def check(self, module, url, dd, keys=None, xml=None):
"""Check that running the metadata module on a url generates the expected dictionary"""
pipeline = cellprofiler.pipeline.Pipeline()
imgs = cellprofiler.modules.images.Images()
imgs.filter_choice.value = cellprofiler.modules.images.FILTER_CHOICE_NONE
imgs.module_num = 1
pipeline.add_module(imgs)
module.module_num = 2
pipeline.add_module(module)
pipeline.add_urls([url])
m = cellprofiler.measurement.Measurements()
workspace = cellprofiler.workspace.Workspace(pipeline, module, None,
None, m, None)
file_list = workspace.file_list
file_list.add_files_to_filelist([url])
if xml is not None:
file_list.add_metadata(url, xml)
ipds = pipeline.get_image_plane_details(workspace)
self.assertEqual(len(ipds), len(dd))
for d, ipd in zip(dd, ipds):
self.assertDictContainsSubset(d, ipd.metadata)
all_keys = list(pipeline.get_available_metadata_keys().keys())
if keys is not None:
for key in keys:
self.assertIn(key, all_keys)
def check(self, module, url, expected):
'''Check filtering of one URL using the module as configured'''
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_urls([url])
module.module_num = 1
pipeline.add_module(module)
m = cellprofiler.measurement.Measurements()
workspace = cellprofiler.workspace.Workspace(pipeline, module, None, None, m, None)
file_list = pipeline.get_filtered_file_list(workspace)
if expected:
self.assertEqual(len(file_list), 1)
self.assertEqual(file_list[0], url)
else:
self.assertEqual(len(file_list), 0)
def check(module, url, expected):
"""Check filtering of one URL using the module as configured"""
pipeline = cellprofiler.pipeline.Pipeline()
pipeline.add_urls([url])
module.set_module_num(1)
pipeline.add_module(module)
m = cellprofiler.measurement.Measurements()
workspace = cellprofiler.workspace.Workspace(pipeline, module, None, None,
m, None)
file_list = pipeline.get_filtered_file_list(workspace)
if expected:
assert len(file_list) == 1
assert file_list[0] == url
else:
assert len(file_list) == 0
def check(self, module, url, dd, keys=None, xml=None):
'''Check that running the metadata module on a url generates the expected dictionary'''
pipeline = cellprofiler.pipeline.Pipeline()
imgs = cellprofiler.modules.images.Images()
imgs.filter_choice.value = cellprofiler.modules.images.FILTER_CHOICE_NONE
imgs.module_num = 1
pipeline.add_module(imgs)
module.module_num = 2
pipeline.add_module(module)
pipeline.add_urls([url])
m = cellprofiler.measurement.Measurements()
workspace = cellprofiler.workspace.Workspace(pipeline, module, None, None, m, None)
file_list = workspace.file_list
file_list.add_files_to_filelist([url])
if xml is not None:
file_list.add_metadata(url, xml)
ipds = pipeline.get_image_plane_details(workspace)
self.assertEqual(len(ipds), len(dd))
for d, ipd in zip(dd, ipds):
self.assertDictContainsSubset(d, ipd.metadata)
all_keys = pipeline.get_available_metadata_keys().keys()
if keys is not None:
for key in keys:
self.assertIn(key, all_keys)