import os
from pkg_resources import resource_filename as pkgrf
from xcp_d.utils import collect_data,select_registrationfile,extract_t1w_seg

fmri_dir =  pkgrf('xcp_d','data/fmriprep')
layout,subj_data = collect_data(bids_dir=fmri_dir,participant_label='sub-colornest001',
                                           task='rest',bids_validate=False)
regfile = pkgrf('xcp_d','data/fmriprep/sub-colornest001/ses-1/anat/sub-colornest001_ses-1_rec-refaced_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5')

bold_file = pkgrf('xcp_d','data/fmriprep/sub-colornest001/ses-1/func/sub-colornest001_ses-1_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz')
custom_confounds = pkgrf('xcp_d','data/fmriprep/sub-colornest001/ses-1/func/sub-colornest001_ses-1_task-rest_run-1_desc-confounds_timeseries.tsv')

tseg = pkgrf('xcp_d','data/fmriprep/sub-colornest001/ses-1/anat/sub-colornest001_ses-1_rec-refaced_desc-preproc_T1w.nii.gz')
t1w = pkgrf('xcp_d','data/fmriprep/sub-colornest001/ses-1/anat/sub-colornest001_ses-1_rec-refaced_dseg.nii.gz')
from xcp_d.workflow.bold import init_boldpostprocess_wf
wf = init_boldpostprocess_wf(
            bold_file = str(bold_file),
            upper_bpf=0.08,
            lower_bpf =0.01,
            bpf_order=2,
            motion_filter_order=4,
            motion_filter_type='notch',
            band_stop_min=0.1,
            band_stop_max=0.2,
            smoothing=5,
            head_radius=50,
            params='27P',
            custom_confounds=custom_confounds,
            omp_nthreads=1,
            dummytime=0,
            output_dir='output_dir',
            fd_thresh=0.3,
            num_bold=1,
            layout=layout,
            mni_to_t1w=regfile,
            despike=None,
            name='bold_postprocess_wf')
wf.inputs.inputnode.t1w = t1w
wf.inputs.inputnode.t1seg = tseg