From a84bfc2023ffaaa389d599e862112e8e9c80b084 Mon Sep 17 00:00:00 2001
From: paulojamorim <paulojamorim@gmail.com>
Date: Fri, 14 May 2010 18:16:10 +0000
Subject: [PATCH] FIX: Inverted 3D from Coronal Slice (#240)

---
 invesalius/data/surface.py         |  9 +++++++--
 invesalius/data/surface_process.py | 26 ++++++++++++++++----------
 invesalius/data/volume.py          | 33 ++++++++++++++++++++-------------
 3 files changed, 43 insertions(+), 25 deletions(-)

diff --git a/invesalius/data/surface.py b/invesalius/data/surface.py
index cb3265e..17fb481 100644
--- a/invesalius/data/surface.py
+++ b/invesalius/data/surface.py
@@ -431,11 +431,16 @@ class SurfaceManager():
         writer.Write()
 
         language = ses.Session().language
-
+        
+        if (prj.Project().original_orientation == const.AXIAL):
+            flip_image = True
+        else:
+            flip_image = False
+            
         pipe_in, pipe_out = multiprocessing.Pipe()
         sp = surface_process.SurfaceProcess(pipe_in, filename_img, mode, min_value, max_value,
                  decimate_reduction, smooth_relaxation_factor,
-                 smooth_iterations, language, fill_holes, keep_largest)
+                 smooth_iterations, language, fill_holes, keep_largest, flip_image)
         sp.start()
 
         while 1:
diff --git a/invesalius/data/surface_process.py b/invesalius/data/surface_process.py
index bb5c8c4..1c0d31a 100644
--- a/invesalius/data/surface_process.py
+++ b/invesalius/data/surface_process.py
@@ -8,7 +8,8 @@ class SurfaceProcess(multiprocessing.Process):
 
     def __init__(self, pipe, filename, mode, min_value, max_value,
                  decimate_reduction, smooth_relaxation_factor,
-                 smooth_iterations, language,  fill_holes, keep_largest):
+                 smooth_iterations, language,  fill_holes, keep_largest, 
+                 flip_image):
 
         multiprocessing.Process.__init__(self)
         self.pipe = pipe
@@ -22,6 +23,7 @@ class SurfaceProcess(multiprocessing.Process):
         self.language = language
         self.fill_holes = fill_holes
         self.keep_largest = keep_largest
+        self.flip_image = flip_image
 
 
     def run(self):
@@ -37,17 +39,21 @@ class SurfaceProcess(multiprocessing.Process):
         reader = vtk.vtkXMLImageDataReader()
         reader.SetFileName(self.filename)
         reader.Update()
-
-        # Flip original vtkImageData
-        flip = vtk.vtkImageFlip()
-        flip.SetInput(reader.GetOutput())
-        flip.SetFilteredAxis(1)
-        flip.FlipAboutOriginOn()
-
+        
+        image = reader.GetOutput()
+        
+        if (self.flip_image):
+            # Flip original vtkImageData
+            flip = vtk.vtkImageFlip()
+            flip.SetInput(reader.GetOutput())
+            flip.SetFilteredAxis(1)
+            flip.FlipAboutOriginOn()
+            image = flip.GetOutput()
+            
         # Create vtkPolyData from vtkImageData
         if self.mode == "CONTOUR":
             contour = vtk.vtkContourFilter()
-            contour.SetInput(flip.GetOutput())
+            contour.SetInput(image)
             contour.SetValue(0, self.min_value) # initial threshold
             contour.SetValue(1, self.max_value) # final threshold
             contour.GetOutput().ReleaseDataFlagOn()
@@ -56,7 +62,7 @@ class SurfaceProcess(multiprocessing.Process):
             polydata = contour.GetOutput()
         else: #mode == "GRAYSCALE":
             mcubes = vtk.vtkMarchingCubes()
-            mcubes.SetInput(flip.GetOutput())
+            mcubes.SetInput(image)
             mcubes.SetValue(0, 255)
             mcubes.ComputeScalarsOn()
             mcubes.ComputeGradientsOn()
diff --git a/invesalius/data/volume.py b/invesalius/data/volume.py
index 9263f25..0aa369a 100755
--- a/invesalius/data/volume.py
+++ b/invesalius/data/volume.py
@@ -450,19 +450,26 @@ class Volume():
         image = proj.imagedata
 
         number_filters = len(self.config['convolutionFilters'])
-        update_progress= vtk_utils.ShowProgress(2 + number_filters)
-
-        # Flip original vtkImageData
-        flip = vtk.vtkImageFlip()
-        flip.SetInput(image)
-        flip.SetFilteredAxis(1)
-        flip.FlipAboutOriginOn()
-        flip.AddObserver("ProgressEvent", lambda obj,evt:
-                            update_progress(flip, "Rendering..."))
-        flip.Update()
-
-        image = flip.GetOutput()
-
+        
+        if (prj.Project().original_orientation == const.AXIAL):
+            flip_image = True
+        else:
+            flip_image = False
+        
+        if (flip_image):    
+            update_progress= vtk_utils.ShowProgress(2 + number_filters) 
+            # Flip original vtkImageData
+            flip = vtk.vtkImageFlip()
+            flip.SetInput(image)
+            flip.SetFilteredAxis(1)
+            flip.FlipAboutOriginOn()
+            flip.AddObserver("ProgressEvent", lambda obj,evt:
+                                update_progress(flip, "Rendering..."))
+            flip.Update()
+            image = flip.GetOutput()
+        else:
+            update_progress= vtk_utils.ShowProgress(1 + number_filters)
+        
         scale = image.GetScalarRange()
         self.scale = scale
 
--
libgit2 0.21.2