Package: pyCEPS
pyCEPSpyCEPS 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 CiteIf you use this software, please consider citing:@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, visitZenodoInstallationPython 3.9 or higher is required. Just usepipto install:python3-mpipinstallpycepsThis will install all necessary dependencies and add a CLI entry point.
To test the installation runpyceps--helpStandard WorkflowTypically, a user wants to import and translate complete EAM data sets, save
a reduced version of the data set to disk (PKL file), 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--systemspecifies the EAM system used for data acquisition.--study-repositorypoints to a (valid) data location, e.g. a ZIP archive
(preferred), or a folder.--convertautomatically loads the data set in its entirety and exports all
data to openCARP compatible formats.--visualizeopens a local HTML site and interactively shows the EAM data.--save-studysaves the (reduced) EAM data set to disk as PKL file, which can
later used (much faster than re-importing the EAM data).To open and work with a previously generated PKL file usepyceps--system"carto"--pkl-file"path_to_pkl"--visualize...
pyceps--system"precision"--pkl-file"path_to_pkl"--visualize...Saving a reduced version of EAM dataUpon 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 PKL format to disk use--save-studyThe PKL 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.Visualizing the dataOnce a data set was imported/loaded it can be visualized using a local HTML
site to evaluate the quality of the data set:--visualizeNote: This will lock the console!Advanced Import/ExportTo 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 PKL file at a later point,
if the study repository (original data) is still accessible. See usage of--change-rootfor details on how to change data location.Specifying the EAM system--system[carto,precision]Specifying the data location--study-repository"path_to_repository"--pkl-file"path_to_pkl"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.To use the following commands, the used EAM system AND the data location
MUST be specified!Specifying what to importTo import single mapping procedures the name of the mapping procedure can be
specified. Optionalallcan 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 exportIt 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-lesionsNote: If--convertis used, this is obsolete since data is exported for all
mapping procedures.Note: Using--dump-point-ecgsneeds access to EAM data repository to load
ECG data!See below how to set a valid path if necessaryChanging the location of original EAM dataWhen opening EAM data from previously generated PKL 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 PKL file is still valid is displayed upon
loading of a PKL 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 ExpertsThe 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.frompycepsimportCartoStudystudy=CartoStudy("path_to_repository")# import all available mapsstudy.import_maps(study.mapNames)...LicenseThis software is made available under the terms of the
GNU General Public License v3.0 (GPLv3+).Whom Do I Talk To?R. ArnoldA. Prassl