From 58534ceb1e1f48178a6c81de4d6a3021ed9122c6 Mon Sep 17 00:00:00 2001
From: tfmoraes <totonixsame@gmail.com>
Date: Thu, 21 Oct 2010 13:21:37 +0000
Subject: [PATCH] ENH: Ported analyze reader to new way to handle slices (using memmap).

---
 invesalius/control.py               | 21 ++++++++++++++++++---
 invesalius/data/imagedata_utils.py  |  3 +--
 invesalius/reader/analyze_reader.py | 37 +++----------------------------------
 3 files changed, 22 insertions(+), 39 deletions(-)

diff --git a/invesalius/control.py b/invesalius/control.py
index 3e4f194..92dbc06 100755
--- a/invesalius/control.py
+++ b/invesalius/control.py
@@ -383,16 +383,31 @@ class Controller():
         ps.Publisher().sendMessage('End busy cursor')
 
     def CreateAnalyzeProject(self, imagedata):
+        header = imagedata.get_header()
         proj = prj.Project()
         proj.name = _("Untitled")
         proj.SetAcquisitionModality("MRI")
-        proj.imagedata = imagedata
         #TODO: Verify if all Analyse are in AXIAL orientation
-        proj.original_orientation =  const.AXIAL
-        proj.threshold_range = imagedata.GetScalarRange()
+
+        if not header['orient']:
+            proj.original_orientation =  const.AXIAL
+        elif header['orient'] == 1:
+            proj.original_orientation = const.CORONAL
+        elif header['orient'] == 2:
+            proj.original_orientation = const.SAGITAL
+
+        proj.threshold_range = (header['glmin'],
+                                header['glmax'])
         proj.window = proj.threshold_range[1] - proj.threshold_range[0]
         proj.level =  (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
 
+        self.Slice = sl.Slice()
+        self.Slice.matrix = imagedata.get_data().swapaxes(0, 2)
+
+        self.Slice.window_level = proj.level
+        self.Slice.window_width = proj.window
+        self.Slice.spacing = header.get_zooms()[:3]
+
 
     def CreateDicomProject(self, imagedata, dicom):
         name_to_const = {"AXIAL":const.AXIAL,
diff --git a/invesalius/data/imagedata_utils.py b/invesalius/data/imagedata_utils.py
index c7a9190..aff6255 100644
--- a/invesalius/data/imagedata_utils.py
+++ b/invesalius/data/imagedata_utils.py
@@ -492,9 +492,8 @@ def dcm2memmap(files, slice_size, orientation):
 
 def to_vtk(n_array, spacing, slice_number, orientation):
     dy, dx = n_array.shape
-    n_array.shape = dx * dy
 
-    v_image = numpy_support.numpy_to_vtk(n_array)
+    v_image = numpy_support.numpy_to_vtk(n_array.flat)
 
     print orientation
     if orientation == 'AXIAL':
diff --git a/invesalius/reader/analyze_reader.py b/invesalius/reader/analyze_reader.py
index 2c91b74..d134904 100644
--- a/invesalius/reader/analyze_reader.py
+++ b/invesalius/reader/analyze_reader.py
@@ -23,43 +23,12 @@ import tempfile
 
 import vtk
 
-from nibabel import AnalyzeHeader
+from nibabel import AnalyzeImage, squeeze_image
 
 def ReadAnalyze(filename):
-    print "Reading analyze file:", filename
+    anlz = squeeze_image(AnalyzeImage.from_filename(filename))
+    return anlz
 
-    # Reading info from analyze header
-    header_file = open(filename)
-    header = AnalyzeHeader.from_fileobj(header_file)
-    xf, yf, zf = header.get_data_shape()[:3]
-    data_type = header.get_data_dtype().name
-    pixel_spacing = header.get_zooms()[:3]
-
-    # Mapping from numpy type to vtk type.
-    anlz_2_vtk_type = {
-                       'int16': 'SetDataScalarTypeToShort',
-                       'uint16': 'SetDataScalarTypeToUnsignedShort',
-                       'float32': 'SetDataScalarTypeToFloat'
-                      }
-
-    print header
-
-    reader = vtk.vtkImageReader()
-    reader.SetFileName(filename[:-3] + 'img')
-
-    # Setting the endiannes based on the analyze header.
-    if header.endianness == '<':
-        reader.SetDataByteOrderToLittleEndian()
-    elif header.endianness == '>':
-        reader.SetDataByteOrderToBigEndian()
-
-    reader.SetFileDimensionality(3)
-    reader.SetDataExtent(0, xf-1, 0, yf-1, 0, zf-1)
-    reader.SetDataSpacing(pixel_spacing)
-    reader.SetHeaderSize(0)
-    # reader.SetTransform(transform)
-    getattr(reader, anlz_2_vtk_type[data_type])()
-    reader.Update()
 
     return reader.GetOutput()
 
--
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