[FIX 🔨] bug fixes and improvement

enigmatoolbox/datasets/base.py

@@ -281,7 +281,7 @@ def fetch_ahba(csvfile=None):
                 Table of gene co-expression data, shape = (82, 15634)
         """
     if csvfile is None:
-        url = 'https://raw.githubusercontent.com/saratheriver/enigma-extra/master/ahba/allgenes.csv'
+        url = 'https://raw.githubusercontent.com/saratheriver/enigma-extra/master/ahba/allgenes_stable.csv'
         return pd.read_csv(url, error_bad_lines=False)
     else:
         return pd.read_csv(csvfile, error_bad_lines=False)

enigmatoolbox/permutation_testing/permutation_testing.py

@@ -84,7 +84,7 @@ def centroid_extraction_sphere(sphere_coords, annotfile, ventricles=False):
     return centroid
 
 
-def rotate_parcellation(coord_l, coord_r, nrot=100):
+def rotate_parcellation(coord_l, coord_r, nrot=1000):
     """
     Rotate parcellation (author: @saratheriver)
 
@@ -95,7 +95,7 @@ def rotate_parcellation(coord_l, coord_r, nrot=100):
     coord_r : ndarray
         Coordinates of right hemisphere regions on the sphere, shape = (m, 3)
     nrot : int, optional
-        Number of rotations. Default is 100.
+        Number of rotations. Default is 1000.
 
     Returns
     -------
@@ -299,7 +299,7 @@ def perm_sphere_p(x, y, perm_id, corr_type='pearson', null_dist=False):
         return p_perm
 
 
-def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot=100,
+def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot=1000,
               type='pearson', null_dist=False, ventricles=False):
     """
     Spin permutation (author: @saratheriver)
@@ -315,7 +315,7 @@ def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot=
     parcellation_name : string, optional
         Parcellation name {'aparc', 'aparc_aseg'}. Default is 'aparc'.
     n_rot : int, optional
-        Number of spin rotations. Default is 100.
+        Number of spin rotations. Default is 1000.
     type : string, optional
         Correlation type {'pearson', 'spearman'}. Default is 'pearson'.
     null_dist : bool, optional
@@ -390,7 +390,7 @@ def spin_test(map1, map2, surface_name='fsa5', parcellation_name='aparc', n_rot=
         return p_spin
 
 
-def shuf_test(map1, map2, n_rot=100, type='pearson', null_dist=False):
+def shuf_test(map1, map2, n_rot=1000, type='pearson', null_dist=False):
     """
     Shuf permuation (author: @saratheriver)
 
@@ -401,7 +401,7 @@ def shuf_test(map1, map2, n_rot=100, type='pearson', null_dist=False):
     map2 : narray, ndarray, or pandas.Series
         The other map to be correlated
     n_rot : int, optional
-        Number of shuffles. Default is 100.
+        Number of shuffles. Default is 1000.
     type : string, optional
         Correlation type {'pearson', 'spearman'}. Default is 'pearson'.
     null_dist : bool, optional

enigmatoolbox/plotting/colormaps.py

@@ -10,12 +10,39 @@
                         [70, 130, 180, 255],
                         [196, 58, 250, 255]], dtype=np.uint8)
 
+eco_kos_colors = np.array([[0, 0, 0, 255],
+                           [126, 40, 127, 255],
+                           [51, 104, 156, 255],
+                           [167, 210, 140, 255],
+                           [254, 205, 8, 255],
+                           [255, 253, 25, 255]], dtype=np.uint8)
+
+spec_5_colors = np.array([[0, 0, 0, 255],
+                         [50, 136, 189, 255],
+                         [171, 221, 164, 255],
+                         [235, 235, 181, 255],
+                         [253, 174, 97, 255],
+                         [213, 62, 79, 255]], dtype=np.uint8)
+
 root_pth = os.path.dirname(__file__)
 TealRd_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'TealRd.csv'))
 GyRd_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'GyRd.csv'))
 GyRd_r_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'GyRd_r.csv'))
 GyBu_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'GyBu.csv'))
 GyBu_r_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'GyBu_r.csv'))
 
+bb_r_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_r.csv'))
+bb_o_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_o.csv'))
+bb_g_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_g.csv'))
+bb_p_colors = np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_p.csv'))
+
+bb_r_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_r.csv')))
+bb_o_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_o.csv')))
+bb_g_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_g.csv')))
+bb_p_r_colors = np.flipud(np.loadtxt(os.path.join(root_pth, 'cmaps', 'bb_p.csv')))
+
 colormaps = {'yeo7': yeo7_colors, 'TealRd': TealRd_colors, 'GyRd': GyRd_colors,
-             'GyRd_r': GyRd_r_colors, 'GyBu': GyBu_colors, 'GyBu_r': GyBu_r_colors}
+             'GyRd_r': GyRd_r_colors, 'GyBu': GyBu_colors, 'GyBu_r': GyBu_r_colors,
+             'eco_kos': eco_kos_colors, 'bb_r': bb_r_colors, 'bb_o': bb_o_colors,
+             'bb_g': bb_g_colors, 'bb_p': bb_p_colors, 'bb_r_r': bb_r_r_colors, 'bb_o_r': bb_o_r_colors,
+             'bb_g_r': bb_g_r_colors, 'bb_p_r': bb_p_r_colors, 'spec_5': spec_5_colors}

enigmatoolbox/utils/parcellation.py

@@ -228,7 +228,7 @@ def parcel_to_surface(source_val, target_lab, mask=None, fill=0, source_lab=None
 
     if mask is not None:
         target_lab2 = target_lab[mask]
-        labs2 = map_to_labels(source_val, target_lab2, source_lab=source_lab)
+        labs2 = parcel_to_surface(source_val, target_lab2, source_lab=source_lab)
         return map_to_mask(labs2, mask, fill=fill)
 
     if source_lab is None: