Added Mask 3D edit

environment.yml

@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+  - pytorch
 dependencies:
   - python==3.11
   - cython==3.0.10

invesalius/constants.py

@@ -621,6 +621,7 @@
 ID_MASK_3D_PREVIEW = wx.NewIdRef()
 ID_MASK_3D_RELOAD = wx.NewIdRef()
 ID_MASK_3D_AUTO_RELOAD = wx.NewIdRef()
+ID_MASK_3D_EDIT = wx.NewIdRef()
 
 ID_GOTO_SLICE = wx.NewIdRef()
 ID_GOTO_COORD = wx.NewIdRef()
@@ -648,6 +649,7 @@
 STATE_MEASURE_DENSITY_POLYGON = 1011
 STATE_NAVIGATION = 1012
 STATE_REGISTRATION = 1013
+STATE_MASK_3D_EDIT = 1014
 
 SLICE_STATE_CROSS = 3006
 SLICE_STATE_SCROLL = 3007
@@ -727,6 +729,8 @@
     STATE_REGISTRATION: 3,
     # Override all other states when in navigation mode.
     STATE_NAVIGATION: 4,
+    # TODO(Henrique): check whether we need to override the previous states
+    STATE_MASK_3D_EDIT: 3,
 }
 
 # ------------ Prefereces options key ------------
@@ -1050,3 +1054,9 @@
 # Pedal
 KEYSTROKE_PEDAL_ENABLED = True
 KEYSTROKE_PEDAL_KEY = wx.WXK_F21
+
+# Mask 3D Edit modes
+
+MASK_3D_EDIT_INCLUDE = 0
+MASK_3D_EDIT_EXCLUDE = 1
+MASK_3D_EDIT_OP_NAME = [_("Include Inside"), _("Exclude Inside")]

invesalius/data/polygon_select.py

@@ -0,0 +1,71 @@
+# --------------------------------------------------------------------------
+# Software:     InVesalius - Software de Reconstrucao 3D de Imagens Medicas
+# Copyright:    (C) 2001  Centro de Pesquisas Renato Archer
+# Homepage:     http://www.softwarepublico.gov.br
+# Contact:      [email protected]
+# License:      GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
+# --------------------------------------------------------------------------
+#    Este programa e software livre; voce pode redistribui-lo e/ou
+#    modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
+#    publicada pela Free Software Foundation; de acordo com a versao 2
+#    da Licenca.
+#
+#    Este programa eh distribuido na expectativa de ser util, mas SEM
+#    QUALQUER GARANTIA; sem mesmo a garantia implicita de
+#    COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
+#    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
+#    detalhes.
+# --------------------------------------------------------------------------
+
+import invesalius.constants as const
+from invesalius.gui.widgets.canvas_renderer import CanvasHandlerBase, Polygon
+
+# import invesalius.session as ses
+
+
+class PolygonSelectCanvas(CanvasHandlerBase):
+    """
+    Inspired on PolygonDensityMeasure, stores and renders a polygon for a canvas
+    """
+
+    def __init__(self, colour=(255, 0, 0, 255), interactive=True):
+        super(PolygonSelectCanvas, self).__init__(None)
+        self.parent = None
+        self.children = []
+        self.layer = 0
+
+        self.colour = colour
+        self.points = []
+
+        self.complete = False
+
+        self.location = const.SURFACE
+        self.index = 0
+
+        self.polygon = Polygon(self, fill=False, closed=False, line_colour=self.colour, is_3d=False)
+        self.polygon.layer = 1
+        self.add_child(self.polygon)
+
+        self.text_box = None
+        self.interactive = interactive
+
+    def draw_to_canvas(self, gc, canvas):
+        pass
+
+    def insert_point(self, point):
+        self.polygon.append_point(point)
+
+    def complete_polygon(self):
+        if len(self.polygon.points) >= 3:
+            self.polygon.closed = True
+            self.complete = True
+
+    def IsComplete(self):
+        return self.complete
+
+    def SetVisibility(self, value):
+        self.polygon.visible = value
+
+    def set_interactive(self, value):
+        self.interactive = bool(value)
+        self.polygon.interactive = self.interactive

invesalius/data/styles_3d.py

@@ -28,10 +28,24 @@
 
 import invesalius.constants as const
 import invesalius.project as prj
+import invesalius.segmentation.mask_3d_edit as m3e
+from invesalius.data.polygon_select import PolygonSelectCanvas
 from invesalius.pubsub import pub as Publisher
 
 PROP_MEASURE = 0.8
 
+import numpy as np
+
+
+# TODO: find a better place
+def vtkarray_to_numpy(m):
+    nm = np.zeros((4, 4))
+    for i in range(4):
+        for j in range(4):
+            nm[i, j] = m.GetElement(i, j)
+
+    return nm
+
 
 class Base3DInteractorStyle(vtkInteractorStyleTrackballCamera):
     def __init__(self, viewer):
@@ -620,6 +634,94 @@ def OnScrollBackward(self, evt, obj):
         super().OnScrollBackward(evt, obj)
 
 
+class Mask3DEditorInteractorStyle(DefaultInteractorStyle):
+    """
+    Interactor style for selecting a polygon of interest and performing a mesh edit based on that.
+    """
+
+    def __init__(self, viewer):
+        super().__init__(viewer)
+        self.viewer = viewer
+
+        # Manages the mask operations
+        self.mask3deditor = m3e.Mask3DEditor()
+
+        self.picker = vtkCellPicker()
+        self.picker.PickFromListOn()
+
+        self.has_open_poly = False
+        self.poly = None
+
+        self.RemoveObservers("LeftButtonPressEvent")
+        self.AddObserver("LeftButtonPressEvent", self.OnInsertPolygonPoint)
+        self.AddObserver("RightButtonPressEvent", self.OnInsertPolygon)
+
+        Publisher.subscribe(self.ClearPolygons, "M3E clear polygons")
+
+    def CleanUp(self):
+        self.RemoveObservers("LeftButtonPressEvent")
+        self.RemoveObservers("RightButtonPressEvent")
+
+    def ClearPolygons(self):
+        self.viewer.canvas.draw_list.clear()
+        self.viewer.UpdateCanvas()
+
+    def OnInsertPolygonPoint(self, obj, evt):
+        interactor = self.viewer.interactor
+        interactor.Render()
+
+        mouse_x, mouse_y = self.viewer.interactor.GetEventPosition()
+
+        if not self.has_open_poly:
+            self.poly = PolygonSelectCanvas()
+            self.has_open_poly = True
+            self.viewer.canvas.draw_list.append(self.poly)
+
+        self.poly.insert_point((mouse_x, mouse_y))
+        self.viewer.UpdateCanvas()
+
+    def __get_cam_parameters(self):
+        w, h = self.viewer.GetSize()
+        self.viewer.ren.Render()
+        cam = self.viewer.ren.GetActiveCamera()
+        near, far = cam.GetClippingRange()
+
+        # This flip around the Y axis was done to countereffect the flip that vtk performs
+        # in volume.py:780. If we do not flip back, what is being displayed is flipped,
+        # although the actual coordinates are the initial ones, so the cutting gets wrong
+        # after rotations around y or x.
+        inv_Y_matrix = np.eye(4)
+        inv_Y_matrix[1, 1] = -1
+
+        # Composite transform world to viewport (projection * view)
+        M = cam.GetCompositeProjectionTransformMatrix(w / float(h), near, far)
+        M = vtkarray_to_numpy(M)
+        M = M @ inv_Y_matrix
+
+        MV = cam.GetViewTransformMatrix()
+        MV = vtkarray_to_numpy(MV)
+        MV = MV @ inv_Y_matrix
+
+        params = {
+            "model_to_screen": M,
+            "model_view": MV,
+            "resolution": (w, h),
+            "clipping_range": (near, far),
+        }
+
+        return params
+
+    def OnInsertPolygon(self, obj, evt):
+        self.poly.complete_polygon()
+        self.has_open_poly = False
+
+        self.viewer.UpdateCanvas()
+        self.viewer.ren.Render()
+
+        Publisher.sendMessage("M3E add polygon", points=self.poly.polygon.points)
+        Publisher.sendMessage("M3E set camera", params=self.__get_cam_parameters())
+
+
 class Styles:
     styles = {
         const.STATE_DEFAULT: DefaultInteractorStyle,
@@ -634,6 +736,7 @@ class Styles:
         const.SLICE_STATE_CROSS: CrossInteractorStyle,
         const.STATE_NAVIGATION: NavigationInteractorStyle,
         const.STATE_REGISTRATION: RegistrationInteractorStyle,
+        const.STATE_MASK_3D_EDIT: Mask3DEditorInteractorStyle,
     }
 
     @classmethod

invesalius/gui/task_slice.py

@@ -758,6 +758,42 @@ def __init__(self, parent):
         self.gradient_thresh = gradient_thresh
         self.bind_evt_gradient = True
 
+        ## LINE 5
+        m3ediv = wx.StaticLine(
+            self, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.LI_HORIZONTAL
+        )
+
+        cbox_mask_edit_3d = wx.CheckBox(self, -1, "Edit in 3D")
+        btn_do_3d_edit = wx.Button(self, -1, _("Cut"))
+        combo_mask_edit_3d_op = wx.ComboBox(
+            self, -1, "", choices=const.MASK_3D_EDIT_OP_NAME, style=wx.CB_DROPDOWN | wx.CB_READONLY
+        )
+        combo_mask_edit_3d_op.SetSelection(const.MASK_3D_EDIT_INCLUDE)
+
+        line5 = wx.BoxSizer(wx.HORIZONTAL)
+        # line5.Add(txt_mesh_edit_3d)
+        line5.Add(cbox_mask_edit_3d)
+        line5.Add(btn_do_3d_edit)
+        line5.Add(combo_mask_edit_3d_op)
+
+        self.cbox_mask_edit_3d = cbox_mask_edit_3d
+        self.btn_do_3d_edit = btn_do_3d_edit
+        self.combo_mask_edit_3d_op = combo_mask_edit_3d_op
+
+        ## LINE 6
+        cbox_mask_edit_3d_depth = wx.CheckBox(self, -1, "Cut with depth")
+        spin_mask_edit_3d_depth = wx.SpinCtrlDouble(self, value="1.0", min=0.0, max=1.0, inc=0.05)
+        btn_clear_3d_poly = wx.Button(self, -1, _("Clear Polygons"))
+
+        line6 = wx.BoxSizer(wx.HORIZONTAL)
+        line6.Add(cbox_mask_edit_3d_depth)
+        line6.Add(spin_mask_edit_3d_depth)
+        line6.Add(btn_clear_3d_poly)
+
+        self.cbox_mask_edit_3d_depth = cbox_mask_edit_3d_depth
+        self.spin_mask_edit_3d_depth = spin_mask_edit_3d_depth
+        self.btn_clear_3d_poly = btn_clear_3d_poly
+
         # Add lines into main sizer
         sizer = wx.BoxSizer(wx.VERTICAL)
         sizer.AddSpacer(7)
@@ -768,6 +804,12 @@ def __init__(self, parent):
         sizer.Add(text_thresh, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
         sizer.AddSpacer(5)
         sizer.Add(gradient_thresh, 0, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
+        sizer.AddSpacer(5)
+        sizer.Add(m3ediv, 0, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
+        sizer.AddSpacer(3)
+        sizer.Add(line5, 0, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
+        sizer.AddSpacer(3)
+        sizer.Add(line6, 0, wx.EXPAND | wx.LEFT | wx.RIGHT, 5)
         sizer.AddSpacer(7)
         sizer.Fit(self)
 
@@ -782,6 +824,12 @@ def __bind_events_wx(self):
         self.btn_brush_format.Bind(wx.EVT_MENU, self.OnMenu)
         self.Bind(grad.EVT_THRESHOLD_CHANGED, self.OnGradientChanged, self.gradient_thresh)
         self.combo_brush_op.Bind(wx.EVT_COMBOBOX, self.OnComboBrushOp)
+        self.cbox_mask_edit_3d.Bind(wx.EVT_CHECKBOX, self.OnCheckMaskEdit3D)
+        self.btn_do_3d_edit.Bind(wx.EVT_BUTTON, self.OnDoMaskEdit3D)
+        self.combo_mask_edit_3d_op.Bind(wx.EVT_COMBOBOX, self.OnComboMaskEdit3DMode)
+        self.cbox_mask_edit_3d_depth.Bind(wx.EVT_CHECKBOX, self.OnUseDepthMaskEdit3D)
+        self.spin_mask_edit_3d_depth.Bind(wx.EVT_SPINCTRLDOUBLE, self.OnSpinDepthMaskEdit3D)
+        self.btn_clear_3d_poly.Bind(wx.EVT_BUTTON, self.OnClearPolyMaskEdit3D)
 
     def __bind_events(self):
         Publisher.subscribe(self.SetThresholdBounds, "Update threshold limits")
@@ -885,6 +933,34 @@ def OnSetUnit(self, evt):
         self.unit = self.txt_unit.GetLabel()
         Publisher.sendMessage("Set edition brush unit", unit=self.unit)
 
+    def OnCheckMaskEdit3D(self, evt):
+        style_id = const.STATE_MASK_3D_EDIT
+
+        if self.cbox_mask_edit_3d.GetValue():
+            Publisher.sendMessage("Enable style", style=style_id)
+            Publisher.sendMessage("Enable mask 3D preview")
+        else:
+            Publisher.sendMessage("Disable style", style=style_id)
+
+    def OnDoMaskEdit3D(self, evt):
+        Publisher.sendMessage("M3E apply edit")
+
+    def OnComboMaskEdit3DMode(self, evt):
+        op_id = evt.GetSelection()
+        Publisher.sendMessage("M3E set edit mode", mode=op_id)
+
+    def OnUseDepthMaskEdit3D(self, evt):
+        cb_val = self.cbox_mask_edit_3d_depth.GetValue()
+        Publisher.sendMessage("M3E use depth", use=cb_val)
+        self.OnSpinDepthMaskEdit3D(evt)  # To pass the set value
+
+    def OnSpinDepthMaskEdit3D(self, evt):
+        spin_val = self.spin_mask_edit_3d_depth.GetValue()
+        Publisher.sendMessage("M3E depth value", value=spin_val)
+
+    def OnClearPolyMaskEdit3D(self, evt):
+        Publisher.sendMessage("M3E clear polygons")
+
 
 class WatershedTool(EditionTools):
     def __init__(self, parent):