(entry_set_class, "getValue",
"()Ljava/lang/Object;")
def wrap_entry_set(o):
return (env.get_string_utf(env.call_method(o, get_key_id)),
env.get_string_utf(env.call_method(o, get_value_id)))
#
# Much of what appears below is optimized to avoid the cost of
# "getting nice arguments" for the Java bridge. The IPDs should be
# in alphabetical order which means that, for stacks, we can
# save the results of OME-XML parsing in the Java ImageFile object.
#
extractor_class = env.find_class(
"org/cellprofiler/imageset/ImagePlaneMetadataExtractor")
extract_metadata_id = env.get_method_id(
extractor_class, "extractMetadata",
"(Ljava/lang/String;IILjava/lang/String;"
"[Lorg/cellprofiler/imageset/filter/ImagePlaneDetails;"
"[Lorg/cellprofiler/imageset/ImageFile;"
")Ljava/util/Iterator;")
extract_metadata_if_id = env.get_method_id(
extractor_class, "extractMetadata",
"(Lorg/cellprofiler/imageset/ImageFile;II"
"[Lorg/cellprofiler/imageset/filter/ImagePlaneDetails;"
")Ljava/util/Iterator;")
ipd_class = env.find_class(
"org/cellprofiler/imageset/filter/ImagePlaneDetails")
if_class = env.find_class("org/cellprofiler/imageset/ImageFile")
clear_xml_document_id = env.get_method_id(if_class, "clearXMLDocument",
"()V")
pIPD = env.make_object_array(1, ipd_class)
pIF = env.make_object_array(1, if_class)
last_url = None
last_if = None
if_has_metadata = False
for ipd in ipds:
series, index = [
x if x is not None else 0 for x in ipd.series, ipd.index
]
if ipd.url != last_url:
if if_has_metadata:
env.call_method(last_if, clear_xml_document_id)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
if_has_metadata = False
xmlmetadata = file_list.get_metadata(ipd.url)
if xmlmetadata is not None:
xmlmetadata = env.new_string_utf(xmlmetadata)
if_has_metadata = True
metadata = env.call_method(extractor, extract_metadata_id,
env.new_string_utf(ipd.url),
int(series), int(index),
xmlmetadata, pIPD, pIF)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
last_url = ipd.url
last_if = env.get_object_array_elements(pIF)[0]
else:
metadata = env.call_method(extractor,
extract_metadata_if_id, last_if,
int(series), int(index), pIPD)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
ipd.metadata.update(J.iterate_java(metadata, wrap_entry_set))
ipd.jipd = env.get_object_array_elements(pIPD)[0]
if if_has_metadata:
env.call_method(last_if, clear_xml_document_id)
x = env.exception_occurred()
if x is not None:
raise J.JavaException(x)
return True
