Streamlined head surface creation

invesalius/constants.py

@@ -618,6 +618,7 @@
 ID_DENSITY_MEASURE = wx.NewIdRef()
 ID_MASK_DENSITY_MEASURE = wx.NewIdRef()
 ID_CREATE_SURFACE = wx.NewIdRef()
+ID_REMOVE_NON_VISIBLE_FACES = wx.NewIdRef()
 ID_CREATE_MASK = wx.NewIdRef()
 ID_MASK_3D_PREVIEW = wx.NewIdRef()
 ID_MASK_3D_RELOAD = wx.NewIdRef()
@@ -820,6 +821,16 @@
 BRAIN_INTENSITY_MTMS = 8
 BRAIN_UUID = 9
 
+# Page order in the coregistration panel
+
+IMPORTS_PAGE = 0
+HEAD_PAGE = 1
+IMAGE_PAGE = 2
+TRACKER_PAGE = 3
+REFINE_PAGE = 4
+STYLUS_PAGE = 5
+STIMULATOR_PAGE = 6
+
 # ------------ Navigation defaults -------------------
 
 MARKER_COLOUR = (1.0, 1.0, 0.0)

invesalius/data/polydata_utils.py

@@ -20,20 +20,33 @@
 import sys
 from typing import Iterable, List
 
-from vtkmodules.vtkCommonDataModel import vtkPolyData
+import numpy as np
+from vtkmodules.util import numpy_support
+from vtkmodules.vtkCommonCore import vtkIdList, vtkIdTypeArray
+from vtkmodules.vtkCommonDataModel import vtkPolyData, vtkSelection, vtkSelectionNode
 from vtkmodules.vtkFiltersCore import (
     vtkAppendPolyData,
     vtkCleanPolyData,
+    vtkIdFilter,
     vtkMassProperties,
     vtkPolyDataConnectivityFilter,
     vtkQuadricDecimation,
     vtkSmoothPolyDataFilter,
     vtkTriangleFilter,
 )
+from vtkmodules.vtkFiltersExtraction import vtkExtractSelection
+from vtkmodules.vtkFiltersGeometry import vtkGeometryFilter
 from vtkmodules.vtkFiltersModeling import vtkFillHolesFilter
 from vtkmodules.vtkIOGeometry import vtkOBJReader, vtkSTLReader
 from vtkmodules.vtkIOPLY import vtkPLYReader
 from vtkmodules.vtkIOXML import vtkXMLPolyDataReader, vtkXMLPolyDataWriter
+from vtkmodules.vtkRenderingCore import (
+    vtkActor,
+    vtkPolyDataMapper,
+    vtkRenderer,
+    vtkRenderWindow,
+    vtkSelectVisiblePoints,
+)
 
 import invesalius.constants as const
 import invesalius.data.vtk_utils as vu
@@ -83,14 +96,18 @@ def ApplySmoothFilter(
     smoother.SetNumberOfIterations(iterations)
     smoother.SetFeatureAngle(80)
     smoother.SetRelaxationFactor(relaxation_factor)
-    smoother.FeatureEdgeSmoothingOn()
-    smoother.BoundarySmoothingOn()
-    smoother.GetOutput().ReleaseDataFlagOn()
+    smoother.FeatureEdgeSmoothingOff()
+    smoother.BoundarySmoothingOff()
+    smoother.Update()
+    filler = vtkFillHolesFilter()
+    filler.SetInputConnection(smoother.GetOutputPort())
+    filler.SetHoleSize(1000)
+    filler.Update()
     smoother.AddObserver(
         "ProgressEvent", lambda obj, evt: UpdateProgress(smoother, "Smoothing surface...")
     )
 
-    return smoother.GetOutput()
+    return filler.GetOutput()
 
 
 def FillSurfaceHole(polydata: vtkPolyData) -> "vtkPolyData":
@@ -262,3 +279,98 @@ def SplitDisconectedParts(polydata: vtkPolyData) -> List[vtkPolyData]:
             UpdateProgress(region, _("Splitting disconnected regions..."))
 
     return polydata_collection
+
+
+def RemoveNonVisibleFaces(
+    polydata,
+    positions=[[1, 0, 0], [-1, 0, 0], [0, 1, 0], [0, -1, 0], [0, 0, 1], [0, 0, -1]],
+    remove_visible=False,
+):
+    polydata.BuildLinks()
+
+    mapper = vtkPolyDataMapper()
+    mapper.SetInputData(polydata)
+    mapper.Update()
+
+    actor = vtkActor()
+    actor.SetMapper(mapper)
+
+    renderer = vtkRenderer()
+    renderer.AddActor(actor)
+
+    render_window = vtkRenderWindow()
+    render_window.AddRenderer(renderer)
+    render_window.SetSize(800, 800)
+    render_window.OffScreenRenderingOn()
+
+    camera = renderer.GetActiveCamera()
+    renderer.ResetCamera()
+
+    pos = np.array(camera.GetPosition())
+    fp = np.array(camera.GetFocalPoint())
+    v = pos - fp
+    mag = np.linalg.norm(v)
+    vn = v / mag
+
+    id_filter = vtkIdFilter()
+    id_filter.SetInputData(polydata)
+    id_filter.PointIdsOn()
+    id_filter.Update()
+
+    set_points = None
+
+    for position in positions:
+        pos = fp + np.array(position) * mag
+        camera.SetPosition(pos.tolist())
+        renderer.ResetCamera()
+        render_window.Render()
+
+        select_visible_points = vtkSelectVisiblePoints()
+        select_visible_points.SetInputData(id_filter.GetOutput())
+        select_visible_points.SetRenderer(renderer)
+        select_visible_points.Update()
+        output = select_visible_points.GetOutput()
+        id_points = numpy_support.vtk_to_numpy(
+            output.GetPointData().GetAbstractArray("vtkIdFilter_Ids")
+        )
+        if set_points is None:
+            set_points = set(id_points.tolist())
+        else:
+            set_points.update(id_points.tolist())
+
+    if remove_visible:
+        set_points = set(range(polydata.GetNumberOfPoints())) - set_points
+    cells_ids = set()
+    for p_id in set_points:
+        id_list = vtkIdList()
+        polydata.GetPointCells(p_id, id_list)
+        for i in range(id_list.GetNumberOfIds()):
+            cells_ids.add(id_list.GetId(i))
+
+    try:
+        id_list = numpy_support.numpy_to_vtkIdTypeArray(np.array(list(cells_ids), dtype=np.int64))
+    except ValueError:
+        id_list = vtkIdTypeArray()
+
+    selection_node = vtkSelectionNode()
+    selection_node.SetFieldType(vtkSelectionNode.CELL)
+    selection_node.SetContentType(vtkSelectionNode.INDICES)
+    selection_node.SetSelectionList(id_list)
+
+    selection = vtkSelection()
+    selection.AddNode(selection_node)
+
+    extract_selection = vtkExtractSelection()
+    extract_selection.SetInputData(0, polydata)
+    extract_selection.SetInputData(1, selection)
+    extract_selection.Update()
+
+    geometry_filter = vtkGeometryFilter()
+    geometry_filter.SetInputData(extract_selection.GetOutput())
+    geometry_filter.Update()
+
+    clean_polydata = vtkCleanPolyData()
+    clean_polydata.SetInputData(geometry_filter.GetOutput())
+    clean_polydata.Update()
+
+    return clean_polydata.GetOutput()

invesalius/data/surface.py

@@ -73,6 +73,7 @@
 from invesalius.data.converters import convert_custom_bin_to_vtk
 from invesalius.gui import dialogs
 from invesalius.i18n import tr as _
+from invesalius.utils import new_name_by_pattern
 
 # TODO: Verificar ReleaseDataFlagOn and SetSource
 
@@ -216,7 +217,9 @@ def __bind_events(self):
         # ----
         Publisher.subscribe(self.OnSplitSurface, "Split surface")
         Publisher.subscribe(self.OnLargestSurface, "Create surface from largest region")
+        Publisher.subscribe(self.OnRemoveNonVisibleFaces, "Remove non-visible faces")
         Publisher.subscribe(self.OnSeedSurface, "Create surface from seeds")
+        Publisher.subscribe(self.OnSmoothSurface, "Create smooth surface")
         Publisher.subscribe(self.GetBrainSurfaceActor, "Get brain surface actor")
 
         Publisher.subscribe(self.OnDuplicate, "Duplicate surfaces")
@@ -292,6 +295,23 @@ def OnSeedSurface(self, seeds):
         Publisher.sendMessage("Show single surface", index=index, visibility=True)
         # self.ShowActor(index, True)
 
+    def OnSmoothSurface(self, overwrite=False, name=""):
+        """
+        Create a new smooth surface, based on the last selected surface.
+        """
+        progress_dialog = dialogs.SmoothSurfaceProgressWindow()
+        progress_dialog.Update()
+        index = self.last_surface_index
+        proj = prj.Project()
+        surface = proj.surface_dict[index]
+
+        new_polydata = pu.ApplySmoothFilter(
+            polydata=surface.polydata, iterations=20, relaxation_factor=0.4
+        )
+        new_index = self.CreateSurfaceFromPolydata(new_polydata, overwrite=overwrite, name=name)
+        Publisher.sendMessage("Show single surface", index=new_index, visibility=True)
+        progress_dialog.Close()
+
     def OnSplitSurface(self):
         """
         Create n new surfaces, based on the last selected surface,
@@ -310,18 +330,45 @@ def OnSplitSurface(self):
 
         Publisher.sendMessage("Show multiple surfaces", index_list=index_list, visibility=True)
 
-    def OnLargestSurface(self):
+    def OnLargestSurface(self, overwrite=False, name=""):
         """
         Create a new surface, based on largest part of the last
         selected surface.
         """
+        progress_dialog = dialogs.SelectLargestSurfaceProgressWindow()
+        progress_dialog.Update()
         index = self.last_surface_index
         proj = prj.Project()
         surface = proj.surface_dict[index]
 
         new_polydata = pu.SelectLargestPart(surface.polydata)
-        new_index = self.CreateSurfaceFromPolydata(new_polydata)
+        new_index = self.CreateSurfaceFromPolydata(new_polydata, overwrite=overwrite, name=name)
         Publisher.sendMessage("Show single surface", index=new_index, visibility=True)
+        progress_dialog.Close()
+
+    def OnRemoveNonVisibleFaces(self):
+        """
+        Create a new surface where non-visible faces have been removed.
+        """
+        progress_dialog = dialogs.RemoveNonVisibleFacesProgressWindow()
+        progress_dialog.Update()
+
+        proj = prj.Project()
+        index = self.last_surface_index
+        surface = proj.surface_dict[index]
+        new_polydata = pu.RemoveNonVisibleFaces(surface.polydata)
+
+        name = new_name_by_pattern(f"{surface.name}_removed_nonvisible")
+        overwrite = True
+
+        Publisher.sendMessage(
+            "Create surface from polydata",
+            polydata=new_polydata,
+            name=name,
+            overwrite=overwrite,
+        )
+        Publisher.sendMessage("Fold surface task")
+        progress_dialog.Close()
 
     def OnImportCustomBinFile(self, filename):
         import os

invesalius/gui/deep_learning_seg_dialog.py

@@ -48,7 +48,14 @@
 
 class DeepLearningSegmenterDialog(wx.Dialog):
     def __init__(
-        self, parent, title, has_torch=True, has_plaidml=True, has_theano=True, segmenter=None
+        self,
+        parent,
+        title,
+        auto_segment=False,
+        has_torch=True,
+        has_plaidml=True,
+        has_theano=True,
+        segmenter=None,
     ):
         wx.Dialog.__init__(
             self,
@@ -68,6 +75,7 @@ def __init__(
         #  self.pg_dialog = None
         self.torch_devices = TORCH_DEVICES
         self.plaidml_devices = PLAIDML_DEVICES
+        self.auto_segment = auto_segment
 
         self.backends = backends
 
@@ -87,6 +95,9 @@ def __init__(
         self.OnSetBackend()
         self.HideProgress()
 
+        if self.auto_segment:
+            self.OnSegment(self)
+
     def _init_gui(self):
         self.cb_backends = wx.ComboBox(
             self,
@@ -332,6 +343,10 @@ def AfterSegment(self):
         self.elapsed_time_timer.Stop()
         self.apply_segment_threshold()
 
+        if self.auto_segment:
+            self.OnClose(self)
+            Publisher.sendMessage("Brain segmentation completed")
+
     def SetProgress(self, progress):
         self.progress.SetValue(int(progress * 100))
         wx.GetApp().Yield()
@@ -361,8 +376,9 @@ def OnTickTimer(self, evt):
             if progress == np.inf:
                 progress = 1
                 self.AfterSegment()
-            progress = max(0, min(progress, 1))
-            self.SetProgress(float(progress))
+            else:
+                progress = max(0, min(progress, 1))
+                self.SetProgress(float(progress))
 
     def OnClose(self, evt):
         #  self.segmenter.stop = True
@@ -393,14 +409,15 @@ def ShowProgress(self):
 
 
 class BrainSegmenterDialog(DeepLearningSegmenterDialog):
-    def __init__(self, parent):
+    def __init__(self, parent, auto_segment=False):
         super().__init__(
             parent=parent,
             title=_("Brain segmentation"),
             has_torch=True,
             has_plaidml=True,
             has_theano=True,
             segmenter=segment.BrainSegmentProcess,
+            auto_segment=auto_segment,
         )
 
 

invesalius/gui/default_tasks.py

@@ -104,7 +104,7 @@ def GetExpandedIconImage():
 # Main panel
 class Panel(wx.Panel):
     def __init__(self, parent):
-        wx.Panel.__init__(self, parent, pos=wx.Point(5, 5), size=wx.Size(350, 656))
+        wx.Panel.__init__(self, parent, pos=wx.Point(5, 5), size=wx.Size(385, 656))
 
         # sizer = wx.BoxSizer(wx.VERTICAL)
         gbs = wx.GridBagSizer(5, 5)
@@ -331,7 +331,6 @@ def __init__(self, parent):
                 elif name == _("Configure 3D surface"):
                     self.__id_surface = item.GetId()
 
-        fold_panel.Expand(fold_panel.GetFoldPanel(0))
         self.fold_panel = fold_panel
         self.image_list = image_list
 
@@ -342,6 +341,12 @@ def __init__(self, parent):
         self.SetSizerAndFit(sizer)
         self.__bind_events()
 
+        # Show the navigation panel in navigation mode; otherwise, show the imports panel
+        if mode == const.MODE_NAVIGATOR:
+            self.fold_panel.Expand(self.fold_panel.GetFoldPanel(1))
+        else:
+            self.fold_panel.Expand(self.fold_panel.GetFoldPanel(0))
+
     def __bind_events(self):
         session = ses.Session()
         mode = session.GetConfig("mode")
@@ -370,9 +375,12 @@ def OnEnableState(self, state):
             self.SetStateProjectClose()
 
     def SetStateProjectClose(self):
+        session = ses.Session()
+        mode = session.GetConfig("mode")
         self.fold_panel.Expand(self.fold_panel.GetFoldPanel(0))
         for item in self.enable_items:
-            item.Disable()
+            if mode != const.MODE_NAVIGATOR:
+                item.Disable()
 
     def SetStateProjectOpen(self):
         session = ses.Session()