def test_fit_with_cache(self):
fit_descriptors = []
for i in range(5):
d = DescriptorMemoryElement(six.b('test'), i)
d.set_vector([-2. + i, -2. + i])
fit_descriptors.append(d)
itq = ItqFunctor(DataMemoryElement(),
DataMemoryElement(),
bit_length=1,
random_seed=0)
itq.fit(fit_descriptors)
# TODO: Explanation as to why this is the expected result.
numpy.testing.assert_array_almost_equal(itq.mean_vec, [0, 0])
numpy.testing.assert_array_almost_equal(itq.rotation,
[[1 / sqrt(2)], [1 / sqrt(2)]])
self.assertIsNotNone(itq.mean_vec_cache_elem)
numpy.testing.assert_array_almost_equal(
numpy.load(six.BytesIO(itq.mean_vec_cache_elem.get_bytes())),
[0, 0])
self.assertIsNotNone(itq.rotation_cache_elem)
numpy.testing.assert_array_almost_equal(
numpy.load(six.BytesIO(itq.rotation_cache_elem.get_bytes())),
[[1 / sqrt(2)], [1 / sqrt(2)]])
def itq(task, folderId, **kwargs):
"""
Celery task for training ITQ on a given folder.
This trains ITQ on all descriptors within the index. Since this
is typically called after computing descriptors, it will often
only contain what's in the folder.
:param task: Celery provided task object.
:param folderId: The folder to train ITQ for, note this is only used to
infer the descriptor index.
"""
task.job_manager.updateProgress(message='Training ITQ', forceFlush=True)
index = descriptorIndexFromFolderId(task.girder_client, folderId)
if not index.count():
# TODO SMQTK should account for this?
raise Exception('Descriptor index is empty, cannot train ITQ.')
smqtkFolder = getCreateFolder(task.girder_client, folderId, '.smqtk')
meanVecFile = initializeItemWithFile(task.girder_client,
createOverwriteItem(task.girder_client, smqtkFolder['_id'], 'mean_vec.npy'))
rotationFile = initializeItemWithFile(task.girder_client,
createOverwriteItem(task.girder_client, smqtkFolder['_id'], 'rotation.npy'))
functor = ItqFunctor(mean_vec_cache=GirderDataElement(meanVecFile['_id'], api_root=task.request.apiUrl,
token=task.request.jobInfoSpec['headers']['Girder-Token']),
rotation_cache=GirderDataElement(rotationFile['_id'], api_root=task.request.apiUrl,
token=task.request.jobInfoSpec['headers']['Girder-Token']))
functor.fit(index.iterdescriptors(), use_multiprocessing=False)
def test_fit_with_cache(self):
fit_descriptors = []
for i in range(5):
d = DescriptorMemoryElement(six.b('test'), i)
d.set_vector([-2. + i, -2. + i])
fit_descriptors.append(d)
itq = ItqFunctor(DataMemoryElement(), DataMemoryElement(),
bit_length=1, random_seed=0)
itq.fit(fit_descriptors)
# TODO: Explanation as to why this is the expected result.
numpy.testing.assert_array_almost_equal(itq.mean_vec, [0, 0])
numpy.testing.assert_array_almost_equal(itq.rotation, [[1 / sqrt(2)],
[1 / sqrt(2)]])
self.assertIsNotNone(itq.mean_vec_cache_elem)
numpy.testing.assert_array_almost_equal(
numpy.load(BytesIO(itq.mean_vec_cache_elem.get_bytes())),
[0, 0]
)
self.assertIsNotNone(itq.rotation_cache_elem)
numpy.testing.assert_array_almost_equal(
numpy.load(BytesIO(itq.rotation_cache_elem.get_bytes())),
[[1 / sqrt(2)],
[1 / sqrt(2)]]
)
def test_fit(self):
fit_descriptors = []
for i in range(5):
d = DescriptorMemoryElement('test', i)
d.set_vector([-2. + i, -2. + i])
fit_descriptors.append(d)
itq = ItqFunctor(bit_length=1, random_seed=0)
itq.fit(fit_descriptors)
# TODO: Explanation as to why this is the expected result.
numpy.testing.assert_array_almost_equal(itq.mean_vec, [0, 0])
numpy.testing.assert_array_almost_equal(itq.rotation,
[[1 / sqrt(2)], [1 / sqrt(2)]])
NT.assert_is_none(itq.mean_vec_cache_elem)
NT.assert_is_none(itq.rotation_cache_elem)
def itq(task, folderId, **kwargs):
"""
Celery task for training ITQ on a given folder.
This trains ITQ on all descriptors within the index. Since this
is typically called after computing descriptors, it will often
only contain what's in the folder.
:param task: Celery provided task object.
:param folderId: The folder to train ITQ for, note this is only used to
infer the descriptor index.
"""
task.job_manager.updateProgress(message='Training ITQ', forceFlush=True)
index = descriptorIndexFromFolderId(task.girder_client, folderId)
if not index.count():
# TODO SMQTK should account for this?
raise Exception('Descriptor index is empty, cannot train ITQ.')
smqtkFolder = getCreateFolder(task.girder_client, folderId, '.smqtk')
meanVecFile = initializeItemWithFile(
task.girder_client,
createOverwriteItem(task.girder_client, smqtkFolder['_id'],
'mean_vec.npy'))
rotationFile = initializeItemWithFile(
task.girder_client,
createOverwriteItem(task.girder_client, smqtkFolder['_id'],
'rotation.npy'))
functor = ItqFunctor(
mean_vec_cache=GirderDataElement(
meanVecFile['_id'],
api_root=task.request.apiUrl,
token=task.request.jobInfoSpec['headers']['Girder-Token']),
rotation_cache=GirderDataElement(
rotationFile['_id'],
api_root=task.request.apiUrl,
token=task.request.jobInfoSpec['headers']['Girder-Token']))
functor.fit(index.iterdescriptors(), use_multiprocessing=False)
