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Add wave PVD files - #3

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MatthewFlamm:add-wave-PVD-zip
Aug 20, 2021
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MatthewFlamm merged 1 commit into
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MatthewFlamm:add-wave-PVD-zip

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This is a zip file with the following structure:

wavy/
    wavy.pvd
    wavy/
        wavy00.vts
        wavy01.vts
        ...

The .vts files were generated with the following script:

import pyvista as pv
import numpy as np

x = np.arange(-10, 10, 0.25)
y = np.arange(-10, 10, 0.25)
x, y = np.meshgrid(x, y)
r = np.sqrt(x ** 2 + y ** 2)
z = np.sin(r)

# Create and structured surface
grid = pv.StructuredGrid(x, y, z)
pts = grid.points
# Update Z and write a frame for each updated position
nframe = 15
for i, phase in enumerate(np.linspace(0, 2 * np.pi, nframe + 1)[:nframe]):
    z = np.sin(r + phase).ravel()
    pts[:, -1] = z
    grid['z'] = z
    grid.save(f"wavy{i:02}.vts")

The .pvd file was created manually.

wavy.pvd

<?xml version="1.0" encoding="UTF-8"?>
<VTKFile type="Collection" version="0.1" byte_order="LittleEndian" compressor="vtkZLibDataCompressor">
    <Collection>
        <DataSet timestep="0.00000e+00" group="" part="0" file="wavy/wavy00.vts"/>
        <DataSet timestep="1.00000e+00" group="" part="0" file="wavy/wavy01.vts"/>

This is being used for pyvista/pyvista#1564.

The .pvd file can be read by Paraview:
image

@MatthewFlamm
MatthewFlamm merged commit 38d8e9d into pyvista:master Aug 20, 2021
@MatthewFlamm
MatthewFlamm deleted the add-wave-PVD-zip branch August 20, 2021 20:53
banesullivan pushed a commit that referenced this pull request Feb 6, 2022
akaszynski added a commit that referenced this pull request Apr 12, 2022
* add FORGE data

* add large volume

* add delaunay points

* add embryo

* add antarctica_velocity.vtp

* add translucent room sruface mesh

* added tree.ply

* converted tree.ply to binary

* added ensight example file

* add skybox2

* add GPR example data

* add thermal probes

* add turbineblade

* add carburetor

* add lobster.ply

* add woman.stl

* Add urn.stl

* add tigerfighter.obj

* add pepper.ply and pepper.obj

* add man_face.stl

* renamed pepper.obj to drill.obj

* add mars and stars

* make mars smaller

* add notch stress FEA example

* add notch displacement

* notch_disp.vtk --> notch_disp.vtu

* actually add file

* add louis

* add nefertiti ply

* name change

* add geo sample data

* add cylinder in crossflow dataset

* add context to data

* add hdr files

* add wave PVD files (#3)

* add osmnx graph

* add pvd files from paraview data

* add lucy

* Add `DICOM_Stack` dataset

This dataset will be used to test improved volume rendering and DICOM
stack reading per pyvista/pyvista-support issue #500.

The Cancer Imaging Archive (TCIA) is a service which de-identifies and
hosts a large archive of medical images of cancer accessible for public
download. The data are organized as “collections”; typically patients’
imaging related by a common disease (e.g. lung cancer), image modality
or type (MRI, CT, digital histopathology, etc) or research focus. DICOM
is the primary file format used by TCIA for radiology imaging.
Supporting data related to the images such as patient outcomes,
treatment details, genomics and expert analyses are also provided when
available.

This dataset is a member of the National Cancer Institute's Clinical
Proteomic Tumor Analysis Consortium Sarcomas (CPTAC-SAR) cohort. CPTAC
is a national effort to accelerate the understanding of the molecular
basis of cancer through the application of large-scale proteome and
genome analysis, or proteogenomics. Radiology and pathology images from
CPTAC patients are being collected and made publicly available by The
Cancer Imaging Archive to enable researchers to investigate cancer
phenotypes which may correlate to corresponding proteomic, genomic and
clinical data.

This data has been published under the `Creative Commons Attribution 3.0
Unported License` and must adhere to the CPTAC Data Use Agreement. Per
the TCIA Data Usage Policy (see License file), all oral or written
presentations, disclosures, or publications must acknowledge the
specific dataset(s) or applicable accession number(s) and the
NIH-designated data repositories through which the investigator
accessed any data. The appropriate citations are included in the
CITATIONS file. The metadata for this dataset is included in
metadata.csv. Questions may be directed to
<help@cancerimagingarchive.net>.

Title: Forearm Sarcoma
DataDescription URI: https://doi.org/10.7937/TCIA.2019.9bt23r95
Number of Images: 3
Total Size: 1.51 MB
File Format: DICOM

Co-authored-by: banesullivan <banesulli@gmail.com>
Co-authored-by: Alex Kaszynski <akascap@gmail.com>
Co-authored-by: Bane Sullivan <banesullivan@gmail.com>
Co-authored-by: Flamm, Matthew H <matthewhflamm@gmail.com>
Co-authored-by: MatthewFlamm <39341281+MatthewFlamm@users.noreply.github.com>
akaszynski added a commit that referenced this pull request Apr 15, 2022
* add FORGE data

* add large volume

* add delaunay points

* add embryo

* add antarctica_velocity.vtp

* add translucent room sruface mesh

* added tree.ply

* converted tree.ply to binary

* added ensight example file

* add skybox2

* add GPR example data

* add thermal probes

* add turbineblade

* add carburetor

* add lobster.ply

* add woman.stl

* Add urn.stl

* add tigerfighter.obj

* add pepper.ply and pepper.obj

* add man_face.stl

* renamed pepper.obj to drill.obj

* add mars and stars

* make mars smaller

* add notch stress FEA example

* add notch displacement

* notch_disp.vtk --> notch_disp.vtu

* actually add file

* add louis

* add nefertiti ply

* name change

* add geo sample data

* add cylinder in crossflow dataset

* add context to data

* add hdr files

* add wave PVD files (#3)

* add osmnx graph

* add pvd files from paraview data

* add lucy

* Put `.dcm` files in separate `data` subfolder

`vtk.vtkDICOMImageReader` cannot parse non-dcm files in a folder.

* Replace `data` folder with `.zip` file

Folders cannot be downloaded using the GitHub API, which is causing
DICOM Reader tests to fail in `pyvista`. Instead, zip the folder.
This will be unzipped when downloaded.

Co-authored-by: banesullivan <banesulli@gmail.com>
Co-authored-by: Alex Kaszynski <akascap@gmail.com>
Co-authored-by: Bane Sullivan <banesullivan@gmail.com>
Co-authored-by: Flamm, Matthew H <matthewhflamm@gmail.com>
Co-authored-by: MatthewFlamm <39341281+MatthewFlamm@users.noreply.github.com>
user27182 added a commit that referenced this pull request Sep 6, 2026
`PVD/wavy.zip` was swept up by the `PVD/**` glob and inherited a ParaView
attribution it never had. Pull request #3 publishes the PyVista script that
wrote its frames, and the grids in the archive match what that script
produces, so it is PyVista's own data under MIT. `vtu_series`, which the
pull request that added it says is a conversion of that archive, follows.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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2 participants