From 521898a2b5969bdb930ed8d4bc2fdc9631473383 Mon Sep 17 00:00:00 2001
From: Nicolas Vuaille <nicolas.vuaille@kitware.com>
Date: Tue, 3 Apr 2018 14:25:56 +0200
Subject: [PATCH] Molecule to polydata conversion
* introduce vtkMoleculeToLinesFilter
** Create polydata with atom == point, bond == line cell. Copy data.
* Fix AtomBall and BondStick conversion:
** set array name for bond orders and atomic numbers
** fix allocated size
---
Domains/Chemistry/CMakeLists.txt | 1 +
Domains/Chemistry/Testing/Cxx/CMakeLists.txt | 1 +
.../Testing/Cxx/TestMoleculeToLines.cxx | 62 +++++++++++++++++++
.../Chemistry/vtkMoleculeToAtomBallFilter.cxx | 4 +-
.../vtkMoleculeToBondStickFilter.cxx | 4 +-
.../Chemistry/vtkMoleculeToLinesFilter.cxx | 50 +++++++++++++++
Domains/Chemistry/vtkMoleculeToLinesFilter.h | 51 +++++++++++++++
7 files changed, 171 insertions(+), 2 deletions(-)
create mode 100644 Domains/Chemistry/Testing/Cxx/TestMoleculeToLines.cxx
create mode 100644 Domains/Chemistry/vtkMoleculeToLinesFilter.cxx
create mode 100644 Domains/Chemistry/vtkMoleculeToLinesFilter.h
diff --git a/Domains/Chemistry/CMakeLists.txt b/Domains/Chemistry/CMakeLists.txt
index 5370210eea0..d9cdfc4aaa6 100644
--- a/Domains/Chemistry/CMakeLists.txt
+++ b/Domains/Chemistry/CMakeLists.txt
@@ -7,6 +7,7 @@ set(Module_SRCS
vtkMoleculeMapper.cxx
vtkMoleculeToAtomBallFilter.cxx
vtkMoleculeToBondStickFilter.cxx
+ vtkMoleculeToLinesFilter.cxx
vtkMoleculeToPolyDataFilter.cxx
vtkPeriodicTable.cxx
vtkPointSetToMoleculeFilter.cxx
diff --git a/Domains/Chemistry/Testing/Cxx/CMakeLists.txt b/Domains/Chemistry/Testing/Cxx/CMakeLists.txt
index c0235cc6722..b78e99f1fe5 100644
--- a/Domains/Chemistry/Testing/Cxx/CMakeLists.txt
+++ b/Domains/Chemistry/Testing/Cxx/CMakeLists.txt
@@ -28,6 +28,7 @@ vtk_add_test_cxx(vtkDomainsChemistryCxxTests tests
TestMoleculeIOLegacy.cxx
TestMoleculeSelection.cxx,NO_VALID
TestMoleculeMapperPropertyUpdate.cxx
+ TestMoleculeToLines.cxx,NO_VALID
TestMultiCylinderOn.cxx
TestMultiCylinderOff.cxx
TestPeriodicTable.cxx,NO_VALID
diff --git a/Domains/Chemistry/Testing/Cxx/TestMoleculeToLines.cxx b/Domains/Chemistry/Testing/Cxx/TestMoleculeToLines.cxx
new file mode 100644
index 00000000000..cd0a7c82511
--- /dev/null
+++ b/Domains/Chemistry/Testing/Cxx/TestMoleculeToLines.cxx
@@ -0,0 +1,62 @@
+/*=========================================================================
+
+ Program: Visualization Toolkit
+ Module: TestMoleculeToLines.cxx
+
+ Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+ All rights reserved.
+ See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notice for more information.
+
+=========================================================================*/
+
+#include "vtkTestUtilities.h"
+
+#include "vtkCMLMoleculeReader.h"
+#include "vtkCellData.h"
+#include "vtkDataSetAttributes.h"
+#include "vtkMolecule.h"
+#include "vtkMoleculeToLinesFilter.h"
+#include "vtkNew.h"
+#include "vtkPointData.h"
+#include "vtkPolyData.h"
+
+#define CheckNumbers(name, first, second) \
+ if (first != second) \
+ { \
+ cerr << "Error : wrong number of " << #name << ". Got " << first << " but expects " << second \
+ << endl; \
+ return EXIT_FAILURE; \
+ }
+
+int TestMoleculeToLines(int argc, char* argv[])
+{
+ char* fileName = vtkTestUtilities::ExpandDataFileName(argc, argv, "Data/porphyrin.cml");
+
+ // read molecule from cml file
+ vtkNew<vtkCMLMoleculeReader> reader;
+ reader->SetFileName(fileName);
+ reader->Update();
+ delete[] fileName;
+ vtkMolecule* molecule = reader->GetOutput();
+
+ // convert
+ vtkNew<vtkMoleculeToLinesFilter> converter;
+ converter->SetInputConnection(reader->GetOutputPort());
+ converter->Update();
+ vtkPolyData* poly = converter->GetOutput();
+
+ // check number of points, lines and associated data
+ CheckNumbers("points", poly->GetNumberOfPoints(), molecule->GetNumberOfAtoms());
+ CheckNumbers("lines", poly->GetNumberOfLines(), molecule->GetNumberOfBonds());
+ CheckNumbers("pointData",
+ poly->GetPointData()->GetNumberOfArrays(),
+ molecule->GetAtomData()->GetNumberOfArrays());
+ CheckNumbers("cellData",
+ poly->GetCellData()->GetNumberOfArrays(),
+ molecule->GetBondData()->GetNumberOfArrays());
+ return EXIT_SUCCESS;
+}
diff --git a/Domains/Chemistry/vtkMoleculeToAtomBallFilter.cxx b/Domains/Chemistry/vtkMoleculeToAtomBallFilter.cxx
index 70a32b21ae6..cb99c2543e9 100644
--- a/Domains/Chemistry/vtkMoleculeToAtomBallFilter.cxx
+++ b/Domains/Chemistry/vtkMoleculeToAtomBallFilter.cxx
@@ -59,6 +59,7 @@ int vtkMoleculeToAtomBallFilter::RequestData(
vtkCellArray *polys = vtkCellArray::New();
vtkPoints *points = vtkPoints::New();
vtkUnsignedShortArray *atomicNums = vtkUnsignedShortArray::New();
+ atomicNums->SetName(input->GetAtomicNumberArrayName());
// Initialize a SphereSource
vtkSphereSource *sphereSource = vtkSphereSource::New();
@@ -71,7 +72,8 @@ int vtkMoleculeToAtomBallFilter::RequestData(
GetNumberOfPoints());
polys->Allocate(numAtoms * sphereSource->GetOutput()->GetPolys()->
GetNumberOfCells());
- atomicNums->Allocate(points->GetNumberOfPoints());
+ atomicNums->Allocate(numAtoms * sphereSource->GetOutput()->GetPoints()->
+ GetNumberOfPoints());
// Initialize some variables for later
vtkIdType numCellPoints, *cellPoints;
diff --git a/Domains/Chemistry/vtkMoleculeToBondStickFilter.cxx b/Domains/Chemistry/vtkMoleculeToBondStickFilter.cxx
index e056c9b73cb..d510229de0a 100644
--- a/Domains/Chemistry/vtkMoleculeToBondStickFilter.cxx
+++ b/Domains/Chemistry/vtkMoleculeToBondStickFilter.cxx
@@ -52,6 +52,7 @@ int vtkMoleculeToBondStickFilter::RequestData(
vtkCellArray *polys = vtkCellArray::New();
vtkPoints *points = vtkPoints::New();
vtkUnsignedShortArray *bondOrders = vtkUnsignedShortArray::New();
+ bondOrders->SetName(input->GetBondOrdersArrayName());
// Initialize a CylinderSource
vtkCylinderSource *cylSource = vtkCylinderSource::New();
@@ -64,7 +65,8 @@ int vtkMoleculeToBondStickFilter::RequestData(
GetNumberOfPoints());
polys->Allocate(3 * numBonds * cylSource->GetOutput()->GetPolys()->
GetNumberOfCells());
- bondOrders->Allocate(points->GetNumberOfPoints());
+ bondOrders->Allocate(3 * numBonds * cylSource->GetOutput()->GetPoints()->
+ GetNumberOfPoints());
// Create a transform object to map the cylinder source to the bond
vtkTransform *xform = vtkTransform::New();
diff --git a/Domains/Chemistry/vtkMoleculeToLinesFilter.cxx b/Domains/Chemistry/vtkMoleculeToLinesFilter.cxx
new file mode 100644
index 00000000000..194f2fb4692
--- /dev/null
+++ b/Domains/Chemistry/vtkMoleculeToLinesFilter.cxx
@@ -0,0 +1,50 @@
+/*=========================================================================
+
+ Program: Visualization Toolkit
+ Module: vtkMoleculeToLinesFilter.cxx
+
+ Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+ All rights reserved.
+ See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notice for more information.
+
+=========================================================================*/
+#include "vtkMoleculeToLinesFilter.h"
+
+#include "vtkCellArray.h"
+#include "vtkCellData.h"
+#include "vtkInformation.h"
+#include "vtkMolecule.h"
+#include "vtkPointData.h"
+
+vtkStandardNewMacro(vtkMoleculeToLinesFilter);
+
+//----------------------------------------------------------------------------
+int vtkMoleculeToLinesFilter::RequestData(vtkInformation*,
+ vtkInformationVector** inputVector,
+ vtkInformationVector* outputVector)
+{
+ vtkMolecule* input = vtkMolecule::SafeDownCast(vtkDataObject::GetData(inputVector[0]));
+ vtkPolyData* output = vtkPolyData::SafeDownCast(vtkDataObject::GetData(outputVector));
+
+ vtkNew<vtkCellArray> bonds;
+ // 2 point ids + 1 VTKCellType = 3 values per bonds
+ bonds->Allocate(3 * input->GetNumberOfBonds());
+
+ for (vtkIdType bondInd = 0; bondInd < input->GetNumberOfBonds(); ++bondInd)
+ {
+ vtkBond bond = input->GetBond(bondInd);
+ vtkIdType ids[2] = { bond.GetBeginAtomId(), bond.GetEndAtomId() };
+ bonds->InsertNextCell(2, ids);
+ }
+
+ output->SetPoints(input->GetAtomicPositionArray());
+ output->SetLines(bonds);
+ output->GetPointData()->DeepCopy(input->GetAtomData());
+ output->GetCellData()->DeepCopy(input->GetBondData());
+
+ return 1;
+}
diff --git a/Domains/Chemistry/vtkMoleculeToLinesFilter.h b/Domains/Chemistry/vtkMoleculeToLinesFilter.h
new file mode 100644
index 00000000000..2f4a225966c
--- /dev/null
+++ b/Domains/Chemistry/vtkMoleculeToLinesFilter.h
@@ -0,0 +1,51 @@
+/*=========================================================================
+
+ Program: Visualization Toolkit
+ Module: vtkMoleculeToLinesFilter.h
+
+ Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+ All rights reserved.
+ See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notice for more information.
+
+=========================================================================*/
+/**
+ * @class vtkMoleculeToLinesFilter
+ * @brief Convert a molecule into a simple polydata with lines.
+ *
+ * vtkMoleculeToLinesFilter is a filter class that takes vtkMolecule as input and
+ * generates polydata on output.
+ * Conversion is done following this rules:
+ * - 1 atom == 1 point
+ * - 1 bond == 1 line (cell of type VTK_LINE)
+ * - atom data is copied as point data
+ * - bond data is copied as cell data
+ */
+
+#ifndef vtkMoleculeToLinesFilter_h
+#define vtkMoleculeToLinesFilter_h
+
+#include "vtkDomainsChemistryModule.h" // For export macro
+#include "vtkMoleculeToPolyDataFilter.h"
+
+class VTKDOMAINSCHEMISTRY_EXPORT vtkMoleculeToLinesFilter : public vtkMoleculeToPolyDataFilter
+{
+public:
+ static vtkMoleculeToLinesFilter* New();
+ vtkTypeMacro(vtkMoleculeToLinesFilter, vtkMoleculeToPolyDataFilter);
+
+protected:
+ vtkMoleculeToLinesFilter() = default;
+ ~vtkMoleculeToLinesFilter() = default;
+
+ int RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) override;
+
+private:
+ vtkMoleculeToLinesFilter(const vtkMoleculeToLinesFilter&) = delete;
+ void operator=(const vtkMoleculeToLinesFilter&) = delete;
+};
+
+#endif
--
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