Rosettasciio

==================

Maintenance
-----------

- Pin zarr to version 2 until zarr version 3 is supported. (`351 <https://github.com/hyperspy/rosettasciio/issues/351>`_)

================

New features
------------

- Add basic support for the Delmic HDF5 format. (`139 <https://github.com/hyperspy/rosettasciio/issues/139>`_)


Enhancements
------------

- :ref:`Direct Electron MRC <mrc-format>`:

- add support for newer version of DE server,
- add support foe discovering metadata file (``*_info.txt``) based on the naming scheme. (`311 <https://github.com/hyperspy/rosettasciio/issues/311>`_)
- Add support for tiff file in :func:`~.utils.tools.get_file_handle`. (`317 <https://github.com/hyperspy/rosettasciio/issues/317>`_)


Bug Fixes
---------

- Set ``signal_type`` to ``LumiTransientSpectrum`` when Hamamatsu ``.img`` files are read and LumiSpy is installed. (`209 <https://github.com/hyperspy/rosettasciio/issues/209>`_)
- Fix lazy reading of some tiff files - fix for `316 <https://github.com/hyperspy/rosettasciio/issues/316>`_. (`#317 <https://github.com/hyperspy/rosettasciio/issues/317>`_)
- Fix scale in white field image in ``renishaw`` reader. (`327 <https://github.com/hyperspy/rosettasciio/issues/327>`_)
- Allow reading of Hamamatsu tiff file with ``ScalingXScalingFile="Other"``. (`347 <https://github.com/hyperspy/rosettasciio/issues/347>`_)


Maintenance
-----------

- Add explicit support for python 3.13. (`339 <https://github.com/hyperspy/rosettasciio/issues/339>`_)

================

Enhancements
------------

- :ref:`DigitalSurf surfaces <digitalsurf-format>`:

- add support for saving file - see :func:`~.digitalsurf.file_writer`
- add the :func:`~.digitalsurf.parse_metadata` function to parse metadata from ``sur`` file
- add series of RGB images / surfaces support. (`280 <https://github.com/hyperspy/rosettasciio/issues/280>`_)


Bug Fixes
---------

- Fixes axes for JPG with no exif_tags. Return of axes while loading isn't emty anymore. (`283 <https://github.com/hyperspy/rosettasciio/issues/283>`_)
- :ref:`EMD Velox <emd_fei-format>` 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`` and ``sum_frames=False``. (`287 <https://github.com/hyperspy/rosettasciio/issues/287>`_)
- :ref:`quantumdetector-format`: Fix signal shape of data acquired in ROI mode. (`289 <https://github.com/hyperspy/rosettasciio/issues/289>`_)


Maintenance
-----------

- Add support for numpy 2 in Renishaw, Semper and Dens reader. (`281 <https://github.com/hyperspy/rosettasciio/issues/281>`_)

================

Enhancements
------------

- :ref:`emd_fei-format`: Enforce setting identical units for the ``x`` and ``y`` axes, as convenience to use the scalebar in HyperSpy. (`243 <https://github.com/hyperspy/rosettasciio/issues/243>`_)
- :ref:`quantumdetector-format`: Add support for dask distributed scheduler. (`267 <https://github.com/hyperspy/rosettasciio/issues/267>`_)


Bug Fixes
---------

- :ref:`emd_fei-format`: Fix conversion of offset units which can sometimes mismatch the scale units. (`243 <https://github.com/hyperspy/rosettasciio/issues/243>`_)
- :ref:`ripple-format`: Fix typo and improve error message for unsupported ``dtype`` in writer. (`251 <https://github.com/hyperspy/rosettasciio/issues/251>`_)
- :ref:`emd_fei-format`: Fix parsing elements from EDS data from velox emd file v11. (`274 <https://github.com/hyperspy/rosettasciio/issues/274>`_)


Maintenance
-----------

- Use ``ruff`` for code formating and linting. (`250 <https://github.com/hyperspy/rosettasciio/issues/250>`_)
- Fix ``tifffile`` deprecation. (`262 <https://github.com/hyperspy/rosettasciio/issues/262>`_)
- Add support for ``python-box`` 7. (`263 <https://github.com/hyperspy/rosettasciio/issues/263>`_)

================

Enhancements
------------

- :ref:`Renishaw wdf <renishaw-format>`:

- 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 <https://github.com/hyperspy/rosettasciio/issues/227>`_)
- Add support for reading :ref:`emd <emd_fei-format>` Velox version 11. (`232 <https://github.com/hyperspy/rosettasciio/issues/232>`_)
- Add :ref:`making test data files <making_test_files>` section to contributing guide, explain characteristics of "good" test data files. (`233 <https://github.com/hyperspy/rosettasciio/issues/233>`_)
- :ref:`Quantum Detector <quantumdetector-format>` 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 <https://github.com/hyperspy/rosettasciio/issues/235>`_)
- Improve setting output size for an image. (`244 <https://github.com/hyperspy/rosettasciio/issues/244>`_)


Bug Fixes
---------

- Fix saving ``hspy`` file with empty array (signal or metadata) and fix closing ``hspy`` file when a error occurs during reading or writing. (`206 <https://github.com/hyperspy/rosettasciio/issues/206>`_)
- Fix saving ragged arrays of vectors from/to a chunked ``hspy`` and ``zspy`` store. Greatly increases the speed of saving and loading ragged arrays from chunked datasets. (`211 <https://github.com/hyperspy/rosettasciio/issues/211>`_)
- Fix saving ragged array of strings in ``hspy`` and ``zspy`` format. (`217 <https://github.com/hyperspy/rosettasciio/issues/217>`_)
- Fix setting beam energy for XRF maps in ``bcf`` files. (`231 <https://github.com/hyperspy/rosettasciio/issues/231>`_)
- :ref:`Quantum Detector <quantumdetector-format>` reader: fix setting chunks. (`235 <https://github.com/hyperspy/rosettasciio/issues/235>`_)


Maintenance
-----------

- Add ``POOCH_BASE_URL`` to specify the base url used by pooch to download test data. This fixes the failure of the ``package_and_test.yml`` workflow in pull requests where test data are added or updated. (`200 <https://github.com/hyperspy/rosettasciio/issues/200>`_)
- Fix documentation links following release of hyperspy 2.0. (`210 <https://github.com/hyperspy/rosettasciio/issues/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 <https://github.com/hyperspy/rosettasciio/issues/222>`_)
- Fix deprecation warnings introduced with numpy 1.25 ("Conversion of an array with ndim > 0 to a scalar is deprecated, ..."). (`230 <https://github.com/hyperspy/rosettasciio/issues/230>`_)
- Fix numpy 2.0 removal (``np.product`` and ``np.string_``). (`238 <https://github.com/hyperspy/rosettasciio/issues/238>`_)
- Fix download test data when using ``pytest --pyargs rsciio -n``. (`245 <https://github.com/hyperspy/rosettasciio/issues/245>`_)

================

New features
------------

- Add :func:`rsciio.set_log_level` to set the logging level of ``RosettaSciIO`` (`69 <https://github.com/hyperspy/rosettasciio/issues/69>`_)
- Added the :func:`~rsciio.utils.distributed.memmap_distributed` function for loading a memmap file
from multiple processes.

- Added the arguments ``distributed`` and ``metadata_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 <https://github.com/hyperspy/rosettasciio/issues/162>`_)
- Add support for saving lazy ragged signals to the :ref:`zspy format<zspy-format>`. (`193 <https://github.com/hyperspy/rosettasciio/pull/193>`_)


Bug Fixes
---------

- Fix error when reading :ref:`pantarhei-format` file with aperture ``"Out"`` (`173 <https://github.com/hyperspy/rosettasciio/issues/173>`_)
- Improvement for installation without ``numba``:

- Fix :ref:`tvips <tvips-format>` reader
- Allow reading and writing :ref:`EMD NCEM <emd_ncem-format>` file
- Fix running test suite without optional dependencies (`182 <https://github.com/hyperspy/rosettasciio/issues/182>`_)
- 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 <https://setuptools-scm.readthedocs.io/en/latest/config>`_ (`#187 <https://github.com/hyperspy/rosettasciio/issues/187>`_)
- Fix ``dwell_time`` reading in :ref:`QuantumDetectors <quantumdetector-format>` reader (``.mib`` file). The
``dwell_time`` is stored in milliseconds, not microseconds as the previous code
assumed. (`189 <https://github.com/hyperspy/rosettasciio/issues/189>`_)


Maintenance
-----------

- Remove usage of deprecated ``distutils`` (`152 <https://github.com/hyperspy/rosettasciio/issues/152>`_)
- Fix installing exspy/hyperspy on GitHub CI and test failing without optional dependencies (`186 <https://github.com/hyperspy/rosettasciio/issues/186>`_)
- Unpin pillow now that imageio supports pillow>=10.1.0 (`188 <https://github.com/hyperspy/rosettasciio/issues/188>`_)
- Simplify GitHub CI workflows by using reusable workflow (`190 <https://github.com/hyperspy/rosettasciio/issues/190>`_)


.. _changes_0.2: