jmag722 / vtk-hdf

Python interface for VTK HDF

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linkedin.com/in/jaredmagnusson

vtk-hdf's Issues

points 2D slice

get points output similar to ImageData but only for 2D slice

support imagedata fielddata

rename project, directories

vtk-hdf
vtkhdf
image
utils

support C-arrays

separate h5 open vs write

allow slices to be written on an already opened file - do not assume all the slices will be written from a 3D array

unit test examples

replace string literals with constants

add tutorial

flesh out readme

fix origin centering zero by any axis

allow user to zero any axis

update metadata

getters for dim-spacing-origin

add getters for dimensions, spacing, origin, extent, bounds, etc

cleanup image module

• organize functions by what they do within the module
• standardize function names - should dimensions imply point dimensions?
• remove utils dependency in image.py
• fix citations
• update examples and readme
• remove sequence import
• replace fielddata key arg with var
• point/cell create_dataset <-- call base private function because they share lots of lines of code
• create set_field_array() function trivial for user to do
• extent2cellshape should be extent2celldimensions
• point2cell_dimension --> point2cell_dimensions : put this in image.py

change extension

use .vtkhdf, not .hdf

https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/release/ParaView-5.12.0.md#new-vtkhdf-extension-for-vtkhdf-files

add docstrings

standardize function names

read_slice output C order

this would be the default, allow an option here

Please rename this VTKHDF implementation

Hi @jmag722 ! I'm a VTK maintainer avec very active in regard to the VTKHDF format.

Thanks a lot for creating this VTKHDF implementation, Its great to see the community embracing it.

However, can I suggest a rename of this project?

VTKHDF is the name of the format.
vtkhdf is the name of the implementation available in the vtkIOHDF module in VTK.

I'm afraid adding yet another similar name will be confusing, wdyt ?

split reading slice from h5py opening

support ImageData celldata

list comprehension compute_axes

update docs, examples

cell and field data examples

Add caching

either add a computable default caching size for z-slices, or method to compute it

float64 default type

set default type to float64, h5py defaults to float32

pytest fixture for write vtkhdf

almost all tests involve first writing dummy data to a tmp_path file. move this functionality into a pytest fixture

add link to vtk hdf info pages

https://vtk.org/doc/nightly/html/VTKHDFFileFormat.html

https://docs.vtk.org/en/latest/design_documents/VTKFileFormats.html

support polydata

see https://docs.vtk.org/en/latest/design_documents/VTKFileFormats.html#hdf-file-formats

access data via class

override h5py.File for simpler API

https://stackoverflow.com/questions/9459730/how-do-i-define-a-python-class-that-i-can-use-with-the-with-statement?rq=3

https://stackoverflow.com/questions/3774328/implementing-use-of-with-object-as-f-in-custom-class-in-python

test read_vtkhdf

add tests

init by position without meshgrid

be able to initialize large ImageData set without meshgrid --> vectorize or for loops with parallelization or numba.

add minimum versions

vtk, pyvista, paraview - put in toml and readme