ENH: Handle sagittal and coronal images.

* Handling sagittal and coronal (not tested) images. Sagittal and coronal images are stored in memmap matrix as axial doing insertion acording to orientation; * Axial, sagittal and coronal are showed in its correspondent plane.

ENH: Handle sagittal and coronal images.
* Handling sagittal and coronal (not tested) images. Sagittal and coronal images are stored in memmap matrix as axial doing insertion acording to orientation; * Axial, sagittal and coronal are showed in its correspondent plane.
tfmoraes
1 parent ff5ac193
Showing 4 changed files with 91 additions and 113 deletions Show diff stats
invesalius/control.py
invesalius/data/imagedata_utils.py
invesalius/data/slice_.py
invesalius/data/viewer_slice.py
@@ -357,7 +357,7 @@ class Controller():
         ps.Publisher().sendMessage('Load slice to viewer',
                         (proj.imagedata,
                         proj.mask_dict))
-        ps.Publisher().sendMessage('Load slice plane')
+        #ps.Publisher().sendMessage('Load slice plane')
         ps.Publisher().sendMessage('Bright and contrast adjustment image',\
                                    (proj.window, proj.level))
         ps.Publisher().sendMessage('Update window level value',\
@@ -409,7 +409,7 @@ class Controller():
                     name_to_const[dicom.image.orientation_label]
         proj.window = float(dicom.image.window)
         proj.level = float(dicom.image.level)
-        proj.threshold_range = imagedata.GetScalarRange()
+        proj.threshold_range = (-1024, 3033)
         ######
@@ -445,14 +445,17 @@ class Controller():
         bits = dicom.image.bits_allocad
         sop_class_uid = dicom.acquisition.sop_class_uid
         xyspacing = dicom.image.spacing
+        orientation = dicom.image.orientation_label
         if sop_class_uid == '1.2.840.10008.5.1.4.1.1.7': #Secondary Capture Image Storage
             use_dcmspacing = 1
         else:
             use_dcmspacing = 0
-        imagedata = utils.CreateImageData(filelist, zspacing, xyspacing,size,
-                                          bits, use_dcmspacing)
+        #imagedata = utils.CreateImageData(filelist, zspacing, xyspacing,size,
+                                          #bits, use_dcmspacing)
+
+        imagedata = None
         # 1(a): Fix gantry tilt, if any
         tilt_value = dicom.acquisition.tilt
@@ -466,10 +469,23 @@ class Controller():
             tilt_value = -1*tilt_value
             imagedata = utils.FixGantryTilt(imagedata, tilt_value)
-        self.matrix, self.filename = utils.dcm2memmap(filelist, size)
+        wl = float(dicom.image.level)
+        ww = float(dicom.image.window)
+
+        self.matrix, self.filename = utils.dcm2memmap(filelist, size,
+                                                      orientation)
         self.Slice = sl.Slice()
         self.Slice.matrix = self.matrix
-        self.Slice.spacing = xyspacing[0], xyspacing[1], zspacing
+
+        if orientation == 'AXIAL':
+            self.Slice.spacing = xyspacing[0], xyspacing[1], zspacing
+        elif orientation == 'CORONAL':
+            self.Slice.spacing = xyspacing[0], zspacing, xyspacing[1]
+        elif orientation == 'SAGITTAL':
+            self.Slice.spacing = zspacing, xyspacing[1], xyspacing[0]
+
+        self.Slice.window_level = wl
+        self.Slice.window_width = ww
         return imagedata, dicom
     def LoadImagedataInfo(self):
@@ -456,13 +456,19 @@ class ImageCreator:
         return imagedata
-def dcm2memmap(files, slice_size):
+def dcm2memmap(files, slice_size, orientation):
     """
     From a list of dicom files it creates memmap file in the temp folder and
     returns it and its related filename.
     """
     temp_file = tempfile.mktemp()
-    shape = len(files), slice_size[1], slice_size[0]
+
+    if orientation == 'SAGITTAL':
+        shape = slice_size[0], slice_size[1], len(files)
+    elif orientation == 'CORONAL':
+        shape = slice_size[1], len(files), slice_size[0]
+    else:
+        shape = len(files), slice_size[1], slice_size[0]
     matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape)
     dcm_reader = vtkgdcm.vtkGDCMImageReader()
@@ -471,25 +477,43 @@ def dcm2memmap(files, slice_size):
         dcm_reader.Update()
         image = dcm_reader.GetOutput()
         array = numpy_support.vtk_to_numpy(image.GetPointData().GetScalars())
-        array.shape = matrix.shape[1], matrix.shape[2]
-        matrix[n] = array
+        if orientation == 'CORONAL':
+            array.shape = matrix.shape[0], matrix.shape[2]
+            matrix[:, n, :] = array
+        elif orientation == 'SAGITTAL':
+            array.shape = matrix.shape[0], matrix.shape[1]
+            matrix[:, :, n] = array
+        else:
+            array.shape = matrix.shape[1], matrix.shape[2]
+            matrix[n] = array
     matrix.flush()
     return matrix, temp_file
-def to_vtk(n_array, spacing):
+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)
+    print orientation
+    if orientation == 'AXIAL':
+        dz = 1
+        extent = (0, dx -1, 0, dy -1, slice_number, slice_number)
+    elif orientation == 'SAGITAL':
+        dx, dy, dz = 1, dx, dy
+        extent = (slice_number, slice_number, 0, dy - 1, 0, dz - 1)
+    elif orientation == 'CORONAL':
+        dx, dy, dz = dx, 1, dy
+        extent = (0, dx - 1, slice_number, slice_number, 0, dz - 1)
+
     # Generating the vtkImageData
     image = vtk.vtkImageData()
-    image.SetDimensions(dx, dy, 1)
     image.SetOrigin(0, 0, 0)
     image.SetSpacing(spacing)
     image.SetNumberOfScalarComponents(1)
-    image.SetExtent(0, dx -1, 0, dy -1, 0, 0)
+    image.SetDimensions(dx, dy, dz)
+    image.SetExtent(extent)
     image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
     image.AllocateScalars()
     image.GetPointData().SetScalars(v_image)
@@ -239,15 +239,11 @@ class Slice(object):
     def GetSlices(self, orientation, slice_number):
         if orientation == 'AXIAL':
             n_array = numpy.array(self.matrix[slice_number])
-            spacing = self.spacing
         elif orientation == 'CORONAL':
             n_array = numpy.array(self.matrix[..., slice_number, ...])
-            spacing = self.spacing[0], self.spacing[2], self.spacing[1]
         elif orientation == 'SAGITAL':
             n_array = numpy.array(self.matrix[..., ..., slice_number])
-            spacing = self.spacing[1], self.spacing[2], self.spacing[0]
-
-        image = iu.to_vtk(n_array, spacing)
+        image = iu.to_vtk(n_array, self.spacing, slice_number, orientation)
         image = self.do_ww_wl(image)
         return image
@@ -619,11 +615,13 @@ class Slice(object):
         ps.Publisher().sendMessage('Update slice viewer')
     def do_ww_wl(self, image):
+        print self.window_width, self.window_level
+        print image.GetScalarRange()
         colorer = vtk.vtkImageMapToWindowLevelColors()
         colorer.SetInput(image)
-        colorer.SetWindow(255)
-        colorer.SetLevel(127)
-        colorer.SetOutputFormatToRGBA()
+        colorer.SetWindow(self.window_width)
+        colorer.SetLevel(self.window_level)
+        colorer.SetOutputFormatToRGB()
         colorer.Update()
         return colorer.GetOutput()
@@ -173,7 +173,6 @@ class Viewer(wx.Panel):
         self.cam = ren.GetActiveCamera()
         self.ren = ren
-
     def SetInteractorStyle(self, state):
         self.state = state
         action = {const.SLICE_STATE_CROSS: 
@@ -1056,26 +1055,26 @@ class Viewer(wx.Panel):
         return cursor
     def SetInput(self, imagedata, mask_dict):
-        pass
-        #self.imagedata = imagedata
+        self.slice_ = sl.Slice()
-        ##ren = self.ren
-        #interactor = self.interactor
+        max_slice_number = sl.Slice().GetNumberOfSlices(self.orientation)
+        self.scroll.SetScrollbar(wx.SB_VERTICAL, 1, max_slice_number,
+                                 max_slice_number)
-        ## Slice pipeline, to be inserted into current viewer
-        #slice_ = sl.Slice()
+        self.actor = vtk.vtkImageActor()
+        self.ren.AddActor(self.actor)
+        self.set_slice_number(0)
+        self.__update_camera()
+        self.ren.ResetCamera()
         #if slice_.imagedata is None:
             #slice_.SetInput(imagedata, mask_dict)
-        actor = vtk.vtkImageActor()
         ##actor.SetInput(slice_.GetOutput())
         #self.LoadRenderers(slice_.GetOutput())
         #self.__configure_renderers()
         #ren = self.slice_data_list[0].renderer
         #actor = self.slice_data_list[0].actor
         #actor_bound = actor.GetBounds()
-        self.actor = actor
-        self.ren.AddActor(self.actor)
         #self.cam = ren.GetActiveCamera()
         #for slice_data in self.slice_data_list:
@@ -1088,12 +1087,10 @@ class Viewer(wx.Panel):
         #if actor.GetSliceNumberMax() % number_of_slices:
             #max_slice_number += 1
-        max_slice_number = sl.Slice().GetNumberOfSlices(self.orientation)
-        self.scroll.SetScrollbar(wx.SB_VERTICAL, 1, max_slice_number,
-                                                     max_slice_number)
         #self.set_scroll_position(0)
         #actor_bound = actor.GetBounds()
+        self.interactor.Render()
         #self.EnableText()
         ## Insert cursor
@@ -1268,43 +1265,23 @@ class Viewer(wx.Panel):
         renderer.AddViewProp(slice_data.box_actor)
         return slice_data
-    def __update_camera(self, slice_data):
+    def __update_camera(self):
         orientation = self.orientation
         proj = project.Project()
-        orig_orien = proj.original_orientation
+        orig_orien = 1 #proj.original_orientation
-        cam = slice_data.renderer.GetActiveCamera()
-        cam.SetFocalPoint(0, 0, 0)
-        cam.SetViewUp(const.SLICE_POSITION[orig_orien][0][self.orientation])
-        cam.SetPosition(const.SLICE_POSITION[orig_orien][1][self.orientation])
-        cam.ComputeViewPlaneNormal()
-        cam.OrthogonalizeViewUp()
-        cam.ParallelProjectionOn()
-
-        self.__update_display_extent(slice_data)
+        self.cam.SetFocalPoint(0, 0, 0)
+        self.cam.SetViewUp(const.SLICE_POSITION[orig_orien][0][self.orientation])
+        self.cam.SetPosition(const.SLICE_POSITION[orig_orien][1][self.orientation])
+        self.cam.ComputeViewPlaneNormal()
+        self.cam.OrthogonalizeViewUp()
+        self.cam.ParallelProjectionOn()
-        slice_data.renderer.ResetCamera()
         #slice_data.renderer.Render()
-    def __update_display_extent(self, slice_data):
-        e = self.imagedata.GetWholeExtent()
-        proj = project.Project()
-
-        pos = slice_data.number
-
-        x = (pos, pos, e[2], e[3], e[4], e[5])
-        y = (e[0], e[1], pos, pos, e[4], e[5])
-        z = (e[0], e[1], e[2], e[3], pos, pos)
-
-        if (proj.original_orientation == const.AXIAL):
-            new_extent = {"SAGITAL": x, "CORONAL": y, "AXIAL": z}
-        elif(proj.original_orientation == const.SAGITAL):
-            new_extent = {"SAGITAL": z,"CORONAL": x,"AXIAL": y}
-        elif(proj.original_orientation == const.CORONAL):
-            new_extent = {"SAGITAL": x,"CORONAL": z,"AXIAL": y}
-
-        slice_data.actor.SetDisplayExtent(new_extent[self.orientation])
-        slice_data.renderer.ResetCameraClippingRange()
+    def __update_display_extent(self, image):
+        self.actor.SetDisplayExtent(image.GetExtent())
+        self.ren.ResetCameraClippingRange()
     def UpdateRender(self, evt):
         self.interactor.Render()
@@ -1341,18 +1318,10 @@ class Viewer(wx.Panel):
     def OnScrollBar(self, evt=None):
         pos = self.scroll.GetThumbPosition()
-        slice_ = sl.Slice()
-        image = slice_.GetSlices(self.orientation, pos)
-        self.actor.SetInput(image)
-        self.ren.ResetCamera()
+        self.set_slice_number(pos)
         self.interactor.Render()
-        print "slice", pos
-        #self.set_slice_number(pos)
-        ##self.UpdateSlice3D(pos)
-        #self.pos = pos
-        #self.interactor.Render()
-        #if evt:
-            #evt.Skip()
+        if evt:
+            evt.Skip()
     def OnScrollBarRelease(self, evt):
         #self.UpdateSlice3D(self.pos)
@@ -1409,43 +1378,14 @@ class Viewer(wx.Panel):
         evt.Skip()
     def set_slice_number(self, index):
-        self.slice_number = index
-        # for m in self.actors_by_slice_number.values():
-            # for actor in m:
-                # actor.SetVisibility(0) 
-        # Removing actor from the previous renderers/slice.
-        for n in self.renderers_by_slice_number:
-            renderer = self.renderers_by_slice_number[n]
-            for actor in self.actors_by_slice_number.get(n, []):
-                renderer.RemoveActor(actor)
-
-        self.renderers_by_slice_number = {}
-
-        for n, slice_data in enumerate(self.slice_data_list):
-            ren = slice_data.renderer
-            actor = slice_data.actor
-            pos = self.layout[0] * self.layout[1] * index + n
-            max = actor.GetSliceNumberMax() + 1
-            if pos < max:
-                self.renderers_by_slice_number[pos] = ren
-                for m_actor in self.actors_by_slice_number.get(pos, []):
-                    ren.AddActor(m_actor)
-                slice_data.SetNumber(pos)
-                # for actor in self.actors_by_slice_number.get(pos, []):
-                    # actor.SetVisibility(1)
-                self.__update_display_extent(slice_data)
-                slice_data.Show()
-            else:
-                slice_data.Hide()
-
-            position = {"SAGITAL": {0: slice_data.number},
-                        "CORONAL": {1: slice_data.number},
-                        "AXIAL": {2: slice_data.number}}
-
-            #if 'DEFAULT' in self.modes:
-            #    ps.Publisher().sendMessage(
-            #        'Update cursor single position in slice',
-            #        position[self.orientation])
+        image = self.slice_.GetSlices(self.orientation, index)
+        self.actor.SetInput(image)
+        self.__update_display_extent(image)
+        print "slice", index
+        print "display extent", self.actor.GetDisplayExtent()
+        print "whole extent", image.GetWholeExtent()
+        print "boundsa", self.actor.GetBounds()
+        print "camera", self.cam.GetPosition(), self.cam.GetFocalPoint()
     def ChangeSliceNumber(self, pubsub_evt):
         index = pubsub_evt.data