def run(self, module_info, pre=None, post=None, **kwargs):
'''Run a module
module_info - the module_info of the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.make_map(kwargs)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run", "(Limagej/module/ModuleInfo;"
"Ljava/util/List;"
"Ljava/util/List;"
"Ljava/util/Map;)"
"Ljava/util/concurrent/Future;", module_info, pre, post,
input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/module/Module;",
future)
def run(self, module_info,
pre = None,
post = None,
**kwargs):
'''Run a module
module_info - the module_info of the module to run
pre - list of PreprocessorPlugins to run before running module
post - list of PostprocessorPlugins to run after running module
*kwargs - names and values for input parameters
'''
input_map = J.make_map(kwargs)
if pre is not None:
pre = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
pre)
if post is not None:
post = J.static_call("java/util/Arrays", "asList",
"([Ljava/lang/Object;)Ljava/util/List;",
post)
future = J.call(
self.o, "run",
"(Limagej/module/ModuleInfo;"
"Ljava/util/List;"
"Ljava/util/List;"
"Ljava/util/Map;)"
"Ljava/util/concurrent/Future;",
module_info, pre, post, input_map)
return J.call(
self.o, "waitFor",
"(Ljava/util/concurrent/Future;)Limagej/module/Module;",
future)
def run_command(self, command_class, inputs, outputs):
'''Run an imageJ command
command_class - the command's dotted class name
inputs - a dictionary of key/value pairs for the command's inputs
outputs - a dictionary of keys to be filled with the command's outputs
'''
module_index = ij2.get_module_service(self.context).getIndex()
module_infos = module_index.getS('imagej.command.CommandInfo')
module_info = filter(lambda x:x.getClassName() == command_class,
module_infos)[0]
svc = ij2.get_command_service(self.context)
input_map = J.make_map(**inputs)
future = svc.run(module_info.o, input_map.o)
module = future.get()
for key in list(outputs):
module_item = module_info.getOutput(key)
outputs[key] = module_item.getValue(module)
def do_teest(self, module, channels, expected_tags, expected_metadata, additional=None):
'''Ensure that NamesAndTypes recreates the column layout when run
module - instance of NamesAndTypes, set up for the test
channels - a dictionary of channel name to list of "ipds" for that
channel where "ipd" is a tuple of URL and metadata dictionary
Entries may appear multiple times (e.g. illumination function)
expected_tags - the metadata tags that should have been generated
by prepare_run.
expected_metadata - a sequence of two-tuples of metadata key and
the channel from which the metadata is extracted.
additional - if present, these are added as ImagePlaneDetails in order
to create errors. Format is same as a single channel of
channels.
'''
ipds = []
urls = set()
url_root = "file:" + urllib.pathname2url(os.path.abspath(os.path.curdir))
channels = dict(channels)
if additional is not None:
channels["Additional"] = additional
for channel_name in list(channels):
channel_data = [(url_root + "/" + path, metadata)
for path, metadata in channels[channel_name]]
channels[channel_name] = channel_data
for url, metadata in channel_data:
if url in urls:
continue
urls.add(url)
ipd = cpp.ImagePlaneDetails(url, None, None, None, **metadata)
jmetadata = J.make_map(**metadata)
ipd.jipd = J.run_script("""
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
var imageFile=new ImageFile(new java.net.URI(url));
var imagePlane=new ImagePlane(imageFile);
new ImagePlaneDetails(imagePlane, metadata);
""", dict(url=url, metadata=jmetadata))
ipds.append(ipd)
if additional is not None:
del channels["Additional"]
ipds.sort(key = lambda x: x.url)
pipeline = cpp.Pipeline()
del pipeline.image_plane_details[:]
pipeline.image_plane_details.extend(ipds)
module.module_num = 1
pipeline.add_module(module)
m = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, m, None, m, None)
self.assertTrue(module.prepare_run(workspace))
tags = m.get_metadata_tags()
self.assertEqual(len(tags), len(expected_tags))
for tag, expected_tag in zip(tags, expected_tags):
for et in expected_tag:
ftr = et if et == cpmeas.IMAGE_NUMBER else \
"_".join((cpmeas.C_METADATA, et))
if ftr == tag:
break
else:
self.fail("%s not in %s" % (tag, ",".join(expected_tag)))
iscds = m.get_channel_descriptors()
self.assertEqual(len(iscds), len(channels))
for channel_name in channels.keys():
iscd_match = filter(lambda x:x.name == channel_name, iscds)
self.assertEquals(len(iscd_match), 1)
iscd = iscd_match[0]
assert isinstance(iscd, cpp.Pipeline.ImageSetChannelDescriptor)
for i, (expected_url, metadata) in enumerate(channels[channel_name]):
image_number = i+1
if iscd.channel_type == iscd.CT_OBJECTS:
url_ftr = "_".join((cpmeas.C_OBJECTS_URL, channel_name))
else:
url_ftr = "_". join((cpmeas.C_URL, channel_name))
self.assertEqual(expected_url, m[cpmeas.IMAGE, url_ftr, image_number])
for key, channel in expected_metadata:
if channel != channel_name:
continue
md_ftr = "_".join((cpmeas.C_METADATA, key))
self.assertEqual(metadata[key],
m[cpmeas.IMAGE, md_ftr, image_number])
def do_teest(self,
module,
channels,
expected_tags,
expected_metadata,
additional=None):
'''Ensure that NamesAndTypes recreates the column layout when run
module - instance of NamesAndTypes, set up for the test
channels - a dictionary of channel name to list of "ipds" for that
channel where "ipd" is a tuple of URL and metadata dictionary
Entries may appear multiple times (e.g. illumination function)
expected_tags - the metadata tags that should have been generated
by prepare_run.
expected_metadata - a sequence of two-tuples of metadata key and
the channel from which the metadata is extracted.
additional - if present, these are added as ImagePlaneDetails in order
to create errors. Format is same as a single channel of
channels.
'''
ipds = []
urls = set()
url_root = "file:" + urllib.pathname2url(
os.path.abspath(os.path.curdir))
channels = dict(channels)
if additional is not None:
channels["Additional"] = additional
for channel_name in list(channels):
channel_data = [(url_root + "/" + path, metadata)
for path, metadata in channels[channel_name]]
channels[channel_name] = channel_data
for url, metadata in channel_data:
if url in urls:
continue
urls.add(url)
ipd = cpp.ImagePlaneDetails(url, None, None, None, **metadata)
jmetadata = J.make_map(**metadata)
ipd.jipd = J.run_script(
"""
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
var imageFile=new ImageFile(new java.net.URI(url));
var imagePlane=new ImagePlane(imageFile);
new ImagePlaneDetails(imagePlane, metadata);
""", dict(url=url, metadata=jmetadata))
ipds.append(ipd)
if additional is not None:
del channels["Additional"]
ipds.sort(key=lambda x: x.url)
pipeline = cpp.Pipeline()
del pipeline.image_plane_details[:]
pipeline.image_plane_details.extend(ipds)
module.module_num = 1
pipeline.add_module(module)
m = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, m, None, m, None)
self.assertTrue(module.prepare_run(workspace))
tags = m.get_metadata_tags()
self.assertEqual(len(tags), len(expected_tags))
for tag, expected_tag in zip(tags, expected_tags):
for et in expected_tag:
ftr = et if et == cpmeas.IMAGE_NUMBER else \
"_".join((cpmeas.C_METADATA, et))
if ftr == tag:
break
else:
self.fail("%s not in %s" % (tag, ",".join(expected_tag)))
iscds = m.get_channel_descriptors()
self.assertEqual(len(iscds), len(channels))
for channel_name in channels.keys():
iscd_match = filter(lambda x: x.name == channel_name, iscds)
self.assertEquals(len(iscd_match), 1)
iscd = iscd_match[0]
assert isinstance(iscd, cpp.Pipeline.ImageSetChannelDescriptor)
for i, (expected_url,
metadata) in enumerate(channels[channel_name]):
image_number = i + 1
if iscd.channel_type == iscd.CT_OBJECTS:
url_ftr = "_".join((cpmeas.C_OBJECTS_URL, channel_name))
else:
url_ftr = "_".join((cpmeas.C_URL, channel_name))
self.assertEqual(expected_url, m[cpmeas.IMAGE, url_ftr,
image_number])
for key, channel in expected_metadata:
if channel != channel_name:
continue
md_ftr = "_".join((cpmeas.C_METADATA, key))
self.assertEqual(metadata[key], m[cpmeas.IMAGE, md_ftr,
image_number])
