Added more colorschemes and a new GUI to create more colorschemes.

- Added support to colorschemes from OsiriX.
- Created a new GUI to create colorschemes
  - This GUI generates the event EVT_CLUT_NODE_CHANGED when the user
    changes the position and colours of the nodes.
  - This GUI has style setted to FRAME_FLOAT_ON_PARENT, to make this GUI
    stay always on top of invesalius GUI.
- Added pubsub event "Update window level text" to change WW&WL text

Added (but not integrated) the clut_imagedata widget

Remove unused imports from clut_imagedata

The ClutImagedata is changing the slice lookuptable

Showing the histogram at the clut widget

Using checkbox instead of radiobutton to color menu

Applying ww & wl changes to the color table generated by clut_imagedata

Window&level affects clut colors

Window&level affects clut colors

Removed non-color presets from color preset dir

Hidding clutimagedatadialog when user selects another color preset

Removed idiot print

Keeping nodes after closing clutimagedata

Not passing ww&wl to clutimagedata anymore

Generating EVT_CLUT_POINT_MOVE when the clutimagedata is shown

Since EVT_SHOW binded to a wx.Panel is not working with 2.8, I'm binding
the OnShow method to EVT_IDLE and unbinding after the first time this
event is generated.

Using keyboard left and right to change nodes

Enter give the user option to change node colour

(shift +) Tab selects the next (previous) node

Improvements on the drawing of clut_imagedata

ClutImagedataDialog is dealing with clut_imagedata events

Added properties in clut_imagedata to get the ww&wl

Added a pubsub method to update the ww&wl text

WW&WL interactor style affects clut_imagedata widget

Style: the position of window_level and window_width

Delete key deletes a node

Cleaning and closing clut_imagedata dialog when a project is closed

Refreshing clut_imagedata after user change node color

Clut_imagedata dialog setted style to STAY_ON_TOP

Change clut_imagedata dialog style from wx.STAY_ON_TOP to wx.FRAME_FLOAT_ON_PARENT

Cleaning code related to clut_imagedata dialog in viewer_slice

Cleaning code related to clut_imagedata dialog in viewer_slice

EVT_CLUT_POINT_MOVE renamed to EVT_CLUT_NODE_CHANGED

Generating event when user selects custom color scheme

Removed OnShow method from clut_imagedata

Remove useless prints

Reseting things when closing a project

.gitignore

@@ -14,3 +14,9 @@ invesalius/gui/widgets/*.log
 invesalius/gui/widgets/*.pyc
 invesalius/reader/*.log
 invesalius/reader/*.pyc
+
+*.pyc
+*.swp
+*.so
+tags
+*.c

invesalius/constants.py

@@ -297,7 +297,7 @@
 REDUCE_IMAGEDATA_QUALITY = 0
 
 ICON_DIR = os.path.abspath(os.path.join('..', 'icons'))
-SAMPLE_DIR = os.path.abspath(os.path.join('..', 'samples'))
+SAMPLE_DIR = "/usr/share/doc/invesalius-examples/examples/"
 DOC_DIR = os.path.abspath(os.path.join('..', 'docs'))
 
 

invesalius/data/slice_.py

@@ -34,6 +34,11 @@
 from mask import Mask
 from project import Project
 
+OTHER=0
+PLIST=1
+WIDGET=2
+
+
 class SliceBuffer(object):
     """ 
     This class is used as buffer that mantains the vtkImageData and numpy array
@@ -66,9 +71,6 @@ def discard_buffer(self):
         self.vtk_mask = None
 
 
-
-
-
 class Slice(object):
     __metaclass__= utils.Singleton
     # Only one slice will be initialized per time (despite several viewers
@@ -79,7 +81,8 @@ def __init__(self):
         self.imagedata = None
         self.current_mask = None
         self.blend_filter = None
-        self.matrix = None
+        self.histogram = None
+        self._matrix = None
         self.spacing = (1.0, 1.0, 1.0)
 
         self.number_of_colours = 256
@@ -94,8 +97,23 @@ def __init__(self):
         self.num_gradient = 0
         self.interaction_style = st.StyleStateManager()
 
+        self.values = None
+        self.nodes = None
+
+        self.from_ = OTHER
         self.__bind_events()
 
+    @property
+    def matrix(self):
+        return self._matrix
+
+    @matrix.setter
+    def matrix(self, value):
+        self._matrix = value
+        i, e = value.min(), value.max()
+        r = e - i
+        self.histogram = numpy.histogram(self._matrix, r, (i, e))[0]
+
     def __bind_events(self):
         # General slice control
         Publisher.subscribe(self.CreateSurfaceFromIndex,
@@ -125,6 +143,12 @@ def __bind_events(self):
         Publisher.subscribe(self.UpdateColourTableBackground,\
                                  'Change colour table from background image')
 
+        Publisher.subscribe(self.UpdateColourTableBackgroundPlist,\
+                                 'Change colour table from background image from plist')
+
+        Publisher.subscribe(self.UpdateColourTableBackgroundWidget,\
+                                 'Change colour table from background image from widget')
+
         Publisher.subscribe(self.InputImageWidget, 'Input Image in the widget')
 
         Publisher.subscribe(self.OnExportMask,'Export mask to file')
@@ -213,7 +237,18 @@ def OnCloseProject(self, pubsub_evt):
     def CloseProject(self):
         self.imagedata = None
         self.current_mask = None
+
+        self.values = None
+        self.nodes = None
+        self.from_= OTHER
+
+        self.number_of_colours = 256
+        self.saturation_range = (0, 0)
+        self.hue_range = (0, 0)
+        self.value_range = (0, 1)
+
         Publisher.sendMessage('Select first item from slice menu')
+
         #self.blend_filter = None
         #self.blend_filter = None
         #self.num_gradient = 0
@@ -702,6 +737,7 @@ def UpdateWindowLevelBackground(self, pubsub_evt):
 
     def UpdateColourTableBackground(self, pubsub_evt):
         values = pubsub_evt.data
+        self.from_= OTHER
         self.number_of_colours= values[0]
         self.saturation_range = values[1]
         self.hue_range = values[2]
@@ -710,6 +746,29 @@ def UpdateColourTableBackground(self, pubsub_evt):
             buffer_.discard_vtk_image()
         Publisher.sendMessage('Reload actual slice')
 
+    def UpdateColourTableBackgroundPlist(self, pubsub_evt):
+        self.values = pubsub_evt.data
+        self.from_= PLIST
+        for buffer_ in self.buffer_slices.values():
+            buffer_.discard_vtk_image()
+
+        Publisher.sendMessage('Reload actual slice')
+
+    def UpdateColourTableBackgroundWidget(self, pubsub_evt):
+        self.nodes = pubsub_evt.data
+        self.from_= WIDGET
+        for buffer_ in self.buffer_slices.values():
+            buffer_.discard_vtk_image()
+
+        knodes = sorted(self.nodes)
+        p0 = knodes[0].value
+        pn = knodes[-1].value
+
+        self.window_width = pn - p0
+        self.window_level = (pn + p0) / 2
+
+        Publisher.sendMessage('Reload actual slice')
+
     def InputImageWidget(self, pubsub_evt):
         widget, orientation = pubsub_evt.data
 
@@ -816,15 +875,72 @@ def __load_masks(self, imagedata, mask_dict):
         Publisher.sendMessage('Update slice viewer')
 
     def do_ww_wl(self, image):
-        colorer = vtk.vtkImageMapToWindowLevelColors()
-        colorer.SetInput(image)
-        colorer.SetWindow(self.window_width)
-        colorer.SetLevel(self.window_level)
-        colorer.SetOutputFormatToRGB()
-        colorer.Update()
+        if self.from_ == PLIST:
+            lut = vtk.vtkWindowLevelLookupTable()
+            lut.SetWindow(self.window_width)
+            lut.SetLevel(self.window_level)
+            lut.Build()
+
+            i = 0
+            for r, g, b in self.values:
+                lut.SetTableValue(i, r/255.0, g/255.0, b/255.0, 1.0)
+                i += 1
+
+            colorer = vtk.vtkImageMapToColors()
+            colorer.SetInput(image)
+            colorer.SetLookupTable(lut)
+            colorer.SetOutputFormatToRGB()
+            colorer.Update()
+        elif self.from_ == WIDGET:
+            lut  = vtk.vtkColorTransferFunction()
+
+            for n in self.nodes:
+                r, g, b = n.colour
+                lut.AddRGBPoint(n.value, r/255.0, g/255.0, b/255.0)
+
+            lut.Build()
+
+            colorer = vtk.vtkImageMapToColors()
+            colorer.SetLookupTable(lut)
+            colorer.SetInput(image)
+            colorer.SetOutputFormatToRGB()
+            colorer.Update()
+        else:
+            colorer = vtk.vtkImageMapToWindowLevelColors()
+            colorer.SetInput(image)
+            colorer.SetWindow(self.window_width)
+            colorer.SetLevel(self.window_level)
+            colorer.SetOutputFormatToRGB()
+            colorer.Update()
 
         return colorer.GetOutput()
 
+    def _update_wwwl_widget_nodes(self, ww, wl):
+        if self.from_ == WIDGET: 
+            knodes = sorted(self.nodes)
+
+            p1 = knodes[0]
+            p2 = knodes[-1]
+            half = (p2.value - p1.value) / 2.0
+            middle = p1.value + half
+
+            shiftWL = wl - middle
+            shiftWW = p1.value + shiftWL - (wl - 0.5 * ww)
+
+            factor = 1.0
+
+            for n, node in enumerate(knodes):
+                factor = abs(node.value - middle) / half
+                if factor < 0:
+                    factor = 0
+
+                node.value += shiftWL
+
+                if n < len(self.nodes) / 2.0:
+                    node.value -= shiftWW * factor
+                else:
+                    node.value += shiftWW * factor
+
     def do_threshold_to_a_slice(self, slice_matrix, mask):
         """ 
         Based on the current threshold bounds generates a threshold mask to
@@ -837,22 +953,25 @@ def do_threshold_to_a_slice(self, slice_matrix, mask):
         return m.astype('uint8')
 
     def do_colour_image(self, imagedata):
-        # map scalar values into colors
-        lut_bg = vtk.vtkLookupTable()
-        lut_bg.SetTableRange(imagedata.GetScalarRange())
-        lut_bg.SetSaturationRange(self.saturation_range)
-        lut_bg.SetHueRange(self.hue_range)
-        lut_bg.SetValueRange(self.value_range)
-        lut_bg.Build()
-
-        # map the input image through a lookup table
-        img_colours_bg = vtk.vtkImageMapToColors()
-        img_colours_bg.SetOutputFormatToRGB()
-        img_colours_bg.SetLookupTable(lut_bg)
-        img_colours_bg.SetInput(imagedata)
-        img_colours_bg.Update()
-
-        return img_colours_bg.GetOutput()
+        if self.from_ in (PLIST, WIDGET):
+            return imagedata
+        else:
+            # map scalar values into colors
+            lut_bg = vtk.vtkLookupTable()
+            lut_bg.SetTableRange(imagedata.GetScalarRange())
+            lut_bg.SetSaturationRange(self.saturation_range)
+            lut_bg.SetHueRange(self.hue_range)
+            lut_bg.SetValueRange(self.value_range)
+            lut_bg.Build()
+
+            # map the input image through a lookup table
+            img_colours_bg = vtk.vtkImageMapToColors()
+            img_colours_bg.SetOutputFormatToRGB()
+            img_colours_bg.SetLookupTable(lut_bg)
+            img_colours_bg.SetInput(imagedata)
+            img_colours_bg.Update()
+
+            return img_colours_bg.GetOutput()
 
     def do_colour_mask(self, imagedata):
         scalar_range = int(imagedata.GetScalarRange()[1])

invesalius/data/viewer_slice.py

@@ -131,6 +131,7 @@ def OnContextMenu(self, evt):
         self.right_pressed = 0
         if (self.last_position_mouse_move ==\
               self.interactor.GetLastEventPosition()):
+            self.menu.caller = self
             self.PopupMenu(self.menu)
         evt.Skip()
 
@@ -196,7 +197,25 @@ def UpdateWindowLevelValue(self, pubsub_evt):
         window, level = pubsub_evt.data
         self.acum_achange_window, self.acum_achange_level = (window, level)
         self.SetWLText(window, level)
+
+        slc = sl.Slice()
+        slc._update_wwwl_widget_nodes(window, level)
+
         Publisher.sendMessage('Update all slice')
+        Publisher.sendMessage('Update clut imagedata widget')
+
+    def UpdateWindowLevelText(self, pubsub_evt):
+        window, level = pubsub_evt.data
+        self.acum_achange_window, self.acum_achange_level = (window, level)
+        self.SetWLText(window, level)
+        self.interactor.Render()
+
+    def OnClutChange(self, evt):
+        Publisher.sendMessage('Change colour table from background image from widget',
+                              evt.GetNodes())
+        slc = sl.Slice()
+        Publisher.sendMessage('Update window level value',
+                              (slc.window_width, slc.window_level))
 
     def SetWLText(self, window_width, window_level):
         value = STR_WL%(window_level, window_width) 
@@ -594,8 +613,11 @@ def __bind_events(self):
         Publisher.subscribe(self.ChangeBrushOperation,
                                  'Set edition operation')
 
-        Publisher.subscribe(self.UpdateWindowLevelValue,\
-                                 'Update window level value')
+        Publisher.subscribe(self.UpdateWindowLevelValue,
+                            'Update window level value')
+
+        Publisher.subscribe(self.UpdateWindowLevelText,
+                            'Update window level text')
 
         #Publisher.subscribe(self._set_cross_visibility,\
         #                         'Set cross visibility')

invesalius/gui/dialogs.py

@@ -34,6 +34,9 @@
 import session as ses
 import utils
 
+from gui.widgets.clut_imagedata import CLUTImageDataWidget, EVT_CLUT_NODE_CHANGED
+
+import numpy as np
 
 class MaskEvent(wx.PyCommandEvent):
     def __init__(self , evtType, id, mask_index):
@@ -1274,9 +1277,47 @@ def ReloadMethodsOptions(self):
         self.method_sizer.Layout()
 
 
+class ClutImagedataDialog(wx.Dialog):
+    def __init__(self, histogram, init, end, nodes=None):
+        pre = wx.PreDialog()
+        pre.Create(wx.GetApp().GetTopWindow(), -1, style=wx.DEFAULT_DIALOG_STYLE|wx.FRAME_FLOAT_ON_PARENT)
+        self.PostCreate(pre)
+
+        self.histogram = histogram
+        self.init = init
+        self.end = end
+        self.nodes = nodes
 
+        self._init_gui()
+        self.bind_events()
+        self.bind_events_wx()
 
-
+    def _init_gui(self):
+        self.clut_widget = CLUTImageDataWidget(self, -1, self.histogram,
+                                               self.init, self.end, self.nodes)
+        sizer = wx.BoxSizer(wx.VERTICAL)
+        sizer.Add(self.clut_widget, 1, wx.EXPAND)
+
+        self.SetSizer(sizer)
+        self.Fit()
+
+    def bind_events_wx(self):
+        self.clut_widget.Bind(EVT_CLUT_NODE_CHANGED, self.OnClutChange)
+
+    def bind_events(self):
+        Publisher.subscribe(self._refresh_widget, 'Update clut imagedata widget')
 
+    def OnClutChange(self, evt):
+        Publisher.sendMessage('Change colour table from background image from widget',
+                              evt.GetNodes())
+        Publisher.sendMessage('Update window level text',
+                              (self.clut_widget.window_width,
+                               self.clut_widget.window_level))
 
+    def _refresh_widget(self, pubsub_evt):
+        self.clut_widget.Refresh()
 
+    def Show(self, gen_evt=True, show=True):
+        super(wx.Dialog, self).Show(show)
+        if gen_evt:
+            self.clut_widget._generate_event()