Dealing with derivatives #45
Conversation
| raise NotADirectoryError( | ||
| f"The input path is not valid. You specified '{input_path}', which is not a directory.") | ||
|
|
||
| # if not(BIDSValidator().is_bids(input_path)): |
There was a problem hiding this comment.
delete commented lines or specify what the missing TODO / FIXME is for those lines
| ) | ||
| return bids_layout, layout_df, dataset_description | ||
|
|
||
| if ("DatasetType" in dataset_description) and (dataset_description["DatasetType"] == "derivative"): |
There was a problem hiding this comment.
since dataset_description["DatasetType"] is only RECOMMENDED this is not a reliable path to check for derivatives.
I would suggest to only go with line 57-66 to determine if derivatives are present. This only works though in the case of derivatives that are provided in a subdirectory of a BIDS raw dataset. In case only derivative data are shared as BIDS dataset, there is no requirement to store those data in a "derivative" subdirectory (if I understand the specifications correctly).
However you can make use of the REQUIREMENT that the dataset_description.json for derivative data MUST have a "GeneratedBy" key specified.
Also note that if derived datasets are stored in a subdirectory of a raw dataset in BIDS, there are two dataset_description.json files: one for the raw data and one for (each) derived dataset.
| return bids_layout, layout_df, dataset_description | ||
|
|
||
| if ("DatasetType" in dataset_description) and (dataset_description["DatasetType"] == "derivative"): | ||
| bids_layout = BIDSLayout(input_path, is_derivative=True) |
There was a problem hiding this comment.
Is this only loading derivatives or all (raw + derivatives)?
| layout_df = bids_layout.to_df() | ||
| return bids_layout, layout_df, dataset_description | ||
|
|
||
| bids_layout = BIDSLayout(input_path) |
There was a problem hiding this comment.
I don't know why you need the upper lines. Based on the specifications, would it not be sufficient enough to state
has_derived_data = False:
if os.path.isdir(os.path.join(input_path, "derivatives")) or
"GeneratedBy" in dataset_description:
has_derived_data = True
bids_layout = BIDSLayout(input_path, is_derivative=has_derived_data)
layout_df = bids_layout.to_df()
?? (please double check the code, not sure I wrote this correctly)
Note that the data types also need to be set in openMINDS (can be an array). Not sure if you do this later somewhere?
| @@ -5,7 +5,8 @@ | |||
| import bids2openminds.converter | |||
|
|
|||
| example_dataset = [("ds003", 13), ("ds000247", 6), | |||
There was a problem hiding this comment.
can you make a comment and explain what the numbers are in the example dataset tuples?
|
Postponed to later, see issue #54 |
This pull request verify if the dataset contains or derivatives or is derived dataset, before calling BIDSLayout.