def __init__(self,
username: str = None,
password: str = None,
serverurl: str = None,
logfile=sys.stdout,
loglevel: int = 1,
statusqueue: queue.Queue = None):
configuration = Configuration()
configuration.username = username
configuration.password = password
configuration.host = serverurl
self.client = ApiClient(configuration=configuration)
self.APIs = ExactAPIs(self.client)
self.configuration = configuration
self.statusqueue = statusqueue
self.progress_denominator = 1
self.progress_offset = 0
self.set_progress_properties(1, 0)
self.multi_threaded = True
self.num_threads = 10
if (self.multi_threaded):
self.jobqueue = queue.Queue()
self.resultQueue = queue.Queue()
self.workers = {}
for k in range(self.num_threads):
self.workers[k] = threading.Thread(target=self.queueWorker,
daemon=True)
self.workers[k].start()
self.logfile = logfile
self.loglevel = loglevel
self.log(
0, f'Created EXM with username {username}, serverurl: {serverurl}')
def cleanup():
client = ApiClient(configuration)
apis = ExactAPIs(client)
imageset = apis.image_sets_api.list_image_sets().results[0].id
# loop through dataset, delete all annotations and images
allImagesInSet = apis.images_api.list_images(omit="annotations").results
# select first image in imageset
for image in allImagesInSet:
annos = apis.annotations_api.list_annotations(id=image.id,
pagination=False).results
for anno in annos:
apis.annotations_api.destroy_annotation(anno.id,
keep_deleted_element=False)
apis.images_api.destroy_image(id=image.id)
product_id = 1
# Delete all previous annotation types
annoTypes = apis.annotation_types_api.list_annotation_types(
product_id).results
for at in annoTypes:
apis.annotation_types_api.destroy_annotation_type(at.id)
assert (len(
apis.annotation_types_api.list_annotation_types(product_id).results) ==
0)
def test_setup():
client = ApiClient(configuration)
apis = ExactAPIs(client)
# annos = image_sets_api.list_image_sets(expand="product_set")
# image_sets_api.retrieve_image_set(1, expand="product_set")
# Delete all previous annotation types
try:
for at in apis.annotation_types_api.list_annotation_types().results:
if not (at.deleted):
apis.annotation_types_api.destroy_annotation_type(id=at.id)
except:
print('Unable to destroy annotation types')
def test_images():
client = ApiClient(configuration)
apis = ExactAPIs(client)
imageset = apis.image_sets_api.list_image_sets().results[0].id
# Delete all images
product_id = 1
allImagesInSet = apis.images_api.list_images(omit="annotations").results
for img in allImagesInSet:
apis.images_api.destroy_image(id=img.id)
allImagesInSet = apis.images_api.list_images(omit="annotations").results
assert (len(allImagesInSet) == 0) # all images gone
# generate dummy image
dummy = np.random.randint(0, 255, (200, 200, 3))
cv2.imwrite('dummy.png', dummy)
apis.images_api.create_image(file_path='dummy.png',
image_type=0,
image_set=imageset).results
allImagesInSet = apis.images_api.list_images(omit="annotations").results
# select first image in imageset
imageid = allImagesInSet[0].id
assert (apis.images_api.retrieve_image(
id=imageid).filename == 'dummy.tiff')
apis.images_api.download_image(id=imageid,
target_path='./dummy-retrieved.png',
original_image=True)
retr = cv2.imread('dummy-retrieved.png')
assert (np.all(retr == dummy))
apis.images_api.destroy_image(id=imageid)
allImagesInSet = apis.images_api.list_images(omit="annotations").results
assert (len(allImagesInSet) == 0) # all images gone
os.remove('dummy.png')
os.remove('dummy-retrieved.png')
def __init__(self, api_client=None):
if api_client is None:
api_client = ApiClient()
self.api_client = api_client
def test_pushannos():
imageset = 1
product_id = 1
client = ApiClient(configuration)
apis = ExactAPIs(client)
randstr = ''.join(
['{:02x}'.format(x) for x in np.random.randint(0, 255, 6)])
imagename = f'dummy{randstr}.png'
imageset = apis.image_sets_api.list_image_sets().results[0].id
# generate dummy image
dummy = np.random.randint(0, 255, (200, 200, 3))
cv2.imwrite(imagename, dummy)
exm = ExactManager(username=configuration.username,
password=configuration.password,
serverurl=configuration.host)
iset = exm.upload_image_to_imageset(imageset_id=imageset,
filename=imagename)
# apis.images_api.create_image(file_path=imagename, image_type=0, image_set=imageset).results
imageset_details = apis.image_sets_api.retrieve_image_set(id=imageset,
expand='images')
imageid = imageset_details.images[0]['id']
DB = Database().create(':memory:')
# Add slide to database
slideuid = DB.insertNewSlide(imagename, '')
DB.insertClass('BB')
DB.insertAnnotator('sliderunner_unittest')
DB.insertAnnotator(
'otherexpert') # we will only send annotations of the marked expert
DB.insertClass('POLY')
coords = np.array([[100, 200], [150, 220], [180, 250]])
DB.insertNewPolygonAnnotation(annoList=coords,
slideUID=1,
classID=2,
annotator=1)
coords = np.array([[150, 250], [350, 220], [0, 250]])
DB.insertNewPolygonAnnotation(annoList=coords,
slideUID=1,
classID=2,
annotator=1)
coords = np.array([[150, 255], [350, 210], [50, 250]])
DB.insertNewPolygonAnnotation(annoList=coords,
slideUID=1,
classID=2,
annotator=2)
DB.setExactPerson(1)
#empty image
annos = apis.annotations_api.list_annotations(id=imageid,
pagination=False).results
for anno in annos:
apis.annotations_api.destroy_annotation(id=anno.id)
# for anno in exm.retrieve_annotations(imageid):
# print(anno)
# All annotations have been removed
assert (len(
apis.annotations_api.list_annotations(id=imageid,
pagination=False).results) == 0)
exm.sync(imageid,
imageset_id=imageset,
product_id=product_id,
slideuid=slideuid,
database=DB)
# Only 2 annotations have been inserted
assert (len(apis.annotations_api.list_annotations(imageid).results) == 2)
uuids = [
x.unique_identifier
for x in apis.annotations_api.list_annotations(imageid).results
]
# All were created with correct guid
for dbanno in list(DB.annotations.keys())[:-1]:
assert (DB.annotations[dbanno].guid in uuids)
print('--- resync ---')
# Sync again
exm.sync(imageid,
imageset_id=imageset,
product_id=product_id,
slideuid=slideuid,
database=DB)
# No change
print('Length is now: ',
len(apis.annotations_api.list_annotations(imageid).results))
assert (len(apis.annotations_api.list_annotations(imageid).results) == 2)
# All were created with correct guid
uuids = [
x.unique_identifier
for x in apis.annotations_api.list_annotations(imageid).results
]
for dbanno in list(DB.annotations.keys())[:-1]:
assert (DB.annotations[dbanno].guid in uuids)
print('--- local update created ---')
# Now let's create a local update - keep same exact_id (crucial!)
DB.loadIntoMemory(1)
DB.setAnnotationLabel(classId=1,
person=1,
annoIdx=1,
entryId=DB.annotations[1].labels[0].uid,
exact_id=DB.annotations[1].labels[0].exact_id)
# Sync again
exm.sync(imageid,
imageset_id=imageset,
product_id=product_id,
slideuid=slideuid,
database=DB)
# check if remote has been updated
# annos = apis.annotations_api.list_annotations(id=imageid, pagination=False).results
annos = np.array(
apis.annotations_api.list_annotations(
imageid, expand='annotation_type').results)
assert (len(annos) > 0)
for anno in annos:
if (anno.id == DB.annotations[1].labels[0].exact_id):
assert (anno.annotation_type['name'] == 'BB')
annotype_id = anno.annotation_type['id']
# Now update remotely and see if changes are reflected
newguid = str(uuid.uuid4())
vector = list_to_exactvector([[90, 80], [20, 30]])
vector['frame'] = 2
lastModified = datetime.datetime.fromtimestamp(
time.time()).strftime("%Y-%m-%dT%H:%M:%S.%f")
annotation = Annotation(annotation_type=annotype_id,
vector=vector,
image=imageid,
unique_identifier=newguid,
last_edit_time=lastModified,
time=lastModified,
description='abcdef')
created = apis.annotations_api.create_annotation(body=annotation)
exm.sync(imageid,
imageset_id=imageset,
product_id=product_id,
slideuid=slideuid,
database=DB)
DB.loadIntoMemory(1, zLevel=None)
found = False
for annoI in DB.annotations:
anno = DB.annotations[annoI]
if (anno.guid == newguid):
found = True
assert (anno.annotationType == AnnotationType.POLYGON)
assert (anno.text == 'abcdef')
assert (anno.labels[0].exact_id == created.id)
assert (found)
# also check in stored database
DB.loadIntoMemory(1)
for annoI in DB.annotations:
anno = DB.annotations[annoI]
if (anno.guid == newguid):
found = True
assert (anno.annotationType == AnnotationType.POLYGON)
assert (anno.labels[0].exact_id == created.id)
annos = apis.annotations_api.list_annotations(id=imageid,
pagination=False).results
for anno in annos:
apis.annotations_api.destroy_annotation(anno.id,
keep_deleted_element=False)
# All gone
assert (len(
apis.annotations_api.list_annotations(id=imageid,
pagination=False).results) == 0)
# Now delete image
apis.images_api.destroy_image(id=imageid)
os.remove(imagename)
exm.terminate()