Esempio n. 1
0
def pearson_correlation(datadir,
                        outdir,
                        usemask=True,
                        excludef='',
                        exclude_idx=-1):

    slidir = datadir + os.path.sep + au.slices_str()

    subjsfile = datadir + os.path.sep + au.subjects_str()
    labelsfile = datadir + os.path.sep + au.labels_str()

    lst = os.listdir(slidir)
    n = au.count_match(lst, au.data_str() + '_' + au.slice_regex())

    exclude_log = ''
    if exclude_idx > -1:
        exclude_log = ' excluding subject ' + str(exclude_idx)

    au.log.info('Calculating correlation of ' + slidir + os.path.sep +
                au.data_str() + '_' + au.slice_regex() + exclude_log)

    for i in range(n):
        slino = au.zeropad(i)

        dataf = slidir + os.path.sep + au.data_str() + '_' + au.slice_str(
        ) + '_' + slino + au.ext_str()
        maskf = slidir + os.path.sep + au.mask_str() + '_' + au.slice_str(
        ) + '_' + slino + au.ext_str()
        outf = outdir + os.path.sep + au.pearson_str() + '_' + au.slice_str(
        ) + '_' + slino

        if exclude_idx > -1:
            outf += '_' + au.excluded_str() + str(exclude_idx) + au.ext_str()
        else:
            outf += au.ext_str()

        if not os.path.isfile(dataf):
            au.log.error('Could not find ' + dataf)
            continue

        if not usemask:
            maskf = ''

        try:
            measure_pearson(dataf, labelsfile, outf, maskf, excludef,
                            exclude_idx)
        except:
            au.log.error(
                'pearson_correlation: Error measuring correlation on ' + dataf)
            au.log.error("Unexpected error: ", sys.exc_info()[0])
            exit(1)
Esempio n. 2
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def pearson_correlation (datadir, outdir, usemask=True, excludef='', exclude_idx=-1):

   slidir = datadir + os.path.sep + au.slices_str()

   subjsfile  = datadir + os.path.sep + au.subjects_str()
   labelsfile = datadir + os.path.sep + au.labels_str()

   lst = os.listdir(slidir)
   n = au.count_match(lst, au.data_str() + '_' + au.slice_regex())

   exclude_log = ''
   if exclude_idx > -1:
      exclude_log = ' excluding subject ' + str(exclude_idx)
   
   au.log.info ('Calculating correlation of ' + slidir + os.path.sep + au.data_str() + '_' + au.slice_regex() + exclude_log)

   for i in range(n):
      slino = au.zeropad(i)

      dataf = slidir + os.path.sep + au.data_str()    + '_' + au.slice_str() + '_' + slino + au.ext_str()
      maskf = slidir + os.path.sep + au.mask_str()    + '_' + au.slice_str() + '_' + slino + au.ext_str()
      outf  = outdir + os.path.sep + au.pearson_str() + '_' + au.slice_str() + '_' + slino

      if exclude_idx > -1:
         outf += '_' + au.excluded_str() + str(exclude_idx) + au.ext_str()
      else:
         outf += au.ext_str()

      if not os.path.isfile(dataf): 
         au.log.error('Could not find ' + dataf)
         continue

      if not usemask:
         maskf = ''

      try:
         measure_pearson(dataf, labelsfile, outf, maskf, excludef, exclude_idx)
      except:
         au.log.error('pearson_correlation: Error measuring correlation on ' + dataf)
         au.log.error("Unexpected error: ", sys.exc_info()[0] )
         exit(1)
Esempio n. 3
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    outf_labels = outdir + os.path.sep + au.labels_str()
    np.savetxt(outf_subjs, subjs, fmt='%s')
    np.savetxt(outf_labels, subjlabels, fmt='%i')

    #creating folder for slices
    slidir = outdir + os.path.sep + au.slices_str()
    if not (os.path.exists(slidir)):
        os.mkdir(slidir)
        #slice the volumes

    #creating group and mask slices
    pre.slice_and_merge(outf_subjs, outf_labels, chkf, outdir, maskf)

    #creating measure output folder
    if measure == 'pea':
        measure_fname = au.pearson_str()
    elif measure == 'bat':
        measure_fname = au.bhattacharyya_str()
    elif measure == 'ttest':
        measure_fname = au.ttest_str()

    #checking the leave parameter
    if leave > (subjsnum - 1):
        au.log.warning('aizkolari_measure: the leave (-l) argument value is ' +
                       str(leave) +
                       ', bigger than the last index of subject: ' +
                       str(subjsnum - 1) + '. Im setting it to -1.')
        leave = -1

    #reading exclusion list
    excluded = parse_exclude_list(excluf, leave)
Esempio n. 4
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   outf_labels = outdir + os.path.sep + au.labels_str()
   np.savetxt(outf_subjs,  subjs,      fmt='%s')
   np.savetxt(outf_labels, subjlabels, fmt='%i')

   #creating folder for slices
   slidir = outdir + os.path.sep + au.slices_str()
   if not(os.path.exists(slidir)):
      os.mkdir(slidir)
      #slice the volumes

   #creating group and mask slices
   pre.slice_and_merge(outf_subjs, outf_labels, chkf, outdir, maskf)

   #creating measure output folder
   if measure == 'pea':
      measure_fname = au.pearson_str()
   elif measure == 'bat':
      measure_fname = au.bhattacharyya_str()
   elif measure == 'ttest':
      measure_fname = au.ttest_str()

   #checking the leave parameter
   if leave > (subjsnum - 1):
      au.log.warning('aizkolari_measure: the leave (-l) argument value is ' + str(leave) + ', bigger than the last index of subject: ' + str(subjsnum - 1) + '. Im setting it to -1.')
      leave = -1

   #reading exclusion list
   excluded = parse_exclude_list (excluf, leave)

   #setting the output folder mdir extension
   mdir = outdir + os.path.sep + measure_fname