Changelog

List of changes in-between dclab releases.

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 0.1.2

  • 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

version