diff --git a/.precommit-config.yaml b/.precommit-config.yaml new file mode 100644 index 0000000..774bf8c --- /dev/null +++ b/.precommit-config.yaml @@ -0,0 +1,9 @@ +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.3.4 + hooks: + # Run the linter. + - id: ruff + # Run the formatter. + - id: ruff-format \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md index 9770343..044df07 100644 --- a/README.md +++ b/README.md @@ -4,29 +4,41 @@ ![](https://github.com/FAIRmat-NFDI/pynxtools-apm/actions/workflows/publish.yml/badge.svg) ![](https://coveralls.io/repos/github/FAIRmat-NFDI/pynxtools_apm/badge.svg?branch=master) -# A reader for atom probe microscopy (APM) data +# A parser and normalizer for atom probe tomography and field-ion microscopy data # Installation +It is recommended to use python 3.11 with a dedicated virtual environment for this package. +Learn how to manage [python versions](https://github.com/pyenv/pyenv) and +[virtual environments](https://realpython.com/python-virtual-environments-a-primer/). -TODO:add installation e.g. following xps, mpes +This package is a reader plugin for [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools) and thus should be installed together with `pynxtools`: +```shell +pip install pynxtools[apm] +``` + +for the latest development version. # Purpose -This reader plugin for [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools) is used to translate diverse file formats from the scientific community and technology partners -within the field of atom probe tomography as well as related field ion microscopy into a standardized representation using the +This reader plugin for [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools) is used to translate diverse file formats from the scientific community and technology partners +within the field of atom probe tomography and field-ion microscopy into a standardized representation using the [NeXus](https://www.nexusformat.org/) application definition [NXapm](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXapm.html#nxapm). ## Supported file formats -TODO: Add table rows which quantity "atom probe jargon", columns readers. +This plugin supports the majority of the file formats that are currently used for atom probe. +A detailed summary is available in the [reference section of the documentation](https://fairmat-nfdi.github.io/pynxtools-apm/pynxtools-apm). # Getting started -TODO: Point to jupyter notebook giving examples. +[A getting started tutorial](https://github.com/FAIRmat-NFDI/pynxtools-apm/tree/main/examples) is offered that guides you +how to use the apm reader for converting your data to NeXus from a Jupyter notebook. Note that not every combination of +supported file formats and input for the parser allows to fill required and recommended fields and attributes of the NXapm +application definition. Therefore, you may need to provide an ELN file that contains the missing values in order for the +validation step of the APM reader to pass. # Contributing We are continously working on adding parsers for other data formats, technology partners, and atom probers. If you would like to implement a parser for your data, feel free to get in contact. ## Development install - Install the package with its dependencies: ```shell @@ -37,7 +49,7 @@ python -m pip install -e . python -m pip install -e ".[dev]" ``` -There is also a [pre-commit hook](https://pre-commit.com/#intro) available + ## Test this software - Especially relevant for developers, there exists a basic test framework written in [pytest](https://docs.pytest.org/en/stable/) which can be used as follows: diff --git a/docs/explanation/learn.md b/docs/explanation/learn.md index 7318198..fd810ff 100644 --- a/docs/explanation/learn.md +++ b/docs/explanation/learn.md @@ -1 +1,12 @@ # Learn + +Pynxtools-apm offers the atom probe community a set of diverse example how a parser can be implemented to provide for a diverse and wide coverage of the (meta)data from the research field of atom probe and field-ion microscopy. We would like to encourage the community to share example files with us. These can be small and come from diverse use cases. + +We are working together with the [International Field Emission Society's (IFES) Atom Probe Technical Committee (APT TC)](https://fieldemission.org/article.php?id=technical_committee) to improve the capabilities of the reader for the benefit of all +atom probers. + +## Workflow + +The following diagram shows how `pynxtools-apm` processes information and interacts with the core routines of `pynxtools`. + + diff --git a/docs/explanation/media/workflow.mermaid b/docs/explanation/media/workflow.mermaid new file mode 100644 index 0000000..fab9b81 --- /dev/null +++ b/docs/explanation/media/workflow.mermaid @@ -0,0 +1,8 @@ +flowchart TD + ELN(eln_data.yaml) -->|Metadata entered via an ELN| APM(pynxtools-apm) + CFG(apm.specific.config.yaml) --> | Configuration inputted via given RDM| APM + RECON(reconstruction) -->|Reconstruction| APM + RANGE(ranging) -->|Ranging definitions| APM + APM --> |Interface to the dataconverter| DCONV(pynxtools) + DCONV --> |Verification of content against NXapm, file I/O thereafter| NXS(NeXus/HDF5 NXapm-compliant) + \ No newline at end of file diff --git a/docs/explanation/media/workflow.png b/docs/explanation/media/workflow.png new file mode 100644 index 0000000..a634f7c Binary files /dev/null and b/docs/explanation/media/workflow.png differ diff --git a/docs/explanation/performance.md b/docs/explanation/performance.md new file mode 100644 index 0000000..56e822a --- /dev/null +++ b/docs/explanation/performance.md @@ -0,0 +1,28 @@ +# Known issues + +## Charge state analysis +When the ranging definitions have molecular ions which are composed from many atoms and elements with many isotopes +it is possible that the interpretation of the ranging definitions can take long. The situation is case dependent. +The reason is that while parsing the reader uses a combinatorial algorithm to identify the charge state(s) from the +ranging definitions. The computation time of this algorithm depends on the total number of possible isotopic combinations +that need evaluation. + +## Verifying instance against cardinality/existence constraints +Performance relevant for only some cases and input is that the verification of the instantiated schema can be slow. +This verification step is executed before the data are written to the NeXus/HDF5 file. The reason for this issue is that +the dataconverter traverses the dependency graph of the already instantiated concepts of the NXapm application definition +to assure that the template is valid, i.e. that all required quantities have been instantiated. Depending on which branches +get instantiated by the input, this evaluation can be slower as more pathes have to be visited. + +Note that this issue is independent of size of the input i.e. how many ions are included in a dataset does not really matter. + +## Molecular ions +The reader currently supports to define up to 255 ranging definitions. In all cases where we have seen range files from +groups across the world where more ranging definitions have been made these were typically duplicated lines in the +ranging definitions file. + +The reader currently supports to define molecular ions with up to 32 atoms which covers for almost all cases of molecular ion +fragments that are typically studied with atom probe. Note that in mass spectrometry fragments with a considerable larger +number of atoms are observed but telling them apart in atom probe would in practice be even more complicated. + +A more detailed overview for resolving molecular ions in atom probe is available [in the literature](https://doi.org/10.1016/j.patter.2020.100192). diff --git a/docs/index.md b/docs/index.md index 6518a1f..d160c4e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -39,6 +39,9 @@ This is the place where to add documentation of [diátaxis](https://diataxis.fr) This is the place where to add documentation of [diátaxis](https://diataxis.fr) content type explanation. +- [Scope and idea](explanation/learn.md) +- [Known performance issues](explanation/performance.md) +
diff --git a/docs/reference/camecaroot.md b/docs/reference/camecaroot.md index 9eaabd6..800d338 100644 --- a/docs/reference/camecaroot.md +++ b/docs/reference/camecaroot.md @@ -5,7 +5,7 @@ with software other than provided by Cameca. We have investigated the situation of metadata have been documented by Cameca. In addition, we have done a successful proof-of-concept to explore a route of reading several pieces of information contained in all of these binary file formats using only Python. The main motivation for this was to explore a route that would enable automated mapping and normalizing of some of the metadata into NeXus via a simpler - programmatic approach - than having users to enter the information via e.g. electronic lab notebooks or supplementary files. -The main motivation to access the binary file structure directly in contrast to using a library from Cern's ROOT ecosystem was that every +The main motivation to access the binary file structure directly in contrast to using a library from [Cern's ROOT](https://root.cern/) ecosystem was that every tool which would include a ROOT-capable pynxtools-apm plugin would also have to install at least some part of the versatile but functionally rich ROOT library that may not be appropriate in all cases when working with already complex research data management system with their own dependencies. diff --git a/mkdocs.yaml b/mkdocs.yaml index b970da3..fb2d8ae 100644 --- a/mkdocs.yaml +++ b/mkdocs.yaml @@ -12,6 +12,7 @@ nav: - how-tos/howto.md - Learn: - explanation/learn.md + - explanation/performance.md - Reference: - reference/contextualization.md - reference/apt.md diff --git a/pynxtools_apm/README.md b/pynxtools_apm/README.md index 6b75796..657dc39 100644 --- a/pynxtools_apm/README.md +++ b/pynxtools_apm/README.md @@ -1,51 +1,5 @@ - -## Contact person in FAIRmat for this reader -Markus Kühbach +comments in the issue list (or drop us an email) to exchange specifically about this topic.-->