def layer_writer_and_data(request):
"""Fixture that supplies layer io utilities for tests.
Parameters
----------
request : _pytest.fixtures.SubRequest
The pytest request object
Returns
-------
tuple
``(writer, layer_data, extension, reader, Layer)``
- writer: a function that can write layerdata to a path
- layer_data: the layerdata tuple for this layer
- extension: an appropriate extension for this layer type
- reader: a function that can read this layer type from a path and
returns a ``(data, meta)`` tuple.
- Layer: the Layer class
"""
if request.param == 'image':
data = np.random.rand(20, 20)
Layer = Image
layer = Image(data)
writer = napari_write_image
extension = '.tif'
def reader(path):
return (io.imread(path), {}, 'image') # metadata
elif request.param == 'labels':
data = np.random.randint(0, 16000, (32, 32), 'uint64')
Layer = Labels
layer = Labels(data)
writer = napari_write_labels
extension = '.tif'
def reader(path):
return (io.imread(path), {}, 'labels') # metadata
elif request.param == 'points':
data = np.random.rand(20, 2)
Layer = Points
layer = Points(data)
writer = napari_write_points
extension = '.csv'
reader = partial(io.csv_to_layer_data, require_type='points')
elif request.param == 'points-with-properties':
data = np.random.rand(20, 2)
Layer = Points
layer = Points(data, properties={'values': np.random.rand(20)})
writer = napari_write_points
extension = '.csv'
reader = partial(io.csv_to_layer_data, require_type='points')
elif request.param == 'shapes':
np.random.seed(0)
data = [
np.random.rand(2, 2),
np.random.rand(2, 2),
np.random.rand(6, 2),
np.random.rand(6, 2),
np.random.rand(2, 2),
]
shape_type = ['ellipse', 'line', 'path', 'polygon', 'rectangle']
Layer = Shapes
layer = Shapes(data, shape_type=shape_type)
writer = napari_write_shapes
extension = '.csv'
reader = partial(io.csv_to_layer_data, require_type='shapes')
else:
return None, None, None, None, None
layer_data = layer.as_layer_data_tuple()
return writer, layer_data, extension, reader, Layer
def layer_writer_and_data(request):
"""Fixture that supplies layer io utilities for tests.
Parameters
----------
request : _pytest.fixtures.SubRequest
The pytest request object
Returns
-------
tuple
``(writer, layer_data, extension, reader, Layer)``
- writer: a function that can write layerdata to a path
- layer_data: the layerdata tuple for this layer
- extension: an appropriate extension for this layer type
- reader: a function that can read this layer type from a path and
returns a ``(data, meta)`` tuple.
- Layer: the Layer class
"""
if request.param == 'image':
data = np.random.rand(20, 20)
Layer = Image
layer = Image(data)
writer = napari_write_image
extension = '.tif'
def reader(path):
return (
io.imread(path),
{}, # metadata
)
elif request.param == 'points':
data = np.random.rand(20, 2)
Layer = Points
layer = Points(data)
writer = napari_write_points
extension = '.csv'
def reader(path):
return (
io.read_csv(path)[0][:, 1:3],
{}, # metadata
)
elif request.param == 'points-with-properties':
data = np.random.rand(20, 2)
Layer = Points
layer = Points(data, properties={'values': np.random.rand(20)})
writer = napari_write_points
extension = '.csv'
def reader(path):
return (
io.read_csv(path)[0][:, 1:3],
{
'properties': {
io.read_csv(path)[1][3]: io.read_csv(path)[0][:, 3]
}
},
)
else:
return None, None, None, None, None
layer_data = layer.as_layer_data_tuple()
return writer, layer_data, extension, reader, Layer
