├── .gitignore ├── .travis.yml ├── CHANGELOG.rst ├── LICENSE.rst ├── MANIFEST.in ├── README.rst ├── conda_recipe └── magni │ ├── bld.bat │ ├── build.sh │ ├── meta.yaml │ ├── run_test.py │ └── setup_py_conda.patch ├── doc ├── Makefile ├── build │ ├── html │ │ ├── _modules │ │ │ ├── index.html │ │ │ └── magni │ │ │ │ ├── afm │ │ │ │ └── reconstruction.html │ │ │ │ ├── cs │ │ │ │ └── phase_transition │ │ │ │ │ ├── _analysis.html │ │ │ │ │ ├── _backup.html │ │ │ │ │ ├── _data.html │ │ │ │ │ ├── _simulation.html │ │ │ │ │ ├── _util.html │ │ │ │ │ ├── io.html │ │ │ │ │ └── plotting.html │ │ │ │ ├── imaging │ │ │ │ ├── _util.html │ │ │ │ ├── domains.html │ │ │ │ ├── evaluation.html │ │ │ │ ├── preprocessing.html │ │ │ │ └── visualisation.html │ │ │ │ ├── reproducibility │ │ │ │ ├── _annotation.html │ │ │ │ └── io.html │ │ │ │ └── utils │ │ │ │ ├── _util.html │ │ │ │ ├── config.html │ │ │ │ ├── matrices.html │ │ │ │ ├── multiprocessing │ │ │ │ ├── _processing.html │ │ │ │ └── _util.html │ │ │ │ └── plotting.html │ │ ├── _static │ │ │ ├── ajax-loader.gif │ │ │ ├── basic.css │ │ │ ├── comment-bright.png │ │ │ ├── comment-close.png │ │ │ ├── comment.png │ │ │ ├── doctools.js │ │ │ ├── down-pressed.png │ │ │ ├── down.png │ │ │ ├── file.png │ │ │ ├── jquery.js │ │ │ ├── minus.png │ │ │ ├── plus.png │ │ │ ├── pygments.css │ │ │ ├── searchtools.js │ │ │ ├── sidebar.js │ │ │ ├── underscore.js │ │ │ ├── up-pressed.png │ │ │ ├── up.png │ │ │ └── websupport.js │ │ ├── examples.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── magni.afm.html │ │ ├── magni.afm.io.html │ │ ├── magni.afm.reconstruction.html │ │ ├── magni.afm.types.html │ │ ├── magni.cs.html │ │ ├── magni.cs.phase_transition._analysis.html │ │ ├── magni.cs.phase_transition._backup.html │ │ ├── magni.cs.phase_transition._data.html │ │ ├── magni.cs.phase_transition._simulation.html │ │ ├── magni.cs.phase_transition._util.html │ │ ├── magni.cs.phase_transition.html │ │ ├── magni.cs.phase_transition.io.html │ │ ├── magni.cs.phase_transition.plotting.html │ │ ├── magni.cs.reconstruction.html │ │ ├── magni.cs.reconstruction.iht.html │ │ ├── magni.cs.reconstruction.sl0.html │ │ ├── magni.html │ │ ├── magni.imaging._util.html │ │ ├── magni.imaging.dictionaries.html │ │ ├── magni.imaging.domains.html │ │ ├── magni.imaging.evaluation.html │ │ ├── magni.imaging.html │ │ ├── magni.imaging.measurements.html │ │ ├── magni.imaging.preprocessing.html │ │ ├── magni.imaging.visualisation.html │ │ ├── magni.reproducibility._annotation.html │ │ ├── magni.reproducibility.html │ │ ├── magni.reproducibility.io.html │ │ ├── magni.utils._util.html │ │ ├── magni.utils.config.html │ │ ├── magni.utils.html │ │ ├── magni.utils.matrices.html │ │ ├── magni.utils.multiprocessing._processing.html │ │ ├── magni.utils.multiprocessing._util.html │ │ ├── magni.utils.multiprocessing.html │ │ ├── magni.utils.plotting.html │ │ ├── magni.utils.validation.html │ │ ├── notation.html │ │ ├── objects.inv │ │ ├── search.html │ │ └── searchindex.js │ └── pdf │ │ └── index.pdf ├── docapi.py └── source │ ├── conf.py │ ├── create_pdf_cover.py │ ├── examples.rst │ ├── index.rst │ ├── magni.afm._config.rst │ ├── magni.afm.io._data_attachment.rst │ ├── magni.afm.io._object_building.rst │ ├── magni.afm.io._stream_conversion.rst │ ├── magni.afm.io._util.rst │ ├── magni.afm.io.rst │ ├── magni.afm.reconstruction.rst │ ├── magni.afm.rst │ ├── magni.afm.types._util.rst │ ├── magni.afm.types.image.rst │ ├── magni.afm.types.rst │ ├── magni.afm.types.spectroscopy.rst │ ├── magni.cs.indicators.rst │ ├── magni.cs.phase_transition._analysis.rst │ ├── magni.cs.phase_transition._backup.rst │ ├── magni.cs.phase_transition._config.rst │ ├── magni.cs.phase_transition._data.rst │ ├── magni.cs.phase_transition._simulation.rst │ ├── magni.cs.phase_transition._util.rst │ ├── magni.cs.phase_transition.io.rst │ ├── magni.cs.phase_transition.plotting.rst │ ├── magni.cs.phase_transition.rst │ ├── magni.cs.reconstruction._config.rst │ ├── magni.cs.reconstruction.amp._algorithm.rst │ ├── magni.cs.reconstruction.amp._config.rst │ ├── magni.cs.reconstruction.amp.rst │ ├── magni.cs.reconstruction.amp.stop_criterion.rst │ ├── magni.cs.reconstruction.amp.threshold_operator.rst │ ├── magni.cs.reconstruction.amp.util.rst │ ├── magni.cs.reconstruction.gamp._algorithm.rst │ ├── magni.cs.reconstruction.gamp._config.rst │ ├── magni.cs.reconstruction.gamp.channel_initialisation.rst │ ├── magni.cs.reconstruction.gamp.input_channel.rst │ ├── magni.cs.reconstruction.gamp.output_channel.rst │ ├── magni.cs.reconstruction.gamp.rst │ ├── magni.cs.reconstruction.gamp.stop_criterion.rst │ ├── magni.cs.reconstruction.iht._config.rst │ ├── magni.cs.reconstruction.iht.rst │ ├── magni.cs.reconstruction.it._algorithm.rst │ ├── magni.cs.reconstruction.it._config.rst │ ├── magni.cs.reconstruction.it._step_size.rst │ ├── magni.cs.reconstruction.it._stop_criterion.rst │ ├── magni.cs.reconstruction.it._threshold.rst │ ├── magni.cs.reconstruction.it._threshold_operators.rst │ ├── magni.cs.reconstruction.it._util.rst │ ├── magni.cs.reconstruction.it.rst │ ├── magni.cs.reconstruction.rst │ ├── magni.cs.reconstruction.sl0._L_start.rst │ ├── magni.cs.reconstruction.sl0._L_update.rst │ ├── magni.cs.reconstruction.sl0._algorithm.rst │ ├── magni.cs.reconstruction.sl0._config.rst │ ├── magni.cs.reconstruction.sl0._mu_start.rst │ ├── magni.cs.reconstruction.sl0._mu_update.rst │ ├── magni.cs.reconstruction.sl0._sigma_start.rst │ ├── magni.cs.reconstruction.sl0.rst │ ├── magni.cs.rst │ ├── magni.imaging._util.rst │ ├── magni.imaging.dictionaries._fastops.rst │ ├── magni.imaging.dictionaries._matrices.rst │ ├── magni.imaging.dictionaries._mtx1D.rst │ ├── magni.imaging.dictionaries._visualisations.rst │ ├── magni.imaging.dictionaries.analysis.rst │ ├── magni.imaging.dictionaries.rst │ ├── magni.imaging.dictionaries.utils.rst │ ├── magni.imaging.domains.rst │ ├── magni.imaging.evaluation.rst │ ├── magni.imaging.measurements._lissajous.rst │ ├── magni.imaging.measurements._matrices.rst │ ├── magni.imaging.measurements._random_line.rst │ ├── magni.imaging.measurements._spiral.rst │ ├── magni.imaging.measurements._square_spiral.rst │ ├── magni.imaging.measurements._uniform_line.rst │ ├── magni.imaging.measurements._uniform_rotated_line.rst │ ├── magni.imaging.measurements._util.rst │ ├── magni.imaging.measurements._visualisation.rst │ ├── magni.imaging.measurements._zigzag.rst │ ├── magni.imaging.measurements.rst │ ├── magni.imaging.preprocessing.rst │ ├── magni.imaging.rst │ ├── magni.imaging.visualisation.rst │ ├── magni.reproducibility._annotation.rst │ ├── magni.reproducibility._chase.rst │ ├── magni.reproducibility.data.rst │ ├── magni.reproducibility.io.rst │ ├── magni.reproducibility.rst │ ├── magni.rst │ ├── magni.utils._util.rst │ ├── magni.utils.config.rst │ ├── magni.utils.matrices.rst │ ├── magni.utils.multiprocessing._config.rst │ ├── magni.utils.multiprocessing._processing.rst │ ├── magni.utils.multiprocessing._util.rst │ ├── magni.utils.multiprocessing.rst │ ├── magni.utils.plotting.rst │ ├── magni.utils.rst │ ├── magni.utils.types.rst │ ├── magni.utils.validation._generic.rst │ ├── magni.utils.validation._levels.rst │ ├── magni.utils.validation._numeric.rst │ ├── magni.utils.validation._util.rst │ ├── magni.utils.validation.rst │ ├── magni.utils.validation.types.rst │ └── notation.rst ├── examples ├── afm-io.ipynb ├── cs-phase_transition-config.ipynb ├── cs-phase_transition.ipynb ├── cs-reconstruction.ipynb ├── data.hdf5 ├── display.py ├── example.mi ├── imaging-dictionaries.ipynb ├── imaging-domains.ipynb ├── imaging-measurements.ipynb ├── imaging-preprocessing.ipynb ├── magni.ipynb ├── reproducibility-data.ipynb ├── reproducibility-io.ipynb ├── utils-matrices.ipynb ├── utils-multiprocessing.ipynb ├── utils-plotting.ipynb └── utils-validation.ipynb ├── magni ├── __init__.py ├── afm │ ├── __init__.py │ ├── _config.py │ ├── io │ │ ├── __init__.py │ │ ├── _data_attachment.py │ │ ├── _object_building.py │ │ ├── _stream_conversion.py │ │ └── _util.py │ ├── reconstruction.py │ └── types │ │ ├── __init__.py │ │ ├── _util.py │ │ ├── image.py │ │ └── spectroscopy.py ├── cs │ ├── __init__.py │ ├── indicators.py │ ├── phase_transition │ │ ├── __init__.py │ │ ├── _analysis.py │ │ ├── _backup.py │ │ ├── _config.py │ │ ├── _data.py │ │ ├── _simulation.py │ │ ├── _util.py │ │ ├── io.py │ │ └── plotting.py │ └── reconstruction │ │ ├── __init__.py │ │ ├── _config.py │ │ ├── amp │ │ ├── __init__.py │ │ ├── _algorithm.py │ │ ├── _config.py │ │ ├── stop_criterion.py │ │ ├── threshold_operator.py │ │ └── util.py │ │ ├── gamp │ │ ├── __init__.py │ │ ├── _algorithm.py │ │ ├── _config.py │ │ ├── channel_initialisation.py │ │ ├── input_channel.py │ │ ├── output_channel.py │ │ └── stop_criterion.py │ │ ├── iht │ │ ├── __init__.py │ │ └── _config.py │ │ ├── it │ │ ├── __init__.py │ │ ├── _algorithm.py │ │ ├── _config.py │ │ ├── _step_size.py │ │ ├── _stop_criterion.py │ │ ├── _threshold.py │ │ ├── _threshold_operators.py │ │ └── _util.py │ │ └── sl0 │ │ ├── _L_start.py │ │ ├── _L_update.py │ │ ├── __init__.py │ │ ├── _algorithm.py │ │ ├── _config.py │ │ ├── _mu_start.py │ │ ├── _mu_update.py │ │ └── _sigma_start.py ├── imaging │ ├── __init__.py │ ├── _util.py │ ├── dictionaries │ │ ├── __init__.py │ │ ├── _fastops.py │ │ ├── _matrices.py │ │ ├── _mtx1D.py │ │ ├── _visualisations.py │ │ ├── analysis.py │ │ └── utils.py │ ├── domains.py │ ├── evaluation.py │ ├── measurements │ │ ├── __init__.py │ │ ├── _lissajous.py │ │ ├── _matrices.py │ │ ├── _random_line.py │ │ ├── _spiral.py │ │ ├── _square_spiral.py │ │ ├── _uniform_line.py │ │ ├── _uniform_rotated_line.py │ │ ├── _util.py │ │ ├── _visualisation.py │ │ └── _zigzag.py │ ├── preprocessing.py │ └── visualisation.py ├── reproducibility │ ├── __init__.py │ ├── _annotation.py │ ├── _chase.py │ ├── data.py │ └── io.py ├── tests │ ├── __init__.py │ ├── build_docs.py │ ├── config.py │ ├── cs_indicators.py │ ├── cs_phase_transition.py │ ├── cs_reconstruction.py │ ├── dep_check.py │ ├── gamp_em_sigma_sq_sols.npz │ ├── gamp_fixed_sigma_sq_sols.npz │ ├── imaging_dictionaries.py │ ├── imaging_evaluation.py │ ├── ipynb_examples.py │ ├── pt_test_data.hdf5 │ ├── reproducibility.py │ ├── run_tests.py │ ├── style_checks.py │ ├── utils_matrices.py │ ├── utils_multiprocessing.py │ ├── utils_plotting.py │ ├── utils_validation.py │ └── wrap_doctests.py └── utils │ ├── __init__.py │ ├── _util.py │ ├── config.py │ ├── matrices.py │ ├── multiprocessing │ ├── __init__.py │ ├── _config.py │ ├── _processing.py │ └── _util.py │ ├── plotting.py │ ├── types.py │ └── validation │ ├── __init__.py │ ├── _generic.py │ ├── _levels.py │ ├── _numeric.py │ ├── _util.py │ └── types.py ├── readthedocs.yml ├── readthedocs_environment.yml └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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