def set_experiment_resource(remote: BossRemote, params: dict) -> ExperimentResource:
"""Use the arguments in the class config to create an experiment resource object"""
if 'name' not in params:
params['name'] = 'experiment{0}'.format(hex(round(time.time()))[2:])
param_names = [str(p.name) for p in inspect.signature(ExperimentResource).parameters.values()]
filtered_params = {k: v for k, v in list(params.items()) if k in param_names} # Filter unexpected arguments
exp_resource = ExperimentResource(**filtered_params)
if exp_resource.name in remote.list_experiments(exp_resource.coll_name):
experiment = remote.update_project(exp_resource.name, exp_resource)
print('Updated experiment {0}'.format(exp_resource.name))
else:
experiment = remote.create_project(exp_resource)
print('Created experiment {0}'.format(exp_resource.name))
return experiment
def set_channel_resource(remote: BossRemote, params: dict) -> ChannelResource:
"""Use the arguments in the class config to create a channel resource object"""
if 'name' not in params:
params['name'] = 'channel{0}'.format(hex(round(time.time()))[2:])
param_names = [str(p.name) for p in inspect.signature(ChannelResource).parameters.values()]
filtered_params = {k: v for k, v in list(params.items()) if k in param_names} # Filter unexpected arguments
chan_resource = ChannelResource(**filtered_params)
if chan_resource.name in remote.list_channels(chan_resource.coll_name, chan_resource.exp_name):
channel = remote.update_project(chan_resource.name, chan_resource)
print('Updated channel {0}'.format(chan_resource.name))
else:
channel = remote.create_project(chan_resource)
print('Created channel {0}'.format(chan_resource.name))
return channel
def set_coordinate_frame_resource(remote: BossRemote, params: dict) -> CoordinateFrameResource:
"""Use the arguments in the class config to create a frame resource object"""
if 'name' not in params:
params['name'] = 'frame{0}'.format(hex(round(time.time()))[2:])
param_names = [str(p.name) for p in inspect.signature(CoordinateFrameResource).parameters.values()]
filtered_params = {k: v for k, v in list(params.items()) if k in param_names} # Filter unexpected arguments
frame_resource = CoordinateFrameResource(**filtered_params)
if frame_resource.name in remote.list_coordinate_frames():
coordinate_frame = remote.update_project(frame_resource.name, frame_resource)
print('Updated frame {0}'.format(frame_resource.name))
else:
coordinate_frame = remote.create_project(frame_resource)
print('Created frame {0}'.format(frame_resource.name))
return coordinate_frame
def ingest_volume(host, token, channel_name, collection, experiment, volume):
"""
Assumes the collection and experiment exists in BOSS.
"""
remote = BossRemote({'protocol': 'https',
'host': host,
'token': token})
if volume.dtype == 'uint64':
dtype = 'uint64'
img_type = 'annotation'
sources = ['empty']
else:
dtype = volume.dtype.name
img_type = 'image'
sources = []
try:
channel_resource = ChannelResource(channel_name, collection, experiment)
channel = remote.get_project(channel_resource)
except:
channel_resource = ChannelResource(channel_name, collection, experiment,
type=img_type,
sources=sources,
datatype=dtype)
channel = remote.create_project(channel_resource)
#Get max size of experiment
exp_resource = ExperimentResource(experiment, collection)
coord_frame = remote.get_project(exp_resource).coord_frame
coord_frame_resource = CoordinateFrameResource(coord_frame)
data = remote.get_project(coord_frame_resource)
y_stop, x_stop = data.y_stop, data.x_stop
for z in range(volume.shape[0]):
print('Uploading {} slice'.format(z))
remote.create_cutout(channel,
0,
(0, x_stop),
(0, y_stop),
(z, z + 1),
volume[z, :, :].reshape((-1, y_stop, x_stop)))
coll_data = {'poc': 'Jane Doe'}
local.create_metadata(Channel1, coll_data)
exp_data = {'weight': '20g', 'diet': 'C2', 'date': '23-May-2016'}
local.create_metadata(Collection1, exp_data)
chan_new_data = {'weight': '45g', 'date': '23-May-2017'}
local.update_metadata(Collection1, chan_new_data)
local.delete_metadata(Channel1, ['poc'])
CollectionMeta = local.list_metadata(Collection1)
print(CollectionMeta)
#Data processing can also be done here before re-upload
#Local to Boss upload of annotated data
chan_setup = get_channel('CHAN_NAME',
'COLL_NAME',
'EXP_NAME',
'image',
datatype='uint16')
chan = BossRemote.create_project(chan_setup)
xspan = [0, 200]
yspan = [0, 90]
zspan = [0, 20]
VolumeLmeta.astype(numpy.uint16)
BossRemote.create_cutout(chan, 0, xspan, yspan, zspan, VolumeLMeta)
def boss_pull_cutout(args):
if args.config:
rmt = BossRemote(args.config)
else:
cfg = _generate_config(args.token, args)
with open("intern.cfg", "w") as f:
cfg.write(f)
rmt = BossRemote("intern.cfg")
COLL_NAME = args.coll
EXP_NAME = args.exp
CHAN_NAME = args.chan
# Create or get a channel to write to
chan_setup = ChannelResource(
CHAN_NAME, COLL_NAME, EXP_NAME, type=args.itype, datatype=args.dtype
)
try:
chan_actual = rmt.get_project(chan_setup)
except HTTPError:
chan_actual = rmt.create_project(chan_setup)
# get coordinate frame to determine padding bounds
cfr = CoordinateFrameResource(args.coord)
cfr_actual = rmt.get_project(cfr)
x_min_bound = cfr_actual.x_start
x_max_bound = cfr_actual.x_stop
y_min_bound = cfr_actual.y_start
y_max_bound = cfr_actual.y_stop
z_min_bound = cfr_actual.z_start
z_max_bound = cfr_actual.z_stop
print("Data model setup.")
xmin = np.max([x_min_bound, args.xmin - args.padding])
xmax = np.min([x_max_bound, args.xmax + args.padding])
x_rng = [xmin, xmax]
ymin = np.max([y_min_bound, args.ymin - args.padding])
ymax = np.min([y_max_bound, args.ymax + args.padding])
y_rng = [ymin, ymax]
zmin = np.max([z_min_bound, args.zmin - args.padding])
zmax = np.min([z_max_bound, args.zmax + args.padding])
z_rng = [zmin, zmax]
# Verify that the cutout uploaded correctly.
attempts = 0
while attempts < 3:
try:
cutout_data = rmt.get_cutout(chan_actual, args.res, x_rng, y_rng, z_rng)
break
except HTTPError as e:
if attempts < 3:
attempts += 1
print("Obtained HTTP error from server. Trial {}".format(attempts))
else:
print("Failed 3 times: {}".format(e))
# Data will be in Z,Y,X format
# Change to X,Y,Z for pipeline
cutout_data = np.transpose(cutout_data, (2, 1, 0))
def _upload(f):
print("Uploading to s3:/{}/{}".format(args.bucket, args.output))
s3 = boto3.resource("s3")
f.seek(0, 0)
s3.Object(args.bucket, args.output).put(Body=f)
# Clean up.
if args.bucket and args.s3_only:
with tempfile.TemporaryFile() as f:
np.save(f, cutout_data)
_upload(f)
else:
with open(args.output, "w+b") as f:
np.save(f, cutout_data)
if args.bucket:
_upload(f)
def boss_merge_xbrain(args):
# Verify that the cutout uploaded correctly.
def pull_margin_cutout(chan_actual, x_rng, y_rng, z_rng):
attempts = 0
while attempts < 3:
try:
cutout_data = rmt.get_cutout(chan_actual, 0, x_rng, y_rng, z_rng)
break
except HTTPError as e:
if attempts < 3:
attempts += 1
print("Obtained HTTP error from server. Trial {}".format(attempts))
else:
print("Failed 3 times: {}".format(e))
# Data will be in Z,Y,X format
# Change to X,Y,Z for pipeline
cutout_data = np.transpose(cutout_data, (2, 1, 0))
return cutout_data
templatesize = args.templatesize
if args.config:
rmt = BossRemote(args.config)
else:
cfg = _generate_config(args.token, args)
with open("intern.cfg", "w") as f:
cfg.write(f)
rmt = BossRemote("intern.cfg")
# data is desired range
if args.bucket:
s3 = boto3.resource("s3")
with tempfile.TemporaryFile() as f:
s3.Bucket(args.bucket).download_fileobj(args.input, f)
f.seek(0, 0)
data = np.load(f)
with tempfile.TemporaryFile() as f:
s3.Bucket(args.bucket).download_fileobj(args.centroids, f)
f.seek(0, 0)
centroids = np.load(f)
else:
data = np.load(args.input)
centroids = np.load(args.centroids)
COLL_NAME = args.coll
EXP_NAME = args.exp
CHAN_NAME = args.chan
# Create or get a channel to write to
chan_setup = ChannelResource(
CHAN_NAME, COLL_NAME, EXP_NAME, type=args.itype, datatype=args.dtype
)
try:
chan_actual = rmt.get_project(chan_setup)
except HTTPError:
chan_actual = rmt.create_project(chan_setup)
# get coordinate frame to determine padding bounds
cfr = CoordinateFrameResource(args.coord)
cfr_actual = rmt.get_project(cfr)
x_min_bound = cfr_actual.x_start
x_max_bound = cfr_actual.x_stop
y_min_bound = cfr_actual.y_start
y_max_bound = cfr_actual.y_stop
z_min_bound = cfr_actual.z_start
z_max_bound = cfr_actual.z_stop
# coordinates of data block in original coordinate frame, before padding
x_block = [args.xmin, args.xmax]
y_block = [args.ymin, args.ymax]
z_block = [args.zmin, args.zmax]
# Coordinates of data block with padding in original coordinate frame
x_block_pad = [
np.amax([args.xmin - args.padding, x_min_bound]),
np.amin([args.xmax + args.padding, x_max_bound]),
]
y_block_pad = [
np.amax([args.ymin - args.padding, y_min_bound]),
np.amin([args.ymax + args.padding, y_max_bound]),
]
z_block_pad = [
np.amax([args.zmin - args.padding, z_min_bound]),
np.amin([args.zmax + args.padding, z_max_bound]),
]
# Coordinates of core data block in local coordinate frame
xstart = np.amin([args.padding, args.xmin - x_min_bound])
xend = np.amax(
[data.shape[0] - args.padding, data.shape[0] - (x_max_bound - args.xmax)]
)
ystart = np.amin([args.padding, args.ymin - y_min_bound])
yend = np.amax(
[data.shape[1] - args.padding, data.shape[1] - (y_max_bound - args.ymax)]
)
zstart = np.amin([args.padding, args.zmin - z_min_bound])
zend = np.amax(
[data.shape[2] - args.padding, data.shape[2] - (z_max_bound - args.zmax)]
)
print("Data model setup.")
# Template size to decide which centroids to eliminate
# Ranges use the Python convention where the number after the : is the stop
# value. Thus, x_rng specifies x values where: 0 <= x < 8.
if args.onesided:
# Only merge on the max side, to prevent duplication of detection
# Binarize Map
data[np.where(data > 0)] = 1
# Search through centroids
# On side of max values, keep anything where centroid is in padded region
# On side of min values, remove anything that is partially in padded region (covered by another block)
n_centers, _ = centroids.shape # n by 4
bad_inds = []
for i in range(0, n_centers):
if centroids[i, 0] < xstart or centroids[i, 0] - templatesize / 2 > xend:
bad_inds.append(i)
elif centroids[i, 1] < ystart or centroids[i, 1] - templatesize / 2 > yend:
bad_inds.append(i)
elif centroids[i, 2] < zstart or centroids[i, 2] - templatesize / 2 > zend:
bad_inds.append(i)
centroids_out = np.delete(centroids, bad_inds, axis=0)
# translate into global coordinates from local data block
centroids_out[:, 0] = centroids_out[:, 0] - xstart + args.xmin
centroids_out[:, 1] = centroids_out[:, 1] - ystart + args.ymin
centroids_out[:, 2] = centroids_out[:, 2] - zstart + args.zmin
# Eliminate any cells form data which overlap with the padding edge
for ind in bad_inds:
xi = np.array(
[
centroids[ind, 0] - np.ceil(templatesize / 2),
centroids[ind, 0] + np.ceil(templatesize / 2),
]
).astype(int)
yi = np.array(
[
centroids[ind, 1] - np.ceil(templatesize / 2),
centroids[ind, 1] + np.ceil(templatesize / 2),
]
).astype(int)
zi = np.array(
[
centroids[ind, 2] - np.ceil(templatesize / 2),
centroids[ind, 2] + np.ceil(templatesize / 2),
]
).astype(int)
data[xi, yi, zi] = 0
# Keep any interior cells, any which overlap original boundary and not padding
# Pull down existing boundary area, if area is valid
# Test side 4
if (
xend < data.shape[0]
): # There is padding on side 4 of cube [xmax+pad:xmax+2*pad,pad:ymax+2*pad,pad:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[1], x_block_pad[1]],
[y_block[0], y_block_pad[1]],
[z_block[0], z_block_pad[1]],
)
data[
xend : data.shape[0], ystart : data.shape[1], zstart : data.shape[2]
] = np.maximum(
data[
xend : data.shape[0], ystart : data.shape[1], zstart : data.shape[2]
],
margin,
)
# Test side 5
if (
yend < data.shape[1]
): # There is padding on side 5 of cube [pad:xmax+2*pad,ymax+pad:ymax+2*pad,pad:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[0], x_block_pad[1]],
[y_block[1], y_block_pad[1]],
[z_block[0], z_block_pad[1]],
)
data[
xstart : data.shape[0], yend : data.shape[1], zstart : data.shape[2]
] = np.maximum(
data[
xstart : data.shape[0], yend : data.shape[1], zstart : data.shape[2]
],
margin,
)
# Test side 6
if (
zend < data.shape[2]
): # There is padding on side 4 of cube [pad:xmax+2*pad,pad:ymax+2*pad,zmax+pad:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[0], x_block_pad[1]],
[y_block[0], y_block_pad[1]],
[z_block[1], z_block_pad[1]],
)
data[
xstart : data.shape[0], ystart : data.shape[1], zend : data.shape[2]
] = np.maximum(
data[
xstart : data.shape[0], ystart : data.shape[1], zend : data.shape[2]
],
margin,
)
# push results over entire padded area
# Pipeline Data will be in X,Y,Z format
# Change to Z,Y,X for upload
data = data[
xstart : data.shape[0], ystart : data.shape[1], zstart : data.shape[2]
]
data = np.transpose(data, (2, 1, 0))
data = data.copy(order="C").astype(eval("np.{}".format(args.dtype)))
# Verify that the cutout uploaded correctly.
rmt.create_cutout(
chan_actual,
0,
[x_block[0], x_block_pad[1]],
[y_block[0], y_block_pad[1]],
[z_block[0], z_block_pad[1]],
data,
)
# Clean up.
else:
# Binarize Map
data[np.where(data > 0)] = 1
# Search through centroids
n_centers, _ = centroids.shape # n by 4
bad_inds = []
for i in range(0, n_centers):
if (
centroids[i, 0] + templatesize / 2 < xstart
or centroids[i, 0] - templatesize / 2 > xend
):
bad_inds.append(i)
elif (
centroids[i, 1] + templatesize / 2 < ystart
or centroids[i, 1] - templatesize / 2 > yend
):
bad_inds.append(i)
elif (
centroids[i, 2] + templatesize / 2 < zstart
or centroids[i, 2] - templatesize / 2 > zend
):
bad_inds.append(i)
centroids_out = np.delete(centroids, bad_inds, axis=0)
# translate into global coordinates from local data block
centroids_out[:, 0] = centroids_out[:, 0] - xstart + args.xmin
centroids_out[:, 1] = centroids_out[:, 1] - ystart + args.ymin
centroids_out[:, 2] = centroids_out[:, 2] - zstart + args.zmin
# Eliminate any cells form data which overlap with the padding edge
for ind in bad_inds:
xi = np.array(
[
centroids[ind, 0] - np.ceil(templatesize / 2),
centroids[ind, 0] + np.ceil(templatesize / 2),
]
).astype(int)
yi = np.array(
[
centroids[ind, 1] - np.ceil(templatesize / 2),
centroids[ind, 1] + np.ceil(templatesize / 2),
]
).astype(int)
zi = np.array(
[
centroids[ind, 2] - np.ceil(templatesize / 2),
centroids[ind, 2] + np.ceil(templatesize / 2),
]
).astype(int)
data[xi, yi, zi] = 0
# Keep any interior cells, any which overlap original boundary and not padding
# Pull down existing boundary area, if area is valid
# Test side 1
if (
xstart > 0
): # There is padding on side 1 of cube [0:pad,0:ymax+2*pad,0:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual, [x_block_pad[0], x_block[0]], y_block_pad, z_block_pad
)
data[0:xstart, :, :] = np.maximum(data[0:xstart, :, :], margin)
# Test side 2
if (
ystart > 0
): # There is padding on side 2 of cube [pad:xmax+2*pad,0:pad,pad:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[0], x_block_pad[1]],
[y_block_pad[0], y_block[0]],
[z_block[0], z_block_pad[1]],
)
data[xstart : data.shape[0], 0:ystart, zstart : data.shape[2]] = np.maximum(
data[xstart : data.shape[0], 0:ystart, zstart : data.shape[1]], margin
)
# Test side 3
if (
zstart > 0
): # There is padding on side 3 of cube [pad:xmax+2*pad,pad:ymax+2*pad,0:pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[0], x_block_pad[1]],
[y_block[0], y_block_pad[1]],
[z_block_pad[0], z_block[0]],
)
data[xstart : data.shape[0], ystart : data.shape[1], 0:zstart] = np.maximum(
data[xstart : data.shape[0], ystart : data.shape[1], 0:zstart], margin
)
# Test side 4
if (
xend < data.shape[0]
): # There is padding on side 4 of cube [xmax+pad:xmax+2*pad,pad:ymax+2*pad,pad:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[1], x_block_pad[1]],
[y_block[0], y_block_pad[1]],
[z_block[0], z_block_pad[1]],
)
data[
xend : data.shape[0], ystart : data.shape[1], zstart : data.shape[2]
] = np.maximum(
data[
xend : data.shape[0], ystart : data.shape[1], zstart : data.shape[2]
],
margin,
)
# Test side 5
if (
yend < data.shape[1]
): # There is padding on side 5 of cube [pad:xmax+2*pad,ymax+pad:ymax+2*pad,pad:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[0], x_block_pad[1]],
[y_block[1], y_block_pad[1]],
[z_block[0], z_block_pad[1]],
)
data[
xstart : data.shape[0], yend : data.shape[1], zstart : data.shape[2]
] = np.maximum(
data[
xstart : data.shape[0], yend : data.shape[1], zstart : data.shape[2]
],
margin,
)
# Test side 6
if (
zend < data.shape[2]
): # There is padding on side 4 of cube [pad:xmax+2*pad,pad:ymax+2*pad,zmax+pad:zmax+2*pad]
margin = pull_margin_cutout(
chan_actual,
[x_block[0], x_block_pad[1]],
[y_block[0], y_block_pad[1]],
[z_block[1], z_block_pad[1]],
)
data[
xstart : data.shape[0], ystart : data.shape[1], zend : data.shape[2]
] = np.maximum(
data[
xstart : data.shape[0], ystart : data.shape[1], zend : data.shape[2]
],
margin,
)
# push results over entire padded area
# Pipeline Data will be in X,Y,Z format
# Change to Z,Y,X for upload
data = np.transpose(data, (2, 1, 0))
data = data.copy(order="C").astype(eval("np.{}".format(args.dtype)))
# Verify that the cutout uploaded correctly.
rmt.create_cutout(chan_actual, 0, x_block_pad, y_block_pad, z_block_pad, data)
# Clean up.
def _upload(f):
print("Uploading to s3:/{}/{}".format(args.bucket, args.output))
s3 = boto3.resource("s3")
f.seek(0, 0)
s3.Object(args.bucket, args.output).put(Body=f)
# Clean up.
if args.bucket and args.s3_only:
with tempfile.TemporaryFile() as f:
np.save(f, centroids_out)
_upload(f)
else:
print("Saving output")
with open(args.output, "w+b") as f:
np.save(f, centroids_out)
if args.bucket:
_upload(f)
return
def boss_push_cutout(args):
if args.config:
rmt = BossRemote(args.config)
else:
cfg = _generate_config(args.token, args)
with open("intern.cfg", "w") as f:
cfg.write(f)
rmt = BossRemote("intern.cfg")
# data is desired range
if args.bucket:
s3 = boto3.resource("s3")
with tempfile.TemporaryFile() as f:
s3.Bucket(args.bucket).download_fileobj(args.input, f)
f.seek(0, 0)
data = np.load(f)
else:
data = np.load(args.input)
numpyType = np.uint8
if args.dtype == "uint32":
numpyType = np.uint32
elif args.dtype == "uint64":
numpyType = np.uint64
if data.dtype != args.dtype:
data = data.astype(numpyType)
sources = []
if args.source:
sources.append(args.source)
COLL_NAME = args.coll
EXP_NAME = args.exp
CHAN_NAME = args.chan
# Create or get a channel to write to
chan_setup = ChannelResource(
CHAN_NAME,
COLL_NAME,
EXP_NAME,
type=args.itype,
datatype=args.dtype,
sources=sources,
)
try:
chan_actual = rmt.get_project(chan_setup)
except HTTPError:
chan_actual = rmt.create_project(chan_setup)
# get coordinate frame to determine padding bounds
cfr = CoordinateFrameResource(args.coord)
cfr_actual = rmt.get_project(cfr)
x_min_bound = cfr_actual.x_start
x_max_bound = cfr_actual.x_stop
y_min_bound = cfr_actual.y_start
y_max_bound = cfr_actual.y_stop
z_min_bound = cfr_actual.z_start
z_max_bound = cfr_actual.z_stop
print("Data model setup.")
# Ranges use the Python convention where the number after the : is the stop
# value. Thus, x_rng specifies x values where: 0 <= x < 8.
data_shape = data.shape # with padding, will be bigger than needed
# find data cutoffs to get rid of padding
# if nmin = 0, this means that the data wasn't padded on there to begin with
xstart = args.padding if args.xmin != 0 else 0
ystart = args.padding if args.ymin != 0 else 0
zstart = args.padding if args.zmin != 0 else 0
xend = data_shape[0] - args.padding
yend = data_shape[1] - args.padding
zend = data_shape[2] - args.padding
# xstart = np.min([args.padding,args.xmin-x_min_bound])
# xend = np.max([data.shape[0]-args.padding,data.shape[0]-(x_max_bound-args.xmax)])
# ystart = np.min([args.padding,args.ymin-y_min_bound])
# yend = np.max([data.shape[1]-args.padding,data.shape[1]-(y_max_bound-args.ymax)])
# zstart = np.min([args.padding,args.zmin-z_min_bound])
# zend = np.max([data.shape[2]-args.padding,data.shape[2]-(z_max_bound-args.zmax)])
# get range which will be uploaded
x_rng = [args.xmin, args.xmax]
y_rng = [args.ymin, args.ymax]
z_rng = [args.zmin, args.zmax]
# Pipeline Data will be in X,Y,Z format
# Change to Z,Y,X for upload
data = np.transpose(data, (2, 1, 0))
data = data[zstart:zend, ystart:yend, xstart:xend]
data = data.copy(order="C")
# Verify that the cutout uploaded correctly.
attempts = 0
while attempts < 3:
try:
rmt.create_cutout(chan_actual, args.res, x_rng, y_rng, z_rng, data)
break
except HTTPError as e:
if attempts < 3:
attempts += 1
print("These are the dimensions: ")
print(data.shape)
print("This is the data type:")
print(data.dtype)
print("Specified data type was:")
print(args.dtype)
print("Specified image type")
print(args.itype)
print("Obtained HTTP error from server. Trial {}".format(attempts))
print("The error: {}".format(e))
else:
raise Exception("Failed 3 times: {}".format(e))
COLL_NAME = 'gray'
EXP_NAME = 'alpha'
CHAN_NAME = 'ex_EM'
# Create or get a channel to write to
chan_setup = ChannelResource(CHAN_NAME,
COLL_NAME,
EXP_NAME,
'image',
'Example channel.',
datatype='uint16')
try:
chan_actual = rmt.get_project(chan_setup)
except HTTPError:
chan_actual = rmt.create_project(chan_setup)
print('Data model setup.')
# Ranges use the Python convention where the number after the : is the stop
# value. Thus, x_rng specifies x values where: 0 <= x < 8.
x_rng = [0, 8]
y_rng = [0, 4]
z_rng = [0, 5]
# Note that the numpy matrix is in Z, Y, X order.
data = numpy.random.randint(1, 3000, (5, 4, 8))
data = data.astype(numpy.uint16)
# Upload the cutout to the channel.
rmt.create_cutout(chan_actual, 0, x_rng, y_rng, z_rng, data)
This script sets up the data model resource used by the example scripts.
To run this example (and create new resources), you must have a user with the resource-manager role!
"""
from intern.remote.boss import BossRemote
from intern.resource.boss.resource import *
from requests import HTTPError
rmt = BossRemote('example.cfg')
coll = CollectionResource('gray', 'Collection used for examples.')
try:
rmt.get_project(coll)
except HTTPError:
rmt.create_project(coll)
coord = CoordinateFrameResource(
'StdFrame', 'Standard coordinate frame for xyz.', 0, 2048, 0, 2048, 0, 64)
try:
coord_actual = rmt.get_project(coord)
except HTTPError:
coord_actual = rmt.create_project(coord)
alpha_exp = ExperimentResource(
'alpha', 'gray', coord_actual.name, 'Alpha example experiment.',
num_time_samples=10)
try:
rmt.get_project(alpha_exp)
except HTTPError:
rmt.create_project(alpha_exp)
class ProjectServiceTest_v1(unittest.TestCase):
"""Integration tests of the Boss resource API.
"""
def setUp(self):
self.rmt = BossRemote('test.cfg', API_VER)
# Turn off SSL cert verification. This is necessary for interacting with
# developer instances of the Boss.
self.rmt.project_service.session_send_opts = {'verify': False}
self.rmt.metadata_service.session_send_opts = {'verify': False}
self.rmt.volume_service.session_send_opts = {'verify': False}
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
coll_name = 'collection2309-{}'.format(random.randint(0, 9999))
self.coll = CollectionResource(coll_name, 'bar')
coll_name_upd = '{}-{}'.format(coll_name, random.randint(0, 9999))
self.coll_upd = CollectionResource(coll_name_upd, 'latest')
cf_name = 'ProjTestFrame{}'.format(random.randint(0, 9999))
self.coord = CoordinateFrameResource(cf_name, 'Test coordinate frame.',
0, 10, -5, 5, 3, 6, 1, 1, 1,
'nanometers')
self.coord_upd = copy.copy(self.coord)
self.coord_upd.name = 'MouseFrame{}'.format(random.randint(0, 9999))
self.coord_upd.description = 'Mouse coordinate frame.'
self.exp = ExperimentResource('exp2309-2',
self.coll.name,
self.coord.name,
'my experiment',
1,
'isotropic',
time_step=2,
time_step_unit='nanoseconds')
self.exp_upd = ExperimentResource('exp2309-2a', self.coll.name,
self.coord.name,
'my first experiment', 2,
'anisotropic')
self.source_chan = ChannelResource('sourceChan', self.coll.name,
self.exp.name, 'image',
'test source channel', 0, 'uint8',
0)
self.related_chan = ChannelResource('relatedChan', self.coll.name,
self.exp.name, 'image',
'test related channel', 0, 'uint8',
0)
self.chan = ChannelResource('myChan',
self.coll.name,
self.exp.name,
'annotation',
'test annotation channel',
0,
'uint8',
0,
sources=['sourceChan'],
related=['relatedChan'])
self.chan_upd = ChannelResource('yourChan',
self.coll.name,
self.exp.name,
'annotation',
'your test annotation channel',
0,
'uint8',
1,
sources=['sourceChan'],
related=['relatedChan'])
def tearDown(self):
try:
self.rmt.delete_project(self.chan_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.chan)
except HTTPError:
pass
try:
self.rmt.delete_project(self.related_chan)
except HTTPError:
pass
try:
self.rmt.delete_project(self.source_chan)
except HTTPError:
pass
try:
self.rmt.delete_project(self.exp_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.exp)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coord_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coord)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coll_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coll)
except HTTPError:
pass
def test_create_coord_frame(self):
cf = self.rmt.create_project(self.coord)
self.assertEqual(self.coord.name, cf.name)
self.assertEqual(self.coord.description, cf.description)
self.assertEqual(self.coord.x_start, cf.x_start)
self.assertEqual(self.coord.x_stop, cf.x_stop)
self.assertEqual(self.coord.y_start, cf.y_start)
self.assertEqual(self.coord.y_stop, cf.y_stop)
self.assertEqual(self.coord.z_start, cf.z_start)
self.assertEqual(self.coord.z_stop, cf.z_stop)
self.assertEqual(self.coord.x_voxel_size, cf.x_voxel_size)
self.assertEqual(self.coord.y_voxel_size, cf.y_voxel_size)
self.assertEqual(self.coord.z_voxel_size, cf.z_voxel_size)
self.assertEqual(self.coord.voxel_unit, cf.voxel_unit)
def test_create_collection(self):
c = self.rmt.create_project(self.coll)
self.assertEqual(self.coll.name, c.name)
self.assertEqual(self.coll.description, c.description)
def test_create_experiment(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
self.assertEqual(self.exp.name, e.name)
self.assertEqual(self.exp.description, e.description)
self.assertEqual(self.coll.name, e.coll_name)
self.assertEqual(self.exp.coord_frame, e.coord_frame)
self.assertEqual(self.exp.hierarchy_method, e.hierarchy_method)
self.assertEqual(self.exp.num_hierarchy_levels, e.num_hierarchy_levels)
self.assertEqual(self.exp.num_time_samples, e.num_time_samples)
self.assertEqual(self.exp.time_step, e.time_step)
self.assertEqual(self.exp.time_step_unit, e.time_step_unit)
def test_create_channel(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
ch = self.rmt.create_project(self.source_chan)
self.assertEqual(self.source_chan.name, ch.name)
self.assertEqual(self.exp.name, ch.exp_name)
self.assertEqual(self.source_chan.description, ch.description)
self.assertEqual(self.coll.name, ch.coll_name)
self.assertEqual(self.source_chan.datatype, ch.datatype)
self.assertEqual(self.source_chan.default_time_sample,
ch.default_time_sample)
self.assertEqual(self.source_chan.base_resolution, ch.base_resolution)
def test_create_annotation_channel_without_source_fails(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
rel_ch = self.rmt.create_project(self.related_chan)
chan = ChannelResource('myChan',
self.coll.name,
self.exp.name,
'annotation',
'test annotation channel',
0,
'uint8',
0,
related=['relatedChan'])
with self.assertRaises(HTTPError):
self.rmt.create_project(chan)
def test_create_annotation_channel(self):
"""Annotation channels require a source channel."""
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
ch = self.rmt.create_project(self.source_chan)
rel_ch = self.rmt.create_project(self.related_chan)
ann_ch = self.rmt.create_project(self.chan)
self.assertEqual(self.chan.name, ann_ch.name)
self.assertEqual(self.exp.name, ann_ch.exp_name)
self.assertEqual(self.chan.description, ann_ch.description)
self.assertEqual(self.coll.name, ann_ch.coll_name)
self.assertEqual(self.chan.datatype, ann_ch.datatype)
self.assertEqual(self.chan.default_time_sample,
ann_ch.default_time_sample)
self.assertEqual(self.chan.base_resolution, ann_ch.base_resolution)
self.assertEqual(self.chan.sources, ann_ch.sources)
self.assertEqual(self.chan.related, ann_ch.related)
def test_get_collection(self):
coll = self.rmt.create_project(self.coll)
c = self.rmt.get_project(self.coll)
self.assertEqual(self.coll.name, c.name)
self.assertEqual(self.coll.description, c.description)
def test_get_coord_frame(self):
coord = self.rmt.create_project(self.coord)
cf = self.rmt.get_project(self.coord)
self.assertEqual(self.coord.name, cf.name)
self.assertEqual(self.coord.description, cf.description)
self.assertEqual(self.coord.x_start, cf.x_start)
self.assertEqual(self.coord.x_stop, cf.x_stop)
self.assertEqual(self.coord.y_start, cf.y_start)
self.assertEqual(self.coord.y_stop, cf.y_stop)
self.assertEqual(self.coord.z_start, cf.z_start)
self.assertEqual(self.coord.z_stop, cf.z_stop)
self.assertEqual(self.coord.x_voxel_size, cf.x_voxel_size)
self.assertEqual(self.coord.y_voxel_size, cf.y_voxel_size)
self.assertEqual(self.coord.z_voxel_size, cf.z_voxel_size)
self.assertEqual(self.coord.voxel_unit, cf.voxel_unit)
def test_get_experiment(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
exp = self.rmt.create_project(self.exp)
e = self.rmt.get_project(self.exp)
self.assertEqual(self.exp.name, e.name)
self.assertEqual(self.exp.description, e.description)
self.assertEqual(self.coll.name, e.coll_name)
self.assertEqual(self.exp.coord_frame, e.coord_frame)
self.assertEqual(self.exp.hierarchy_method, e.hierarchy_method)
self.assertEqual(self.exp.num_hierarchy_levels, e.num_hierarchy_levels)
self.assertEqual(self.exp.num_time_samples, e.num_time_samples)
self.assertEqual(self.exp.time_step, e.time_step)
self.assertEqual(self.exp.time_step_unit, e.time_step_unit)
def test_get_channel(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
chan = self.rmt.create_project(self.source_chan)
ch = self.rmt.get_project(self.source_chan)
self.assertEqual(self.source_chan.name, ch.name)
self.assertEqual(self.exp.name, ch.exp_name)
self.assertEqual(self.source_chan.description, ch.description)
self.assertEqual(self.coll.name, ch.coll_name)
self.assertEqual(self.source_chan.datatype, ch.datatype)
self.assertEqual(self.source_chan.default_time_sample,
ch.default_time_sample)
self.assertEqual(self.source_chan.base_resolution, ch.base_resolution)
def test_get_channel_helper(self):
"""
Test the helper get_channel() as opposed to getting a channel via get_project().
"""
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
chan = self.rmt.create_project(self.source_chan)
actual = self.rmt.get_channel(chan.name, chan.coll_name, chan.exp_name)
# This is not an exhaustive list of attributes, but they are the
# important ones for correct interaction with the volume service.
self.assertTrue(actual.cutout_ready)
self.assertEqual(chan.datatype, actual.datatype)
self.assertEqual(chan.default_time_sample, actual.default_time_sample)
self.assertEqual(chan.base_resolution, actual.base_resolution)
self.assertEqual(chan.downsample_status, actual.downsample_status)
self.assertEqual(chan.type, actual.type)
self.assertEqual(chan.name, actual.name)
self.assertEqual(chan.coll_name, actual.coll_name)
self.assertEqual(chan.exp_name, actual.exp_name)
def test_update_collection(self):
coll = self.rmt.create_project(self.coll)
c = self.rmt.update_project(self.coll.name, self.coll_upd)
self.assertEqual(self.coll_upd.name, c.name)
self.assertEqual(self.coll_upd.description, c.description)
def test_update_coord_frame(self):
c = self.rmt.create_project(self.coll)
coord = self.rmt.create_project(self.coord)
cf = self.rmt.update_project(self.coord.name, self.coord_upd)
self.assertEqual(self.coord_upd.name, cf.name)
self.assertEqual(self.coord_upd.description, cf.description)
def test_update_experiment(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
eup = self.rmt.update_project(self.exp.name, self.exp_upd)
self.assertEqual(self.exp_upd.name, eup.name)
self.assertEqual(self.exp_upd.description, eup.description)
self.assertEqual(self.coll.name, eup.coll_name)
self.assertEqual(self.exp_upd.coord_frame, eup.coord_frame)
self.assertEqual(self.exp_upd.hierarchy_method, eup.hierarchy_method)
self.assertEqual(self.exp_upd.num_hierarchy_levels,
eup.num_hierarchy_levels)
self.assertEqual(self.exp_upd.num_time_samples, eup.num_time_samples)
self.assertEqual(self.exp.time_step, eup.time_step)
self.assertEqual(self.exp.time_step_unit, eup.time_step_unit)
def test_update_channel(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
source_ch = self.rmt.create_project(self.source_chan)
rel_ch = self.rmt.create_project(self.related_chan)
chan = self.rmt.create_project(self.chan)
ch = self.rmt.update_project(self.chan.name, self.chan_upd)
self.assertEqual(self.chan_upd.name, ch.name)
self.assertEqual(self.exp.name, ch.exp_name)
self.assertEqual(self.chan_upd.description, ch.description)
self.assertEqual(self.coll.name, ch.coll_name)
self.assertEqual(self.chan_upd.datatype, ch.datatype)
self.assertEqual(self.chan_upd.default_time_sample,
ch.default_time_sample)
self.assertEqual(self.chan_upd.base_resolution, ch.base_resolution)
self.assertEqual(self.chan_upd.sources, ch.sources)
self.assertEqual(self.chan_upd.related, ch.related)
def test_list_collections(self):
coll = self.rmt.create_project(self.coll)
coll_list = self.rmt.list_collections()
c = [name for name in coll_list if name == self.coll.name]
self.assertEqual(1, len(c))
self.assertEqual(self.coll.name, c[0])
def test_list_coord_frames(self):
cf = self.rmt.create_project(self.coord)
cf_list = self.rmt.list_coordinate_frames()
c = [name for name in cf_list if name == self.coord.name]
self.assertEqual(1, len(c))
self.assertEqual(self.coord.name, c[0])
def test_list_experiments(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
exp = self.rmt.create_project(self.exp)
exp_list = self.rmt.list_experiments(self.coll.name)
e = [name for name in exp_list if name == self.exp.name]
self.assertEqual(1, len(e))
self.assertEqual(self.exp.name, e[0])
#def test_list_channels(self):
# c = self.rmt.create_project(self.coll)
# cf = self.rmt.create_project(self.coord)
# e = self.rmt.create_project(self.exp)
# chan = self.rmt.create_project(self.chan)
# chan_list = self.rmt.list_channels(self.coll.name, self.exp.name)
# ch = [name for name in chan_list if name == self.chan.name]
# self.assertEqual(1, len(ch))
# self.assertEqual(self.chan.name, ch[0])
def test_delete_all(self):
"""Formally test delete at all levels of the data model.
Delete happens all the time in the tearDown() but specifically test
it here.
"""
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
ch = self.rmt.create_project(self.source_chan)
self.rmt.delete_project(self.source_chan)
self.rmt.delete_project(self.exp)
self.rmt.delete_project(self.coord)
self.rmt.delete_project(self.coll)
ymax = 4
zmax = 5
tmax = 10
COLL_NAME = 'gray'
EXP_NAME = 'timeseries_test'
CHAN_NAME = 'Ch1'
COORD_FRAME = COLL_NAME + '_' + EXP_NAME
coord = CoordinateFrameResource(
COORD_FRAME, '', 0, xmax, 0, ymax, 0, zmax)
try:
coord_actual = rmt.get_project(coord)
except HTTPError:
coord_actual = rmt.create_project(coord)
# Create or get experiment
chan_setup = ExperimentResource(
EXP_NAME, COLL_NAME, coord_frame=COORD_FRAME,
num_time_samples=tmax, time_step=1)
try:
chan_actual = rmt.get_project(chan_setup)
except HTTPError:
chan_actual = rmt.create_project(chan_setup)
# Create or get a channel to write to
chan_setup = ChannelResource(
CHAN_NAME, COLL_NAME, EXP_NAME, 'image', '', datatype='uint16')
from intern.remote.boss import BossRemote
from intern.resource.boss.resource import *
CONFIG_FILE = "demo_cfg.json"
rmt = BossRemote("./boss.cfg")
# Load Configuration File
with open(os.path.join("./db_configs", CONFIG_FILE), 'rt') as cfg:
config = json.load(cfg)
# Create a collection
collection = CollectionResource(config["collection"]["name"], config["collection"]["description"])
try:
collection = rmt.create_project(collection)
except Exception as e:
collection = rmt.get_project(collection)
# Create a coord frame
coord = CoordinateFrameResource(config["coordinate_frame"]["name"],
config["coordinate_frame"]["description"],
config["coordinate_frame"]["x_start"],
config["coordinate_frame"]["x_stop"],
config["coordinate_frame"]["y_start"],
config["coordinate_frame"]["y_stop"],
config["coordinate_frame"]["z_start"],
config["coordinate_frame"]["z_stop"],
config["coordinate_frame"]["voxel_size_x"],
config["coordinate_frame"]["voxel_size_y"],
config["coordinate_frame"]["voxel_size_z"])
coll_list = rmt.list_collections()
print("Collections: {}".format(coll_list))
# For resources below the collection level, the parents must be specified.
# For example to list all the channels that are part of the gray collection
# and alpha experiment:
chan_list = rmt.list_channels('gray', 'alpha')
print("Channels in Collection - gray and Experiment - alpha: {}".format(
chan_list))
# When creating a new resource, the corresponding resource object will need
# the required attributes populated.
# For example, to add an "image" style channel named beta to the alpha experiment referenced
# in the previous example:
betaChan = ChannelResource('beta', 'gray', 'alpha', 'image')
newBetaChan = rmt.create_project(betaChan)
# Note that the create method returns a new instance of the ChannelResource.
# The new instance has its `raw` attribute populated with all the JSON data
# returned by the Boss API.
# Display raw channel data from the Boss API:
print(newBetaChan.raw)
# We forgot, to indicate that this channel is related to the omega channel.
# Let's fix that by updating the channel.
newBetaChan.related = ['omega']
betaChanUpdated = rmt.update_project(newBetaChan.name, newBetaChan)
# Let's verify the data type was updated.
print(betaChanUpdated.related)
class BossResParams:
def __init__(self, ingest_job, get_only=True):
self.ingest_job = ingest_job
self.coord_frame_name = '_'.join(
(ingest_job.coll_name, ingest_job.exp_name))
self.rmt = BossRemote(self.ingest_job.boss_config_file)
self.coll_resource = self.setup_boss_collection(get_only=get_only)
self.coord_frame_resource = self.setup_boss_coord_frame(
get_only=get_only)
self.exp_resource = self.setup_boss_experiment(get_only=get_only)
self.ch_resource = self.setup_boss_channel(get_only=get_only)
def get_boss_project(self, proj_setup, get_only):
try:
proj_actual = self.rmt.get_project(proj_setup)
except HTTPError as e:
if get_only is False:
try:
proj_actual = self.rmt.create_project(proj_setup)
except Exception as e:
print(type(e), e)
raise (e)
else:
print(type(e), e)
raise e
except Exception as e:
print(type(e), e)
raise (e)
return proj_actual
def setup_boss_collection(self, get_only=True):
coll_setup = CollectionResource(self.ingest_job.coll_name)
return self.get_boss_project(coll_setup, get_only)
def setup_boss_coord_frame(self, get_only=True):
# if we don't know the coordinate frame parameters, get the one with the same name
if get_only:
coord_setup = CoordinateFrameResource(self.coord_frame_name)
else:
coord_setup = CoordinateFrameResource(
self.coord_frame_name, '',
self.ingest_job.coord_frame_x_extent[0],
self.ingest_job.coord_frame_x_extent[1],
self.ingest_job.coord_frame_y_extent[0],
self.ingest_job.coord_frame_y_extent[1],
self.ingest_job.coord_frame_z_extent[0],
self.ingest_job.coord_frame_z_extent[1],
self.ingest_job.voxel_size[0], self.ingest_job.voxel_size[1],
self.ingest_job.voxel_size[2], self.ingest_job.voxel_unit)
coord_frame_resource = self.get_boss_project(coord_setup, get_only)
if get_only:
# matching ingest_job values to coordinate frame values (if they weren't specified, they are now populated)
self.ingest_job.voxel_size = [
coord_frame_resource.x_voxel_size,
coord_frame_resource.y_voxel_size,
coord_frame_resource.z_voxel_size
]
self.ingest_job.voxel_unit = coord_frame_resource.voxel_unit
return coord_frame_resource
def setup_boss_experiment(self, get_only=True):
# if we don't know the coordinate frame parameters, get the one with the same name
if get_only:
exp_setup = ExperimentResource(self.ingest_job.exp_name,
self.ingest_job.coll_name,
self.coord_frame_name)
else:
# if all elements are the same, isotropic, otherwise anisotropic
if len(set(self.ingest_job.voxel_size)) <= 1:
hierarchy_method = 'isotropic'
else:
hierarchy_method = 'anisotropic'
num_hierarchy_levels = self.calc_hierarchy_levels()
exp_setup = ExperimentResource(self.ingest_job.exp_name,
self.ingest_job.coll_name,
self.coord_frame_name, '',
num_hierarchy_levels,
hierarchy_method)
exp_resource = self.get_boss_project(exp_setup, get_only)
# record the offset (if there is any) into BOSS metadata field for experiment
self.record_offsets(exp_resource)
return exp_resource
def record_offsets(self, exp_resource):
if any([a > 0 for a in self.ingest_job.offsets]):
offsets_dict = {'offsets': self.ingest_job.offsets}
try:
self.rmt.create_metadata(exp_resource, offsets_dict)
except HTTPErrorList: # keys already exist
self.rmt.update_metadata(exp_resource, offsets_dict)
def setup_boss_channel(self, ch_description='', get_only=True):
ch_args = [
self.ingest_job.ch_name, self.ingest_job.coll_name,
self.ingest_job.exp_name
]
if not get_only:
ch_args.extend(
(self.ingest_job.ch_type, ch_description, 0,
self.ingest_job.boss_datatype, self.ingest_job.res))
# annotation data
if self.ingest_job.source_channel is not None:
ch_args.append([self.ingest_job.source_channel])
# checking to make sure source channel exists (creating if needed)
try:
source_args = [
self.ingest_job.source_channel,
self.ingest_job.coll_name, self.ingest_job.exp_name
]
source_setup = ChannelResource(*source_args)
self.get_boss_project(source_setup, True)
except:
self.ingest_job.send_msg(
'Creating a dummy source channel for this annotation because none exists yet'
)
source_args.extend(('image', '', 0, 'uint8', 0))
source_setup = ChannelResource(*source_args)
self.get_boss_project(source_setup, False)
ch_setup = ChannelResource(*ch_args)
ch_resource = self.get_boss_project(ch_setup, get_only)
if get_only:
self.ingest_job.boss_datatype = ch_resource.datatype
if self.ingest_job.datatype is None:
self.ingest_job.datatype = ch_resource.datatype
self.ingest_job.res = ch_resource.base_resolution
return ch_resource
def calc_hierarchy_levels(self, lowest_res=512):
img_size = [
self.coord_frame_resource.x_stop -
self.coord_frame_resource.x_start,
self.coord_frame_resource.y_stop -
self.coord_frame_resource.y_start,
self.coord_frame_resource.z_stop -
self.coord_frame_resource.z_start
]
max_xy = max(img_size[0:1])
# we add one because 0 is included in the number of downsampling levels
num_levels = max(1, math.ceil(math.log(max_xy / lowest_res, 2)) + 1)
return num_levels
