def test_atlas_value_to_name():
structure_df = load_structures_as_df(structures_csv)
assert "Interpeduncular nucleus" == structures_tree.atlas_value_to_name(
100, structure_df)
with pytest.raises(structures_tree.UnknownAtlasValue):
structures_tree.atlas_value_to_name(100000, structure_df)
def display_brain_region_name(layer, structures_df):
val = layer.get_value()
if val != 0 and val is not None:
try:
region = atlas_value_to_name(val, structures_df)
msg = f"{region}"
except UnknownAtlasValue:
msg = "Unknown region"
else:
msg = "No label here!"
layer.help = msg
def get_connected_component_shape(layer, event):
val = layer.get_value()
if val != 0 and val is not None:
try:
region = atlas_value_to_name(val, structures_df)
msg = f"{region}"
except UnknownAtlasValue:
msg = "Unknown region"
else:
msg = "No label here!"
layer.help = msg
def add_structure_volume_to_df(
df,
atlas_value,
structures_reference_df,
unique_vals_left,
unique_vals_right,
counts_left,
counts_right,
voxel_volume,
total_volume_voxels=None,
):
name = atlas_value_to_name(atlas_value, structures_reference_df)
left_volume, left_percentage = get_volume_in_hemisphere(
atlas_value,
unique_vals_left,
counts_left,
total_volume_voxels,
voxel_volume,
)
right_volume, right_percentage = get_volume_in_hemisphere(
atlas_value,
unique_vals_right,
counts_right,
total_volume_voxels,
voxel_volume,
)
if total_volume_voxels is not None:
total_percentage = left_percentage + right_percentage
else:
total_percentage = 0
df = df.append(
{
"structure_name": name,
"left_volume_mm3": left_volume,
"left_percentage_of_total": left_percentage,
"right_volume_mm3": right_volume,
"right_percentage_of_total": right_percentage,
"total_volume_mm3": left_volume + right_volume,
"percentage_of_total": total_percentage,
},
ignore_index=True,
)
return df
def add_structure_volume_to_df(
df,
atlas_value,
structures_reference_df,
unique_vals_left,
unique_vals_right,
counts_left,
counts_right,
voxel_volume,
):
name = atlas_value_to_name(atlas_value, structures_reference_df)
try:
left_index = np.where(unique_vals_left == atlas_value)[0][0]
left_volume = counts_left[left_index] * voxel_volume
except IndexError:
logging.warning("Atlas value: {} not found in registered atlas. "
"Setting registered volume to 0.".format(atlas_value))
left_volume = 0
try:
right_index = np.where(unique_vals_right == atlas_value)[0][0]
right_volume = counts_right[right_index] * voxel_volume
except IndexError:
logging.warning("Atlas value: {} not found in registered atlas. "
"Setting registered volume to 0.".format(atlas_value))
right_volume = 0
df = df.append(
{
"structure_name": name,
"left_volume_mm3": left_volume,
"right_volume_mm3": right_volume,
"total_volume_mm3": left_volume + right_volume,
},
ignore_index=True,
)
return df