Code

Add data read#85

Code

Draft

oruebel wants to merge 163 commits intomainNeurodataWithoutBorders/aqnwb:mainfrom add_readNeurodataWithoutBorders/aqnwb:add_readCopy head branch name to clipboard

+4,173-1,024

Commits

Commits on Aug 31, 2024

• Define base classes for reading

  oruebel

  committed
  1e1f041

• First draft of reading datasets and attributes

  oruebel

  committed
  e58f50f

• Split reading of attribute and dataset to separate functions

  oruebel

  committed
  250a66b

• Remove debug print

  oruebel

  committed
  e1bfa2e

• Add functions to construct ReadDatasetWrapper and ReadAttributeWrapper from BaseIO

  oruebel

  committed
  4aedefd

• Fix formatting

  oruebel

  committed
  4dae171

• Add test for using the ReadDatasetWrapper

  oruebel

  committed
  140809e

• Start refactor containers for read

  oruebel

  committed
  4d7b1ea

• Fix format

  oruebel

  committed
  2db4bfe

Commits on Sep 1, 2024

• Read ElectricalSeries.data example working

  oruebel

  committed
  b2959d2

• Revert change to tests used for debugging

  oruebel

  committed
  37d30d3

• Fix codespell issue

  oruebel

  committed
  6cfe416

• Move read example to an example file

  oruebel

  committed
  3d86aff

• Fix bug in Container::create

  oruebel

  committed
  3fc1d7a

• Add example for data read

  oruebel

  committed
  b09a4fa

• Fix spelling error

  oruebel

  committed
  970f4c8

• Add user docs for data read

  oruebel

  committed
  26fbae9

• Update read user docs

  oruebel

  committed
  4299f99

Commits on Sep 2, 2024

• Add toc

  oruebel

  committed
  9c9301c

• Add read software design figure and more details on the design

  oruebel

  committed
  447337a

• Some adjustment to the edges in the fig

  oruebel

  committed
  e3d4330

• Some adjustment to the edges in the fig

  oruebel

  committed
  77f0861

• Add intro for data read page

  oruebel

  committed
  5190731

Commits on Sep 3, 2024

• Make Container::create inline

  oruebel

  committed
  f08e42f

• Make DataBlock::fromGeneric inline

  oruebel

  committed
  1a754b9

• Implement function to allow us to get the storage object type for a given path

  oruebel

  committed
  ebfbdf1

• Rename getObjectType to getStroageObjectType

  oruebel

  committed
  3022861

• Fix reading of attributes and add TimeSeries.resolution read

  oruebel

  committed
  6ba32a5

• Add example for reading an attribute

  oruebel

  committed
  1fb5d95

• Add ReadDataWrapperBase as common base class for ReadDatasetWrapper and ReadAttributeWrapper

  oruebel

  committed
  676b978

• Fix docstring

  oruebel

  committed
  14c8362

• Minor fixed to docs

  oruebel

  committed
  d2b1c23

• Mention ReadDataWrapperBase in the read dox page

  oruebel

  committed
  78825f2

• Merge branch 'main' into add_read

  oruebel

  committed
  85db320

• Fix unit tests after merge

  oruebel

  committed
  5c2faae

• Remove NWBFile.identifierText property

  oruebel

  committed
  c481260

Commits on Sep 4, 2024

• Allow setting of value type template parameter for ReadDataWrapperBase and subtypes

  oruebel

  committed
  b418149

• Save the std::type_index as part of the DataBlock to support runtime checking

  oruebel

  committed
  1f3ad24

Commits on Sep 5, 2024

• Fix #88 move io classes to their own module

  oruebel

  committed
  99b5d4e

• Refactor to add IO namespace to match folder structure

  oruebel

  committed
  04117e9

• Move HDF5RecordingData to its own hpp/cpp files

  oruebel

  committed
  82a4c08

• Moved read I/O classes to new ReadIO.hpp

  oruebel

  committed
  6554e29

• Refactor the read data wrappers to use a single ReadDataWrapper class for both Attributes and Datasets

  oruebel

  committed
  bff7121

Commits on Sep 6, 2024

• Replace redundant ReadObjectType with StorageObjectType

  oruebel

  committed
  53365ff

• Add traits for ReadObjectWrapper to prevent instantiation for Group and Undefined types

  oruebel

  committed
  c66b3bc

• Fix formatting

  oruebel

  committed
  0da4800

• Fix spelling error

  oruebel

  committed
  d161c47

• Inline functions in ReadIO.hpp

  oruebel

  committed
  58e5afb

• Some minor fixes

  oruebel

  committed
  b7cc149

Commits on Sep 7, 2024

• Merge branch 'main' into add_read

  oruebel

  authored
  b9c6c9b

Commits on Sep 8, 2024

• First draft of Container registry

  oruebel

  committed
  0e8ef12

• Update ElectrodGroup to provide standard Container constructor and move args to initalize

  oruebel

  committed
  69c3c4e

• Fix formatting

  oruebel

  committed
  e75c7ad

• Merge branch 'add_read' into add_container_read

  oruebel

  committed
  eeaceae

• Register subtypes

  oruebel

  committed
  e62164b

• Move the registry to a new RegisteredType class to also cover non-Group types, e.g., Data, VectorData etc.

  oruebel

  committed
  e99feee

• Fix formatting

  oruebel

  committed
  3683921

• Ensure all neurodata_types are registered correctly

  oruebel

  committed
  20050c7

• Add unittest for RegisteredTrype

  oruebel

  committed
  cf9c017

• Add developer docs for RegisteredTypes

  oruebel

  committed
  be29fb6

• Fix name of the unit test file for RegisteredType

  oruebel

  committed
  779c2af

• Add example code for RegisteredType

  oruebel

  committed
  3179c4b

• Use both namespace and type name to register and access subtypes

  oruebel

  committed
  dbdd945

• Update documentation to clarify the use of namespace::classname to manage container classes

  oruebel

  committed
  4a7197f

• Update read test to use the registry to construct the class

  oruebel

  committed
  d11870b

• Minor dox fixes

  oruebel

  committed
  7a64982

Commits on Sep 9, 2024

• Fix getTypeName and getNamespace and use them instead of hard-coded values

  oruebel

  committed
  b42065b

• Update docs for getTypeName add getNamespace

  oruebel

  committed
  501bc32

• Merge branch 'main' into add_read

  oruebel

  committed
  5ab8464

• Fix ElectricalSeries

  oruebel

  committed
  803dfcf

• Merge branch 'add_read' into add_container_read

  oruebel

  committed
  5d959bd

• Attempt to fix reading of string attribute

  oruebel

  committed
  a1dc63d

• Fix read neurodata_type attribute read test

  oruebel

  committed
  bba4a79

• Add test for reading a TimeSeries Container back

  oruebel

  committed
  a58a44a

• Add RegisteredType::create method to read a type from file

  oruebel

  committed
  3ac8ca4

• Fix path ecephys read test

  oruebel

  committed
  5f0bdd6

• Change RegisteredType::create to return shared pointer to support casting

  oruebel

  committed
  edc45cf

• Update ecephys read example

  oruebel

  committed
  7184f96

• Updated read tutorial and example

  oruebel

  committed
  bda279d

• Add missing comment

  oruebel

  committed
  db8c652

• Clarify read docs and rename workflow docs

  oruebel

  committed
  cf06a19

Commits on Sep 19, 2024

• Run test workflows on all PRs

  oruebel

  committed
  cdffc74

• Merge branch 'add_read' into add_container_read

  oruebel

  committed
  b0a28f9

• Fix static assert for ReadDataWrapper

  oruebel

  committed
  89f6d29

• Sync add_read with main branch (#101)

  Show description for 5608c5a
  oruebel

  authored
  5608c5a

• Merge branch 'add_read' into add_container_read

  oruebel

  authored
  8bbecb8

• Merge branch 'main' into add_read

  oruebel

  committed
  c7ced4e

Commits on Sep 20, 2024

• Merge branch 'main' into add_read

  oruebel

  committed
  dd01ad3

• Fix formatting and docs error after merge with main

  oruebel

  committed
  968fcf0

• Merge branch 'add_read' into add_container_read

  oruebel

  committed
  b424eaf

• Fix formatting after merge

  oruebel

  committed
  8aa5680

• Remove SpikeEventSeries.neurodata_type

  oruebel

  committed
  5798145

• Register SpikeEventSeries as a type

  oruebel

  committed
  8832b04

Commits on Sep 21, 2024

• Updated RegisterTypes to allow overwrite of the typename to use and overwrite the typename for ElectrodeTable

  oruebel

  committed
  f244d8c

• Fix code formatting

  oruebel

  committed
  c78e7cb

• Add missing description for DynamicTableRegion

  oruebel

  committed
  9d7f408

• Fix #109 Add missing axis attribute for channel_conversion and remove extra attributes

  oruebel

  committed
  435866c

• Remove undefined functions from Device

  oruebel

  committed
  ce3227c

• Rename member variable in ElectricalSeries

  oruebel

  committed
  cc0cd84

• Rename member variable in SpikeEventSeries

  oruebel

  committed
  f99ed91

• Added mergePaths functions and made functions in Utils.hpp static inline

  oruebel

  committed
  6a4876f

• Updated ElectrodeTable to use mergePaths method

  oruebel

  committed
  af28b29

• Updated DynamicTable to use mergePaths method

  oruebel

  committed
  c222955

• Update ElectrodeGroup to use mergePaths

  oruebel

  committed
  0d402f3

• Updated ElectricalSeries to use mergePaths

  oruebel

  committed
  156910c

• Updated TimerSeries to use mergePaths function

  oruebel

  committed
  962faaa

• Updated NWBFile to use the mergePaths function

  oruebel

  committed
  8f13baf

Commits on Sep 22, 2024

• Updated ElectrodeTable static paths to not used trailing / for consistency

  oruebel

  committed
  bf92ce2

• Fix Doxygen error by extracting also static members in the docs

  oruebel

  committed
  c2251a8

• Fix section level in install.dox

  oruebel

  committed
  f3e30cd

• Update ReadDataWrapper to use m_ member naming convention

  oruebel

  committed
  cea343b

• Updated DataBlock / DataBlockGeneric to avoid shadowing of constructor args

  oruebel

  committed
  7c884d4

• Fix reference error in read.dox

  oruebel

  committed
  8145382

• Add ReadDataWrapper isType, getPath, getIO methods and update docstrings

  oruebel

  committed
  078c4f9

• Create macro DEFINE_FIELD to simplify creating access methods for fields in RegisteredType subclasses

  oruebel

  committed
  98377cb

• Replace previous field access methods in TimeSeries with DEFINE_FIELD macro calls

  oruebel

  committed
  281375c

• Replace TimeSeries.dataLazy and resolutionLazy with DEFINE_FIELD definitions

  oruebel

  committed
  9eb00cf

• Update the Doxygen built to expand the DEFINE_FIELD macro to document the generated functions

  oruebel

  committed
  90803a8

• Fix spellcheck

  oruebel

  committed
  4dfb541

• Fix section levels in read.dox

  oruebel

  committed
  9b9c8c3

• Add docs for using the DEFINE_FIELD macro

  oruebel

  committed
  3c4b2d7

• Added attributeExists method on IO and ReadDataWrapper::exists methods to check that an object actually exists

  oruebel

  committed
  aad6928

• Add TimeSeries.descriptionLazy field to test that reading string attributes works

  oruebel

  committed
  5a411c4

• Added function getGroupObjects to the I/O to allow gettings all objects contained in a group

  oruebel

  committed
  daca8f2

• Add BaseIO::findTypes method to search for neurodata_types in a file

  oruebel

  committed
  1f81e6d

Commits on Sep 23, 2024

• Add example for searching for typed objects

  oruebel

  committed
  3affcca

• Update ElectrodeTable to use m_ member names

  oruebel

  committed
  30e1226

• Added field definitions for TimeSeries

  oruebel

  committed
  fa6a981

Commits on Sep 24, 2024

• Add some design docs about reading registered types

  oruebel

  committed
  a0e02b2

• Update read types design figure

  oruebel

  committed
  fbed92c

• Minor update to docs of RegisteredType

  oruebel

  committed
  d4c2e64

• Update docs/pages/userdocs/read.dox

  Show description for bfaabb8
  

  oruebel

  and

  stephprince

  authored
  bfaabb8

• Update src/io/ReadIO.hpp

  Show description for a439212
  

  oruebel

  and

  stephprince

  authored
  a439212

• Update src/io/ReadIO.hpp

  oruebel

  authored
  5f28fb0

• Rename ReadDataWrapper.is_dataset

  oruebel

  committed
  a9725b2

• Update src/io/hdf5/HDF5IO.hpp

  Show description for e70949c
  

  oruebel

  and

  stephprince

  authored
  e70949c

• Remove duplicate code in NWBFile

  oruebel

  committed
  d1da5d1

• Remove outdated ToDo item

  oruebel

  committed
  12a86a5

Commits on Oct 2, 2024

• Apply suggestions on docs from code review

  Show description for 423f3d7
  

  oruebel

  and

  stephprince

  authored
  423f3d7

Commits on Oct 22, 2024

• Merge branch 'main' into add_read

  oruebel

  committed
  ae66f33

• Fix build error after merge

  oruebel

  committed
  69df3e0

• Merge branch 'add_read' into add_container_read

  oruebel

  authored
  415926c

• Fix build error due to error during merge with base branch

  oruebel

  committed
  a93cadd

• Apply suggestions from code review

  Show description for 2554667
  

  oruebel

  and

  stephprince

  authored
  2554667

Commits on Oct 23, 2024

• Fix read.dox figure based on suggestion

  oruebel

  committed
  6c57527

• Fix docs based on code review

  oruebel

  committed
  a7cf936

Commits on Dec 12, 2024

• update getAttribute method to detect object type

  stephprince

  committed
  3d89d78

• update read example

  stephprince

  committed
  c22d658

• add file mode options and readonly mode to io

  stephprince

  committed
  a91cc91

• update example to use readonly

  stephprince

  committed
  b20388c

Commits on Dec 18, 2024

• add getter functions to Container classes with attributes

  stephprince

  committed
  20afbae

• fix formatting

  stephprince

  committed
  20813c2

• update lint workflow

  stephprince

  committed
  f211978

Commits on Dec 19, 2024

• add NWBFile fields

  stephprince

  committed
  0b7d181

• update filenames

  stephprince

  committed
  a5cda51

• remove duplicate file mode checks

  stephprince

  committed
  6a7bb45

• Merge pull request #91 from NeurodataWithoutBorders/add_container_read

  Show description for bfa740a
  stephprince

  authored
  bfa740a

Commits on Dec 22, 2024

• Merge branch 'main' into add_read

  oruebel

  committed
  ddb8f50

• Fix spelling and complete merge

  oruebel

  committed
  54d55da

• Fix missing merge in file

  oruebel

  committed
  8492bf7

• Install Boost multi-array in windows action

  oruebel

  committed
  9ed9bd3

• Use std::vector instead of variable-length arrays to avoid Windows built errors

  oruebel

  committed
  f6b306b

• Add note to docs to clarify non-virtual DEFINE_FIELD

  oruebel

  committed
  7b88122