def test_cells_xml_to_dataframe():
cells_df = cell_io.cells_xml_to_df(xml_path)
assert len(cells_df) == 65
assert cells_df.type.tolist() == type_vals
assert cells_df.x.tolist() == x_vals
assert cells_df.y.tolist() == y_vals
assert cells_df.z.tolist() == z_vals
def get_cell_arrays(cells_file):
df = cells_xml_to_df(cells_file)
non_cells = df[df["type"] == Cell.UNKNOWN]
cells = df[df["type"] == Cell.CELL]
cells = cells_df_as_np(cells)
non_cells = cells_df_as_np(non_cells)
return cells, non_cells
def get_cell_labels_arrays(cells_file,
new_order=[2, 1, 0],
type_column="type"):
df = cells_xml_to_df(cells_file)
labels = df[type_column]
labels = labels.to_numpy()
cells_df = df.drop(columns=[type_column])
cells = cells_df[cells_df.columns[new_order]]
cells = cells.to_numpy()
# convert to boolean
labels = labels == 2
return cells, labels