mbirjax 0.2.0__tar.gz

mbirjax-0.2.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Charles A. Bouman and Gregery T. Buzzard
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

mbirjax-0.2.0/MBIRJAX.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: mbirjax
+Version: 0.2.0
+Summary: High-performance tomographic reconstruction
+Author-email: MBIRJAX development team <buzzard@purdue.edu>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, Charles A. Bouman and Gregery T. Buzzard
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: homepage, https://mbirjax.readthedocs.io
+Project-URL: source, https://github.com/cabouman/mbirjax
+Keywords: tomography,tomographic reconstruction,computed tomography
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: setuptools
+Requires-Dist: jax
+Requires-Dist: jaxlib
+Requires-Dist: ruamel.yaml
+Requires-Dist: psutil
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
+Requires-Dist: sphinx-book-theme>=1.0.1; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+
+.. docs-include-ref
+
+MBIRJAX
+=======
+
+Model-Based Iterative Reconstruction (MBIR) for tomographic reconstruction that is based on the `JAX <https://github.com/google/jax>`__ library.
+Full documentation is available at https://mbirjax.readthedocs.io .
+
+Installing from PyPI
+--------------------
+
+    .. code-block::
+
+        pip install mbirjax
+
+Installing from Source
+----------------------
+
+1. *Clone the repository:*
+
+    .. code-block::
+
+        git clone git@github.com:cabouman/mbirjax.git
+
+2. Install the conda environment and package
+
+    a. Option 1: Clean install using dev_scripts - We provide bash scripts that will do a clean install of MBIRJAX in a new conda environment using the commands:
+
+        .. code-block::
+
+            cd dev_scripts
+            source clean_install_all.sh
+
+    b. Option 2: Manual install - You can also manually install MBIRJAX from the main directory of the repository with the following commands:
+
+        .. code-block::
+
+            conda create --name mbirjax python=3.10
+            conda activate mbirjax
+            pip install -r requirements.txt
+            pip install .
+
+Running Demo(s)
+---------------
+
+Run any of the available demo scripts with something like the following:
+
+    .. code-block::
+
+        python demo/<demo_file>.py
+

mbirjax-0.2.0/MBIRJAX.egg-info/SOURCES.txt

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+LICENSE
+README.rst
+pyproject.toml
+MBIRJAX.egg-info/PKG-INFO
+MBIRJAX.egg-info/SOURCES.txt
+MBIRJAX.egg-info/dependency_links.txt
+MBIRJAX.egg-info/requires.txt
+MBIRJAX.egg-info/top_level.txt
+demo/demo_cone_beam_shepp_logan.py
+demo/demo_parbeam_shepp_logan.py
+demo/demo_slice_viewer.py
+docs/build/html/_static/new_model_template.py
+docs/source/conf.py
+docs/source/_static/new_model_template.py
+experiments/cone_beam_dev.py
+experiments/parallel_model_dev.py
+experiments/prox_test.py
+experiments/recon_experiments.py
+experiments/cvpr-2024/vcd_figs_for_abst.py
+experiments/gpu_performance/cumulative_memory.py
+experiments/gpu_performance/display_results.py
+experiments/gpu_performance/evaluate_over_indices.py
+experiments/gpu_performance/initialize_evaluation.py
+mbirjax/__init__.py
+mbirjax/_utils.py
+mbirjax/cone_beam.py
+mbirjax/memory_stats.py
+mbirjax/parallel_beam.py
+mbirjax/parameter_handler.py
+mbirjax/plot_utils.py
+mbirjax/projectors.py
+mbirjax/tomography_model.py
+mbirjax/vcd_utils.py
+mbirjax.egg-info/PKG-INFO
+mbirjax.egg-info/SOURCES.txt
+mbirjax.egg-info/dependency_links.txt
+mbirjax.egg-info/requires.txt
+mbirjax.egg-info/top_level.txt
+tests/test_projectors.py

mbirjax-0.2.0/MBIRJAX.egg-info/dependency_links.txt

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+

mbirjax-0.2.0/MBIRJAX.egg-info/requires.txt

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+matplotlib
+numpy
+setuptools
+jax
+jaxlib
+ruamel.yaml
+psutil
+
+[docs]
+sphinx
+sphinxcontrib-bibtex
+sphinx-book-theme>=1.0.1
+sphinx-design
+sphinx-copybutton
+
+[test]
+pytest

mbirjax-0.2.0/MBIRJAX.egg-info/top_level.txt

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+demo
+dev_scripts
+dist
+docs
+experiments
+mbirjax
+tests

mbirjax-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: mbirjax
+Version: 0.2.0
+Summary: High-performance tomographic reconstruction
+Author-email: MBIRJAX development team <buzzard@purdue.edu>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, Charles A. Bouman and Gregery T. Buzzard
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: homepage, https://mbirjax.readthedocs.io
+Project-URL: source, https://github.com/cabouman/mbirjax
+Keywords: tomography,tomographic reconstruction,computed tomography
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: setuptools
+Requires-Dist: jax
+Requires-Dist: jaxlib
+Requires-Dist: ruamel.yaml
+Requires-Dist: psutil
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
+Requires-Dist: sphinx-book-theme>=1.0.1; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+
+.. docs-include-ref
+
+MBIRJAX
+=======
+
+Model-Based Iterative Reconstruction (MBIR) for tomographic reconstruction that is based on the `JAX <https://github.com/google/jax>`__ library.
+Full documentation is available at https://mbirjax.readthedocs.io .
+
+Installing from PyPI
+--------------------
+
+    .. code-block::
+
+        pip install mbirjax
+
+Installing from Source
+----------------------
+
+1. *Clone the repository:*
+
+    .. code-block::
+
+        git clone git@github.com:cabouman/mbirjax.git
+
+2. Install the conda environment and package
+
+    a. Option 1: Clean install using dev_scripts - We provide bash scripts that will do a clean install of MBIRJAX in a new conda environment using the commands:
+
+        .. code-block::
+
+            cd dev_scripts
+            source clean_install_all.sh
+
+    b. Option 2: Manual install - You can also manually install MBIRJAX from the main directory of the repository with the following commands:
+
+        .. code-block::
+
+            conda create --name mbirjax python=3.10
+            conda activate mbirjax
+            pip install -r requirements.txt
+            pip install .
+
+Running Demo(s)
+---------------
+
+Run any of the available demo scripts with something like the following:
+
+    .. code-block::
+
+        python demo/<demo_file>.py
+

mbirjax-0.2.0/README.rst

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+.. docs-include-ref
+
+MBIRJAX
+=======
+
+Model-Based Iterative Reconstruction (MBIR) for tomographic reconstruction that is based on the `JAX <https://github.com/google/jax>`__ library.
+Full documentation is available at https://mbirjax.readthedocs.io .
+
+Installing from PyPI
+--------------------
+
+    .. code-block::
+
+        pip install mbirjax
+
+Installing from Source
+----------------------
+
+1. *Clone the repository:*
+
+    .. code-block::
+
+        git clone git@github.com:cabouman/mbirjax.git
+
+2. Install the conda environment and package
+
+    a. Option 1: Clean install using dev_scripts - We provide bash scripts that will do a clean install of MBIRJAX in a new conda environment using the commands:
+
+        .. code-block::
+
+            cd dev_scripts
+            source clean_install_all.sh
+
+    b. Option 2: Manual install - You can also manually install MBIRJAX from the main directory of the repository with the following commands:
+
+        .. code-block::
+
+            conda create --name mbirjax python=3.10
+            conda activate mbirjax
+            pip install -r requirements.txt
+            pip install .
+
+Running Demo(s)
+---------------
+
+Run any of the available demo scripts with something like the following:
+
+    .. code-block::
+
+        python demo/<demo_file>.py
+

mbirjax-0.2.0/demo/demo_cone_beam_shepp_logan.py

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+import numpy as np
+import time
+import jax.numpy as jnp
+import matplotlib.pyplot as plt
+import mbirjax.plot_utils as pu
+import mbirjax.parallel_beam
+
+if __name__ == "__main__":
+    """
+    This is a script to develop, debug, and tune the vcd reconstruction with a parallel beam projector
+    """
+    # Set parameters
+    num_views = 256
+    num_det_rows = 20
+    num_det_channels = 256
+    source_detector_dist = 4 * num_det_channels
+    source_iso_dist = source_detector_dist
+
+    start_angle = -np.pi*(1/2)
+    end_angle = np.pi*(1/2)
+    sharpness = 0.0
+
+    # Initialize sinogram
+    sinogram = jnp.zeros((num_views, num_det_rows, num_det_channels))
+    angles = jnp.linspace(start_angle, end_angle, num_views, endpoint=False)
+
+    # Set up parallel beam model
+    cone_model = mbirjax.ConeBeamModel(sinogram.shape, angles, source_detector_dist=source_detector_dist, source_iso_dist=source_iso_dist)
+
+    # Generate 3D Shepp Logan phantom
+    print('Creating phantom')
+    phantom = cone_model.gen_modified_3d_sl_phantom()
+
+    # Generate synthetic sinogram data
+    print('Creating sinogram')
+    sinogram = cone_model.forward_project(phantom)
+
+    # View sinogram
+    pu.slice_viewer(sinogram.transpose((1, 2, 0)), title='Original sinogram')
+
+    # Generate weights array
+    weights = cone_model.gen_weights(sinogram / sinogram.max(), weight_type='transmission_root')
+
+    # Set reconstruction parameter values
+    cone_model.set_params(sharpness=sharpness, verbose=1)
+
+    # Print out model parameters
+    cone_model.print_params()
+
+    # ##########################
+    # Perform VCD reconstruction
+    print('Starting recon')
+    time0 = time.time()
+    recon, recon_params = cone_model.recon(sinogram, weights=weights)
+
+    recon.block_until_ready()
+    elapsed = time.time() - time0
+    print('Elapsed time for recon is {:.3f} seconds'.format(elapsed))
+    # ##########################
+
+    # Display results
+    pu.slice_viewer(phantom, recon, title='Phantom (left) vs VCD Recon (right)')
+

mbirjax-0.2.0/demo/demo_parbeam_shepp_logan.py

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+import numpy as np
+import time
+import jax.numpy as jnp
+import matplotlib.pyplot as plt
+import mbirjax.plot_utils as pu
+import mbirjax.parallel_beam
+
+if __name__ == "__main__":
+    """
+    This is a script to develop, debug, and tune the parallel beam mbirjax code.
+    """
+    # Set parameters
+    num_views = 256
+    num_det_rows = 20
+    num_det_channels = 256
+    start_angle = -np.pi*(1/2)
+    end_angle = np.pi*(1/2)
+    sharpness = 0.0
+
+    # Initialize sinogram
+    sinogram = jnp.zeros((num_views, num_det_rows, num_det_channels))
+    angles = jnp.linspace(start_angle, end_angle, num_views, endpoint=False)
+
+    # Set up parallel beam model
+    parallel_model = mbirjax.ParallelBeamModel(sinogram.shape, angles)
+
+    # Generate 3D Shepp Logan phantom
+    print('Creating phantom')
+    phantom = parallel_model.gen_modified_3d_sl_phantom()
+
+    # Generate synthetic sinogram data
+    print('Creating sinogram')
+    sinogram = parallel_model.forward_project(phantom)
+
+    # View sinogram
+    pu.slice_viewer(sinogram.transpose((1, 2, 0)), title='Original sinogram')
+
+    # Generate weights array
+    weights = parallel_model.gen_weights(sinogram / sinogram.max(), weight_type='transmission_root')
+
+    # Set reconstruction parameter values
+    parallel_model.set_params(sharpness=sharpness, verbose=1)
+
+    # Print out model parameters
+    parallel_model.print_params()
+
+    # ##########################
+    # Perform VCD reconstruction
+    time0 = time.time()
+    recon, recon_params = parallel_model.recon(sinogram, weights=weights)
+
+    recon.block_until_ready()
+    elapsed = time.time() - time0
+    print('Elapsed time for recon is {:.3f} seconds'.format(elapsed))
+    # ##########################
+
+    # Display results
+    pu.slice_viewer(phantom, recon, title='Phantom (left) vs VCD Recon (right)')
+

mbirjax-0.2.0/demo/demo_slice_viewer.py

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+import numpy as np
+import jax.numpy as jnp
+import mbirjax.plot_utils as pu
+import mbirjax.parallel_beam
+
+if __name__ == "__main__":
+    """
+    This is a script to demonstrate the built-in slice viewer
+    """
+    # Set parameters
+    num_views = 128
+    num_det_rows = 128
+    num_det_channels = 128
+    source_detector_dist = 4 * num_det_channels
+    source_iso_dist = source_detector_dist
+
+    detector_cone_angle = 2 * np.arctan2(num_det_channels / 2, source_detector_dist)
+    start_angle = -(np.pi + detector_cone_angle) * (1/2)
+    end_angle = (np.pi + detector_cone_angle) * (1/2)
+    sharpness = 0.0
+
+    # Initialize sinogram
+    sinogram = jnp.zeros((num_views, num_det_rows, num_det_channels))
+    angles = jnp.linspace(start_angle, end_angle, num_views, endpoint=False)
+
+    # Set up parallel beam model
+    cone_model = mbirjax.ConeBeamModel(sinogram.shape, angles, source_detector_dist=source_detector_dist, source_iso_dist=source_iso_dist)
+
+    # Generate 3D Shepp Logan phantom
+    print('Creating phantom')
+    phantom = cone_model.gen_modified_3d_sl_phantom()
+
+    # View the phantom
+    pu.slice_viewer(phantom, phantom.transpose((1, 2, 0)), title='Phantom axial and coronal', slice_label='View')
+
+    # Generate synthetic sinogram data
+    print('Creating sinogram')
+    sinogram = cone_model.forward_project(phantom)
+
+    # View sinogram
+    pu.slice_viewer(sinogram, title='Sinogram', slice_axis=0)