[AymericGaudin]

In this PR, I add features that compress cat12 outputs from .nii to .nii.gz, and that delete the input .nii, which is a (uncompressed) copy of a rawdata. This occurs directly after the computation is over and before the checks.

[AymericGaudin]

J'ai pas fait le ruff check sur le bon dossier... Je corrige tout ça

[AGrigis]

In interfaces.utils we can define a more generic compression function:

@step(
    hooks=[
        CoerceparamsHook(),
        LogRuntimeHook(
            bunched=False
        ),
        CommandLineWrapperHook(),
        SignatureHook(),
    ]
)
def compressfiles(
        root_dir: Directory, 
        extensions: list[str] = (".nii", ), 
    ) -> list[str]:
    """
    Recursively scan a directory to compress specified neuroimaging files into
    .gz.

    Parameters
    ----------
    root_dir : Directory
        Path to the root directory to scan.
    extensions : list[str]
        A list of file extensions to target for compression.
        Default `(".nii", )`.
    """
    if not root_dir.is_dir():
        raise ValueError(
            f"The specified path is not a valid directory: {root_dir}"
        )

    clean_extensions = [
        ext.lstrip(".")
        for ext in extensions
    ]

    command = [
        "find",
        str(root_dir),
        "-type f",
        "\\(",
    ]
    for cnt, ext in enumerate(clean_extensions):
        if cnt > 0:
            command.append("-o")
        command.extend([
            "-name",
            f"*.{ext}",
        ])  
    command.extend([
        "\\)",
        "!", "-name", "*.gz",
        "-exec", "gzip", "-v", "{}", "\\;",
    ])

    return command

[AGrigis]

Must be decoracted @step.

[AGrigis]

Already handle by CoerceparamsHook.

[AGrigis]

In the main workflow we build the batch so have a direct access to these files in 't1_files' and the root 'output_dir.parent'. Can we avoid parsing the batch file?