bids2table is a python library for efficiently indexing large Neuroimaging datasets. It can be used in CPAC to replace some of these functions in order to provide abstraction and much cleaner looking code.
Project sub-parts and estimates
Mapping the functions in CPAC/utils/bids_utils.py and finding out which ones can be replaced or reimplemented.
Functions that could be replaced
collect_bids_files_configs
bids_gen_cpac_sublist
update
RPool object in engine.py is built directly from BIDSTable
The subject and session rows are grouped and then passed to the engine with a for loop.
Previous data_config_file is replaced the BIDSTable.
For each row in the BIDSTable a Resource object is initialized with attributes similar and in addition to the BIDSFile, BIDSEntity dataclasses. In future may be inherit from these classes.
To do
add write_to_disk(path) method to the Resource or the ResourcePool class
Implement StratPool
Timeline notes
No response
Timesink notes
No response
Frustration notes
No response
Design decisions and notes
Planning to add Resource and StratPool classes to abstract the bids data.
Looked into BIDSEntity , BIDSFile etc. classes in the bids2table library. It looks like Resource class can inherit one of these classes and we can add more methods to it like for e.g. write_to_disk(path)
User interface changes
bids2table is a python library for efficiently indexing large Neuroimaging datasets. It can be used in CPAC to replace some of these functions in order to provide abstraction and much cleaner looking code.
Project sub-parts and estimates
CPAC/utils/bids_utils.pyand finding out which ones can be replaced or reimplemented.update
engine.pyis built directly fromBIDSTabledata_config_fileis replaced the BIDSTable.BIDSTableaResourceobject is initialized with attributes similar and in addition to the BIDSFile, BIDSEntity dataclasses. In future may be inherit from these classes.To do
write_to_disk(path)method to theResourceor theResourcePoolclassStratPoolTimeline notes
No response
Timesink notes
No response
Frustration notes
No response
Design decisions and notes
bids2tablelibrary. It looks like Resource class can inherit one of these classes and we can add more methods to it like for e.g.write_to_disk(path)