Release Notes#
Changelog entries for the development version are available at https://rosettasciio.readthedocs.io/en/latest/changes.html
[UNRELEASED] (2024-11-03)#
New features#
Add basic support for the Delmic HDF5 format. (#139)
Enhancements#
Add support for tiff file in
get_file_handle()
. (#317)
Bug Fixes#
0.6 (2024-07-11)#
Enhancements#
-
add support for saving file - see
file_writer()
add the
parse_metadata()
function to parse metadata fromsur
fileadd series of RGB images / surfaces support. (#280)
Bug Fixes#
Fixes axes for JPG with no exif_tags. Return of axes while loading isn’t emty anymore. (#283)
EMD Velox fixes for reading files containing multiple EDS streams:
fix reading multiple EDS streams lazily with
sum_EDS_detectors=True
,fix reading separate EDS stream and individual frames when using
sum_EDS_detectors=False
andsum_frames=False
. (#287)
Quantum Detector: Fix signal shape of data acquired in ROI mode. (#289)
Maintenance#
Add support for numpy 2 in Renishaw, Semper and Dens reader. (#281)
0.5 (2024-06-15)#
Enhancements#
EMD (Velox): Enforce setting identical units for the
x
andy
axes, as convenience to use the scalebar in HyperSpy. (#243)Quantum Detector: Add support for dask distributed scheduler. (#267)
Bug Fixes#
EMD (Velox): Fix conversion of offset units which can sometimes mismatch the scale units. (#243)
Ripple format: Fix typo and improve error message for unsupported
dtype
in writer. (#251)EMD (Velox): Fix parsing elements from EDS data from velox emd file v11. (#274)
Maintenance#
0.4 (2024-04-02)#
Enhancements#
-
return survey image instead of saving it to the metadata and add marker of the mapping area on the survey image.
Add support for reading data with invariant axis, for example when the values of the Z axis doesn’t change.
Parse calibration of
jpg
images saved with Renishaw Wire software. (#227)
Add making test data files section to contributing guide, explain characteristics of “good” test data files. (#233)
Quantum Detector reader: use timestamps to get navigation shape when the navigation shape is not available - for example, acquisition with pixel trigger or scan shape not in metadata. (#235)
Improve setting output size for an image. (#244)
Bug Fixes#
Fix saving
hspy
file with empty array (signal or metadata) and fix closinghspy
file when a error occurs during reading or writing. (#206)Fix saving ragged arrays of vectors from/to a chunked
hspy
andzspy
store. Greatly increases the speed of saving and loading ragged arrays from chunked datasets. (#211)Fix saving ragged array of strings in
hspy
andzspy
format. (#217)Fix setting beam energy for XRF maps in
bcf
files. (#231)Quantum Detector reader: fix setting chunks. (#235)
Maintenance#
Add
POOCH_BASE_URL
to specify the base url used by pooch to download test data. This fixes the failure of thepackage_and_test.yml
workflow in pull requests where test data are added or updated. (#200)Fix documentation links following release of hyperspy 2.0. (#210)
Run test suite on osx arm64 on GitHub CI and speed running test suite using all available CPUs (3 or 4) instead of only 2. (#222)
Fix deprecation warnings introduced with numpy 1.25 (“Conversion of an array with ndim > 0 to a scalar is deprecated, …”). (#230)
Fix numpy 2.0 removal (
np.product
andnp.string_
). (#238)Fix download test data when using
pytest --pyargs rsciio -n
. (#245)
0.3 (2023-12-12)#
New features#
Add
rsciio.set_log_level()
to set the logging level ofRosettaSciIO
(#69)Added the
memmap_distributed()
function for loading a memmap file from multiple processes.Added the arguments
distributed
andmetadata_file
to the .mrc file reader for loading metadata save from DirectElectron detectors.Speed up to the .mrc file reader for large .mrc files by removing the need to reshape and transpose the data. (#162)
Add support for saving lazy ragged signals to the zspy format. (#193)
Bug Fixes#
Fix error when reading CEOS Panta Rhei (PRZ) file with aperture
"Out"
(#173)Improvement for installation without
numba
:Fix getting version on debian/ubuntu in system-wide install. Add support for installing from git archive and improve getting development version using setuptools fallback_version (#187)
Fix
dwell_time
reading in QuantumDetectors reader (.mib
file). Thedwell_time
is stored in milliseconds, not microseconds as the previous code assumed. (#189)
Maintenance#
0.2 (2023-11-09)#
New features#
Add support for reading the
.img
-format from Hamamatsu. (#87)Add support for reading the
.mib
-format from Quantum Detector Merlin camera. (#174)
Bug Fixes#
Improved Documentation#
Enhancements#
Maintenance#
Add
sidpy
dependency and pin it to <0.12.1 as a workaround to fixpyusid
import (#155)Update hspy/zspy plugins to new markers API introduced in HyperSpy 2.0 (#164)
Pin pillow<10.1.0 until imageio supports newer pillow version - see imageio/imageio#1044 (#175)
Update the test suite and the CI workflows to work with and without exspy installed (#176)
Add badges that became available after first release (#177)
0.1 (2023-06-06)#
New features#
Add support for reading the
.xml
-format from Horiba Jobin Yvon’s LabSpec software. (#25)Add support for reading the
.tvf
-format from TriVista. (#27)Add support for reading the
.wdf
-format from Renishaw’s WIRE software. (#55)Added subclassing of
.sur
files in CL signal type and updated metadata parsing (#98)Add optional kwarg to tiff reader
multipage_as_list
which when set to True usespages
interface and returns list of signal for every page with full metadata. (#104)Add file reader and writer for PRZ files generated by CEOS PantaRhei (HyperSpy #2896)
Bug Fixes#
Ensure that the
.msa
plugin handlesSIGNALTYPE
values according to the official format specification. (#39)Fix error when reading Velox file containing FFT with an odd number of pixels (#49)
Fix error when reading JEOL
.pts
file with un-ordered frame list or when length offrame_start_index
is smaller than the sweep count (#68)Fix exporting scalebar with reciprocal units containing space (#90)
Fix array indexing bug when loading a
sur
file format containing spectra series. (#98)For more robust xml to dict conversion,
convert_xml_to_dict
is replaced byXmlToDict
(introduced by PR #111). (#101)Fix bugs with reading non-FEI and Velox
mrc
files, improve documentation ofmrc
andmrcz
file format. Closes #71, #91, #93, #96, #130. (#131)
Improved Documentation#
Deprecations#
Remove deprecated
record_by
attribute from file readers where remaining (#102)
Enhancements#
Recognise both byte and string object for
NXdata
tag in NeXus reader (#112)
API changes#
Move, enhance and share xml to dict/list translation and other tools (new api for devs) from
Bruker._api
to utils:utils.date_time_tools.msfiletime_to_unix
function to convert the uint64 MSFILETIME to datetime.datetime object.utils.tools.sanitize_msxml_float
function to sanitize some MSXML generated xml where comma is used as float decimal separator.utils.tools.XmlToDict
Xml to dict/list translator class with rich customization options as kwargs, and main method for translationdictionarize
(#111)
Maintenance#
Initiate GitHub actions for tests and documentation. (#1)
Initiate towncrier changelog and create templates for PRs and issues. (#3)
Add github CI workflow to check links, build docs and push to the
gh-pages
branch. Fix links and add EDAX reference file specification (#4)Add azure pipelines CI to run test suite using conda-forge packages. Add pytest and coverage configuration in
pyproject.toml
(#6)Fix minimum install, add corresponding tests build and tidy up leftover code (#13)
Fixes and code consistency improvements based on analysis provided by lgtm.org (#23)
Added github action for code scanning using the codeQL engine. (#26)
Following the deprecation cycle announced in HyperSpy, the following keywords and attributes have been removed:
Bruker composite file (BCF): The
'spectrum'
option for theselect_type
parameter was removed. Use ‘spectrum_image’ instead.Electron Microscopy Dataset (EMD) NCEM: Using the keyword
'dataset_name'
was removed, use'dataset_path'
instead.NeXus data format: The
dataset_keys
,dataset_paths
andmetadata_keys
keywords were removed. Usedataset_key
,dataset_path
andmetadata_key
instead. (#30)
Unify the
format_name
scheme of IO plugins usingname
instead and addname_aliases
(list) for backwards compatibility. (#35)Add drone CI to test on
arm64
/aarch64
platform (#42)Unify naming of folders/submodules to match documented format
name
(#81)Add black as a development dependency. Add pre-commit configuration file with black code style check, which when installed will require changes to pass a style check before commiting. (#86)
Add support for python-box 7 (#100)
Migrate to API v3 of
imageio.v3
(#106)Add explicit support for python 3.11 and drop support for python 3.6, 3.7 (#109)
Remove test data from packaging and download them when necessary (#123)
Define packaging in
pyproject.toml
and keepsetup.py
to handle compilation of C extension (#125)Add release GitHub workflow to automate release process and add corresponding documentation in releasing_guide.md (#126)
Add pre-commit hook to update test data registry and pre-commit.ci to run from pull request (#129)
Tidy up
rsciio
namespace: privatisedocstrings
, moveconftest.py
andexceptions
to tests and utils folder, respectively (#132)
Initiation (2022-07-23)#
RosettaSciIO was split out of the HyperSpy repository on July 23, 2022. The IO-plugins and related functions so far developed in HyperSpy were moved to this new repository.