├── .gitattributes ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── TomoPyUI.bat ├── app └── app.ipynb ├── bench └── Benchmarking.ipynb ├── docker └── Dockerfile ├── docs ├── environment.yml └── source │ ├── _static │ ├── images │ │ ├── logo.png │ │ ├── tomopy-favicon.ico │ │ └── tomopy-favicon.svg │ ├── theme.css │ └── videos │ │ ├── align_new.mp4 │ │ ├── alignment.mp4 │ │ ├── center-multiple.webm │ │ ├── center.mp4 │ │ ├── center_new.mp4 │ │ ├── data_explorer_fast.mp4 │ │ ├── front_page.mp4 │ │ ├── import.mp4 │ │ ├── import_viewer.mp4 │ │ ├── intro.mp4 │ │ ├── looking_at_data_fast.mp4 │ │ └── subdirs.mp4 │ ├── _templates │ ├── demo.html │ └── sidebar-nav-bs-index.html │ ├── conf.py │ ├── contributing.md │ ├── how-to.md │ ├── howitworks.md │ ├── index.md │ ├── install.md │ └── usage.ipynb ├── environment-nocuda.yml ├── environment.yml ├── examples ├── data │ ├── ALS_832_Data │ │ ├── fake_als_data.h5 │ │ └── make_fake_als_data.py │ ├── tiff_image │ │ └── tomo77_downsampled0p5.tif │ └── tiff_sequence │ │ ├── tomo77_000.tiff │ │ ├── tomo77_001.tiff │ │ ├── tomo77_002.tiff │ │ ├── tomo77_003.tiff │ │ ├── tomo77_004.tiff │ │ ├── tomo77_005.tiff │ │ ├── tomo77_006.tiff │ │ ├── tomo77_007.tiff │ │ ├── tomo77_008.tiff │ │ ├── tomo77_009.tiff │ │ ├── tomo77_010.tiff │ │ ├── tomo77_011.tiff │ │ ├── tomo77_012.tiff │ │ ├── tomo77_013.tiff │ │ ├── tomo77_014.tiff │ │ ├── tomo77_015.tiff │ │ ├── tomo77_016.tiff │ │ ├── tomo77_017.tiff │ │ ├── tomo77_018.tiff │ │ ├── tomo77_019.tiff │ │ ├── tomo77_020.tiff │ │ ├── tomo77_021.tiff │ │ ├── tomo77_022.tiff │ │ ├── tomo77_023.tiff │ │ ├── tomo77_024.tiff │ │ ├── tomo77_025.tiff │ │ ├── tomo77_026.tiff │ │ ├── tomo77_027.tiff │ │ ├── tomo77_028.tiff │ │ ├── tomo77_029.tiff │ │ ├── tomo77_030.tiff │ │ ├── tomo77_031.tiff │ │ ├── tomo77_032.tiff │ │ ├── tomo77_033.tiff │ │ ├── tomo77_034.tiff │ │ ├── tomo77_035.tiff │ │ ├── tomo77_036.tiff │ │ ├── tomo77_037.tiff │ │ ├── tomo77_038.tiff │ │ ├── tomo77_039.tiff │ │ ├── tomo77_040.tiff │ │ ├── tomo77_041.tiff │ │ ├── tomo77_042.tiff │ │ ├── tomo77_043.tiff │ │ ├── tomo77_044.tiff │ │ ├── tomo77_045.tiff │ │ ├── tomo77_046.tiff │ │ ├── tomo77_047.tiff │ │ ├── tomo77_048.tiff │ │ ├── tomo77_049.tiff │ │ ├── tomo77_050.tiff │ │ ├── tomo77_051.tiff │ │ ├── tomo77_052.tiff │ │ ├── tomo77_053.tiff │ │ ├── tomo77_054.tiff │ │ ├── tomo77_055.tiff │ │ ├── tomo77_056.tiff │ │ ├── tomo77_057.tiff │ │ ├── tomo77_058.tiff │ │ ├── tomo77_059.tiff │ │ ├── tomo77_060.tiff │ │ ├── tomo77_061.tiff │ │ ├── tomo77_062.tiff │ │ ├── tomo77_063.tiff │ │ ├── tomo77_064.tiff │ │ ├── tomo77_065.tiff │ │ ├── tomo77_066.tiff │ │ ├── tomo77_067.tiff │ │ ├── tomo77_068.tiff │ │ ├── tomo77_069.tiff │ │ ├── tomo77_070.tiff │ │ ├── tomo77_071.tiff │ │ ├── tomo77_072.tiff │ │ ├── tomo77_073.tiff │ │ ├── tomo77_074.tiff │ │ ├── tomo77_075.tiff │ │ ├── tomo77_076.tiff │ │ ├── tomo77_077.tiff │ │ ├── tomo77_078.tiff │ │ ├── tomo77_079.tiff │ │ ├── tomo77_080.tiff │ │ ├── tomo77_081.tiff │ │ ├── tomo77_082.tiff │ │ ├── tomo77_083.tiff │ │ ├── tomo77_084.tiff │ │ ├── tomo77_085.tiff │ │ ├── tomo77_086.tiff │ │ ├── tomo77_087.tiff │ │ ├── tomo77_088.tiff │ │ ├── tomo77_089.tiff │ │ ├── tomo77_090.tiff │ │ ├── tomo77_091.tiff │ │ ├── tomo77_092.tiff │ │ ├── tomo77_093.tiff │ │ ├── tomo77_094.tiff │ │ ├── tomo77_095.tiff │ │ ├── tomo77_096.tiff │ │ ├── tomo77_097.tiff │ │ ├── tomo77_098.tiff │ │ ├── tomo77_099.tiff │ │ ├── tomo77_100.tiff │ │ ├── tomo77_101.tiff │ │ ├── tomo77_102.tiff │ │ ├── tomo77_103.tiff │ │ ├── tomo77_104.tiff │ │ ├── tomo77_105.tiff │ │ ├── tomo77_106.tiff │ │ ├── tomo77_107.tiff │ │ ├── tomo77_108.tiff │ │ ├── tomo77_109.tiff │ │ ├── tomo77_110.tiff │ │ ├── tomo77_111.tiff │ │ ├── tomo77_112.tiff │ │ ├── tomo77_113.tiff │ │ ├── tomo77_114.tiff │ │ ├── tomo77_115.tiff │ │ ├── tomo77_116.tiff │ │ ├── tomo77_117.tiff │ │ ├── tomo77_118.tiff │ │ ├── tomo77_119.tiff │ │ ├── tomo77_120.tiff │ │ ├── tomo77_121.tiff │ │ ├── tomo77_122.tiff │ │ ├── tomo77_123.tiff │ │ ├── tomo77_124.tiff │ │ ├── tomo77_125.tiff │ │ ├── tomo77_126.tiff │ │ ├── tomo77_127.tiff │ │ ├── tomo77_128.tiff │ │ ├── tomo77_129.tiff │ │ ├── tomo77_130.tiff │ │ ├── tomo77_131.tiff │ │ ├── tomo77_132.tiff │ │ ├── tomo77_133.tiff │ │ ├── tomo77_134.tiff │ │ ├── tomo77_135.tiff │ │ ├── tomo77_136.tiff │ │ ├── tomo77_137.tiff │ │ ├── tomo77_138.tiff │ │ ├── tomo77_139.tiff │ │ ├── tomo77_140.tiff │ │ ├── tomo77_141.tiff │ │ ├── tomo77_142.tiff │ │ ├── tomo77_143.tiff │ │ ├── tomo77_144.tiff │ │ ├── tomo77_145.tiff │ │ ├── tomo77_146.tiff │ │ ├── tomo77_147.tiff │ │ ├── tomo77_148.tiff │ │ ├── tomo77_149.tiff │ │ ├── tomo77_150.tiff │ │ ├── tomo77_151.tiff │ │ ├── tomo77_152.tiff │ │ ├── tomo77_153.tiff │ │ ├── tomo77_154.tiff │ │ ├── tomo77_155.tiff │ │ ├── tomo77_156.tiff │ │ ├── tomo77_157.tiff │ │ ├── tomo77_158.tiff │ │ ├── tomo77_159.tiff │ │ ├── tomo77_160.tiff │ │ ├── tomo77_161.tiff │ │ ├── tomo77_162.tiff │ │ ├── tomo77_163.tiff │ │ ├── tomo77_164.tiff │ │ ├── tomo77_165.tiff │ │ ├── tomo77_166.tiff │ │ ├── tomo77_167.tiff │ │ ├── tomo77_168.tiff │ │ ├── tomo77_169.tiff │ │ ├── tomo77_170.tiff │ │ ├── tomo77_171.tiff │ │ ├── tomo77_172.tiff │ │ ├── tomo77_173.tiff │ │ ├── tomo77_174.tiff │ │ ├── tomo77_175.tiff │ │ ├── tomo77_176.tiff │ │ ├── tomo77_177.tiff │ │ ├── tomo77_178.tiff │ │ ├── tomo77_179.tiff │ │ ├── tomo77_180.tiff │ │ ├── tomo77_181.tiff │ │ ├── tomo77_182.tiff │ │ ├── tomo77_183.tiff │ │ ├── tomo77_184.tiff │ │ ├── tomo77_185.tiff │ │ ├── tomo77_186.tiff │ │ ├── tomo77_187.tiff │ │ ├── tomo77_188.tiff │ │ ├── tomo77_189.tiff │ │ ├── tomo77_190.tiff │ │ ├── tomo77_191.tiff │ │ ├── tomo77_192.tiff │ │ ├── tomo77_193.tiff │ │ ├── tomo77_194.tiff │ │ ├── tomo77_195.tiff │ │ ├── tomo77_196.tiff │ │ ├── tomo77_197.tiff │ │ ├── tomo77_198.tiff │ │ ├── tomo77_199.tiff │ │ ├── tomo77_200.tiff │ │ ├── tomo77_201.tiff │ │ ├── tomo77_202.tiff │ │ ├── tomo77_203.tiff │ │ ├── tomo77_204.tiff │ │ ├── tomo77_205.tiff │ │ ├── tomo77_206.tiff │ │ ├── tomo77_207.tiff │ │ ├── tomo77_208.tiff │ │ ├── tomo77_209.tiff │ │ ├── tomo77_210.tiff │ │ ├── tomo77_211.tiff │ │ ├── tomo77_212.tiff │ │ ├── tomo77_213.tiff │ │ ├── tomo77_214.tiff │ │ ├── tomo77_215.tiff │ │ ├── tomo77_216.tiff │ │ ├── tomo77_217.tiff │ │ ├── tomo77_218.tiff │ │ ├── tomo77_219.tiff │ │ ├── tomo77_220.tiff │ │ ├── tomo77_221.tiff │ │ ├── tomo77_222.tiff │ │ ├── tomo77_223.tiff │ │ ├── tomo77_224.tiff │ │ ├── tomo77_225.tiff │ │ ├── tomo77_226.tiff │ │ ├── tomo77_227.tiff │ │ ├── tomo77_228.tiff │ │ ├── tomo77_229.tiff │ │ ├── tomo77_230.tiff │ │ ├── tomo77_231.tiff │ │ ├── tomo77_232.tiff │ │ ├── tomo77_233.tiff │ │ ├── tomo77_234.tiff │ │ ├── tomo77_235.tiff │ │ ├── tomo77_236.tiff │ │ ├── tomo77_237.tiff │ │ ├── tomo77_238.tiff │ │ ├── tomo77_239.tiff │ │ ├── tomo77_240.tiff │ │ ├── tomo77_241.tiff │ │ ├── tomo77_242.tiff │ │ ├── tomo77_243.tiff │ │ ├── tomo77_244.tiff │ │ ├── tomo77_245.tiff │ │ ├── tomo77_246.tiff │ │ ├── tomo77_247.tiff │ │ ├── tomo77_248.tiff │ │ ├── tomo77_249.tiff │ │ ├── tomo77_250.tiff │ │ ├── tomo77_251.tiff │ │ ├── tomo77_252.tiff │ │ ├── tomo77_253.tiff │ │ ├── tomo77_254.tiff │ │ ├── tomo77_255.tiff │ │ ├── tomo77_256.tiff │ │ ├── tomo77_257.tiff │ │ ├── tomo77_258.tiff │ │ ├── tomo77_259.tiff │ │ ├── tomo77_260.tiff │ │ ├── tomo77_261.tiff │ │ ├── tomo77_262.tiff │ │ ├── tomo77_263.tiff │ │ ├── tomo77_264.tiff │ │ ├── tomo77_265.tiff │ │ ├── tomo77_266.tiff │ │ ├── tomo77_267.tiff │ │ ├── tomo77_268.tiff │ │ ├── tomo77_269.tiff │ │ ├── tomo77_270.tiff │ │ ├── tomo77_271.tiff │ │ ├── tomo77_272.tiff │ │ ├── tomo77_273.tiff │ │ ├── tomo77_274.tiff │ │ ├── tomo77_275.tiff │ │ ├── tomo77_276.tiff │ │ ├── tomo77_277.tiff │ │ ├── tomo77_278.tiff │ │ ├── tomo77_279.tiff │ │ ├── tomo77_280.tiff │ │ ├── tomo77_281.tiff │ │ ├── tomo77_282.tiff │ │ ├── tomo77_283.tiff │ │ ├── tomo77_284.tiff │ │ ├── tomo77_285.tiff │ │ ├── tomo77_286.tiff │ │ ├── tomo77_287.tiff │ │ ├── tomo77_288.tiff │ │ ├── tomo77_289.tiff │ │ ├── tomo77_290.tiff │ │ ├── tomo77_291.tiff │ │ ├── tomo77_292.tiff │ │ ├── tomo77_293.tiff │ │ ├── tomo77_294.tiff │ │ ├── tomo77_295.tiff │ │ ├── tomo77_296.tiff │ │ ├── tomo77_297.tiff │ │ ├── tomo77_298.tiff │ │ ├── tomo77_299.tiff │ │ ├── tomo77_300.tiff │ │ ├── tomo77_301.tiff │ │ ├── tomo77_302.tiff │ │ ├── tomo77_303.tiff │ │ ├── tomo77_304.tiff │ │ ├── tomo77_305.tiff │ │ ├── tomo77_306.tiff │ │ ├── tomo77_307.tiff │ │ ├── tomo77_308.tiff │ │ ├── tomo77_309.tiff │ │ ├── tomo77_310.tiff │ │ ├── tomo77_311.tiff │ │ ├── tomo77_312.tiff │ │ ├── tomo77_313.tiff │ │ ├── tomo77_314.tiff │ │ ├── tomo77_315.tiff │ │ ├── tomo77_316.tiff │ │ ├── tomo77_317.tiff │ │ ├── tomo77_318.tiff │ │ ├── tomo77_319.tiff │ │ ├── tomo77_320.tiff │ │ ├── tomo77_321.tiff │ │ ├── tomo77_322.tiff │ │ ├── tomo77_323.tiff │ │ ├── tomo77_324.tiff │ │ ├── tomo77_325.tiff │ │ ├── tomo77_326.tiff │ │ ├── tomo77_327.tiff │ │ ├── tomo77_328.tiff │ │ ├── tomo77_329.tiff │ │ ├── tomo77_330.tiff │ │ ├── tomo77_331.tiff │ │ ├── tomo77_332.tiff │ │ ├── tomo77_333.tiff │ │ ├── tomo77_334.tiff │ │ ├── tomo77_335.tiff │ │ ├── tomo77_336.tiff │ │ ├── tomo77_337.tiff │ │ ├── tomo77_338.tiff │ │ ├── tomo77_339.tiff │ │ ├── tomo77_340.tiff │ │ ├── tomo77_341.tiff │ │ ├── tomo77_342.tiff │ │ ├── tomo77_343.tiff │ │ ├── tomo77_344.tiff │ │ ├── tomo77_345.tiff │ │ ├── tomo77_346.tiff │ │ ├── tomo77_347.tiff │ │ ├── tomo77_348.tiff │ │ ├── tomo77_349.tiff │ │ ├── tomo77_350.tiff │ │ ├── tomo77_351.tiff │ │ ├── tomo77_352.tiff │ │ ├── tomo77_353.tiff │ │ ├── tomo77_354.tiff │ │ ├── tomo77_355.tiff │ │ ├── tomo77_356.tiff │ │ ├── tomo77_357.tiff │ │ ├── tomo77_358.tiff │ │ ├── tomo77_359.tiff │ │ ├── tomo77_360.tiff │ │ ├── tomo77_361.tiff │ │ ├── tomo77_362.tiff │ │ ├── tomo77_363.tiff │ │ ├── tomo77_364.tiff │ │ ├── tomo77_365.tiff │ │ ├── tomo77_366.tiff │ │ ├── tomo77_367.tiff │ │ ├── tomo77_368.tiff │ │ ├── tomo77_369.tiff │ │ ├── tomo77_370.tiff │ │ ├── tomo77_371.tiff │ │ ├── tomo77_372.tiff │ │ ├── tomo77_373.tiff │ │ ├── tomo77_374.tiff │ │ ├── tomo77_375.tiff │ │ ├── tomo77_376.tiff │ │ ├── tomo77_377.tiff │ │ ├── tomo77_378.tiff │ │ ├── tomo77_379.tiff │ │ ├── tomo77_380.tiff │ │ ├── tomo77_381.tiff │ │ ├── tomo77_382.tiff │ │ ├── tomo77_383.tiff │ │ ├── tomo77_384.tiff │ │ ├── tomo77_385.tiff │ │ ├── tomo77_386.tiff │ │ ├── tomo77_387.tiff │ │ ├── tomo77_388.tiff │ │ ├── tomo77_389.tiff │ │ ├── tomo77_390.tiff │ │ ├── tomo77_391.tiff │ │ ├── tomo77_392.tiff │ │ ├── tomo77_393.tiff │ │ ├── tomo77_394.tiff │ │ ├── tomo77_395.tiff │ │ ├── tomo77_396.tiff │ │ ├── tomo77_397.tiff │ │ ├── tomo77_398.tiff │ │ ├── tomo77_399.tiff │ │ ├── tomo77_400.tiff │ │ ├── tomo77_401.tiff │ │ ├── tomo77_402.tiff │ │ ├── tomo77_403.tiff │ │ ├── tomo77_404.tiff │ │ ├── tomo77_405.tiff │ │ ├── tomo77_406.tiff │ │ ├── tomo77_407.tiff │ │ ├── tomo77_408.tiff │ │ ├── tomo77_409.tiff │ │ ├── tomo77_410.tiff │ │ ├── tomo77_411.tiff │ │ ├── tomo77_412.tiff │ │ ├── tomo77_413.tiff │ │ ├── tomo77_414.tiff │ │ ├── tomo77_415.tiff │ │ ├── tomo77_416.tiff │ │ ├── tomo77_417.tiff │ │ ├── tomo77_418.tiff │ │ ├── tomo77_419.tiff │ │ ├── tomo77_420.tiff │ │ ├── tomo77_421.tiff │ │ ├── tomo77_422.tiff │ │ ├── tomo77_423.tiff │ │ ├── tomo77_424.tiff │ │ ├── tomo77_425.tiff │ │ ├── tomo77_426.tiff │ │ ├── tomo77_427.tiff │ │ ├── tomo77_428.tiff │ │ ├── tomo77_429.tiff │ │ ├── tomo77_430.tiff │ │ ├── tomo77_431.tiff │ │ ├── tomo77_432.tiff │ │ ├── tomo77_433.tiff │ │ ├── tomo77_434.tiff │ │ ├── tomo77_435.tiff │ │ ├── tomo77_436.tiff │ │ ├── tomo77_437.tiff │ │ ├── tomo77_438.tiff │ │ ├── tomo77_439.tiff │ │ ├── tomo77_440.tiff │ │ ├── tomo77_441.tiff │ │ ├── tomo77_442.tiff │ │ ├── tomo77_443.tiff │ │ ├── tomo77_444.tiff │ │ ├── tomo77_445.tiff │ │ ├── tomo77_446.tiff │ │ ├── tomo77_447.tiff │ │ ├── tomo77_448.tiff │ │ ├── tomo77_449.tiff │ │ └── tomo77_450.tiff ├── hdf_browser.ipynb ├── scripts │ └── multi_energy_script.py └── shift_projections.ipynb ├── pyproject.toml ├── setup.cfg ├── setup.py └── tomopyui ├── __init__.py ├── _sharedvars.py ├── _version.py ├── backend ├── __init__.py ├── hdf_handler.py ├── io.py ├── io_multienergy.py ├── runanalysis.py └── util │ ├── __init__.py │ ├── center.py │ ├── dask_downsample.py │ ├── dxchange │ ├── __init__.py │ └── reader.py │ ├── padding.py │ └── registration │ ├── __init__.py │ ├── _masked_phase_cross_correlation_cupy.py │ ├── _phase_cross_correlation_cucim.py │ ├── _phase_cross_correlation_cupy.py │ ├── fft.py │ └── fft_cucim.py ├── gpu ├── __init__.py ├── prep │ ├── __init__.py │ ├── alignment.py │ └── sampling.py └── recon │ ├── __init__.py │ └── algorithm.py └── widgets ├── __init__.py ├── analysis.py ├── center.py ├── dataexplorer.py ├── hdf_imports.py ├── hdf_tree.py ├── hdf_viewer.py ├── helpers.py ├── imports.py ├── main.py ├── prep.py ├── styles.py ├── tools.py └── view.py /.gitattributes: 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