def test_roi_instantiation(ophys_plane_data_fixture):
schema_dict = ophys_plane_data_fixture
ct = 0
for meta_pair in schema_dict['coupled_planes']:
pair = meta_pair['planes']
for plane in pair:
for roi_args in plane['rois']:
_ = OphysROI.from_schema_dict(roi_args)
ct += 1
assert ct == 8
def from_schema_dict(cls, schema_dict):
"""
Create an OphysPlane from a dict taken from the module's argschema
Parameters
----------
schema_dict -- a dict codifying the plane, as read from argschema, i.e.
{ # start of ophys_experiment
"ophys_experiment_id": ,# an int
"motion_corrected_stack": , # path to h5 movie file
"motion_border": { # border widths
"x0": , # a float
"x1": , # a float
"y0": , # a float
"y1": , # a float
},
"rois": [ # list of dicts definining the ROIs for this experiment
{ # start of individual ROI
"id": , # an int
"x": , # an int
"y": , # an int
"width": , # an int
"height": , # an int
"valid_roi": , # boolean
"mask_matrix": [[]] # 2-D array of booleans
}, # end of individual ROI,
{
"id": ,
"x": ,
"y": ,
"width": ,
"height": ,
"valid_roi": ,
"mask_matrix": [[]]
},
...
]
}
"""
roi_list = []
for roi in schema_dict['rois']:
roi_list.append(OphysROI.from_schema_dict(roi))
max_path = None
if 'maximum_projection_image_file' in schema_dict:
max_path = schema_dict['maximum_projection_image_file']
return cls(experiment_id=schema_dict['ophys_experiment_id'],
movie_path=schema_dict['motion_corrected_stack'],
motion_border=schema_dict['motion_border'],
roi_list=roi_list,
max_projection_path=max_path)