ADD: Edit mask pixel tool (erase) in default mode - not working

tatiana
1 parent 159f813a
Showing 4 changed files with 195 additions and 9 deletions Show diff stats
.gitattributes
invesalius/data/cursor_actors.py
invesalius/data/slice_.py
invesalius/data/viewer_slice.py
@@ -73,6 +73,7 @@ invesalius/.svnignore -text
 invesalius/constants.py -text
 invesalius/control.py -text
 invesalius/data/__init__.py -text
+invesalius/data/cursor_actors.py -text
 invesalius/data/editor.py -text
 invesalius/data/imagedata_utils.py -text
 invesalius/data/mask.py -text
@@ -0,0 +1,111 @@
+from  math import *
+
+import vtk
+
+class CursorCircle:
+   # TODO: Think and try to change this class to an actor
+   # CursorCircleActor(vtk.vtkActor)
+    
+    def __init__(self):
+        
+        self.colour = (0.0, 0.0, 1.0)
+        self.opacity = 1
+        self.radius = 20
+        self.position = (0 ,0, 1)
+        self.points = []
+        self.orientation = "AXIAL"
+        
+        self.mapper = vtk.vtkPolyDataMapper()
+        self.disk = vtk.vtkDiskSource()
+        self.actor = vtk.vtkActor()
+        
+        self.__build_actor()
+        self.__calculate_area_pixels()
+
+    def __build_actor(self):
+        """
+        Function to plot the circle
+        """
+        
+        disk = self.disk
+        disk.SetInnerRadius(self.radius)
+        disk.SetOuterRadius(0) # filled
+        disk.SetRadialResolution(50)
+        disk.SetCircumferentialResolution(50)
+     
+        mapper = self.mapper
+        mapper.SetInput(disk.GetOutput())
+        
+        actor = self.actor      
+        actor.SetMapper(mapper)
+        actor.GetProperty().SetOpacity(self.opacity)
+        actor.GetProperty().SetColor(self.colour) 
+        actor.SetPosition(self.position)
+        actor.SetVisibility(1)
+        actor.PickableOff()
+        
+    def __calculate_area_pixels(self):
+        """
+        Return the cursor's pixels.
+        This method scans the circle line by line.
+        Extracted equation. 
+        http://www.mathopenref.com/chord.html
+        """
+        xc = 0
+        yc = 0
+        z = 0
+        self.pixel_list = []
+        radius = int(self.radius)
+        for i in xrange(int(yc - radius), int(yc + radius)):
+            # distance from the line to the circle's center
+            d = yc - i
+            # line size
+            line = sqrt(round(radius ** 2) - round(d ** 2)) * 2
+            # line initial x
+            xi = int(xc - line/2)
+            # line final
+            xf = int(line/2 + xc)
+            yi = i
+            for k in xrange(xi,xf):
+                self.pixel_list.append((k, yi))
+
+    def SetSize(self, radius):
+        self.radius = radius
+        disk.SetInnerRadius(radius)
+        self.__calculate_area_pixels()
+        
+    def SetColour(self, colour):
+        self.actor.GetProperty().SetColor(self.colour)
+
+    def SetOrientation(self, orientation):
+        self.orientation = orientation
+
+        if orientation == "CORONAL":
+            self.actor.RotateX(90)
+
+        if orientation == "SAGITAL":
+            self.actor.RotateY(90)
+
+    def SetPosition(self, position):
+    
+        #if self.orientation == "AXIAL":
+        #    z = 1
+        #elif self.orientation == "CORONAL":
+        #    y = 1
+        #elif self.orientation == "SAGITAL":
+        #    x = 1
+        self.position = position
+        self.actor.SetPosition(position)
+
+    def GetPixels(self):
+        px, py, pz = self.position
+        orient = self.orientation
+        for pixel_0,pixel_1 in self.pixel_list:
+            # The position of the pixels in this list is relative (based only on
+            # the area, and not the cursor position).
+            # Let's calculate the absolute position
+            # TODO: Optimize this!!!!
+            absolute_pixel = {"AXIAL": (px + pixel_0, py + pixel_1, pz),
+                              "CORONAL": (px + pixel_0, py, pz + pixel_1),
+                              "SAGITAL": (px, py + pixel_0, pz + pixel_1)}
+            yield absolute_pixel[orient]
@@ -33,6 +33,12 @@ class Slice(object):
                                  'Update cursor position in slice')
         ps.Publisher().subscribe(self.ShowMask, 'Show mask')
         ps.Publisher().subscribe(self.ChangeMaskName, 'Change mask name')
+        ps.Publisher().subscribe(self.EraseMaskPixel, 'Erase mask pixel')
+        
+        
+    def EraseMaskPixel(self, pubsub_evt):
+        position = pubsub_evt.data
+        self.ErasePixel(position)
     def ChangeMaskName(self, pubsub_evt):
         index, name = pubsub_evt.data
@@ -118,6 +124,8 @@ class Slice(object):
             ps.Publisher().sendMessage('Select mask name in combo', mask_index)
             ps.Publisher().sendMessage('Update slice viewer')
+
+
     def ChangeCurrentMaskColour(self, colour, update=True):
         # This is necessary because wx events are calling this before it was created
         if self.current_mask:
@@ -358,27 +366,31 @@ class Slice(object):
     #    thresh_min, thresh_max = evt.data
     #    self.current_mask.edition_threshold_range = thresh_min, thresh_max
-    def ErasePixel(self, x, y, z):
+    def ErasePixel(self, position):
         """
         Delete pixel, based on x, y and z position coordinates.
         """
-        colour = imagedata.GetScalarRange()[0]
-        self.imagedata.SetScalarComponentFromDouble(x, y, z, 0, colour)
-        self.imagedata.Update()
+        x, y, z = position
+        imagedata = self.current_mask.imagedata
+        colour = imagedata.GetScalarRange()[0]# - 1 # Important to effect erase
+        imagedata.SetScalarComponentFromDouble(x, y, z, 0, colour)
+        imagedata.Update()
     def DrawPixel(self, x, y, z, colour=None):
         """
         Draw pixel, based on x, y and z position coordinates.
         """
+        imagedata = self.current_mask.imagedata
         if colour is None:
             colour = imagedata.GetScalarRange()[1]
-        self.imagedata.SetScalarComponentFromDouble(x, y, z, 0, colour)
+        imagedata.SetScalarComponentFromDouble(x, y, z, 0, colour)
     def EditPixelBasedOnThreshold(self, x, y, z):
         """
         Erase or draw pixel based on edition threshold range.
         """
-        pixel_colour = self.imagedata.GetScalarComponentAsDouble(x, y, z, 0)
+        
+        pixel_colour = imagedata.GetScalarComponentAsDouble(x, y, z, 0)
         thresh_min, thresh_max = self.current_mask.edition_threshold_range
         if (pixel_colour >= thresh_min) and (pixel_colour <= thresh_max):
@@ -26,6 +26,7 @@ import wx.lib.pubsub as ps
 import data.slice_ as sl
 import constants as const
 import project
+import cursor_actors as ca
 class Viewer(wx.Panel):
@@ -36,7 +37,7 @@ class Viewer(wx.Panel):
         self.SetBackgroundColour(colour)
         # Interactor aditional style
-        self.modes = []
+        self.modes = ['DEFAULT']
         self.mouse_pressed = 0
         self.__init_gui()
@@ -83,7 +84,7 @@ class Viewer(wx.Panel):
         self.cam = ren.GetActiveCamera()
         self.ren = ren
-        self.AppendMode('DEFAULT')
+        self.AppendMode('EDITOR')
     def AppendMode(self, mode):
@@ -115,6 +116,19 @@ class Viewer(wx.Panel):
                 # Bind event
                 style.AddObserver(event,
                                   action[mode][event])
+
+        # Insert cursor
+        cursor = ca.CursorCircle()
+        cursor.SetOrientation(self.orientation)
+        coordinates = {"SAGITAL": [self.slice_number, 0, 0],
+                       "CORONAL": [0, self.slice_number, 0],
+                       "AXIAL": [0, 0, self.slice_number]}
+        cursor.SetPosition(coordinates[self.orientation])
+        self.ren.AddActor(cursor.actor)
+        self.ren.Render()
+        
+        self.cursor = cursor
+
     def OnMouseClick(self, obj, evt_vtk):
@@ -129,9 +143,15 @@ class Viewer(wx.Panel):
         print "Edit pixel region based on origin:", coord
     def OnBrushMove(self, obj, evt_vtk):
-        coord = self.GetCoordinate()
+        coord = self.GetCoordinateCursor()
+        self.cursor.SetPosition(coord)
+        self.ren.Render()
         if self.mouse_pressed:
             print "Edit pixel region based on origin:", coord
+            pixels = self.cursor.GetPixels()
+            for coord in pixels:
+                ps.Publisher().sendMessage('Erase mask pixel', coord)
+            self.interactor.Render()
     def OnCrossMove(self, obj, evt_vtk):
         coord = self.GetCoordinate()
@@ -187,6 +207,48 @@ class Viewer(wx.Panel):
         #print "New coordinate: ", coord
         return coord
+     
+     
+    def GetCoordinateCursor(self):
+    
+        # Find position
+        mouse_x, mouse_y = self.interactor.GetEventPosition()
+        self.pick.Pick(mouse_x, mouse_y, 0, self.ren)
+        x, y, z = self.pick.GetPickPosition()
+        
+        # First we fix the position origin, based on vtkActor bounds
+        bounds = self.actor.GetBounds()
+        bound_xi, bound_xf, bound_yi, bound_yf, bound_zi, bound_zf = bounds
+        x = float(x - bound_xi)
+        y = float(y - bound_yi)
+        z = float(z - bound_zi)
+        
+        # Then we fix the porpotion, based on vtkImageData spacing
+        #spacing_x, spacing_y, spacing_z = self.imagedata.GetSpacing()
+        #x = x/spacing_x
+        #y = y/spacing_y
+        #z = z/spacing_z
+        
+        # Based on the current orientation, we define 3D position
+        coordinates = {"SAGITAL": [self.slice_number, y, z],
+                       "CORONAL": [x, self.slice_number, z],
+                       "AXIAL": [x, y, self.slice_number]}
+        coord = [int(coord) for coord in coordinates[self.orientation]]
+        
+        # According to vtkImageData extent, we limit min and max value
+        # If this is not done, a VTK Error occurs when mouse is pressed outside
+        # vtkImageData extent
+        #extent = self.imagedata.GetWholeExtent()
+        #extent_min = extent[0], extent[2], extent[4]
+        #extent_max = extent[1], extent[3], extent[5]
+        #for index in xrange(3):
+        #    if coord[index] > extent_max[index]:
+        #        coord[index] = extent_max[index]
+        #    elif coord[index] < extent_min[index]:
+        #        coord[index] = extent_min[index]
+        #print "New coordinate: ", coord
+        
+        return coord
     def __bind_events(self):
         ps.Publisher().subscribe(self.LoadImagedata, 'Load slice to viewer')
@@ -0,0 +1,111 @@		@@ -0,0 +1,111 @@
	1	+from math import *
	2	+
	3	+import vtk
	4	+
	5	+class CursorCircle:
	6	+ # TODO: Think and try to change this class to an actor
	7	+ # CursorCircleActor(vtk.vtkActor)
	8	+
	9	+ def __init__(self):
	10	+
	11	+ self.colour = (0.0, 0.0, 1.0)
	12	+ self.opacity = 1
	13	+ self.radius = 20
	14	+ self.position = (0 ,0, 1)
	15	+ self.points = []
	16	+ self.orientation = "AXIAL"
	17	+
	18	+ self.mapper = vtk.vtkPolyDataMapper()
	19	+ self.disk = vtk.vtkDiskSource()
	20	+ self.actor = vtk.vtkActor()
	21	+
	22	+ self.__build_actor()
	23	+ self.__calculate_area_pixels()
	24	+
	25	+ def __build_actor(self):
	26	+ """
	27	+ Function to plot the circle
	28	+ """
	29	+
	30	+ disk = self.disk
	31	+ disk.SetInnerRadius(self.radius)
	32	+ disk.SetOuterRadius(0) # filled
	33	+ disk.SetRadialResolution(50)
	34	+ disk.SetCircumferentialResolution(50)
	35	+
	36	+ mapper = self.mapper
	37	+ mapper.SetInput(disk.GetOutput())
	38	+
	39	+ actor = self.actor
	40	+ actor.SetMapper(mapper)
	41	+ actor.GetProperty().SetOpacity(self.opacity)
	42	+ actor.GetProperty().SetColor(self.colour)
	43	+ actor.SetPosition(self.position)
	44	+ actor.SetVisibility(1)
	45	+ actor.PickableOff()
	46	+
	47	+ def __calculate_area_pixels(self):
	48	+ """
	49	+ Return the cursor's pixels.
	50	+ This method scans the circle line by line.
	51	+ Extracted equation.
	52	+ http://www.mathopenref.com/chord.html
	53	+ """
	54	+ xc = 0
	55	+ yc = 0
	56	+ z = 0
	57	+ self.pixel_list = []
	58	+ radius = int(self.radius)
	59	+ for i in xrange(int(yc - radius), int(yc + radius)):
	60	+ # distance from the line to the circle's center
	61	+ d = yc - i
	62	+ # line size
	63	+ line = sqrt(round(radius 2) - round(d 2)) * 2
	64	+ # line initial x
	65	+ xi = int(xc - line/2)
	66	+ # line final
	67	+ xf = int(line/2 + xc)
	68	+ yi = i
	69	+ for k in xrange(xi,xf):
	70	+ self.pixel_list.append((k, yi))
	71	+
	72	+ def SetSize(self, radius):
	73	+ self.radius = radius
	74	+ disk.SetInnerRadius(radius)
	75	+ self.__calculate_area_pixels()
	76	+
	77	+ def SetColour(self, colour):
	78	+ self.actor.GetProperty().SetColor(self.colour)
	79	+
	80	+ def SetOrientation(self, orientation):
	81	+ self.orientation = orientation
	82	+
	83	+ if orientation == "CORONAL":
	84	+ self.actor.RotateX(90)
	85	+
	86	+ if orientation == "SAGITAL":
	87	+ self.actor.RotateY(90)
	88	+
	89	+ def SetPosition(self, position):
	90	+
	91	+ #if self.orientation == "AXIAL":
	92	+ # z = 1
	93	+ #elif self.orientation == "CORONAL":
	94	+ # y = 1
	95	+ #elif self.orientation == "SAGITAL":
	96	+ # x = 1
	97	+ self.position = position
	98	+ self.actor.SetPosition(position)
	99	+
	100	+ def GetPixels(self):
	101	+ px, py, pz = self.position
	102	+ orient = self.orientation
	103	+ for pixel_0,pixel_1 in self.pixel_list:
	104	+ # The position of the pixels in this list is relative (based only on
	105	+ # the area, and not the cursor position).
	106	+ # Let's calculate the absolute position
	107	+ # TODO: Optimize this!!!!
	108	+ absolute_pixel = {"AXIAL": (px + pixel_0, py + pixel_1, pz),
	109	+ "CORONAL": (px + pixel_0, py, pz + pixel_1),
	110	+ "SAGITAL": (px, py + pixel_0, pz + pixel_1)}
	111	+ yield absolute_pixel[orient]
	@@ -26,6 +26,7 @@ import wx.lib.pubsub as ps		@@ -26,6 +26,7 @@ import wx.lib.pubsub as ps
26	import data.slice_ as sl	26	import data.slice_ as sl
27	import constants as const	27	import constants as const
28	import project	28	import project
		29	+import cursor_actors as ca
29		30
30	class Viewer(wx.Panel):	31	class Viewer(wx.Panel):
31		32
	@@ -36,7 +37,7 @@ class Viewer(wx.Panel):		@@ -36,7 +37,7 @@ class Viewer(wx.Panel):
36	self.SetBackgroundColour(colour)	37	self.SetBackgroundColour(colour)
37		38
38	# Interactor aditional style	39	# Interactor aditional style
39	- self.modes = []	40	+ self.modes = ['DEFAULT']
40	self.mouse_pressed = 0	41	self.mouse_pressed = 0
41		42
42	self.__init_gui()	43	self.__init_gui()
	@@ -83,7 +84,7 @@ class Viewer(wx.Panel):		@@ -83,7 +84,7 @@ class Viewer(wx.Panel):
83	self.cam = ren.GetActiveCamera()	84	self.cam = ren.GetActiveCamera()
84	self.ren = ren	85	self.ren = ren
85		86
86	- self.AppendMode('DEFAULT')	87	+ self.AppendMode('EDITOR')
87		88
88	def AppendMode(self, mode):	89	def AppendMode(self, mode):
89		90
	@@ -115,6 +116,19 @@ class Viewer(wx.Panel):		@@ -115,6 +116,19 @@ class Viewer(wx.Panel):
115	# Bind event	116	# Bind event
116	style.AddObserver(event,	117	style.AddObserver(event,
117	action[mode][event])	118	action[mode][event])
		119	+
		120	+ # Insert cursor
		121	+ cursor = ca.CursorCircle()
		122	+ cursor.SetOrientation(self.orientation)
		123	+ coordinates = {"SAGITAL": [self.slice_number, 0, 0],
		124	+ "CORONAL": [0, self.slice_number, 0],
		125	+ "AXIAL": [0, 0, self.slice_number]}
		126	+ cursor.SetPosition(coordinates[self.orientation])
		127	+ self.ren.AddActor(cursor.actor)
		128	+ self.ren.Render()
		129	+
		130	+ self.cursor = cursor
		131	+
118		132
119		133
120	def OnMouseClick(self, obj, evt_vtk):	134	def OnMouseClick(self, obj, evt_vtk):
	@@ -129,9 +143,15 @@ class Viewer(wx.Panel):		@@ -129,9 +143,15 @@ class Viewer(wx.Panel):
129	print "Edit pixel region based on origin:", coord	143	print "Edit pixel region based on origin:", coord
130		144
131	def OnBrushMove(self, obj, evt_vtk):	145	def OnBrushMove(self, obj, evt_vtk):
132	- coord = self.GetCoordinate()	146	+ coord = self.GetCoordinateCursor()
		147	+ self.cursor.SetPosition(coord)
		148	+ self.ren.Render()
133	if self.mouse_pressed:	149	if self.mouse_pressed:
134	print "Edit pixel region based on origin:", coord	150	print "Edit pixel region based on origin:", coord
		151	+ pixels = self.cursor.GetPixels()
		152	+ for coord in pixels:
		153	+ ps.Publisher().sendMessage('Erase mask pixel', coord)
		154	+ self.interactor.Render()
135		155
136	def OnCrossMove(self, obj, evt_vtk):	156	def OnCrossMove(self, obj, evt_vtk):
137	coord = self.GetCoordinate()	157	coord = self.GetCoordinate()
	@@ -187,6 +207,48 @@ class Viewer(wx.Panel):		@@ -187,6 +207,48 @@ class Viewer(wx.Panel):
187	#print "New coordinate: ", coord	207	#print "New coordinate: ", coord
188		208
189	return coord	209	return coord
		210	+
		211	+
		212	+ def GetCoordinateCursor(self):
		213	+
		214	+ # Find position
		215	+ mouse_x, mouse_y = self.interactor.GetEventPosition()
		216	+ self.pick.Pick(mouse_x, mouse_y, 0, self.ren)
		217	+ x, y, z = self.pick.GetPickPosition()
		218	+
		219	+ # First we fix the position origin, based on vtkActor bounds
		220	+ bounds = self.actor.GetBounds()
		221	+ bound_xi, bound_xf, bound_yi, bound_yf, bound_zi, bound_zf = bounds
		222	+ x = float(x - bound_xi)
		223	+ y = float(y - bound_yi)
		224	+ z = float(z - bound_zi)
		225	+
		226	+ # Then we fix the porpotion, based on vtkImageData spacing
		227	+ #spacing_x, spacing_y, spacing_z = self.imagedata.GetSpacing()
		228	+ #x = x/spacing_x
		229	+ #y = y/spacing_y
		230	+ #z = z/spacing_z
		231	+
		232	+ # Based on the current orientation, we define 3D position
		233	+ coordinates = {"SAGITAL": [self.slice_number, y, z],
		234	+ "CORONAL": [x, self.slice_number, z],
		235	+ "AXIAL": [x, y, self.slice_number]}
		236	+ coord = [int(coord) for coord in coordinates[self.orientation]]
		237	+
		238	+ # According to vtkImageData extent, we limit min and max value
		239	+ # If this is not done, a VTK Error occurs when mouse is pressed outside
		240	+ # vtkImageData extent
		241	+ #extent = self.imagedata.GetWholeExtent()
		242	+ #extent_min = extent[0], extent[2], extent[4]
		243	+ #extent_max = extent[1], extent[3], extent[5]
		244	+ #for index in xrange(3):
		245	+ # if coord[index] > extent_max[index]:
		246	+ # coord[index] = extent_max[index]
		247	+ # elif coord[index] < extent_min[index]:
		248	+ # coord[index] = extent_min[index]
		249	+ #print "New coordinate: ", coord
		250	+
		251	+ return coord
190		252
191	def __bind_events(self):	253	def __bind_events(self):
192	ps.Publisher().subscribe(self.LoadImagedata, 'Load slice to viewer')	254	ps.Publisher().subscribe(self.LoadImagedata, 'Load slice to viewer')