fixed colors.py and added scripts directly calling colors.py and converting to mipav lut

Author: Shuo Han

colors_script/calc_colormap.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+sys.path.append('../mindboggle/mio')
+import colors
+import numpy as np
+import os
+import pickle
+
+filename = 'label.nii.gz'
+matrix_filename = 'matrix.pickle'
+colormap_filename = 'colormap.npy'
+
+if not os.path.isfile(matrix_filename):
+    print('finding adjacency maps')
+    IDs, matrix, output = colors.label_adjacency_matrix(filename, ignore_values=[])
+    pickle.dump(matrix, open(matrix_filename, 'wb'))
+    np.save('IDs', IDs)
+else:
+    IDs = np.load('IDs.npy')
+    matrix = pickle.load(open(matrix_filename, 'rb'))
+
+matrix = matrix.as_matrix()
+matrix = matrix[:, 1:]
+
+print('finding colormap')
+if not os.path.isfile(colormap_filename):
+    colormap = colors.distinguishable_colors(ncolors=len(IDs),
+                                            backgrounds=[[0,0,0],[1,1,1]],
+                                            save_csv=False)
+    np.save(colormap_filename, colormap)
+else:
+    colormap = np.load(colormap_filename)
+
+print(colormap.shape)
+
+colors = colors.group_colors(colormap, 'cerebellum', IDs=IDs,
+                             adjacency_matrix=matrix)
+np.save('colors', colors)

colors_script/convert_to_mipav_lut.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import numpy as np
+
+colormap_filename = 'colors.npy'
+labels_filename = 'IDs.npy'
+lut_filename = 'colors.lut'
+
+labels = np.load(labels_filename)
+colors = np.load(colormap_filename)
+colors = colors * 255
+
+contents = list()
+contents.append('<LUT>')
+contents.append('256\t# Size of LUT Arrays')
+
+for i in range(256):
+    if i in labels:
+        idx = np.where(labels == i)
+        c = colors[idx].tolist()[0]
+    else:
+        c = [0.0, 0.0, 0.0]
+    c_str = [str(cc) for cc in c]
+    line = '\t'.join([str(i), '1.0', *c_str])
+    contents.append(line)
+
+with open(lut_filename, 'w') as file:
+    file.write('\n'.join(contents))

mindboggle/mio/colors.py

@@ -8,6 +8,8 @@
 Copyright 2016,  Mindboggle team (http://mindboggle.info), Apache v2.0 License
 
 """
+import sys
+sys.path.append('/Users/shuo/Code/git_repo/mindboggle')
 
 
 def distinguishable_colors(ncolors, backgrounds=[[0,0,0],[1,1,1]],
@@ -502,11 +504,11 @@ def group_colors(colormap, colormap_name, description='', adjacency_matrix=[],
     nlabels = np.shape(colors)[0]
     new_colors = np.copy(colors)
 
-    if not IDs:
+    if len(IDs) == 0:
         IDs = range(nlabels)
-    if not names:
+    if len(names) == 0:
         names = [str(x) for x in range(nlabels)]
-    if not groups:
+    if len(groups) == 0:
         groups = [1 for x in range(nlabels)]
 
     # ------------------------------------------------------------------------
@@ -1188,4 +1190,4 @@ def viridis_colormap():
         [0.983868, 0.904867, 0.136897],
         [0.993248, 0.906157, 0.143936]]
 
-    return viridis
+    return viridis