def test_get_filename_without_ext(self):
self.assertEqual(libmag.get_filename_without_ext("foo/bar/item.py"),
"item")
self.assertEqual(libmag.get_filename_without_ext("foo/bar/item"),
"item")
self.assertEqual(
libmag.get_filename_without_ext("foo/bar/item.file.py"),
"item.file")
def export_common_labels(img_paths, output_path):
"""Export data frame combining all label IDs from the given atlases,
showing the presence of labels in each atlas.
Args:
img_paths: Image paths from which to load the corresponding
labels images.
output_path: Path to export data frame to .csv.
Returns:
Data frame with label IDs as indices, column for each atlas, and
cells where 1 indicates that the given atlas has the corresponding
label.
"""
labels_dict = {}
for img_path in img_paths:
name = libmag.get_filename_without_ext(img_path)
labels_np = sitk_io.load_registered_img(
img_path, config.RegNames.IMG_LABELS.value)
# only use pos labels since assume neg labels are merely mirrored
labels_unique = np.unique(labels_np[labels_np >= 0])
labels_dict[name] = pd.Series(np.ones(len(labels_unique), dtype=int),
index=labels_unique)
df = pd.DataFrame(labels_dict)
df.sort_index()
df.to_csv(output_path)
print("common labels exported to {}".format(output_path))
return df
def merge_excels(paths, out_path, names=None):
"""Merge Excel files into separate sheets of a single Excel output file.
Args:
paths (List[str]): Sequence of paths to Excel files to load.
out_path (str): Path to output file.
names (List[str]): Sequence of sheet names corresponding to ``paths``.
If None, the filenames without extensions in ``paths`` will be
used.
"""
libmag.backup_file(out_path)
with pd.ExcelWriter(out_path) as writer:
if not names:
names = [libmag.get_filename_without_ext(p) for p in paths]
for path, name in zip(paths, names):
# TODO: styling appears to be lost during the read step
df = pd.read_excel(path, index_col=0, engine="openpyxl")
df.to_excel(writer, sheet_name=name, index=False)