Permalink
Fetching contributors…
Cannot retrieve contributors at this time
executable file 232 lines (148 sloc) 8.32 KB

Change Log

All notable changes to this project will be documented in this file.

[0.14.5] = 2018-06-14

Changed

  • bumped lower limit of pandas to 0.17, removed upper limit
  • changed CellTypesCache cell data structure to be less nested, more flat. Requires update to manifest and re-download of cells.json.
  • simplified MouseConnectivityCache data structure. Requires update to manifest and re-download of experiments.json.
  • stopped using deprecated function in SimpleTree

Added

  • regression tests for Brain Observatory analysis

[0.14.4] - 2018-01-30

Changed

  • Numerous Python 2/3 compatibility fixes
  • Improved spike filtering in ephys.ephys_features

[0.14.3] - 2017-10-19

Added

  • CellTypesCache.get_cells has a new species argument.

Changed

  • MouseConnectivityCache downloads structure masks instead of computing them.

[0.14.2] - 2017-08-17

Added

  • ABS-64; Jupyterhub Dockerfiles
  • PR #13; Manifest error check

Changed

ABS-132; changed to Allen Institute Software License ABS-129; StructureTree converts color hex triplet to 8-bit color triplet ABS-125; update expected data for unmocked tests PBS-358; update extract_trace module to deal with motion border case ABS-85; allow variable long square start time in ephys feature extractor

[0.13.2] - 2017-06-15

Added

  • BrainObservatoryNwbDataSet.get_demixed_traces
  • BrainObservatoryNwbDataSet.get_pupil_location
  • BrainObservatoryNwbDataSet.get_pupil_size
  • BrainObservatoryApi.get_cell_specimen_id_mapping
  • allensdk.brain_observatory.receptive_field_analysis
  • allensdk.brain_observatory.demixer

Changed

  • BrainObservatoryCache.get_ophys_experiments returns "acquisition_age_days" instead of "age_days". The new field describes the age of the animal on the day of experiment acquisition.
  • BrainObservatoryCache.get_experiment_containers no longer returns "age_days".
  • BrainObservatoryCache.get_ophys_experiments accepts a list of cell_specimen_ids for additional filtering
  • json_utilities uses simplejson for better NaN handling

[0.13.1] - 2017-03-20

Fixed

  • issue #42: Caching behavior in MouseConnectivityCache for CCF volumes fixed
  • GLIF examples, documentation fixed

[0.13.0] - 2017-03-16

Added

  • ReferenceSpace is a new class for relating structure graphs and annotation volumes.
  • Standardized caching and paging decorators

Changed

  • Ontology has been deprecated in favor of StructureTree.
  • MouseConnectivityCache uses StructureTree internally (ontology-based methods are deprecated)
  • CellTypesCache and MouseConnectivityCache use cacher decorator
  • GlifApi has stateless methods now. Old methods are deprecated.

Fixed

  • Github issue #35 - MouseConnectivityCache's manifest now uses CCF-version- and resolution-specific file names for masks. The masks now live inside the CCF version directory. Users must download a new manifest.

[0.12.4] - 2016-10-28

Fixed

  • Github issues #23, #28 - added a new dependency "requests_toolbelt" and upgraded API database for more reliable large file downloads.
  • Github issue #26 - better documentation for structure unionize records.
  • Github issue #25 - documentation errors in brain observatory analysis.

Changed

  • New CCF annotation volume with complete cortical areas and layers.
  • Mouse Connectivity structure unionize records have been computed for new CCF. Previous records are available here: http://download.alleninstitute.org/informatics-archive/june-2016/mouse_projection/
  • Github issue #27 - MouseConnectivityCache.get_structure_unionizes returns only requested structures, not all descendants. Added a separate argument for descendant inclusion.

Added

  • MouseConnectivityCache has a new constructor argument for specifying CCF version.

[0.12.2] - 2016-9-1

Fixed

  • Github issue #16 (jinja2 requirement)
  • Github pull request #21 (spurious "i" typo) in r_neuropil.py

[0.12.1] - 2016-8-17

Changed

  • neuropil subtraction algorithm (brain_observatory.r_neuropil) faster and more robust
  • formatting changes for better PEP8 compliance
  • preparation for Python 3 support
  • updated Dockerfiles

Fixed

  • Github issue #17 (scipy requirement)

[0.12.0] - 2016-6-9

Added

  • Support for the Allen Brain Observatory data (BrainObservatoryCache and BrainObservatoryApi classes).
  • Code for neurpil subtraction, dF/F estimation, and tuning analysis.
  • New ephys feature extractor (ephys_features.py, ephys_extractor.py). The old one is still there (feature_extractor.py) but should be considered deprecated.

[0.11.0] - 2016-3-3

Added

  • CellTypesCache.get_cells has a new argument 'reporter_status', which accepts one or more ReporterStatus values.
  • CellTypesApi.save_reconstruction_marker and CellTypesCache.get_reconstruction_marker download and open files containing positions that mark special points in reconstruction (truncation, early termination of reconstruction, etc).
  • swc.read_marker_file for reading in marker files
  • Morphology has new methods for manipulating the morphology tree structure
  • allensdk.model.biophysical package supports active and passive models

Changed

  • Morphology compartments are now Compartment objects that behave like dictionaries
  • Compartment.children stores references to immediate descendant Compartments
  • spike times in NWB files are stored in "analysis/spike_times" instead of "analysis/aibs_spike_times"
  • NwbDataSet looks for spike times in both locations ("spike_times" first)
  • glif_neuron_methods.py function names have been changed to be more standardized
  • allensdk.model.biophysical_perisomatic package renamed to allensdk.model.biophysical
  • NEURON dependency updated to 7.4 release 1370

Fixed

  • MouseConnectivityCache.get_structure_mask bug fixed (github issue 8)
  • CellTypesApi.get_ephys_sweeps returns sweeps in sweep number order (github issue 11)
  • NwbDataSet.set_spike_times added maxshape(None,) to create_dataset (github issue 7)

[0.10.1] - 2015-9-24

Added

  • MouseConnectivityCache.get_projection_matrix, method for building a signal matrix from injection structure to projection structure.
  • CellTypesCache.get_morphology_features, method for retrieving morphology features for all cells
  • CellTypesCache.get_all_features, method for retrieving both morphology and ephys features for all cells in a single table
  • new RmaTemplate class enables construction of queries with jinja2 template library.
  • Jupyter notebook examples added to documentation.

Fixed

  • Api.retrieve_parsed_json_over_http respects post parameter.
  • improved installation of dependencies.

Changed

  • Ontology.get_child_ids and Ontology.get_descendant_ids accept a list of ids instead of a variable length argument list.
  • API Access/Data API Client documentation better reflects new 0.10.x allensdk.api.query modules.
  • Cache.wrap method defaults to save_as_json=False.
  • Cache.wrap method defaults to returning json rather than a pandas dataframe (new parameter return_dataframe=False).
  • BiophysicalApi.cache_data throws an exception if no data is found for a neuronal model id.
  • Replaced brainscales Dockerfile with neuralenseble Dockerfiles.

[0.10.1] - 2015-x-x

Added

  • MouseConnectivityCache.get_projection_matrix, method for building a signal matrix from injection structure to projection structure.
  • CellTypesCache.get_morphology_features, method for retrieving morphology features for all cells
  • CellTypesCache.get_all_features, method for retrieving both morphology and ephys features for all cells in a single table

Changed

  • Ontology.get_child_ids and Ontology.get_descendant_ids accept a list of ids instead of a variable length argument list.

[0.10.0] - 2015-8-20

Added

  • Manifest and Cache classes for keeping track of files
  • MouseConnectivityApi class for downloading data from the Mouse Connectivity Atlas
  • MouseConnectivityCache fclass or keeping track of files
  • CellTypesCache for keeping track of cell types files
  • Ontology class for manipulating structures
  • Rma class for formalizing API queries
  • GridDataApi for downloading expression and projection grid volumes
  • EphysFeatureExtractor module for computing ephys features used in Cell Types Database

Fixed

  • json_utilities has better numpy data type serialization support

[0.9.1] - 2015-5-13

Changed

  • Documentation updated

Fixed

  • Installation/Makefile bug

[0.9.0] - 2015-5-12

Added

  • Everything: initial release!