Changelog¶
List of changes in-between dclab releases.
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¶
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 0.10.5¶
- 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