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‎.gitignore/.gitignore

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# Various IDE folders
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.idea
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.vscode
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.vscode
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# Astra source files
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src/astra

‎docs/images/Cone_beam.jpg

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‎docs/images/Figures.ai

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‎docs/images/Laminography_parallel.jpg

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‎docs/imageset.rst

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Constructor for the :class:`CALCreateImageSet` class that creates an image set given a :class:`ProjObj` and structure of image transformation parameters.
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:Parameters: * projection_obj - :class:`ProjObj` containing the projections OR a "plain" 3D projection matrix (FOR BACKWARD COMPATIBILITY)
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* image_params - structure of image transformation parameters (refer to image at the end of this section for visual depiction of some of the parameters)

‎docs/projectors.rst

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:Parameters: * target_obj - :class:`TargetObj` containing the target (output from :func:`CALPrepTarget`)
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* proj_params - structure of projection parameters defining the projection configuration
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* proj_params.angles - vector of angles at which to perform forward and back projection
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* proj_params.CUDA - en/disables usage of Astra toolbox GPU accelerated projector
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* proj_params.inclination_angle - angle of elevation from normal tomographic plane
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* proj_params.cone_angle - angle of maximum ray divergence along rotation axis in cone beam geometry
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* parallel - whether or not to use parallel processing when performing forward and back projection
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:Returns: * ProjectorObj - :class:`ProjectorObj` that links to the correct projector depending on the target dimensions
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3D
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--
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3D (Matlab)
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-----------
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.. class:: Projector3D(proj_params,parallel)
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.. class:: Projector3DParallel(proj_params,parallel)
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Constructs a :class:`Projector3D` object for performing 3D forward and back projection.
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Constructs a :class:`Projector3DParallel` object for performing 3D forward and back projection with **parallel ray geometry** using Matlab's ``radon`` and ``iradon`` functions.
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:Parameters: * proj_params - structure of projection parameters defining the projection configuration
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* proj_params.angles - vector of angles at which to perform forward and back projection
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* parallel - whether or not to use parallel processing when performing forward and back projection
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:Returns: * obj - :class:`Projector3D`
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:Returns: * obj - :class:`Projector3DParallel`
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.. classmethod:: forward(x)
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:Returns: * x - 3D matrix of reconstruction. Dimensions will be ``[nT,nT,nZ]`` where ``nT`` is the number of elements in the transverse/radial direction and ``nZ`` is the number of z-slices
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2D
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--
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3D (Astra)
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----------
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.. class:: Projector3DCUDA(proj_params)
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Constructs a :class:`Projector3DCUDA` object for performing 3D forward and back projection with **parallel and cone beam geometry** using Astra Toolbox GPU accelerated projectors.
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:Parameters: * proj_params - structure of projection parameters defining the projection configuration
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* proj_params.angles - vector of angles at which to perform forward and back projection
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* proj_params.CUDA - en/disables usage of Astra toolbox GPU accelerated projector
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* proj_params.inclination_angle - angle of elevation from normal tomographic plane
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* proj_params.cone_angle - angle of maximum ray divergence along rotation axis in cone beam geometry
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:Returns: * obj - :class:`Projector3DCUDA`
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.. classmethod:: forward(x)
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Performs 3D forward projection using Astra's GPU accelerated 3D projectors.
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:Parameters: * x - 3D matrix of target
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:Returns: * b - 3D matrix of sinograms. Dimensions will be ``[nT,nTheta,nZ]`` where ``nT`` is the number of elements in the transverse/radial direction, ``nTheta`` is the number of angles, and ``nZ`` is the number of z-slices
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.. classmethod:: backward(b)
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Performs 3D back projection using Astra's GPU accelerated 3D projectors.
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:Parameters: * b - 3D matrix of sinograms
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:Returns: * x - 3D matrix of reconstruction. Dimensions will be ``[nT,nT,nZ]`` where ``nT`` is the number of elements in the transverse/radial direction and ``nZ`` is the number of z-slices
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2D (Matlab)
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-----------
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.. class:: Projector2D(proj_params)
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.. class:: Projector2DParallel(proj_params)
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Constructs a :class:`Projector2D` object for performing 2D forward and back projection.
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Constructs a :class:`Projector2DParallel` object for performing 2D forward and back projection with **parallel beam geometry** using Matlab's :func:`radon` and :func:`iradon` functions.
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:Parameters: * proj_params - structure of projection parameters defining the projection configuration
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* proj_params.angles - vector of angles at which to perform forward and back projection
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:Returns: * obj - :class:`Projector2D`
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:Returns: * obj - :class:`Projector2DParallel`
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.. classmethod:: forward(x)
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‎docs/sec_setup.rst

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::
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CALtest()
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You should see the following if the installation succeeded:
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This function will test the basic functionality of the toolbox and check if a GPU is available for the use of the `Astra toolbox`_ which is included in this toolbox.
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You should see the following if installation was successful:
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::
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CAL-software-Matlab Toolbox installed successfully!
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Getting GPU info...
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Testing basic CPU 2D functionality...
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Testing basic CUDA 2D functionality...
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Testing basic CUDA 3D functionality...
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If your computer has a NVIDIA GPU the CUDA 2D and 3D functionality should say "Ok".
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Now the toolbox can be used like any other Matlab toolbox. You do not need to be in a particular working directory to access the functions of the toolbox.
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Astra Toolbox
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-------------
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`Astra toolbox`_ is a toolbox for GPU-accelerated tomography which has very flexible projector geometries that can be used for non-standard CAL systems. If Astra installation fails, go to the Astra Github repository and download the `Mex and Tools`_ folders and place them in a folder inside the source folder in which CAL-software-Matlab is installed.
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.. _`CAL-software-Matlab`: https://github.com/computed-axial-lithography/CAL-software-Matlab
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.. _`release`: https://github.com/computed-axial-lithography/CAL-software-Matlab/releases
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.. _`Astra toolbox`: https://github.com/astra-toolbox/astra-toolbox
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.. _`Mex and Tools`: https://github.com/astra-toolbox/astra-toolbox/tree/master/matlab
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Uninstallation
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--------------

‎docs/sec_usage_projopt.rst

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Projection generation and optimization
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######################################
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Projection
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----------
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With the target prepared, the projection generation and optimization can begin. The class :class:`CALOptimize` is used to perform projection generation and optimization. First, define the projection parameters and the optimization parameters (these are just some examples for demonstration, more information about these parameters can be found in the :ref:`optimization` code reference:
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::
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% define projection parameters
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opt_params.threshold = 0.8;
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opt_params.learning_rate = 0.005;
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The default projection geometry is parallel beam perpendicular to the axis of rotation. However, there are other possible projections geometries including cone beam and laminographic (parallel or cone beam) geometries. These are selected by specifying non-zero ``proj_params``: ``cone_angle`` and/or ``incline_angle`` in degrees. **Additionally,** ``proj_params.CUDA`` **must be set to true to enable these geometries (which implies that your PC has a NVIDIA CUDA GPU).** These geometries are depicted in the figure below.
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Parallel beam laminography where :math:`\varphi` is the incline angle which is set with the parameter ``proj_params.incline_angle`` = :math:`\varphi`.
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.. image:: images/Laminography_parallel.jpg
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:width: 500
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Cone beam where :math:`\beta` is the maximum cone angle along the z-axis which is set with the parameter ``proj_params.cone_angle`` = :math:`\beta`.
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.. image:: images/Cone_beam.jpg
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:width: 500
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Optimization
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------------
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Then initialize the class :class:`CALOptimize` with these parameters and the :class:`TargetObj` created above:
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% instantiate the optimization class

‎package_files/.gitattributes

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CAL-software-Matlab.mltbx filter=lfs diff=lfs merge=lfs -text

‎package_files/CAL-software-Matlab.mltbx

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‎package_files/CAL-software-Matlab.prj

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This code package is provided to support the generation of the light projections and the control of a DLP projector through Matlab.</param.description>
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<param.screenshot>F:\Github\CAL-software-Matlab\docs\images\title.png</param.screenshot>
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<param.version>1.4.1</param.version>
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<param.version>1.5.0</param.version>
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<param.output>${PROJECT_ROOT}\CAL-software-Matlab.mltbx</param.output>
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<param.products.name />
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<param.products.id />
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<fileset.rootfiles>
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<file>F:\Github\CAL-software-Matlab\src\.gitignore</file>
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<file>F:\Github\CAL-software-Matlab\src\archive</file>
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<file>F:\Github\CAL-software-Matlab\src\astra</file>
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<file>F:\Github\CAL-software-Matlab\src\astratesting.m</file>
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<file>F:\Github\CAL-software-Matlab\src\autoArrangeFigures_bin</file>
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<file>F:\Github\CAL-software-Matlab\src\CALCreateImageSet.m</file>
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<file>F:\Github\CAL-software-Matlab\src\CALMetrics.m</file>
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<file>F:\Github\CAL-software-Matlab\src\CALProjectorConstructor.m</file>
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<file>F:\Github\CAL-software-Matlab\src\CALSetup.m</file>
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<file>F:\Github\CAL-software-Matlab\src\CALtest.m</file>
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<file>F:\Github\CAL-software-Matlab\src\clipToCircle.m</file>
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<file>F:\Github\CAL-software-Matlab\src\colormaps_bin</file>
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<file>F:\Github\CAL-software-Matlab\src\createTarget.m</file>
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<file>F:\Github\CAL-software-Matlab\src\Display.m</file>
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<file>F:\Github\CAL-software-Matlab\src\imshow_3D_bin</file>
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<file>F:\Github\CAL-software-Matlab\src\LICENSE.txt</file>
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<file>F:\Github\CAL-software-Matlab\src\loadExStlFilename.m</file>
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<file>F:\Github\CAL-software-Matlab\src\Projector2D.m</file>
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<file>F:\Github\CAL-software-Matlab\src\Projector3D.m</file>
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<file>F:\Github\CAL-software-Matlab\src\Projector2DParallel.m</file>
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<file>F:\Github\CAL-software-Matlab\src\Projector3DConeCUDA.m</file>
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<file>F:\Github\CAL-software-Matlab\src\Projector3DParallel.m</file>
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<file>F:\Github\CAL-software-Matlab\src\Projector3DParallelCUDA.m</file>
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<file>F:\Github\CAL-software-Matlab\src\ReconObj.m</file>

‎src/CALCreateImageSet.m

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%{
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Copyright (C) 2020-2021 Hayden Taylor Lab, University of California, Berkeley
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Website https://github.com/computed-axial-lithography/CAL-software-Matlab
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This file is part of the CAL-software-Matlab toolbox.
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%}
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classdef CALCreateImageSet
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‎src/CALMetrics.m

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%{
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Copyright (C) 2020-2021 Hayden Taylor Lab, University of California, Berkeley
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Website https://github.com/computed-axial-lithography/CAL-software-Matlab
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This file is part of the CAL-software-Matlab toolbox.
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%}
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classdef CALMetrics
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‎src/CALOptimize.m

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%{
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Copyright (C) 2020-2021 Hayden Taylor Lab, University of California, Berkeley
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Website https://github.com/computed-axial-lithography/CAL-software-Matlab
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This file is part of the CAL-software-Matlab toolbox.
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%}
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classdef CALOptimize
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obj.thresholds = zeros(1,opt_params.max_iter);
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function [obj] = parseParams(obj,opt_params,proj_params)
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mu = curr_threshold;
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mu_dilated = (1-obj.opt_params.Rho)*curr_threshold;
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mu_eroded = (1+obj.opt_params.Rho)*curr_threshold;
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% mu_dilated = (1-obj.opt_params.Rho)*curr_threshold;
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% mu_eroded = (1+obj.opt_params.Rho)*curr_threshold;
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x_thresh = obj.sigmoid((x-mu), obj.opt_params.sigmoid);
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x_thresh_eroded = obj.sigmoid((x-mu_eroded), obj.opt_params.sigmoid);
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x_thresh_dilated = obj.sigmoid((x-mu_dilated), obj.opt_params.sigmoid);
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% x_thresh_eroded = obj.sigmoid((x-mu_eroded), obj.opt_params.sigmoid);
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% x_thresh_dilated = obj.sigmoid((x-mu_dilated), obj.opt_params.sigmoid);
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delta_x = (x_thresh - obj.target_obj.target).*obj.target_obj.target_care_area; % Target space error
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delta_x_eroded = (x_thresh_eroded - obj.target_obj.target).*obj.target_obj.target_care_area; % Eroded version
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delta_x_feedback = (delta_x + delta_x_eroded + delta_x_dilated)/3;
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delta_x = (x_thresh - obj.target_obj.target);%.*obj.target_obj.target_care_area; % Target space error
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% delta_x_eroded = (x_thresh_eroded - obj.target_obj.target).*obj.target_obj.target_care_area; % Eroded version
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% delta_x_dilated = (x_thresh_dilated - obj.target_obj.target).*obj.target_obj.target_care_area; % Dilated version
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% delta_x_feedback = (delta_x + delta_x_eroded + delta_x_dilated)/3;
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delta_x_feedback = delta_x;
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obj.error(curr_iter) = CALMetrics.calcVER(obj.target_obj.target,x);
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delta_b = obj.A.forward(delta_x_feedback);

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