Download as
Browse Code »

Commit 7c80274f085e948751ea02c174aa811faa07e4b7

Authored by Thiago Franco de Moraes
1 parent 8d9b272f
Exists in measure

Reading and applying osirix preset colours

Showing 4 changed files with 97 additions and 23 deletions   Show diff stats
invesalius/constants.py
  Diff comments   View file @7c80274
@@ -295,7 +295,7 @@ WINDOW_LEVEL = {_("Abdomen"):(350,50), @@ -295,7 +295,7 @@ WINDOW_LEVEL = {_("Abdomen"):(350,50),
295 REDUCE_IMAGEDATA_QUALITY = 0 295 REDUCE_IMAGEDATA_QUALITY = 0
296 296
297 ICON_DIR = os.path.abspath(os.path.join('..', 'icons')) 297 ICON_DIR = os.path.abspath(os.path.join('..', 'icons'))
298 -SAMPLE_DIR = os.path.abspath(os.path.join('..', 'samples')) 298 +SAMPLE_DIR = "/usr/share/doc/invesalius-examples/examples/"
299 DOC_DIR = os.path.abspath(os.path.join('..', 'docs')) 299 DOC_DIR = os.path.abspath(os.path.join('..', 'docs'))
300 300
301 301
invesalius/data/slice_.py
  Diff comments   View file @7c80274
@@ -94,6 +94,8 @@ class Slice(object): @@ -94,6 +94,8 @@ class Slice(object):
94 self.num_gradient = 0 94 self.num_gradient = 0
95 self.interaction_style = st.StyleStateManager() 95 self.interaction_style = st.StyleStateManager()
96 96
  97 + self.from_plist = False
  98 +
97 self.__bind_events() 99 self.__bind_events()
98 100
99 def __bind_events(self): 101 def __bind_events(self):
@@ -125,6 +127,9 @@ class Slice(object): @@ -125,6 +127,9 @@ class Slice(object):
125 Publisher.subscribe(self.UpdateColourTableBackground,\ 127 Publisher.subscribe(self.UpdateColourTableBackground,\
126 'Change colour table from background image') 128 'Change colour table from background image')
127 129
  130 + Publisher.subscribe(self.UpdateColourTableBackgroundPlist,\
  131 + 'Change colour table from background image from plist')
  132 +
128 Publisher.subscribe(self.InputImageWidget, 'Input Image in the widget') 133 Publisher.subscribe(self.InputImageWidget, 'Input Image in the widget')
129 134
130 Publisher.subscribe(self.OnExportMask,'Export mask to file') 135 Publisher.subscribe(self.OnExportMask,'Export mask to file')
@@ -702,6 +707,7 @@ class Slice(object): @@ -702,6 +707,7 @@ class Slice(object):
702 707
703 def UpdateColourTableBackground(self, pubsub_evt): 708 def UpdateColourTableBackground(self, pubsub_evt):
704 values = pubsub_evt.data 709 values = pubsub_evt.data
  710 + self.from_plist = False
705 self.number_of_colours= values[0] 711 self.number_of_colours= values[0]
706 self.saturation_range = values[1] 712 self.saturation_range = values[1]
707 self.hue_range = values[2] 713 self.hue_range = values[2]
@@ -710,6 +716,13 @@ class Slice(object): @@ -710,6 +716,13 @@ class Slice(object):
710 buffer_.discard_vtk_image() 716 buffer_.discard_vtk_image()
711 Publisher.sendMessage('Reload actual slice') 717 Publisher.sendMessage('Reload actual slice')
712 718
  719 + def UpdateColourTableBackgroundPlist(self, pubsub_evt):
  720 + self.values = pubsub_evt.data
  721 + self.from_plist = True
  722 + for buffer_ in self.buffer_slices.values():
  723 + buffer_.discard_vtk_image()
  724 + Publisher.sendMessage('Reload actual slice')
  725 +
713 def InputImageWidget(self, pubsub_evt): 726 def InputImageWidget(self, pubsub_evt):
714 widget, orientation = pubsub_evt.data 727 widget, orientation = pubsub_evt.data
715 728
@@ -816,12 +829,31 @@ class Slice(object): @@ -816,12 +829,31 @@ class Slice(object):
816 Publisher.sendMessage('Update slice viewer') 829 Publisher.sendMessage('Update slice viewer')
817 830
818 def do_ww_wl(self, image): 831 def do_ww_wl(self, image):
819 - colorer = vtk.vtkImageMapToWindowLevelColors()  
820 - colorer.SetInput(image)  
821 - colorer.SetWindow(self.window_width)  
822 - colorer.SetLevel(self.window_level)  
823 - colorer.SetOutputFormatToRGB()  
824 - colorer.Update() 832 + if self.from_plist:
  833 + lut = vtk.vtkWindowLevelLookupTable()
  834 + lut.SetWindow(self.window_width)
  835 + lut.SetLevel(self.window_level)
  836 + lut.Build()
  837 +
  838 + i = 0
  839 + for r, g, b in self.values:
  840 + lut.SetTableValue(i, r/255.0, g/255.0, b/255.0, 1.0)
  841 + i += 1
  842 +
  843 + print i, r, g, b
  844 +
  845 + colorer = vtk.vtkImageMapToColors()
  846 + colorer.SetInput(image)
  847 + colorer.SetLookupTable(lut)
  848 + colorer.SetOutputFormatToRGB()
  849 + colorer.Update()
  850 + else:
  851 + colorer = vtk.vtkImageMapToWindowLevelColors()
  852 + colorer.SetInput(image)
  853 + colorer.SetWindow(self.window_width)
  854 + colorer.SetLevel(self.window_level)
  855 + colorer.SetOutputFormatToRGB()
  856 + colorer.Update()
825 857
826 return colorer.GetOutput() 858 return colorer.GetOutput()
827 859
@@ -837,22 +869,25 @@ class Slice(object): @@ -837,22 +869,25 @@ class Slice(object):
837 return m.astype('uint8') 869 return m.astype('uint8')
838 870
839 def do_colour_image(self, imagedata): 871 def do_colour_image(self, imagedata):
840 - # map scalar values into colors  
841 - lut_bg = vtk.vtkLookupTable()  
842 - lut_bg.SetTableRange(imagedata.GetScalarRange())  
843 - lut_bg.SetSaturationRange(self.saturation_range)  
844 - lut_bg.SetHueRange(self.hue_range)  
845 - lut_bg.SetValueRange(self.value_range)  
846 - lut_bg.Build()  
847 -  
848 - # map the input image through a lookup table  
849 - img_colours_bg = vtk.vtkImageMapToColors()  
850 - img_colours_bg.SetOutputFormatToRGB()  
851 - img_colours_bg.SetLookupTable(lut_bg)  
852 - img_colours_bg.SetInput(imagedata)  
853 - img_colours_bg.Update()  
854 -  
855 - return img_colours_bg.GetOutput() 872 + if self.from_plist:
  873 + return imagedata
  874 + else:
  875 + # map scalar values into colors
  876 + lut_bg = vtk.vtkLookupTable()
  877 + lut_bg.SetTableRange(imagedata.GetScalarRange())
  878 + lut_bg.SetSaturationRange(self.saturation_range)
  879 + lut_bg.SetHueRange(self.hue_range)
  880 + lut_bg.SetValueRange(self.value_range)
  881 + lut_bg.Build()
  882 +
  883 + # map the input image through a lookup table
  884 + img_colours_bg = vtk.vtkImageMapToColors()
  885 + img_colours_bg.SetOutputFormatToRGB()
  886 + img_colours_bg.SetLookupTable(lut_bg)
  887 + img_colours_bg.SetInput(imagedata)
  888 + img_colours_bg.Update()
  889 +
  890 + return img_colours_bg.GetOutput()
856 891
857 def do_colour_mask(self, imagedata): 892 def do_colour_mask(self, imagedata):
858 scalar_range = int(imagedata.GetScalarRange()[1]) 893 scalar_range = int(imagedata.GetScalarRange()[1])
invesalius/gui/widgets/slice_menu.py
  Diff comments   View file @7c80274
@@ -24,6 +24,7 @@ import sys @@ -24,6 +24,7 @@ import sys
24 import wx 24 import wx
25 from wx.lib.pubsub import pub as Publisher 25 from wx.lib.pubsub import pub as Publisher
26 import constants as const 26 import constants as const
  27 +import presets
27 28
28 class SliceMenu(wx.Menu): 29 class SliceMenu(wx.Menu):
29 def __init__(self): 30 def __init__(self):
@@ -56,6 +57,7 @@ class SliceMenu(wx.Menu): @@ -56,6 +57,7 @@ class SliceMenu(wx.Menu):
56 self.ID_TO_TOOL_ITEM[new_id] = wl_item 57 self.ID_TO_TOOL_ITEM[new_id] = wl_item
57 58
58 59
  60 +
59 #----------- Sub menu of the save and load options --------- 61 #----------- Sub menu of the save and load options ---------
60 #submenu_wl.AppendSeparator() 62 #submenu_wl.AppendSeparator()
61 #options = [_("Save current values"), 63 #options = [_("Save current values"),
@@ -84,6 +86,13 @@ class SliceMenu(wx.Menu): @@ -84,6 +86,13 @@ class SliceMenu(wx.Menu):
84 name, kind=wx.ITEM_RADIO) 86 name, kind=wx.ITEM_RADIO)
85 submenu_pseudo_colours.AppendItem(color_item) 87 submenu_pseudo_colours.AppendItem(color_item)
86 self.ID_TO_TOOL_ITEM[new_id] = color_item 88 self.ID_TO_TOOL_ITEM[new_id] = color_item
  89 +
  90 + self.plist_presets = presets.get_wwwl_presets()
  91 + for name in sorted(self.plist_presets):
  92 + new_id = wx.NewId()
  93 + color_item = wx.MenuItem(submenu_wl, new_id, name, kind=wx.ITEM_RADIO)
  94 + submenu_pseudo_colours.AppendItem(color_item)
  95 + self.ID_TO_TOOL_ITEM[new_id] = color_item
87 96
88 flag_tiling = False 97 flag_tiling = False
89 #------------ Sub menu of the image tiling --------------- 98 #------------ Sub menu of the image tiling ---------------
@@ -160,6 +169,11 @@ class SliceMenu(wx.Menu): @@ -160,6 +169,11 @@ class SliceMenu(wx.Menu):
160 Publisher.sendMessage('Change colour table from background image', values) 169 Publisher.sendMessage('Change colour table from background image', values)
161 Publisher.sendMessage('Update slice viewer') 170 Publisher.sendMessage('Update slice viewer')
162 171
  172 + elif key in self.plist_presets:
  173 + values = presets.get_wwwl_preset_colours(self.plist_presets[key])
  174 + Publisher.sendMessage('Change colour table from background image from plist', values)
  175 + Publisher.sendMessage('Update slice viewer')
  176 +
163 elif(key in const.IMAGE_TILING.keys()): 177 elif(key in const.IMAGE_TILING.keys()):
164 print "c" 178 print "c"
165 values = const.IMAGE_TILING[key] 179 values = const.IMAGE_TILING[key]
invesalius/presets.py
  Diff comments   View file @7c80274
@@ -16,9 +16,12 @@ @@ -16,9 +16,12 @@
16 # PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais 16 # PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
17 # detalhes. 17 # detalhes.
18 #-------------------------------------------------------------------------- 18 #--------------------------------------------------------------------------
  19 +import glob
19 import os 20 import os
20 import plistlib 21 import plistlib
21 22
  23 +import constants as const
  24 +
22 from wx.lib.pubsub import pub as Publisher 25 from wx.lib.pubsub import pub as Publisher
23 26
24 from utils import TwoWaysDictionary 27 from utils import TwoWaysDictionary
@@ -164,3 +167,25 @@ class Presets(): @@ -164,3 +167,25 @@ class Presets():
164 self.thresh_ct = TwoWaysDictionary(thresh_ct_new) 167 self.thresh_ct = TwoWaysDictionary(thresh_ct_new)
165 168
166 169
  170 +
  171 +def get_wwwl_presets():
  172 + files = glob.glob(os.path.join('..', 'presets', 'raycasting', 'color_list', '*.plist'))
  173 + presets = {}
  174 + for f in files:
  175 + p = os.path.splitext(os.path.basename(f))[0]
  176 + presets[p] = f
  177 + return presets
  178 +
  179 +
  180 +def get_wwwl_preset_colours(pfile):
  181 + preset = plistlib.readPlist(pfile)
  182 + ncolours = len(preset['Blue'])
  183 + colours = []
  184 + for i in xrange(ncolours):
  185 + r = preset['Red'][i]
  186 + g = preset['Green'][i]
  187 + b = preset['Blue'][i]
  188 +
  189 + colours.append((r, g, b))
  190 +
  191 + return colours