os.mkdir(func_dir)
for exam in exams:
exam_dir = os.path.join(source, exam)
for rt, dirs, files in os.walk(exam_dir):
for d in dirs:
for str in ["spgr", "SPGR", '_166_', '_160_', '_164', 'f166']:
if str in d or str in root:
src_dir = os.path.join(rt, d)
dest_dir = os.path.join(anat_dir, d)
shutil.copytree(src_dir, dest_dir)
path_list = uf.splitall(src_dir)
ind = path_list.find('SocCog_Raw_Data_By_Exam_Number')
exam = path_list(ind + 1)
ex_dir = path_list(ind + 2)
with open(os.path.join(dest_dir, exam + 'txt')) as recfile:
recfile.write(''.join([exam, '\n', ex_dir]))
with open('/media/katie/SocCog/working_data/copyrec1.txt', 'a+') as copyrec:
copyrec.write(''.join(["d", d, '\n', "src", src_dir, '\n', "dest", dest_dir]))
for str in ['M', 'L', '_1904', '_1960', '_5610', 'f5610', 'f1903', '_1848', '_5455', '_4522', '_2234', '_3374'\
'_5236', '_442', '_2550', '_6528', '_3094']:
if str in d:
src_dir = os.path.join(rt, d)
dest_dir = os.path.join(func_dir, d)
shutil.copytree(src_dir, dest_dir)
with open(os.path.join(root, 'copyrec1.txt', 'a+')) as copyrec:
copyrec.write(''.join(["d", d, '\n', "src", src_dir, '\n', "dest", dest_dir]))
uf.done(root, "getRawfromExamDir.py, program to retrieve files from raw exam directories, has finished")
# done = True
###RENAME IMG###
###MOVE IMG####
with open(os.path.join(scripts_dir, q_string), 'w+') as q:
q.write("""
#!/bin/bash
#$ -S /bin/bash
#$ -l mem=4G,time=24:00:00
#$ -cwd
""")
q.write('#$ -N j' + ser_id + '\n#$ -j y\n#$ -o ' + ser_id + '.txt\n')
q.write('''\
echo "Starting on : $(date)"
echo "Running on node : $(hostname)"
echo "Current directory : $(pwd)"
echo "Current job ID : $JOB_ID"
echo "Current job name : $JOB_NAME"
#The following is the job to be performed:
''')
q.write("python " + p_path)
uf.done(os.path.join(dst_root, 'done.txt'), "SocCogMasterSort.py, program to sort has completed")
__author__ = 'katie'
root = '/media/truecrypt2/sample/7436test'
import os, uf
for rt, dirs, files in os.walk(root):
for f in files:
if (f[-3:] == 'img' or f[-3:] == 'hdr') and ('L' in f or 'M' in f):
old = os.path.join(rt, f)
newname = 'f' + f[-10:]
new = os.path.join(rt, newname)
os.rename(old, new)
print old
print new
print ' '
if (f[-3:] == 'img' or f[-3:] == 'hdr') and ('anat' in f and f[0] == 's'):
old = os.path.join(rt, f)
newname = 's' + f[-10:]
new = os.path.join(rt, newname)
os.rename(old, new)
print old
print new
print ' '
uf.done('/media/truecrypt2/sample/7436new/done.txt')
if (f[-3:] == 'img' or f[-3:] == 'hdr') and ('anat' in dst_path):
newname = 's' + f[-13:-7] + f[-4:]
new = os.path.join(dst_path, newname)
os.rename(old, new)
files = [f for f in os.listdir(dst_path) if len(f) <= 12]
logline['Renamed'] = 'Renamed_' + str(len(files)) + '_files_' + os.path.join(dst_path, files[0])
###MOVE IMG####
ult_path = uf.buildtree(ult_root, dst_path_lst)
for f in os.listdir(dst_path):
if (f[-3:] == 'img' or f[-3:] == 'hdr'):
old = os.path.join(dst_path, f)
new = os.path.join(ult_path, f)
print old
print new
print ' '
os.rename(old, new)
files = [f for f in os.listdir(ult_path)]
logline['Moved'] = 'Moved_' + str(len(files)) + '_files_' + os.path.join(ult_path, files[0])
#del(logline[''])
with open(logfile,'a+') as log:
dw = csv.DictWriter(log, delimiter='\t', fieldnames=ordered_fieldnames)
dw.writerow(logline)
uf.done(os.path.join(dst_root, 'done.txt'), "ks_mastersort_no_clust.py, program to sort has completed")
os.mkdir(func_dir)
for exam in exams:
exam_dir = os.path.join(source, exam)
for rt, dirs, files in os.walk(exam_dir):
for d in dirs:
for str in ["spgr", "SPGR", '_166_', '_160_', '_164', 'f166']:
if str in d or str in root:
src_dir = os.path.join(rt, d)
dest_dir = os.path.join(anat_dir, d)
shutil.copytree(src_dir, dest_dir)
path_list = uf.splitall(src_dir)
ind = path_list.find('SocCog_Raw_Data_By_Exam_Number')
exam = path_list(ind + 1)
ex_dir = path_list(ind + 2)
with open(os.path.join(dest_dir, exam + 'txt')) as recfile:
recfile.write(''.join([exam, '\n', ex_dir]))
with open('/media/katie/SocCog/working_data/copyrec1.txt', 'a+') as copyrec:
copyrec.write(''.join(["d", d, '\n', "src", src_dir, '\n', "dest", dest_dir]))
for str in ['M', 'L', '_1904', '_1960', '_5610', 'f5610', 'f1903', '_1848', '_5455', '_4522', '_2234', '_3374'\
'_5236', '_442', '_2550', '_6528', '_3094']:
if str in d:
src_dir = os.path.join(rt, d)
dest_dir = os.path.join(func_dir, d)
shutil.copytree(src_dir, dest_dir)
with open(os.path.join(root, 'copyrec1.txt', 'a+')) as copyrec:
copyrec.write(''.join(["d", d, '\n', "src", src_dir, '\n', "dest", dest_dir]))
uf.done(root, "SocCogMasterSort.py, program to sort ")
