aerosim-cfdmod 1.1.2__tar.gz

aerosim_cfdmod-1.1.2/LICENSE

@@ -0,0 +1,202 @@
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aerosim_cfdmod-1.1.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: aerosim-cfdmod
+Version: 1.1.2
+Summary: Tools for analysis of CFD cases
+Home-page: https://github.com/AeroSim-CFD/cfdmod
+License: Apache-2.0
+Author: Waine Oliveira Jr
+Author-email: waine@aerosim.io
+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
+Classifier: Programming Language :: Python :: 3.13
+Provides-Extra: docs
+Provides-Extra: geometry
+Provides-Extra: lnas
+Provides-Extra: notebook
+Provides-Extra: vtk
+Requires-Dist: aerosim-lnas (>=0.6.0,<0.7.0)
+Requires-Dist: colorama (>=0.4.6,<0.5.0)
+Requires-Dist: ipykernel (>=6.25.2,<7.0.0) ; extra == "notebook"
+Requires-Dist: ipython (>=8.15.0,<9.0.0) ; extra == "notebook"
+Requires-Dist: jupyter (>=1.0.0,<2.0.0) ; extra == "notebook"
+Requires-Dist: matplotlib (>=3.7.3,<4.0.0)
+Requires-Dist: myst-parser (>=2.0.0,<3.0.0) ; extra == "docs"
+Requires-Dist: nbsphinx (>=0.9.3,<0.10.0) ; extra == "docs"
+Requires-Dist: numpy (>=1.26.0,<2.0.0)
+Requires-Dist: pandas (>=2.1.0,<3.0.0)
+Requires-Dist: pyarrow (>=15.0.0,<16.0.0)
+Requires-Dist: pydantic (>=2.3,<3.0)
+Requires-Dist: pymeshlab (>=2023,<2024) ; extra == "geometry"
+Requires-Dist: pyvista (>=0.43.1,<0.44.0) ; extra == "vtk"
+Requires-Dist: ruamel-yaml (>=0.18.5,<0.19.0)
+Requires-Dist: scipy (>=1.11.2,<2.0.0)
+Requires-Dist: sphinx-autobuild (>=2021.3.14,<2022.0.0) ; extra == "docs"
+Requires-Dist: sphinx-book-theme (>=1.0.1,<2.0.0) ; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex (>=2.6.1,<3.0.0) ; extra == "docs"
+Requires-Dist: tables (>=3.9.1,<4.0.0)
+Requires-Dist: trimesh (>=3.23.5,<4.0.0) ; extra == "geometry"
+Requires-Dist: vtk (>=9.2.6,<10.0.0) ; extra == "vtk"
+Project-URL: Repository, https://github.com/AeroSim-CFD/cfdmod
+Description-Content-Type: text/markdown
+
+# cfdmod
+
+[![Testing Pipeline](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/testing.yaml/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/testing.yaml)
+[![Docs Deploy](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/pages/pages-build-deployment)
+[![Linting Workflow](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/linting.yaml/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/linting.yaml)
+[![Release artifacts](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/build_and_deploy_artifacts.yaml/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/build_and_deploy_artifacts.yaml)
+
+Package to provide analysis and processing tools for CFD cases
+
+## Tests
+
+This codebase uses Pytest framework and it features tests for loft, cp, s1profile, config_models and altimetry modules. To run the tests via CLI:
+
+```bash
+poetry run pytest <path/to/tests>
+```
+
+The tests can also be automated to run in different environments, and include dist build commands using <a href="https://tox.wiki/en/stable/" target="_blank">tox</a>:
+
+```bash
+poetry run tox
+```
+
+## Memory usage profiling
+
+In order to check memory usage, _memory-profiler_ library is used.
+First, install memory-profiler:
+
+```bash
+pip install -U memory-profiler
+```
+
+And activate the poetry virtual environment:
+
+```bash
+poetry shell
+```
+
+Then, run:
+
+```bash
+mprof run -C -M python path_to_script.py
+mprof plot
+```
+
+That will plot the latest profiling data.
+
+## Generating schemas
+
+Schema files serve as a guide to fill config files.
+To generate a schema file for every config model, use the following command:
+
+```bash
+poetry run python -m scripts.generate_schemas
+```
+
+In order to setup the schema in VSCode, edit `settings.json`, or the workspace file, to include:
+
+```bash
+"yaml.schemas": {
+    "file:///path/to/cfdmod/output/schema-cfdmod.json": "**/cfdmod/**/\*.yaml"
+}
+```
+

aerosim_cfdmod-1.1.2/README.md

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+# cfdmod
+
+[![Testing Pipeline](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/testing.yaml/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/testing.yaml)
+[![Docs Deploy](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/pages/pages-build-deployment)
+[![Linting Workflow](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/linting.yaml/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/linting.yaml)
+[![Release artifacts](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/build_and_deploy_artifacts.yaml/badge.svg)](https://github.com/AeroSim-CFD/cfdmod/actions/workflows/build_and_deploy_artifacts.yaml)
+
+Package to provide analysis and processing tools for CFD cases
+
+## Tests
+
+This codebase uses Pytest framework and it features tests for loft, cp, s1profile, config_models and altimetry modules. To run the tests via CLI:
+
+```bash
+poetry run pytest <path/to/tests>
+```
+
+The tests can also be automated to run in different environments, and include dist build commands using <a href="https://tox.wiki/en/stable/" target="_blank">tox</a>:
+
+```bash
+poetry run tox
+```
+
+## Memory usage profiling
+
+In order to check memory usage, _memory-profiler_ library is used.
+First, install memory-profiler:
+
+```bash
+pip install -U memory-profiler
+```
+
+And activate the poetry virtual environment:
+
+```bash
+poetry shell
+```
+
+Then, run:
+
+```bash
+mprof run -C -M python path_to_script.py
+mprof plot
+```
+
+That will plot the latest profiling data.
+
+## Generating schemas
+
+Schema files serve as a guide to fill config files.
+To generate a schema file for every config model, use the following command:
+
+```bash
+poetry run python -m scripts.generate_schemas
+```
+
+In order to setup the schema in VSCode, edit `settings.json`, or the workspace file, to include:
+
+```bash
+"yaml.schemas": {
+    "file:///path/to/cfdmod/output/schema-cfdmod.json": "**/cfdmod/**/\*.yaml"
+}
+```

aerosim_cfdmod-1.1.2/cfdmod/analysis/inflow/__init__.py

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+"""Inflow analysis module"""

aerosim_cfdmod-1.1.2/cfdmod/analysis/inflow/functions.py

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+from typing import Literal
+
+import numpy as np
+import pandas as pd
+import scipy
+from scipy.ndimage import gaussian_filter
+
+from cfdmod.analysis.inflow.profile import InflowData, NormalizationParameters
+
+VelocityComponents = Literal["ux", "uy", "uz"]
+
+
+def spectral_density_function(
+    velocity_signal: np.ndarray,
+    timestamps: np.ndarray,
+    reference_velocity: float,
+    characteristic_length: float,
+) -> tuple[np.ndarray, np.ndarray]:
+    """Perform a FFT over a velocity signal
+
+    Args:
+        velocity_signal (np.ndarray): Array of instantaneous velocity signal
+        timestamps (np.ndarray): Array of timestamps of the signal
+        reference_velocity (float): Value for reference velocity. For normalization
+        characteristic_length (float): Value for Characteristic length. For normalization
+
+    Returns:
+        tuple[np.ndarray, np.ndarray]: Tuple with spectral density values array and normalized frequency values array
+    """
+
+    def filter_avg_data(data: np.ndarray) -> np.ndarray:
+        filtered_data = gaussian_filter(data, sigma=3)  # Sigma smooths the curve
+        return filtered_data
+
+    delta_t = timestamps[1] - timestamps[0]
+    signal_frequency = 1 / delta_t
+
+    (xf, yf) = scipy.signal.periodogram(velocity_signal, signal_frequency, scaling="density")
+    st = np.std(velocity_signal)
+    yf = xf * yf / st**2
+    xf = xf * characteristic_length / reference_velocity  # Stroulhall number N = f * L / U
+
+    # Get the filter coefficients so we can check its frequency response.
+    yf = filter_avg_data(yf)
+    return xf[2:], yf[2:]
+
+
+def calculate_mean_velocity(
+    inflow_data: InflowData, for_components: list[VelocityComponents]
+) -> pd.DataFrame:
+    """Calculates the turbulence intensity for each component given
+    The inflow data dataframe must contain the columns selected by for_components (ux, uy, uz)
+
+    Args:
+        inflow_data (InflowData): Inflow data structure containing points and hist series
+        for_components (list[VelocityComponents]): List of components to calculate mean velocity from
+
+    Returns:
+        pd.DataFrame: Mean Velocity dataframe with columns for each for_components suffixed by *_mean
+    """
+    if not all(
+        [component in inflow_data.data.columns for component in for_components + ["point_idx"]]
+    ):
+        raise ValueError("Components must be inside inflow profile data columns")
+
+    group_by_point_idx = inflow_data.data.groupby("point_idx")
+    velocity_data = group_by_point_idx.agg(
+        {component: "mean" for component in for_components}
+    ).reset_index()
+    # Rename columns
+    velocity_data.columns = [
+        col + "_mean" if col in for_components else col for col in velocity_data.columns
+    ]
+    return velocity_data
+
+
+def calculate_turbulence_intensity(
+    inflow_data: InflowData, for_components: list[VelocityComponents]
+) -> pd.DataFrame:
+    """Calculates the turbulence intensity for each component given
+    The inflow data dataframe must contain the columns selected by for_components (ux, uy, uz)
+
+    Args:
+        inflow_data (InflowData): Inflow data structure containing points and hist series
+        for_components (list[VelocityComponents]): List of components to calculate turbulence intensity from
+
+    Returns:
+        pd.DataFrame: Turbulence intensity dataframe with columns for each for_components preffixed by I_*
+    """
+    if not all(
+        [component in inflow_data.data.columns for component in for_components + ["point_idx"]]
+    ):
+        raise ValueError("Components must be inside inflow profile data columns")
+
+    group_by_point_idx = inflow_data.data.groupby("point_idx")
+    turbulence_data = group_by_point_idx.agg(
+        {component: ["mean", "std"] for component in for_components}
+    ).reset_index()
+    # Rename columns
+    turbulence_data.columns = [
+        "_".join(col) if col[1] != "" else col[0] for col in turbulence_data.columns
+    ]
+    for component in for_components:
+        turbulence_data[f"I_{component}"] = (
+            turbulence_data[f"{component}_std"] / turbulence_data[f"{component}_mean"]
+        )
+
+    return turbulence_data[
+        ["point_idx"] + [f"I_{component}" for component in for_components]
+    ].copy()
+
+
+def calculate_spectral_density(
+    inflow_data: InflowData,
+    target_index: int,
+    for_components: list[VelocityComponents],
+    normalization_params: NormalizationParameters,
+) -> pd.DataFrame:
+    """Calculates the spectral density for a given target point index
+    The inflow data dataframe must contain the columns selected by for_components (ux, uy, uz)
+
+    Args:
+        inflow_data (InflowData): Inflow data structure containing points and hist series
+        target_index (int): Index of the target point
+        for_components (list[VelocityComponents]): List of components to calculate turbulence intensity from
+        normalization_params (NormalizationParameters): Parameters for spectral density normalization
+
+    Returns:
+        pd.DataFrame: Spectral density data with columns S (*) and f (*) for each for_components
+    """
+    spectral_data = pd.DataFrame()
+    for component in for_components:
+        point_data = inflow_data.data.loc[inflow_data.data["point_idx"] == target_index]
+        vel_arr = point_data[component].to_numpy()
+        time_arr = point_data["time_step"].to_numpy()
+
+        spec_dens, norm_freq = spectral_density_function(
+            velocity_signal=vel_arr,
+            timestamps=time_arr,
+            reference_velocity=normalization_params.reference_velocity,
+            characteristic_length=normalization_params.characteristic_length,
+        )
+        spectral_data[f"S ({component})"] = spec_dens
+        spectral_data[f"f ({component})"] = norm_freq
+
+    return spectral_data
+
+
+def calculate_autocorrelation(
+    inflow_data: InflowData, anchor_point_idx: int, for_components: list[VelocityComponents]
+) -> pd.DataFrame:
+    """Calculates the autocorrelation from an anchor point
+
+    Args:
+        inflow_data (InflowData): Inflow data structure containing points and hist series
+        anchor_point_idx (int): Index of the anchor point
+        for_components (list[VelocityComponents]): List of components to calculate turbulence intensity from
+
+    Returns:
+        pd.DataFrame: Autocorrelation data with columns for each for_components preffixed by coef_*
+    """
+    anchor_data = inflow_data.data.loc[inflow_data.data["point_idx"] == anchor_point_idx].copy()
+    anchor_data = anchor_data[for_components + ["point_idx", "time_step"]]
+    for component in for_components:
+        anchor_data[f"{component}_a"] = anchor_data[f"{component}"]
+        anchor_data[f"{component}_a^2"] = anchor_data[f"{component}"] ** 2
+    data_to_merge = anchor_data[
+        ["time_step"]
+        + [f"{component}_a{symbol}" for component in for_components for symbol in ["^2", ""]]
+    ]
+    merged_data = pd.merge(inflow_data.data, data_to_merge, on="time_step", how="left")
+    for component in for_components:
+        merged_data[f"{component}_{component}_a"] = (
+            merged_data[f"{component}"] * merged_data[f"{component}_a"]
+        )
+    avg_data = merged_data.groupby("point_idx").mean()
+    for component in for_components:
+        avg_data[f"coef_{component}"] = (
+            avg_data[f"{component}_{component}_a"]
+            - avg_data[f"{component}"] * avg_data[f"{component}_a"]
+        ) / (avg_data[f"{component}_a^2"] - avg_data[f"{component}_a"] ** 2)
+    autocorrelation = avg_data[[f"coef_{c}" for c in for_components]].reset_index()
+    return autocorrelation

aerosim_cfdmod-1.1.2/cfdmod/analysis/inflow/profile.py

@@ -0,0 +1,51 @@
+from __future__ import annotations
+
+import pathlib
+from dataclasses import dataclass
+
+import pandas as pd
+
+
+@dataclass
+class NormalizationParameters:
+    reference_velocity: float
+    characteristic_length: float
+
+
+class InflowData:
+    def __init__(self, data: pd.DataFrame, points: pd.DataFrame):
+        self.data = data
+        self.points = points
+
+    @classmethod
+    def from_files(cls, hist_series_path: pathlib.Path, points_path: pathlib.Path) -> InflowData:
+        """Reads data from file and builds a InflowData
+        The inflow data dataframe must contain the columns (ux, uy, uz)
+        If any are missing, it won't be able to perform calculations over the components that are missing,
+        but will be able to perform calculations over the components that are present
+
+        Args:
+            hist_series_path (pathlib.Path): Path of the historic series (point_idx, ux, uy, uz velocities)
+            points_path (pathlib.Path): Path of the points information (idx, x, y, z coordinates)
+
+        Returns:
+            InflowData: Inflow data object
+        """
+        hist_series_format = hist_series_path.name.split(".")[-1]
+        if hist_series_format == "csv":
+            data = pd.read_csv(hist_series_path)
+        elif hist_series_format == "h5":
+            data_dfs = []
+            with pd.HDFStore(hist_series_path, mode="r") as data_store:
+                for key in data_store.keys():
+                    df = data_store.get(key)
+                    data_dfs.append(df)
+
+            data = pd.concat(data_dfs)
+            data.sort_values(
+                by=[col for col in ["time_step", "point_idx"] if col in data.columns], inplace=True
+            )
+        else:
+            raise Exception(f"Extension {hist_series_format} not supported for hist series!")
+        points = pd.read_csv(points_path)
+        return InflowData(data=data, points=points)

aerosim_cfdmod-1.1.2/cfdmod/api/configs/hashable.py

@@ -0,0 +1,16 @@
+import hashlib
+
+from pydantic import BaseModel
+
+
+class HashableConfig(BaseModel):
+    def sha256(self) -> str:
+        """Hash config dict and returns a string with the hash hexcode
+
+        Returns:
+            str: Config data object hash
+        """
+        hash_sha256 = hashlib.sha256()
+        hash_sha256.update(self.model_dump_json().encode("utf-8"))
+
+        return hash_sha256.hexdigest()