ENH: Support for Mesh serialization #3154

PranjalSahu · 2022-02-03T02:27:49Z

This PR adds the functionality of mesh serialization.

SetPoints method is added for 1D array input argument in PointSet. Used for numpy interface.
SetCellsArray and GetCellsArray are added in Mesh. To provider a simpler API for creating mesh having only one type of cell, additional SetCellsArray(cell_vector_container, itk.CommonEnums.CellGeometry) is added.
CreateCell private method is added that creates a new cell given its type. The function can be reused for other purposes. Future additions of new kinds of cells should add an entry here to support the Python focussed APIs.
For serialization, we follow the approach similar to the MeshFileWriter where first the cell type is passed, followed by the count of points in that cell and finally the point ids. The count of points is needed here as the itkPolygonCell can take a variable number of points.
The functions (SetPoints, SetCellsArray) take as argument 1D VectorContainer which can be easily converted to a numpy and reverse.
For pickle-based serialization, getstate and setstate methods are added in python (both for mesh and pointset)(refer ENH: pickle serialization for itk images (issue 1091) #2829).
Support for key based updation of points, cells, point data, and cell data in the mesh is also added.
Test for consistency of points and cells using the newly added functions is added. The newly added API should perform seamlessly with older APIs and the results should be consistent.
Python Tests have also been added for mesh serialization, point set serialization, dict based methods in python, and for the conversion from VTK Mesh to ITK Mesh.

PR Checklist

No API changes were made (or the changes have been approved)
No major design changes were made (or the changes have been approved)
Added test (or behavior not changed)
Updated API documentation (or API not changed)
Added license to new files (if any)
Added Python wrapping to new files (if any) as described in ITK Software Guide Section 9.5
Added ITK examples for all new major features (if any)

Refer to the ITK Software Guide for
further development details if necessary.

thewtex · 2022-02-03T11:46:28Z

@PranjalSahu awesome! The data structure should follow:

https://insightsoftwareconsortium.github.io/itk-wasm/api/Mesh.html

GenevieveBuckley · 2022-02-04T05:24:58Z

I'm slightly confused about why I've been requested as a reviewer, I don't do a whole lot with meshes (maybe will do more in the near future, but not a lot right now). Can you elaborate on what you were hoping for from me, @thewtex ?

thewtex · 2022-02-04T21:14:49Z

@GenevieveBuckley , no expectations, but since you did such an amazing job on the Image serialization :-), your eyes may see pickling issues here. But, it is more just a heads-up that we are building on the work that you did for other data structures.

GenevieveBuckley

Ok, I've had a look over it now. It seems like nice work overall.
I know it says above this is still a work in progress. Before it is merged, my two biggest suggestions are that:

The itkMeshSetGetCellTest.py test assertions need to be strengthened, and
The dictionary returned on serialization currently includes a lot of empty string values, so it looks like there would be a fair bit of metadata loss upon serialization/de-serialization. This should also be addressed (and it will require a few new test assertions for these as well)

I don't feel like I can provide feedback on the header files, so I haven't left comments there.

Wrapping/Generators/Python/PyBase/pyBase.i

Modules/Core/Mesh/wrapping/test/itkMeshSetGetCellTest.py

GenevieveBuckley · 2022-02-08T23:51:27Z

Wrapping/Generators/Python/PyBase/pyBase.i

+                    elif key == 'direction':
+                        self.SetDirection(np.flip(value, axis=None))
+                    else:
+                        self.GetMetaDataDictionary()[key] = value


There's no SetMetaDataDictionary option?
Assuming that's the case, this is a nice workaround.

Wrapping/Generators/Python/PyBase/pyBase.i

Wrapping/Generators/Python/itk/support/extras.py

PranjalSahu · 2022-02-14T01:00:11Z

@thewtex I found that we have Object name functionality present for all objects. I am thinking of using that instead of using a new field for name in the PointSet. If you agree then I will remove the addition of new name field from this PR.

Also, I have not added the support for QuadEdge Mesh in the wasm data structure in this PR.

PranjalSahu · 2022-02-14T01:02:33Z

Also I realized for code coverage I should instantiate all types of Cells while testing SetCellsAsArray.

dzenanz

Mostly looks good.

Wrapping/Generators/Python/itk/support/helpers.py

Modules/Core/Mesh/include/itkMesh.hxx

thewtex

Looking great!!!

A few comments inline.

Could we also please add a test for serialization of a PointSet?

Modules/Core/Common/include/itkPointSet.h

Modules/Core/Common/include/itkPointSet.hxx

Modules/Core/Common/include/itkPointSet.h

Modules/Core/Mesh/include/itkMesh.h

dzenanz

LGTM, assuming CI passes.

Modules/Core/Mesh/include/itkMesh.hxx

thewtex · 2022-03-08T17:40:54Z

@PranjalSahu could you please rebase on master?

PranjalSahu · 2022-03-08T17:53:14Z

yes working on it.

thewtex · 2022-03-08T22:28:03Z

To investigate: Wrap PyVectorContainer for Point , direct copy, change Python test code to use SetPoints instead of SetPointsArray, etc.

Set Method needed for better Python support and Mesh serialization. Already present GetPoints can be used in Python without any issues and therefore no additional method is needed.

Needed for better Python support and Mesh serialization using numpy.

PranjalSahu · 2022-03-14T15:47:59Z

@thewtex SetPointsArray is replaced with SetPoints. There are two versions for it now one
with argument type (itkVectorContainerULPF3 *) and other with (itkVectorContainerULF *).

The one with itkVectorContainerULF makes it easier to directly use NumPy arrays for setting
the points (no conversion to itkPoint needed). So the output from other libraries like scikit etc. (ex. Nx3 Numpy arrays) can be plugged directly.

I used the reinterpret_cast for this inside the newly added SetPoints:
auto * pointsPtr = reinterpret_cast<PointsContainer *>(points);

No need for assign operation is needed. Also, I found that for DynamicTraits it wasn't compiling as it
does not support direct assign operation (map).

Sample usage in Python:

points_vc = itk.vector_container_from_array(arr.flatten())
mesh.SetPoints(points_vc)

thewtex

We have converged on an excellent outcome. @PranjalSahu thanks for your hard work. @GenevieveBuckley thanks for the review.

@PranjalSahu awesome to see the PointSet serialization here, too!

thewtex · 2022-03-16T17:23:59Z

Modules/Core/Common/wrapping/test/itkPointSetSerializationTest.py

+
+
+# Check the serialization of mesh
+serialize_deserialize = pickle.loads(pickle.dumps(point_set))


N-Dekker · 2024-09-11T17:28:50Z

Modules/Core/Common/include/itkPointSet.hxx

+  {
+    itkExceptionMacro("Number of entries in given 1d array incompatible with the point dimension");
+  }
+  auto * pointsPtr = reinterpret_cast<PointsContainer *>(points);


I'm sorry but this reinterpret_cast<PointsContainer *>(points) very much looks like undefined behavior to me. (It tries to "reinterpret" the bits of an itk::VectorContainer of scalars as an itk::VectorContainer of itk::Point.) How did you find out that it seemed to work at all?

This can be tested by using a 1D array. I can write a small test case here if it is not present already.
I am checking if this is covered under test or not.

Thanks @PranjalSahu I'm glad to see that you already tested this code:

ITK/Modules/Core/Common/test/itkPointSetTest.cxx

Lines 102 to 127 in 9a5dade

// Insert the points using SetPointArray.

PointsVectorContainerPointer pointsArray = PointsVectorContainer::New();

// Test for in-compatible input array dimension

pointsArray->InsertElement(0, 1.0);

ITK_TRY_EXPECT_EXCEPTION(pset->SetPoints(pointsArray));

pointsArray->Reserve(numOfPoints * pointDimension);

int index = 0;

for (int i = 0; i < numOfPoints; ++i)

{

pointsArray->SetElement(index++, 1.0);

pointsArray->SetElement(index++, 2.0);

pointsArray->SetElement(index++, 3.0);

}

pset->SetPoints(pointsArray);

// Check the count of points after insertion using SetPoints.

pointsArrayAfter = pset->GetPoints();

if (static_cast<int>(pointsArrayAfter->Size()) != numOfPoints)

{

std::cerr << "Mismatch in count after inserting points." << std::endl;

return EXIT_FAILURE;

}

Nevertheless, it's officially undefined behavior. Sorry 🤷. The C++ Standard does not guarantee that it works. In theory, it might do anything. And in practice, undefined behavior does lead to trouble. I just asked about a similar example at the ACCU mailing list, and Jonathan Wakely (@jwakely) confirmed that it is indeed undefined behavior.

So I would prefer to see the reinterpret_cast<PointsContainer *> "trick" removed. But otherwise (at least), a note should be added that this function is unsafe.

PranjalSahu · 2024-09-12T21:23:54Z

Modules/Core/Mesh/wrapping/test/itkMeshSerializationTest.py

+for i in range(NumberOfCells):
+    cells_array[i, :] = [i * 1, (i + 1) * 2, (i + 2) * 3]
+
+# Insert the cells in mesh by converting to 1D array


One similar test case is here which uses a 1D input array.

thewtex requested a review from GenevieveBuckley February 3, 2022 11:44

GenevieveBuckley reviewed Feb 9, 2022

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PranjalSahu force-pushed the pranjal21 branch from 71591ef to 5bfcf7b Compare February 14, 2022 00:15

PranjalSahu changed the title ~~WIP: Support for Mesh serialization~~ ENH: Support for Mesh serialization Feb 14, 2022

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thewtex mentioned this pull request Mar 10, 2022

Make itk.Transform pickle-able #3269

Closed

ENH: Adding SetPoints in PointSet for 1D input array

6827360

Set Method needed for better Python support and Mesh serialization. Already present GetPoints can be used in Python without any issues and therefore no additional method is needed.

PranjalSahu force-pushed the pranjal21 branch from ca6fcb8 to a0a751a Compare March 13, 2022 03:14

PranjalSahu added 5 commits March 13, 2022 14:45

ENH: Adding Set/GetCellsArray in Mesh

ff3c0b6

Needed for better Python support and Mesh serialization using numpy.

ENH: Adding set/getstate in Python for Mesh serialization

a8ca6fb

ENH: Adding test for Mesh serialization

bf8336d

ENH: Adding set/getstate in Python for PointSet serialization

22661e0

ENH: Adding test for PointSet serialization

6ec7ada

PranjalSahu force-pushed the pranjal21 branch from a0a751a to 6ec7ada Compare March 13, 2022 18:48

thewtex approved these changes Mar 16, 2022

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thewtex merged commit 0e1c2c3 into InsightSoftwareConsortium:master Mar 16, 2022

jhlegarreta mentioned this pull request Mar 31, 2022

DOC: Document methods in header file #3351

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PranjalSahu deleted the pranjal21 branch July 19, 2022 18:29

N-Dekker reviewed Sep 11, 2024

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PranjalSahu commented Sep 12, 2024

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N-Dekker mentioned this pull request Sep 13, 2024

PointSet::SetPoints(PointsVectorContainer *) overload leads to undefined behavior #4848

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ENH: Support for Mesh serialization #3154

ENH: Support for Mesh serialization #3154

PranjalSahu commented Feb 3, 2022 •

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		# Check the serialization of mesh
		serialize_deserialize = pickle.loads(pickle.dumps(point_set))

	// Insert the points using SetPointArray.
	PointsVectorContainerPointer pointsArray = PointsVectorContainer::New();

	// Test for in-compatible input array dimension
	pointsArray->InsertElement(0, 1.0);
	ITK_TRY_EXPECT_EXCEPTION(pset->SetPoints(pointsArray));

	pointsArray->Reserve(numOfPoints * pointDimension);

	int index = 0;
	for (int i = 0; i < numOfPoints; ++i)
	{
	pointsArray->SetElement(index++, 1.0);
	pointsArray->SetElement(index++, 2.0);
	pointsArray->SetElement(index++, 3.0);
	}

	pset->SetPoints(pointsArray);

	// Check the count of points after insertion using SetPoints.
	pointsArrayAfter = pset->GetPoints();
	if (static_cast<int>(pointsArrayAfter->Size()) != numOfPoints)
	{
	std::cerr << "Mismatch in count after inserting points." << std::endl;
	return EXIT_FAILURE;
	}

ENH: Support for Mesh serialization #3154

ENH: Support for Mesh serialization #3154

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