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moveDICOMS.py
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moveDICOMS.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Jul 07 11:29:08 2015
@author: windows
"""
import sys, os
import string
import shutil
import itertools
import stat
import glob ##Unix style pathname pattern expansion
import time
import re
from os.path import join
from os import listdir, rmdir
from shutil import copy2, move, rmtree
import subprocess
import re
from sqlalchemy.orm import sessionmaker
from mylocalbase import mynewengine
import mylocaldatabase
def moveDICOMS(rootdir, patpath, lesionpath, lesionindicat, cadID, accessionN, dicomN, iside, dynID, T2ID):
'''
patpath = massdir+os.sep+str(cadID)
lesionpath = massdir+os.sep+str(cadID)+os.sep+str(accessionN)
'''
# out files/folders
os.chdir(str(rootdir))
if not os.path.exists(str(cadID)):
os.makedirs(str(cadID))
os.chdir(str(cadID))
cmd = 'cp '+patpath+os.sep+lesionindicat+' '+lesionindicat
print cmd
p1 = subprocess.Popen(cmd, shell=False, stdin=subprocess.PIPE)
p1.wait()
if not os.path.exists(str(accessionN)):
os.makedirs(str(accessionN))
os.chdir(str(accessionN))
# parse throuh the DCE-MRI series
phases_series=[]
testSID = str(dynID)
if 'S' in str(testSID):
#print testSID[1:]
chosen_phase = int(testSID[1:])
else:
chosen_phase = int(testSID)
if(testSID[0] == 'S'):
phases_series.append('S'+str(chosen_phase))
for chSer in [chosen_phase+1, chosen_phase+2, chosen_phase+3, chosen_phase+4]:
phases_series.append( 'S'+str(chSer) )
else:
phases_series.append(str(chosen_phase))
for chSer in [chosen_phase+1, chosen_phase+2, chosen_phase+3, chosen_phase+4]:
phases_series.append( str(chSer) )
for kseries in range(len(phases_series)):
print "moving ... %s " % lesionpath+os.sep+phases_series[kseries]
move(lesionpath+os.sep+phases_series[kseries], phases_series[kseries])
# now process T2ID
print "moving ... %s " % lesionpath+os.sep+T2ID
move(lesionpath+os.sep+T2ID, T2ID)
if T2ID =='S4' and iside in ['Right','R']:
otherT2ID = 'S3'
nonfatT1 = 'S5'
if T2ID =='S4' and iside in ['Left','L']:
otherT2ID = 'S5'
nonfatT1 = 'S6'
if T2ID =='S3' and iside in ['Left','L']:
otherT2ID = 'S4'
nonfatT1 = 'S5'
if T2ID =='S5' and iside in ['Left','L']:
otherT2ID = 'S6'
nonfatT1 = 'S7'
if T2ID =='S5' and iside in ['Right','R']:
otherT2ID = 'S4'
nonfatT1 = 'S6'
if T2ID =='S6' and iside in ['Right','R']:
otherT2ID = 'S5'
nonfatT1 = 'S7'
if T2ID =='S7' and iside in ['Left','L']:
otherT2ID = 'S8'
nonfatT1 = 'S9'
if T2ID =='S7' and iside in ['Right','R']:
otherT2ID = 'S6'
nonfatT1 = 'S8'
if T2ID =='003' and iside in ['Left','L']:
otherT2ID = '004'
nonfatT1 = '005'
if T2ID =='004' and iside in ['Right','R']:
otherT2ID = '003'
nonfatT1 = '005'
# now process T2ID
print "moving ... %s " % lesionpath+os.sep+otherT2ID
move(lesionpath+os.sep+otherT2ID, otherT2ID)
# now process T2ID
print "moving ... %s " % lesionpath+os.sep+nonfatT1
move(lesionpath+os.sep+nonfatT1, nonfatT1)
return
##############################################################################
# Create the database: the Session.
Session = sessionmaker()
Session.configure(bind=mynewengine) # once engine is available
session = Session() #instantiate a Session
#process masses
massdatainfo = []
for cad_case, lesion in session.query(mylocaldatabase.Lesion_record, mylocaldatabase.Mass_record).order_by(mylocaldatabase.Lesion_record.lesion_id).\
filter(mylocaldatabase.Lesion_record.lesion_id==mylocaldatabase.Mass_record.lesion_id).all():
print cad_case.lesion_id, cad_case.cad_pt_no_txt, cad_case.exam_a_number_txt, cad_case.exam_img_dicom_txt, cad_case.exam_dt_datetime, cad_case.exam_find_side_int, lesion.DynSeries_id, lesion.T2Series_id
massdatainfo.append([cad_case.lesion_id, cad_case.cad_pt_no_txt, cad_case.exam_a_number_txt, cad_case.exam_img_dicom_txt, cad_case.exam_dt_datetime, cad_case.exam_find_side_int, lesion.DynSeries_id, lesion.T2Series_id] )
#process non-masses
nonmassdatainfo = []
for cad_case, lesion in session.query(mylocaldatabase.Lesion_record, mylocaldatabase.Nonmass_record).order_by(mylocaldatabase.Lesion_record.lesion_id).\
filter(mylocaldatabase.Lesion_record.lesion_id==mylocaldatabase.Nonmass_record.lesion_id).all():
print cad_case.lesion_id, cad_case.cad_pt_no_txt, cad_case.exam_a_number_txt, cad_case.exam_img_dicom_txt, cad_case.exam_dt_datetime, cad_case.exam_find_side_int, lesion.DynSeries_id, lesion.T2Series_id
nonmassdatainfo.append([cad_case.lesion_id, cad_case.cad_pt_no_txt, cad_case.exam_a_number_txt, cad_case.exam_img_dicom_txt, cad_case.exam_dt_datetime, cad_case.exam_find_side_int, lesion.DynSeries_id, lesion.T2Series_id] )
# start to move series to
rootdir = 'Z:\Breast\DICOMS'
massdir = 'Z:'+os.sep+'Cristina'+os.sep+'MassNonmass'+os.sep+'\mass'
nonmassdir = 'Z:'+os.sep+'Cristina'+os.sep+'MassNonmass'+os.sep+'nonmass'
for j in range(216):
nonmassdatainfo.pop(0)
for i in range(len(nonmassdatainfo)):
print nonmassdatainfo[i]
ilesion = nonmassdatainfo[i]
cadID = int(ilesion[1])
try: accessionN = int(ilesion[2])
except: accessionN = 0
dicomN = str(ilesion[3])
idatetime = ilesion[4]
iside = str(ilesion[5])
dynID = str(ilesion[6])
T2ID = str(ilesion[7])
# check first if DICOMS already moved to destination
if not os.path.exists(rootdir+os.sep+str(cadID)+os.sep+str(accessionN)) or os.path.exists(rootdir+os.sep+str(cadID)+os.sep+str(dicomN)):
# in files/folders
patpath = nonmassdir+os.sep+str(cadID)
# account for dicomN instead of AccessionN
if os.path.exists( nonmassdir+os.sep+str(cadID)+os.sep+str(accessionN) ):
lesionpath = nonmassdir+os.sep+str(cadID)+os.sep+str(accessionN)
lesionindicat = str(accessionN)+'_seriesStudy.txt'
else:
lesionpath = nonmassdir+os.sep+str(cadID)+os.sep+str(dicomN)
lesionindicat = str(dicomN)+'_seriesStudy.txt'
moveDICOMS(rootdir, patpath, lesionpath, lesionindicat, cadID, accessionN, dicomN, iside, dynID, T2ID)
#if int(raw_input('input 1 to continue or 0 to skip removing files: ')):
# deal with the rest
alldirs = listdir(lesionpath)
# exclude DynPhases
remainingdirs = [x for x in alldirs if x not in 'DynPhases']
for idir in remainingdirs:
# check if directory
if os.path.isdir(lesionpath+os.sep+str(idir)):
print "removing .. %s" % idir
files = listdir(lesionpath+os.sep+str(idir))
## to delete any directory recursively...
for ifile in files:
if ifile == '.' or ifile == '..': continue
ipath = lesionpath + os.sep + str(idir) + os.sep + ifile
os.unlink(ipath)
rmtree(lesionpath+os.sep+idir)
# deal with remaining folders inside DynPhases
allDyn = listdir(lesionpath+os.sep+'DynPhases')
remainingdirs = [x for x in allDyn if not re.search('VOI', x, re.IGNORECASE)]
for idir in remainingdirs:
# check if directory
if os.path.isdir(lesionpath+os.sep+'DynPhases'+os.sep+str(idir)):
print "removing .. %s" % idir
files = listdir(lesionpath+os.sep+'DynPhases'+os.sep+str(idir))
## to delete any directory recursively...
for ifile in files:
if ifile == '.' or ifile == '..': continue
ipath = lesionpath + os.sep + 'DynPhases' + os.sep + str(idir) + os.sep + ifile
os.unlink(ipath)
rmtree(lesionpath+os.sep+'DynPhases'+os.sep+idir)