Search.setIndex({"alltitles": {"0. 1D and 2D integration": [[104, "0.-1D-and-2D-integration"]], "0.10.0: 10/2014": [[20, "id31"]], "0.10.1: 10/2014": [[20, "id30"]], "0.10.2: 11/2014": [[20, "id29"]], "0.10.3: 03/2015": [[20, "id28"]], "0.11.0: 07/2015": [[20, "id27"]], "0.12.0: 06/06/2016": [[20, "id26"]], "0.13.0: 01/12/2016": [[20, "id25"]], "0.14.0: 20/07/2017": [[20, "id24"]], "0.14.1: 25/07/2017": [[20, "id23"]], "0.14.2: 14/09/2017": [[20, "id22"]], "0.15.0: 01/02/2018": [[20, "id21"]], "0.16.0: 26/10/2018": [[20, "id20"]], "0.17.0 19/12/2018": [[20, "id19"]], "0.18.0 15/05/2019": [[20, "id18"]], "0.19.0 31/01/2020": [[20, "id17"]], "0.1: 05/2011": [[20, "id44"]], "0.20.0 22/01/2021": [[20, "id16"]], "0.21.0 20/01/2022": [[20, "id15"]], "0.21.1 02/02/2022": [[20, "id14"]], "0.21.2 03/02/2022": [[20, "id13"]], "0.21.3 24/03/2022": [[20, "id12"]], "0.2: 07/2011": [[20, "id43"]], "0.3: 11/2011": [[20, "id42"]], "0.4: 06/2012": [[20, "id41"]], "0.5: 06/2012": [[20, "id40"]], "0.6: 07/2012": [[20, "id39"]], "0.7.2: 08/2012": [[20, "id37"]], "0.7: 07/2012": [[20, "id38"]], "0.8: 10/2012": [[20, "id36"]], "0.9.2: (01/2014)": [[20, "id34"]], "0.9.3:  02/2014": [[20, "id33"]], "0.9.4:  06/2014": [[20, "id32"]], "0.9: 10/2013": [[20, "id35"]], "1. Description of the computer.": [[95, "1.-Description-of-the-computer."]], "1. Generate images with the 4 orientations:": [[94, "1.-Generate-images-with-the-4-orientations:"]], "1. Separation based on 2D integration": [[104, "1.-Separation-based-on-2D-integration"]], "1D azimuthal integration": [[90, "1D-azimuthal-integration"]], "2. Separation based on 1D integration:": [[104, "2.-Separation-based-on-1D-integration:"]], "2. Setup the enviroment:": [[95, "2.-Setup-the-enviroment:"]], "2023.01 16/01/2023": [[20, "id11"]], "2023.02 27/02/2023": [[20, "id10"]], "2023.03 22/03/2023": [[20, "id9"]], "2023.05 16/05/2023": [[20, "id8"]], "2023.08 30/08/2023 BUGGY, DO NOT USE !!!": [[20, "buggy-do-not-use"]], "2023.09 08/09/2023": [[20, "id7"]], "2024.01 18/01/2024": [[20, "id6"]], "2024.02 01/02/2024": [[20, "id5"]], "2024.05 21/05/2024": [[20, "id4"]], "2024.09 12/09/2024": [[20, "id3"]], "2025.01 31/01/2025": [[20, "id2"]], "2025.03 14/03/2025": [[20, "id1"]], "2D Integration in non-azimuthal space": [[122, null]], "2D integration or Caking": [[90, "2D-integration-or-Caking"]], "3. Rebuild the isotropic and anisotropic contribution": [[104, "3.-Rebuild-the-isotropic-and-anisotropic-contribution"]], "3. Writing the test dataset on disk.": [[95, "3.-Writing-the-test-dataset-on-disk."]], "3D rendering": [[60, "d-rendering"]], "4. Implementation of sigma-clipping using pure 1D integrators.": [[104, "4.-Implementation-of-sigma-clipping-using-pure-1D-integrators."]], "4. Reading the dataset using the h5py/HDF5 library:": [[95, "4.-Reading-the-dataset-using-the-h5py/HDF5-library:"]], "4.1 Using the h5py API in a natural way": [[95, "4.1-Using-the-h5py-API-in-a-natural-way"]], "4.2 Pre-allocate the output buffer (for h5py)": [[95, "4.2-Pre-allocate-the-output-buffer-(for-h5py)"]], "5. Decouple HDF5 chunk reading from decompression.": [[95, "5.-Decouple-HDF5-chunk-reading-from-decompression."]], "5. Variance assessement from deviation to the mean": [[104, "5.-Variance-assessement-from-deviation-to-the-mean"]], "5.1 Benchmarking of the chunk reading using the read_direct_chunk from h5py": [[95, "5.1-Benchmarking-of-the-chunk-reading-using-the-read_direct_chunk-from-h5py"]], "5.2 Benchmarking of the decompression (single threaded)": [[95, "5.2-Benchmarking-of-the-decompression-(single-threaded)"]], "5.3 Benchmark the analysis of the HDF5 file": [[95, "5.3-Benchmark-the-analysis-of-the-HDF5-file"]], "5.4 Benchmark the chunk reading using the h5py direct chunk read": [[95, "5.4-Benchmark-the-chunk-reading-using-the-h5py-direct-chunk-read"]], "5.5 Benchmark the chunk reading using numpy.memmap": [[95, "5.5-Benchmark-the-chunk-reading-using-numpy.memmap"]], "5.5 Benchmark the chunk reading using the Python file interface": [[95, "5.5-Benchmark-the-chunk-reading-using-the-Python-file-interface"]], "6. Azimuthal integration": [[95, "6.-Azimuthal-integration"]], "6. Towards lossy compression of single crystal diffraction data": [[104, "6.-Towards-lossy-compression-of-single-crystal-diffraction-data"]], "6.1 Serial workflow": [[95, "6.1-Serial-workflow"]], "6.1.1 Prepare the azimuthal integrator": [[95, "6.1.1-Prepare-the-azimuthal-integrator"]], "6.1.2 Benchmarking of the serial workflow": [[95, "6.1.2-Benchmarking-of-the-serial-workflow"]], "6.2 Pool of threads, queues,": [[95, "6.2-Pool-of-threads,-queues,"]], "6.3 Parallelize decompression + processing": [[95, "6.3-Parallelize-decompression-+-processing"]], "6.3 Parallelize read + decompression + processing": [[95, "6.3-Parallelize-read-+-decompression-+-processing"]], "6.3.1 Parallelize read + decompression + processing using the Python file interface": [[95, "6.3.1-Parallelize-read-+-decompression-+-processing-using-the-Python-file-interface"]], "6.3.1 Parallelize read + decompression + processing using the numpy.memmap interface": [[95, "6.3.1-Parallelize-read-+-decompression-+-processing-using-the-numpy.memmap-interface"]], "7. Conclusion": [[104, "7.-Conclusion"]], "7. Display some results": [[95, "7.-Display-some-results"]], "7. Evolution of the performances with the number of threads": [[95, "7.-Evolution-of-the-performances-with-the-number-of-threads"]], "8. Conclusion": [[95, "8.-Conclusion"]], "APIs for integrate1d using the exit angles and polar angles": [[80, "APIs-for-integrate1d-using-the-exit-angles-and-polar-angles"]], "About Microsoft Visual Studio Compiler": [[53, "about-microsoft-visual-studio-compiler"]], "About OpenMP": [[52, "about-openmp"]], "About statstics": [[117, "About-statstics"]], "Absorption coeficient at 17.8 keV": [[116, "Absorption-coeficient-at-17.8-keV"]], "Abstract": [[23, "abstract"]], "Accumulators": [[58, "accumulators"]], "Acknowledgments": [[57, "acknowledgments"]], "Acquire some more control points": [[59, "acquire-some-more-control-points"]], "Advanced video tutorial": [[60, "advanced-video-tutorial"]], "All other Modules": [[108, "All-other-Modules"]], "And also getting the intensity profile integrated across the polar angle (be careful, by default the fiber integration is vertical)": [[93, "And-also-getting-the-intensity-profile-integrated-across-the-polar-angle-(be-careful,-by-default-the-fiber-integration-is-vertical)"]], "AppVeyor": [[55, "appveyor"]], "Application manuals": [[48, null]], "As most of the Python projects:": [[55, "as-most-of-the-python-projects"]], "Automatic calibration": [[83, "Automatic-calibration"]], "Automatic peak-extraction": [[60, "automatic-peak-extraction"]], "Azimuthal Integration": [[120, "Azimuthal-Integration"]], "Azimuthal average": [[58, "azimuthal-average"]], "Azimuthal averaging in log-scaled bins": [[91, null]], "Azimuthal averaging using pyFAI": [[63, "Azimuthal-averaging-using-pyFAI"]], "Azimuthal integration for powder diffraction": [[64, "Azimuthal-integration-for-powder-diffraction"]], "Azimuthal integration for small angle data": [[64, "Azimuthal-integration-for-small-angle-data"]], "Azimuthal integration methods": [[23, "azimuthal-integration-methods"]], "Azimuthal integration options": [[65, "azimuthal-integration-options"]], "Azimuthal integration using the graphical user interface": [[65, null]], "Azimuthal integration with pixel splitting": [[119, "Azimuthal-integration-with-pixel-splitting"]], "Azimuthal regrouping using pyFAI": [[63, "Azimuthal-regrouping-using-pyFAI"]], "Azimuthal sigma-clipping": [[67, "Azimuthal-sigma-clipping"]], "AzimuthalIntegrator": [[23, "azimuthalintegrator"], [29, "azimuthalintegrator"]], "Basic usage of pyFAI": [[63, "Basic-usage-of-pyFAI"]], "Benchmarking and optimization of the parameters": [[89, "Benchmarking-and-optimization-of-the-parameters"]], "Bibliography": [[18, null]], "Blob detection": [[19, "blob-detection"]], "Bubble": [[26, "bubble"]], "Bugs:": [[34, "bugs"]], "Build dependencies": [[55, "build-dependencies"]], "Build dependencies:": [[50, "build-dependencies"]], "Build from sources": [[51, "build-from-sources"]], "Building procedure": [[50, "building-procedure"], [55, "building-procedure"]], "CCD calibration": [[73, null]], "Cake and Integration": [[60, "cake-and-integration"]], "Calculate the approximate correction of the other positions": [[81, "Calculate-the-approximate-correction-of-the-other-positions"]], "Calibrant selection and generation": [[70, null]], "Calibration": [[19, null], [29, "calibration"], [57, "calibration"]], "Calibration of a 2 theta arm with a Pilatus 100k detector": [[85, null]], "Calibration of a detector on a translation table": [[87, null]], "Calibration of a diffraction setup using Jupyter notebooks": [[61, null]], "Calibration of a diffraction setup using the Command Line Interface (CLI)": [[59, null]], "Calibration of a diffraction setup using the Graphical User Interface (GUI)": [[60, null]], "Calibration of a very large Pilatus detector with overlapping grid position": [[76, null]], "Calibration of all frames in automatic mode:": [[84, "Calibration-of-all-frames-in-automatic-mode:"]], "Calibration of the 9-Mythen detector at the Cristal beamline at Soleil": [[108, null]], "Calibration of the central position": [[81, "Calibration-of-the-central-position"]], "Calibration of the pixel position for a Pilatus detector": [[77, null]], "Calibration tool: MX-calibrate": [[31, null]], "Calibration tool: check_calib": [[32, null]], "Calibration tool: pyFAI-calib": [[40, null]], "Calibration tool: pyFAI-calib2": [[41, null]], "Calibration tool: pyFAI-recalib": [[45, null]], "Change-log of versions": [[20, null]], "Common tool for azimuthal intration": [[64, "Common-tool-for-azimuthal-intration"]], "Comparison with the original \u201cpeakfinder8\u201d": [[103, "Comparison-with-the-original-%22peakfinder8%22"]], "Complex detectors": [[25, "complex-detectors"]], "Conclusion": [[25, "conclusion"], [57, "conclusion"], [58, "conclusion"], [60, "conclusion"], [61, "Conclusion"], [63, "Conclusion"], [64, "Conclusion"], [67, "Conclusion"], [68, "Conclusion"], [69, "Conclusion"], [71, "Conclusion"], [72, "Conclusion"], [73, "Conclusion"], [74, "Conclusion"], [75, "Conclusion"], [76, "Conclusion"], [77, "Conclusion"], [79, "Conclusion"], [82, "Conclusion"], [85, "Conclusion"], [87, "Conclusion"], [89, "Conclusion"], [90, "Conclusion"], [91, "Conclusion"], [92, "Conclusion"], [93, "Conclusion"], [94, "Conclusion"], [96, "Conclusion"], [97, "Conclusion"], [98, "Conclusion"], [100, "Conclusion"], [101, "Conclusion"], [102, "Conclusion"], [103, "Conclusion"], [108, "Conclusion"], [112, "Conclusion"], [113, "Conclusion"], [117, "Conclusion"], [119, "Conclusion"], [123, "conclusion"]], "Conclusion of the raytracing part:": [[116, "Conclusion-of-the-raytracing-part:"]], "Conclusion on deconvolution using least-squares:": [[113, "Conclusion-on-deconvolution-using-least-squares:"]], "Conclusion:": [[84, "Conclusion:"], [114, "Conclusion:"]], "Conclusions": [[80, "Conclusions"], [83, "Conclusions"]], "Construction of a synthetic dataset": [[119, "Construction-of-a-synthetic-dataset"]], "Content of the file": [[71, "Content-of-the-file"]], "Continuous integration": [[55, "continuous-integration"]], "Conventions": [[21, null]], "Conventions from the detector manufacturer": [[21, "conventions-from-the-detector-manufacturer"]], "Conversion": [[28, "conversion"]], "Converting the calibration from Dioptas to process data with pyFAI": [[21, "converting-the-calibration-from-dioptas-to-process-data-with-pyfai"]], "Cookbook recipes": [[62, null]], "Coordinates": [[28, "coordinates"], [28, "id2"], [28, "id5"]], "Creation of a calibrant file": [[71, null]], "Creation of a new calibrant": [[69, null], [72, null]], "Creation of a new radial unit": [[91, "Creation-of-a-new-radial-unit"]], "Creation of diffraction images": [[92, "Creation-of-diffraction-images"], [93, "Creation-of-diffraction-images"]], "Creation of the MultiGeometry": [[92, "Creation-of-the-MultiGeometry"]], "Creation of the image": [[89, "Creation-of-the-image"]], "DESCRIPTION": [[36, "description"], [42, "description"], [45, "description"]], "Dahu": [[26, "dahu"]], "Deconvolution of the Thickness effect": [[113, null]], "Default geometry in pyFAI": [[27, "default-geometry-in-pyfai"]], "Define the detector": [[68, "Define-the-detector"]], "Define the right mask": [[75, "Define-the-right-mask"]], "Defining a detector from a spline file": [[74, "Defining-a-detector-from-a-spline-file"]], "Defining the mask": [[60, "defining-the-mask"]], "Definition of the geometry transformation": [[85, "Definition-of-the-geometry-transformation"]], "Demo of usage of the MultiGeometry class of pyFAI": [[92, null]], "Demo of usage of the MultiGeometryFiber class of pyFAI": [[93, null]], "Demonstration": [[82, "Demonstration"]], "Dependencies": [[50, "dependencies"]], "Design of AzimuthalIntegrator": [[23, null]], "Design of the library": [[24, null]], "Detailed installation procedure": [[50, "detailed-installation-procedure"]], "Detector": [[23, "detector"], [28, null], [28, "id1"], [29, "detector"], [57, "detector"]], "Detector D-matrix": [[28, "detector-d-matrix"]], "Detector definition files as NeXus files": [[74, "Detector-definition-files-as-NeXus-files"]], "Detector definitions": [[74, "Detector-definitions"]], "Detector distortion corrections": [[74, null]], "Detector geometric distortions and corrections": [[78, null]], "Detector orientation": [[21, "detector-orientation"]], "Detector position": [[27, "detector-position"]], "Detectors classes": [[25, "detectors-classes"]], "Dioptas": [[26, "dioptas"]], "Discard wronly assigned peaks": [[108, "Discard-wronly-assigned-peaks"]], "Display of an image and its headers": [[85, "Display-of-an-image-and-its-headers"]], "Display some results": [[96, "Display-some-results"]], "Distortion": [[29, "distortion"]], "Distortion correction": [[74, "Distortion-correction"]], "Distortion of Eiger2 CdTe detector from ID11": [[75, null]], "Dpdak": [[26, "dpdak"]], "EDNA": [[26, "edna"]], "Ecosystem": [[26, null]], "Effect of pixel splitting on 2D integration": [[100, "Effect-of-pixel-splitting-on-2D-integration"]], "Environment variables": [[50, "environment-variables"]], "Error model validator": [[118, null]], "Estimation of the pixel size:": [[73, "Estimation-of-the-pixel-size:"]], "Evaluation of the peak-profile": [[85, "Evaluation-of-the-peak-profile"]], "Example of Pixel-detectors:": [[74, "Example-of-Pixel-detectors:"]], "Example of usage": [[66, null]], "Example of usage:": [[40, "example-of-usage"]], "Examples": [[123, "examples"]], "Experiment description": [[57, "experiment-description"]], "Experiment settings": [[60, "experiment-settings"]], "Experimental setup": [[68, "Experimental-setup"]], "Experimental setup options:": [[37, "experimental-setup-options"], [49, "experimental-setup-options"]], "Experimental validation of the Formula:": [[120, "Experimental-validation-of-the-Formula:"]], "Extract the flatfield for all positions": [[81, "Extract-the-flatfield-for-all-positions"]], "Extracting ellipse parameters from rings": [[79, null]], "FReLoN detector": [[74, "FReLoN-detector"]], "FabIO": [[26, "fabio"]], "Fast Azimuthal Integration using Python": [[30, null]], "Feedback from integrated result to improve the mask": [[60, "feedback-from-integrated-result-to-improve-the-mask"]], "FiberIntegrator": [[80, "FiberIntegrator"]], "FiberIntegrator introduces three new parameters:": [[80, "FiberIntegrator-introduces-three-new-parameters:"]], "FiberIntegrator methods use non-pixel-splitting by default": [[80, "FiberIntegrator-methods-use-non-pixel-splitting-by-default"]], "Filtering signal in azimuthal space": [[67, null]], "Fit all modules of the central grid position:": [[76, "Fit-all-modules-of-the-central-grid-position:"]], "Fit all modules of the left grid position:": [[76, "Fit-all-modules-of-the-left-grid-position:"]], "Fit all modules of the right grid position:": [[76, "Fit-all-modules-of-the-right-grid-position:"]], "Fit all modules togeather": [[76, "Fit-all-modules-togeather"]], "Fit the grid on a reference module for each position": [[76, "Fit-the-grid-on-a-reference-module-for-each-position"]], "Fitting wavelength with multiple sample-detector distances": [[83, null]], "Flatfield calibration": [[81, null]], "For ESRF staff and users": [[90, "For-ESRF-staff-and-users"]], "From silx repository": [[51, "from-silx-repository"]], "General introduction": [[57, null]], "Generate an azimuthal integrator, integrate and look at the background:": [[102, "Generate-an-azimuthal-integrator,-integrate-and-look-at-the-background:"]], "Generation of diffraction images": [[92, "Generation-of-diffraction-images"], [93, "Generation-of-diffraction-images"]], "Geometries in pyFAI": [[82, null]], "Geometry": [[23, "geometry"], [29, "geometry"], [57, "geometry"]], "Geometry conversion": [[57, "geometry-conversion"]], "Geometry definition of ImageD11": [[28, "geometry-definition-of-imaged11"]], "Geometry definition of pyFAI": [[28, "geometry-definition-of-pyfai"]], "Geometry fitting": [[60, "geometry-fitting"]], "Get Python": [[53, "get-python"]], "Get all additional data": [[59, "get-all-additional-data"]], "Getting access to the notebook:": [[90, "Getting-access-to-the-notebook:"]], "Getting help": [[55, "getting-help"]], "Getting trained in using the notebook": [[90, "Getting-trained-in-using-the-notebook"]], "Glossary": [[29, null]], "Goniometer and translation table calibration": [[88, null]], "Grid assignment": [[75, "Grid-assignment"], [76, "Grid-assignment"], [77, "Grid-assignment"]], "Grid spot position measurement.": [[75, "Grid-spot-position-measurement."]], "Guinier-like scatterer image": [[91, "Guinier-like-scatterer-image"]], "Half a FReLoN CCD image of Lantanide hexaboride taken at ESRF-ID11:": [[40, "half-a-frelon-ccd-image-of-lantanide-hexaboride-taken-at-esrf-id11"]], "Hardware requirement": [[50, "hardware-requirement"]], "High performance computing": [[99, null]], "How it works": [[123, "how-it-works"]], "How to fill-up gaps in arrays of pixel detectors during 2D integration": [[92, "How-to-fill-up-gaps-in-arrays-of-pixel-detectors-during-2D-integration"]], "How to retrieve dynamically masked pixels during sigma-clipping": [[107, null]], "How to use pyFAI to display or reduce data from grazing-incidence/fiber scattering experiments": [[80, "How-to-use-pyFAI-to-display-or-reduce-data-from-grazing-incidence/fiber-scattering-experiments"]], "Idea": [[123, "idea"]], "If we choose polar units, we can cake (remap) the image in the classic but taking into account the missing wedge": [[93, "If-we-choose-polar-units,-we-can-cake-(remap)-the-image-in-the-classic-but-taking-into-account-the-missing-wedge"]], "ImXPAD S540 detector at D2AM": [[86, null]], "Image": [[29, "image"]], "Image decompression and azimuthal integration on the GPU": [[96, null]], "Image processing": [[76, "Image-processing"], [77, "Image-processing"]], "Image representation in Python": [[27, null]], "Implementation of PeakFinder8 on GPU": [[103, null]], "Indices and tables": [[30, "indices-and-tables"]], "Initalize azimuthal integrator with different orientation:": [[94, "Initalize-azimuthal-integrator-with-different-orientation:"]], "Initialization and loading of the libraries": [[85, "Initialization-and-loading-of-the-libraries"]], "Initialization of the notebook for matplotlib integration:": [[63, "Initialization-of-the-notebook-for-matplotlib-integration:"]], "Inpainting": [[89, "Inpainting"]], "Inpainting missing data": [[89, null]], "Install Python3:": [[52, "install-python3"]], "Install pyFAI from sources": [[53, "install-pyfai-from-sources"]], "Install pyFAI via PIP": [[53, "install-pyfai-via-pip"]], "Installation": [[50, null]], "Installation from sources": [[52, "installation-from-sources"]], "Installation procedure on Debian/Ubuntu": [[51, "installation-procedure-on-debian-ubuntu"]], "Installation procedure on Linux": [[51, null]], "Installation procedure on MacOSX": [[52, null]], "Installation procedure on Windows": [[53, null]], "Installation procedure on other linux distibution": [[51, "installation-procedure-on-other-linux-distibution"]], "Integrate a bunch of images": [[65, "integrate-a-bunch-of-images"]], "Integration of a bunch of files using pyFAI": [[90, "Integration-of-a-bunch-of-files-using-pyFAI"]], "Integration of images in the SAXS appoximation:": [[119, "Integration-of-images-in-the-SAXS-appoximation:"]], "Integration of images with solid angle correction/polarization correction": [[119, "Integration-of-images-with-solid-angle-correction/polarization-correction"]], "Integration of the pattern for the two extreme cases": [[68, "Integration-of-the-pattern-for-the-two-extreme-cases"]], "Integration tool: diff_map": [[34, null]], "Integration tool: diff_tomo": [[35, null]], "Integration tool: pyFAI-integrate": [[44, null]], "Integration tool: pyFAI-saxs": [[46, null]], "Integration tool: pyFAI-waxs": [[47, null]], "Integration with Python": [[63, null]], "Interpolation of the fitted data": [[73, "Interpolation-of-the-fitted-data"]], "Introducing the new generation of azimuthal integrator \u2026 in production since 0.20": [[119, "Introducing-the-new-generation-of-azimuthal-integrator-...-in-production-since-0.20"]], "Introduction": [[57, "introduction"]], "Introduction to diffraction image analysis using the notebook": [[90, "Introduction-to-diffraction-image-analysis-using-the-notebook"]], "Introduction to the tutorials": [[90, null]], "Inversion: Finding where a scattered beam hits the detector": [[28, "inversion-finding-where-a-scattered-beam-hits-the-detector"]], "Investigation on the rotations:": [[82, "Investigation-on-the-rotations:"]], "Jupyter in the cloud": [[90, "Jupyter-in-the-cloud"]], "LImA": [[26, "lima"]], "Laue diffraction peak identification": [[102, null]], "Least squares refinement of the pseudo-inverse": [[116, "Least-squares-refinement-of-the-pseudo-inverse"]], "Linux": [[55, "linux"]], "List of contributors in code": [[55, 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