From 0472084d41b97b131211bd725a65cd3df8818e1d Mon Sep 17 00:00:00 2001
From: Thiago Franco de Moraes <totonixsame@gmail.com>
Date: Tue, 18 Aug 2015 15:21:22 -0300
Subject: [PATCH] User can use the whitaker smoothing

---
 invesalius/data/surface.py         | 23 ++++++++++++++++++++---
 invesalius/data/surface_process.py |  5 ++++-
 invesalius/gui/dialogs.py          |  3 ++-
 3 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/invesalius/data/surface.py b/invesalius/data/surface.py
index 68ac6ca..272720e 100644
--- a/invesalius/data/surface.py
+++ b/invesalius/data/surface.py
@@ -24,6 +24,7 @@ import random
 import tempfile
 import weakref
 
+import numpy as np
 import vtk
 import wx
 from wx.lib.pubsub import pub as Publisher
@@ -37,6 +38,8 @@ import surface_process
 import utils as utl
 import vtk_utils as vu
 
+from data import smooth_cy
+
 try:
     import ca_smoothing
 except ImportError:
@@ -465,13 +468,27 @@ class SurfaceManager():
         q_in = multiprocessing.Queue()
         q_out = multiprocessing.Queue()
 
+        if algorithm == 'Whitaker':
+            iteractions = 10
+            bsize = 4
+            mask_tfile = tempfile.mktemp()
+            mmask = np.memmap(mask_tfile, shape=mask.matrix.shape, dtype='float64', mode='w+')
+            smooth_cy.smooth(mask.matrix, iteractions, bsize, mmask)
+            mmask[0, :, :] = -1
+            mmask[:, 0, :] = -1
+            mmask[:, :, 0] = -1
+
+        else:
+            mask_tfile = mask.temp_file
+            mmask = mask.matrix
+
         p = []
         for i in xrange(n_processors):
             sp = surface_process.SurfaceProcess(pipe_in, filename_img,
                                                 matrix.shape, matrix.dtype,
-                                                mask.temp_file,
-                                                mask.matrix.shape,
-                                                mask.matrix.dtype,
+                                                mask_tfile,
+                                                mmask.shape,
+                                                mmask.dtype,
                                                 spacing,
                                                 mode, min_value, max_value,
                                                 decimate_reduction,
diff --git a/invesalius/data/surface_process.py b/invesalius/data/surface_process.py
index 63a1378..7df5e51 100644
--- a/invesalius/data/surface_process.py
+++ b/invesalius/data/surface_process.py
@@ -151,7 +151,10 @@ class SurfaceProcess(multiprocessing.Process):
         contour.SetInputData(image)
         #contour.SetInput(flip.GetOutput())
         if self.from_binary:
-            contour.SetValue(0, 127) # initial threshold
+            if self.algorithm == 'Whitaker':
+                contour.SetValue(0, 0.0) # initial threshold
+            else:
+                contour.SetValue(0, 127) # initial threshold
         else:
             contour.SetValue(0, self.min_value) # initial threshold
             contour.SetValue(1, self.max_value) # final threshold
diff --git a/invesalius/gui/dialogs.py b/invesalius/gui/dialogs.py
index 0be6b39..7b0178d 100644
--- a/invesalius/gui/dialogs.py
+++ b/invesalius/gui/dialogs.py
@@ -1307,7 +1307,8 @@ class SurfaceMethodPanel(wx.Panel):
         self.mask_edited = mask_edited
         self.alg_types = {_(u'Default'): 'Default',
                           _(u'Context aware smoothing'): 'ca_smoothing',
-                          _(u'Binary'): 'Binary'}
+                          _(u'Binary'): 'Binary',
+                          _(u'Reducing Aliasing'): 'Whitaker'}
         self.edited_imp = [_(u'Default'), ]
 
         self._build_widgets()
--
libgit2 0.21.2