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CHANGELOG
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0.14.4
- setup: require Python 3.10
0.14.3
- setup: require qpretrieve 0.3.0
0.14.2
- fix: keep a reference of the reference data for the QLSI
series file format, which enables qpretrieve 0.2.10 to make
use of its caching feature
0.14.1
- fix: support "logs" key in QLSI and OAH HDF5 file formats
0.14.0
- feat: support QLSI data with `qlsi_pitch_term` metadata
- tests: cleanup
- setup: bump h5py from 2.7.0 to 3.5.0 (no timestamps written)
- setup: bump qpimage from 0.8.5 to 0.9.1 (QLSI processing)
0.13.2
- setup: bump qpimage from 0.8.3 to 0.8.5
0.13.1
- ref: deprecate get_time in favor of get_metadata
0.13.0
- BREAKING CHANGE: renamed all file format classes
- feat: add file format class for QLSI data
- feat: support series files in SeriesFolder format
- setup: bump qpimage from 0.7.7 to 0.8.3
- ref: simplify submodule structure and detection of file formats
- ref: deprecate `holo_kw`
0.12.1
- maintenance release
0.12.0
- feat: implement reader for new HDF5-based raw off-axis hologram
file format
- fix: support optional meta data keys from qpimage
- setup: drop support for all Python versions below 3.9
- setup: migrate from qpimage 0.7.4 to 0.7.7
0.11.0
- feat: implement FDTD/Meep reader for data from ODTbrain paper
- fix: remove call to deprecated Element.getchildren
- setup: bump qpimage from 0.6.2 to 0.7.4 (new metadata keys)
0.10.9
- ref: minor code cleanup
- setup: remove unneccessary requirements from setup.py
0.10.8
- fix: wavelength could not be extracted for some phasics files
(section name "analyse data" vs "analyse data v1")
- fix: time could not be parsed due to comma instead of dot
in phasics meta data
0.10.7
- ci: migrate to GHA
- docs: fix sphinx build
- setup: setup.py test is deprecated
0.10.6
- maintenance release
0.10.5
- setup: bump qpimage from 0.6.1 to 0.6.2
- setup: change dependency of scikit-image to tifffile 2020.5.25
- ref: make code work with latest version of tifffile
0.10.4
- setup: bump qpimage from 0.5.0 to 0.6.1
0.10.3
- fix: missing keyword argument `idx` in `SingleTifHolo.get_time`
- fix: correctly pass precision to phasics and hologram zip file
formats
- fix: add file size to dataset identifier hashing process
- example: add conversion script to hdf5 qpimage data
0.10.2
- fix: SeriesFolder did not pass on holo_kw when loading hologram data
0.10.1
- fix: SeriesHdf5Qpimage did not correctly load meta data "time"
0.10.0
- feat: allow to specify a time interval or a series slice in
SeriesData.saveh5
- fix: seek to zero before computing a data identifier for an
io.IOBase object
- fix: only write series identifier in SeriesData.saveh5 if
the keyword arguments for slice extraction are not set
- ref: fix deprecated `.value` (h5py)
- tests: fix date extraction from zip file
0.9.0
- feat: allow to specify a slice in SeriesData.saveh5 (useful
when only a specific region needs to be extracted)
0.8.0
- feat: allow tracking the progress of SeriesData.saveh5 using
multiprocessing.Value objects
0.7.1
- docs: fix missing changelog files
0.7.0
- feat: added command-line entry point "qpinfo"
- feat: support subjoined QPSeries file format
- docs: minor update
0.6.4
- fix: ignore None or nan values in given meta data
0.6.3
- enh: introduce BadFileFormatError
0.6.2
- maintenance release
0.6.1
- tests: fix bad identification of data types
0.6.0
- BREAKING CHANGE: SeriesFolder file format does not load data files
recursively anymore
0.5.1
- fix: falsely detected datasets in SeriesFolder file format
0.5.0
- feat: use file modification time as fallback for TIFF files when
the file format does not implement `get_time`
- fix: return "nan" instead of "0" when the time is not defined for
a measurement
0.4.4
- fix: SeriesFolder file format should not support folders containing
no usable data
- fix: verify file format given by user
0.4.3
- fix: "identifier" not always set for generated instances of QPImage
0.4.2
- fix: implement `get_name` method for SeriesFolder format
- enh: start identifier/name indexing at 1 instead of 0
0.4.1
- fix: do not allow intensity values less than zero for SingleTifPhasics
0.4.0
- feat: extract meta data from QPSeries/QPImage data files
0.3.5
- fix: single_tif_phaiscs (SID4Bio) contains two phase images, the second
of which is recorded at a different time point than the intensity
image. The first image is recorded in wavelengths and not in
nanometers and thus is converted using phasics metadata first.
If this metadata is not available, the second image is used.
0.3.4
- fix: qpimage file formats: override identifiers (clean solution)
- fix: add check for valid meta_data keys
- docs: document attributes of SeriesData
0.3.3
- fix: qpimage file formats: identifiers were not unique, but simply
copied from the input hdf5 file
0.3.2
- setup: add qpimage version dependency
0.3.1
- ci: automate PyPI release with travis-ci
0.3.0
- docs: automatically document all file format classes
- docs: add introduction and file format overview
- tests: improve coverage
0.2.1
- fix: regression when loading data from zip file
0.2.0
- drop support for Python 3.5
- fix: SeriesHdf5Qpimage blocked hdf5 file for reading
- fix: background datasets did not get hologram keyword arguments
- feat: allow to cast input data type (qpimage version 0.2.0)
0.1.6
- code cleanup
0.1.5
- fix: raw phasics tif files were not ignored in `SeriesFolder` (#3)
- feat: reduce length of dataset hashes to six chars for user convenience
- feat: switch order of name and index in identifier for user convenience
0.1.4
- feat: new file format for zipped hologram tif files
- feat: add "storage_type" property describing which type of data
is stored originally in a dataset
- feat: add hologram file formats: HyperSpy and tif-based
- fix: use hologram keyword arguments to generate dataset identifer
0.1.3
- feat: save memory by hard-linking background image data in QPSeries
- fix: format series and single hdf5: override raw meta data
- fix: include background data in determination of data set identifiers
0.1.2
- feat: change API for SingleData ("idx=0" for user convenience)
- feat: implement SeriesData.saveh5 (export as qpimage.QPSeries) (#2)
- feat: add unique part of file name to SeriesFolder image identifiers (#2)
- feat: extract identifiers from hdf5 files
0.1.1
- feat: support pathlib
- feat: add SeriesData.identifier
0.1.0
- initial release