integrate-module 0.2.15__tar.gz

integrate_module-0.2.15/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023-2025 Thomas Mejer Hansen and INTEGRATE Working Group
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

integrate_module-0.2.15/PKG-INFO

@@ -0,0 +1,157 @@
+Metadata-Version: 2.4
+Name: integrate_module
+Version: 0.2.15
+Summary: Localized probabilistic data integration
+Author-email: Thomas Mejer Hansen <tmeha@geo.au.dk>
+License: MIT
+Keywords: inversion,electromagnetic,geophysics,geology,prior,tarantola
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: h5py
+Requires-Dist: scipy
+Requires-Dist: psutil
+Requires-Dist: tqdm
+Requires-Dist: requests
+Requires-Dist: ga-aem-forward-win; platform_system == "Windows"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Provides-Extra: all
+Requires-Dist: jupyter>=1.0.0; extra == "all"
+Requires-Dist: jupytext; extra == "all"
+Requires-Dist: pandas; extra == "all"
+Requires-Dist: pyvista; extra == "all"
+Dynamic: license-file
+
+# INTEGRATE Python Module
+
+[![PyPI version](https://badge.fury.io/py/integrate_module.svg)](https://badge.fury.io/py/integrate_module)
+[![Test PyPI](https://img.shields.io/badge/Test%20PyPI-integrate__module-orange.svg)](https://test.pypi.org/project/integrate-module/)
+[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://cultpenguin.github.io/integrate_module/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+This repository holds the INTEGRATE Python module
+
+
+## Installation 
+
+Assuming you allready have python 3.10 installed
+
+    pip install -i https://test.pypi.org/simple/ integrate_module
+
+On Windows this will also install the python wrapper for the ga-aem (1D EM forward modeling - GPL v2 code) --> [ga-aem-forward-win](https://pypi.org/project/ga-aem-forward-win/)
+
+
+### PIP (from pypi)
+
+    # Install python3 venv
+    sudo apt install python3-venv
+    
+    # Create virtual environment
+    python3 -m venv ~/integrate
+    source ~/integrate/bin/activate
+    pip install --upgrade pip
+    
+    # Install integrate module
+    pip install -i https://test.pypi.org/simple/ integrate_module
+    
+### PIP (from source)
+
+    # Install python3 venv
+    sudo apt install python3-venv
+    
+    # Create virtual environment
+    python3 -m venv ~/integrate
+    source ~/integrate/bin/activate
+    pip install --upgrade pip
+    
+    # Install integrate module
+    cd path/to/integrate module
+    pip install -e .
+
+### Conda + PIP (from pypi)
+
+Create a Conda environment (called integrate) and install the required modules, using 
+
+    conda create --name integrate python=3.10 numpy pandas matplotlib scipy tqdm requests h5py psutil
+    conda activate integrate
+    pip install -i https://test.pypi.org/simple/ integrate_module
+    
+    
+    
+### Conda + PIP (from source)
+
+Create a Conda environment (called integrate) and install the required modules, using 
+
+    conda create --name integrate python=3.10 numpy pandas matplotlib scipy tqdm requests h5py psutil
+    conda activate integrate
+    pip install -e .
+
+
+## GA-AEM
+
+In order to use GA-AEM for forward EM modeling, the 'gatdaem1d' Python module must be installed. Follow instructions at [https://github.com/GeoscienceAustralia/ga-aem](https://github.com/GeoscienceAustralia/ga-aem) or use the information below.
+
+
+### pypi paackage for windows
+
+In Windows the [ga-aem-forward-win](https://pypi.org/project/ga-aem-forward-win/) package will be autoamtically installed that provides access to the GA-AEM forward code. It can be installed manually using
+
+    pip install ga-aem-forward-win
+
+### Pre-Compiled Python module in Windows
+
+Download pre-compiled version of GA-AEM for windows through the latest  release from https://github.com/GeoscienceAustralia/ga-aem/releases as GA-AEM.zip
+
+Download precompiled FFTW3 windows dlls from https://www.fftw.org/install/windows.html as fftw-3.3.5-dll64.zip 
+
+unzip GA-AEM.zip to get GA-AEM
+
+unzip fftw-3.3.5-dll64.zip to get fftw-3.3.5-dll64
+
+Copy fftw-3.3.5-dll64/*.dll to GA-AEM/python/gatdaem1d/
+
+    cp fftw-3.3.5-dll64/*.dll GA-AEM/python/gatdaem1d/
+
+Install the python gatdaem1d module
+
+    cd GA-AEM/python/
+    pip install -e .
+
+    # test the installaion
+    cd examples
+    python skytem_example.py
+
+
+
+### Compile ga-aem Python module in Ubuntu/Linux
+
+
+A script that downloads and install GA-AEM is located in 'scripts/cmake_build_script_ubuntu_gatdaem1d.sh'. Be sure to use the appropriate Python environment and then run
+
+    sh scripts/cmake_build_script_ubuntu_gatdaem1d.sh
+    cd ga-aem/install-ubuntu/python
+    pip install .
+    
+### Compile ga-aem Python module in OSX/Homebrew
+
+First install homebrew, then run 
+
+    sh ./scripts/cmake_build_script_homebrew_gatdaem1d.sh
+    cd ga-aem/install-homebrew/python
+    pip install .
+
+
+## Development
+
+The main branch should be the most stable, and updates, less frequent, but with larger changes.
+
+The develop branch contains the current development code and may be updated frequently, and some functions and examples may be broken.
+
+
+

integrate_module-0.2.15/README.md

@@ -0,0 +1,128 @@
+# INTEGRATE Python Module
+
+[![PyPI version](https://badge.fury.io/py/integrate_module.svg)](https://badge.fury.io/py/integrate_module)
+[![Test PyPI](https://img.shields.io/badge/Test%20PyPI-integrate__module-orange.svg)](https://test.pypi.org/project/integrate-module/)
+[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://cultpenguin.github.io/integrate_module/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+This repository holds the INTEGRATE Python module
+
+
+## Installation 
+
+Assuming you allready have python 3.10 installed
+
+    pip install -i https://test.pypi.org/simple/ integrate_module
+
+On Windows this will also install the python wrapper for the ga-aem (1D EM forward modeling - GPL v2 code) --> [ga-aem-forward-win](https://pypi.org/project/ga-aem-forward-win/)
+
+
+### PIP (from pypi)
+
+    # Install python3 venv
+    sudo apt install python3-venv
+    
+    # Create virtual environment
+    python3 -m venv ~/integrate
+    source ~/integrate/bin/activate
+    pip install --upgrade pip
+    
+    # Install integrate module
+    pip install -i https://test.pypi.org/simple/ integrate_module
+    
+### PIP (from source)
+
+    # Install python3 venv
+    sudo apt install python3-venv
+    
+    # Create virtual environment
+    python3 -m venv ~/integrate
+    source ~/integrate/bin/activate
+    pip install --upgrade pip
+    
+    # Install integrate module
+    cd path/to/integrate module
+    pip install -e .
+
+### Conda + PIP (from pypi)
+
+Create a Conda environment (called integrate) and install the required modules, using 
+
+    conda create --name integrate python=3.10 numpy pandas matplotlib scipy tqdm requests h5py psutil
+    conda activate integrate
+    pip install -i https://test.pypi.org/simple/ integrate_module
+    
+    
+    
+### Conda + PIP (from source)
+
+Create a Conda environment (called integrate) and install the required modules, using 
+
+    conda create --name integrate python=3.10 numpy pandas matplotlib scipy tqdm requests h5py psutil
+    conda activate integrate
+    pip install -e .
+
+
+## GA-AEM
+
+In order to use GA-AEM for forward EM modeling, the 'gatdaem1d' Python module must be installed. Follow instructions at [https://github.com/GeoscienceAustralia/ga-aem](https://github.com/GeoscienceAustralia/ga-aem) or use the information below.
+
+
+### pypi paackage for windows
+
+In Windows the [ga-aem-forward-win](https://pypi.org/project/ga-aem-forward-win/) package will be autoamtically installed that provides access to the GA-AEM forward code. It can be installed manually using
+
+    pip install ga-aem-forward-win
+
+### Pre-Compiled Python module in Windows
+
+Download pre-compiled version of GA-AEM for windows through the latest  release from https://github.com/GeoscienceAustralia/ga-aem/releases as GA-AEM.zip
+
+Download precompiled FFTW3 windows dlls from https://www.fftw.org/install/windows.html as fftw-3.3.5-dll64.zip 
+
+unzip GA-AEM.zip to get GA-AEM
+
+unzip fftw-3.3.5-dll64.zip to get fftw-3.3.5-dll64
+
+Copy fftw-3.3.5-dll64/*.dll to GA-AEM/python/gatdaem1d/
+
+    cp fftw-3.3.5-dll64/*.dll GA-AEM/python/gatdaem1d/
+
+Install the python gatdaem1d module
+
+    cd GA-AEM/python/
+    pip install -e .
+
+    # test the installaion
+    cd examples
+    python skytem_example.py
+
+
+
+### Compile ga-aem Python module in Ubuntu/Linux
+
+
+A script that downloads and install GA-AEM is located in 'scripts/cmake_build_script_ubuntu_gatdaem1d.sh'. Be sure to use the appropriate Python environment and then run
+
+    sh scripts/cmake_build_script_ubuntu_gatdaem1d.sh
+    cd ga-aem/install-ubuntu/python
+    pip install .
+    
+### Compile ga-aem Python module in OSX/Homebrew
+
+First install homebrew, then run 
+
+    sh ./scripts/cmake_build_script_homebrew_gatdaem1d.sh
+    cd ga-aem/install-homebrew/python
+    pip install .
+
+
+## Development
+
+The main branch should be the most stable, and updates, less frequent, but with larger changes.
+
+The develop branch contains the current development code and may be updated frequently, and some functions and examples may be broken.
+
+
+

integrate_module-0.2.15/integrate/__init__.py

@@ -0,0 +1,79 @@
+# Import rejection sampling functions from new module
+from integrate.integrate_rejection import integrate_rejection
+from integrate.integrate_rejection import integrate_rejection_range
+from integrate.integrate_rejection import integrate_posterior_chunk
+from integrate.integrate_rejection import integrate_posterior_main
+from integrate.integrate_rejection import likelihood_gaussian_diagonal
+from integrate.integrate_rejection import likelihood_gaussian_full
+from integrate.integrate_rejection import likelihood_multinomial
+from integrate.integrate_rejection import select_subset_for_inversion
+from integrate.integrate_rejection import cleanup_shared_memory
+from integrate.integrate_rejection import reconstruct_shared_arrays
+from integrate.integrate_rejection import create_shared_memory
+
+# Import other functions from main module
+from integrate.integrate import integrate_update_prior_attributes   
+from integrate.integrate import integrate_posterior_stats
+from integrate.integrate import logl_T_est
+from integrate.integrate import lu_post_sample_logl
+from integrate.integrate import prior_data
+from integrate.integrate import prior_data_gaaem
+from integrate.integrate import prior_data_identity
+from integrate.integrate import forward_gaaem
+from integrate.integrate import synthetic_case
+from integrate.integrate import prior_model_layered
+from integrate.integrate import prior_model_workbench
+from integrate.integrate import prior_model_workbench_direct
+from integrate.integrate import posterior_cumulative_thickness
+#from integrate.integrate import integrate_rejection_multi  
+from integrate.integrate import use_parallel
+from integrate.integrate import get_weight_from_position
+from integrate.integrate import entropy
+from integrate.integrate import class_id_to_idx
+from integrate.integrate import is_notebook
+from integrate.integrate import get_hypothesis_probability
+from integrate.integrate import sample_posterior_multiple_hypotheses
+
+from integrate.integrate_io import load_prior
+from integrate.integrate_io import load_prior_data
+from integrate.integrate_io import save_prior_data
+from integrate.integrate_io import load_prior_model
+from integrate.integrate_io import save_prior_model
+from integrate.integrate_io import load_data
+from integrate.integrate_io import get_geometry 
+from integrate.integrate_io import read_gex
+from integrate.integrate_io import gex_to_stm
+from integrate.integrate_io import get_gex_file_from_data
+from integrate.integrate_io import write_stm_files
+from integrate.integrate_io import post_to_csv
+from integrate.integrate_io import copy_hdf5_file
+from integrate.integrate_io import hdf5_scan
+from integrate.integrate_io import get_case_data
+from integrate.integrate_io import write_data_gaussian
+from integrate.integrate_io import write_data_multinomial
+from integrate.integrate_io import check_data
+from integrate.integrate_io import merge_data
+from integrate.integrate_io import merge_posterior
+from integrate.integrate_io import read_usf
+from integrate.integrate_io import read_usf_mul
+from integrate.integrate_io import test_read_usf
+
+from integrate.integrate_plot import plot_geometry
+from integrate.integrate_plot import plot_profile
+from integrate.integrate_plot import plot_profile_continuous
+from integrate.integrate_plot import plot_profile_discrete
+from integrate.integrate_plot import plot_cumulative_probability_profile
+from integrate.integrate_plot import plot_T_EV
+from integrate.integrate_plot import plot_data_xy
+from integrate.integrate_plot import plot_data
+from integrate.integrate_plot import plot_data_prior_post
+from integrate.integrate_plot import plot_data_prior
+from integrate.integrate_plot import plot_prior_stats
+from integrate.integrate_plot import plot_feature_2d
+from integrate.integrate_plot import plot_posterior_cumulative_thickness
+from integrate.integrate_plot import get_clim_cmap
+
+# REMOVE CLI IMPORTS - These cause circular dependencies
+# from . import integrate_cli
+# from . import integrate_timing
+