def setup_class(self):
"""Create the unittest database"""
makeunitdb.createTestDB(p.token,
channel_list=p.channels,
public=True,
readonly=0)
cutout1 = "0/2,5/1,3/0,2"
cutout2 = "0/1,3/4,6/2,5"
cutout3 = "0/4,6/2,5/5,7"
cutout4 = "0/6,8/5,9/2,4"
syn_segments1 = [
[7, 3],
]
syn_segments2 = [
[7, 4],
]
syn_segments3 = [
[3, 9],
]
syn_segments4 = [
[5, 4],
]
f1 = createSpecificSynapse(1, syn_segments1, cutout1)
putid = putAnnotation(p, f1)
f2 = createSpecificSynapse(2, syn_segments2, cutout2)
putid = putAnnotation(p, f2)
f3 = createSpecificSynapse(3, syn_segments3, cutout3)
putid = putAnnotation(p, f3)
f4 = createSpecificSynapse(4, syn_segments4, cutout4)
putid = putAnnotation(p, f4)
def test_anno_minmal(self):
"""Upload a minimal and maximal annotation. Verify fields."""
# Create an in-memory HDF5 file
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File ( tmpfile.name )
# Create the top level annotation id namespace
idgrp = h5fh.create_group ( str(0) )
h5fh.flush()
tmpfile.seek(0)
p.annoid = putAnnotation(p, tmpfile)
h5ret = getAnnotation(p)
idgrpret = h5ret.get(str(p.annoid))
assert idgrpret
assert ( idgrpret['ANNOTATION_TYPE'][0] == 1 )
assert not idgrpret.get('RESOLUTION')
assert not idgrpret.get('XYZOFFSET')
assert not idgrpret.get('VOXELS')
assert not idgrpret.get('CUTOUT')
mdgrpret = idgrpret['METADATA']
assert mdgrpret
assert ( mdgrpret['CONFIDENCE'][0] == 0.0 )
assert ( mdgrpret['STATUS'][0] == 0 )
assert ( mdgrpret['KVPAIRS'][:] == '' )
assert ( mdgrpret['AUTHOR'][:] == 'unknown' )
def test_anno_minmal(self):
"""Upload a minimal and maximal annotation. Verify fields."""
# Create an in-memory HDF5 file
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File(tmpfile.name)
# Create the top level annotation id namespace
idgrp = h5fh.create_group(str(0))
h5fh.flush()
tmpfile.seek(0)
p.annoid = putAnnotation(p, tmpfile)
h5ret = getAnnotation(p)
idgrpret = h5ret.get(str(p.annoid))
assert idgrpret
assert (idgrpret['ANNOTATION_TYPE'][0] == 1)
assert not idgrpret.get('RESOLUTION')
assert not idgrpret.get('XYZOFFSET')
assert not idgrpret.get('VOXELS')
assert not idgrpret.get('CUTOUT')
mdgrpret = idgrpret['METADATA']
assert mdgrpret
assert (mdgrpret['CONFIDENCE'][0] == 0.0)
assert (mdgrpret['STATUS'][0] == 0)
assert (mdgrpret['KVPAIRS'][:] == '')
assert (mdgrpret['AUTHOR'][:] == 'unknown')
def setup_class(self):
"""Create the unittest database"""
makeunitdb.createTestDB(p.token,
channel_list=p.channels,
public=True,
readonly=0,
ximagesize=100,
yimagesize=100,
zimagesize=100)
cutout1 = "0/2,5/1,3/1,3"
cutout2 = "0/1,3/4,6/2,5"
cutout3 = "0/4,6/2,5/5,7"
cutout4 = "0/6,8/5,9/2,4"
syn_segments1 = [7, 3]
syn_segments2 = [7, 4]
syn_segments3 = [3, 9]
syn_segments4 = [5, 4]
# syn_presegments1 = [7, 3, 5]
# syn_presegments2 = [7, 4, 2, 8]
# syn_presegments3 = [3, 9]
# syn_presegments4 = [5]
# syn_postsegments1 = [7, 3, 5]
# syn_postsegments2 = [7, 4, 2, 8]
# syn_postsegments3 = [3, 9]
# syn_postsegments4 = [5]
# RB COMMENT Old RAMON schema list of lists.
# syn_segments1 = [[7, 3],]
# syn_segments2 = [[7, 4],]
# syn_segments3 = [[3, 9],]
# syn_segments4 = [[5, 4],]
f1 = createSpecificSynapse(1, syn_segments1, cutout1)
putid = putAnnotation(p, f1)
f2 = createSpecificSynapse(2, syn_segments2, cutout2)
putid = putAnnotation(p, f2)
f3 = createSpecificSynapse(3, syn_segments3, cutout3)
putid = putAnnotation(p, f3)
f4 = createSpecificSynapse(4, syn_segments4, cutout4)
putid = putAnnotation(p, f4)
def test_anno_upload( self ):
"""Upload all different kinds of annotations and retrieve"""
for anntype in [ 1, 2, 3, 4, 5, 6]:
annoid = 0
f = H5AnnotationFile ( anntype, annoid )
putid1 = putAnnotation(p, f)
# this assumes that +1 is available (which it is)
newid = putid1 + 1
f = H5AnnotationFile ( anntype, newid )
putid2 = putAnnotation(p, f)
# retrieve both annotations
p.annoid = putid1
assert ( putid1 == getId(p) )
p.annoid = putid2
assert ( putid2 == getId(p) )
def test_anno_upload(self):
"""Upload all different kinds of annotations and retrieve"""
for anntype in [1, 2, 3, 4, 5, 6]:
annoid = 0
f = H5AnnotationFile(anntype, annoid)
putid1 = putAnnotation(p, f)
# this assumes that +1 is available (which it is)
newid = putid1 + 1
f = H5AnnotationFile(anntype, newid)
putid2 = putAnnotation(p, f)
# retrieve both annotations
p.annoid = putid1
assert (putid1 == getId(p))
p.annoid = putid2
assert (putid2 == getId(p))
def setup_class(self):
"""Create the unittest database"""
makeunitdb.createTestDB(p.token, channel_list=p.channels, public=True, readonly=0)
cutout1 = "0/2,5/1,3/0,2"
cutout2 = "0/1,3/4,6/2,5"
cutout3 = "0/4,6/2,5/5,7"
cutout4 = "0/6,8/5,9/2,4"
syn_segments1 = [[7, 3], ]
syn_segments2 = [[7, 4], ]
syn_segments3 = [[3, 9], ]
syn_segments4 = [[5, 4], ]
f1 = createSpecificSynapse(1, syn_segments1, cutout1)
putid = putAnnotation(p, f1)
f2 = createSpecificSynapse(2, syn_segments2, cutout2)
putid = putAnnotation(p, f2)
f3 = createSpecificSynapse(3, syn_segments3, cutout3)
putid = putAnnotation(p, f3)
f4 = createSpecificSynapse(4, syn_segments4, cutout4)
putid = putAnnotation(p, f4)
def test_anno_update(self):
"""Upload a Updated file with new data"""
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File(tmpfile.name)
# Create the top level annotation id namespace
idgrp = h5fh.create_group(str(p.annoid))
# Create a metadata group
mdgrp = idgrp.create_group("METADATA")
# now lets add a bunch of random values for the specific annotation type
ann_status = random.randint(0, 4)
ann_confidence = random.random()
ann_author = 'unittest_author2'
# Annotation type
idgrp.create_dataset("ANNOTATION_TYPE", (1, ), np.uint32, data=1)
# Set Annotation specific metadata
mdgrp.create_dataset("STATUS", (1, ), np.uint32, data=ann_status)
mdgrp.create_dataset("CONFIDENCE", (1, ),
np.float,
data=ann_confidence)
mdgrp.create_dataset("AUTHOR", (1, ),
dtype=h5py.special_dtype(vlen=str),
data=ann_author)
h5fh.flush()
tmpfile.seek(0)
p.field = 'update'
p.annoid = putAnnotation(p, tmpfile)
p.field = None
h5ret = getAnnotation(p)
idgrpret = h5ret.get(str(p.annoid))
assert idgrpret
assert (idgrpret['ANNOTATION_TYPE'][0] == 1)
assert not idgrpret.get('RESOLUTION')
assert not idgrpret.get('XYZOFFSET')
assert not idgrpret.get('VOXELS')
assert not idgrpret.get('CUTOUT')
mdgrpret = idgrpret['METADATA']
assert mdgrpret
assert (abs(mdgrpret['CONFIDENCE'][0] - ann_confidence) < 0.0001)
#assert ( mdgrpret['CONFIDENCE'][0] == ann_confidence )
assert (mdgrpret['STATUS'][0] == ann_status)
assert (mdgrpret['AUTHOR'][:] == ann_author)
def test_anno_update (self):
"""Upload a Updated file with new data"""
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File ( tmpfile.name )
# Create the top level annotation id namespace
idgrp = h5fh.create_group ( str(p.annoid) )
# Create a metadata group
mdgrp = idgrp.create_group ( "METADATA" )
# now lets add a bunch of random values for the specific annotation type
ann_status = random.randint(0,4)
ann_confidence = random.random()
ann_author = 'unittest_author2'
# Annotation type
idgrp.create_dataset ( "ANNOTATION_TYPE", (1,), np.uint32, data=1 )
# Set Annotation specific metadata
mdgrp.create_dataset ( "STATUS", (1,), np.uint32, data=ann_status )
mdgrp.create_dataset ( "CONFIDENCE", (1,), np.float, data=ann_confidence )
mdgrp.create_dataset ( "AUTHOR", (1,), dtype=h5py.special_dtype(vlen=str), data=ann_author )
h5fh.flush()
tmpfile.seek(0)
p.field = 'update'
p.annoid = putAnnotation(p, tmpfile)
p.field = None
h5ret = getAnnotation(p)
idgrpret = h5ret.get(str(p.annoid))
assert idgrpret
assert ( idgrpret['ANNOTATION_TYPE'][0] == 1 )
assert not idgrpret.get('RESOLUTION')
assert not idgrpret.get('XYZOFFSET')
assert not idgrpret.get('VOXELS')
assert not idgrpret.get('CUTOUT')
mdgrpret = idgrpret['METADATA']
assert mdgrpret
assert ( abs(mdgrpret['CONFIDENCE'][0] - ann_confidence) < 0.0001 )
#assert ( mdgrpret['CONFIDENCE'][0] == ann_confidence )
assert ( mdgrpret['STATUS'][0] == ann_status )
assert ( mdgrpret['AUTHOR'][:] == ann_author )
def test_bigint_json(self):
"""Test the annotation (RAMON) JSON interface with a large ID"""
# create hdf5 file and post it
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File(tmpfile.name)
ann_status = random.randint(0, 4)
ann_confidence = random.random()
ann_author = 'unittest_author'
ann_annoid = 10025
# create annotation id namespace
idgrp = h5fh.create_group(str(ann_annoid))
# annotation type
idgrp.create_dataset("ANNOTATION_TYPE", (1, ), np.uint32, data=1)
mdgrp = idgrp.create_group("METADATA")
# set annotation metadata
mdgrp.create_dataset("STATUS", (1, ), np.uint32, data=ann_status)
mdgrp.create_dataset("CONFIDENCE", (1, ),
np.float,
data=ann_confidence)
mdgrp.create_dataset("AUTHOR", (1, ),
dtype=h5py.special_dtype(vlen=str),
data=ann_author)
h5fh.flush()
tmpfile.seek(0)
p.annoid = putAnnotation(p, tmpfile)
# fetching the JSON info
f = getURL("https://{}/ca/{}/{}/{}/json/".format(
SITE_HOST, p.token, p.channels[0], ann_annoid))
# read the JSON file
ann_info = json.loads(f.content)
assert (ann_info.keys()[0] == str(ann_annoid))
assert (str(
ann_info[str(ann_annoid)]['ann_status']) == str(ann_status))
assert (str(ann_info[str(ann_annoid)]['ann_confidence'])[:5] == str(
ann_confidence)[:5])
assert (ann_info[str(ann_annoid)]['ann_author'] == str(ann_author))
def makeAnno ( p, anntype ): """Helper make an annotation""" # Create an annotation tmpfile = tempfile.NamedTemporaryFile() h5fh = h5py.File ( tmpfile.name ) # Create the top level annotation id namespace idgrp = h5fh.create_group ( str(0) ) mdgrp = idgrp.create_group ( "METADATA" ) ann_author='Unit Test' mdgrp.create_dataset ( "AUTHOR", (1,), dtype=h5py.special_dtype(vlen=str), data=ann_author ) idgrp.create_dataset ( "ANNOTATION_TYPE", (1,), np.uint32, data=anntype ) h5fh.flush() tmpfile.seek(0) p.annoid = putAnnotation (p, tmpfile) tmpfile.close()
def makeAnno ( p, anntype ): """Helper make an annotation""" # Create an annotation tmpfile = tempfile.NamedTemporaryFile() h5fh = h5py.File ( tmpfile.name ) # Create the top level annotation id namespace idgrp = h5fh.create_group ( str(0) ) mdgrp = idgrp.create_group ( "METADATA" ) ann_author='Unit Test' mdgrp.create_dataset ( "AUTHOR", (1,), dtype=h5py.special_dtype(vlen=str), data=ann_author ) idgrp.create_dataset ( "ANNOTATION_TYPE", (1,), np.uint32, data=anntype ) h5fh.flush() tmpfile.seek(0) p.annoid = putAnnotation (p, tmpfile) tmpfile.close()
def test_bigint_json(self):
"""Test the annotation (RAMON) JSON interface with a large ID"""
# create hdf5 file and post it
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File( tmpfile.name )
ann_status = random.randint(0,4)
ann_confidence = random.random()
ann_author = 'unittest_author'
ann_annoid = 10025
# create annotation id namespace
idgrp = h5fh.create_group ( str(ann_annoid) )
# annotation type
idgrp.create_dataset ( "ANNOTATION_TYPE", (1,), np.uint32, data=1 )
mdgrp = idgrp.create_group( "METADATA" )
# set annotation metadata
mdgrp.create_dataset ( "STATUS", (1,), np.uint32, data=ann_status )
mdgrp.create_dataset ( "CONFIDENCE", (1,), np.float, data=ann_confidence )
mdgrp.create_dataset ( "AUTHOR", (1,), dtype=h5py.special_dtype(vlen=str), data=ann_author )
h5fh.flush()
tmpfile.seek(0)
p.annoid = putAnnotation(p, tmpfile)
# fetching the JSON info
f = getURL("https://{}/ca/{}/{}/{}/json/".format(SITE_HOST, p.token, p.channels[0], ann_annoid))
# read the JSON file
ann_info = json.loads(f.content)
assert( ann_info.keys()[0] == str(ann_annoid) )
assert( str(ann_info[str(ann_annoid)]['ann_status']) == str(ann_status) )
assert( str(ann_info[str(ann_annoid)]['ann_confidence'])[:5] == str(ann_confidence)[:5] )
assert( ann_info[str(ann_annoid)]['ann_author'] == str(ann_author) )
def test_multiple_json(self):
"""Test the annotation (RAMON) JSON interface with multiple objects"""
number_of_annotations = 3 # Note: these are 1-indexed
anno_objs = {}
for i in range(number_of_annotations):
# create hdf5 file and post it
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File( tmpfile.name )
ann_status = random.randint(0,4)
ann_confidence = random.random()
ann_author = 'unittest_author'
ann_annoid = (i + 1)*10 # we multiply by 10 to avoid conflicts with above test
anno_objs[ str(ann_annoid) ] = {
'ann_status': ann_status,
'ann_confidence': ann_confidence,
'ann_author': ann_author
}
# create annotation id namespace
idgrp = h5fh.create_group ( str(ann_annoid) )
# annotation type
idgrp.create_dataset ( "ANNOTATION_TYPE", (1,), np.uint32, data=1 )
mdgrp = idgrp.create_group( "METADATA" )
# set annotation metadata
mdgrp.create_dataset ( "STATUS", (1,), np.uint32, data=ann_status )
mdgrp.create_dataset ( "CONFIDENCE", (1,), np.float, data=ann_confidence )
mdgrp.create_dataset ( "AUTHOR", (1,), dtype=h5py.special_dtype(vlen=str), data=ann_author )
h5fh.flush()
tmpfile.seek(0)
p.annoid = putAnnotation(p, tmpfile)
# fetching the JSON info
ann_id_str = ''
for i in range(number_of_annotations):
ann_id_str += '{}'.format( (i + 1)*10 )
if i < number_of_annotations - 1:
ann_id_str += ','
f = getURL("https://{}/ca/{}/{}/{}/json/".format(SITE_HOST, p.token, p.channels[0], ann_id_str))
# read the JSON file
ann_info = json.loads(f.content)
for i in range(number_of_annotations):
# make sure we have all the relevant annotation objects
assert( str( (i + 1)*10 ) in ann_info.keys() )
chosen_id = (i + 1)*10
chosen_obj = anno_objs[str( chosen_id )]
assert( str(ann_info[str(chosen_id)]['ann_status']) == str(chosen_obj['ann_status']) )
assert( str(ann_info[str(chosen_id)]['ann_confidence'])[:5] == str(chosen_obj['ann_confidence'])[:5] )
assert( ann_info[str(chosen_id)]['ann_author'] == str(chosen_obj['ann_author']) )
# pick an annotation object at random and check its properties
chosen_id = random.randint(1,number_of_annotations)*10
chosen_obj = anno_objs[str(chosen_id)]
assert( str(ann_info[str(chosen_id)]['ann_status']) == str(chosen_obj['ann_status']) )
assert( str(ann_info[str(chosen_id)]['ann_confidence'])[:5] == str(chosen_obj['ann_confidence'])[:5] )
assert( ann_info[str(chosen_id)]['ann_author'] == str(chosen_obj['ann_author']) )
def test_multiple_json(self):
"""Test the annotation (RAMON) JSON interface with multiple objects"""
number_of_annotations = 3 # Note: these are 1-indexed
anno_objs = {}
for i in range(number_of_annotations):
# create hdf5 file and post it
tmpfile = tempfile.NamedTemporaryFile()
h5fh = h5py.File(tmpfile.name)
ann_status = random.randint(0, 4)
ann_confidence = random.random()
ann_author = 'unittest_author'
ann_annoid = (
i +
1) * 10 # we multiply by 10 to avoid conflicts with above test
anno_objs[str(ann_annoid)] = {
'ann_status': ann_status,
'ann_confidence': ann_confidence,
'ann_author': ann_author
}
# create annotation id namespace
idgrp = h5fh.create_group(str(ann_annoid))
# annotation type
idgrp.create_dataset("ANNOTATION_TYPE", (1, ), np.uint32, data=1)
mdgrp = idgrp.create_group("METADATA")
# set annotation metadata
mdgrp.create_dataset("STATUS", (1, ), np.uint32, data=ann_status)
mdgrp.create_dataset("CONFIDENCE", (1, ),
np.float,
data=ann_confidence)
mdgrp.create_dataset("AUTHOR", (1, ),
dtype=h5py.special_dtype(vlen=str),
data=ann_author)
h5fh.flush()
tmpfile.seek(0)
p.annoid = putAnnotation(p, tmpfile)
# fetching the JSON info
ann_id_str = ''
for i in range(number_of_annotations):
ann_id_str += '{}'.format((i + 1) * 10)
if i < number_of_annotations - 1:
ann_id_str += ','
f = getURL("https://{}/ca/{}/{}/{}/json/".format(
SITE_HOST, p.token, p.channels[0], ann_id_str))
# read the JSON file
ann_info = json.loads(f.content)
for i in range(number_of_annotations):
# make sure we have all the relevant annotation objects
assert (str((i + 1) * 10) in ann_info.keys())
chosen_id = (i + 1) * 10
chosen_obj = anno_objs[str(chosen_id)]
assert (str(ann_info[str(chosen_id)]['ann_status']) == str(
chosen_obj['ann_status']))
assert (str(ann_info[str(chosen_id)]['ann_confidence'])[:5] == str(
chosen_obj['ann_confidence'])[:5])
assert (ann_info[str(chosen_id)]['ann_author'] == str(
chosen_obj['ann_author']))
# pick an annotation object at random and check its properties
chosen_id = random.randint(1, number_of_annotations) * 10
chosen_obj = anno_objs[str(chosen_id)]
assert (str(ann_info[str(chosen_id)]['ann_status']) == str(
chosen_obj['ann_status']))
assert (str(ann_info[str(chosen_id)]['ann_confidence'])[:5] == str(
chosen_obj['ann_confidence'])[:5])
assert (ann_info[str(chosen_id)]['ann_author'] == str(
chosen_obj['ann_author']))
