arrhythpy 1.0.0__py3-none-any.whl

arrhythpy/__init__.py

@@ -0,0 +1,36 @@
+"""
+Arrhythpy
+=========
+
+Arrhythpy is an open-source Python program to quantify and classify
+arrhythmias in calcium transients in an automated manner.
+
+See the paper: https://doi.org/10.1152/ajpheart.00414.2025
+
+This package exposes the core analysis functions so Arrhythpy can be
+used as a library, in addition to its GUI and command-line tools:
+
+    >>> from arrhythpy import run, analyse_single, load_transient
+"""
+from .core import (
+    run,
+    analyse_single,
+    load_transient,
+    is_numeric,
+    calc_accuracy,
+    get_threshold_freq,
+    get_threshold_arrythmia,
+)
+
+__version__ = "1.0.0"
+
+__all__ = [
+    "run",
+    "analyse_single",
+    "load_transient",
+    "is_numeric",
+    "calc_accuracy",
+    "get_threshold_freq",
+    "get_threshold_arrythmia",
+    "__version__",
+]

arrhythpy/batch_cli.py

@@ -0,0 +1,82 @@
+"""
+Command-line entry point for running Arrhythpy over many sub-folders at
+once. Equivalent to running the original ``run_folders.py`` script.
+"""
+import glob
+import os
+
+import yaml
+
+from .core import run, is_numeric
+
+
+def main():
+    print('\n')
+    path = input('Path:\t')
+    print('\n')
+
+    file_path = os.path.join(path, "config.yaml")
+    if os.path.exists(file_path):
+        print("Parameter file found in folder: " + os.path.basename(path))
+        with open(os.path.join(path, "config.yaml"), 'r') as yaml_file:
+            params = yaml.safe_load(yaml_file)
+            frequency = params["frequency"]
+            duration = params["duration"]
+            threshold_freq = params["threshold_freq"]
+            threshold_arrythmia = params["threshold_arrythmia"]
+
+            show = params["show"]
+            sigma0 = params["sigma0"]
+            threshold_abs = params["threshold_abs"]
+            prominence = params["prominence"]
+            varfreq_weight = params["varfreq_weight"]
+            scale = params["scale"]
+    else:
+        print("No paramter file found. Specify the following paramters:\n")
+        frequency = input('Pacing / Eigen frequency:\t')
+        if is_numeric(frequency):
+            frequency = float(frequency)
+        print('\n')
+        duration = float(input('Duration of signal in sec:\t'))
+        print('\n')
+        threshold_freq = float(input('Threshold for Tachycardia / Bradicardia in Hz:\t'))
+        print('\n')
+        threshold_arrythmia = float(input('Threshold for Arrythmia:\t'))
+        print('\n')
+
+        show = False
+        sigma0 = .01
+        threshold_abs = .1
+        prominence = 0.05
+        varfreq_weight = 0.5
+        scale = 1.
+
+        params = {
+            'frequency': frequency,
+            'duration': duration,
+            'threshold_freq': threshold_freq,
+            'threshold_arrythmia': threshold_arrythmia,
+            'show': show,                           # set to True if you want to check the plots and edit them.
+            'sigma0': sigma0,                       # inital width of gaussian smoothing
+            'threshold_abs': threshold_abs,         # threshold for peak detection of wavelet transform
+            'prominence': prominence,               # omit any peaks in the correlation smaller than this value
+            'varfreq_weight': varfreq_weight,       # weight of VF in weight sum of IMC and VF
+            'scale': scale                          # scales the VF distribution before cropping to e [0,1]
+        }
+        with open(os.path.join(path, 'config.yaml'), 'w') as yaml_file:
+            yaml.dump(params, yaml_file)
+
+    directories = [os.path.join(path, name) for name in os.listdir(path) if os.path.isdir(os.path.join(path, name))]
+
+    files = []
+    for p in directories:
+        files_single = glob.glob(os.path.join(p, '*'))
+        files += files_single
+
+    run(files, frequency=frequency, threshold_freq=threshold_freq, prominence=prominence,
+        threshold_arrythmia=threshold_arrythmia, duration=duration, sigma0=sigma0,
+        threshold_abs=threshold_abs, path=path, show=show)
+
+
+if __name__ == "__main__":
+    main()

arrhythpy/cli.py

@@ -0,0 +1,78 @@
+"""
+Command-line entry point for running Arrhythpy on a single folder of
+line scans (or a folder of split CSV transients).
+
+Equivalent to running the original ``main.py`` script directly.
+"""
+import glob
+import os
+
+import yaml
+
+from .core import run, is_numeric
+
+
+def main():
+    print('\n')
+    path = input('Path:\t')
+    print('\n')
+
+    file_path = os.path.join(path, "config.yaml")
+    if os.path.exists(file_path):
+        print("Parameter file found in folder: " + os.path.basename(path))
+        with open(os.path.join(path, "config.yaml"), 'r') as yaml_file:
+            params = yaml.safe_load(yaml_file)
+            frequency = params["frequency"]
+            duration = params["duration"]
+            threshold_freq = params["threshold_freq"]
+            threshold_arrythmia = params["threshold_arrythmia"]
+
+            show = params["show"]
+            sigma0 = params["sigma0"]
+            threshold_abs = params["threshold_abs"]
+            prominence = params["prominence"]
+            varfreq_weight = params["varfreq_weight"]
+            scale = params["scale"]
+    else:
+        print("No paramter file found. Specify the following paramters:\n")
+        frequency = input('Pacing / Eigen frequency:\t')
+        if is_numeric(frequency):
+            frequency = float(frequency)
+        print('\n')
+        duration = float(input('Duration of signal in sec:\t'))
+        print('\n')
+        threshold_freq = float(input('Threshold for Tachycardia / Bradicardia in Hz:\t'))
+        print('\n')
+        threshold_arrythmia = float(input('Threshold for Arrythmia:\t'))
+        print('\n')
+
+        show = False
+        sigma0 = .01
+        threshold_abs = .1
+        prominence = 0.05
+        varfreq_weight = 0.5
+        scale = 1.
+
+        params = {
+            'frequency': frequency,
+            'duration': duration,
+            'threshold_freq': threshold_freq,
+            'threshold_arrythmia': threshold_arrythmia,
+            'show': show,                           # set to True if you want to check the plots and edit them.
+            'sigma0': sigma0,                       # inital width of gaussian smoothing
+            'threshold_abs': threshold_abs,         # threshold for peak detection of wavelet transform
+            'prominence': prominence,               # omit any peaks in the correlation smaller than this value
+            'varfreq_weight': varfreq_weight,       # weight of VF in weight sum of IMC and VF
+            'scale': scale                          # scales the VF distribution before cropping to e [0,1]
+        }
+        with open(os.path.join(path, 'config.yaml'), 'w') as yaml_file:
+            yaml.dump(params, yaml_file)
+
+    files = glob.glob(os.path.join(path, '*'))
+    run(files, frequency=frequency, threshold_freq=threshold_freq, threshold_arrythmia=threshold_arrythmia,
+        duration=duration, sigma0=sigma0, prominence=prominence, threshold_abs=threshold_abs,
+        varfreq_weight=varfreq_weight, scale=scale, show=show)
+
+
+if __name__ == "__main__":
+    main()