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welcome to atomap s documentation atomap 0 4 3 dev1 documentation atomap installing start atomap finding the atom lattice analysing atom lattices dumbbell lattice several phases gui functionality automation of the analysis examples quantification working with atomic models quantify scan distortions making datasets for testing plotting for publications various tools become a contributor development guide api documentation atomap welcome to atomap s documentation view page source welcome to atomap s documentation news 2025 1 18 atomap has moved to github the development of atomap has moved from https gitlab com atomap atomap to https github com atomap dev atomap while gitlab has been a good home for atomap most of the hyperspy community is on github so this move will make collaboration with the rest of the community easier 2025 1 5 atomap 0 4 2 released this is a small release which greatly improves the performance of remove_atoms_from_image_using_2d_gaussian making it easier to work with large images with multiple sublattices it also includes several minor style and linting fixes about atomap atomap is a python library for analysing atomic resolution scanning transmission electron microscopy images it relies in fitting 2 d gaussian functions to every atomic column in an image and automatically find all major symmetry axes the full procedure is explained in the article atomap a new software tool for the automated analysis of atomic resolution images using two dimensional gaussian fitting the easiest way to try atomap is via binder introductory jupyter notebook to install atomap on your own computer see the install instructions measuring the ellipticity of atomic columns more info mapping the variation in distance between oxygen columns more information atomap is under development and still in alpha so bugs and errors can be expected bug reports and feature requests are welcome on the issue tracker contributors are welcome too if you publish scientific articles using atomap please consider citing the article atomap a new software tool for the automated analysis of atomic resolution images using two dimensional gaussian fitting m nord et al advanced structural and chemical imaging 2017 3 9 atomap is available under the gnu gpl v3 license the source code is found in the github repository contents on this webpage installing hyperspy bundle anaconda python distribution pypi installation development version start atomap tutorials finding the atom lattice a simple cubic structure images with more than one sublattice finding the oxygen sublattice analysing atom lattices fantasite the dummy structure the atom_lattice object ellipticity distance between monolayers atom distance difference angle between atoms integration of atomic columns line profiles finding polarization plotting a pair distribution function dumbbell lattice dumbbell vector making the dumbbell lattice analysing the image several phases precipitate matrix analysing the sublattices gui functionality selecting atoms with gui adding atoms using gui toggle atom refine automation of the analysis finding atom lattices with process parameters making process parameters examples dumbbell example nanoparticle example precipitate example perovskite oxide quantification absolute integrator statistical method working with atomic models exporting to atomic models importing atomic models quantify scan distortions making datasets for testing large amount of atoms plotting for publications saving specific data matplotlib various tools rotating image and points working with single atom sublattices become a contributor why contribute what to contribute version control first steps setting up git second steps adding something learn more development guide testing style checks generating the sphinx page continuous integration api documentation classes modules index module index old news 2024 10 20 atomap 0 4 1 released this is a maintenance release making atomap work with numpy 2 0 it also updates atomap to use pyproject toml instead of setup py 2024 02 17 atomap 0 4 0 released this release is the first to work with the new 2 0 0 version of hyperspy the major change is a large improvement in plotting speed for example sublattice plot or sublattice plot_planes thanks to a reimplementation of hyperspy s marker functionality thanks to carter francis for the merge request there has also been some minor updates of the install instructions and fixes for deprecation warnings 2023 11 18 atomap 0 3 4 released this release has a large performance improvement for the 2d gaussian refinement which is especially noticeable for large images with many atoms a new parameter nearest_neighbors has been added to sublattice construct_zone_axes increasing it will give more atomic planes note due to a new api breaking version of hyperspy 2 0 0 this atomap release will be the last which will work with the older hyperspy versions 1 x x thus the next releases will only work with hyperspy 2 0 0 or higher most users should not notice any differences 2023 5 17 atomap 0 3 3 released this is a small maintenance release fixing some deprecation warning style issues and fixing a plotting bug when visualizing vectors 2022 4 28 atomap 0 3 2 released this is a maintenance release updating atomap to work with the newly released hyperspy 1 7 2021 6 11 atomap 0 3 1 released this is a small release with one bug fix from tom slater and two performance improvements from niels cautaerts the latter are related to finding the initial atomic column positions and will especially improve the processing time for large images 2021 4 23 try atomap without having to install anything via binder introductory jupyter notebook 2021 1 30 atomap 0 3 0 released information about the 3d structure of sublattices can now be added allowing for 3d atomic models to be converted into an atom_lattice via the atomic simulation environment and vice versa this 3d information can be set manually or via the intensity for homogeneous structures see statistical method and working with atomic models for more info thanks to tom slater and eoghan o connell for implementing this the performance of atomic column integration has been greatly improved atomap integrate and atom_lattice integrate_column_intensity will be much faster now thanks to thomas aarholt set_scale method in atom_lattice and sublattice has been added for easily setting the scale and unit better support for visualizing atom_lattice and sublattice objects with scaled units thanks to eoghan o connell for adding this 2020 1 29 atomap 0 2 1 released new method for getting a pair distribution function see the documentation for more info thanks to tom slater for implementing this add a method for getting the local often high frequency scanning distortions utilizing the shape of the atomic columns quantify scan distortions improved the progressbar when using atomap in jupyter notebooks thanks to alexander skorikov 2019 10 17 atomap 0 2 0 released greatly improved documentation notebook and several new functions for analysing images with dumbbell features like si or gaas new gui tool for selection a subset of atom positions making it easier to work on images with several phases statistical quantification using gaussian mixture model thanks to tom slater for implementing this functions in the atom_position class calculate_max_intensity and calculate_min_intensity thanks to eoghan o connell for implementing this 2019 03 05 atomap 0 1 4 released this release includes functions to find shifts within unit cells often seen in materials with polarization this can for example be used to find shifts in b cations in relation to the a cations in a perovskite structure finding polarization big optimization in refining the atom positions using centre of mass which makes it much easier to work with images containing a large number of atoms for smaller images the improvement is around 5 10 times while for larger ones it is 1000 times faster thanks to thomas aarholt for implementing this similar optimizations to get_model_image which is primarily used to generate test data via the dummy data module this means generating test data like get_fantasite is 60 times faster with even bigger improvements to larger test data thanks to annick de backer at emat for tips on how to improve this another optimization for the integration of atomic columns functionality is in the pipeline with a merge request from thomas aarholt 2018 11 26 atomap 0 1 3 released major features in this release includes a gui function for adding and removing atoms which makes it easier to set up the initial atom positions see adding atoms using gui for more information a gui function for toggling if atom positions should be refined or not see toggle atom refine better handling of hexagonal structures by adding a adding a vector_fraction parameter to find_missing_atoms_from_zone_vector thanks to eoghan o connell for the suggestion the addition of mask_radius to the refine functions which makes it easier to work with non perodic atom positions for example working with single atom sublattices 2018 06 13 atomap 0 1 2 released this is a minor release including a signal attribute in sublattice and atom_lattice classes minor changes in package dependencies and some improvements to the documentation 2018 03 25 atomap 0 1 1 released the major new features are methods for integrating atomic column intensity and quantifying this intensity in adf stem images see integration of atomic columns and absolute integrator for more info thanks to katherine e macarthur for adding this other features include tools for rotating atomic positions for plotting purposes rotating image and points and reduced memory use when processing data with many atoms 2017 11 16 atomap 0 1 0 released we are happy to announce a new atomap release it includes a major makeover of the tutorial start with finding the atom lattice new features in this release are methods for finding atomic column intensity new and simple plotting tools and a module for generating test data 2017 07 03 version 0 0 8 released new features ability to process dumbbell structures fitting of multiple 2d gaussians at the same time improved background subtraction during 2d gaussian fitting and processing of nanoparticles next copyright 2024 magnus nord built with sphinx using a theme provided by read the docs