Changelog
List of changes in-between qpformat releases.
version 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)
version 0.10.9
ref: minor code cleanup
setup: remove unneccessary requirements from setup.py
version 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
version 0.10.7
ci: migrate to GHA
docs: fix sphinx build
setup: setup.py test is deprecated
version 0.10.6
maintenance release
version 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
version 0.10.4
setup: bump qpimage from 0.5.0 to 0.6.1
version 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
version 0.10.2
fix: SeriesFolder did not pass on holo_kw when loading hologram data
version 0.10.1
fix: SeriesHdf5Qpimage did not correctly load meta data “time”
version 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
version 0.9.0
feat: allow to specify a slice in SeriesData.saveh5 (useful when only a specific region needs to be extracted)
version 0.8.0
feat: allow tracking the progress of SeriesData.saveh5 using multiprocessing.Value objects
version 0.7.1
docs: fix missing changelog files
version 0.7.0
feat: added command-line entry point “qpinfo”
feat: support subjoined QPSeries file format
docs: minor update
version 0.6.4
fix: ignore None or nan values in given meta data
version 0.6.3
enh: introduce BadFileFormatError
version 0.6.2
maintenance release
version 0.6.1
tests: fix bad identification of data types
version 0.6.0
BREAKING CHANGE: SeriesFolder file format does not load data files recursively anymore
version 0.5.1
fix: falsely detected datasets in SeriesFolder file format
version 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
version 0.4.4
fix: SeriesFolder file format should not support folders containing no usable data
fix: verify file format given by user
version 0.4.3
fix: “identifier” not always set for generated instances of QPImage
version 0.4.2
fix: implement get_name method for SeriesFolder format
enh: start identifier/name indexing at 1 instead of 0
version 0.4.1
fix: do not allow intensity values less than zero for SingleTifPhasics
version 0.4.0
feat: extract meta data from QPSeries/QPImage data files
version 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.
version 0.3.4
fix: qpimage file formats: override identifiers (clean solution)
fix: add check for valid meta_data keys
docs: document attributes of SeriesData
version 0.3.3
fix: qpimage file formats: identifiers were not unique, but simply copied from the input hdf5 file
version 0.3.2
setup: add qpimage version dependency
version 0.3.1
ci: automate PyPI release with travis-ci
version 0.3.0
docs: automatically document all file format classes
docs: add introduction and file format overview
tests: improve coverage
version 0.2.1
fix: regression when loading data from zip file
version 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)
version 0.1.6
code cleanup
version 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
version 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
version 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
version 0.1.2
version 0.1.1
feat: support pathlib
feat: add SeriesData.identifier
version 0.1.0
initial release