-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #2 from atomprobe-tc/add_ato_and_pyccapt_support
Release 3.11 constraint and added ATO v3, v5, and pyccapt file format support
- Loading branch information
Showing
8 changed files
with
530 additions
and
23 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| # POS file format reader used by atom probe microscopists. | ||
| # | ||
| # Copyright The NOMAD Authors. | ||
| # | ||
| # This file is part of NOMAD. See https://nomad-lab.eu for further info. | ||
| # | ||
| # 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. | ||
| # | ||
|
|
||
| # pylint: disable=no-member,duplicate-code | ||
|
|
||
| import os | ||
|
|
||
| import numpy as np | ||
|
|
||
| from ifes_apt_tc_data_modeling.nexus.nx_field import NxField | ||
| from ifes_apt_tc_data_modeling.utils.mmapped_io import get_memory_mapped_data | ||
|
|
||
|
|
||
| class ReadAtoFileFormat(): | ||
| """Read Rouen group *.ato file format.""" | ||
|
|
||
| def __init__(self, filename: str): | ||
| assert len(filename) > 4, "ATO file incorrect filename ending!" | ||
| assert filename.lower().endswith(".ato"), \ | ||
| "ATO file incorrect file type!" | ||
| self.filename = filename | ||
|
|
||
| self.filesize = os.path.getsize(self.filename) | ||
| self.number_of_events = None | ||
| self.version = None | ||
| retval = self.get_ato_version() | ||
| if retval in [3, 5]: | ||
| # there also seems to exist a version 4 but I have never seen an example for it | ||
| self.version = retval | ||
| print(f"ATO file is in a supported version {self.version}") | ||
| if self.version == 3: | ||
| assert (self.filesize - 2 * 4) % 14 * 4 == 0, \ | ||
| "ATO v3 filesize not integer multiple of 14*4B!" | ||
| self.number_of_events = np.uint32((self.filesize - 2 * 4) / (14 * 4)) | ||
| print(f"ATO file contains {self.number_of_events} entries") | ||
| if self.version == 5: | ||
| assert (self.filesize - 5000) % 40 == 0, \ | ||
| "ATO v5 filesize not integer multiple of 40B!" | ||
| self.number_of_events = np.uint32((self.filesize - 5000) / 40) | ||
| print(f"ATO file contains {self.number_of_events} entries") | ||
| else: | ||
| raise ValueError("ATO file unsupported version!") | ||
| # https://zenodo.org/records/8382828 | ||
| # details three versions of the Rouen/GPM ato format v3, v4, v5 | ||
| # Cameca/AMETEK's runrootl/FileConvert utility know two ATO flavours: | ||
| # CamecaRoot v18.46.533g built Marc, 21, 2022 against ROOT 5.34/36 | ||
| # v3 LAWATOP and v5 current GPM | ||
| # specifically an earlier parser | ||
| # https://hg.sr.ht/~mycae/libatomprobe/browse/src/io/dataFiles.cpp?rev=tip | ||
| # mentions that storage format may not be robust enough against overflow and | ||
| # suggests that additional polishing of results is needed | ||
|
|
||
| def get_ato_version(self): | ||
| header = get_memory_mapped_data(self.filename, "<u4", 0, 4, 2) | ||
| if header[1] in [3, 4, 5]: | ||
| return header[1] | ||
| return None | ||
|
|
||
| def get_reconstructed_positions(self): | ||
| """Read xyz columns.""" | ||
|
|
||
| xyz = NxField() | ||
| xyz.typed_value = np.zeros( | ||
| [self.number_of_events, 3], np.float32) | ||
| xyz.unit = "nm" | ||
|
|
||
| if self.version == 3: | ||
| for dim in [0, 1, 2]: | ||
| xyz.typed_value[:, dim] = \ | ||
| get_memory_mapped_data(self.filename, "<f4", | ||
| 2 * 4 + dim * 4, 14 * 4, self.number_of_events) | ||
| # wpx -> x, wpy -> y, fpz -> z | ||
| if self.version == 5: | ||
| # publicly available sources are inconclusive whether coordinates are in angstroem or nm | ||
| # based on the evidence of usa_denton_smith Si.epos converted to v5 ATO via CamecaRoot | ||
| # the resulting x, y coordinates suggests that v5 ATO stores in angstroem, while fpz is stored in nm? | ||
| # however https://zenodo.org/records/8382828 reports the reconstructed positions to be named | ||
| # not at all wpx, wpy and fpz but x, y, z instead and here claims the nm | ||
| xyz.typed_value[:, 0] = \ | ||
| np.float32(get_memory_mapped_data(self.filename, "<i2", | ||
| 5000 + 0, 40, self.number_of_events) * 0.1) # wpx -> x | ||
| xyz.typed_value[:, 1] = \ | ||
| np.float32(get_memory_mapped_data(self.filename, "<i2", | ||
| 5000 + 2, 40, self.number_of_events) * 0.1) # wpy -> y | ||
| xyz.typed_value[:, 2] = \ | ||
| get_memory_mapped_data(self.filename, "<f4", | ||
| 5000 + 4, 40, self.number_of_events) # fpz -> z | ||
| return xyz | ||
|
|
||
| def get_mass_to_charge_state_ratio(self): | ||
| """Read mass-to-charge-state-ratio column.""" | ||
|
|
||
| m_n = NxField() | ||
| m_n.typed_value = np.zeros( | ||
| [self.number_of_events, 1], np.float32) | ||
| m_n.unit = "Da" | ||
|
|
||
| if self.version == 3: | ||
| m_n.typed_value[:, 0] = \ | ||
| get_memory_mapped_data(self.filename, "<f4", | ||
| 2 * 4 + 3 * 4, 14 * 4, self.number_of_events) | ||
| if self.version == 5: | ||
| m_n.typed_value[:, 0] = \ | ||
| get_memory_mapped_data(self.filename, "<f4", | ||
| 5000 + 8, 40, self.number_of_events) | ||
| return m_n |
Oops, something went wrong.