Merge branch 'master' of github.com:scilus/scilpy into convert_trks_t…

…o_hdf5

scilpy/image/labels.py

@@ -1,12 +1,26 @@
 # -*- coding: utf-8 -*-
+import importlib.resources as resources
 import inspect
+import json
 import logging
 import os
 
 import numpy as np
 from scipy.spatial import cKDTree
 
 
+def load_wmparc_labels():
+    """
+    Load labels dictionary of different parcellations from the Desikan-Killiany
+    atlas.
+    """
+    lut_package = resources.files('data').joinpath('LUT')
+    labels_path = lut_package.joinpath('dk_aggregate_structures.json')
+    with open(labels_path) as labels_file:
+        labels = json.load(labels_file)
+    return labels
+
+
 def get_data_as_labels(in_img):
     """
     Get data as label (force type np.uint16), check data type before casting.
@@ -33,6 +47,26 @@ def get_data_as_labels(in_img):
                       'image'.format(basename, curr_type))
 
 
+def get_binary_mask_from_labels(atlas, label_list):
+    """
+    Get a binary mask from labels.
+
+    Parameters
+    ----------
+    atlas: numpy.ndarray
+        The image will all labels as values (ex, result from
+        get_data_as_labels).
+    label_list: list[int]
+        The labels to get.
+    """
+    mask = np.zeros(atlas.shape, dtype=np.uint16)
+    for label in label_list:
+        is_label = atlas == label
+        mask[is_label] = 1
+
+    return mask
+
+
 def get_lut_dir():
     """
     Return LUT directory in scilpy repository