def _read_position_list(self):
"""Open a Micromanager acquired position file and return a list of X, Y positions"""
if self.pl_path is None:
return [], []
acquisition_dict = util.read_json(self.pl_path)
return clean_position_text(acquisition_dict)
def read_metadata(image_path: Path):
"""Read a metadata dictionary from a file and return it, or return None if not found"""
metadata_path = Path(image_path.parent, image_path.stem + '_metadata.txt')
try:
metadata = util.read_json(metadata_path)
return metadata
except:
return None
def get_xy_origin(pl_path, params=None):
"""Read an micromanager position list and get the XY origin"""
raw_pos_list = util.read_json(pl_path)
pos_list = clean_position_text(raw_pos_list)[0]
xy_origin = np.min(pos_list, 0)
if params is not None:
xy_origin[0] = xy_origin[
0] - 0.5 * params['raylines'] * params['transducer spacing']
return xy_origin
def _read_delays(self):
"""
Find a delays file if it exists and read it in instead of calculating
:return:
"""
temp_params = util.read_json(self.params_path)
if self.params == temp_params:
self.delays = sp.load_npz(self.delays_path)
else:
raise (
"The parameters do not match.\n Point to the right file or to an unused file name"
)
def test_read_string_io(self, tmpdir, file_content, expected):
path = tmpdir.join('test.json')
with open(str(path), 'w') as file:
json.dump(file_content, file)
output = util.read_json(path)
assert output == expected