'''

This function runs the main routine

'''

# Import packages

from indi_aws import fetch_creds

import os

import yaml

# Init variables

creds_path = '/home/ubuntu/secure-creds/aws-keys/fcp-indi-keys2.csv'

bucket = fetch_creds.return_bucket('fcp-indi', creds_path)

bucket_prefix = 'data/Projects/ABIDE_Initiative/Outputs/cpac/raw_outputs_rerun'

sub_fp = '/home/ubuntu/abide/preprocessing/yamls/subs_list.yml'

sub_list = yaml.load(open(sub_fp, 'r'))

example_subid = '0050002_session_1'

# Populate list of files to link to

#src_list = []

#src_list = gather_files_tosort(src_list, bucket, bucket_prefix)

# Derivatives dictionary {name: (no_files_per_strategy, filt_str)}

strat_dict = {'nofilt_noglobal' : ['pipeline_abide_rerun', 'global0'],

'nofilt_global' : ['pipeline_abide_rerun', 'global1'],

'filt_noglobal' : ['pipeline_abide_rerun__freq-filter', 'global0'],

'filt_global' : ['pipeline_abide_rerun__freq-filter', 'global1']}

derivs_dict = {'alff' : (1, 'alff_to_standard_smooth', 'nii.gz'),

'degree_binarize' : (1, 'centrality_outputs_smoothed', 'degree_centrality_binarize'),

'degree_weighted' : (1, 'centrality_outputs_smoothed', 'degree_centrality_weighted'),

'dual_regression' : (1, 'dr_tempreg_maps_zstat_stack_to_standard_smooth', 'nii.gz'),

'eigenvector_binarize' : (1, 'centrality_outputs_smoothed', 'eigenvector_centrality_binarize'),

'eigenvector_weighted' : (1, 'centrality_outputs_smoothed', 'eigenvector_centrality_weighted'),

'falff' : (1, 'falff_to_standard_smooth', 'nii.gz'),

'func_mask' : (1, 'functional_brain_mask_to_standard', 'nii.gz'),

'func_mean' : (1, 'mean_functional_in_mni', 'nii.gz'),

'func_preproc' : (1, 'functional_mni', '.nii.gz'),

'lfcd' : (1, 'centrality_outputs_smoothed', 'lfcd_binarize'),

'reho' : (1, 'reho_to_standard_smooth', 'nii.gz'),

'rois_aal' : (4, 'roi_timeseries', 'aal'),

'rois_cc200' : (4, 'roi_timeseries', 'CC200'),

'rois_cc400' : (4, 'roi_timeseries', 'CC400'),

'rois_dosenbach160' : (4, 'roi_timeseries', 'rois_3mm'),

'rois_ez' : (4, 'roi_timeseries', 'ez'),

'rois_ho' : (4, 'roi_timeseries', 'ho_'),

'rois_tt' : (4, 'roi_timeseries', 'tt'),

'vmhc' : (1, 'vmhc_fisher_zstd_zstat_map', 'nii.gz')}

# Create error and output dictionaries

out_dict = {k : {kk : [] for kk in derivs_dict.keys()} for k in strat_dict.keys()}

err_dict = {k : {kk : [] for kk in derivs_dict.keys()} for k in strat_dict.keys()}

# Iterate through strategies

for strat, filts in strat_dict.items():

print('building %s...' % strat)

filt = filts[0]

g_sig = filts[1]

strat_prefix = os.path.join(bucket_prefix, filt, example_subid)

# Iterate through derivatives

for deriv, v in derivs_dict.items():

num_files = v[0]

deriv_folder = v[1]

name_filter = v[2]

deriv_prefix = os.path.join(strat_prefix, deriv_folder)

keys_list = []

for key in bucket.list(prefix=deriv_prefix):

k_name = str(key.name)

# If global signal regression was used or didnt need to be

if (g_sig in k_name or 'global' not in k_name) and \

name_filter in k_name:

keys_list.append(k_name)

# Grab only wanted results from keys

if len(keys_list) == num_files:

out_dict[strat][deriv] = [k for k in keys_list if '.nii.gz' in k or '.1D' in k][0]

else:

err_dict[strat][deriv] = keys_list

print('error in number of files!')

# Go through dictionary and build paths

mapping_dict = {}

s = 1

# For each subject

for sub in sub_list:

subid = sub.split('_')[-1] + '_session_1'

print('populating %s...%d' % (subid, s))

# For each strategy

for strat, deriv_dict in out_dict.items():

strat_prefix = os.path.join(bucket_prefix, strat)

# For each derivative, generate src and dst filepaths

d = 0

for deriv, filepath in deriv_dict.items():

deriv_prefix = os.path.join(strat_prefix, deriv, sub + '_' + deriv)

# Check extensions

if filepath.endswith('.nii.gz'):

dst_path = deriv_prefix + '.nii.gz'

elif filepath.endswith('.1D'):

dst_path = deriv_prefix + '.1D'

else:

raise Exception('Bad extension type')

# Get sub id from filepath

src_path = filepath.replace(example_subid, subid)

mapping_dict[src_path] = dst_path

d += 1

if d != 20:

print(d)

raw_input('not enough dervivs')

s += 1

# Return