Repository: gift-surg/NiftyMIC Branch: master Commit: 553bce0824e7 Files: 127 Total size: 1020.4 KB Directory structure: gitextract_rkx8168q/ ├── .gitattributes ├── .gitignore ├── .gitlab-ci.yml ├── .gitmodules ├── LICENSE ├── MANIFEST.in ├── README.md ├── data/ │ └── templates/ │ ├── LICENSE │ ├── README │ └── templates_info.json ├── doc/ │ └── doxyfile ├── docker/ │ ├── docker-compose.yml │ ├── itk_niftymic/ │ │ ├── .dockerignore │ │ └── Dockerfile │ ├── niftymic/ │ │ ├── .dockerignore │ │ └── Dockerfile │ └── simplereg_dependencies/ │ ├── .dockerignore │ └── Dockerfile ├── niftymic/ │ ├── __about__.py │ ├── __init__.py │ ├── application/ │ │ ├── __init__.py │ │ ├── correct_bias_field.py │ │ ├── correct_intensities.py │ │ ├── multiply.py │ │ ├── nifti2dicom.py │ │ ├── propagate_mask.py │ │ ├── reconstruct_volume.py │ │ ├── reconstruct_volume_from_slices.py │ │ ├── register_image.py │ │ ├── rsfmri_estimate_motion.py │ │ ├── rsfmri_reconstruct_volume_from_slices.py │ │ ├── run_reconstruction_parameter_study.py │ │ ├── run_reconstruction_pipeline.py │ │ ├── segment_fetal_brains.py │ │ └── show_slice_coverage.py │ ├── base/ │ │ ├── __init__.py │ │ ├── data_reader.py │ │ ├── data_writer.py │ │ ├── exceptions.py │ │ ├── psf.py │ │ ├── slice.py │ │ └── stack.py │ ├── definitions.py │ ├── reconstruction/ │ │ ├── __init__.py │ │ ├── admm_solver.py │ │ ├── linear_operators.py │ │ ├── primal_dual_solver.py │ │ ├── scattered_data_approximation.py │ │ ├── solver.py │ │ └── tikhonov_solver.py │ ├── registration/ │ │ ├── __init__.py │ │ ├── flirt.py │ │ ├── intra_stack_registration.py │ │ ├── niftyreg.py │ │ ├── registration_method.py │ │ ├── simple_itk_registration.py │ │ ├── stack_registration_base.py │ │ ├── transform_initializer.py │ │ └── wrap_itk_registration.py │ ├── utilities/ │ │ ├── __init__.py │ │ ├── binary_mask_from_mask_srr_estimator.py │ │ ├── brain_stripping.py │ │ ├── data_preprocessing.py │ │ ├── input_arparser.py │ │ ├── intensity_correction.py │ │ ├── joint_image_mask_builder.py │ │ ├── motion_updater.py │ │ ├── n4_bias_field_correction.py │ │ ├── outlier_rejector.py │ │ ├── parameter_normalization.py │ │ ├── segmentation_propagation.py │ │ ├── siena.py │ │ ├── stack_mask_morphological_operations.py │ │ ├── target_stack_estimator.py │ │ ├── template_stack_estimator.py │ │ ├── toolkit_executor.py │ │ └── volumetric_reconstruction_pipeline.py │ └── validation/ │ ├── __init__.py │ ├── evaluate_image_similarity.py │ ├── evaluate_simulated_stack_similarity.py │ ├── evaluate_slice_residual_similarity.py │ ├── export_side_by_side_simulated_vs_original_slice_comparison.py │ ├── image_similarity_evaluator.py │ ├── motion_evaluator.py │ ├── motion_simulator.py │ ├── residual_evaluator.py │ ├── show_evaluated_simulated_stack_similarity.py │ ├── simulate_stacks_from_reconstruction.py │ ├── slice_acquisition.py │ ├── slice_coverage.py │ └── write_random_motion_transforms.py ├── niftymic_correct_bias_field.py ├── niftymic_multiply.py ├── niftymic_nifti2dicom.py ├── niftymic_reconstruct_volume.py ├── niftymic_reconstruct_volume_from_slices.py ├── niftymic_register_image.py ├── niftymic_rsfmri_estimate_motion.py ├── niftymic_rsfmri_reconstruct_volume_from_slices.py ├── niftymic_run_reconstruction_parameter_study.py ├── niftymic_run_reconstruction_pipeline.py ├── niftymic_segment_fetal_brains.py ├── niftymic_show_reconstruction_parameter_study.py ├── requirements-monaifbs.txt ├── requirements.txt ├── setup.py └── tests/ ├── __init__.py ├── brain_stripping_test.py ├── case_study_fetal_brain_test.py ├── case_study_rsfmri_test.py ├── data_reader_test.py ├── image_similarity_evaluator_test.py ├── installation_test.py ├── installation_test_fetal_brain_seg.py ├── installation_test_monaifbs.py ├── intensity_correction_test.py ├── intra_stack_registration_test.py ├── linear_image_quality_transfer_test.py ├── linear_operators_test.py ├── niftyreg_test.py ├── parameter_normalization_test.py ├── registration_test.py ├── residual_evaluator_test.py ├── run_tests.py ├── segmentation_propagation_test.py ├── simulator_slice_acquisition_test.py └── stack_test.py ================================================ FILE CONTENTS ================================================ ================================================ FILE: .gitattributes ================================================ *.pt filter=lfs diff=lfs merge=lfs -text ================================================ FILE: .gitignore ================================================ build/ html/ data/tests/ dist/ latex/ monaifbs/models/ prototyping/ *.nii *.nii.gz *.tar.gz *.deb *.zip *.pyc *iterate.dat *.egg-info *.idea *.wiki /.project .DS_Store **/.DS_Store ================================================ FILE: .gitlab-ci.yml ================================================ # -----------------------------------Set Up------------------------------------ variables: PY_VERSION: 3 PRIVATE: 0 TMPDIR: ./tmp DATADIR: /home/mebner/data/ci/FetalBrain VENV: pysitk-test-py${PY_VERSION} ITK_DIR: /mnt/shared/mebner/environment/ITK/ITK_NiftyMIC-python${PY_VERSION}-build FSL_DIR: /mnt/shared/mebner/environment/FSL/fsl TEST_DIR: /home/mebner/Development/NiftyMIC/data/tests NIFTYREG_INSTALL: /mnt/shared/mebner/environment/NiftyReg/NiftyReg-master-install CONVERT3D_INSTALL: /mnt/shared/mebner/environment/Convert3D/c3d-git-install before_script: # add NiftyReg to PATH - export PATH="${NIFTYREG_INSTALL}/bin:$PATH" # add FSL - PATH=${FSL_DIR}/bin:${PATH} - export PATH="${FSL_INSTALL}/bin:$PATH" - export FSLOUTPUTTYPE=NIFTI_GZ # add Convert3D to PATH - export PATH="${CONVERT3D_INSTALL}/bin:$PATH" # save current folder path - cwd_dir=$(pwd) # create virtual environment - rm -rf ${VENV} - mypython=$(which python${PY_VERSION}) - virtualenv -p $mypython ${VENV} - cd ${VENV} - venv_dir=$(pwd) - source bin/activate # print Python version to CI output - which python - python --version # copy ITK_NiftyMIC-build WrapITK to site-packages of python venv - py_sitepkg=${venv_dir}/lib/python*/site-packages - cp -v ${ITK_DIR}/Wrapping/Generators/Python/WrapITK.pth ${py_sitepkg} - cd $cwd_dir # If PRIVATE is used: # add CI_JOB_TOKEN for cloning dependent repositories in requirements.txt # (https://docs.gitlab.com/ee/user/project/new_ci_build_permissions_model.html#dependent-repositories) - > (if [ ${PRIVATE} == 1 ]; then sed -i -- "s#github.com/gift-surg#gitlab-ci-token:${CI_JOB_TOKEN}@PRIVATE.cs.ucl.ac.uk/GIFT-Surg#g" requirements.txt; fi); # install requirements - pip install -r requirements.txt # set environment variables for installation - export NIFTYMIC_ITK_DIR=$ITK_DIR # run installation - pip install -e . # replace TEST_DIR in niftymic/definitions.py file - sed -i -- 's:DIR_TEST = os.path.join(DIR_ROOT, "data", "tests"):DIR_TEST = "'"$TEST_DIR"'":g' niftymic/definitions.py - cat niftymic/definitions.py after_script: # delete tmp-directory - rm -rfv ${TMPDIR} # ----------------------------------Test Jobs---------------------------------- builddocs: # only: # - master script: - cd doc - doxygen doxyfile tags: - gift-adelie installation: # only: # - master script: - python -m nose tests/installation_test.py tags: - gift-adelie reconstruct_volume_tk1l2: # only: # - master script: - > niftymic_reconstruct_volume --filenames ${DATADIR}/input_data/axial.nii.gz ${DATADIR}/input_data/coronal.nii.gz ${DATADIR}/input_data/sagittal.nii.gz --output ${TMPDIR}/srr_from_slices_tk1l2.nii.gz --suffix-mask _mask --verbose 0 --isotropic-resolution 2 --reconstruction-type TK1L2 --two-step-cycles 1 --iter-max 2 --iter-max-first 2 tags: - gift-adelie reconstruct_volume_huberl2: # only: # - master script: - > niftymic_reconstruct_volume --filenames ${DATADIR}/input_data/axial.nii.gz ${DATADIR}/input_data/coronal.nii.gz ${DATADIR}/input_data/sagittal.nii.gz --output ${TMPDIR}/srr_from_slices_huberl2.nii.gz --suffix-mask _mask --verbose 0 --isotropic-resolution 2 --reconstruction-type HuberL2 --two-step-cycles 1 --iter-max 2 --iter-max-first 2 --iterations 1 tags: - gift-adelie reconstruct_volume_from_slices: # only: # - master script: - > niftymic_reconstruct_volume_from_slices --filenames ${DATADIR}/input_data/axial.nii.gz ${DATADIR}/input_data/coronal.nii.gz ${DATADIR}/input_data/sagittal.nii.gz --dir-input-mc ${DATADIR}/motion_correction_oriented --suffix-mask _mask --reconstruction-space ${DATADIR}/SRR_stacks3_TK1_lsmr_alpha0p03_itermax10_oriented.nii.gz --output ${TMPDIR}/srr_from_slices.nii.gz --verbose 0 --isotropic-resolution 2 --iter-max 2 tags: - gift-adelie run_reconstruction_pipeline: # only: # - master script: - > niftymic_run_reconstruction_pipeline --filenames ${DATADIR}/input_data/axial.nii.gz --filenames-masks ${DATADIR}/input_data/axial_mask.nii.gz --dir-output ${TMPDIR} --suffix-mask _mask --bias-field-correction 1 --two-step-cycles 0 --iter-max 1 --run-diagnostics 1 --slice-thicknesses 3.85 --verbose 0 tags: - gift-adelie param_study_huberl2: # only: # - master script: - recon_type=HuberL2 - > niftymic_run_reconstruction_parameter_study --filenames ${DATADIR}/input_data/axial.nii.gz ${DATADIR}/input_data/coronal.nii.gz ${DATADIR}/input_data/sagittal.nii.gz --dir-input-mc ${DATADIR}/motion_correction_oriented --suffix-mask _mask --reference ${DATADIR}/SRR_stacks3_TK1_lsmr_alpha0p03_itermax10_oriented.nii.gz --dir-output ${TMPDIR}/param_study --alphas 0.01 0.05 --iter-max 2 --verbose 0 --iterations 2 --reconstruction-type ${recon_type} tags: - gift-adelie rsfmri_estimate_motion: # only: # - master script: - recon_type=HuberL2 - > niftymic_rsfmri_estimate_motion --filename ${DATADIR}/rsfmri/bold.nii.gz --filename-mask ${DATADIR}/rsfmri/bold_4Dmask.nii.gz --dir-output ${TMPDIR}/rsfmri --two-step-cycles 1 --iterations 2 --sda --alpha 1 --verbose 0 --prototyping tags: - gift-adelie rsfmri_reconstruct_volume_from_slices: # only: # - master script: - recon_type=TK1L2 - > niftymic_rsfmri_reconstruct_volume_from_slices --filename ${DATADIR}/rsfmri/bold.nii.gz --filename-mask ${DATADIR}/rsfmri/bold_4Dmask.nii.gz --output ${TMPDIR}/rsfmri/foo.nii.gz --alpha 0.05 --iter-max 2 --verbose 0 --reconstruction-type ${recon_type} --reconstruction-spacing 2 2 5 --use-masks-srr 1 --prototyping tags: - gift-adelie ## # Results can (slightly) change depending on the downloaded library version; # enough so that the accuracy limits are not met. Run them locally instead. # unit_tests: # # only: # # - master # script: # - python -m nose tests/brain_stripping_test.py # - python -m nose tests/case_study_fetal_brain_test.py # - python -m nose tests/data_reader_test.py # - python -m nose tests/image_similarity_evaluator_test.py # - python -m nose tests/intensity_correction_test.py # - python -m nose tests/linear_operators_test.py # - python -m nose tests/niftyreg_test.py # - python -m nose tests/residual_evaluator_test.py # - python -m nose tests/segmentation_propagation_test.py # - python -m nose tests/simulator_slice_acquisition_test.py # - python -m nose tests/stack_test.py # tags: # - gift-adelie ================================================ FILE: .gitmodules ================================================ [submodule "MONAIfbs"] path = MONAIfbs url = https://github.com/gift-surg/MONAIfbs ================================================ FILE: LICENSE ================================================ Copyright (c) 2017, University College London 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. ================================================ FILE: MANIFEST.in ================================================ include LICENSE include requirements.txt ================================================ FILE: README.md ================================================ # Motion Correction and Volumetric Image Reconstruction of 2D Ultra-fast MRI NiftyMIC is a Python-based open-source toolkit for research developed within the [GIFT-Surg][giftsurg] project to reconstruct an isotropic, high-resolution volume from multiple, possibly motion-corrupted, stacks of low-resolution 2D slices. The framework relies on slice-to-volume registration algorithms for motion correction and reconstruction-based Super-Resolution (SR) techniques for the volumetric reconstruction. The algorithm and software were developed by [Michael Ebner][mebner] at the [Wellcome/EPSRC Centre for Interventional and Surgical Sciences][weiss], [University College London (UCL)][ucl] (2015 -- 2019), and the [Department of Surgical and Interventional Sciences][sie], [King's College London (KCL)][kcl] (since 2019). A detailed description of the NiftyMIC algorithm is found in [EbnerWang2020][ebner-wang-2020]: * Ebner, M., Wang, G., Li, W., Aertsen, M., Patel, P. A., Aughwane, R., Melbourne, A., Doel, T., Dymarkowski, S., De Coppi, P., David, A. L., Deprest, J., Ourselin, S., Vercauteren, T. (2020). An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI. NeuroImage, 206, 116324. A later extension to this paper for fetal brain automatic segmentation building on [MONAI][monai] was provided by [Marta B.M. Ranzini][martaranzini]. More information about `MONAIfbs` can be found [here][monaifbs]. An extension of NiftyMIC for fetal functional MRI was developed in collaboration with members of the [Computational Image Research Lab][cir], Department of Biomedical Imaging and Image-guided Therapy at the [Medical University of Vienna][muw]. A detailed description of the NiftyMIC algorithm for fetal fMRI is found in [Sobotka2022][sobotka-2022]: * Sobotka, D., Ebner, M., Schwartz, E., Nenning, K.-H., Taymourtash, A., Vercauteren, T., Ourselin, S., Kasprian, G., Prayer, D., Langs, G., Licandro, R. (2022). Motion Correction and Volumetric Reconstruction for Fetal fMRI. arXiv. If you have any questions or comments, please drop an email to `michael.ebner@kcl.ac.uk`. ## NiftyMIC applied to Fetal Brain MRI Given a set of low-resolution, possibly motion-corrupted, stacks of 2D slices, NiftyMIC produces an isotropic, high-resolution 3D volume. As an example, we illustrate its use for fetal MRI by computing a high-resolution visualization of the brain for a neck mass subject. Standard clinical HASTE sequences were used to acquire the low-resolution images in multiple orientations. The associated brain masks for motion correction can be obtained with the included automated segmentation tool [MONAIfbs][monaifbs] (a legacy method for automated segmentation can also be found in the [fetal_brain_seg][fetal_brain_seg] package). Full working examples on automated segmentation and high-resolution reconstruction of fetal brain MRI using NiftyMIC is described in the [Usage](https://github.com/gift-surg/NiftyMIC#automatic-segmentation-and-high-resolution-reconstruction-of-fetal-brain-mri) section below.

Figure 1. NiftyMIC -- a volumetric MRI reconstruction tool based on rigid slice-to-volume registration and outlier-robust super-resolution reconstruction steps -- applied to fetal brain MRI.

Figure 2. Qualitative comparison of the original low-resolution input data and the obtained high-resolution volumetric reconstructions in both the original patient-specific and standard anatomical orientations. Five input stacks (two axial, one coronal and two sagittal) were used.

## Algorithm Several methods have been implemented to solve the **Robust Super-Resolution Reconstruction (SRR)** problem

to obtain the (vectorized) high-resolution 3D MRI volume ![img](http://latex.codecogs.com/svg.latex?%5Cvec%7Bx%7D%5Cin%5Cmathbb%7BR%7D%5EN) from multiple, possibly motion corrupted, low-resolution stacks of (vectorized) 2D MR slices ![img](http://latex.codecogs.com/svg.latex?%5Cvec%7By%7D_k%5Cin%5Cmathbb%7BR%7D%5E%7BN_k%7D) with ![img](http://latex.codecogs.com/svg.latex?N_k%5Cll%7BN%7D) for ![img](https://latex.codecogs.com/svg.latex?k\in\mathcal{K}:=\\{1,\dots,K\\}) for a variety of regularizers ![img](http://latex.codecogs.com/svg.latex?%5Ctext%7BReg%7D) and data loss functions ![img](http://latex.codecogs.com/svg.latex?%5Cvarrho). The linear operator ![img](http://latex.codecogs.com/svg.latex?A_k%3A%3DD_kB_kW_k) represents the combined operator describing the (rigid) motion ![img](http://latex.codecogs.com/svg.latex?W_k), the blurring operator ![img](http://latex.codecogs.com/svg.latex?B_k) and the downsampling operator ![img](http://latex.codecogs.com/svg.latex?D_k). The toolkit relies on an iterative motion-correction/reconstruction approach whereby **complete outlier rejection** of misregistered slices is achieved by iteratively solving the SRR problem for a slice-index set ![img](https://latex.codecogs.com/svg.latex?\mathcal{K}_\sigma:=\\{1\le&space;k&space;\le&space;K:&space;\text{Sim}(A_k^{\iota}\vec{x}^{\iota},&space;\vec{y}^{\iota}_k)\ge\sigma\\}\subset&space;\mathcal{K}) containing only slices that are in high agreement with their simulated counterparts projected from a previous high-resolution iterate ![img](http://latex.codecogs.com/svg.latex?\vec{x}^{\iota}) according to a similarity measure ![img](http://latex.codecogs.com/svg.latex?\text{Sim}) and parameter ![img](http://latex.codecogs.com/svg.latex?\sigma>0). In the current implementation, the similarity measure ![img](http://latex.codecogs.com/svg.latex?\text{Sim}) corresponds to Normalized Cross Correlation (NCC). --- The provided **data loss functions** ![img](http://latex.codecogs.com/svg.latex?%5Cvarrho) are motivated by [SciPy](https://docs.scipy.org/doc/scipy-0.19.0/reference/generated/scipy.optimize.least_squares.html) and allow for additional robust outlier handling during the SRR step. Implemented data loss functions are: * `linear`: * `soft_l1`: * `huber`: * `arctan`: * `cauchy`: --- The **available regularizers** include * Zeroth-order Tikhonov (TK0): * First-order Tikhonov (TK1): * Isotropic Total Variation (TV): * Huber Function: --- Additionally, the choice of finding **optimal reconstruction parameters** is facilitated by the [Numerical Solver Library (NSoL)][nsol]. ## Disclaimer NiftyMIC supports medical image registration and volumetric reconstruction for ultra-fast 2D MRI. **NiftyMIC is not intended for clinical use**. ## How to cite If you use this software in your work for structural MRI reconstruction, please cite * [[EbnerWang2020]][ebner-wang-2020] Ebner, M., Wang, G., Li, W., Aertsen, M., Patel, P. A., Aughwane, R., Melbourne, A., Doel, T., Dymarkowski, S., De Coppi, P., David, A. L., Deprest, J., Ourselin, S., Vercauteren, T. (2020). An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI. NeuroImage, 206, 116324. * [[EbnerWang2018]][ebner-wang-2018] Ebner, M., Wang, G., Li, W., Aertsen, M., Patel, P. A., Melbourne, A., Doel, T., David, A. L., Deprest, J., Ourselin, S., Vercauteren, T. (2018). An Automated Localization, Segmentation and Reconstruction Framework for Fetal Brain MRI. In Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2018 (pp. 313–320). Springer. * [[Ebner2018]](https://www.sciencedirect.com/science/article/pii/S1053811917308042) Ebner, M., Chung, K. K., Prados, F., Cardoso, M. J., Chard, D. T., Vercauteren, T., Ourselin, S. (2018). Volumetric reconstruction from printed films: Enabling 30 year longitudinal analysis in MR neuroimaging. NeuroImage, 165, 238–250. If you use this software in your work for functional MRI reconstruction, please cite * [[Sobotka2022]][sobotka-2022] Sobotka, D., Ebner, M., Schwartz, E., Nenning, K.-H., Taymourtash, A., Vercauteren, T., Ourselin, S., Kasprian, G., Prayer, D., Langs, G., Licandro, R. (2022). Motion Correction and Volumetric Reconstruction for Fetal fMRI. arXiv. * [[EbnerWang2020]][ebner-wang-2020] Ebner, M., Wang, G., Li, W., Aertsen, M., Patel, P. A., Aughwane, R., Melbourne, A., Doel, T., Dymarkowski, S., De Coppi, P., David, A. L., Deprest, J., Ourselin, S., Vercauteren, T. (2020). An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI. NeuroImage, 206, 116324. ## Installation ### From Source NiftyMIC was developed in Ubuntu 16.04, 18.04 and Mac OS X 10.12 and tested for Python 2.7, 3.5 and 3.6. It builds on a couple of additional libraries developed within the [GIFT-Surg][giftsurg] project including * [NSoL][nsol] * [SimpleReg][simplereg] * [PySiTK][pysitk] * [ITK_NiftyMIC][itkniftymic] whose installation requirements need to be met. Therefore, the local installation comes in three steps: 1. [Installation of ITK_NiftyMIC][itkniftymic] 1. [Installation of SimpleReg dependencies][simplereg-dependencies] 1. [Installation of NiftyMIC (including optional MONAIfbs)][niftymic-install] Note: The optional use of the automated fetal brain segmentation tool [MONAIfbs][monaifbs] requires Python version >= 3.6. ### Virtual Machine and Docker To avoid manual installation from source, NiftyMIC is also available as a [virtual machine][niftymic-vm] and [Docker image][niftymic-docker]. ## Usage Provided the input MR image data in NIfTI format (`nii` or `nii.gz`), NiftyMIC can reconstruct an isotropic, high-resolution volume from multiple, possibly motion-corrupted, stacks of low-resolution 2D slices. A recommended workflow is [associated applications in square brackets]: 1. Segmentation of the anatomy of interest for all input images. For fetal brain MRI reconstructions, we recommend the use of the fully automatic segmentation tool [MONAIfbs][monaifbs] already integrated in NiftyMIC [`niftymic_segment_fetal_brains`]. 1. Bias-field correction [`niftymic_correct_bias_field`] 1. Volumetric reconstruction in subject space using two-step iterative approach based on rigid slice-to-volume registration and SRR cycles [`niftymic_reconstruct_volume`] In case reconstruction in a template space is desired (like for fetal MRI) additional steps could be: 1. Register obtained SRR to template and update respective slice motion corrections [`niftymic_register_image`] 1. Volumetric reconstruction in template space [`niftymic_reconstruct_volume_from_slices`] Additional information on how to use NiftyMIC and its applications is provided in the following. ### Volumetric MR Reconstruction from Motion Corrupted 2D Slices Leveraging a two-step registration-reconstruction approach an isotropic, high-resolution 3D volume can be generated from multiple stacks of low-resolution slices. An example for a basic usage reads ``` niftymic_reconstruct_volume \ --filenames path-to-stack-1.nii.gz ... path-to-stack-N.nii.gz \ --filenames-masks path-to-stack-1_mask.nii.gz ... path-to-stack-N_mask.nii.gz \ --output path-to-srr.nii.gz \ ``` whereby complete outlier removal during SRR is activated by default (`--outlier-rejection 1`). A more elaborate example could be ``` niftymic_reconstruct_volume \ --filenames path-to-stack-1.nii.gz ... path-to-stack-N.nii.gz \ --filenames-masks path-to-stack-1_mask.nii.gz ... path-to-stack-N_mask.nii.gz \ --alpha 0.01 \ --outlier-rejection 1 \ --threshold-first 0.5 \ --threshold 0.85 \ --intensity-correction 1 \ --isotropic-resolution 0.8 \ --two-step-cycles 3 \ --output path-to-output-dir/srr.nii.gz \ --subfolder-motion-correction motion_correction \ # created in 'path-to-output-dir' --verbose 1 ``` The obtained motion-correction transformations in `motion_correction` can be used for further processing, e.g. by using `niftymic_reconstruct_volume_from_slices.py` to solve the SRR problem for a variety of different regularization and data loss function types. ### Transformation to Template Space If a template is available, it is possible to obtain a SRR in its associated standard anatomical space. Using the subject-space SRR outcome of `niftymic_reconstruct_volume` a rigid alignment step maps all slice motion correction transformations accordingly using ``` niftymic_register_image \ --fixed path-to-template.nii.gz \ --fixed-mask path-to-template_mask.nii.gz \ --moving path-to-subject-space-srr.nii.gz \ --moving-mask path-to-subject-space-srr_mask.nii.gz \ --dir-input-mc dir-to-motion_correction \ --output path-to-registration-transform.txt ``` For fetal brain template space alignment, a [spatio-temporal atlas][gholipour_atlas] is provided in [`data/templates`](data/templates). If you make use of it, please cite * Gholipour, A., Rollins, C. K., Velasco-Annis, C., Ouaalam, A., Akhondi-Asl, A., Afacan, O., Ortinau, C. M., Clancy, S., Limperopoulos, C., Yang, E., Estroff, J. A. & Warfield, S. K. (2017). A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth. Scientific Reports 7, 476. and abide by the license agreement as described in [`data/templates/LICENSE`](data/templates/LICENSE). ### SRR Methods for Motion Corrected (or Static) Data After performed/updated motion correction (or having static data in the first place) several options are available: * Volumetric reconstruction in template space * Parameter tuning for SRR: * different solvers and regularizers can be used to solve the SRR problem for comparison * parameter studies can be performed to find optimal reconstruction parameters. #### SRR from Motion Corrected (or Static) Slice Acquisitions Solve the SRR problem for motion corrected data (or static data if `--dir-input-mc` is omitted): ``` niftymic_reconstruct_volume_from_slices \ --filenames path-to-stack-1.nii.gz ... path-to-stack-N.nii.gz \ --filenames-masks path-to-stack-1_mask.nii.gz ... path-to-stack-N_mask.nii.gz \ --dir-input-mc dir-to-motion_correction \ # optional --output path-to-srr.nii.gz \ --reconstruction-type TK1L2 \ --reconstruction-space path-to-template.nii.gz \ # optional --alpha 0.01 ``` ``` niftymic_reconstruct_volume_from_slices \ --filenames path-to-stack-1.nii.gz ... path-to-stack-N.nii.gz \ --dir-input-mc dir-to-motion_correction \ --output path-to-srr.nii.gz \ --reconstruction-type HuberL2 \ --alpha 0.003 ``` Slices that were rejected during the `niftymic_reconstruct_volume` run are recognized as outliers based on the content of `dir-input-mc` and will not be incorporated during the volumetric reconstruction. #### Parameter Studies to Determine Optimal SRR Parameters The optimal choice for reconstruction parameters like the regularization parameter or data loss function can be found by running parameter studies. This includes L-curve studies and direct comparison against a reference volume for various cost functions. In case a reference is available, similarity measures are evaluated against this "ground-truth" as well. Example are: ``` niftymic_run_reconstruction_parameter_study \ --filenames path-to-stack-1.nii.gz ... path-to-stack-N.nii.gz \ --filenames-masks path-to-stack-1_mask.nii.gz ... path-to-stack-N_mask.nii.gz \ --dir-input-mc dir-to-motion_correction \ --dir-output dir-to-param-study-output \ --reconstruction-type TK1L2 \ --reconstruction-space path-to-reconstruction-space.nii.gz \ # define reconstruction space --alphas 0.005 0.01 0.02 0.05 0.1 # regularization parameters to sweep through --append # if given, append a previously performed parameter study in output directory (if available) ``` ``` niftymic_run_reconstruction_parameter_study \ --filenames path-to-stack-1.nii.gz ... path-to-stack-N.nii.gz \ --filenames-masks path-to-stack-1_mask.nii.gz ... path-to-stack-N_mask.nii.gz \ --dir-input-mc dir-to-motion_correction \ --dir-output dir-to-param-study-output \ --reconstruction-type HuberL2 \ --reference path-to-reference-volume.nii.gz \ # in case reference ("ground-truth") is available (reconstruction space is defined by this reference) --measures MAE RMSE PSNR NCC NMI SSIM \ # evaluate reconstruction similarities against reference --reference-mask path-to-reference-volume_mask.nii.gz \ # if given, evaluate similarities (--measures) on masked region only --alphas 0.001 0.003 0.005 0.001 0.003 \ # regularization parameters to sweep through --append # if given, append a previously performed parameter study in output directory (if available) ``` The results can be assessed by accessing the [NSoL][nsol]-script `show_parameter_study.py` via ``` niftymic_show_parameter_study \ --dir-input dir-to-param-study-output \ --study-name TK1L2 \ --dir-output-figures dir-to-figures ``` ### Automatic Segmentation and High-Resolution Reconstruction of Fetal Brain MRI An automated framework is implemented to obtain a high-resolution fetal brain MRI reconstruction in the standard anatomical planes (Figure 2). This includes two main subsequent blocks: 1. Automatic segmentation to generate fetal brain masks 2. Automatic high-resolution reconstruction. The latter is based on the work described in [EbnerWang2018][ebner-wang-2018] and [EbnerWang2020][ebner-wang-2020]. Compared to the segmentation approach proposed in [EbnerWang2020][ebner-wang-2020], a new automated segmentation tool has been included in the NiftyMIC package, called [MONAIfbs][monaifbs]. This implements a single-step segmentation approach based on the [dynUNet][dynUNet] implemented in [MONAI][monai]. The current NiftyMIC version is still compatible with the older segmentation pipeline based on the [fetal_brain_seg][fetal_brain_seg] package and presented in [EbnerWang2020][ebner-wang-2020]. Details on its use are available at [this wiki page][wikifetalbrainseg], although `MONAIfbs` is the recommended option. #### Automatic segmentation Provided the dependencies for `MONAIfbs` are [installed][niftymic-install], create the automatic fetal brain masks of HASTE-like images: ``` niftymic_segment_fetal_brains \ --filenames \ nifti/name-of-stack-1.nii.gz \ nifti/name-of-stack-2.nii.gz \ nifti/name-of-stack-N.nii.gz \ --filenames-masks \ seg/name-of-stack-1.nii.gz \ seg/name-of-stack-2.nii.gz \ seg/name-of-stack-N.nii.gz ``` #### Automatic reconstruction Afterwards, four consecutive steps including 1. bias field correction (`niftymic_correct_bias_field`), 1. subject-space reconstruction (`niftymic_reconstruct_volume`), 1. template-space alignment (`niftymic_register_image`), and 1. template-space reconstruction (`niftymic_reconstruct_volume_from_slices`) are performed to create a high-resolution fetal brain MRI reconstruction in the standard anatomical planes: ``` niftymic_run_reconstruction_pipeline \ --filenames \ nifti/name-of-stack-1.nii.gz \ nifti/name-of-stack-2.nii.gz \ nifti/name-of-stack-N.nii.gz \ --filenames-masks \ seg/name-of-stack-1.nii.gz \ seg/name-of-stack-2.nii.gz \ seg/name-of-stack-N.nii.gz \ --dir-output srr ``` Additional parameters such as the regularization parameter `alpha` can be specified too. For more information please execute `niftymic_run_reconstruction_pipeline -h`. *Note*: In case a suffix distinguishes image segmentation (`--filenames-masks`) from the associated image filenames (`--filenames`), the argument `--suffix-mask` needs to be provided for reconstructing the HR brain volume mask as part of the pipeline. E.g. if images `name-of-stack-i.nii.gz` are associated with the mask `name-of-stack-i_mask.nii.gz`, then the additional argument `--suffix-mask _mask` needs to be specified. ### NiftyMIC applied to Fetal Brain Functional MRI An extension of NiftyMIC for fetal functional MRI is described in [Sobotka2022][sobotka-2022]:

Figure 3: Overview of the proposed motion correction and volumetric reconstruction algorithm for rs-fMRI. With the first n=15 (default) time points a HR reference volume with outlier rejection is estimated (Ebner, Wang et al., 2020). Afterwards each slice of a time point is registered to the HR reference volume following which individual time points are reconstructed using Huber L2 regularization.

Figure 4: Qualitative comparison of the original low-resolution input sequence (top row) and the obtained volumetric reconstruction of the functional MRI (bottom row) in patient-specific orientation. A sequence of axial stacks were used as input.

A recommended workflow is [associated applications in square brackets]: 1. Volumetric segmentation of the fetal brain for all input images in the sequence. We tested the algorithm with fetal functional brains masks created using the Brain Extraction Tool incorporated in the [FSL Toolbox][fsl] (Smith et al. 2002). 1. Motion estimation [`rsfmri_estimate_motion`] ``` rsfmri_estimate_motion \ --filename path-to-bold.nii.gz \ --filename-mask path-to-bold_mask.nii.gz \ --dir-output path-to-dir-output ``` 1. Functional volumetric reconstruction [`rsfmri_reconstruct_volume_from_slices`] An example for a basic usage reads ``` rsfmri_reconstruct_volume_from_slices \ --filename path-to-bold.nii.gz \ --filename-mask path-to-bold_mask.nii.gz \ --dir-input-mc path-to-motion_correction \ # created in `dir-output` in step 2 above --output path-to-bold_reconstructed.nii.gz ``` A more elaborate example using a different reconstruction approach `HuberL2` could be ``` rsfmri_reconstruct_volume_from_slices \ --filename path-to-bold.nii.gz \ --filename-mask path-to-bold_mask.nii.gz \ --dir-input-mc path-to-motion_correction \ # created in `dir-output` in step 2 above --output path-to-bold_reconstructed.nii.gz \ --reconstruction-type HuberL2 --alpha 0.1 \ --iter-max 20 ``` If you have any questions or comments with regards to the use of NiftyMIC for functional MRI, please drop an email to `daniel.sobotka@meduniwien.ac.at`. ## Licensing and Copyright Copyright (c) 2022 Michael Ebner and contributors. This framework is made available as free open-source software under the [BSD-3-Clause License][bsd]. Other licenses may apply for dependencies. ## Funding This work is partially funded by the UCL [Engineering and Physical Sciences Research Council (EPSRC)][epsrc] Centre for Doctoral Training in Medical Imaging (EP/L016478/1), the Innovative Engineering for Health award ([Wellcome Trust][wellcometrust] [WT101957] and [EPSRC][epsrc] [NS/A000027/1]), and supported by researchers at the [National Institute for Health Research][nihr] [University College London Hospitals (UCLH)][uclh] Biomedical Research Centre. ## References Selected publications associated with NiftyMIC are: * [[Sobotka2022]][sobotka-2022] Sobotka, D., Ebner, M., Schwartz, E., Nenning, K.-H., Taymourtash, A., Vercauteren, T., Ourselin, S., Kasprian, G., Prayer, D., Langs, G., Licandro, R. (2022). Motion Correction and Volumetric Reconstruction for Fetal fMRI. arXiv. * [[EbnerWang2020]][ebner-wang-2020] Ebner, M., Wang, G., Li, W., Aertsen, M., Patel, P. A., Aughwane, R., Melbourne, A., Doel, T., Dymarkowski, S., De Coppi, P., David, A. L., Deprest, J., Ourselin, S., Vercauteren, T. (2020). An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI. NeuroImage, 206, 116324. * [[Ebner2019]](https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.27852) Ebner, M., Patel, P. A., Atkinson, D., Caselton, C., Firmin, F., Amin, Z., Bainbridge, A., De Coppi, P., Taylor, S. A., Ourselin, S., Chouhan, M. D., Vercauteren, T. (2019). Super‐resolution for upper abdominal MRI: Acquisition and post‐processing protocol optimization using brain MRI control data and expert reader validation. Magnetic Resonance in Medicine, 82(5), 1905–1919. * [[Sobotka2019]](http://link.springer.com/10.1007/978-3-030-32875-7_14) Sobotka, D., Licandro, R., Ebner, M., Schwartz, E., Vercauteren, T., Ourselin, S., Kasprian, G., Prayer, D., Langs, G. (2019). Reproducibility of Functional Connectivity Estimates in Motion Corrected Fetal fMRI. Smart Ultrasound Imaging and Perinatal, Preterm and Paediatric Image Analysis (pp. 123–132). Cham: Springer International Publishing. * [[EbnerWang2018]][ebner-wang-2018] Ebner, M., Wang, G., Li, W., Aertsen, M., Patel, P. A., Melbourne, A., Doel, T., David, A. L., Deprest, J., Ourselin, S., Vercauteren, T. (2018). An Automated Localization, Segmentation and Reconstruction Framework for Fetal Brain MRI. In Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2018 (pp. 313–320). Springer * [[Ebner2018]](https://www.sciencedirect.com/science/article/pii/S1053811917308042) Ebner, M., Chung, K. K., Prados, F., Cardoso, M. J., Chard, D. T., Vercauteren, T., Ourselin, S. (2018). Volumetric reconstruction from printed films: Enabling 30 year longitudinal analysis in MR neuroimaging. NeuroImage, 165, 238–250. * [[Ranzini2017]](https://mski2017.files.wordpress.com/2017/09/miccai-mski2017.pdf) Ranzini, M. B., Ebner, M., Cardoso, M. J., Fotiadou, A., Vercauteren, T., Henckel, J., Hart, A., Ourselin, S., and Modat, M. (2017). Joint Multimodal Segmentation of Clinical CT and MR from Hip Arthroplasty Patients. MICCAI Workshop on Computational Methods and Clinical Applications in Musculoskeletal Imaging (MSKI) 2017. * [[Ebner2017]](https://link.springer.com/chapter/10.1007%2F978-3-319-52280-7_1) Ebner, M., Chouhan, M., Patel, P. A., Atkinson, D., Amin, Z., Read, S., Punwani, S., Taylor, S., Vercauteren, T., Ourselin, S. (2017). Point-Spread-Function-Aware Slice-to-Volume Registration: Application to Upper Abdominal MRI Super-Resolution. In Zuluaga, M. A., Bhatia, K., Kainz, B., Moghari, M. H., and Pace, D. F., editors, Reconstruction, Segmentation, and Analysis of Medical Images. RAMBO 2016, volume 10129 of Lecture Notes in Computer Science, pages 3–13. Springer International Publishing. [bsd]: https://opensource.org/licenses/BSD-3-Clause [cir]: https://www.cir.meduniwien.ac.at/ [cmic]: http://cmic.cs.ucl.ac.uk [dynUNet]: https://github.com/Project-MONAI/tutorials/blob/master/modules/dynunet_tutorial.ipynb [ebner-wang-2018]: http://link.springer.com/10.1007/978-3-030-00928-1_36 [ebner-wang-2020]: https://www.sciencedirect.com/science/article/pii/S1053811919309152 [epsrc]: http://www.epsrc.ac.uk [fetal_brain_seg]: https://github.com/gift-surg/fetal_brain_seg [fsl]: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET [gholipour_atlas]: https://www.nature.com/articles/s41598-017-00525-w [giftsurg]: http://www.gift-surg.ac.uk [guarantors]: https://guarantorsofbrain.org/ [itkniftymic]: https://github.com/gift-surg/ITK_NiftyMIC/wikis/home [kcl]: https://www.kcl.ac.uk [martaranzini]: https://www.linkedin.com/in/marta-bianca-maria-ranzini [mebner]: https://www.linkedin.com/in/ebnermichael [monai]: https://monai.io/ [monaifbs]: https://github.com/gift-surg/MONAIfbs [mssociety]: https://www.mssociety.org.uk/ [muw]: https://www.meduniwien.ac.at [niftymic-docker]: https://hub.docker.com/r/renbem/niftymic [niftymic-install]: https://github.com/gift-surg/NiftyMIC/wikis/niftymic-installation [niftymic-vm]: https://github.com/gift-surg/NiftyMIC/wiki/niftymic-virtualbox [nihr]: http://www.nihr.ac.uk/research [nsol]: https://github.com/gift-surg/NSoL [pysitk]: https://github.com/gift-surg/PySiTK [sie]: https://www.kcl.ac.uk/bmeis/our-departments/surgical-interventional-engineering [simplereg-dependencies]: https://github.com/gift-surg/SimpleReg/wikis/simplereg-dependencies [simplereg]: https://github.com/gift-surg/SimpleReg [sobotka-2022]: https://arxiv.org/abs/2202.05863 [ucl]: http://www.ucl.ac.uk [uclh]: http://www.uclh.nhs.uk [weiss]: https://www.ucl.ac.uk/interventional-surgical-sciences [wellcometrust]: http://www.wellcome.ac.uk [wikifetalbrainseg]: https://github.com/gift-surg/NiftyMIC/wiki/Legacy-Segmentation-Tool-(fetal_brain_seg) ================================================ FILE: data/templates/LICENSE ================================================ CRL (Computational Radiology Laboratory) hereby grants a license to use, including the right to share, copy, distribute, and transmit, the information, images and data that appears on this webpage solely for non-commercial educational and research purposes, subject to the following restrictions: (1) You must at all times acknowledge and attribute ownership of the information, images and data to CRL, including reproducing CRL's copyright to the extent that the same appears thereon; for publications referencing the fetal structural atlas, cite Gholipour et al., Scientific Reports, 2017; for publications referencing the DTI atlas, cite Khan et al., NeuroImage, 2018 and Khan et al., MICCAI, 2018 (full citations found on the Fetal Brain Atlas webpage); and (2) You may not post the information, images and data on any website, electronic bulletin board or any other electronic medium without the express written permission of CRL or required acknowledgements. As the information, images and data is experimental in nature and is being provided solely to facilitate academic and scientific research, you agree that you will use this information, images and data at your own risk and without liability of any kind to CRL. CRL MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESSED OR IMPLIED WITH RESPECT TO THE INFORMATION, IMAGES AND DATA, AND THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Use of the information, images or data for any commercial purposes is strictly prohibited without the express written consent of CRL. By requesting access through submitting this form, you acknowledge that you understand and accept all the terms and conditions in this license agreement. ================================================ FILE: data/templates/README ================================================ 2016 Fetal Brain Atlas Copyright 2016, Computational Radiology Lab, Boston Childrens Hospital Contact: Ali Gholipour: Ali.Gholipour@childrens.harvard.edu Clemente Velasco-Annis: Clemente.Velasco-Annis@childrens.harvard.edu This version of the Spatio-Temporal Atlas (STA) was last edited on 11/21/16 This spatio-temporal atlas and the included parcellations are not intended for medical use and have no warranty. Structures received varying amounts of attention and refinement based on the research goals at the time of creation and thus no guarantees can be made regarding the accuracy or precision of the segmentations, nor the withholding to any particular labeling convention or protocol between structures. Any output derived from the use of these atlases or parcellations shouled be checked in order to validate the accuracy of the results. # # # # # # # # # # # # # # # # # # # # # # New to this update (11/21/16) "Olympic edition": CHANGES TO LABELING SCHEME: The parcellation scheme (label numbers) has been reorganized All atlas images now share the same label key The full key can be found below Left and right white matter have been separated into separate labels Labels for left and right internal capsule have been added to all images REFINEMENT TO PARCELLATIONS: "Miscellanous_brain_tissue" has been mostly removed as most of the label was internal capsule Developing white matter zones (SP, IZ & VZ) have been removed from STA31-33 because they were not felt to be accurate (differentiation between layers was arbitrary) *There are two versions of the STA30 parcellation, one with developing white matter zones, one without* Cortical plate was reduced in the region anterior to the corpus callosum (reduced the portion "wrapping" into hemisphere) Subplate has been expanded to the appropriate width as per reviewer feedback The intermediate zone/ventricular zone has been edited to shrink the ventricular zone in line with reviewer feedback Deep gray matter structures have been edited to increase segmentation consistency between gestational ages # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # New to this update (06/07/16): White and gray cerebellum have been recombined because we could not ensure the accuracy of the delineation (very little refinement had been done since initial propagation of the parcellation scheme to this atlas). The files have been renamed slightly. # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # New to this update (03/30/16): ADDED TEMPLATES: There are now atlas images and labels for gestational age (GA) weeks 21-37. DEVELOPING WHITE MATTER ZONES: Labels for developing white matter zones have been added for GA 21-33 This includes left and right "ventricular zone", "intermediate zone" (similar to subventricular zone), and "subplate" In these images, label 51 is now "miscellaneous brain tissue", mostly deep gray matter found between the larger subcortical structures Images with the labeling convention are marked with "wmz"; for example, STA27_WMZparc.nii.gz There are two versions of labels for STA31, STA32, and STA33 STA31_parc.nii.gz = All white matter is label 51 STA31_WMZparc.nii.gz = Developing white matter layers have been separated into miscellaneous brain tissue (#51), subplate (#73,74), intermediate zone (#75,76), and ventricular zone (#77,78) Note: As the white matter homogenizes in composition during development, the visual differentiation between the layers also decreases. Because of this the accuracy of the developmental layers may not be great for the older brains (i.e. STA30-33). This primarily pertains to the border between intermediate zone and subplate. ADDITIONAL ADDED LABELS: #5: Hippocampal commisure #6: Fornix LABEL REFINEMENTS: Many of the labels have been refined to increase accuracy, in particular: hippocampus caudate thalamus lentiform corpus callosum cortical plate # # # # # # # # # # # # # # # # # # # # # # Label key (all images): 37 Hippocampus_L 38 Hippocampus_R 41 Amygdala_L 42 Amygdala_R 71 Caudate_L 72 Caudate_R 73 Lentiform_L 74 Lentiform_R 77 Thalamus_L 78 Thalamus_R 91 CorpusCallosum 92 Lateral_Ventricle_L 93 Lateral_Ventricle_R 94 Brainstem 100 Cerebellum_L 101 Cerebellum_R 108 Subthalamic_Nuc_L 109 Subthalamic_Nuc_R 110 Hippocampal_Comm 111 Fornix 112 Cortical_Plate_L 113 Cortical_Plate_R 114 Subplate_L 115 Subplate_R 116 Inter_Zone_L 117 Inter_Zone_R 118 Vent_Zone_L 119 Vent_Zone_R 120 White_Matter_L 121 White_Matter_R 122 Internal_Capsule_L 123 Internal_Capsule_R 124 CSF 125 Misc # # # # # # # # # # # # # # # # # # # # # # Michael Ebner, Feb 16, 2018: - All image headers have been updated using fslreorient2std using `for i in *.nii.gz; do echo $i; fslreorient2std $i $i; done` - _mask: binarized image labels - _mask_dil: dilated binary masks; applied to SRR it approximates brain tissue only - templates_info.json: Additional information on templates like volume ================================================ FILE: data/templates/templates_info.json ================================================ { "21": { "image": "STA21.nii.gz", "mask": "STA21_mask.nii.gz", "mask_dil": "STA21_mask_dil.nii.gz", "volume_mask": 89246.38487071976, "volume_mask_dil": 120038.46124333153 }, "22": { "image": "STA22.nii.gz", "mask": "STA22_mask.nii.gz", "mask_dil": "STA22_mask_dil.nii.gz", "volume_mask": 101490.30689354343, "volume_mask_dil": 134909.44540126887 }, "23": { "image": "STA23.nii.gz", "mask": "STA23_mask.nii.gz", "mask_dil": "STA23_mask_dil.nii.gz", "volume_mask": 106235.50507484014, "volume_mask_dil": 140715.503598928 }, "24": { "image": "STA24.nii.gz", "mask": "STA24_mask.nii.gz", "mask_dil": "STA24_mask_dil.nii.gz", "volume_mask": 130878.99653601555, "volume_mask_dil": 170357.1202916332 }, "25": { "image": "STA25.nii.gz", "mask": "STA25_mask.nii.gz", "mask_dil": "STA25_mask_dil.nii.gz", "volume_mask": 178492.25774336213, "volume_mask_dil": 227175.59493246424 }, "26": { "image": "STA26.nii.gz", "mask": "STA26_mask.nii.gz", "mask_dil": "STA26_mask_dil.nii.gz", "volume_mask": 201635.08283969283, "volume_mask_dil": 253806.15093200956 }, "27": { "image": "STA27.nii.gz", "mask": "STA27_mask.nii.gz", "mask_dil": "STA27_mask_dil.nii.gz", "volume_mask": 210435.81779203523, "volume_mask_dil": 263941.1528740433 }, "28": { "image": "STA28.nii.gz", "mask": "STA28_mask.nii.gz", "mask_dil": "STA28_mask_dil.nii.gz", "volume_mask": 233175.18840337868, "volume_mask_dil": 290329.5337829808 }, "29": { "image": "STA29.nii.gz", "mask": "STA29_mask.nii.gz", "mask_dil": "STA29_mask_dil.nii.gz", "volume_mask": 257051.194746539, "volume_mask_dil": 317684.56706204003 }, "30": { "image": "STA30.nii.gz", "mask": "STA30_mask.nii.gz", "mask_dil": "STA30_mask_dil.nii.gz", "volume_mask": 282285.5319890282, "volume_mask_dil": 346364.6513653975 }, "31": { "image": "STA31.nii.gz", "mask": "STA31_mask.nii.gz", "mask_dil": "STA31_mask_dil.nii.gz", "volume_mask": 312587.62620157294, "volume_mask_dil": 380993.6413300073 }, "32": { "image": "STA32.nii.gz", "mask": "STA32_mask.nii.gz", "mask_dil": "STA32_mask_dil.nii.gz", "volume_mask": 340744.4484698328, "volume_mask_dil": 413634.54276009236 }, "33": { "image": "STA33.nii.gz", "mask": "STA33_mask.nii.gz", "mask_dil": "STA33_mask_dil.nii.gz", "volume_mask": 356126.40670901025, "volume_mask_dil": 430765.4864316511 }, "34": { "image": "STA34.nii.gz", "mask": "STA34_mask.nii.gz", "mask_dil": "STA34_mask_dil.nii.gz", "volume_mask": 392819.77292167663, "volume_mask_dil": 472869.6483262277 }, "35": { "image": "STA35.nii.gz", "mask": "STA35_mask.nii.gz", "mask_dil": "STA35_mask_dil.nii.gz", "volume_mask": 418491.86852033855, "volume_mask_dil": 502023.33085117553 }, "36": { "image": "STA36.nii.gz", "mask": "STA36_mask.nii.gz", "mask_dil": "STA36_mask_dil.nii.gz", "volume_mask": 422497.7414778769, "volume_mask_dil": 506874.512634493 }, "37": { "image": "STA37.nii.gz", "mask": "STA37_mask.nii.gz", "mask_dil": "STA37_mask_dil.nii.gz", "volume_mask": 390531.14151572104, "volume_mask_dil": 470833.9439705052 } } ================================================ FILE: doc/doxyfile ================================================ # Doxyfile 1.8.9.1 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project. # # All text after a double hash (##) is considered a comment and is placed in # front of the TAG it is preceding. # # All text after a single hash (#) is considered a comment and will be ignored. # The format is: # TAG = value [value, ...] # For lists, items can also be appended using: # TAG += value [value, ...] # Values that contain spaces should be placed between quotes (\" \"). #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- # This tag specifies the encoding used for all characters in the config file # that follow. The default is UTF-8 which is also the encoding used for all text # before the first occurrence of this tag. Doxygen uses libiconv (or the iconv # built into libc) for the transcoding. See http://www.gnu.org/software/libiconv # for the list of possible encodings. # The default value is: UTF-8. DOXYFILE_ENCODING = UTF-8 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded by # double-quotes, unless you are using Doxywizard) that should identify the # project for which the documentation is generated. This name is used in the # title of most generated pages and in a few other places. # The default value is: My Project. PROJECT_NAME = "Motion Correction and Volumetric Image Reconstruction of 2D Ultra-fast MRI" # The PROJECT_NUMBER tag can be used to enter a project or revision number. This # could be handy for archiving the generated documentation or if some version # control system is used. PROJECT_NUMBER = # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a # quick idea about the purpose of the project. Keep the description short. PROJECT_BRIEF = # With the PROJECT_LOGO tag one can specify a logo or an icon that is included # in the documentation. The maximum height of the logo should not exceed 55 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy # the logo to the output directory. PROJECT_LOGO = # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path # into which the generated documentation will be written. If a relative path is # entered, it will be relative to the location where doxygen was started. If # left blank the current directory will be used. OUTPUT_DIRECTORY = "./" # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- # directories (in 2 levels) under the output directory of each output format and # will distribute the generated files over these directories. Enabling this # option can be useful when feeding doxygen a huge amount of source files, where # putting all generated files in the same directory would otherwise causes # performance problems for the file system. # The default value is: NO. CREATE_SUBDIRS = NO # If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII # characters to appear in the names of generated files. If set to NO, non-ASCII # characters will be escaped, for example _xE3_x81_x84 will be used for Unicode # U+3044. # The default value is: NO. ALLOW_UNICODE_NAMES = NO # The OUTPUT_LANGUAGE tag is used to specify the language in which all # documentation generated by doxygen is written. Doxygen will use this # information to generate all constant output in the proper language. # Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, # Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), # Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, # Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), # Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, # Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, # Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, # Ukrainian and Vietnamese. # The default value is: English. OUTPUT_LANGUAGE = English # If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member # descriptions after the members that are listed in the file and class # documentation (similar to Javadoc). Set to NO to disable this. # The default value is: YES. BRIEF_MEMBER_DESC = YES # If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief # description of a member or function before the detailed description # # Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the # brief descriptions will be completely suppressed. # The default value is: YES. REPEAT_BRIEF = YES # This tag implements a quasi-intelligent brief description abbreviator that is # used to form the text in various listings. Each string in this list, if found # as the leading text of the brief description, will be stripped from the text # and the result, after processing the whole list, is used as the annotated # text. Otherwise, the brief description is used as-is. If left blank, the # following values are used ($name is automatically replaced with the name of # the entity):The $name class, The $name widget, The $name file, is, provides, # specifies, contains, represents, a, an and the. ABBREVIATE_BRIEF = "The $name class" \ "The $name widget" \ "The $name file" \ is \ provides \ specifies \ contains \ represents \ a \ an \ the # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then # doxygen will generate a detailed section even if there is only a brief # description. # The default value is: NO. ALWAYS_DETAILED_SEC = NO # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all # inherited members of a class in the documentation of that class as if those # members were ordinary class members. Constructors, destructors and assignment # operators of the base classes will not be shown. # The default value is: NO. INLINE_INHERITED_MEMB = YES # If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path # before files name in the file list and in the header files. If set to NO the # shortest path that makes the file name unique will be used # The default value is: YES. FULL_PATH_NAMES = YES # The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. # Stripping is only done if one of the specified strings matches the left-hand # part of the path. The tag can be used to show relative paths in the file list. # If left blank the directory from which doxygen is run is used as the path to # strip. # # Note that you can specify absolute paths here, but also relative paths, which # will be relative from the directory where doxygen is started. # This tag requires that the tag FULL_PATH_NAMES is set to YES. STRIP_FROM_PATH = # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the # path mentioned in the documentation of a class, which tells the reader which # header file to include in order to use a class. If left blank only the name of # the header file containing the class definition is used. Otherwise one should # specify the list of include paths that are normally passed to the compiler # using the -I flag. STRIP_FROM_INC_PATH = # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but # less readable) file names. This can be useful is your file systems doesn't # support long names like on DOS, Mac, or CD-ROM. # The default value is: NO. SHORT_NAMES = NO # If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the # first line (until the first dot) of a Javadoc-style comment as the brief # description. If set to NO, the Javadoc-style will behave just like regular Qt- # style comments (thus requiring an explicit @brief command for a brief # description.) # The default value is: NO. JAVADOC_AUTOBRIEF = NO # If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first # line (until the first dot) of a Qt-style comment as the brief description. If # set to NO, the Qt-style will behave just like regular Qt-style comments (thus # requiring an explicit \brief command for a brief description.) # The default value is: NO. QT_AUTOBRIEF = NO # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a # multi-line C++ special comment block (i.e. a block of //! or /// comments) as # a brief description. This used to be the default behavior. The new default is # to treat a multi-line C++ comment block as a detailed description. Set this # tag to YES if you prefer the old behavior instead. # # Note that setting this tag to YES also means that rational rose comments are # not recognized any more. # The default value is: NO. MULTILINE_CPP_IS_BRIEF = NO # If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the # documentation from any documented member that it re-implements. # The default value is: YES. INHERIT_DOCS = YES # If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new # page for each member. If set to NO, the documentation of a member will be part # of the file/class/namespace that contains it. # The default value is: NO. SEPARATE_MEMBER_PAGES = NO # The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen # uses this value to replace tabs by spaces in code fragments. # Minimum value: 1, maximum value: 16, default value: 4. TAB_SIZE = 4 # This tag can be used to specify a number of aliases that act as commands in # the documentation. An alias has the form: # name=value # For example adding # "sideeffect=@par Side Effects:\n" # will allow you to put the command \sideeffect (or @sideeffect) in the # documentation, which will result in a user-defined paragraph with heading # "Side Effects:". You can put \n's in the value part of an alias to insert # newlines. ALIASES = # This tag can be used to specify a number of word-keyword mappings (TCL only). # A mapping has the form "name=value". For example adding "class=itcl::class" # will allow you to use the command class in the itcl::class meaning. TCL_SUBST = # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources # only. Doxygen will then generate output that is more tailored for C. For # instance, some of the names that are used will be different. The list of all # members will be omitted, etc. # The default value is: NO. OPTIMIZE_OUTPUT_FOR_C = NO # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or # Python sources only. Doxygen will then generate output that is more tailored # for that language. For instance, namespaces will be presented as packages, # qualified scopes will look different, etc. # The default value is: NO. OPTIMIZE_OUTPUT_JAVA = YES # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran # sources. Doxygen will then generate output that is tailored for Fortran. # The default value is: NO. OPTIMIZE_FOR_FORTRAN = NO # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL # sources. Doxygen will then generate output that is tailored for VHDL. # The default value is: NO. OPTIMIZE_OUTPUT_VHDL = NO # Doxygen selects the parser to use depending on the extension of the files it # parses. With this tag you can assign which parser to use for a given # extension. Doxygen has a built-in mapping, but you can override or extend it # using this tag. The format is ext=language, where ext is a file extension, and # language is one of the parsers supported by doxygen: IDL, Java, Javascript, # C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: # FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: # Fortran. In the later case the parser tries to guess whether the code is fixed # or free formatted code, this is the default for Fortran type files), VHDL. For # instance to make doxygen treat .inc files as Fortran files (default is PHP), # and .f files as C (default is Fortran), use: inc=Fortran f=C. # # Note: For files without extension you can use no_extension as a placeholder. # # Note that for custom extensions you also need to set FILE_PATTERNS otherwise # the files are not read by doxygen. EXTENSION_MAPPING = # If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments # according to the Markdown format, which allows for more readable # documentation. See http://daringfireball.net/projects/markdown/ for details. # The output of markdown processing is further processed by doxygen, so you can # mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in # case of backward compatibilities issues. # The default value is: YES. MARKDOWN_SUPPORT = YES # When enabled doxygen tries to link words that correspond to documented # classes, or namespaces to their corresponding documentation. Such a link can # be prevented in individual cases by putting a % sign in front of the word or # globally by setting AUTOLINK_SUPPORT to NO. # The default value is: YES. AUTOLINK_SUPPORT = YES # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want # to include (a tag file for) the STL sources as input, then you should set this # tag to YES in order to let doxygen match functions declarations and # definitions whose arguments contain STL classes (e.g. func(std::string); # versus func(std::string) {}). This also make the inheritance and collaboration # diagrams that involve STL classes more complete and accurate. # The default value is: NO. BUILTIN_STL_SUPPORT = NO # If you use Microsoft's C++/CLI language, you should set this option to YES to # enable parsing support. # The default value is: NO. CPP_CLI_SUPPORT = NO # Set the SIP_SUPPORT tag to YES if your project consists of sip (see: # http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen # will parse them like normal C++ but will assume all classes use public instead # of private inheritance when no explicit protection keyword is present. # The default value is: NO. SIP_SUPPORT = NO # For Microsoft's IDL there are propget and propput attributes to indicate # getter and setter methods for a property. Setting this option to YES will make # doxygen to replace the get and set methods by a property in the documentation. # This will only work if the methods are indeed getting or setting a simple # type. If this is not the case, or you want to show the methods anyway, you # should set this option to NO. # The default value is: YES. IDL_PROPERTY_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC # tag is set to YES then doxygen will reuse the documentation of the first # member in the group (if any) for the other members of the group. By default # all members of a group must be documented explicitly. # The default value is: NO. DISTRIBUTE_GROUP_DOC = NO # Set the SUBGROUPING tag to YES to allow class member groups of the same type # (for instance a group of public functions) to be put as a subgroup of that # type (e.g. under the Public Functions section). Set it to NO to prevent # subgrouping. Alternatively, this can be done per class using the # \nosubgrouping command. # The default value is: YES. SUBGROUPING = YES # When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions # are shown inside the group in which they are included (e.g. using \ingroup) # instead of on a separate page (for HTML and Man pages) or section (for LaTeX # and RTF). # # Note that this feature does not work in combination with # SEPARATE_MEMBER_PAGES. # The default value is: NO. INLINE_GROUPED_CLASSES = NO # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions # with only public data fields or simple typedef fields will be shown inline in # the documentation of the scope in which they are defined (i.e. file, # namespace, or group documentation), provided this scope is documented. If set # to NO, structs, classes, and unions are shown on a separate page (for HTML and # Man pages) or section (for LaTeX and RTF). # The default value is: NO. INLINE_SIMPLE_STRUCTS = NO # When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or # enum is documented as struct, union, or enum with the name of the typedef. So # typedef struct TypeS {} TypeT, will appear in the documentation as a struct # with name TypeT. When disabled the typedef will appear as a member of a file, # namespace, or class. And the struct will be named TypeS. This can typically be # useful for C code in case the coding convention dictates that all compound # types are typedef'ed and only the typedef is referenced, never the tag name. # The default value is: NO. TYPEDEF_HIDES_STRUCT = NO # The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This # cache is used to resolve symbols given their name and scope. Since this can be # an expensive process and often the same symbol appears multiple times in the # code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small # doxygen will become slower. If the cache is too large, memory is wasted. The # cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range # is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 # symbols. At the end of a run doxygen will report the cache usage and suggest # the optimal cache size from a speed point of view. # Minimum value: 0, maximum value: 9, default value: 0. LOOKUP_CACHE_SIZE = 0 #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- # If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in # documentation are documented, even if no documentation was available. Private # class members and static file members will be hidden unless the # EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. # Note: This will also disable the warnings about undocumented members that are # normally produced when WARNINGS is set to YES. # The default value is: NO. EXTRACT_ALL = YES # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will # be included in the documentation. # The default value is: NO. EXTRACT_PRIVATE = YES # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal # scope will be included in the documentation. # The default value is: NO. EXTRACT_PACKAGE = YES # If the EXTRACT_STATIC tag is set to YES, all static members of a file will be # included in the documentation. # The default value is: NO. EXTRACT_STATIC = YES # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined # locally in source files will be included in the documentation. If set to NO, # only classes defined in header files are included. Does not have any effect # for Java sources. # The default value is: YES. EXTRACT_LOCAL_CLASSES = YES # This flag is only useful for Objective-C code. If set to YES, local methods, # which are defined in the implementation section but not in the interface are # included in the documentation. If set to NO, only methods in the interface are # included. # The default value is: NO. EXTRACT_LOCAL_METHODS = YES # If this flag is set to YES, the members of anonymous namespaces will be # extracted and appear in the documentation as a namespace called # 'anonymous_namespace{file}', where file will be replaced with the base name of # the file that contains the anonymous namespace. By default anonymous namespace # are hidden. # The default value is: NO. EXTRACT_ANON_NSPACES = NO # If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all # undocumented members inside documented classes or files. If set to NO these # members will be included in the various overviews, but no documentation # section is generated. This option has no effect if EXTRACT_ALL is enabled. # The default value is: NO. HIDE_UNDOC_MEMBERS = NO # If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all # undocumented classes that are normally visible in the class hierarchy. If set # to NO, these classes will be included in the various overviews. This option # has no effect if EXTRACT_ALL is enabled. # The default value is: NO. HIDE_UNDOC_CLASSES = NO # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend # (class|struct|union) declarations. If set to NO, these declarations will be # included in the documentation. # The default value is: NO. HIDE_FRIEND_COMPOUNDS = NO # If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any # documentation blocks found inside the body of a function. If set to NO, these # blocks will be appended to the function's detailed documentation block. # The default value is: NO. HIDE_IN_BODY_DOCS = NO # The INTERNAL_DOCS tag determines if documentation that is typed after a # \internal command is included. If the tag is set to NO then the documentation # will be excluded. Set it to YES to include the internal documentation. # The default value is: NO. INTERNAL_DOCS = NO # If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file # names in lower-case letters. If set to YES, upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows # and Mac users are advised to set this option to NO. # The default value is: system dependent. CASE_SENSE_NAMES = NO # If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with # their full class and namespace scopes in the documentation. If set to YES, the # scope will be hidden. # The default value is: NO. HIDE_SCOPE_NAMES = NO # If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will # append additional text to a page's title, such as Class Reference. If set to # YES the compound reference will be hidden. # The default value is: NO. HIDE_COMPOUND_REFERENCE= NO # If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of # the files that are included by a file in the documentation of that file. # The default value is: YES. SHOW_INCLUDE_FILES = YES # If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each # grouped member an include statement to the documentation, telling the reader # which file to include in order to use the member. # The default value is: NO. SHOW_GROUPED_MEMB_INC = NO # If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include # files with double quotes in the documentation rather than with sharp brackets. # The default value is: NO. FORCE_LOCAL_INCLUDES = NO # If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the # documentation for inline members. # The default value is: YES. INLINE_INFO = YES # If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the # (detailed) documentation of file and class members alphabetically by member # name. If set to NO, the members will appear in declaration order. # The default value is: YES. SORT_MEMBER_DOCS = YES # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief # descriptions of file, namespace and class members alphabetically by member # name. If set to NO, the members will appear in declaration order. Note that # this will also influence the order of the classes in the class list. # The default value is: NO. SORT_BRIEF_DOCS = NO # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the # (brief and detailed) documentation of class members so that constructors and # destructors are listed first. If set to NO the constructors will appear in the # respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. # Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief # member documentation. # Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting # detailed member documentation. # The default value is: NO. SORT_MEMBERS_CTORS_1ST = NO # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy # of group names into alphabetical order. If set to NO the group names will # appear in their defined order. # The default value is: NO. SORT_GROUP_NAMES = NO # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by # fully-qualified names, including namespaces. If set to NO, the class list will # be sorted only by class name, not including the namespace part. # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. # Note: This option applies only to the class list, not to the alphabetical # list. # The default value is: NO. SORT_BY_SCOPE_NAME = NO # If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper # type resolution of all parameters of a function it will reject a match between # the prototype and the implementation of a member function even if there is # only one candidate or it is obvious which candidate to choose by doing a # simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still # accept a match between prototype and implementation in such cases. # The default value is: NO. STRICT_PROTO_MATCHING = NO # The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo # list. This list is created by putting \todo commands in the documentation. # The default value is: YES. GENERATE_TODOLIST = YES # The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test # list. This list is created by putting \test commands in the documentation. # The default value is: YES. GENERATE_TESTLIST = YES # The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug # list. This list is created by putting \bug commands in the documentation. # The default value is: YES. GENERATE_BUGLIST = YES # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) # the deprecated list. This list is created by putting \deprecated commands in # the documentation. # The default value is: YES. GENERATE_DEPRECATEDLIST= YES # The ENABLED_SECTIONS tag can be used to enable conditional documentation # sections, marked by \if ... \endif and \cond # ... \endcond blocks. ENABLED_SECTIONS = # The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the # initial value of a variable or macro / define can have for it to appear in the # documentation. If the initializer consists of more lines than specified here # it will be hidden. Use a value of 0 to hide initializers completely. The # appearance of the value of individual variables and macros / defines can be # controlled using \showinitializer or \hideinitializer command in the # documentation regardless of this setting. # Minimum value: 0, maximum value: 10000, default value: 30. MAX_INITIALIZER_LINES = 30 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated at # the bottom of the documentation of classes and structs. If set to YES, the # list will mention the files that were used to generate the documentation. # The default value is: YES. SHOW_USED_FILES = YES # Set the SHOW_FILES tag to NO to disable the generation of the Files page. This # will remove the Files entry from the Quick Index and from the Folder Tree View # (if specified). # The default value is: YES. SHOW_FILES = YES # Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces # page. This will remove the Namespaces entry from the Quick Index and from the # Folder Tree View (if specified). # The default value is: YES. SHOW_NAMESPACES = YES # The FILE_VERSION_FILTER tag can be used to specify a program or script that # doxygen should invoke to get the current version for each file (typically from # the version control system). Doxygen will invoke the program by executing (via # popen()) the command command input-file, where command is the value of the # FILE_VERSION_FILTER tag, and input-file is the name of an input file provided # by doxygen. Whatever the program writes to standard output is used as the file # version. For an example see the documentation. FILE_VERSION_FILTER = # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed # by doxygen. The layout file controls the global structure of the generated # output files in an output format independent way. To create the layout file # that represents doxygen's defaults, run doxygen with the -l option. You can # optionally specify a file name after the option, if omitted DoxygenLayout.xml # will be used as the name of the layout file. # # Note that if you run doxygen from a directory containing a file called # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE # tag is left empty. LAYOUT_FILE = # The CITE_BIB_FILES tag can be used to specify one or more bib files containing # the reference definitions. This must be a list of .bib files. The .bib # extension is automatically appended if omitted. This requires the bibtex tool # to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. # For LaTeX the style of the bibliography can be controlled using # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the # search path. See also \cite for info how to create references. CITE_BIB_FILES = #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages #--------------------------------------------------------------------------- # The QUIET tag can be used to turn on/off the messages that are generated to # standard output by doxygen. If QUIET is set to YES this implies that the # messages are off. # The default value is: NO. QUIET = NO # The WARNINGS tag can be used to turn on/off the warning messages that are # generated to standard error (stderr) by doxygen. If WARNINGS is set to YES # this implies that the warnings are on. # # Tip: Turn warnings on while writing the documentation. # The default value is: YES. WARNINGS = YES # If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate # warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag # will automatically be disabled. # The default value is: YES. WARN_IF_UNDOCUMENTED = YES # If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for # potential errors in the documentation, such as not documenting some parameters # in a documented function, or documenting parameters that don't exist or using # markup commands wrongly. # The default value is: YES. WARN_IF_DOC_ERROR = YES # This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that # are documented, but have no documentation for their parameters or return # value. If set to NO, doxygen will only warn about wrong or incomplete # parameter documentation, but not about the absence of documentation. # The default value is: NO. WARN_NO_PARAMDOC = NO # The WARN_FORMAT tag determines the format of the warning messages that doxygen # can produce. The string should contain the $file, $line, and $text tags, which # will be replaced by the file and line number from which the warning originated # and the warning text. Optionally the format may contain $version, which will # be replaced by the version of the file (if it could be obtained via # FILE_VERSION_FILTER) # The default value is: $file:$line: $text. WARN_FORMAT = "$file:$line: $text" # The WARN_LOGFILE tag can be used to specify a file to which warning and error # messages should be written. If left blank the output is written to standard # error (stderr). WARN_LOGFILE = #--------------------------------------------------------------------------- # Configuration options related to the input files #--------------------------------------------------------------------------- # The INPUT tag is used to specify the files and/or directories that contain # documented source files. You may enter file names like myfile.cpp or # directories like /usr/src/myproject. Separate the files or directories with # spaces. # Note: If this tag is empty the current directory is searched. INPUT = "../niftymic" # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses # libiconv (or the iconv built into libc) for the transcoding. See the libiconv # documentation (see: http://www.gnu.org/software/libiconv) for the list of # possible encodings. # The default value is: UTF-8. INPUT_ENCODING = UTF-8 # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and # *.h) to filter out the source-files in the directories. If left blank the # following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, # *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, # *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, # *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, # *.qsf, *.as and *.js. FILE_PATTERNS = *.c \ *.cc \ *.cxx \ *.cpp \ *.c++ \ *.java \ *.ii \ *.ixx \ *.ipp \ *.i++ \ *.inl \ *.idl \ *.ddl \ *.odl \ *.h \ *.hh \ *.hxx \ *.hpp \ *.h++ \ *.cs \ *.d \ *.php \ *.php4 \ *.php5 \ *.phtml \ *.inc \ *.m \ *.markdown \ *.md \ *.mm \ *.dox \ *.py \ *.f90 \ *.f \ *.for \ *.tcl \ *.vhd \ *.vhdl \ *.ucf \ *.qsf \ *.as \ *.js # The RECURSIVE tag can be used to specify whether or not subdirectories should # be searched for input files as well. # The default value is: NO. RECURSIVE = YES # The EXCLUDE tag can be used to specify files and/or directories that should be # excluded from the INPUT source files. This way you can easily exclude a # subdirectory from a directory tree whose root is specified with the INPUT tag. # # Note that relative paths are relative to the directory from which doxygen is # run. EXCLUDE = # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded # from the input. # The default value is: NO. EXCLUDE_SYMLINKS = NO # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. # # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories for example use the pattern */test/* EXCLUDE_PATTERNS = # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the # output. The symbol name can be a fully qualified name, a word, or if the # wildcard * is used, a substring. Examples: ANamespace, AClass, # AClass::ANamespace, ANamespace::*Test # # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories use the pattern */test/* EXCLUDE_SYMBOLS = # The EXAMPLE_PATH tag can be used to specify one or more files or directories # that contain example code fragments that are included (see the \include # command). EXAMPLE_PATH = # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and # *.h) to filter out the source-files in the directories. If left blank all # files are included. EXAMPLE_PATTERNS = * # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude commands # irrespective of the value of the RECURSIVE tag. # The default value is: NO. EXAMPLE_RECURSIVE = NO # The IMAGE_PATH tag can be used to specify one or more files or directories # that contain images that are to be included in the documentation (see the # \image command). IMAGE_PATH = # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command: # # # # where is the value of the INPUT_FILTER tag, and is the # name of an input file. Doxygen will then use the output that the filter # program writes to standard output. If FILTER_PATTERNS is specified, this tag # will be ignored. # # Note that the filter must not add or remove lines; it is applied before the # code is scanned, but not when the output code is generated. If lines are added # or removed, the anchors will not be placed correctly. INPUT_FILTER = # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern # basis. Doxygen will compare the file name with each pattern and apply the # filter if there is a match. The filters are a list of the form: pattern=filter # (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how # filters are used. If the FILTER_PATTERNS tag is empty or if none of the # patterns match the file name, INPUT_FILTER is applied. FILTER_PATTERNS = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using # INPUT_FILTER) will also be used to filter the input files that are used for # producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). # The default value is: NO. FILTER_SOURCE_FILES = NO # The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file # pattern. A pattern will override the setting for FILTER_PATTERN (if any) and # it is also possible to disable source filtering for a specific pattern using # *.ext= (so without naming a filter). # This tag requires that the tag FILTER_SOURCE_FILES is set to YES. FILTER_SOURCE_PATTERNS = # If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that # is part of the input, its contents will be placed on the main page # (index.html). This can be useful if you have a project on for instance GitHub # and want to reuse the introduction page also for the doxygen output. USE_MDFILE_AS_MAINPAGE = #--------------------------------------------------------------------------- # Configuration options related to source browsing #--------------------------------------------------------------------------- # If the SOURCE_BROWSER tag is set to YES then a list of source files will be # generated. Documented entities will be cross-referenced with these sources. # # Note: To get rid of all source code in the generated output, make sure that # also VERBATIM_HEADERS is set to NO. # The default value is: NO. SOURCE_BROWSER = YES # Setting the INLINE_SOURCES tag to YES will include the body of functions, # classes and enums directly into the documentation. # The default value is: NO. INLINE_SOURCES = NO # Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any # special comment blocks from generated source code fragments. Normal C, C++ and # Fortran comments will always remain visible. # The default value is: YES. STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES then for each documented # function all documented functions referencing it will be listed. # The default value is: NO. REFERENCED_BY_RELATION = NO # If the REFERENCES_RELATION tag is set to YES then for each documented function # all documented entities called/used by that function will be listed. # The default value is: NO. REFERENCES_RELATION = NO # If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set # to YES then the hyperlinks from functions in REFERENCES_RELATION and # REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will # link to the documentation. # The default value is: YES. REFERENCES_LINK_SOURCE = YES # If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the # source code will show a tooltip with additional information such as prototype, # brief description and links to the definition and documentation. Since this # will make the HTML file larger and loading of large files a bit slower, you # can opt to disable this feature. # The default value is: YES. # This tag requires that the tag SOURCE_BROWSER is set to YES. SOURCE_TOOLTIPS = YES # If the USE_HTAGS tag is set to YES then the references to source code will # point to the HTML generated by the htags(1) tool instead of doxygen built-in # source browser. The htags tool is part of GNU's global source tagging system # (see http://www.gnu.org/software/global/global.html). You will need version # 4.8.6 or higher. # # To use it do the following: # - Install the latest version of global # - Enable SOURCE_BROWSER and USE_HTAGS in the config file # - Make sure the INPUT points to the root of the source tree # - Run doxygen as normal # # Doxygen will invoke htags (and that will in turn invoke gtags), so these # tools must be available from the command line (i.e. in the search path). # # The result: instead of the source browser generated by doxygen, the links to # source code will now point to the output of htags. # The default value is: NO. # This tag requires that the tag SOURCE_BROWSER is set to YES. USE_HTAGS = NO # If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a # verbatim copy of the header file for each class for which an include is # specified. Set to NO to disable this. # See also: Section \class. # The default value is: YES. VERBATIM_HEADERS = YES # If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the # clang parser (see: http://clang.llvm.org/) for more accurate parsing at the # cost of reduced performance. This can be particularly helpful with template # rich C++ code for which doxygen's built-in parser lacks the necessary type # information. # Note: The availability of this option depends on whether or not doxygen was # compiled with the --with-libclang option. # The default value is: NO. CLANG_ASSISTED_PARSING = NO # If clang assisted parsing is enabled you can provide the compiler with command # line options that you would normally use when invoking the compiler. Note that # the include paths will already be set by doxygen for the files and directories # specified with INPUT and INCLUDE_PATH. # This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES. CLANG_OPTIONS = #--------------------------------------------------------------------------- # Configuration options related to the alphabetical class index #--------------------------------------------------------------------------- # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all # compounds will be generated. Enable this if the project contains a lot of # classes, structs, unions or interfaces. # The default value is: YES. ALPHABETICAL_INDEX = YES # The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in # which the alphabetical index list will be split. # Minimum value: 1, maximum value: 20, default value: 5. # This tag requires that the tag ALPHABETICAL_INDEX is set to YES. COLS_IN_ALPHA_INDEX = 5 # In case all classes in a project start with a common prefix, all classes will # be put under the same header in the alphabetical index. The IGNORE_PREFIX tag # can be used to specify a prefix (or a list of prefixes) that should be ignored # while generating the index headers. # This tag requires that the tag ALPHABETICAL_INDEX is set to YES. IGNORE_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the HTML output #--------------------------------------------------------------------------- # If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output # The default value is: YES. GENERATE_HTML = YES # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of # it. # The default directory is: html. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_OUTPUT = html # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each # generated HTML page (for example: .htm, .php, .asp). # The default value is: .html. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_FILE_EXTENSION = .html # The HTML_HEADER tag can be used to specify a user-defined HTML header file for # each generated HTML page. If the tag is left blank doxygen will generate a # standard header. # # To get valid HTML the header file that includes any scripts and style sheets # that doxygen needs, which is dependent on the configuration options used (e.g. # the setting GENERATE_TREEVIEW). It is highly recommended to start with a # default header using # doxygen -w html new_header.html new_footer.html new_stylesheet.css # YourConfigFile # and then modify the file new_header.html. See also section "Doxygen usage" # for information on how to generate the default header that doxygen normally # uses. # Note: The header is subject to change so you typically have to regenerate the # default header when upgrading to a newer version of doxygen. For a description # of the possible markers and block names see the documentation. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_HEADER = # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each # generated HTML page. If the tag is left blank doxygen will generate a standard # footer. See HTML_HEADER for more information on how to generate a default # footer and what special commands can be used inside the footer. See also # section "Doxygen usage" for information on how to generate the default footer # that doxygen normally uses. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_FOOTER = # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style # sheet that is used by each HTML page. It can be used to fine-tune the look of # the HTML output. If left blank doxygen will generate a default style sheet. # See also section "Doxygen usage" for information on how to generate the style # sheet that doxygen normally uses. # Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as # it is more robust and this tag (HTML_STYLESHEET) will in the future become # obsolete. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_STYLESHEET = # The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined # cascading style sheets that are included after the standard style sheets # created by doxygen. Using this option one can overrule certain style aspects. # This is preferred over using HTML_STYLESHEET since it does not replace the # standard style sheet and is therefore more robust against future updates. # Doxygen will copy the style sheet files to the output directory. # Note: The order of the extra style sheet files is of importance (e.g. the last # style sheet in the list overrules the setting of the previous ones in the # list). For an example see the documentation. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_EXTRA_STYLESHEET = # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or # other source files which should be copied to the HTML output directory. Note # that these files will be copied to the base HTML output directory. Use the # $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these # files. In the HTML_STYLESHEET file, use the file name only. Also note that the # files will be copied as-is; there are no commands or markers available. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_EXTRA_FILES = # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen # will adjust the colors in the style sheet and background images according to # this color. Hue is specified as an angle on a colorwheel, see # http://en.wikipedia.org/wiki/Hue for more information. For instance the value # 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 # purple, and 360 is red again. # Minimum value: 0, maximum value: 359, default value: 220. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_COLORSTYLE_HUE = 220 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors # in the HTML output. For a value of 0 the output will use grayscales only. A # value of 255 will produce the most vivid colors. # Minimum value: 0, maximum value: 255, default value: 100. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_COLORSTYLE_SAT = 100 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the # luminance component of the colors in the HTML output. Values below 100 # gradually make the output lighter, whereas values above 100 make the output # darker. The value divided by 100 is the actual gamma applied, so 80 represents # a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not # change the gamma. # Minimum value: 40, maximum value: 240, default value: 80. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_COLORSTYLE_GAMMA = 80 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML # page will contain the date and time when the page was generated. Setting this # to NO can help when comparing the output of multiple runs. # The default value is: YES. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_TIMESTAMP = YES # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML # documentation will contain sections that can be hidden and shown after the # page has loaded. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_DYNAMIC_SECTIONS = NO # With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries # shown in the various tree structured indices initially; the user can expand # and collapse entries dynamically later on. Doxygen will expand the tree to # such a level that at most the specified number of entries are visible (unless # a fully collapsed tree already exceeds this amount). So setting the number of # entries 1 will produce a full collapsed tree by default. 0 is a special value # representing an infinite number of entries and will result in a full expanded # tree by default. # Minimum value: 0, maximum value: 9999, default value: 100. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_INDEX_NUM_ENTRIES = 100 # If the GENERATE_DOCSET tag is set to YES, additional index files will be # generated that can be used as input for Apple's Xcode 3 integrated development # environment (see: http://developer.apple.com/tools/xcode/), introduced with # OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a # Makefile in the HTML output directory. Running make will produce the docset in # that directory and running make install will install the docset in # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at # startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html # for more information. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. GENERATE_DOCSET = NO # This tag determines the name of the docset feed. A documentation feed provides # an umbrella under which multiple documentation sets from a single provider # (such as a company or product suite) can be grouped. # The default value is: Doxygen generated docs. # This tag requires that the tag GENERATE_DOCSET is set to YES. DOCSET_FEEDNAME = "Doxygen generated docs" # This tag specifies a string that should uniquely identify the documentation # set bundle. This should be a reverse domain-name style string, e.g. # com.mycompany.MyDocSet. Doxygen will append .docset to the name. # The default value is: org.doxygen.Project. # This tag requires that the tag GENERATE_DOCSET is set to YES. DOCSET_BUNDLE_ID = org.doxygen.Project # The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify # the documentation publisher. This should be a reverse domain-name style # string, e.g. com.mycompany.MyDocSet.documentation. # The default value is: org.doxygen.Publisher. # This tag requires that the tag GENERATE_DOCSET is set to YES. DOCSET_PUBLISHER_ID = org.doxygen.Publisher # The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. # The default value is: Publisher. # This tag requires that the tag GENERATE_DOCSET is set to YES. DOCSET_PUBLISHER_NAME = Publisher # If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three # additional HTML index files: index.hhp, index.hhc, and index.hhk. The # index.hhp is a project file that can be read by Microsoft's HTML Help Workshop # (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on # Windows. # # The HTML Help Workshop contains a compiler that can convert all HTML output # generated by doxygen into a single compiled HTML file (.chm). Compiled HTML # files are now used as the Windows 98 help format, and will replace the old # Windows help format (.hlp) on all Windows platforms in the future. Compressed # HTML files also contain an index, a table of contents, and you can search for # words in the documentation. The HTML workshop also contains a viewer for # compressed HTML files. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. GENERATE_HTMLHELP = NO # The CHM_FILE tag can be used to specify the file name of the resulting .chm # file. You can add a path in front of the file if the result should not be # written to the html output directory. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. CHM_FILE = # The HHC_LOCATION tag can be used to specify the location (absolute path # including file name) of the HTML help compiler (hhc.exe). If non-empty, # doxygen will try to run the HTML help compiler on the generated index.hhp. # The file has to be specified with full path. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. HHC_LOCATION = # The GENERATE_CHI flag controls if a separate .chi index file is generated # (YES) or that it should be included in the master .chm file (NO). # The default value is: NO. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. GENERATE_CHI = NO # The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) # and project file content. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. CHM_INDEX_ENCODING = # The BINARY_TOC flag controls whether a binary table of contents is generated # (YES) or a normal table of contents (NO) in the .chm file. Furthermore it # enables the Previous and Next buttons. # The default value is: NO. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. BINARY_TOC = NO # The TOC_EXPAND flag can be set to YES to add extra items for group members to # the table of contents of the HTML help documentation and to the tree view. # The default value is: NO. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. TOC_EXPAND = NO # If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and # QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that # can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help # (.qch) of the generated HTML documentation. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. GENERATE_QHP = NO # If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify # the file name of the resulting .qch file. The path specified is relative to # the HTML output folder. # This tag requires that the tag GENERATE_QHP is set to YES. QCH_FILE = # The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help # Project output. For more information please see Qt Help Project / Namespace # (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). # The default value is: org.doxygen.Project. # This tag requires that the tag GENERATE_QHP is set to YES. QHP_NAMESPACE = org.doxygen.Project # The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt # Help Project output. For more information please see Qt Help Project / Virtual # Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- # folders). # The default value is: doc. # This tag requires that the tag GENERATE_QHP is set to YES. QHP_VIRTUAL_FOLDER = doc # If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom # filter to add. For more information please see Qt Help Project / Custom # Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- # filters). # This tag requires that the tag GENERATE_QHP is set to YES. QHP_CUST_FILTER_NAME = # The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the # custom filter to add. For more information please see Qt Help Project / Custom # Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- # filters). # This tag requires that the tag GENERATE_QHP is set to YES. QHP_CUST_FILTER_ATTRS = # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this # project's filter section matches. Qt Help Project / Filter Attributes (see: # http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). # This tag requires that the tag GENERATE_QHP is set to YES. QHP_SECT_FILTER_ATTRS = # The QHG_LOCATION tag can be used to specify the location of Qt's # qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the # generated .qhp file. # This tag requires that the tag GENERATE_QHP is set to YES. QHG_LOCATION = # If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be # generated, together with the HTML files, they form an Eclipse help plugin. To # install this plugin and make it available under the help contents menu in # Eclipse, the contents of the directory containing the HTML and XML files needs # to be copied into the plugins directory of eclipse. The name of the directory # within the plugins directory should be the same as the ECLIPSE_DOC_ID value. # After copying Eclipse needs to be restarted before the help appears. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. GENERATE_ECLIPSEHELP = NO # A unique identifier for the Eclipse help plugin. When installing the plugin # the directory name containing the HTML and XML files should also have this # name. Each documentation set should have its own identifier. # The default value is: org.doxygen.Project. # This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. ECLIPSE_DOC_ID = org.doxygen.Project # If you want full control over the layout of the generated HTML pages it might # be necessary to disable the index and replace it with your own. The # DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top # of each HTML page. A value of NO enables the index and the value YES disables # it. Since the tabs in the index contain the same information as the navigation # tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. DISABLE_INDEX = NO # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index # structure should be generated to display hierarchical information. If the tag # value is set to YES, a side panel will be generated containing a tree-like # index structure (just like the one that is generated for HTML Help). For this # to work a browser that supports JavaScript, DHTML, CSS and frames is required # (i.e. any modern browser). Windows users are probably better off using the # HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can # further fine-tune the look of the index. As an example, the default style # sheet generated by doxygen has an example that shows how to put an image at # the root of the tree instead of the PROJECT_NAME. Since the tree basically has # the same information as the tab index, you could consider setting # DISABLE_INDEX to YES when enabling this option. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. GENERATE_TREEVIEW = YES # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that # doxygen will group on one line in the generated HTML documentation. # # Note that a value of 0 will completely suppress the enum values from appearing # in the overview section. # Minimum value: 0, maximum value: 20, default value: 4. # This tag requires that the tag GENERATE_HTML is set to YES. ENUM_VALUES_PER_LINE = 4 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used # to set the initial width (in pixels) of the frame in which the tree is shown. # Minimum value: 0, maximum value: 1500, default value: 250. # This tag requires that the tag GENERATE_HTML is set to YES. TREEVIEW_WIDTH = 250 # If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to # external symbols imported via tag files in a separate window. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. EXT_LINKS_IN_WINDOW = NO # Use this tag to change the font size of LaTeX formulas included as images in # the HTML documentation. When you change the font size after a successful # doxygen run you need to manually remove any form_*.png images from the HTML # output directory to force them to be regenerated. # Minimum value: 8, maximum value: 50, default value: 10. # This tag requires that the tag GENERATE_HTML is set to YES. FORMULA_FONTSIZE = 10 # Use the FORMULA_TRANPARENT tag to determine whether or not the images # generated for formulas are transparent PNGs. Transparent PNGs are not # supported properly for IE 6.0, but are supported on all modern browsers. # # Note that when changing this option you need to delete any form_*.png files in # the HTML output directory before the changes have effect. # The default value is: YES. # This tag requires that the tag GENERATE_HTML is set to YES. FORMULA_TRANSPARENT = YES # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see # http://www.mathjax.org) which uses client side Javascript for the rendering # instead of using pre-rendered bitmaps. Use this if you do not have LaTeX # installed or if you want to formulas look prettier in the HTML output. When # enabled you may also need to install MathJax separately and configure the path # to it using the MATHJAX_RELPATH option. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. USE_MATHJAX = NO # When MathJax is enabled you can set the default output format to be used for # the MathJax output. See the MathJax site (see: # http://docs.mathjax.org/en/latest/output.html) for more details. # Possible values are: HTML-CSS (which is slower, but has the best # compatibility), NativeMML (i.e. MathML) and SVG. # The default value is: HTML-CSS. # This tag requires that the tag USE_MATHJAX is set to YES. MATHJAX_FORMAT = HTML-CSS # When MathJax is enabled you need to specify the location relative to the HTML # output directory using the MATHJAX_RELPATH option. The destination directory # should contain the MathJax.js script. For instance, if the mathjax directory # is located at the same level as the HTML output directory, then # MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax # Content Delivery Network so you can quickly see the result without installing # MathJax. However, it is strongly recommended to install a local copy of # MathJax from http://www.mathjax.org before deployment. # The default value is: http://cdn.mathjax.org/mathjax/latest. # This tag requires that the tag USE_MATHJAX is set to YES. MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax # extension names that should be enabled during MathJax rendering. For example # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols # This tag requires that the tag USE_MATHJAX is set to YES. MATHJAX_EXTENSIONS = # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces # of code that will be used on startup of the MathJax code. See the MathJax site # (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an # example see the documentation. # This tag requires that the tag USE_MATHJAX is set to YES. MATHJAX_CODEFILE = # When the SEARCHENGINE tag is enabled doxygen will generate a search box for # the HTML output. The underlying search engine uses javascript and DHTML and # should work on any modern browser. Note that when using HTML help # (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) # there is already a search function so this one should typically be disabled. # For large projects the javascript based search engine can be slow, then # enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to # search using the keyboard; to jump to the search box use + S # (what the is depends on the OS and browser, but it is typically # , /