paradigma 0.1.5__py3-none-any.whl → 0.3.0__py3-none-any.whl

paradigma/windowing.py

@@ -0,0 +1,219 @@
+import pandas as pd
+import numpy as np
+import math
+
+from typing import Union, List
+
+
+def create_window(
+        df: pd.DataFrame,
+        time_column_name: str,
+        window_nr: int,
+        lower_index: int,
+        upper_index: int,
+        data_point_level_cols: list,
+        segment_nr: int,
+        sampling_frequency: int = 100
+    ) -> list:
+    """Transforms (a subset of) a dataframe into a single row
+
+    Parameters
+    ----------
+    df: pd.DataFrame
+        The original dataframe to be windowed
+    time_column_name: str
+        The name of the time column
+    window_nr: int
+        The identification of the window
+    lower_index: int
+        The dataframe index of the first sample to be windowed
+    upper_index: int
+        The dataframe index of the final sample to be windowed
+    data_point_level_cols: list
+        The columns in sensor_df that are to be kept as individual datapoints in a list instead of aggregates
+    segment_nr: int
+        The identification of the segment
+    sampling_frequency: int, optional
+        The sampling frequency (Hz) of the data (default: 100)
+
+    Returns
+    -------
+    list
+        Rows corresponding to single windows
+    """
+    t_start_window = df.loc[lower_index, time_column_name]
+
+    df_subset = df.loc[lower_index:upper_index, data_point_level_cols].copy()
+    t_start = t_start_window
+    t_end = upper_index/sampling_frequency + t_start_window
+
+    if segment_nr is None:
+        l_subset_squeezed = [window_nr+1, t_start, t_end] + df_subset.values.T.tolist()
+    else:
+        l_subset_squeezed = [segment_nr, window_nr+1, t_start, t_end] + df_subset.values.T.tolist()
+
+    return l_subset_squeezed
+
+
+def tabulate_windows(
+        df: pd.DataFrame,
+        time_column_name: str,
+        data_point_level_cols: list,
+        window_length_s: Union[int, float] = 6,
+        window_step_size_s: Union[int, float] = 1,
+        sampling_frequency: int = 100,
+        segment_nr_colname: Union[str, None] = None,
+        segment_nr: Union[int, None] = None,
+    ) -> pd.DataFrame:
+    """Compiles multiple windows into a single dataframe
+
+    Parameters
+    ----------
+    df: pd.DataFrame
+        The original dataframe to be windowed
+    time_column_name: str
+        The name of the time column
+    data_point_level_cols: list
+        The names of the columns that are to be kept as individual datapoints in a list instead of aggregates
+    window_length_s: int | float, optional
+        The number of seconds a window constitutes (default: 6)
+    window_step_size_s: int | float, optional
+        The number of seconds between the end of the previous and the start of the next window (default: 1)
+    sampling_frequency: int, optional
+        The sampling frequency of the data (default: 100)
+    segment_nr_colname: str, optional
+        The name of the column that identifies the segment; set to None if not applicable (default: None)
+    segment_nr: int, optional
+        The identification of the segment; set to None if not applicable (default: None)
+    
+
+    Returns
+    -------
+    pd.DataFrame
+        Dataframe with each row corresponding to an individual window
+    """
+    window_length = sampling_frequency * window_length_s - 1
+    window_step_size = sampling_frequency * window_step_size_s
+
+    df = df.reset_index(drop=True)
+
+    if window_step_size <= 0:
+        raise Exception("Step size should be larger than 0.")
+    if window_length > df.shape[0]:
+        return 
+
+    l_windows = []
+    n_windows = math.floor(
+        (df.shape[0] - window_length) / 
+         window_step_size
+        ) + 1
+
+    for window_nr in range(n_windows):
+        lower = window_nr * window_step_size
+        upper = window_nr * window_step_size + window_length
+        l_windows.append(
+            create_window(
+                df=df,
+                time_column_name=time_column_name,
+                window_nr=window_nr,
+                lower_index=lower,
+                upper_index=upper,
+                data_point_level_cols=data_point_level_cols,
+                segment_nr=segment_nr,
+                sampling_frequency=sampling_frequency
+            )
+        )
+
+    if segment_nr is None:
+        df_windows = pd.DataFrame(l_windows, columns=['window_nr', 'window_start', 'window_end'] + data_point_level_cols)
+    else:
+        df_windows = pd.DataFrame(l_windows, columns=[segment_nr_colname, 'window_nr', 'window_start', 'window_end'] + data_point_level_cols)
+            
+    return df_windows.reset_index(drop=True)
+
+
+def create_segments(
+        df: pd.DataFrame,
+        time_colname: str,
+        segment_nr_colname: str,
+        minimum_gap_s: int,
+    ) -> pd.DataFrame:
+    """Create segments based on the time column of the dataframe. Segments are defined as continuous time periods.
+    
+    Parameters
+    ----------
+    df: pd.DataFrame
+        The dataframe to be segmented
+    time_colname: str
+        The name of the time column
+    minimum_gap_s: int
+        The minimum gap in seconds to split up the time periods into segments
+
+    Returns
+    -------
+    pd.DataFrame
+        The dataframe with additional columns related to segments
+    """
+    array_new_segments = np.where((df[time_colname] - df[time_colname].shift() > minimum_gap_s), 1, 0)
+    df['new_segment_cumsum'] = array_new_segments.cumsum()
+    df_segments = pd.DataFrame(df.groupby('new_segment_cumsum')[time_colname].count()).reset_index()
+    df_segments.columns = [segment_nr_colname, 'length_segment_s']
+    df_segments[segment_nr_colname] += 1
+
+    df = df.drop(columns=['new_segment_cumsum'])
+
+    cols_to_append = [segment_nr_colname, 'length_segment_s']
+
+    for col in cols_to_append:
+        df[col] = 0
+
+    index_start = 0
+    for _, row in df_segments.iterrows():
+        len_segment = row['length_segment_s']
+
+        for col in cols_to_append:
+            df.loc[index_start:index_start+len_segment-1, col] = row[col]
+
+        index_start += len_segment
+
+    return df
+
+
+def discard_segments(
+        df: pd.DataFrame,
+        time_colname: str,
+        segment_nr_colname: str,
+        minimum_segment_length_s: int,
+    ) -> pd.DataFrame:
+    """Discard segments that are shorter than a specified length.
+    
+    Parameters
+    ----------
+    df: pd.DataFrame
+        The dataframe containing information about the segments
+    time_colname: str
+        The column name of the time column
+    segment_nr_colname: str
+        The column name of the column containing the segment numbers
+    minimum_segment_length_s: int
+        The minimum required length of a segment in seconds
+    
+    Returns
+    -------
+    pd.DataFrame
+        The dataframe with segments that are longer than the specified length
+    """
+    segment_length_bool = df.groupby(segment_nr_colname)[time_colname].apply(lambda x: x.max() - x.min()) > minimum_segment_length_s
+
+    df = df.loc[df[segment_nr_colname].isin(segment_length_bool.loc[segment_length_bool.values].index)]
+
+    # reorder the segments - starting at 1
+    for segment_nr in df[segment_nr_colname].unique():
+        df.loc[df[segment_nr_colname]==segment_nr, f'{segment_nr_colname}_ordered'] = np.where(df[segment_nr_colname].unique()==segment_nr)[0][0] + 1
+
+    df[f'{segment_nr_colname}_ordered'] = df[f'{segment_nr_colname}_ordered'].astype(int)
+
+    df = df.drop(columns=[segment_nr_colname])
+    df = df.rename(columns={f'{segment_nr_colname}_ordered': segment_nr_colname})
+
+    return df

paradigma-0.3.0.dist-info/LICENSE

@@ -0,0 +1,192 @@
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+
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+

paradigma-0.3.0.dist-info/METADATA

@@ -0,0 +1,79 @@
+Metadata-Version: 2.1
+Name: paradigma
+Version: 0.3.0
+Summary: Paradigma - a toolbox for Digital Biomarkers for Parkinson's Disease
+License: Apache-2.0
+Author: Peter Kok
+Author-email: p.kok@esciencecenter.nl
+Requires-Python: >=3.10,<4.0
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: pandas (>=2.1.4,<3.0.0)
+Requires-Dist: pytype (>=2024.4.11,<2025.0.0)
+Requires-Dist: scikit-learn (>=1.3.2,<2.0.0)
+Requires-Dist: tsdf (>=0.5.2,<0.6.0)
+Description-Content-Type: text/markdown
+
+# paradigma
+
+| Badges | |
+|:----:|----|
+| **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/biomarkersparkinson/paradigma.svg)](https://github.com/biomarkersparkinson/paradigma/releases/latest) [![PyPI](https://img.shields.io/pypi/v/paradigma.svg)](https://pypi.python.org/pypi/paradigma/)  [![Static Badge](https://img.shields.io/badge/RSD-paradigma-lib)](https://research-software-directory.org/software/paradigma) |
+| **Build Status** | [![](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/) [![Build and test](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml) [![pages-build-deployment](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment) |
+| **License** |  [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/paradigma)](https://github.com/biomarkersparkinson/paradigma/blob/main/LICENSE) |
+<!-- | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7867899.svg)](https://doi.org/10.5281/zenodo.7867899) | -->
+<!-- | **Fairness** |  [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/8083/badge)](https://www.bestpractices.dev/projects/8083) | -->
+
+Digital Biomarkers for Parkinson's Disease Toolbox
+
+A package ([documentation](https://biomarkersparkinson.github.io/paradigma/)) to process wearable sensor data for Parkinson's disease.
+
+## Installation
+
+The package is available in PyPi and requires [Python 3.10](https://www.python.org/downloads/) or higher. It can be installed using:
+
+```bash
+pip install paradigma
+```
+
+## Usage
+
+See our [extended documentation](https://biomarkersparkinson.github.io/paradigma/).
+
+
+## Development
+
+### Installation
+The package requires Python 3.10 or higher. Use [Poetry](https://python-poetry.org/docs/#installation) to set up the environment and install the dependencies:
+
+```bash
+poetry install
+```
+
+### Testing
+
+```bash
+poetry run pytest
+```
+
+### Building documentation
+
+```bash
+poetry run make html --directory docs/
+```
+
+## Contributing
+
+Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.
+
+## License
+
+`paradigma` was created by Peter Kok, Vedran Kasalica, Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers. It is licensed under the terms of the Apache License 2.0 license.
+
+## Credits
+
+`paradigma` was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).
+

paradigma-0.3.0.dist-info/RECORD

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paradigma/dummy.py

@@ -1,3 +0,0 @@
-
-def hello_world():
-    return "Hello, world!"