def test_rectmask():
rect = np.ones([3, 3])
testrect = np.zeros([5, 5])
rect1 = 1 * testrect
rect1[0:3, 0:3] = rect
rect2 = 1 * testrect
rect2[0:3, 2:5] = rect
rect3 = 1 * testrect
rect3[2:5, 0:3] = rect
rect4 = 1 * testrect
rect4[2:5, 2:5] = rect
assert np.allclose(m.rectangular(2, 2, 3, 3, 5, 5), rect4)
assert np.allclose(m.rectangular(2, 2, -3, 3, 5, 5), rect3)
assert np.allclose(m.rectangular(2, 2, 3, -3, 5, 5), rect2)
assert np.allclose(m.rectangular(2, 2, -3, -3, 5, 5), rect1)
def get_roi(params, shape):
if "roi" not in params or ("shape" not in params["roi"]):
return None
params = params["roi"]
ny, nx = tuple(shape)
if params["shape"] == "disk":
roi = masks.circular(
params["cx"],
params["cy"],
nx,
ny,
params["r"],
)
elif params["shape"] == "rect":
roi = masks.rectangular(
params["x"],
params["y"],
params["width"],
params["height"],
nx,
ny,
)
else:
raise NotImplementedError("unknown shape %s" % params["shape"])
return roi
def get_sd_roi(self):
if "roi" not in self.parameters:
return None
params = self.parameters["roi"]
ny, nx = tuple(self.dataset.shape.nav)
if params["shape"] == "rect":
roi = masks.rectangular(
params["x"],
params["y"],
params["width"],
params["height"],
nx, ny,
)
else:
raise NotImplementedError("unknown shape %s" % params["shape"])
return roi
def test_sd_roi(hdf5_ds_2, tmpdir_factory, lt_ctx):
datadir = tmpdir_factory.mktemp('template_tests')
conn = {'connection': {'type': 'local'}}
path = hdf5_ds_2.path
dataset = _get_hdf5_params(path)
roi_params = {
"shape": "rect",
"x": 1,
"y": 2,
"width": 6,
"height": 6
}
analysis = [{
"analysisType": 'SD_FRAMES',
"parameters": {
"roi": roi_params
}
}]
notebook = notebook_generator(conn, dataset, analysis, save=True)
notebook = io.StringIO(notebook.getvalue())
nb = nbformat.read(notebook, as_version=4)
ep = ExecutePreprocessor(timeout=600)
out = ep.preprocess(nb, {"metadata": {"path": datadir}})
data_path = os.path.join(datadir, 'sd_result.npy')
results = np.load(data_path)
nx, ny = hdf5_ds_2.shape.nav
roi = masks.rectangular(
X=roi_params["x"],
Y=roi_params["y"],
Width=roi_params["width"],
Height=roi_params["height"],
imageSizeX=nx,
imageSizeY=ny)
udf = StdDevUDF()
expected = lt_ctx.run_udf(dataset=hdf5_ds_2, udf=udf, roi=roi)
assert np.allclose(
results,
expected['varsum'].raw_data,
)
def test_empty_rectmask():
assert not np.any(m.rectangular(2, 2, 0, 3, 5, 5))
assert not np.any(m.rectangular(2, 2, 3, 0, 5, 5))
assert not np.any(m.rectangular(2, 2, 0, 0, 5, 5))
