ECGProcess 1.1.0__tar.gz → 1.2.0__tar.gz

ecgprocess-1.2.0/ECGProcess.egg-info/PKG-INFO

@@ -0,0 +1,224 @@
+Metadata-Version: 2.4
+Name: ECGProcess
+Version: 1.2.0
+Summary: A python module to process and standardise ECG data
+Author-email: "A. Floriaan Schmidt" <floriaanschmidt@gmail.com>
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://gitlab.com/SchmidtAF/ECGProcess
+Project-URL: Documentation, https://SchmidtAF.gitlab.io/ECGProcess/
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENCE.txt
+Requires-Dist: lxml>=5
+Requires-Dist: xmltodict>=1.0.3
+Requires-Dist: pandas>=2.1.1
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.7
+Requires-Dist: pydicom>=2
+Requires-Dist: matplotlib>=3.9
+Provides-Extra: dev
+Requires-Dist: pytest>=6; extra == "dev"
+Requires-Dist: pytest-mock>=3.0; extra == "dev"
+Requires-Dist: pytest-dependency>=0.5; extra == "dev"
+Requires-Dist: codespell; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: bump2version>=1; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: sphinx-bootstrap-theme; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Requires-Dist: myst-parser; extra == "dev"
+Requires-Dist: nbsphinx; extra == "dev"
+Requires-Dist: nbsphinx-link; extra == "dev"
+Requires-Dist: sphinx-argparse; extra == "dev"
+Requires-Dist: numpydoc; extra == "dev"
+Requires-Dist: docutils<0.21; extra == "dev"
+Requires-Dist: notebook; extra == "dev"
+Requires-Dist: jupyter; extra == "dev"
+Provides-Extra: tensorflow
+Requires-Dist: tensorflow>=2.16; extra == "tensorflow"
+Provides-Extra: wfdb
+Requires-Dist: wfdb<5,>=4.3.1; extra == "wfdb"
+Provides-Extra: all
+Requires-Dist: tensorflow>=2.16; extra == "all"
+Requires-Dist: wfdb<5,>=4.3.1; extra == "all"
+Dynamic: license-file
+
+<!-- TODO once dev is merged into master and the pages job redeploys, switch
+     this back to the Sphinx-published URL:
+     https://SchmidtAF.gitlab.io/ECGProcess/_static/ecgp_logo.png -->
+<img src="https://gitlab.com/SchmidtAF/ECGProcess/-/raw/d853ccf/docs/source/_static/ecgp_logo.png" alt="ECGProcess icon" width="250"/>
+
+# An ECG processing module
+__version__: `1.2.0`
+
+Supports Python 3.11-3.13; the test suite runs against all three versions
+in CI.
+
+
+This repository hosts a collection of functions for processing
+electrocardiogram (ECG) data and preparing it for analysis.
+
+At a glance, ECGProcess is driven by three units:
+
+* A **processor** unit, reads individual ECG files and based on 
+  a user-supplied configuration file extracts waveform
+  signals, median beats, and metadata to python dictionaries; see [Configuration files](https://SchmidtAF.gitlab.io/ECGProcess/configuration_files.html)).
+* The **table** unit, `ECGTable`, loops over a directory of ECG files, 
+  calls the reader for each one, while applying optional engineering steps
+  (e.g. resampling, calibration, lead correction), and again optionally 
+  concatenating multiple files together.
+* A **writer** unit, tells `ECGTable` what to write to disk
+  (tables, NumPy arrays, WFDB records, images, ...). 
+
+Together these units implement an application programming interface (API),
+mapping ECG data from distinct file types to class attributes
+providing a fixed interface for downstream processing. 
+The package ships with boilerplate classes and validation utilities,
+letting the user expand **processing** of additional file types,
+build custom **engineering** (e.g. standardisation) pipelines, as well as 
+create custom **writers**.
+
+Please consult the [documentation](https://SchmidtAF.gitlab.io/ECGProcess/)
+for the full picture.
+
+## Installation 
+The package is available on PyPI, and conda, with the latest source code 
+available on gitlab. 
+
+### Installation using PyPI
+
+To install the package from PyPI, run:
+
+```bash
+pip install ecgprocess
+```
+
+This installs the latest stable release along with its dependencies.
+
+### Installation using conda
+
+A Conda package is maintained in my personal Conda channel.
+To install from this channel, run:
+
+```bash
+conda install afschmidt::ecgprocess
+```
+
+### Installation using gitlab
+
+If you require the latest updates, potentially not yet formally released,
+you can install the package directly from GitLab.
+
+First, clone the repository and move into its root directory:
+
+```bash
+git clone git@gitlab.com:SchmidtAF/ecgprocess.git
+cd ecgprocess
+```
+
+Install the dependencies:
+
+```bash
+# From the root of the repository
+conda env create --file ./resources/conda/envs/conda_create.yaml
+```
+
+To add to an existing environment use:
+
+```bash
+# From the root of the repository
+conda env update --file ./resources/conda/envs/conda_update.yaml
+```
+
+Next the package can be installed: 
+
+```bash
+make install
+```
+
+#### Development
+For development work, install the package in editable mode, with its
+development dependencies (`pytest`, `codespell`, `sphinx`, ...) and Git
+commit hooks configured:
+
+```bash
+make install-dev
+```
+
+This command installs the package in editable mode with the `[dev]`
+extras and configures Git commit hooks, allowing you to run `git pull`
+to update the repository or switch branches without reinstalling.
+
+Alternatively, you can install manually. This is exactly equivalent
+to `make install-dev`:
+
+```bash
+python -m pip install -e ".[dev]"
+python .githooks/.setup_git_hooks.py
+```
+
+#### Git Hooks Configuration
+
+
+When setting up a development environment, the `setup-hooks` command 
+configures Git hooks to enforce conventional commit message formatting and 
+spell check using `codespell`.
+
+To view the commit message format requirements, run:
+
+```bash
+./.githooks/commit-msg -help
+```
+
+For frequent use, add this function to your shell configuration (`~/.bashrc` 
+or `~/.zshrc`):
+
+```bash
+commit-format-help() {
+    local git_root
+    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
+    
+    if [ -z "$git_root" ]; then
+        echo "Error: Not inside a git repository"
+        return 1
+    fi
+    
+    local hook_path="$git_root/.githooks/commit-msg"
+    
+    if [ ! -f "$hook_path" ]; then
+        echo "Error: commit-msg hook not found"
+        return 1
+    fi
+    
+    "$hook_path" --help
+}
+```
+
+## Next steps...
+If you installed with `make install-dev`, you might wish to run `pytest` to 
+confirm everything is in working order. 
+
+```sh
+# From the root of the repository
+pytest tests
+```
+
+## Usage
+
+Please have a look at the [example](https://SchmidtAF.gitlab.io/ECGProcess/examples.html)
+ recipes. 
+
+## Icon
+
+The package icon features the Etruscan shrew, one of the smallest
+mammals, whose heart can beat over 1,500 times a minute, the fastest
+heart rate of any mammal.

{ecgprocess-1.1.0 → ecgprocess-1.2.0}/ECGProcess.egg-info/SOURCES.txt

@@ -2,6 +2,8 @@ LICENCE.txt
 README.md
 pyproject.toml
 requirements-dev.txt
+requirements-tensorflow.txt
+requirements-wfdb.txt
 requirements.txt
 ECGProcess.egg-info/PKG-INFO
 ECGProcess.egg-info/SOURCES.txt
@@ -29,10 +31,21 @@ ecgprocess/example_data/example_datasets/example-XML1.xml
 ecgprocess/example_data/example_datasets/example-XML1.xsd
 ecgprocess/example_data/example_datasets/example-XML1_error.xsd
 ecgprocess/example_data/example_datasets/example-XML1_wrong.xsd
+ecgprocess/example_data/example_datasets/example-XMLWriter1.json
+ecgprocess/example_data/example_datasets/example-XMLWriter1.xsd
 ecgprocess/example_data/example_datasets/string_data.txt
 ecgprocess/utils/__init__.py
 ecgprocess/utils/config_tools.py
 ecgprocess/utils/ecg_tools.py
 ecgprocess/utils/engineering_tools.py
 ecgprocess/utils/general.py
-ecgprocess/utils/reader_tools.py
+ecgprocess/utils/reader_tools.py
+ecgprocess/writer/__init__.py
+ecgprocess/writer/writer_base.py
+ecgprocess/writer/writer_figure.py
+ecgprocess/writer/writer_numpy.py
+ecgprocess/writer/writer_pixel.py
+ecgprocess/writer/writer_table.py
+ecgprocess/writer/writer_tfrecord.py
+ecgprocess/writer/writer_wfdb.py
+ecgprocess/writer/writer_xml.py

{ecgprocess-1.1.0 → ecgprocess-1.2.0}/ECGProcess.egg-info/requires.txt

@@ -1,12 +1,15 @@
 lxml>=5
-xmltodict>=0.14
+xmltodict>=1.0.3
 pandas>=2.1.1
 numpy>=1.26
 scipy>=1.7
-tensorflow>=2.16
 pydicom>=2
 matplotlib>=3.9
 
+[all]
+tensorflow>=2.16
+wfdb<5,>=4.3.1
+
 [dev]
 pytest>=6
 pytest-mock>=3.0
@@ -28,3 +31,9 @@ numpydoc
 docutils<0.21
 notebook
 jupyter
+
+[tensorflow]
+tensorflow>=2.16
+
+[wfdb]
+wfdb<5,>=4.3.1

ecgprocess-1.2.0/PKG-INFO

@@ -0,0 +1,224 @@
+Metadata-Version: 2.4
+Name: ECGProcess
+Version: 1.2.0
+Summary: A python module to process and standardise ECG data
+Author-email: "A. Floriaan Schmidt" <floriaanschmidt@gmail.com>
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://gitlab.com/SchmidtAF/ECGProcess
+Project-URL: Documentation, https://SchmidtAF.gitlab.io/ECGProcess/
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENCE.txt
+Requires-Dist: lxml>=5
+Requires-Dist: xmltodict>=1.0.3
+Requires-Dist: pandas>=2.1.1
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.7
+Requires-Dist: pydicom>=2
+Requires-Dist: matplotlib>=3.9
+Provides-Extra: dev
+Requires-Dist: pytest>=6; extra == "dev"
+Requires-Dist: pytest-mock>=3.0; extra == "dev"
+Requires-Dist: pytest-dependency>=0.5; extra == "dev"
+Requires-Dist: codespell; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: bump2version>=1; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: sphinx-bootstrap-theme; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Requires-Dist: myst-parser; extra == "dev"
+Requires-Dist: nbsphinx; extra == "dev"
+Requires-Dist: nbsphinx-link; extra == "dev"
+Requires-Dist: sphinx-argparse; extra == "dev"
+Requires-Dist: numpydoc; extra == "dev"
+Requires-Dist: docutils<0.21; extra == "dev"
+Requires-Dist: notebook; extra == "dev"
+Requires-Dist: jupyter; extra == "dev"
+Provides-Extra: tensorflow
+Requires-Dist: tensorflow>=2.16; extra == "tensorflow"
+Provides-Extra: wfdb
+Requires-Dist: wfdb<5,>=4.3.1; extra == "wfdb"
+Provides-Extra: all
+Requires-Dist: tensorflow>=2.16; extra == "all"
+Requires-Dist: wfdb<5,>=4.3.1; extra == "all"
+Dynamic: license-file
+
+<!-- TODO once dev is merged into master and the pages job redeploys, switch
+     this back to the Sphinx-published URL:
+     https://SchmidtAF.gitlab.io/ECGProcess/_static/ecgp_logo.png -->
+<img src="https://gitlab.com/SchmidtAF/ECGProcess/-/raw/d853ccf/docs/source/_static/ecgp_logo.png" alt="ECGProcess icon" width="250"/>
+
+# An ECG processing module
+__version__: `1.2.0`
+
+Supports Python 3.11-3.13; the test suite runs against all three versions
+in CI.
+
+
+This repository hosts a collection of functions for processing
+electrocardiogram (ECG) data and preparing it for analysis.
+
+At a glance, ECGProcess is driven by three units:
+
+* A **processor** unit, reads individual ECG files and based on 
+  a user-supplied configuration file extracts waveform
+  signals, median beats, and metadata to python dictionaries; see [Configuration files](https://SchmidtAF.gitlab.io/ECGProcess/configuration_files.html)).
+* The **table** unit, `ECGTable`, loops over a directory of ECG files, 
+  calls the reader for each one, while applying optional engineering steps
+  (e.g. resampling, calibration, lead correction), and again optionally 
+  concatenating multiple files together.
+* A **writer** unit, tells `ECGTable` what to write to disk
+  (tables, NumPy arrays, WFDB records, images, ...). 
+
+Together these units implement an application programming interface (API),
+mapping ECG data from distinct file types to class attributes
+providing a fixed interface for downstream processing. 
+The package ships with boilerplate classes and validation utilities,
+letting the user expand **processing** of additional file types,
+build custom **engineering** (e.g. standardisation) pipelines, as well as 
+create custom **writers**.
+
+Please consult the [documentation](https://SchmidtAF.gitlab.io/ECGProcess/)
+for the full picture.
+
+## Installation 
+The package is available on PyPI, and conda, with the latest source code 
+available on gitlab. 
+
+### Installation using PyPI
+
+To install the package from PyPI, run:
+
+```bash
+pip install ecgprocess
+```
+
+This installs the latest stable release along with its dependencies.
+
+### Installation using conda
+
+A Conda package is maintained in my personal Conda channel.
+To install from this channel, run:
+
+```bash
+conda install afschmidt::ecgprocess
+```
+
+### Installation using gitlab
+
+If you require the latest updates, potentially not yet formally released,
+you can install the package directly from GitLab.
+
+First, clone the repository and move into its root directory:
+
+```bash
+git clone git@gitlab.com:SchmidtAF/ecgprocess.git
+cd ecgprocess
+```
+
+Install the dependencies:
+
+```bash
+# From the root of the repository
+conda env create --file ./resources/conda/envs/conda_create.yaml
+```
+
+To add to an existing environment use:
+
+```bash
+# From the root of the repository
+conda env update --file ./resources/conda/envs/conda_update.yaml
+```
+
+Next the package can be installed: 
+
+```bash
+make install
+```
+
+#### Development
+For development work, install the package in editable mode, with its
+development dependencies (`pytest`, `codespell`, `sphinx`, ...) and Git
+commit hooks configured:
+
+```bash
+make install-dev
+```
+
+This command installs the package in editable mode with the `[dev]`
+extras and configures Git commit hooks, allowing you to run `git pull`
+to update the repository or switch branches without reinstalling.
+
+Alternatively, you can install manually. This is exactly equivalent
+to `make install-dev`:
+
+```bash
+python -m pip install -e ".[dev]"
+python .githooks/.setup_git_hooks.py
+```
+
+#### Git Hooks Configuration
+
+
+When setting up a development environment, the `setup-hooks` command 
+configures Git hooks to enforce conventional commit message formatting and 
+spell check using `codespell`.
+
+To view the commit message format requirements, run:
+
+```bash
+./.githooks/commit-msg -help
+```
+
+For frequent use, add this function to your shell configuration (`~/.bashrc` 
+or `~/.zshrc`):
+
+```bash
+commit-format-help() {
+    local git_root
+    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
+    
+    if [ -z "$git_root" ]; then
+        echo "Error: Not inside a git repository"
+        return 1
+    fi
+    
+    local hook_path="$git_root/.githooks/commit-msg"
+    
+    if [ ! -f "$hook_path" ]; then
+        echo "Error: commit-msg hook not found"
+        return 1
+    fi
+    
+    "$hook_path" --help
+}
+```
+
+## Next steps...
+If you installed with `make install-dev`, you might wish to run `pytest` to 
+confirm everything is in working order. 
+
+```sh
+# From the root of the repository
+pytest tests
+```
+
+## Usage
+
+Please have a look at the [example](https://SchmidtAF.gitlab.io/ECGProcess/examples.html)
+ recipes. 
+
+## Icon
+
+The package icon features the Etruscan shrew, one of the smallest
+mammals, whose heart can beat over 1,500 times a minute, the fastest
+heart rate of any mammal.

ecgprocess-1.2.0/README.md

@@ -0,0 +1,170 @@
+<!-- TODO once dev is merged into master and the pages job redeploys, switch
+     this back to the Sphinx-published URL:
+     https://SchmidtAF.gitlab.io/ECGProcess/_static/ecgp_logo.png -->
+<img src="https://gitlab.com/SchmidtAF/ECGProcess/-/raw/d853ccf/docs/source/_static/ecgp_logo.png" alt="ECGProcess icon" width="250"/>
+
+# An ECG processing module
+__version__: `1.2.0`
+
+Supports Python 3.11-3.13; the test suite runs against all three versions
+in CI.
+
+
+This repository hosts a collection of functions for processing
+electrocardiogram (ECG) data and preparing it for analysis.
+
+At a glance, ECGProcess is driven by three units:
+
+* A **processor** unit, reads individual ECG files and based on 
+  a user-supplied configuration file extracts waveform
+  signals, median beats, and metadata to python dictionaries; see [Configuration files](https://SchmidtAF.gitlab.io/ECGProcess/configuration_files.html)).
+* The **table** unit, `ECGTable`, loops over a directory of ECG files, 
+  calls the reader for each one, while applying optional engineering steps
+  (e.g. resampling, calibration, lead correction), and again optionally 
+  concatenating multiple files together.
+* A **writer** unit, tells `ECGTable` what to write to disk
+  (tables, NumPy arrays, WFDB records, images, ...). 
+
+Together these units implement an application programming interface (API),
+mapping ECG data from distinct file types to class attributes
+providing a fixed interface for downstream processing. 
+The package ships with boilerplate classes and validation utilities,
+letting the user expand **processing** of additional file types,
+build custom **engineering** (e.g. standardisation) pipelines, as well as 
+create custom **writers**.
+
+Please consult the [documentation](https://SchmidtAF.gitlab.io/ECGProcess/)
+for the full picture.
+
+## Installation 
+The package is available on PyPI, and conda, with the latest source code 
+available on gitlab. 
+
+### Installation using PyPI
+
+To install the package from PyPI, run:
+
+```bash
+pip install ecgprocess
+```
+
+This installs the latest stable release along with its dependencies.
+
+### Installation using conda
+
+A Conda package is maintained in my personal Conda channel.
+To install from this channel, run:
+
+```bash
+conda install afschmidt::ecgprocess
+```
+
+### Installation using gitlab
+
+If you require the latest updates, potentially not yet formally released,
+you can install the package directly from GitLab.
+
+First, clone the repository and move into its root directory:
+
+```bash
+git clone git@gitlab.com:SchmidtAF/ecgprocess.git
+cd ecgprocess
+```
+
+Install the dependencies:
+
+```bash
+# From the root of the repository
+conda env create --file ./resources/conda/envs/conda_create.yaml
+```
+
+To add to an existing environment use:
+
+```bash
+# From the root of the repository
+conda env update --file ./resources/conda/envs/conda_update.yaml
+```
+
+Next the package can be installed: 
+
+```bash
+make install
+```
+
+#### Development
+For development work, install the package in editable mode, with its
+development dependencies (`pytest`, `codespell`, `sphinx`, ...) and Git
+commit hooks configured:
+
+```bash
+make install-dev
+```
+
+This command installs the package in editable mode with the `[dev]`
+extras and configures Git commit hooks, allowing you to run `git pull`
+to update the repository or switch branches without reinstalling.
+
+Alternatively, you can install manually. This is exactly equivalent
+to `make install-dev`:
+
+```bash
+python -m pip install -e ".[dev]"
+python .githooks/.setup_git_hooks.py
+```
+
+#### Git Hooks Configuration
+
+
+When setting up a development environment, the `setup-hooks` command 
+configures Git hooks to enforce conventional commit message formatting and 
+spell check using `codespell`.
+
+To view the commit message format requirements, run:
+
+```bash
+./.githooks/commit-msg -help
+```
+
+For frequent use, add this function to your shell configuration (`~/.bashrc` 
+or `~/.zshrc`):
+
+```bash
+commit-format-help() {
+    local git_root
+    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
+    
+    if [ -z "$git_root" ]; then
+        echo "Error: Not inside a git repository"
+        return 1
+    fi
+    
+    local hook_path="$git_root/.githooks/commit-msg"
+    
+    if [ ! -f "$hook_path" ]; then
+        echo "Error: commit-msg hook not found"
+        return 1
+    fi
+    
+    "$hook_path" --help
+}
+```
+
+## Next steps...
+If you installed with `make install-dev`, you might wish to run `pytest` to 
+confirm everything is in working order. 
+
+```sh
+# From the root of the repository
+pytest tests
+```
+
+## Usage
+
+Please have a look at the [example](https://SchmidtAF.gitlab.io/ECGProcess/examples.html)
+ recipes. 
+
+## Icon
+
+The package icon features the Etruscan shrew, one of the smallest
+mammals, whose heart can beat over 1,500 times a minute, the fastest
+heart rate of any mammal.