def test_create_render_resource_wrong_channel(self):
owner = "Forrest"
project = "M247514_Rorb_1"
stack = "Site3Align2_LENS_Session1"
channel = "notAchannel"
with pytest.raises(AssertionError):
renderResource(
owner,
project,
stack,
self.baseURL,
self.datatype,
channel=channel,
scale=self.scale,
)
def test_create_render_resource(self):
render_obj = renderResource(
self.owner,
self.project,
self.stack,
self.baseURL,
self.datatype,
scale=self.scale,
)
assert render_obj.x_rng == self.x_rng
assert render_obj.y_rng == self.y_rng
assert render_obj.z_rng == self.z_rng
assert render_obj.datatype == "uint8"
def test_create_render_resource_half_scale(self):
self.scale = 0.5
render_obj = renderResource(
self.owner,
self.project,
self.stack,
self.baseURL,
self.datatype,
scale=self.scale,
)
assert render_obj.scale == self.scale
assert render_obj.x_rng == [round(x * self.scale) for x in self.x_rng]
assert render_obj.y_rng == [round(x * self.scale) for x in self.y_rng]
assert render_obj.z_rng == self.z_rng
def test_get_render_tile_channel_scale(self):
self.setup_render_channel()
self.scale = 0.125
render_obj = renderResource(
self.owner,
self.project,
self.stack,
self.baseURL,
self.datatype,
channel=self.channel,
scale=self.scale,
)
x = 4200
y = 6500
z = 24
x_width = 1024
y_width = 1024
window = [0, 5000]
# GET /v1/owner/{owner}/project/{project}/stack/{stack}/z/{z}/box/{x},{y},{width},{height},{scale}/png-image
tile_url = "{}owner/{}/project/{}/stack/{}/z/{}/box/{},{},{},{},{}/png-image?channels={}&minIntensity={}&maxIntensity={}".format(
self.baseURL,
self.owner,
self.project,
self.stack,
z,
x,
y,
x_width,
y_width,
self.scale,
self.channel,
window[0],
window[1],
)
r = requests.get(tile_url)
test_img = Image.open(BytesIO(r.content))
# dim 3 is RGBA (A=alpha), for grayscale, RGB values are all the same
test_data = np.asarray(test_img)[:, :, 0]
# getting tile from render resource
data = render_obj.get_render_tile(z, x, y, x_width, y_width, window)
assert data.shape == (y_width * self.scale, x_width * self.scale)
assert np.array_equal(data, test_data)
def test_create_render_resource_channel(self):
# metadata:
# http://render-dev-eric.neurodata.io/render-ws/v1/owner/Forrest/project/M247514_Rorb_1/stack/Site3Align2_LENS_Session1
self.setup_render_channel()
render_obj = renderResource(
self.owner,
self.project,
self.stack,
self.baseURL,
self.datatype,
channel=self.channel,
scale=self.scale,
)
assert render_obj.x_rng == [-27814, 63397]
assert render_obj.y_rng == [-67750, 69699]
assert render_obj.z_rng == [0, 50]
def test_get_render_tile(self):
x = 1024
y = 512
z = 17
x_width = 512
y_width = 1024
window = [0, 10000]
# GET /v1/owner/{owner}/project/{project}/stack/{stack}/z/{z}/box/{x},{y},{width},{height},{scale}/png-image
tile_url = "{}owner/{}/project/{}/stack/{}/z/{}/box/{},{},{},{},{}/png-image?minIntensity={}&maxIntensity={}".format(
self.baseURL,
self.owner,
self.project,
self.stack,
z,
x,
y,
x_width,
y_width,
self.scale,
window[0],
window[1],
)
r = requests.get(tile_url)
test_img = Image.open(BytesIO(r.content))
# dim 3 is RGBA (A=alpha), for grayscale, RGB values are all the same
test_data = np.asarray(test_img)[:, :, 0]
render_obj = renderResource(
self.owner,
self.project,
self.stack,
self.baseURL,
self.datatype,
scale=self.scale,
)
data = render_obj.get_render_tile(z, x, y, x_width, y_width, window)
assert data.shape == (y_width, x_width)
assert np.array_equal(data, test_data)
def test_get_render_tile_no_window_uint16(self):
x = 50
y = 512
z = 17
x_width = 512
y_width = 1024
datatype = "uint16"
# GET /v1/owner/{owner}/project/{project}/stack/{stack}/z/{z}/box/{x},{y},{width},{height},{scale}/tiff16-image
tile_url = "{}owner/{}/project/{}/stack/{}/z/{}/box/{},{},{},{},{}/tiff16-image".format(
self.baseURL,
self.owner,
self.project,
self.stack,
z,
x,
y,
x_width,
y_width,
self.scale,
)
print(tile_url)
r = requests.get(tile_url)
test_img = Image.open(BytesIO(r.content))
# dim 3 is RGBA (A=alpha), for grayscale, RGB values are all the same
test_data = np.asarray(test_img)
render_obj = renderResource(
self.owner,
self.project,
self.stack,
self.baseURL,
datatype,
scale=self.scale,
)
data = render_obj.get_render_tile(z, x, y, x_width, y_width)
assert data.shape == (y_width, x_width)
assert np.array_equal(data, test_data)
def __init__(self, args_namespace):
# args is a Namespace (argparse)
# convert to dict in order to use the get method (returns None if not present in dict)
args = vars(args_namespace)
self.datasource = args.get('datasource')
self.slack_usr = args.get('slack_usr')
self.s3_bucket_name = args.get('s3_bucket_name')
self.create_resources = args.get('create_resources')
self.coll_name = args.get('collection')
self.exp_name = args.get('experiment')
self.ch_name = args.get('channel')
self.datatype = args.get('datatype')
self.warn_missing_files = args.get('warn_missing_files')
self.z_range = args.get('z_range')
self.limit_x = args.get('limit_x')
self.limit_y = args.get('limit_y')
self.limit_z = args.get('limit_z')
self.voxel_size = args.get('voxel_size')
self.voxel_unit = args.get('voxel_unit')
self.res = args.get('res')
self.source_channel = args.get('source_channel')
if self.source_channel is not None:
self.boss_datatype = 'uint64' # force boss datatype to uint64 for annotations
self.ch_type = 'annotation'
else:
# image channels don't have a source
try:
assert self.datatype == 'uint8' or self.datatype == 'uint16' or self.datatype is None
except AssertionError:
raise ValueError(
'image channels in the BOSS only support uint8 or uint16')
self.boss_datatype = self.datatype
self.ch_type = 'image'
if self.datasource == 'render':
# create a render resource which will populate some of the variables
render_owner = args.get('render_owner')
render_project = args.get('render_project')
render_stack = args.get('render_stack')
render_channel = args.get('render_channel')
render_baseURL = args.get('render_baseURL')
render_scale = args.get('render_scale')
self.render_window = args.get('render_window')
# create the render object in order to get the xyz extents
self.render_obj = renderResource(render_owner,
render_project,
render_stack,
render_baseURL,
self.datatype,
channel=render_channel,
scale=render_scale,
limit_x=self.limit_x,
limit_y=self.limit_y,
limit_z=self.limit_z)
self.x_extent = self.render_obj.x_rng
self.y_extent = self.render_obj.y_rng
self.z_extent = self.render_obj.z_rng
self.z_step = 1
# render resource is set to return PNGs
self.extension = 'png'
if self.z_range is None: # if the user isn't specifying the z range for ingest, we just get the entire extent
self.z_range = self.z_extent
# otherwise it's image data
elif self.datasource == 's3' or self.datasource == 'local':
self.base_fname = args.get('base_filename')
self.base_path = args.get('base_path')
self.extension = args.get('extension')
self.x_extent = args.get('x_extent')
self.y_extent = args.get('y_extent')
self.z_extent = args.get('z_extent')
self.validate_xyz_limits()
self.apply_limits()
self.z_step = args.get('z_step')
# initialize offset to zero (x,y,z)
self.offsets = [0, 0, 0]
self.forced_offsets = args.get('forced_offsets')
# if user specified, we calculate the offset
if args.get('offset_extents') or self.forced_offsets is not None:
# calculate and store offsets
self.offsets = self.calc_offsets()
# create new extents
self.offset_extents()
self.set_img_size()
self.coord_frame_x_extent = args.get('coord_frame_x_extent')
self.coord_frame_y_extent = args.get('coord_frame_y_extent')
self.coord_frame_z_extent = args.get('coord_frame_z_extent')
self.set_coord_frame_extents()
self.get_extents = args.get('get_extents')
self.validate_coord_frames()
# creating the slack session
self.slack_obj = self.create_slack_session(
args.get('slack_token_file'))
if self.datasource == 's3':
self.s3_res = self.create_s3_res(
aws_profile=args.get('aws_profile'))
else:
self.s3_res = None
self.boss_config_file = args.get('boss_config_file')
self.num_READ_failures = 0
self.num_POST_failures = 0
# Document the arguments passed
self.send_msg('{} Command parameters used: {}'.format(
get_formatted_datetime(), args))
def test_wrong_stack(self):
owner = "6_ribbon_experiments"
project = "M321160_Ai139_smallvol"
stack = "DOES_NOT_EXIST"
with pytest.raises(ConnectionError):
renderResource(owner, project, stack, self.baseURL, self.datatype)
