pyelq 1.1.0__py3-none-any.whl

pyelq/support_functions/spatio_temporal_interpolation.py

@@ -0,0 +1,229 @@
+# SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# -*- coding: utf-8 -*-
+"""Spatio-temporal interpolation module.
+
+Support function to perform interpolation in various ways
+
+"""
+import warnings
+from typing import Tuple, Union
+
+import numpy as np
+import pandas as pd
+from scipy.interpolate import griddata
+
+
+def interpolate(
+    location_in: np.ndarray = None,
+    time_in: Union[np.ndarray, pd.arrays.DatetimeArray] = None,
+    values_in: np.ndarray = None,
+    location_out: np.ndarray = None,
+    time_out: Union[np.ndarray, pd.arrays.DatetimeArray] = None,
+    **kwargs,
+) -> np.ndarray:
+    """Interpolates data based on input.
+
+    Interpolation using scipy.griddata function. Which in turn uses linear barycentric interpolation.
+
+    It is assumed that the shape of location_in, time_in and values_in is consistent
+
+    When time_out has the same size as number of rows of location_out, it is assumed these are aligned and be treated as
+    consistent, hence the output will be a column vector.
+    If this is not the case an interpolation will be performed for all combinations of rows in location out with times
+    of time_out and output wil be shaped as [nof_location_values x dimension]
+
+    If location_out == None, we only perform temporal (1D) interpolation.
+    If time_out == None we only perform spatial  interpolation
+
+    If linear interpolation is not possible for spatio or spatiotemporal interpolation, we use nearest neighbor
+    interpolation, a warning will be displayed
+
+    Args:
+        location_in (np.ndarray): Array of size [nof_values x dimension] with locations to interpolate from
+        time_in (Union[np.ndarray, pd.arrays.DatetimeArray]): Array of size [nof_values x 1] with timestamps or some
+            form of time values (seconds) to interpolate from
+        values_in (np.ndarray): Array of size [nof_values x 1] with values to interpolate from
+        location_out (np.ndarray): Array of size [nof_location_values x dimension] with locations to interpolate to
+        time_out (Union[np.ndarray, pd.arrays.DatetimeArray]): Array of size [nof_time_values x 1] with
+            timestamps or some form of time values (seconds) to interpolate to
+        **kwargs (dict): Other keyword arguments which get passed into the griddata interpolation function
+
+    Returns:
+        result (np.ndarray): Array of size [nof_location_values x nof_time_values] with interpolated values
+
+    """
+    _sense_check_interpolate_inputs(
+        location_in=location_in, time_in=time_in, values_in=values_in, location_out=location_out, time_out=time_out
+    )
+
+    if (
+        time_out is not None
+        and isinstance(time_out, pd.arrays.DatetimeArray)
+        and isinstance(time_in, pd.arrays.DatetimeArray)
+    ):
+        min_time_out = np.amin(time_out)
+        time_out = (time_out - min_time_out).total_seconds()
+        time_in = (time_in - min_time_out).total_seconds()
+
+    if location_out is None:
+        return _griddata(points_in=time_in, values=values_in, points_out=time_out, **kwargs)
+
+    if time_out is None:
+        return _griddata(points_in=location_in, values=values_in, points_out=location_out, **kwargs)
+
+    if location_in.shape[0] != time_in.size:
+        raise ValueError("Location and time are do not have consistent sizes")
+
+    if location_out.shape[0] != time_out.size:
+        location_temp = np.tile(location_out, (time_out.size, 1))
+        time_temp = np.repeat(time_out.squeeze(), location_out.shape[0])
+        out_array = np.column_stack((location_temp, time_temp))
+    else:
+        out_array = np.column_stack((location_out, time_out))
+
+    in_array = np.column_stack((location_in, time_in))
+
+    result = _griddata(points_in=in_array, values=values_in, points_out=out_array, **kwargs)
+
+    if location_out.shape[0] != time_out.size:
+        result = result.reshape((location_out.shape[0], time_out.size), order="C")
+
+    return result
+
+
+def _sense_check_interpolate_inputs(
+    location_in: np.ndarray,
+    time_in: Union[np.ndarray, pd.arrays.DatetimeArray],
+    values_in: np.ndarray,
+    location_out: np.ndarray,
+    time_out: Union[np.ndarray, pd.arrays.DatetimeArray],
+):
+    """Helper function to sense check inputs and raise errors when applicable.
+
+    Args:
+        location_in (np.ndarray): Array of size [nof_values x dimension] with locations to interpolate from
+        time_in (Union[np.ndarray, pd.arrays.DatetimeArray]): Array of size [nof_values x 1] with timestamps or some
+            form of time values (seconds) to interpolate from
+        values_in (np.ndarray): Array of size [nof_values x 1] with values to interpolate from
+        location_out (np.ndarray): Array of size [nof_location_values x dimension] with locations to interpolate to
+        time_out (Union[np.ndarray, pd.arrays.DatetimeArray]): Array of size [nof_time_values x 1] with
+        timestamps or some form of time values (seconds) to interpolate to
+
+    Raises:
+        ValueError: When inputs do not match up.
+
+    """
+    if location_out is not None and location_in is None:
+        raise ValueError("Cannot specify output location without input location")
+    if time_out is not None and time_in is None:
+        raise ValueError("Cannot specify output time without input time")
+    if values_in is None:
+        raise ValueError("Must provide values_in")
+    if location_out is None and time_out is None:
+        raise ValueError("location_out or time_out not specified. Need to specify somewhere to interpolate to")
+
+
+def _griddata(points_in: np.ndarray, values: np.ndarray, points_out: np.ndarray, **kwargs):
+    """Wrapped function to handle special cases around the gridded interpolate.
+
+    Will try nearest neighbour method when few enough points that spatial cases fail.
+
+    Syntax like scipy.griddata
+
+    Args:
+        points_in (np.ndarray): 2-D ndarray of floats with shape (n, D), or length D tuple of 1-D
+        nd-arrays with shape (n,). Data point coordinates.
+        values (np.ndarray): _ndarray of float or complex, shape (n,). Data values
+        points_out (np.ndarray): 2-D ndarray of floats with shape (m, D), or length D tuple of nd-arrays
+          broadcastable to the same shape. Points at which to interpolate data.
+
+    Returns:
+        ndarray: Array of interpolated values.
+
+    """
+    if values.size == 1:
+        return np.ones((points_out.shape[0], 1)) * values
+
+    try:
+        return griddata(points=points_in, values=values.flatten(), xi=points_out, **kwargs)
+    except RuntimeError:
+        warnings.warn(
+            "Warning linear interpolation did not succeed, most likely too few input points (<5),"
+            "trying again with method==nearest"
+        )
+        if "method" in kwargs:
+            del kwargs["method"]
+        return griddata(points=points_in, values=values, xi=points_out, method="nearest", **kwargs)
+
+
+def temporal_resampling(
+    time_in: Union[np.ndarray, pd.arrays.DatetimeArray],
+    values_in: np.ndarray,
+    time_bin_edges: Union[np.ndarray, pd.arrays.DatetimeArray],
+    aggregate_function: str = "mean",
+    side: str = "center",
+) -> Tuple[Union[np.ndarray, pd.arrays.DatetimeArray], np.ndarray]:
+    """Resamples data into a set of time bins.
+
+    Checks which values of time_in are withing 2 consecutive values of time_bin_edges and performs the aggregate
+    function on the corresponding values from values_in. time_in values outside the time_bin_edges are ignored.
+    Empty bins will be assigned a 'NaN' value.
+
+    When 'time_in' is a sequence of time stamps, a DatetimeArray should be used. Otherwise, a np.ndarray should be used.
+
+    Args:
+        time_in (Union[np.ndarray, pd.arrays.DatetimeArray]): A vector of times which correspond to values_in.
+        values_in (np.ndarray): A vector of the values to be resampled.
+        time_bin_edges (Union[np.ndarray, pd.arrays.DatetimeArray]): A vector of times which define the edges of the
+                                                                     bins into which the data will be resampled.
+        aggregate_function (str, optional): The function which is used to aggregate the data after it has been
+                                            sorted into bins. Defaults to mean.
+        side (str, optional): Which side of the time bins should be used to generate times_out. Possible values are:
+                              'left', 'center', and 'right'. Defaults to 'center'.
+
+    Returns:
+        time_out (Union[np.ndarray, pd.arrays.DatetimeArray]): Vector-like object containing the times of the resampled
+                                                               values consistent with time_in dtype and side input
+                                                               argument.
+        values_out (np.ndarray): A vector of resampled values, according to the time bins and the aggregate function.
+
+    Raises:
+        ValueError: If any of the input arguments are not of the correct type or shape, this error is raised.
+
+    """
+    if not isinstance(time_bin_edges, type(time_in)) or values_in.size != time_in.size:
+        raise ValueError("Arguments 'time_in', 'time_bin_edges' and/or 'values_in' are not of consistent type or size.")
+
+    if not isinstance(aggregate_function, str):
+        raise ValueError("The supplied 'aggregate_function' is not a string.")
+
+    if side == "center":
+        time_out = np.diff(time_bin_edges) / 2 + time_bin_edges[:-1]
+    elif side == "left":
+        time_out = time_bin_edges[:-1]
+    elif side == "right":
+        time_out = time_bin_edges[1:]
+    else:
+        raise ValueError(f"The 'side' argument must be 'left', 'center', or 'right', but received '{side}'.")
+
+    zero_value = 0
+    if isinstance(time_bin_edges, pd.arrays.DatetimeArray):
+        zero_value = np.array(0).astype("<m8[ns]")
+
+    if not np.all(np.diff(time_bin_edges) > zero_value):
+        raise ValueError("Argument 'time_bin_edges' does not monotonically increase.")
+
+    if np.any(time_in < time_bin_edges[0]) or np.any(time_in > time_bin_edges[-1]):
+        warnings.warn("Values in time_in are outside of range of time_bin_edges. These values will be ignored.")
+
+    index = np.searchsorted(time_bin_edges, time_in, side="left")
+    grouped_vals = pd.Series(values_in).groupby(index).agg(aggregate_function)
+    grouped_vals = grouped_vals.drop(index=[0, time_bin_edges.size], errors="ignore").sort_index()
+
+    values_out = np.full(time_out.shape, np.nan)
+    values_out[grouped_vals.index - 1] = grouped_vals.to_numpy()
+
+    return time_out, values_out

pyelq-1.1.0.dist-info/LICENSE.md

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pyelq-1.1.0.dist-info/LICENSES/Apache-2.0.txt

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pyelq-1.1.0.dist-info/METADATA

@@ -0,0 +1,127 @@
+Metadata-Version: 2.3
+Name: pyelq
+Version: 1.1.0
+Summary: Package for detection, localization and quantification code.
+License: Apache-2.0
+Keywords: gas dispersion,emission,detection,localization,quantification
+Author: Bas van de Kerkhof
+Requires-Python: >=3.9,<3.12
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Dist: geojson (>=3.2.0)
+Requires-Dist: numpy (>=2.0.2)
+Requires-Dist: openmcmc (==1.0.5)
+Requires-Dist: pandas (>=2.2.3)
+Requires-Dist: plotly (>=6.0.0)
+Requires-Dist: pymap3d (>=3.1.0)
+Requires-Dist: scikit-learn (>=1.6.1)
+Requires-Dist: scipy (>=1.13.1)
+Requires-Dist: shapely (>=2.0.7)
+Project-URL: Documentation, https://sede-open.github.io/pyELQ/
+Project-URL: Homepage, https://sede-open.github.io/pyELQ/
+Project-URL: Repository, https://github.com/sede-open/pyELQ
+Description-Content-Type: text/markdown
+
+<!--
+SPDX-FileCopyrightText: 2024 Shell Global Solutions International B.V. All Rights Reserved.
+
+SPDX-License-Identifier: Apache-2.0
+-->
+
+<div align="center">
+
+[![PyPI version](https://img.shields.io/pypi/v/pyelq.svg?logo=pypi&logoColor=FFE873)](https://pypi.org/project/pyelq/)
+[![Supported Python versions](https://img.shields.io/pypi/pyversions/pyelq.svg?logo=python&logoColor=FFE873)](https://pypi.org/project/pyelq/)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Code Style Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=pyelq_pyelq&metric=coverage)](https://sonarcloud.io/summary/new_code?id=pyelq_pyelq)
+[![Vulnerabilities](https://sonarcloud.io/api/project_badges/measure?project=pyelq_pyelq&metric=vulnerabilities)](https://sonarcloud.io/summary/new_code?id=pyelq_pyelq)
+[![Bugs](https://sonarcloud.io/api/project_badges/measure?project=pyelq_pyelq&metric=bugs)](https://sonarcloud.io/summary/new_code?id=pyelq_pyelq)
+[![Lines of Code](https://sonarcloud.io/api/project_badges/measure?project=pyelq_pyelq&metric=ncloc)](https://sonarcloud.io/summary/new_code?id=pyelq_pyelq)
+[![Duplicated Lines (%)](https://sonarcloud.io/api/project_badges/measure?project=pyelq_pyelq&metric=duplicated_lines_density)](https://sonarcloud.io/summary/new_code?id=pyelq_pyelq)
+[![Code Smells](https://sonarcloud.io/api/project_badges/measure?project=pyelq_pyelq&metric=code_smells)](https://sonarcloud.io/summary/new_code?id=pyelq_pyelq)
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+</div>
+
+# pyELQ
+This repository contains the Python Emission Localization and Quantification software we call pyELQ. It is code used 
+for gas dispersion modelling, in particular methane emissions detection, localization and quantification. 
+
+***
+# Background
+The **py**thon **E**mission **L**ocalization and **Q**uantification (pyELQ) code aims to maximize effective use of 
+existing measurement data, especially from continuous monitoring solutions. The code has been developed to detect, 
+localize, and quantify methane emissions from concentration and wind measurements. It can be used in combination with 
+point or beam sensors that are placed strategically on an area of interest.
+
+The algorithms in the pyELQ code are based a Bayesian statistics framework. pyELQ can ingest long-term concentration 
+and wind data, and it performs an inversion to predict the likely strengths and locations of persistent methane sources. 
+The goal is to arrive at a plausible estimate of methane emissions from an area of interest that matches the measured 
+data. The predictions from pyELQ come with uncertainty ranges that are representative of probability density functions 
+sampled by a Markov Chain Monte Carlo method. Time series of varying length can be processed by pyELQ: in general, 
+the Bayesian inversion leads to a more constrained solution if more high-precision measurement data is available. 
+We have tested our code under controlled conditions as well as in operating oil and gas facilities.
+
+The information on the strength and the approximate location of methane emission sources provided by pyELQ can help 
+operators with more efficient identification and quantification of (unexpected) methane sources, in order to start 
+appropriate mitigating actions accordingly. The pyELQ code is being made available in an open-source environment, 
+to support various assets in their quest to reduce methane emissions.
+
+Use cases where the pyELQ code has been applied are described in the following papers:
+
+* IJzermans, R., Jones, M., Weidmann, D. et al. "Long-term continuous monitoring of methane emissions at an oil and gas facility using a multi-open-path laser dispersion spectrometer." Sci Rep 14, 623 (2024). (https://doi.org/10.1038/s41598-023-50081-9)
+
+* Weidmann, D., Hirst, B. et al. "Locating and Quantifying Methane Emissions by Inverse Analysis of Path-Integrated Concentration Data Using a Markov-Chain Monte Carlo Approach." ACS Earth and Space Chemistry 2022 6 (9), 2190-2198  (https://doi.org/10.1021/acsearthspacechem.2c00093)
+
+## Deployment design
+The pyELQ code needs high-quality methane concentration and wind data to be able to provide reliable output on location 
+and quantification of methane emission sources. This requires methane concentration sensors of sufficiently high 
+precision in a layout that allows the detection of relevant methane emission sources, in combination with wind 
+measurements of high enough frequency and accuracy. The optimal sensor layout typically depends on the prevailing 
+meteorological conditions at the site of interest and requires multiple concentration sensors to cover the site under 
+different wind directions. 
+
+## pyELQ data interpretation
+The results from pyELQ come with uncertainty ranges that are representative of probability density functions sampled 
+by a Markov Chain Monte Carlo method. One should take these uncertainty ranges into account when interpreting the pyELQ 
+output data. Remember that absence of evidence for methane emissions does not always imply evidence for absence of 
+methane emissions; for instance, when meteorological conditions are such that there is no sensor downwind of a methane 
+source during the selected monitoring period, then it will be impossible to detect, localize and quantify 
+this particular source. 
+Also, there are limitations to the forward dispersion model which is used in the analysis. 
+For example, the performance of the Gaussian plume dispersion model will degrade at lower wind speeds. 
+Therefore, careful interpretation of the data is always required. 
+
+***
+# Installing pyELQ as a package
+Suppose you want to use this pyELQ package in a different project.
+You can install it from [PyPi](https://pypi.org/project/pyelq/) through pip 
+`pip install pyelq`.
+Or you could clone the repository and install it from the source code. 
+After activating the environment you want to install pyELQ in, open a terminal, move to the main pyELQ folder
+where pyproject.toml is located and run `pip install .`, optionally you can pass the `-e` flag is for editable mode.
+All the main options, info and settings for the package are found in the pyproject.toml file which sits in this repo
+as well.
+
+***
+
+# Examples
+For some examples on how to use this package please check out these [Examples](https://github.com/sede-open/pyELQ/blob/main/examples)
+
+***
+
+# Contribution
+This project welcomes contributions and suggestions. If you have a suggestion that would make this better you can simply open an issue with a relevant title. Don't forget to give the project a star! Thanks again!
+
+For more details on contributing to this repository, see the [Contributing guide](https://github.com/sede-open/pyELQ/blob/main/CONTRIBUTING.md).
+
+***
+# Licensing
+
+Distributed under the Apache License Version 2.0. See the [license file](https://github.com/sede-open/pyELQ/blob/main/LICENSE.md) for more information.
+