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Add read for neurodata_types, e.g., Container, TimeSeries #91

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merged 87 commits into from
Dec 19, 2024
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0e8ef12
First draft of Container registry
oruebel Sep 8, 2024
eeaceae
Merge branch 'add_read' into add_container_read
oruebel Sep 8, 2024
e62164b
Register subtypes
oruebel Sep 8, 2024
e99feee
Move the registry to a new RegisteredType class to also cover non-Gro…
oruebel Sep 8, 2024
3683921
Fix formatting
oruebel Sep 8, 2024
20050c7
Ensure all neurodata_types are registered correctly
oruebel Sep 8, 2024
cf9c017
Add unittest for RegisteredTrype
oruebel Sep 8, 2024
be29fb6
Add developer docs for RegisteredTypes
oruebel Sep 8, 2024
779c2af
Fix name of the unit test file for RegisteredType
oruebel Sep 8, 2024
3179c4b
Add example code for RegisteredType
oruebel Sep 8, 2024
dbdd945
Use both namespace and type name to register and access subtypes
oruebel Sep 8, 2024
4a7197f
Update documentation to clarify the use of namespace::classname to ma…
oruebel Sep 8, 2024
d11870b
Update read test to use the registry to construct the class
oruebel Sep 8, 2024
7a64982
Minor dox fixes
oruebel Sep 8, 2024
b42065b
Fix getTypeName and getNamespace and use them instead of hard-coded v…
oruebel Sep 9, 2024
501bc32
Update docs for getTypeName add getNamespace
oruebel Sep 9, 2024
5d959bd
Merge branch 'add_read' into add_container_read
oruebel Sep 9, 2024
a1dc63d
Attempt to fix reading of string attribute
oruebel Sep 9, 2024
bba4a79
Fix read neurodata_type attribute read test
oruebel Sep 9, 2024
a58a44a
Add test for reading a TimeSeries Container back
oruebel Sep 9, 2024
3ac8ca4
Add RegisteredType::create method to read a type from file
oruebel Sep 9, 2024
5f0bdd6
Fix path ecephys read test
oruebel Sep 9, 2024
edc45cf
Change RegisteredType::create to return shared pointer to support cas…
oruebel Sep 9, 2024
7184f96
Update ecephys read example
oruebel Sep 9, 2024
bda279d
Updated read tutorial and example
oruebel Sep 9, 2024
db8c652
Add missing comment
oruebel Sep 9, 2024
cf06a19
Clarify read docs and rename workflow docs
oruebel Sep 9, 2024
b0a28f9
Merge branch 'add_read' into add_container_read
oruebel Sep 19, 2024
8bbecb8
Merge branch 'add_read' into add_container_read
oruebel Sep 19, 2024
b424eaf
Merge branch 'add_read' into add_container_read
oruebel Sep 20, 2024
8aa5680
Fix formatting after merge
oruebel Sep 20, 2024
5798145
Remove SpikeEventSeries.neurodata_type
oruebel Sep 20, 2024
8832b04
Register SpikeEventSeries as a type
oruebel Sep 20, 2024
f244d8c
Updated RegisterTypes to allow overwrite of the typename to use and o…
oruebel Sep 21, 2024
c78e7cb
Fix code formatting
oruebel Sep 21, 2024
9d7f408
Add missing description for DynamicTableRegion
oruebel Sep 21, 2024
435866c
Fix #109 Add missing axis attribute for channel_conversion and remove…
oruebel Sep 21, 2024
ce3227c
Remove undefined functions from Device
oruebel Sep 21, 2024
cc0cd84
Rename member variable in ElectricalSeries
oruebel Sep 21, 2024
f99ed91
Rename member variable in SpikeEventSeries
oruebel Sep 21, 2024
6a4876f
Added mergePaths functions and made functions in Utils.hpp static inline
oruebel Sep 21, 2024
af28b29
Updated ElectrodeTable to use mergePaths method
oruebel Sep 21, 2024
c222955
Updated DynamicTable to use mergePaths method
oruebel Sep 21, 2024
0d402f3
Update ElectrodeGroup to use mergePaths
oruebel Sep 21, 2024
156910c
Updated ElectricalSeries to use mergePaths
oruebel Sep 21, 2024
962faaa
Updated TimerSeries to use mergePaths function
oruebel Sep 21, 2024
8f13baf
Updated NWBFile to use the mergePaths function
oruebel Sep 21, 2024
bf92ce2
Updated ElectrodeTable static paths to not used trailing / for consis…
oruebel Sep 22, 2024
c2251a8
Fix Doxygen error by extracting also static members in the docs
oruebel Sep 22, 2024
f3e30cd
Fix section level in install.dox
oruebel Sep 22, 2024
cea343b
Update ReadDataWrapper to use m_ member naming convention
oruebel Sep 22, 2024
7c884d4
Updated DataBlock / DataBlockGeneric to avoid shadowing of constructo…
oruebel Sep 22, 2024
8145382
Fix reference error in read.dox
oruebel Sep 22, 2024
078c4f9
Add ReadDataWrapper isType, getPath, getIO methods and update docstrings
oruebel Sep 22, 2024
98377cb
Create macro DEFINE_FIELD to simplify creating access methods for fie…
oruebel Sep 22, 2024
281375c
Replace previous field access methods in TimeSeries with DEFINE_FIELD…
oruebel Sep 22, 2024
9eb00cf
Replace TimeSeries.dataLazy and resolutionLazy with DEFINE_FIELD defi…
oruebel Sep 22, 2024
90803a8
Update the Doxygen built to expand the DEFINE_FIELD macro to document…
oruebel Sep 22, 2024
4dfb541
Fix spellcheck
oruebel Sep 22, 2024
9b9c8c3
Fix section levels in read.dox
oruebel Sep 22, 2024
3c4b2d7
Add docs for using the DEFINE_FIELD macro
oruebel Sep 22, 2024
aad6928
Added attributeExists method on IO and ReadDataWrapper::exists method…
oruebel Sep 22, 2024
5a411c4
Add TimeSeries.descriptionLazy field to test that reading string attr…
oruebel Sep 22, 2024
daca8f2
Added function getGroupObjects to the I/O to allow gettings all objec…
oruebel Sep 22, 2024
1f81e6d
Add BaseIO::findTypes method to search for neurodata_types in a file
oruebel Sep 22, 2024
3affcca
Add example for searching for typed objects
oruebel Sep 23, 2024
30e1226
Update ElectrodeTable to use m_ member names
oruebel Sep 23, 2024
fa6a981
Added field definitions for TimeSeries
oruebel Sep 23, 2024
a0e02b2
Add some design docs about reading registered types
oruebel Sep 24, 2024
fbed92c
Update read types design figure
oruebel Sep 24, 2024
d4c2e64
Minor update to docs of RegisteredType
oruebel Sep 24, 2024
423f3d7
Apply suggestions on docs from code review
oruebel Oct 2, 2024
415926c
Merge branch 'add_read' into add_container_read
oruebel Oct 22, 2024
a93cadd
Fix build error due to error during merge with base branch
oruebel Oct 22, 2024
2554667
Apply suggestions from code review
oruebel Oct 22, 2024
6c57527
Fix read.dox figure based on suggestion
oruebel Oct 23, 2024
a7cf936
Fix docs based on code review
oruebel Oct 23, 2024
3d89d78
update getAttribute method to detect object type
stephprince Dec 12, 2024
c22d658
update read example
stephprince Dec 12, 2024
a91cc91
add file mode options and readonly mode to io
stephprince Dec 12, 2024
b20388c
update example to use readonly
stephprince Dec 12, 2024
20afbae
add getter functions to Container classes with attributes
stephprince Dec 18, 2024
20813c2
fix formatting
stephprince Dec 18, 2024
f211978
update lint workflow
stephprince Dec 18, 2024
0b7d181
add NWBFile fields
stephprince Dec 19, 2024
a5cda51
update filenames
stephprince Dec 19, 2024
6a7bb45
remove duplicate file mode checks
stephprince Dec 19, 2024
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Merge branch 'add_read' into add_container_read
oruebel authored Oct 22, 2024

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature.
commit 415926cd2688eae95269d743e3b4b63c4c16ac5a
1 change: 1 addition & 0 deletions src/nwb/ecephys/ElectricalSeries.cpp
Original file line number Diff line number Diff line change
@@ -65,6 +65,7 @@ void ElectricalSeries::initialize(const IO::BaseDataType& dataType,
m_io->createAttribute(IO::BaseDataType::I32,
&axis_value,
AQNWB::mergePaths(getPath(), "channel_conversion"),
this->getPath() + "/channel_conversion",
"axis",
1);

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