ENH: Loading images from memmap in viewer slices without the masks.

* The images are being loaded in viewer slices without the masks; * The imagedata with all slices are being loaded too, but not showed * The images are loaded with a hardcoded WL & WW

ENH: Loading images from memmap in viewer slices without the masks.
* The images are being loaded in viewer slices without the masks; * The imagedata with all slices are being loaded too, but not showed * The images are loaded with a hardcoded WL & WW
tfmoraes
1 parent fe94b6bb
Showing 4 changed files with 134 additions and 66 deletions Show diff stats
invesalius/control.py
invesalius/data/imagedata_utils.py
invesalius/data/slice_.py
invesalius/data/viewer_slice.py
@@ -27,6 +27,7 @@ import constants as const
 import data.imagedata_utils as utils
 import data.mask as msk
 import data.measures
+import data.slice_ as sl
 import data.surface as srf
 import data.volume as volume
 import gui.dialogs as dialog
@@ -76,7 +77,6 @@ class Controller():
         ps.Publisher().subscribe(self.OnOpenProject, 'Open project')
         ps.Publisher().subscribe(self.OnOpenRecentProject, 'Open recent project')
         ps.Publisher().subscribe(self.OnShowAnalyzeFile, 'Show analyze dialog')
-        
     def OnCancelImport(self, pubsub_evt):
         #self.cancel_import = True
@@ -466,6 +466,10 @@ class Controller():
             tilt_value = -1*tilt_value
             imagedata = utils.FixGantryTilt(imagedata, tilt_value)
+        self.matrix, self.filename = utils.dcm2memmap(filelist, size)
+        self.Slice = sl.Slice()
+        self.Slice.matrix = self.matrix
+        self.Slice.spacing = xyspacing[0], xyspacing[1], zspacing
         return imagedata, dicom
     def LoadImagedataInfo(self):
@@ -524,7 +528,3 @@ class Controller():
                                   preset_name + '.plist')
         plistlib.writePlist(preset, preset_dir)
-
-
-
-
@@ -478,7 +478,7 @@ def get_numpy_array_type(gdcm_pixel_format):
 def dcm2memmap(files, slice_size):
     """
     From a list of dicom files it creates memmap file in the temp folder and
-    returns.
+    returns it and its related filename.
     """
     temp_file = tempfile.mktemp()
     shape = len(files), slice_size[0], slice_size[1]
@@ -498,3 +498,30 @@ def dcm2memmap(files, slice_size):
         array = numpy.frombuffer(dcm_array, dtype)
         array.shape = slice_size
         matrix[n] = array
+
+    matrix.flush()
+    return matrix, temp_file
+
+def to_vtk(n_array, spacing):
+    dy, dx = n_array.shape
+    n_array.shape = dx * dy
+
+    v_image = numpy_support.numpy_to_vtk(n_array)
+
+    # 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.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
+    image.AllocateScalars()
+    image.GetPointData().SetScalars(v_image)
+    image.Update()
+
+    image_copy = vtk.vtkImageData()
+    image_copy.DeepCopy(image)
+    image_copy.Update()
+
+    return image_copy
@@ -16,6 +16,7 @@
 #    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
 #    detalhes.
 #--------------------------------------------------------------------------
+import numpy
 import vtk
 import wx.lib.pubsub as ps
@@ -38,6 +39,7 @@ class Slice(object):
         self.imagedata = None
         self.current_mask = None
         self.blend_filter = None
+        self.matrix = None
         self.num_gradient = 0
         self.interaction_style = st.StyleStateManager()
@@ -234,6 +236,28 @@ class Slice(object):
     # END PUBSUB_EVT METHODS
     #---------------------------------------------------------------------------
+    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 = self.do_ww_wl(image)
+        return image
+
+    def GetNumberOfSlices(self, orientation):
+        if orientation == 'AXIAL':
+            return self.matrix.shape[0]
+        elif orientation == 'CORONAL':
+            return self.matrix.shape[1]
+        elif orientation == 'SAGITAL':
+            return self.matrix.shape[2]
     def SetMaskColour(self, index, colour, update=True):
         "Set a mask colour given its index and colour (RGB 0-1 values)"
@@ -448,8 +472,6 @@ class Slice(object):
         self.window_level.SetInput(self.imagedata)
     def __create_background(self, imagedata):
-        self.imagedata = imagedata
-
         thresh_min, thresh_max = imagedata.GetScalarRange()
         ps.Publisher().sendMessage('Update threshold limits list', (thresh_min,
                                     thresh_max))
@@ -471,21 +493,21 @@ class Slice(object):
         return img_colours_bg.GetOutput()
     def UpdateWindowLevelBackground(self, pubsub_evt):
+        pass
+        #window, level = pubsub_evt.data
+        #window_level = self.window_level
-        window, level = pubsub_evt.data
-        window_level = self.window_level
-
-        if not((window == window_level.GetWindow()) and\
-                (level == window_level.GetLevel())):
+        #if not((window == window_level.GetWindow()) and\
+                #(level == window_level.GetLevel())):
-            window_level.SetWindow(window)
-            window_level.SetLevel(level)
-            window_level.SetOutputFormatToLuminance()
-            window_level.Update()
+            #window_level.SetWindow(window)
+            #window_level.SetLevel(level)
+            #window_level.SetOutputFormatToLuminance()
+            #window_level.Update()
-            thresh_min, thresh_max = window_level.GetOutput().GetScalarRange()
-            self.lut_bg.SetTableRange(thresh_min, thresh_max)
-            self.img_colours_bg.SetInput(window_level.GetOutput())
+            #thresh_min, thresh_max = window_level.GetOutput().GetScalarRange()
+            #self.lut_bg.SetTableRange(thresh_min, thresh_max)
+            #self.img_colours_bg.SetInput(window_level.GetOutput())
     def UpdateColourTableBackground(self, pubsub_evt):
         values = pubsub_evt.data
@@ -502,15 +524,16 @@ class Slice(object):
     def InputImageWidget(self, pubsub_evt):
-        widget = pubsub_evt.data
+        #widget = pubsub_evt.data
-        flip = vtk.vtkImageFlip()
-        flip.SetInput(self.window_level.GetOutput())
-        flip.SetFilteredAxis(1)
-        flip.FlipAboutOriginOn()
-        flip.Update()
+        #flip = vtk.vtkImageFlip()
+        #flip.SetInput(self.window_level.GetOutput())
+        #flip.SetFilteredAxis(1)
+        #flip.FlipAboutOriginOn()
+        #flip.Update()
-        widget.SetInput(flip.GetOutput())
+        #widget.SetInput(flip.GetOutput())
+        pass
     def CreateMask(self, imagedata=None, name=None, colour=None,
@@ -595,6 +618,16 @@ class Slice(object):
         ps.Publisher().sendMessage('Change mask selected', mask.index)
         ps.Publisher().sendMessage('Update slice viewer')
+    def do_ww_wl(self, image):
+        colorer = vtk.vtkImageMapToWindowLevelColors()
+        colorer.SetInput(image)
+        colorer.SetWindow(255)
+        colorer.SetLevel(127)
+        colorer.SetOutputFormatToRGBA()
+        colorer.Update()
+
+        return colorer.GetOutput()
+
     def __build_mask(self, imagedata, create=True):
         # create new mask instance and insert it into project
         if create:
@@ -88,7 +88,7 @@ class Viewer(wx.Panel):
         self.on_wl = False
         self.on_text = False
         # VTK pipeline and actors
-        #self.__config_interactor()
+        self.__config_interactor()
         self.pick = vtk.vtkPropPicker()
         self.cross_actor = vtk.vtkActor()
@@ -102,7 +102,6 @@ class Viewer(wx.Panel):
         scroll = wx.ScrollBar(self, -1, style=wx.SB_VERTICAL)
         self.scroll = scroll
-
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         sizer.Add(interactor, 1, wx.EXPAND|wx.GROW)
@@ -164,10 +163,11 @@ class Viewer(wx.Panel):
         self.SetLayout(layout)
     def __config_interactor(self):
-
         ren = vtk.vtkRenderer()
+        style = vtk.vtkInteractorStyleImage()
         interactor = self.interactor
+        interactor.SetInteractorStyle(style)
         interactor.GetRenderWindow().AddRenderer(ren)
         self.cam = ren.GetActiveCamera()
@@ -1056,48 +1056,50 @@ class Viewer(wx.Panel):
         return cursor
     def SetInput(self, imagedata, mask_dict):
-        self.imagedata = imagedata
+        pass
+        #self.imagedata = imagedata
-        #ren = self.ren
-        interactor = self.interactor
+        ##ren = self.ren
+        #interactor = self.interactor
-        # Slice pipeline, to be inserted into current viewer
-        slice_ = sl.Slice()
-        if slice_.imagedata is None:
-            slice_.SetInput(imagedata, mask_dict)
+        ## Slice pipeline, to be inserted into current viewer
+        #slice_ = sl.Slice()
+        #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()
+        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 = ren
-        self.cam = ren.GetActiveCamera()
+        self.ren.AddActor(self.actor)
+        #self.cam = ren.GetActiveCamera()
-        for slice_data in self.slice_data_list:
-            self.__update_camera(slice_data)
-            self.Reposition(slice_data)
+        #for slice_data in self.slice_data_list:
+            #self.__update_camera(slice_data)
+            #self.Reposition(slice_data)
-        number_of_slices = self.layout[0] * self.layout[1]
-        max_slice_number = actor.GetSliceNumberMax() + 1/ \
-                number_of_slices
+        #number_of_slices = self.layout[0] * self.layout[1]
+        #max_slice_number = actor.GetSliceNumberMax() + 1/ \
+                #number_of_slices
-        if actor.GetSliceNumberMax() % number_of_slices:
-            max_slice_number += 1
+        #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)
+        #self.set_scroll_position(0)
-        actor_bound = actor.GetBounds()
+        #actor_bound = actor.GetBounds()
-        self.EnableText()
-        # Insert cursor
-        self.SetInteractorStyle(const.STATE_DEFAULT)
+        #self.EnableText()
+        ## Insert cursor
+        #self.SetInteractorStyle(const.STATE_DEFAULT)
-        self.__build_cross_lines()
+        #self.__build_cross_lines()
     def __build_cross_lines(self):
         actor = self.slice_data_list[0].actor
@@ -1339,15 +1341,21 @@ class Viewer(wx.Panel):
     def OnScrollBar(self, evt=None):
         pos = self.scroll.GetThumbPosition()
-        self.set_slice_number(pos)
-        #self.UpdateSlice3D(pos)
-        self.pos = pos
+        slice_ = sl.Slice()
+        image = slice_.GetSlices(self.orientation, pos)
+        self.actor.SetInput(image)
+        self.ren.ResetCamera()
         self.interactor.Render()
-        if evt:
-            evt.Skip()
+        print "slice", pos
+        #self.set_slice_number(pos)
+        ##self.UpdateSlice3D(pos)
+        #self.pos = pos
+        #self.interactor.Render()
+        #if evt:
+            #evt.Skip()
     def OnScrollBarRelease(self, evt):
-        self.UpdateSlice3D(self.pos)
+        #self.UpdateSlice3D(self.pos)
         evt.Skip()
     def OnKeyDown(self, evt=None, obj=None):
	@@ -478,7 +478,7 @@ def get_numpy_array_type(gdcm_pixel_format):		@@ -478,7 +478,7 @@ def get_numpy_array_type(gdcm_pixel_format):
478	def dcm2memmap(files, slice_size):	478	def dcm2memmap(files, slice_size):
479	"""	479	"""
480	From a list of dicom files it creates memmap file in the temp folder and	480	From a list of dicom files it creates memmap file in the temp folder and
481	- returns.	481	+ returns it and its related filename.
482	"""	482	"""
483	temp_file = tempfile.mktemp()	483	temp_file = tempfile.mktemp()
484	shape = len(files), slice_size[0], slice_size[1]	484	shape = len(files), slice_size[0], slice_size[1]
	@@ -498,3 +498,30 @@ def dcm2memmap(files, slice_size):		@@ -498,3 +498,30 @@ def dcm2memmap(files, slice_size):
498	array = numpy.frombuffer(dcm_array, dtype)	498	array = numpy.frombuffer(dcm_array, dtype)
499	array.shape = slice_size	499	array.shape = slice_size
500	matrix[n] = array	500	matrix[n] = array
		501	+
		502	+ matrix.flush()
		503	+ return matrix, temp_file
		504	+
		505	+def to_vtk(n_array, spacing):
		506	+ dy, dx = n_array.shape
		507	+ n_array.shape = dx * dy
		508	+
		509	+ v_image = numpy_support.numpy_to_vtk(n_array)
		510	+
		511	+ # Generating the vtkImageData
		512	+ image = vtk.vtkImageData()
		513	+ image.SetDimensions(dx, dy, 1)
		514	+ image.SetOrigin(0, 0, 0)
		515	+ image.SetSpacing(spacing)
		516	+ image.SetNumberOfScalarComponents(1)
		517	+ image.SetExtent(0, dx -1, 0, dy -1, 0, 0)
		518	+ image.SetScalarType(numpy_support.get_vtk_array_type(n_array.dtype))
		519	+ image.AllocateScalars()
		520	+ image.GetPointData().SetScalars(v_image)
		521	+ image.Update()
		522	+
		523	+ image_copy = vtk.vtkImageData()
		524	+ image_copy.DeepCopy(image)
		525	+ image_copy.Update()
		526	+
		527	+ return image_copy