Changelog¶
List of changes in-between dclab releases.
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¶
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¶
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 0.2.7¶
- 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:
- 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¶
version 0.2.2¶
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¶
- Fix regressions with filtering. https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/issues/43
- Ignore empty columns in .tdms files (#1)
- Moved RTDC_DataSet and PolygonFilter classes to separate files
- Introduce more transparent caching - improves speed in some cases
version 0.1.4¶
- Added support for 3-channel fluorescence data (FL-1..3 max/width)
version 0.1.3¶
- Fixed minor polygon filter problems.
- Fix a couple of Shape-Out-related issues:
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