proadv 2.0.2__tar.gz → 2.1.2__tar.gz

{proadv-2.0.2 → proadv-2.1.2}/PKG-INFO

@@ -1,24 +1,24 @@
 Metadata-Version: 2.1
 Name: proadv
-Version: 2.0.2
+Version: 2.1.2
 Summary: Process Acoustic Doppler Velocimeter data with advanced despiking and analysis tools
 Home-page: https://github.com/farzadasgari/proadv
 Author: Farzad Asgari
 Author-email: std_farzad.asgari@alumni.khu.ac.ir
-Project-URL: Bug Tracker, https://github.com/farzadasgari/proadv/issues
-Project-URL: Documentation, https://github.com/farzadasgari/proadv/tree/main/docs
+Project-URL: Download URL, https://pypi.org/project/proadv/
 Project-URL: Source Code, https://github.com/farzadasgari/proadv
+Project-URL: Documentation, https://proadv.readthedocs.io/en/latest/
 Keywords: ProADV,python,signal processing,data processing,acoustic Doppler velocimeter,ADV,Denoising,Despiking
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Description-Content-Type: text/markdown
 Requires-Dist: numpy>=1.0
 Requires-Dist: scipy>=1.0
@@ -30,9 +30,8 @@ Requires-Dist: fastkde
 [![GitHub forks](https://img.shields.io/github/forks/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/network)
 [![GitHub issues](https://img.shields.io/github/issues/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/issues)
 [![GitHub license](https://img.shields.io/github/license/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/blob/main/LICENSE)
-[![PyPI version](https://badge.fury.io/py/proadv.svg)](https://badge.fury.io/py/proadv)
-[![conda](https://img.shields.io/conda/vn/conda-forge/proadv.svg)](https://anaconda.org/conda-forge/proadv)
-[![PyPI - Downloads](https://img.shields.io/pypi/dm/proadv)](https://pypi.org/project/proadv/)
+[![PyPI version](https://img.shields.io/pypi/v/proadv.svg)](https://pypi.org/project/proadv/)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/proadv.svg)](https://pypi.org/project/proadv/)
 [![GitHub contributors](https://img.shields.io/github/contributors/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/graphs/contributors)
 [![GitHub pull requests](https://img.shields.io/github/issues-pr/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/pulls)
 [![GitHub closed pull requests](https://img.shields.io/github/issues-pr-closed/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/pulls?q=is%3Apr+is%3Aclosed)
@@ -60,6 +59,14 @@ Requires-Dist: fastkde
         * **LI (Linear Interpolation):** Uses linear interpolation between surrounding points to estimate the missing value.
         * **12PP (12 Points Cubic Polynomial):** Employs a 12-point cubic polynomial to fit a smoother curve and replace spikes.
 
+
+<div>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/trivariate-kernel.png" alt="trivariate-kernel" style="width:300px;"/>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/spectrum.png" alt="trivariate-kernel" style="width:300px;"/>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/phase-space.png" alt="trivariate-kernel" style="width:300px;"/>
+</div>
+
+
 * **Statistical Analysis:** ProADV equips you with essential statistical tools to characterize your ADV data:
     * **Minimum, Maximum:** Provides the range of measured velocities.
     * **Mean, Median, Mode:** Calculates central tendency measures.
@@ -68,6 +75,7 @@ Requires-Dist: fastkde
 * **Advanced Analysis:** In addition to cleaning and basic statistics, ProADV offers advanced functionalities for deeper insights:
     * **Moving Average:** Smooths out data fluctuations for better visualization and trend analysis. Provided in simple moving average, exponential moving average, and weighted moving average methods. 
     * **SSA (Singular Spectrum Analysis):** Extracts underlying patterns and trends from time series data.
+    * **Kalman Filter:** Implements the Kalman filter algorithm for state estimation and prediction in time series data. 
     * **PR (Pollution Rate) Calculation:** Estimates the level of noise or pollution within the data.
     * **Spectral Analysis:**
         * **PSD (Power Spectral Density):** Analyzes the distribution of energy across different frequencies within the data.
@@ -75,21 +83,21 @@ Requires-Dist: fastkde
     * **Normality Test:** Evaluates whether your data follows a normal distribution.
     * **Normalization:** Scales data to a common range for further analysis or visualization.
 
+<div>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/singular-spectrum.png" alt="singular-spectrum" style="width:300px;"/>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/kalman.png" alt="kalman-filter" style="width:300px;"/>
+</div>
+
 ### Installation
 
-There are three convenient ways to install ProADV:
+There are two convenient ways to install ProADV:
 
 1. **Using pip (recommended):**
    ```bash
    pip install proadv
    ```
 
-2. **Using conda-forge:**
-   ```bash
-   conda install -c conda-forge proadv
-   ```
-
-3. **From source code:**
+2. **From source code:**
 
    a. Clone the repository:
       ```bash
@@ -125,6 +133,7 @@ For further information and in-depth understanding of the algorithms employed in
 
 ### Acknowledgment
 - This project was developed under the supervision of **[Dr. Seyed Hossein Mohaeri](https://khu.ac.ir/cv/1139/Seyed-Hossein-Mohajeri)** and **[Dr. Mojtaba Mehraein](https://khu.ac.ir/cv/279/Mojtaba-Mehraein)**.
+- We extend our deepest gratitude to **[Dr. Bimlesh Kumar](https://www.researchgate.net/profile/Bimlesh-Kumar)** and **[Dr. Luis Cea](https://www.researchgate.net/profile/Luis-Cea)** for their invaluable guidance and unwavering support throughout our journey.
 - Special thanks to [Parvaneh Yaghoubi](https://github.com/parvanehyaghoubi), [Hossein Abazari](https://github.com/HossA12), [Narges Yaghoubi](https://github.com/nargesyaghoubi), [Mojtaba Karimi](https://github.com/mojikarimi), and [Hiva Yarandi](https://github.com/Hivayrn) for their valuable contributions to this project.
 
 
@@ -133,6 +142,7 @@ For any inquiries, please contact:
 - std_farzad.asgari@alumni.khu.ac.ir
 - khufarzadasgari@gmail.com
 
+
 ### Links
 
 ##### Farzad Asgari

{proadv-2.0.2 → proadv-2.1.2}/README.md

@@ -4,9 +4,8 @@
 [![GitHub forks](https://img.shields.io/github/forks/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/network)
 [![GitHub issues](https://img.shields.io/github/issues/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/issues)
 [![GitHub license](https://img.shields.io/github/license/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/blob/main/LICENSE)
-[![PyPI version](https://badge.fury.io/py/proadv.svg)](https://badge.fury.io/py/proadv)
-[![conda](https://img.shields.io/conda/vn/conda-forge/proadv.svg)](https://anaconda.org/conda-forge/proadv)
-[![PyPI - Downloads](https://img.shields.io/pypi/dm/proadv)](https://pypi.org/project/proadv/)
+[![PyPI version](https://img.shields.io/pypi/v/proadv.svg)](https://pypi.org/project/proadv/)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/proadv.svg)](https://pypi.org/project/proadv/)
 [![GitHub contributors](https://img.shields.io/github/contributors/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/graphs/contributors)
 [![GitHub pull requests](https://img.shields.io/github/issues-pr/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/pulls)
 [![GitHub closed pull requests](https://img.shields.io/github/issues-pr-closed/farzadasgari/proadv)](https://github.com/farzadasgari/proadv/pulls?q=is%3Apr+is%3Aclosed)
@@ -34,6 +33,14 @@
         * **LI (Linear Interpolation):** Uses linear interpolation between surrounding points to estimate the missing value.
         * **12PP (12 Points Cubic Polynomial):** Employs a 12-point cubic polynomial to fit a smoother curve and replace spikes.
 
+
+<div>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/trivariate-kernel.png" alt="trivariate-kernel" style="width:300px;"/>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/spectrum.png" alt="trivariate-kernel" style="width:300px;"/>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/phase-space.png" alt="trivariate-kernel" style="width:300px;"/>
+</div>
+
+
 * **Statistical Analysis:** ProADV equips you with essential statistical tools to characterize your ADV data:
     * **Minimum, Maximum:** Provides the range of measured velocities.
     * **Mean, Median, Mode:** Calculates central tendency measures.
@@ -42,6 +49,7 @@
 * **Advanced Analysis:** In addition to cleaning and basic statistics, ProADV offers advanced functionalities for deeper insights:
     * **Moving Average:** Smooths out data fluctuations for better visualization and trend analysis. Provided in simple moving average, exponential moving average, and weighted moving average methods. 
     * **SSA (Singular Spectrum Analysis):** Extracts underlying patterns and trends from time series data.
+    * **Kalman Filter:** Implements the Kalman filter algorithm for state estimation and prediction in time series data. 
     * **PR (Pollution Rate) Calculation:** Estimates the level of noise or pollution within the data.
     * **Spectral Analysis:**
         * **PSD (Power Spectral Density):** Analyzes the distribution of energy across different frequencies within the data.
@@ -49,21 +57,21 @@
     * **Normality Test:** Evaluates whether your data follows a normal distribution.
     * **Normalization:** Scales data to a common range for further analysis or visualization.
 
+<div>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/singular-spectrum.png" alt="singular-spectrum" style="width:300px;"/>
+   <img src="https://raw.githubusercontent.com/farzadasgari/proadv/main/examples/plots/kalman.png" alt="kalman-filter" style="width:300px;"/>
+</div>
+
 ### Installation
 
-There are three convenient ways to install ProADV:
+There are two convenient ways to install ProADV:
 
 1. **Using pip (recommended):**
    ```bash
    pip install proadv
    ```
 
-2. **Using conda-forge:**
-   ```bash
-   conda install -c conda-forge proadv
-   ```
-
-3. **From source code:**
+2. **From source code:**
 
    a. Clone the repository:
       ```bash
@@ -99,6 +107,7 @@ For further information and in-depth understanding of the algorithms employed in
 
 ### Acknowledgment
 - This project was developed under the supervision of **[Dr. Seyed Hossein Mohaeri](https://khu.ac.ir/cv/1139/Seyed-Hossein-Mohajeri)** and **[Dr. Mojtaba Mehraein](https://khu.ac.ir/cv/279/Mojtaba-Mehraein)**.
+- We extend our deepest gratitude to **[Dr. Bimlesh Kumar](https://www.researchgate.net/profile/Bimlesh-Kumar)** and **[Dr. Luis Cea](https://www.researchgate.net/profile/Luis-Cea)** for their invaluable guidance and unwavering support throughout our journey.
 - Special thanks to [Parvaneh Yaghoubi](https://github.com/parvanehyaghoubi), [Hossein Abazari](https://github.com/HossA12), [Narges Yaghoubi](https://github.com/nargesyaghoubi), [Mojtaba Karimi](https://github.com/mojikarimi), and [Hiva Yarandi](https://github.com/Hivayrn) for their valuable contributions to this project.
 
 
@@ -107,6 +116,7 @@ For any inquiries, please contact:
 - std_farzad.asgari@alumni.khu.ac.ir
 - khufarzadasgari@gmail.com
 
+
 ### Links
 
 ##### Farzad Asgari

proadv-2.1.2/proadv/__init__.py

@@ -0,0 +1 @@
+from . import statistics, kernel, filtration

proadv-2.1.2/proadv/filtration/__init__.py

@@ -0,0 +1 @@
+from . import detection, replacement

proadv-2.1.2/proadv/filtration/detection/__init__.py

@@ -0,0 +1 @@
+from . import poincare, pollution, spherical, phasespace, correlation, acceleration, bivariatekernel, trivariatekernel

{proadv-2.0.2 → proadv-2.1.2}/proadv/filtration/detection/acceleration.py

@@ -6,7 +6,7 @@ def acceleration_thresholding(velocities, frequency, tag, gravity=980, k_gravity
     """
     Detects acceleration events based on velocity data.
 
-    This function calculates acceleration events based on velocity data, considering thresholds
+    Calculate acceleration events based on velocity data, considering thresholds
         for acceleration magnitude and velocity deviation from mean.
 
     Parameters

{proadv-2.0.2 → proadv-2.1.2}/proadv/filtration/detection/bivariatekernel.py

@@ -51,3 +51,13 @@ def _cutoff(density_profile, velocity_profile, c1_threshold, c2_threshold, force
     upper_cutoff_velocity = velocity_profile[upper_cutoff_index]
 
     return lower_cutoff_velocity, upper_cutoff_velocity
+
+
+def _derivative(data):
+    data_size = data.size
+    derivative = np.zeros(data_size)
+    for i in range(1, data_size - 1):
+        backward = data[i] - data[i - 1]
+        forward = data[i + 1] - data[i]
+        derivative[i] = forward if abs(backward) > abs(forward) else backward
+    return derivative

proadv-2.1.2/proadv/filtration/replacement/__init__.py

@@ -0,0 +1 @@
+from . import replacements

{proadv-2.0.2 → proadv-2.1.2}/proadv/filtration/replacement/replacements.py

@@ -66,22 +66,18 @@ def linear_interpolation(velocities, spike_indices, decimals=4):
 
     Parameters
     ------
-    velocities : (array_like)
-        An array-like object containing velocity values. It should be a one-dimensional
+    velocities (array_like):  An array-like object containing velocity values. It should be a one-dimensional
         array of numerical data representing velocities.
-    spike_indices : (array_like)
-        An array-like object containing the indices of detected spike events. It should
+    spike_indices (array_like): An array-like object containing the indices of detected spike events. It should
         be a one-dimensional array of integers where each integer represents the index
         in 'velocities' that corresponds to a spike.
-    decimals : int, optional
-        The number of decimal places to round the interpolated values to. This allows
+    decimals (int, optional): The number of decimal places to round the interpolated values to. This allows
         the output data to be presented with a consistent level of precision. The default
         value is 4, but this can be adjusted as needed.
 
     Returns
     ------
-    modified_data (array_like):
-        An array containing the modified velocity data with spikes replaced by
+    modified_data (array_like): An array containing the modified velocity data with spikes replaced by
         interpolated values. The shape and type of the array are the same as the
         input 'velocities' array.
 

proadv-2.1.2/proadv/kernel/__init__.py

@@ -0,0 +1 @@
+from . import bivariate

{proadv-2.0.2 → proadv-2.1.2}/proadv/kernel/bivariate.py

@@ -366,14 +366,14 @@ def bivariate_kernel(data, hx, hy, grid):
     Compute the bivariate kernel density estimation.
 
     Parameters
-    ----------
+    ------
     data (array_like): Input data array.
     hx (float): Bandwidth along the x-axis.
     hy (float): Bandwidth along the y-axis.
     grid (int): Number of bins along each dimension for histogram computation.
 
     Returns
-    -------
+    ------
     density_mx (array_like): Bivariate kernel density estimation.
     x_mx (array_like): Meshgrid of x values.
     y_mx (array_like): Meshgrid of y values.

proadv-2.1.2/proadv/statistics/__init__.py

@@ -0,0 +1,2 @@
+from . import descriptive, spread, series, moment
+from . import signal, optimize, distributions

{proadv-2.0.2 → proadv-2.1.2}/proadv/statistics/descriptive.py

@@ -51,16 +51,15 @@ def min(data):
     """
 
     for i in data:
-        if isinstance(i, str):  # isinstance returns True if the specified object is of the specified type, otherwise False.
+        if isinstance(i,
+                      str):  # isinstance returns True if the specified object is of the specified type, otherwise False
             raise TypeError("String cannot be placed as an element of an array")
     if np.isnan(data).any():
         raise ValueError("The array contains NaN values. The min function cannot be applied to arrays with NaN values.")
-    if data.ndim != 1:  # Optional check for 1D array
-        raise ValueError("Data array must be a 1D array.")   
-    if np.size(data) == 0: # The array cannot be empty
+    if np.size(data) == 0:  # The array cannot be empty
         raise ValueError("cannot calculate minimum with empty array")
-      
-    minimum = np.min(data) # Calculate the minimum
+
+    minimum = np.min(data)  # Calculate the minimum
     return minimum
 
 
@@ -116,22 +115,20 @@ def max(data):
     >>> maximum
     9
     """
-    
+
     for i in data:
-        if isinstance(i, str): # isinstance returns True if the specified object is of the specified type, otherwise False.
+        if isinstance(i,
+                      str):  # isinstance returns True if the specified object is of the specified type, otherwise False.
             raise TypeError("String cannot be placed as an element of an array")
 
     if np.isnan(data).any():
         raise ValueError("The array contains NaN values. The max function cannot be applied to arrays with NaN values.")
-    
-    if data.ndim != 1:  # Optional check for 1D array
-        raise ValueError("Data array must be a 1D array.")
-    
+
     if np.size(data) == 0:
         # The array cannot be empty
         raise ValueError("cannot calculate maximum with empty array")
     maximum = np.max(data)  # Calculate the maximum
-    
+
     return maximum
 
 

proadv-2.1.2/proadv/statistics/distributions/__init__.py

@@ -0,0 +1 @@
+from . import normal