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cartoreader-lite

Lightweight reader with little to no postprocessing to read the CARTO3 file format from Biosense Webster.

https://github.com/thomgrand/cartoreader-lite

Science Score: 67.0%

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    .zenodo.json file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (15.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Lightweight reader with little to no postprocessing to read the CARTO3 file format from Biosense Webster.

Basic Info
  • Host: GitHub
  • Owner: thomgrand
  • License: agpl-3.0
  • Language: Python
  • Default Branch: public
  • Size: 94.7 KB
Statistics
  • Stars: 4
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 4 years ago · Last pushed about 4 years ago
Metadata Files
Readme License Citation

README.md

CARTOreader - lite

CI Tests codecov DOI

This repository is an inofficial reader to easily process exported CARTO3 data in Python. It does not provide the more extensive capabilities to analyze the signals, such as OpenEP, but is rather meant as a simple reader to import CARTO data. The loaded time data is imported in pandas and the meshes in VTK provided through PyVista, allowing for easy access, export and interoperatibility with existing software.

Installation

To install cartoreader_lite, you can simply install the package from PyPI:

bash pip install cartoreader-lite

Alternatively, you can clone the repository and install the libary using pip.

bash git clone https://github.com/thomgrand/cartoreader-lite cd cartoreader-lite pip install -e .

Usage

To test the library, you first need to get CARTO3 data. None is provided with this repository, but you can download the testing data provided by OpenEP to quickly try out the library (make sure the libary was installed first):

bash python tests/generate_test_data.py

```python from cartoreader_lite import CartoStudy import pyvista as pv import numpy as np

studydir = "openep-testingdata/Carto/ExportStudy-1-11252021-15-01-32" studyname = "Study 1 11252021 15-01-32.xml" study = CartoStudy(studydir, studyname, cartomapkwargs={"discardinvalidpoints": False} #All points of the example are outside the WOI, which would be by default discarded ) ablationpoints = pv.PolyData(np.stack(study.ablationdata.sessionavgdata["pos"].tonumpy())) ablationpoints.pointdata["RFIndex"] = study.ablationdata.sessionavgdata["RFIndex"] plotter = pv.Plotter() plotter.addmesh(ablationpoints, cmap="jet") plotter.addmesh(study.maps[2].mesh) plotter.show() ```

You should see the recorded map of the OpenEP example, together with its recorded points like below.

openep-example

Documentation

https://cartoreader-lite.readthedocs.io/en/latest

Citation

If you use the library in your scientific projects, please cite the associated Zenodo archive: https://zenodo.org/record/5918396.

bibtex @software{grandits_2022_5918396, author = {Thomas Grandits}, title = {CARTOreader - lite}, month = jan, year = 2022, publisher = {Zenodo}, version = {v1.0.1}, doi = {10.5281/zenodo.5918396}, url = {https://doi.org/10.5281/zenodo.5918396} }

Owner

  • Name: Thomas G.
  • Login: thomgrand
  • Kind: user

Citation (citation.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Grandits"
  given-names: "Thomas"
title: "CARTOreader - lite"
version: 1.0.1
doi: 10.5281/zenodo.5918396
date-released: 2022-01-29
url: "https://github.com/thomgrand/cartoreader-lite"

GitHub Events

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  • Watch event: 1

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Last synced: 11 months ago

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  • Total pull request authors: 1
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  • Average comments per pull request: 1.0
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 7 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
pypi.org: cartoreader-lite

Cartoreader-lite provides a simplified and easy low-level access to CARTO3 studies.

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 7 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.5%
Stargazers count: 23.1%
Forks count: 29.8%
Average: 30.2%
Downloads: 66.6%
Maintainers (1)
tomdev
Last synced: 10 months ago

Dependencies

setup.py pypi
  • numpy *
  • trimesh *