Changelog

List of changes in-between dclab releases.

version 0.36.1

  • setup: bump h5py version to 3.0 (issue with integer chunk argument)

version 0.36.0

  • feat: introduce new RTDCWriter class (#144)

  • fix: in some rare cases, an empty .rtdc file could be generated when splitting an .rtdc file via the CLI dclab-split

  • fix: user-defined metadata were not copied with CLI repack

  • fix: support exporting non-scalar plugin features to HDF5 (#143)

  • enh: implement consistent .shape property for contour data (partially #117)

  • enh: improve export speed of contour data

  • enh: improve export speed if data filtering is disabled

  • ref: disable time_offset of internal export.hdf5_append function

  • ref: deprecate write_hdf5.write function

  • ref: deprecate export.hdf5_autocomplete_config function

  • ref: deprecate export.hdf5_append function

version 0.35.8

  • fix: write logs to fixed-length strings in HDF5 files (HDF5 never supported variable length string datasets with fletcher32 or compression filters)

  • fix: non-scalar features that are not defined in dclab were silently ignored upon export; temporarily raise a ValueError instead (#143)

  • setup: release pinning of h5py

version 0.35.7

  • fix: more Shape-In versions are affected by the medium-write bug addressed in 0.33.1

  • enh: improve error handling when loading rpy2

  • enh: add checks for negative or zero-valued metadata

  • tests: fix broken example dataset with zero-valued metadata (#137)

version 0.35.6

  • fix: config converters were not applied to raw metadata (#139)

version 0.35.5

  • enh: add sanity_check method to IntegrityChecker

version 0.35.4

  • enh: implement function for obtaining the description of a configuration key get_config_value_descr

version 0.35.3

  • enh: implement dumping of Configuration to json

version 0.35.2

  • enh: allow to compress, condense, and repack without checking for the input file suffix

  • docs: fixed example data (sphinx encountered unexpected warnings)

version 0.35.1

  • fix: ignore empty logs (raised IndexError before)

  • tests: increase coverage (#136)

version 0.35.0

  • enh: support new configuration keys for online polygon filtering in the form of “[online_filter]: area_um,deform polygon points” (#134)

  • enh: new helper functions in dclab.definitions: get_config_value_type, get_config_value_func, and config_key_exists

  • ref: issue a warning when the data type of a configuration key is not correct

version 0.34.6

  • fix: make get_job_info and get_command_log available in cli submodule

  • tests: add documentation for test data (#119)

version 0.34.5

  • fix: cast data to float when filling with nan values when checking the size of ancillary features

  • fix: dclab-split did not work when nptdms is not installed

  • tests: skip tests that require nptdms, requests, or rpy2 if those

  • enh: add check to warn users from setting None-type config values packaages are not installed

  • tests: add test for non-scalar plugin feature

  • ci: run tests with different setup.py-extras installed

version 0.34.4

  • fix: use temporary file names during CLI operations

version 0.34.3

  • fix: workaround for when rpy2 finds R_HOME, but R doesn’t

version 0.34.2

  • fix: slicing of non-scalar features for hierarchy children (#128)

  • fix: passing a directory to the CLI tdms2rtdc did not work

  • enh: support slicing of non-scalar features for DCOR data (#132)

  • enh: support slicing of the contour feature for HDF5 data (#132)

  • enh: support slicing of LazyContour for contour AncillaryFeature (#132)

  • enh: minor optimizations of the DCOR format

  • ref: raise NotImplementedError for futile attempts to slice the image, contour, or mask features for .tdms data (#132)

  • ref: cleanup CLI code

  • tests: increase coverage of CLI (#116)

version 0.34.1

  • enh: introduce user-defined “user” configuration section (#125)

  • scripts: refactor fem2lutiso_std.py and fem2iso_volume.py so that model-specific post-processing is done in hooks named after the FEM identifier, e.g. fem_hooks/LE-2D-FEM-19.py (#90)

  • docs: new LUT data version 10.6084/m9.figshare.12155064.v3

  • ref: minor code cleanup

version 0.34.0

  • feat: introduce user-defined plugin features (#105)

  • fix: dclab-verify-dataset now also prints other errors it encounters

  • fix: installing the “lmer” R package failed, because “statmod” was not installed

  • fix: correct data types for “fluorescence:sample rate”, “imaging: roi position x”, and “imaging: roi position y” (#124)

  • enh: support new .rtdc attribute “online_contour:bg empty” which is True when the online background image is computed only from frames that do not contain any events (#124)

  • enh: AncillaryFeature now populates other ancillary features when they share the same method (#104)

  • enh: dclab-verify-dataset now returns a non-zero exit code if there were errors, alerts, or violations (#120)

  • ref: streamlined dataset check function for missing meta data keys

version 0.33.3

  • fix: add “chip identifier” to “setup” configuration section and make it optional during dataset checks (#109)

  • fix: ignore empty metadata strings (partly #109); removed the check_metadata_empty_string check function because it does not apply anymore

version 0.33.2

  • fix: some datasets with unknown feature names could not be opened (AssertionError regression in 0.33.1)

  • fix: workaround for sporadic JSONDecodeError when accessing DCOR

  • ref: cleanup cli.py

  • ref: cleanup util.py and deprecate hash_class argument in hashfile

version 0.33.1

  • fix: add dataset check for wrong medium written to .rtdc file by Shape-In

  • fix: filters were ignored when exporting trace data to hdf5 (#112)

  • enh: allow to set ICue identifier for integrity checking

  • ref: code cleanup in export.py

version 0.33.0

  • feat: introduce user-defined temporary features (point 2 in #98)

  • fix: catch errors for integrity checks on non-raw datasets (#102)

  • fix: add check for negative fluorescence values (#101)

  • enh: add metadata keys for baseline offset (#107)

  • setup: remove deprecated setup.py test

version 0.32.5

  • fix: add check for zero-flow rate in dclab-verify-dataset

  • setup: added new file CREDITS for docs and only use maintainer in setup.py

  • docs: add autodoc to constant variables (#94)

  • docs: add “features_innate” and “features_loaded” to scripting goodies section

  • ref: cleanup of RTDCBase class

  • ref: int/bool deprecation warnings in numpy 1.20.0 (#93)

  • tests: test for area_cvx as a float, consistent with output from Shape-In (#96)

version 0.32.4

  • fix: TypeError when registering emodulus LUT (#91)

  • ref: minor cleanup

version 0.32.3

  • build: use oldest-supported-numpy in pyproject.toml

version 0.32.2

  • fix: export trace data in chunks to avoid out-of-memory errors when compressing large files

  • ref: introduce CHUNK_SIZE in write_hdf5.py and use it when exporting to .rtdc

version 0.32.1

  • enh: dclab-compress now by default does not compress any input files that are already fully compressed (fully compressed means that all HDF5 datasets are compressed somehow); to get the old behavior back (compress in any case, use the “force” keyword argument)

version 0.32.0

  • feat: allow to register external look-up tables for Young’s modulus computation (#88)

  • ref: restructure look-up table file handling

  • ref: deprecated [calculation]: “emodulus model” metadata key in favor of the more descriptive “emodulus lut” key.

  • ref: the “method” argument in the context of isoelasticity lines is deprecated in favor of the “lut_identifier” argument

version 0.31.5

  • fix: writing “filtering” and “calculation” metadata sections to .rtdc files should not be allowed

version 0.31.4

  • ci: fix rtd builds

  • ci: fix PyPI releases

version 0.31.3

  • ci: migrate to GitHub Actions

version 0.31.2

  • enh: add soft type check (assertion) for “emodulus medium” key in ancillary features (#86)

  • fix: make sure that strings are not written as bytes in hdf5 files

version 0.31.1

  • enh: add boolean “model converged” key to return dictionary of Rlme4.fit (#85)

version 0.31.0

  • feat: implement (generalized) linear mixed-effects models via a wrapper around R/lme4 using rpy2 (install with extra “lme4”)

version 0.30.1

  • fix: new_dataset attempts to load DCOR dataset when given a non-existent path as a string (#81)

version 0.30.0

  • BREAKING CHANGE: drop support for Python 2 (#34)

  • feat: new machine learning (ML) submodule dclab.ml

  • feat: implement ML model file format .modc (#78)

  • feat: add tensorflow helper functions for RT-DC data

  • setup: bump numpy>=1.17.0

  • ref: minor improvements of code readability

  • tests: set global temp dir and remove it after testing

version 0.29.1

  • enh: lift restrictions on valid options for [setup]:medium (can now be any arbitrary string)

version 0.29.0

  • feat: support the “image_bg” feature which contains the rolling mean background image computed by Shape-In

version 0.28.0

  • feat: new CLI command dclab-split to split a large dataset into multiple smaller datasets

version 0.27.11

  • fix: do not cache hierarchy child feature values; this might lead to intransparent situations where a child has different features than its parent (you cannot always rely on the user to call apply_filter)

  • fix: hierarchy child configuration section “calculation” was not updated with the hierarchy parent values

  • docs: add example for loading data from DCOR and computing the Young’s modulus

version 0.27.10

  • fix: support unicode characters when writing HDF5 in Python2

version 0.27.9

  • docs: add artwork

  • fix: support unicode characters in sample names in Python2

version 0.27.8

  • docs: add more information on emodulus computation

  • docs: add script for visualizing emodulus LUTs

version 0.27.7

  • ref: replace deprecated .tostring() with .tobytes()

version 0.27.6

  • fix: video seek issue workaround also for the first 100 frames

  • cli: also skip the final event in tdms2rtdc if the image is empty

  • cli: renamed kwarg –include-initial-empty-image to include-empty-boundary-images

  • enh: improve detection and recovery of missing images for fmt_tdms

version 0.27.5

  • maintenance build

version 0.27.4

  • maintenance build

version 0.27.3

  • fix: ignore ResourceWarning due to unknown _io.BufferedReader in third-party software when converting .tdms to .rtdc

version 0.27.2

  • maintenance build

version 0.27.1

  • setup: bump imageio to 2.8.0 for Python>=3.4

  • ref: removed NoImageWarning during export (warning is already issued by fmt_tdms.event_image)

version 0.27.0

  • feat: introduce new feature names ml_score_??? where ? can be a digit or a lower-case letter of the alphabet (#77)

  • feat: introduce new functions dclab.definitions.feature_exists and dclab.definitions.scalar_feature_exists for checking the existence of features (including the ml_score_??? features which are not in dclab.definitions.feature_names)

  • feat: introduce ancillary feature ml_class which is defined by the ml_score_??? features

  • enh: fmt_dict automatically converts scalar features to arrays

  • ref: replace check for dclab.definitions.feature_names by dclab.definitions.feature_exists where applicable

  • ref: replace access of dclab.definitions.feature_name2label by dclab.definitions.get_feature_label where applicable

  • ref: do not automatically fill up all the box filtering ranges in RTDCBase.config[“filtering”] with zeros; raise ValueError if user forgets to set both ranges

  • docs: major revision (promote Shape-Out 2 and DCOR)

version 0.26.2

  • fix: kde_methods.bin_num_doane now uses 5 as default if it ecounters nan or zero-division

  • docs: updates related to Young’s modulus computation

version 0.26.1

  • enh: cache more online data in fmt_dcor

  • enh: add dclab.warn.PipelineWarning which is used as a parent class for warnings that a user might be interested in

  • fix: temperature warnings during emodulus computation revealed only the lower temperature limit of the data

version 0.26.0

  • feat: implement volume-deformation isoelasticity lines (#70)

  • fix: specifying an external LUT as ndarray did not work

  • scripts: finish ‘fem2iso_volume.py’ for extracting volume- deformation isoelasticity lines

  • scripts: add ‘pixelation_correction.py’ for visualizing pixelation effects on area_um, volume, and emodulus

  • ref: renamed isoelasticity line text files

version 0.25.0

  • fix: appending data to an hdf5 file results in a broken “index” feature (re-enumeration from 0), if the given dataset contains the “index_online” feature

  • enh: allow to set external LUT files or LUT data when computing the Young’s modulus with the lut_data keyword argument in dclab.features.emodulus.get_emodulus.

  • ref: refactored features.emodulus: New submodules pxcorr and scale_linear; convert is deprecated in favor of scale_feature

version 0.24.8

  • setup: include Python 3.8 builds and remove Python<=3.5 builds

  • scripts: renamed ‘extract_lut_and_iso.py’ to ‘fem2lutiso_std.py’

version 0.24.7

  • fix: ConfigurationDict.update did not take into account invalid keys (everything is now done with (__setitem__`)

version 0.24.6

  • maintenance release

version 0.24.5

  • maintenance release

version 0.24.4

  • maintenance release

version 0.24.3

  • fix: ConfigurationDict.update did not actually perform the requested update (does not affect Configuration.update)

  • enh: also use points_in_polygon from scikit-image to determine contour levels

version 0.24.2

  • build: import new skimage submodules so that PyInstaller will find and use them

version 0.24.1

  • enh: improve polygon filter speed by roughly two orders of magnitude with a cython version taken from scikit-image; there are only minor differences to the old implementation (top right point included vs. lower left point included), so this is not a breaking change (#23)

version 0.24.0

  • data: refurbished LUT for linear elastic spheres provided by Dominic Mokbel and Lucas Wittwer (based on the FEM simulation results from https://doi.org/10.6084/m9.figshare.12155064.v2); compared to the old LUT, there is a relative error in Young’s modulus below 0.1 %, which should not cause any breaking changes

  • data: updated isoelasticity lines (better spacing): analytical data was made available by Christoph Herold, numerical data was interpolated from the new LUT

  • scripts: added ‘scripts/extract_lut_and_iso.py’ for extracting Young’s modulus LUT and isoelastics from FEM simulation data provided by Lucas Wittwer; this is now the default method for extracting new LUTs and isoelastics

  • scripts: added ‘scripts/fem2rtdc.py’ for generating in-silico .rtdc datasets from FEM simulation data provided by Lucas Wittwer

  • fix: dclab-verify-dataset failed when the “logs” group was not present in HDF5 files

  • fix: use predefined chunks when writing HDF5 data to avoid exploding file sizes when writing one event at a time

  • fix: create a deep copy of the metadata dictionary when writing HDF5 data because it leaked to subsequent calls

  • ref: changed the way isoelasticity lines and emodulus LUTs are stored and loaded (e.g. json metadata and a few more sanity checks)

version 0.23.0

  • feat: enable emodulus extrapolation for area_um/deform values outside of the given LUT.

version 0.22.7

  • enh: dclab-verify-dataset now also checks whether the sheath and sample flow rates add up to the channel flow rate

  • ref: Configuration does not anymore load unknown meta data keyword arguments, but ignores them. This implies that dclab-verify-dataset will not anymore check them actively. Instead, any warning issued when opening a file is added to the list of cues.

  • setup: bump nptdms to 0.23.0

version 0.22.6

  • fix: data export to HDF5 did not work when the “frame rate” is not given in the configuration

version 0.22.5

  • enh: add checks for valid keys in the Configuration dictionary of a dataset RTDCBase().config; unknown keys will issue an UnknownConfigurationKeyWarning (#58)

  • ref: moved rtdc_dataset.fmt_hdf5.UnknownKeyWarning to rtdc_dataset.config.UnknownConfigurationKeyWarning

  • ref: renamed rtdc_dataset.config.CaseInsensitiveDict to rtdc_dataset.config.ConfigurationDict and added option to check new keys

version 0.22.4

  • fix: disable computation of Young’s modulus for reservoir measurements (#75)

  • enh: new keyword argument req_func for AncillaryFeature to define additional logic for checking whether a feature is available for a given instance of RTDCBase.

version 0.22.3

  • enh: add data property to ICues (and use it when checking for compression)

version 0.22.2

  • fix: when computing the contour from the mask image, always use the longest contour - critical when the mask image contains artefacts

  • fix: minor issue with dclab-verify-dataset when nptdms was not installed and an exception occured

  • enh: dclab-verify-dataset shows some info on data compression

version 0.22.1

  • enh: remember working API Key

  • docs: document DCOR format

version 0.22.0

  • feat: implement DCOR client

  • enh: improved .rtdc file format detection (with wrong extension)

version 0.21.2

  • enh: dclab-verify-dataset now also checks HDF5 “mask” feature attributes

  • setup: bump h5py to 2.10.0 (need <object>.attrs.get_id)

version 0.21.1

  • fix: correct type of HDF5 image attributes for “mask” feature

version 0.21.0

  • feat: implement new CLI dclab-repack

  • fix: don’t write “logs” group to HDF5 files if there aren’t any

  • fix: support HDF5 files that have no “logs” group

  • docs: fix docstring of dclab-join

version 0.20.8

  • fix: regression where old .tmds data could not be opened if they did not contain the “area_msd” feature

  • fix: convert bytes logs to string in fmt_hdf5

  • enh: support len(ds.logs) for fmt_hdf5

  • enh: replace “info” by “build” in CLI job info

version 0.20.7

  • fix: ensure file extension is .rtdc in dclab-join

  • fix: correct “frame” and “index_online” features when exporting to hdf5

  • enh: allow to set metadata dictionary in dclab.cli.join

version 0.20.6

  • fix: typo in contour check resulted in small tolerance

version 0.20.5

  • fix: be more trustful when it comes to contour data in the tdms file format; instead of raising errors, issue warnings (#72)

version 0.20.4

  • ref: move integrity checks to new class check.IntegrityChecker

  • docs: document remaining dictionaries in dclab.dfn

version 0.20.3

  • docs: fix bad anchors

version 0.20.2

  • ref: using temperature values outside the range for viscosity computation now issues a warning instead of raising an error; warnings were added for the CellCarrier buffers

  • fix: handle number detection correctly in get_emodulus

version 0.20.1

  • fix: always return an array when computing the KDE

  • ref: make accessible static function RTDCBase.get_kde_spacing

version 0.20.0

  • feat: compute elastic modulus from “temp” feature (#51)

  • enh: computing isoelastics from datasets can use [setup]: “temperature” to compute the viscosity/emodulus (#51)

  • enh: define new meta data key [setup]: “temperature”

  • docs: add an advanced section on Young’s modulus computation (#51)

version 0.19.1

  • fix: hierarchy children did not pass force argument to hierarchy parent when apply_filter is called

  • fix: revert histogram2d “density” argument to “normed” to support numpy 1.10 (Shape-Out 1)

  • fix: implement unambiguous RTDCBase.__repr__

version 0.19.0

  • feat: added better contour spacing computation based on percentiles (dclab.kde_methods.bin_width_percentile)

  • feat: add feature “index_online” which may be missing values (#71)

  • feat: implement __getstate__ and __setstate__ for polygon filters

  • fix: write UTF-8 BOM when exporting to .tsv

  • enh: add check whether unique_id exists in PolygonFilter

version 0.18.0

  • fix: correctly handle filtering when features are removed from a dataset

  • ref: move dclab.rtdc_dataset.util to dclab.util

  • ref: minor cleanup in computation of viscosity (support lower-case medum values, add dclab.features.emodulus_viscosity.KNOWN_MEDIA)

  • ref: cleanup dclab.rtdc_dataset.filter (use logical operators, correctly display nan-warning messages, keep track of polygon filters, add consistency checks, improve readability)

version 0.17.1

  • maintenance release

version 0.17.0

  • feat: add command line script for compressing HDF5 (.rtdc) data “dclab-compress”

  • enh: record warnings under “/log” for all command line scripts

  • enh: set gzip data compression for all command line scripts

version 0.16.1

  • fix: circumvent UnicodeDecodeErrors which occured in frozen macOS binaries that use dclab

  • enh: support subsecond accuracy in the the configuration key [experiment] time (e.g. “HH:MM:SS.SSS” instead of “HH:MM:SS”)

  • enh: store the correct, relative measurement time in dclab-join (#63)

version 0.16.0

  • fix: RTDCBase.downsample_scatter with ret_mask=True did not return boolean array of len(RTDCBase) as indicated in the docs

  • ref: remove RTDCBase._plot_filter, which was confusing anyway

  • ref: deprecate usage of RTDCBase._filter

version 0.15.0

  • feat: add method RTDCBase.reset_filter

  • feat: implement RTDCBase.features_loaded

  • feat: allow to instantiate RTDC_Hierarchy without initially applying the filter

  • fix: non-scalar columns of RTDC_Hierarchy did not implement len()

  • docs: add an example script dedicated to data plotting

  • ref: remove circular references between Filter and RTDCBase

version 0.14.8

  • fix: Ignore feature “trace” when the trace folder exists but is empty (HDF5 format)

  • fix: If no contour can be found, raise an error before other ancillary features produce cryptic errors

version 0.14.7

  • enh: allow to add meta data when exporting to .fcs or .tsv (dclab version is saved by default)

  • setup: bump fcswrite from 0.4.1 to 0.5.0

version 0.14.6

  • fix: improved handling of tdms trace data (split trace with fixed samples per event to avoid ValueError when exporting to hdf5)

  • fix: transposed roi size x/y config value when exporting to hdf5

version 0.14.5

  • cli: write warning messages to logs in tdms2rtdc

  • ref: increase verbosity of warning messages

version 0.14.4

  • fix: discard trace data when “samples per event” has multiple values for tdms data

  • fix: prefer image shape over config keywords when determining the shape of the event mask and check the shape in dclab-verify-dataset

  • fix: avoid ContourIndexingError by also searching the neighboring (+2/-2) events when the contour frame number does not match (#67)

version 0.14.3

  • enh: explicitly check contour data when testing whether to include the first event in tdms2rtdc

version 0.14.2

  • ref: convert said ValueError to ContourIndexingError

version 0.14.1

  • fix: ValueError when verifying contour frame index due to comparison of float with int

version 0.14.0

  • feat: new command line script for creating a scalar-feature-only dataset with all available ancillary features “dclab-condense”

  • enh: enable scalar feature compression for hdf5 export

  • docs: fix doc string for dclab-tdms2rtdc (–include-initial-empty-image falsely shown as “enabled by default”)

version 0.13.0

  • feat: allow to obtain a mask representing the filtered data with the ret_mask kwarg in RTDCBase.get_downsampled_scatter

  • feat: allow to force-exclude invalid (inf/nan) events when downsampling using the remove_invalid keyword argument

  • feat: exclude empty initial images in dclab-tdms2rtdc; they may optionally be included with “–include-initial-empty-image”

  • feat: new property RTDCBase.features_innate (measuerd feature)

  • enh: log which ancillary features were computed in dclab-tdms2rtdc (#65)

  • enh: improved tdms meta data import (also affects dclab-tdms2rtdc)

  • enh: update channel count and samples per event when writing hdf5 data

  • enh: dclab-verify-dataset now recognizes invalid tdms data

  • enh: several other improvements when reading tdms data

  • enh: group meta data in log files (dclab-tdms2rtdc and dclab-join)

  • fix: correctly handle hdf5 export when the image or contour columns have incorrect sizes (affects dclab-tdms2rtdc)

  • fix: ignore empty configuration values when loading tdms data

  • fix: image/contour files were searched recursively instead of only in the directory of the tdms file

  • fix: check for precence of “time” feature before using it to correct measurement date and time

  • fix: ancillary feature computation for brightness had wrong dependency coded (contour instead of mask)

  • fix: ancillary feature computation when contour data is involved lead to error, because LazyContourList did not implement identifier (see #61)

  • ref: remove NoContourDataWarning for tdms file format

  • tests: improve dataset checks (#64)

version 0.12.0

  • feat: add command line script for joining measurements “dclab-join” (#57)

  • feat: make log files available as RTDCBase.logs

  • feat: include log data in “dclab-join” and “dclab-tdms2rtdc”

  • fix: features property for tdms file format falsely contains the keys “contour”, “image”, “mask”, and “trace” when they are actually not available.

  • enh: support loading TDMS data using the ‘with’ statement

  • docs: add example for joining measurements

  • docs: other minor improvements

  • setup: add Python 3.7 wheels for Windows (#62)

  • setup: remove Python 2 wheels for macOS

version 0.11.1

  • docs: add example for fluorescence trace visualization

  • docs: restructure advanced usage section

  • ref: make dclab in principle compatible with imageio>=2.5.0; Dependencies are pinned due to segfaults during testing

  • setup: make tdms format support and data export dependency optional; To get the previous behavior, use pip install dclab[all]

version 0.11.0

  • feat: compute contours lazily (#61)

version 0.10.5

  • setup: migrate to PEP 517 (pyproject.toml)

version 0.10.4

  • enh: ignore defective feature “aspect” from Shape-In 2.0.6 and 2.0.7

  • enh: support loading HDF5 data using the ‘with’ statement (e.g. with dclab.new_dataset(rtdc_path) as ds:)

version 0.10.3

  • fix: add numpy build dependency (setup_requires)

version 0.10.2

  • fix: HDF5-export did not re-enumerate “index” feature

version 0.10.1

  • fix: support nan-valued events when computing quantile levels in submodule kde_contours

version 0.10.0

  • BREAKING CHANGE: Change np.meshgrid indexing in RTDCBase.get_kde_contour from “xy” to “ij”

  • feat: new submodule kde_contours for computing kernel density contour lines at specific data percentiles (#60)

  • fix: range for contour KDE computation did not always contain end value (RTDCBase.get_kde_contour)

  • fix: positions keyword argument in RTDCBase.get_kde_scatter was not correctly scaled in the logarithmic case

  • ref: cleanup and document PolygonFilter.point_in_poly

  • ref: move skimage code to separate submodule “external”

  • ref: drop dependency on statsmodels and move relevant code to submodule “external”

version 0.9.1

  • fix: all-zero features were treated as non-existent due to relic from pre-0.3.3 era

  • fix: correct extraction of start time from tdms format (1h offset from local time and measurement duration offset)

  • fix: correct extraction of module composition from tdms format (replace “+” with “,”)

  • enh: add configuration key mapping for tdms format to simplify conversion to hdf5 format (see fmt_tdms.naming)

  • enh: do not add laser info for unused lasers for tdms format

  • enh: dclab-verify-dataset checks for image attribute dtype

  • enh: include original software version when exporting to rtdc format

version 0.9.0

  • feat: add new feature: gravitational force, temperature, and ambient temperature

  • ref: remove unused has_key function in rtdc_dataset.config.CaseInsensitiveDict

  • setup: require numpy>=1.10.0 because of equal_nan argument in allclose

version 0.8.0

  • fix: usage of “xor” (^) instead of “or” (|) in statistics

  • feat: support remove_invalid=False in downsampling.downsample_rand (#27)

  • feat: add keyword arguments xscale and yscale to improve data visualization in RTDCBase.get_downsampled_scatter, RTDCBase.get_kde_contour, and RTDCBase.get_kde_scatter (#55)

  • enh: make downsampling code more transparent

  • BREAKING CHANGE: low-level downsampling methods refactored

    • downsampling.downsample_grid: removed keyword argument remove_invalid, because setting it to False makes no sense in this context

    • downsampling.downsample_rand: changed default value of remove_invalid to False, because this is more objective

    • rename keyword argument retidx to ret_idx

    • these changes do not affect any other higher level functionalities in dclab.rtdc_dataset or in Shape-Out

version 0.7.0

  • feat: add new ancillary feature: principal inertia ratio (#46)

  • feat: add new ancillary feature: absolute tilt (#53)

  • feat: add computation of viscosity for water (#52)

version 0.6.3

  • fix: channel width not correctly identified for old tdms files

version 0.6.2

  • ci: automate release to PyPI with appveyor and travis-ci

version 0.6.0

  • fix: image export as .avi did not have option to use unfiltered data

  • fix: avoid a few unicode gotchas

  • feat: use Doane’s formula for kernel density estimator defaults (#42)

  • docs: usage examples, advanced scripting, and code reference update (#49)

version 0.5.2

  • Migrate from os.path to pathlib (#50)

  • fmt_hdf5: Add run index to title

version 0.5.1

  • Setup: add dependencies for statsmodels

  • Tests: filter known warnings

  • fmt_hdf5: import unknown keys such that “dclab-verify-dataset” can complain about them

version 0.5.0

  • BREAKING CHANGES:

    • definitions.feature_names now contains non-scalar features (inlcuding “image”, “contour”, “mask”, and “trace”). To test for scalar features, use definitions.scalar_feature_names.

    • features bright_* are computed from mask instead of from contour

  • Bugfixes:

    • write correct event count in exported hdf5 data files

    • improve implementation of video file handling in fmt_tdms

  • add new non-scalar feature “mask” (#48)

  • removed configuration key [online_contour]: “bin margin” (#47)

  • minor improvements for the tdms file format

version 0.4.0

  • Bugfix: CLI “dclab-tdms2rtdc” did not work for single tdms files (#45)

  • update configuration keys:

    • added new keys for [fluorescence]

    • added [setup]: “identifier”

    • removed [imaging]: “exposure time”, “flash current”

    • removed [setup]: “temperature”, “viscosity”

  • renamed feature “ncells” to “nevents”

version 0.3.3

  • ref: do not import missing features as zeros in fmt_tdms

  • CLI:

    • add tdms-to-rtdc converter “dclab-tdms2rtdc” (#36)

    • improve “dclab-verify-dataset” user experience

  • Bugfixes:

    • “limit events” filtering must be integer not boolean (#41)

    • Support opening tdms files with capitalized “userDef” column names

    • OSError when trying to open files from repository root

version 0.3.2

  • CLI: add rudimentary dataset checker “dclab-verify-dataset” (#37)

  • Add logic to compute parent/root/child event indices of RTDC_Hierarchy

    • Hierarchy children now support contour, image, and traces

    • Hierarchy children now support and remember manual filters (#22)

  • Update emodulus look-up table with larger values for deformation

  • Implement pixel size correction for emodulus computation

  • Allow to add pixelation error to isoelastics (add_px_err=True) (#28)

  • Bugfixes:

    • Pixel size not read from tdms-based measurements

    • Young’s modulus computation wrong due to faulty FEM simulations (#39)

version 0.3.1

  • Remove all-zero dummy columns from dict format

  • Implement hdf5-based RT-DC data reader (#32)

  • Implement hdf5-based RT-DC data writer (#33)

  • Bugfixes:

    • Automatically fix inverted box filters

    • RTDC_TDMS trace data contained empty arrays when no trace data was present (trace key should not have been accessible)

    • Not possible to get isoelastics for circularity

version 0.3.0

  • New fluorescence crosstalk correction feature recipe (#35)

  • New ancillary features “fl1_max_ctc”, “fl2_max_ctc”, “fl3_max_ctc” (#35)

  • Add priority for multiple ancillary features with same name

  • Bugfixes:

    • Configuration key values were not hashed for ancillary features

  • Code cleanup:

    • Refactoring: Put ancillary columns into a new folder module

    • Refactoring: Use the term “feature” consistently

    • Unify trace handling in dclab (#30)

    • Add functions to convert input config data

version 0.2.9

  • Bugfixes:

    • Regression when loading configuration strings containing quotes

    • Parameters missing when loading ShapeIn 2.0.1 tdms data

version 0.2.8

  • Refactor configuration class to support new format (#26)

version 0.2.7

  • New submodule and classes for managing isoelastics

  • New ancillary columns “inert_ratio_raw” and “inert_ratio_cvx”

  • Bugfixes:

    • Typo when finding contour data files (tdms file format)

  • Rrefactoring:

    • “features” submodule with basic methods for ancillary columns

version 0.2.6

  • Return event images as gray scale (#17)

  • Bugfixes:

    • Shrink ancillary column size if it exceeds dataset size

    • Generate random RTDCBase.identifier (do not use RTDCBase.hash) to fix problem with identical identifiers for hierarchy children

    • Correctly determine contour data files (tdms file format)

    • Allow contour data indices larger than uint8

version 0.2.5

  • Add ancillary columns “bright_avg” and “bright_sd” (#18, #19)

  • Standardize attributes of RTDCBase subclasses (#12)

  • Refactoring:

    • New column names and removal of redundant column identifiers (#16)

    • Minor improvements towards PEP8 (e.g. #15)

    • New class for handling filters (#13)

  • Bugfixes:

    • Hierarchy child computed all ancillary columns of parent upon checking availability of a column

version 0.2.4

  • Replace OpenCV with imageio

  • Add (ancilliary) computation of volume (#11)

  • Add convenience methods for Configuration

  • Refactoring (#8):

    • Separate classes for .tdms, dict-based, and hierarchy datasets

    • Introduce “_events” attribute for stored data

    • Data columns (including image, trace, contour) are accessed via keys instead of attributes.

    • Make space for new hdf5-based file format

    • Introduce ancilliary columns that are computed on-the-fly (new “_ancilliaries” attribute and “ancilliary_columns.py”)

version 0.2.3

  • Add look-up table for elastic modulus (#7)

  • Add filtering option “remove invalid events” to remove nan/inf

  • Support nan and inf in data analysis

  • Improve downsampling performance

  • Refactor downsampling methods (#6)

version 0.2.2

  • Add new histogram-based kernel density estimator (#2)

  • Refactoring:

    • Configuration fully handled by RTDC_DataSet module (#5)

    • Simplify video export function (#4)

    • Removed “Plotting” configuration key

    • Removed .cfg configuration files

version 0.2.1

  • Support npTDMS 0.9.0

  • Add AVI-Export function

  • Add lazy submodule for event trace data and rename RTDC_DataSet.traces to RTDC_DataSet.trace

  • Add “Event index” column

version 0.2.0

  • Compute sensible default configuration parameters for KDE estimation and contour plotting

  • Speed-up handling of contour text files

  • Add support for “User Defined” column in tdms files

version 0.1.9

  • Implement hierarchical instantiation of RTDC_DataSet

  • Bugfix: Prevent instances of PolygonFilter that have same id

  • Load InertiaRatio and InertiaRatioRaw from tdms files

version 0.1.8

  • Allow to instantiate RTDC_DataSet without a tdms file

  • Add statistics submodule

  • Bugfixes:

    • Faulty hashing strategy in RTDC_DataSet.GetDownSampledScatter

  • Code cleanup (renamed methods, cleaned structure)

  • Corrections/additions in definitions (fRT-DC)

version 0.1.7

  • Added channel: distance between to first fl. peaks

  • Added fluorescence channels: peak position, peak area, number of peaks

  • Allow to disable KDE computation

  • Add filter array for manual (user-defined) filtering

  • Add config parameters for log axis scaling

  • Add channels: bounding box x- and y-size

  • Bugfixes:

    • cached.py did not handle None

    • Limiting number of events caused integer/bool error

version 0.1.6

  • Added RTDC_DataSet.ExportTSV for data export

  • Bugfixes:

    • Correct determination of video file in RTDCDataSet

    • Fix multivariate KDE computation

    • Contour accuracy for Defo overridden by that of Circ

version 0.1.5

version 0.1.4

  • Added support for 3-channel fluorescence data (FL-1..3 max/width)

version 0.1.3

version 0.1.2

  • Add support for limiting amount of data points analyzed with the configuration keyword “Limit Events”

  • Comments refer to “events” instead of “points” from now on