pyCEPS

pyCEPS provides an interface to import, visualize and translate clinical mapping data (EAM data). Supported mapping systems are: CARTO^®3 (Biosense Webster) and EnSite Precision^™ (Abbot).

How To Cite

If you use this software, please consider citing:

@article{Arnold_pyCEPS_A_cross-platform_2024, author = {Arnold, Robert and Prassl, Anton J. and Neic, Aurel and Thaler, Franz and Augustin, Christoph M. and Gsell, Matthias A.F. and Gillette, Karli and Manninger, Martin and Scherr, Daniel and Plank, Gernot}, doi = {10.1016/j.cmpb.2024.108299}, journal = {Computer Methods and Programs in Biomedicine}, title = {{pyCEPS: A cross-platform electroanatomic mapping data to computational model conversion platform for the calibration of digital twin models of cardiac electrophysiology}}, volume = {254}, year = {2024} }

@software{arnold_2024_10606341, author = {Arnold, Robert and Prassl, Anton J and Plank, Gernot}, title = {{pyCEPS: A cross-platform Electroanatomic Mapping Data to Computational Model Conversion Platform for the Calibration of Digital Twin Models of Cardiac Electrophysiology}}, month = feb, year = 2024, publisher = {Zenodo}, doi = {10.5281/zenodo.10606340}, url = {https://doi.org/10.5281/zenodo.10606340} }

To cite a specific software version, visit Zenodo

Installation

Python 3.8 or higher is required. Just use pip to install:

python3 -m pip install pyceps

This will install all necessary dependencies and add a CLI entry point. To test the installation run

pyceps --help

Standard Workflow

Typically, a user wants to import and translate complete EAM data sets, save a reduced version of the data set to disk, and visualize the data.

pyceps --system "carto" --study-repository "path_to_repository" --convert --visualize --save-study
pyceps --system "precision" --study-repository "path_to_repository" --convert --visualize --save-study

--system specifies the EAM system used for data acquisition.
--study-repository points to a (valid) data location, e.g. a ZIP archive (preferred), or a folder.
--convert automatically loads the data set in its entirety and exports all data to openCARP compatible formats.
--visualize opens a local HTML site and interactively shows the EAM data.
--save-study saves the (reduced) EAM data set to disk as .pyceps file, which can be used later (much faster than re-importing the EAM data).

To open and work with a previously generated .pyceps file use

pyceps --study-file "path_to_file" --visualize ...
pyceps --study-file "path_to_file" --visualize ...

Quick preview of studies

EAM data sets can be quickly visualized to preview anatomical shells, recording point locations, and ablation lesions:

pyceps --system "carto" --study-repository "path_to_repository" --quick

Note: Any other input/output arguments will be ignored!

Saving a reduced version of EAM data

Upon import of EAM data, a data representation is built which can be saved to disk for later usage. This data object does not contain the entirety of data available in the EAM data set (e.g. not all ECG and EGM data is read) but can therefore be loaded very quickly. To save the data representation in .pyceps format to disk use

--save-study

The file is automatically saved in the folder above the repository path (if EAM data resides in a folder), or in the same folder if data is imported from ZIP archives. Optionally, a different location can be given.

By default, any ECG data associated with recording points is not saved in the output file. If you wish to save ECG data as well for later usage and/or visualization you can add the option

--keep-ecg

Note: files will grow drastically in size if many recording points are present

Visualizing the data

Once a data set was imported/loaded it can be visualized using a local HTML site to evaluate the quality of the data set:

--visualize

Note: This will lock the console!

Advanced Import/Export

To control which data, i.e. mapping procedures, are imported from an EAM data set and which data are exported, the commands described below can be chained together. It is also possible to add data to an existing .pyceps file at a later point, if the study repository (original data) is still accessible. See usage of --change-root for details on how to change data location if needed.

Specifying the EAM system

--system [carto, precision]

This is used only when importing data from an EAM data repository.

Specifying the data location

--study-repository "path_to_repository"
--study-file "path_to_file"

Using these commands will gather basic information from the data set, (i.e. name of the study, performed mapping procedures, etc.) and display this information on the command line.

Specifying what to import

To import single mapping procedures the name of the mapping procedure can be specified. Optional all can be used to import all mapping procedures (same as using --convert).

pyceps.py ... --import-map "map_name"
pyceps.py ... --import-map "all"

All information related to the mapping procedure is loaded, i.e. anatomical shell, mapping points, ablation lesions, etc.

Specifying what to export

It is possible to export specific items from the data set. This works only for single mapping procedures, therefore a mapping procedure to work with has to be specified first using

--map "map_name"

All following commands are then applied to this mapping procedure only.

--dump-mesh
--dump-point-data
--dump-point-egms
--dump-point-ecgs
--dump-map-ecgs
--dump-surface-maps
--dump-lesions

Note: If --convert is used, this is obsolete since data is exported for all mapping procedures.

Note: Using --dump-point-ecgs needs access to EAM data repository to load ECG data!
See below how to set a valid path if necessary

Changing the location of original EAM data

When opening EAM data from previously generated .pyceps files, the original EAM data set might not be accessible or the path might have changed (e.g. when using mounted devices). Information if the path stored in the .pyceps file is still valid is displayed upon loading of a .pyceps file. To change the path to an EAM data repository use

--change-root "path_to_repository"

This will check if the new path is valid and set it accordingly.

For Experts

The data contained in exported data sets differs for different mapping systems. Exporting data via the CLI accesses only data common to every mapping system. To access the entirety of imported data, Python scripts have to be used.

from pyceps import CartoStudy

study = CartoStudy("path_to_repository",
                   pwd='password',
                   encoding='encoding')
study.import_study()
# import all available maps
study.import_maps(study.mapNames)
...

License

This software is made available under the terms of the GNU General Public License v3.0 (GPLv3+).

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