scanLevel.py

#vim: set tabstop=4 expandtab shgftwidth=4 softtabstop=4 mouse=a autoindent hlsearch
#vim: filetype plugin indent on
from glob import glob
import re
import os
import sys
import argparse
import time

#import Initialization.initialization as init
from workflows import Workflows

"""
.. module:: scanLevel
    :platform: Unix
    :synopsis: Module to launch scan level analysis.
.. moduleauthor:: Thomas Funck <tffunck@gmail.com>
"""
def run_scan_level(opts,args): 
    ###Define args with exiting subject and condition combinations
    sub_valid_args, task_valid_args=gen_args(opts, args)
    
    scan_level_workflow = Workflows(opts)

    scan_level_workflow.initialize(opts) 

    #Run the work flow
    if opts.num_threads > 1 :
        scan_level_workflow.workflow.run(plugin='MultiProc', plugin_args={'n_procs': opts.num_threads})
    else : 
        print(scan_level_workflow.workflow._get_all_nodes())
        scan_level_workflow.workflow.run()
        print("Done.")
    return 0


def gen_args(opts, subjects):
    session_ids = opts.sessionList 
    task_ids = opts.taskList 
    run_ids = opts.runList
    acq = opts.acq 
    rec = opts.rec
    
    task_args=[]
    sub_ses_args=[]
    sub_ses_dict={}
    if len(session_ids) == 0 : session_ids=['']
    if len(task_ids) == 0 : task_ids=['']
    if len(run_ids) == 0 : run_ids=['']

    for sub in subjects:
        if opts.verbose >= 2: print("Sub:", sub)
        for ses in session_ids:
            if opts.verbose >= 2: print("Ses:",ses)
            for task in task_ids:
                if opts.verbose >= 2: print("Task:",task)
                for run in run_ids:
                    sub_arg='sub-'+sub
                    rec_arg=acq_arg=""

                    pet_fn=mri_fn=""
                    if  not acq == '': acq_arg='acq-'+acq
                    if  not rec == '': rec_arg='rec-'+rec
                    if ses == '' :
                        pet_string=opts.sourceDir+os.sep+ sub_arg + os.sep + 'pet/*_pet.nii*'
                        mri_string=opts.sourceDir + os.sep + sub_arg + os.sep + 'anat/*_T1w.nii*'
                    else :
                        ses_arg='ses-'+ses
                        pet_string=opts.sourceDir+os.sep+ sub_arg + os.sep+ '*'+ ses_arg + os.sep+ 'pet/*_pet.nii*'
                        mri_string=opts.sourceDir + os.sep + sub_arg + os.sep + '*/anat/*_T1w.nii*'
                    #pet_string_gz=opts.sourceDir+os.sep+ sub_arg + os.sep+ '*'+ ses_arg + os.sep+ 'pet/*_pet.'+opts.img_ext+'.gz'
                    pet_list=glob(pet_string) 
                    print(pet_string)
                    mri_arg_list = ['sub-'+sub]
                    arg_list = ['sub-'+sub ]
                    if not ses == '' :
                        arg_list += ['ses-'+ses]
                        mri_arg_list += ['ses-'+ses]
                    if not task == '': arg_list += ['task-'+task]
                    if not acq == '': arg_list += ['acq-'+acq]
                    if not rec == '': arg_list += ['rec-'+rec]
                    if not run == '': arg_list += ['run-'+run]
                    if opts.verbose >= 2: print( "Arguments for indentifying images:", arg_list );
                    print(pet_list)
                    if pet_list != []:
                        pet_fn = unique_file(pet_list, arg_list, opts.verbose )
                
                    print("mri_string :", mri_string)
                    mri_list=glob(mri_string )
                    print(mri_list)
                    if mri_list != []:
                        mri_fn = unique_file(mri_list, mri_arg_list )

                    if os.path.exists(pet_fn) and os.path.exists(mri_fn):
                        d={'task':task, 'ses':ses, 'sid':sub, 'run':run} 
                        sub_ses_dict[sub]=ses
                        if opts.verbose >= 2 :
                            print(pet_fn, os.path.exists(pet_fn))
                            print(mri_fn, os.path.exists(mri_fn))
                            print('Adding to dict of valid args',d)
                        task_args.append(d)
                    else:
                        if not os.path.exists(pet_fn) and opts.verbose >= 1:
                            print("Could not find PET for ", sub, ses, task, pet_fn)
                        if not os.path.exists(mri_fn) and opts.verbose >= 1:
                            print( "Could not find T1 for ", sub, mri_fn)

    for key, val in sub_ses_dict.items() :
        sub_ses_args.append({"sid":key,"ses":ses})

    if opts.verbose >= 2:
        print("Scans on which APPIAN will be run")
        print( task_args)
    
    opts.sub_valid_args = sub_ses_args
    opts.task_valid_args = task_args

    return sub_ses_args, task_args


def unique_file(files, attributes, verbose=1):

    out_files=[]
    
    for f in files :
        missing_attributes=[]
        for a in attributes :
            if not a in f :
                if verbose >= 2 : 
                    print(a, "not in ", f)
                missing_attributes.append(a)
                break
        if verbose >= 2 : 
            if len(missing_attributes) == 0 :
                print("Valid file", f)
            else :
                print("File missing attributes " +";".join(missing_attributes) +" skipping:",f)

        if  len(missing_attributes) == 0 :
            out_files.append(f)
    print("out files", out_files)
    if attributes == [] or len(out_files) == 0 : return ''

    # If there are 2 out_files, check if one is a compressed version of the other
    # If so keep the compressed version
    if len(out_files) == 2  :
        if out_files[0] == out_files[1] + '.gz' :
            out_files=[out_files[1]+'.gz']
        elif out_files[1] == out_files[0] + '.gz' : 
            out_files=[out_files[0]+'.gz']
		

    if len(out_files) > 1 :
        print("Error: File is not uniquely specified. Multiple files found for the attributes ", attributes)
        print("For PET images, you can used --acq and --rec to specify the acquisition and receptor")
        print(out_files)
        exit(1)

    return( out_files[0] )