"""
Run Freesurfer's recon-all on the THINGS-fMRI dataset. Mostly intended for documentation.
"""

import stat
import sys
from distutils.dir_util import copy_tree
from os import pardir, getcwd, chmod
from os.path import join as pjoin

from nipype.interfaces.freesurfer.preprocess import ReconAll
from nipype.interfaces.utility import Function
from nipype.pipeline.engine import Node, Workflow


def grabanat(bidsroot, subject):
    """Grab anatomical data for given subject"""
    import sys
    from os.path import join as pjoin
    from dataset import ThingsMRIdataset
    sys.path.insert(0, pjoin(bidsroot, 'code', 'things', 'mri'))
    thingsmri = ThingsMRIdataset(bidsroot)
    t1files = thingsmri.layout.get(subject=subject, return_type='file', extension='.nii.gz', suffix='T1w',
                                   reconstruction='pydeface', acquisition='prescannormalized')
    t2file = thingsmri.layout.get(subject=subject, return_type='file', extension='.nii.gz', suffix='T2w',
                                  reconstruction='pydeface', acquisition='prescannormalized')[0]
    return t1files, t2file


def make_reconall_wf(
        subject,
        wdir,
        bidsroot,
        directive='all',
        nprocs=12
) -> Workflow:
    """return very simple workflow running reconall for one subject"""
    wf = Workflow(name='reconall_wf',
                  base_dir=wdir)
    datagrabber = Node(
        Function(function=grabanat,
                 input_names=['bidsroot', 'subject'],
                 output_names=['t1files', 't2file']),
        name='datagrabber')
    datagrabber.inputs.subject = subject
    datagrabber.inputs.bidsroot = bidsroot
    reconall = Node(ReconAll(use_T2=True, directive=directive, openmp=nprocs), name='reconall')
    wf.connect([
        (datagrabber, reconall, [('t1files', 'T1_files'), ('t2file', 'T2_file')])
    ])
    return wf


def main(
        subject,
        nprocs,
        bidsroot,  # path within container "preproc"
        free_permissions=True,  # free permissions for workdir and output (bc docker has different user than host)
) -> None:
    """Run Reconall for one subject and copy the output to the bids derivatives"""
    wdir = pjoin(bidsroot, pardir, 'reconall_workdir', f'sub-{subject}')
    derivdir = pjoin(bidsroot, 'derivatives', 'reconall', f'sub-{subject}')
    # make and run workflow
    wf = make_reconall_wf(
        subject=subject,
        bidsroot=bidsroot,
        wdir=wdir,
        nprocs=nprocs)
    wf.write_graph(graph2use='colored', simple_form=True)
    wf.run()
    # copy output to derivatives manually to preserve typical reconall output structure
    ra_nodedir = pjoin(wdir, 'reconall_wf', 'reconall', 'recon_all')
    copy_tree(ra_nodedir, derivdir, preserve_mode=False)
    if free_permissions:
        for d in [wdir, derivdir]:
            chmod(d, stat.S_IRWXO)
    return None