def test_set_tag(self):
experiment = self._create_experiment()
experiment.set_tag('Population', False)
exp2 = Experiment(os.path.join(self.tst_experiment_dir,
'myexperiment',
'experiment.md.json'))
self.assertTrue('Population' in exp2.metadata.tags)
def test_create_experiment(self):
experiment = Experiment()
metadata = create_experiment()
experiment.create(metadata.name, metadata.author, metadata.date,
self.tst_experiment_dir)
t1 = os.path.isdir(os.path.join(self.tst_experiment_dir,
'myexperiment'))
t2 = os.path.isfile(os.path.join(self.tst_experiment_dir,
'myexperiment',
'experiment.md.json'))
t3 = os.path.isdir(os.path.join(self.tst_experiment_dir,
'myexperiment',
'data'))
t4 = os.path.isfile(os.path.join(self.tst_experiment_dir,
'myexperiment',
'data',
'rawdataset.md.json'))
self.assertTrue(t1*t2*t3*t4)
def _import_image(self, experiment: Experiment, image):
# read metadata from omero
rawdatasetdir = os.path.dirname(experiment.md_uri)
filename = os.path.join(rawdatasetdir, 'data', image.getName())
author = image.getAuthor()
date = image.getDate().strftime('%Y-%m-%d %I:%M %S %p')
extension = os.path.splitext(image.getName())[1][1:]
tags = dict()
for ann in image.listAnnotations():
if ann.OMERO_TYPE == omero.model.MapAnnotationI:
for kv in ann.getValue():
tags[kv[0]] = kv[1]
# print('readed tags:')
# print('\t author:', author)
# print('\t date:', date)
# print('\t extension:', extension)
# print('\t tags:', tags)
# write metadata to the experiment
experiment.import_data(
filename,
image.getName(),
author=author,
format=extension,
date=date,
tags=tags,
copy=False,
)
# register tag to experiment if not exists
for tag in tags:
experiment.set_tag(tag, False)
# copy image
channel = 0
imageData = _get_data(image, channel)
tif = TIFF.open(filename, mode='w')
for t in range(imageData.shape[0]):
for z in range(imageData.shape[1]):
tif.write_image(imageData[t, z, :, :])
tif.close()
def test_write_experiment(self):
experiment = Experiment(self.tst_experiment_file)
experiment.metadata = create_experiment()
experiment.write()
self.assertTrue(filecmp.cmp(self.tst_experiment_file,
self.ref_experiment_file, shallow=False))
def test_read_experiment(self):
read_experiment = Experiment(self.ref_experiment_file)
ref_experiment_container = create_experiment()
self.assertEqual(read_experiment.metadata.serialize(),
ref_experiment_container.serialize())
def _create_experiment(self):
experiment = Experiment()
metadata = create_experiment()
experiment.create(metadata.name, metadata.author, metadata.date,
self.tst_experiment_dir)
return experiment
def test_get_dataset2(self):
# processed dataset
experiment = Experiment(self.ref_experiment_file)
raw_dataset = experiment.get_dataset('process1')
self.assertEqual(raw_dataset.metadata.name, 'process1')
def test_get_dataset1(self):
# raw dataset
experiment = Experiment(self.ref_experiment_file)
raw_dataset = experiment.get_dataset('data')
self.assertEqual(raw_dataset.metadata.name, 'data')