Support VTK 9, drop support for VTK <6, fix CI test build on macOS (#733

)

* fix: Support VTK 9

* enh: Drop support for VTK<6

* fix: Replace deprecated bind2nd

* fix: Missing include in Viewer source file

* fixup: Missing include of vtkIdList.h

* fixup: Add missing include of vtkNew.h

* fix: Download URL of VTK, use curl -L flag to follow redirects

* enh: Use VTK 8.2.0 for CI test build on macOS

* fix: Use Homebrew to install VTK 8.2 or 9.0 on macOS

* fixup: Use keg-only [email protected] Homebrew installation if available

* fixup: brew install [email protected] has no —without-python flag

* fixup: Homebrew vtk formula has no —without-python flag

* fixup: travis.sh script syntax

* enh: Remove vtk_prefix before building VTK from source files

* tmp: Enable verbose Bash output for install_depends.sh

* fixup: Use VTK 8.2.0 build from source files

* enh: Add Travis CI environment variable DEBUG_VTK_BUILD

* fix: Set CMake policy CMP0057 to NEW for Boost installed by homebrew [email protected]

* tmp

* fix: install_depends.sh renamed VTK 9 cache variables

* fix: VTK 9 CMake cache variable options

* ci: Use VTK 9.0 installed with Homebrew

* fix: Remove unused variable from install_depends.h

* fix: Prefix rm command with “run”

* fixup: Add missing include of vtkVersionMacros.h

* fix: member access into incomplete type 'vtkIdTypeArray'

.travis.yml

@@ -20,7 +20,7 @@ env:
   # - On Ubuntu, use default version installed by apt-get
   # - On macOS, build recent VTK version from sources and cache installation
   - LINUX_VTK_VERSION=6.0.0
-  - MACOS_VTK_VERSION=8.1.0
+  - MACOS_VTK_VERSION=9.0  # Homebrew versions: 8.2, 9.0; otherwise build from sources
   - WITH_CCACHE=ON    # speed up MIRTK build itself using ccache
   - WITH_ARPACK=OFF   # requires time consuming build of gcc on macOS
   - WITH_UMFPACK=OFF  # ARPACK & UMFPACK dependencies come in pairs

Applications/config/Depends.cmake

@@ -57,15 +57,15 @@
 if (MIRTK_Image_FOUND)
   # command: calculate
   if (MIRTK_Image_WITH_VTK)
-    basis_find_package(VTK 8|7|6 REQUIRED COMPONENTS vtkCommonCore vtkCommonDataModel)
+    basis_find_package(VTK REQUIRED COMPONENTS vtkCommonCore vtkCommonDataModel)
   endif ()
 endif ()
 
 # ----------------------------------------------------------------------------
 # Dependencies of point set commands
 if (MIRTK_PointSet_FOUND)
   # command: all point set commands, info
-  basis_find_package(VTK 8|7|6 REQUIRED
+  basis_find_package(VTK REQUIRED
     COMPONENTS
       vtkCommonCore
       vtkCommonDataModel

Applications/src/aggregate-images.cc

@@ -369,7 +369,7 @@ double GiniCoefficient(Array<T> &samples)
   if (shift <= static_cast<T>(0)) {
     if (numeric_limits<T>::is_integer) shift -= static_cast<T>(1);
     else                               shift -= static_cast<T>(1e-6);
-    Transform(samples, bind2nd(minus<T>(), shift));
+    Transform(samples, bind(minus<T>(), std::placeholders::_1, shift));
   }
   Sort(samples);
   for (int i = 0; i < n; ++i) {
@@ -408,7 +408,7 @@ double EntropyIndex(Array<T> &samples, int alpha = 1)
   if (shift <= static_cast<T>(0)) {
     if (numeric_limits<T>::is_integer) shift -= static_cast<T>(1);
     else                               shift -= static_cast<T>(1e-6);
-    Transform(samples, bind2nd(minus<T>(), shift));
+    Transform(samples, bind(minus<T>(), std::placeholders::_1, shift));
   }
   // Compute mean value
   double mean = 0.;

Applications/src/calculate-surface-attributes.cc

@@ -249,18 +249,17 @@ BorderPointMask(vtkPolyData *surface, vtkDataArray *point_labels,
   mask = NewVtkDataArray(VTK_UNSIGNED_CHAR, surface->GetNumberOfPoints(), 1, "BorderMask");
   double label;
   if (cell_labels) {
-    vtkPolyDataGetPointCellsNumCellsType ncells;
-    vtkIdType *cells;
+    vtkNew<vtkIdList> cellIds;
     for (vtkIdType ptId = 0; ptId < surface->GetNumberOfPoints(); ++ptId) {
-      surface->GetPointCells(ptId, ncells, cells);
-      if (ncells == 1) {
+      surface->GetPointCells(ptId, cellIds.GetPointer());
+      if (cellIds->GetNumberOfIds() == 1) {
         mask->SetComponent(ptId, 0, 1.);
       } else {
         mask->SetComponent(ptId, 0, 0.);
-        if (ncells > 0) {
-          label = cell_labels->GetComponent(cells[0], 0);
-          for (vtkPolyDataGetPointCellsNumCellsType i = 1; i < ncells; ++i) {
-            if (cell_labels->GetComponent(cells[i], 0) != label) {
+        if (cellIds->GetNumberOfIds() > 0) {
+          label = cell_labels->GetComponent(cellIds->GetId(0), 0);
+          for (vtkIdType i = 1; i < cellIds->GetNumberOfIds(); ++i) {
+            if (cell_labels->GetComponent(cellIds->GetId(i), 0) != label) {
               mask->SetComponent(ptId, 0, 1.);
               break;
             }
@@ -307,18 +306,17 @@ BorderCellMask(vtkPolyData *surface, vtkDataArray *cell_labels, bool edge_nbrs =
       }
     }
   } else {
-    vtkPolyDataGetPointCellsNumCellsType ncells;
-    vtkIdType npts, *pts, *cells;
+    vtkNew<vtkIdList> cellIds, ptIds;
     for (vtkIdType cellId = 0; cellId < surface->GetNumberOfCells(); ++cellId) {
       mask->SetComponent(cellId, 0, 0.);
       label = cell_labels->GetComponent(cellId, 0);
-      surface->GetCellPoints(cellId, npts, pts);
-      for (vtkIdType i = 0; i < npts; ++i) {
-        surface->GetPointCells(pts[i], ncells, cells);
-        for (vtkPolyDataGetPointCellsNumCellsType j = 0; j < ncells; ++j) {
-          if (cell_labels->GetComponent(cells[j], 0) != label) {
+      surface->GetCellPoints(cellId, ptIds.GetPointer());
+      for (vtkIdType i = 0; i < ptIds->GetNumberOfIds(); ++i) {
+        surface->GetPointCells(ptIds->GetId(i), cellIds.GetPointer());
+        for (vtkIdType j = 0; j < cellIds->GetNumberOfIds(); ++j) {
+          if (cell_labels->GetComponent(cellIds->GetId(j), 0) != label) {
             mask->SetComponent(cellId, 0, 1.);
-            i = npts; // break all inner loops
+            i = ptIds->GetNumberOfIds(); // break all inner loops
             break;
           }
         }

Applications/src/convert-pointset-to-mat.cc

@@ -25,6 +25,7 @@
 #include "mirtk/PointSetIO.h"
 #include "mirtk/PointSetUtils.h"
 
+#include "vtkNew.h"
 #include "vtkSmartPointer.h"
 #include "vtkPolyData.h"
 #include "vtkCellArray.h"
@@ -172,9 +173,11 @@ int main(int argc, char *argv[])
     vtkIdType i = 0;
     vtkCellArray *cells = polydata->GetPolys();
     cells->InitTraversal();
-    vtkIdType npts, *pts;
-    while (cells->GetNextCell(npts, pts)) {
-      F(i, 0) = pts[0]+1, F(i, 1) = pts[1]+1, F(i, 2) = pts[2]+1;
+    vtkNew<vtkIdList> ptIds;
+    while (cells->GetNextCell(ptIds.GetPointer())) {
+      F(i, 0) = ptIds->GetId(0) + 1;
+      F(i, 1) = ptIds->GetId(1) + 1;
+      F(i, 2) = ptIds->GetId(2) + 1;
       ++i;
     }
     mxArray *var = MatrixToMxArray(F);

Applications/src/convert-pointset.cc

@@ -27,6 +27,7 @@
 #include "mirtk/PointSetUtils.h"
 #include "mirtk/EuclideanDistanceTransform.h"
 
+#include "vtkNew.h"
 #include "vtkPolyData.h"
 #include "vtkUnstructuredGrid.h"
 #include "vtkImageData.h"

Applications/src/copy-pointset-attributes.cc

@@ -23,6 +23,7 @@
 #include "mirtk/PointSetIO.h"
 #include "mirtk/PointSetUtils.h"
 
+#include "vtkNew.h"
 #include "vtkSmartPointer.h"
 #include "vtkPointSet.h"
 #include "vtkPointData.h"
@@ -249,9 +250,9 @@ ConvertPointToCellLabels(vtkPointSet *pset, vtkDataArray *labels,
       double label;
       OrderedMap<double, int> hist;
       OrderedMap<double, int>::iterator bin;
-      vtkSmartPointer<vtkIdList> ptIds = vtkSmartPointer<vtkIdList>::New();
+      vtkNew<vtkIdList> ptIds;
       for (vtkIdType cellId = 0; cellId < pset->GetNumberOfCells(); ++cellId) {
-        pset->GetCellPoints(cellId, ptIds);
+        pset->GetCellPoints(cellId, ptIds.GetPointer());
         for (int j = 0; j < labels->GetNumberOfComponents(); ++j) {
           hist.clear();
           for (vtkIdType i = 0; i < ptIds->GetNumberOfIds(); ++i) {
@@ -274,9 +275,9 @@ ConvertPointToCellLabels(vtkPointSet *pset, vtkDataArray *labels,
     case UnanimousVote: {
       const double invalid = NaN;
       double       label;
-      vtkSmartPointer<vtkIdList> ptIds = vtkSmartPointer<vtkIdList>::New();
+      vtkNew<vtkIdList> ptIds;
       for (vtkIdType cellId = 0; cellId < pset->GetNumberOfCells(); ++cellId) {
-        pset->GetCellPoints(cellId, ptIds);
+        pset->GetCellPoints(cellId, ptIds.GetPointer());
         for (int j = 0; j < labels->GetNumberOfComponents(); ++j) {
           if (ptIds->GetNumberOfIds() == 0) {
             label = invalid;
@@ -319,9 +320,9 @@ ConvertCellToPointLabels(vtkPointSet *pset, vtkDataArray *labels,
       double label;
       OrderedMap<double, int> hist;
       OrderedMap<double, int>::iterator bin;
-      vtkSmartPointer<vtkIdList> cellIds = vtkSmartPointer<vtkIdList>::New();
+      vtkNew<vtkIdList> cellIds;
       for (vtkIdType ptId = 0; ptId < pset->GetNumberOfPoints(); ++ptId) {
-        pset->GetPointCells(ptId, cellIds);
+        pset->GetPointCells(ptId, cellIds.GetPointer());
         for (int j = 0; j < labels->GetNumberOfComponents(); ++j) {
           hist.clear();
           for (vtkIdType i = 0; i < cellIds->GetNumberOfIds(); ++i) {
@@ -344,9 +345,9 @@ ConvertCellToPointLabels(vtkPointSet *pset, vtkDataArray *labels,
     case UnanimousVote: {
       double       label;
       const double invalid = NaN;
-      vtkSmartPointer<vtkIdList> cellIds = vtkSmartPointer<vtkIdList>::New();
+      vtkNew<vtkIdList> cellIds;
       for (vtkIdType ptId = 0; ptId < pset->GetNumberOfPoints(); ++ptId) {
-        pset->GetPointCells(ptId, cellIds);
+        pset->GetPointCells(ptId, cellIds.GetPointer());
         for (int j = 0; j < labels->GetNumberOfComponents(); ++j) {
           if (cellIds->GetNumberOfIds() == 0) {
             label = invalid;

Applications/src/evaluate-distance.cc

@@ -468,15 +468,14 @@ int main(int argc, char *argv[])
       vtkNew<vtkCellLocator> locator;
       locator->SetDataSet(target);
       locator->BuildLocator();
-      vtkSmartPointer<vtkIdList> ptIds;
-      ptIds = vtkSmartPointer<vtkIdList>::New();
+      vtkNew<vtkIdList> ptIds;
 
       for (vtkIdType ptId = 0; ptId < target->GetNumberOfPoints(); ++ptId) {
         source->GetPoint(ptId, a);
         locator->FindClosestPoint(a, b, cellId, subId, dist);
         dist = sqrt(dist);
         if (mask) {
-          target->GetCellPoints(cellId, ptIds);
+          target->GetCellPoints(cellId, ptIds.GetPointer());
           for (vtkIdType i = 0; i < ptIds->GetNumberOfIds(); ++i) {
             if (mask->GetComponent(ptIds->GetId(i), 0) != 0.) {
               if (dist > hausdorff_dist) hausdorff_dist = dist;

Applications/src/evaluate-distortion.cc

@@ -97,19 +97,20 @@ enum DistortionMeasure
 // -----------------------------------------------------------------------------
 double Angle(vtkPolyData *mesh, vtkIdType cellId, vtkIdType ptId)
 {
-  vtkIdType npts, *pts, i[3] = {0, 1, 2};
-  mesh->GetCellPoints(cellId, npts, pts);
-  for (vtkIdType j = 0; j < npts; ++j) {
-    if (pts[j] == ptId) {
+  vtkIdType i[3] = {0, 1, 2};
+  vtkNew<vtkIdList> ptIds;
+  mesh->GetCellPoints(cellId, ptIds.GetPointer());
+  for (vtkIdType j = 0; j < ptIds->GetNumberOfIds(); ++j) {
+    if (ptIds->GetId(j) == ptId) {
       i[0] = i[j];
       i[j] = 0;
       break;
     }
   }
   double p[3][3], ab, ac, bc;
-  mesh->GetPoint(pts[0], p[i[0]]);
-  mesh->GetPoint(pts[1], p[i[1]]);
-  mesh->GetPoint(pts[2], p[i[2]]);
+  mesh->GetPoint(ptIds->GetId(0), p[i[0]]);
+  mesh->GetPoint(ptIds->GetId(1), p[i[1]]);
+  mesh->GetPoint(ptIds->GetId(2), p[i[2]]);
   ab = pow(p[1][0] - p[0][0], 2) + pow(p[1][1] - p[0][1], 2) + pow(p[1][2] - p[0][2], 2);
   ac = pow(p[2][0] - p[0][0], 2) + pow(p[2][1] - p[0][1], 2) + pow(p[2][2] - p[0][2], 2);
   bc = pow(p[2][0] - p[1][0], 2) + pow(p[2][1] - p[1][1], 2) + pow(p[2][2] - p[1][2], 2);
@@ -131,37 +132,38 @@ AngularDistortion(vtkPolyData *orig, vtkPolyData *mesh)
   array->SetNumberOfComponents(2);
   array->SetNumberOfTuples(npoints);
 
-  vtkPolyDataGetPointCellsNumCellsType ncells1, ncells2;
-  vtkIdType      *cells1, *cells2;
+  vtkNew<vtkIdList> cellIds1, cellIds2;
+
   double         sum1,    sum2;
   Array<double>  angles1, angles2;
   double         ratio, avg_ratio, max_ratio;
 
   for (vtkIdType ptId = 0; ptId < npoints; ++ptId) {
-    orig->GetPointCells(ptId, ncells1, cells1);
-    mesh->GetPointCells(ptId, ncells2, cells2);
-    if (ncells1 != ncells2) {
+    orig->GetPointCells(ptId, cellIds1.GetPointer());
+    mesh->GetPointCells(ptId, cellIds2.GetPointer());
+    if (cellIds1->GetNumberOfIds() != cellIds2->GetNumberOfIds()) {
       FatalError("AngularDistortion: Point " << ptId << " belongs to different number of cells in the two meshes!");
     }
-    angles1.resize(ncells1);
-    angles2.resize(ncells2);
-    for (vtkPolyDataGetPointCellsNumCellsType i = 0; i < ncells1; ++i) {
-      if (cells1[i] != cells2[i]) {
+    const vtkIdType ncells = cellIds1->GetNumberOfIds();
+    angles1.resize(ncells);
+    angles2.resize(ncells);
+    for (vtkIdType i = 0; i < ncells; ++i) {
+      if (cellIds1->GetId(i) != cellIds2->GetId(i)) {
         FatalError("AngularDistortion: Lists of cell IDs to which point " << ptId << " belongs differ!");
       }
-      angles1[i] = Angle(orig, cells1[i], ptId);
-      angles2[i] = Angle(mesh, cells2[i], ptId);
+      angles1[i] = Angle(orig, cellIds1->GetId(i), ptId);
+      angles2[i] = Angle(mesh, cellIds2->GetId(i), ptId);
     }
     sum1 = Accumulate(angles1);
     sum2 = Accumulate(angles2);
     avg_ratio = .0;
     max_ratio = .0;
-    for (vtkPolyDataGetPointCellsNumCellsType i = 0; i < ncells1; ++i) {
+    for (vtkIdType i = 0; i < ncells; ++i) {
       ratio = (angles1[i] / sum1) / (angles2[i] / sum2);
       max_ratio = max(max_ratio, ratio);
       avg_ratio += ratio;
     }
-    avg_ratio /= ncells1;
+    avg_ratio /= ncells;
     array->SetComponent(ptId, 0, avg_ratio);
     array->SetComponent(ptId, 1, max_ratio);
   }

Applications/src/evaluate-surface-mesh.cc

@@ -356,16 +356,17 @@ int main(int argc, char *argv[])
     surface.TakeReference(input->NewInstance());
     surface->SetPoints(input->GetPoints());
     surface->Allocate(input->GetNumberOfCells());
-    vtkIdType cellId, npts, *pts;
+    vtkIdType cellId;
+    vtkNew<vtkIdList> ptIds;
     vtkSmartPointer<vtkIdTypeArray> origCellIds;
     origCellIds = vtkSmartPointer<vtkIdTypeArray>::New();
     origCellIds->SetName("OriginalIds");
     origCellIds->SetNumberOfComponents(1);
     origCellIds->SetNumberOfTuples(selection.size());
     surface->GetCellData()->AddArray(origCellIds);
     for (auto origCellId : selection) {
-      input->GetCellPoints(origCellId, npts, pts);
-      cellId = surface->InsertNextCell(input->GetCellType(origCellId), npts, pts);
+      input->GetCellPoints(origCellId, ptIds.GetPointer());
+      cellId = surface->InsertNextCell(input->GetCellType(origCellId), ptIds.GetPointer());
       origCellIds->SetValue(cellId, origCellId);
     }
     surface->BuildLinks();
@@ -442,14 +443,14 @@ int main(int argc, char *argv[])
             input->GetPointData()->RemoveArray(pointIds->GetName());
             input->GetPointData()->AddArray(pointIds);
             // Add surface component IDs cell data
-            vtkIdType npts, *pts;
+            vtkNew<vtkIdList> ptIds;
             output->BuildLinks();
             cellIds = NewVtkDataArray(ncomp < 256 ? VTK_UNSIGNED_CHAR :
                                         (ncomp < 65535 ? VTK_UNSIGNED_SHORT : VTK_INT),
                                       surface->GetNumberOfCells(), 1, COMPONENT_ID);
             for (vtkIdType cellId = 0; cellId < output->GetNumberOfCells(); ++cellId) {
-              output->GetCellPoints(cellId, npts, pts);
-              cellIds->SetComponent(cellId, 0, (npts == 0 ? 0. : compIds->GetComponent(pts[0], 0)));
+              output->GetCellPoints(cellId, ptIds.GetPointer());
+              cellIds->SetComponent(cellId, 0, (ptIds->GetNumberOfIds() == 0 ? 0. : compIds->GetComponent(ptIds->GetId(0), 0)));
             }
             AddCellData(input, surface, cellIds);
           }
@@ -601,15 +602,14 @@ int main(int argc, char *argv[])
         collisions.Run();
 
         if (output_name) {
-          vtkIdType *cells;
-          vtkPolyDataGetPointCellsNumCellsType ncells;
+          vtkNew<vtkIdList> cellIds;
           vtkSmartPointer<vtkDataArray> mask;
           mask = NewVtkDataArray(VTK_UNSIGNED_CHAR, surface->GetNumberOfPoints(), 1, "CollisionMask");
           for (vtkIdType ptId = 0; ptId < surface->GetNumberOfPoints(); ++ptId) {
             mask->SetComponent(ptId, 0, 0.);
-            surface->GetPointCells(ptId, ncells, cells);
-            for (vtkPolyDataGetPointCellsNumCellsType i = 0; i < ncells; ++i) {
-              if (collisions.GetCollisionType(cells[i]) != SurfaceCollisions::NoCollision) {
+            surface->GetPointCells(ptId, cellIds.GetPointer());
+            for (vtkIdType i = 0; i < cellIds->GetNumberOfIds(); ++i) {
+              if (collisions.GetCollisionType(cellIds->GetId(i)) != SurfaceCollisions::NoCollision) {
                 mask->SetComponent(ptId, 0, 1.);
                 break;
               }

Applications/src/extract-connected-points.cc

@@ -29,6 +29,7 @@
 #include "vtkPolyDataWriter.h"
 #include "vtkPolyDataConnectivityFilter.h"
 #include "vtkCleanPolyData.h"
+#include "vtkIdTypeArray.h"
 
 using namespace mirtk;
 

Applications/src/info.cc

@@ -201,8 +201,8 @@ struct CountTriangleTriangleIntersections
     vtkSmartPointer<vtkIdList>      ptIds   = vtkSmartPointer<vtkIdList>::New();
     vtkSmartPointer<vtkIdList>      cellIds = vtkSmartPointer<vtkIdList>::New();
 
-    vtkPolyDataGetPointCellsNumCellsType ncells;
-    vtkIdType *cells, cellId2;
+    vtkIdType cellId2;
+    vtkNew<vtkIdList> ptCellIds;
     double r1, c1[3], v1[3], v2[3], v3[3], u1[3], u2[3], u3[3];
 
     for (vtkIdType cellId1 = re.begin(); cellId1 != re.end(); ++cellId1) {
@@ -215,9 +215,9 @@ struct CountTriangleTriangleIntersections
       _PointLocator->FindPointsWithinRadius(3.0 * r1, c1, ptIds);
       cellIds->Reset();
       for (vtkIdType i = 0; i < ptIds->GetNumberOfIds(); ++i) {
-        _DataSet->GetPointCells(ptIds->GetId(i), ncells, cells);
-        for (vtkPolyDataGetPointCellsNumCellsType j = 0; j < ncells; ++j) {
-          cellIds->InsertUniqueId(cells[j]);
+        _DataSet->GetPointCells(ptIds->GetId(i), ptCellIds.GetPointer());
+        for (vtkIdType j = 0; j < ptCellIds->GetNumberOfIds(); ++j) {
+          cellIds->InsertUniqueId(ptCellIds->GetId(j));
         }
       }
       for (vtkIdType i = 0; i < cellIds->GetNumberOfIds(); ++i) {