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do_results_DB.py
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do_results_DB.py
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#! /usr/bin/env python
# -*- coding: utf-8 -*-
import common as c
import do_common, os
#import re
import Cenir_DB
import sys
#pour le send dicom (check)
from netdicom.applicationentity import AE
from netdicom.SOPclass import *
from dicom.dataset import Dataset, FileDataset
from dicom.UID import ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian
#import netdicom
import tempfile
from do_common import alpha_num_str
import glob
def add_options(parser):
parser.add_option("--res_dir", action="store_true", dest="res_dir",default='/export/dataCENIR/dicom/nifti_proc/',
help="result rootdir default /export/dataCENIR/dicom/nifti_proc/")
parser.add_option("--set_results", action="store_true", dest="set_results",default=False,
help="parse the serie database an set the results table ")
#parser.add_option("-r","--rootdir", action="store", dest="rootdir", default='/servernas/nasDicom/dicom_raw',
# help="full path to the root directorie dicom files (protocol dir) default='/nasDicom/dicom_raw'")
parser.add_option("--check_send", action="store_true", dest="check_send",default=False,
help="Dicom query verio and prisma and compare to dicom dir ")
parser.add_option("--patient_search", action="store", dest="patient_search", default='*',
help="define the string to search for patient in remote dicom server default='*'")
parser.add_option("--create_tar", action="store_true", dest="create_tar",default=False,
help="create series directorie tar file in the dicom suj dir ")
return parser
# call back
def OnAssociateResponse(association):
print "Association response received"
def OnAssociateRequest(association):
print "Association resquested"
return True
def OnReceiveStore(SOPClass, DS):
print "Received C-STORE", DS.PatientName
try:
# do something with dataset. For instance, store it.
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.2'
file_meta.MediaStorageSOPInstanceUID = "1.2.3" # !! Need valid UID here
file_meta.ImplementationClassUID = "1.2.3.4" # !!! Need valid UIDs here
filename = '%s/%s.dcm' % (tempfile.gettempdir(), DS.SOPInstanceUID)
ds = FileDataset(filename, {}, file_meta=file_meta, preamble="\0" * 128)
ds.update(DS)
ds.save_as(filename)
print "File %s written" % filename
except:
pass
# must return appropriate status
return SOPClass.Success
class Results_DB:
'Class to handel DataBase of results'
def __init__(self,verbose=True,log=0,opt=None):
self.verbose = verbose
self.log = log
if opt is not None:
self.db_name = opt.db_name
self.db_host = opt.db_host
self.res_dir = opt.res_dir
self.opt = opt
self.rootdir = opt.rootdir
self.patient_search = opt.patient_search
def set_results_DB(self):
CDB = Cenir_DB.Cenir_DB(log=self.log,opt=self.opt)
con,cur = CDB.open_sql_connection()
cur2 = con.cursor()
#sqlcmd="select Sid, ExamName, PatientsName, SName,SNumber,dicom_dir,dicom_sdir from ExamSerie where SeqType like 'MPRAGE';";
sqlcmd="select Sid,nifti_dir from ExamSerie where SeqType like 'MPRAGE';";
cur.execute(sqlcmd)
rows = cur.fetchall()
self.log.info('checking %d rows',len(rows))
found=0
res_list=[]
for row in rows:
if row['nifti_dir'] is None:
log.info('Serie Sid %d has no nifti',row['Sid'])
else:
pp,ser = os.path.split(row['nifti_dir'])
pp,suj = os.path.split(pp)
pp,proto = os.path.split(pp)
procdir = os.path.join(self.res_dir,proto,suj,ser,'vbm8')
if os.path.isdir(procdir):
found+=1
res = {}
res["Sid"] = row['Sid']
res['dir_path'] = procdir
restext = c.get_subdir_regex_files(procdir,'.*seg8.txt')
if len(restext)==1:
res['status'] = 1
text_file = open(restext[0], "r")
# si plusieur tab text_list = re.split(r'\t+',line)
line = text_file.readline().split('\t')
if len(line)>3:
res['vbmgrayvol'] = line[0]
res['vbmwhitevol'] =line[1]
res['vbmcsfvol'] = line[2]
else :
#self.log.info("corrupt seg8 files %s ",restext)
res['status'] = 0
text_file.close()
else:
res['status'] = 0
res_list.append(res)
else:
#print "mising " + procdir
pass
self.log.info("found %d vbm dir",found)
for res in res_list:
exist_line = CDB.get_sql_select_line('results_anat',"Sid",res["Sid"],cur)
if len(exist_line)==0:
sqlcmd = CDB.get_sql_insert_cmd_from_dict(res,'results_anat')
else:
sqlcmd = CDB.get_sql_update_cmd_from_dict(res,'results_anat','Sid',exist_line['Sid'])
cur2.execute(sqlcmd)
con.commit()
con.close()
def set_results_DB_dicomdir_test(self):
#il n'ent trouve que 6997 7142 soit 145 mauvaise dicomdir name
CDB = Cenir_DB.Cenir_DB(log=self.log,opt=self.opt)
con,cur = CDB.open_sql_connection()
#sqlcmd="select Sid, ExamName, PatientsName, SName,SNumber,dicom_dir,dicom_sdir from ExamSerie where SeqType like 'MPRAGE';";
sqlcmd="select Sid,dicom_dir,dicom_sdir from ExamSerie where SeqType like 'MPRAGE';";
sqlcmd="select Sid,dicom_dir,dicom_sdir from ExamSerie where SeqType like 'MPRAGE';";
cur.execute(sqlcmd)
rows = cur.fetchall()
self.log.info('checking %d rows',len(rows))
found=0
for row in rows:
pp,suj = os.path.split(row['dicom_dir'])
pp,proto = os.path.split(pp)
procdir = os.path.join(self.res_dir,proto,suj,row['dicom_sdir'],'vbm8')
if os.path.isdir(procdir):
found+=1
else:
#print "mising " + procdir
pass
self.log.info("found %d vbm dir",found)
def get_exam_suj_ser_from_dicom_dataset(self,ds):
#identical to get_exam_suj_ser_from_dicom_meta in Exam_info just from an other input
# (se.StudyDescription, se.StudyDate, se.PatientName, se.SeriesNumber, se.SeriesDescription)
# if "StudyDescription" not in meta : #Service patient on prisma has none
# exa = "ServicePatient"
# str_date = str(meta["AcquisitionDate"])
# str_date = str_date[0:4]+'_'+str_date[4:6] + '_' + str_date[6:8]
# suj = str_date + '_' + alpha_num_str(meta["PatientName"])
# ser = 'S%02d' % meta.get('SeriesNumber')
# return(exa,suj,ser)
# else:
# exa = alpha_num_str(meta["StudyDescription"])
exa = alpha_num_str(ds.StudyDescription)
#exa = alpha_num_str(ds.AcquisitionDate)
# study_date = str(meta["StudyDate"])
# study_date = study_date[0:4]+'_'+study_date[4:6] + '_' + study_date[6:8]
#
# if "AcquisitionDate" not in meta :
# str_date = study_date
# else:
# str_date = str(meta["AcquisitionDate"])
# str_date = str_date[0:4]+'_'+str_date[4:6] + '_' + str_date[6:8]
#
# #dicom bug only for DTI tensor : AcquisitionDate is bad and anterior
# if study_date > str_date :
# str_date = study_date
str_date = ds.StudyDate
str_date = str_date[0:4]+'_'+str_date[4:6] + '_' + str_date[6:8]
#suj = str_date + '_' + alpha_num_str(meta["PatientName"])
suj = str_date + '_' + alpha_num_str(ds.PatientName)
exaid = ds.StudyID
if len(exaid)>1 : #Service patient has strange Eid
suj += '_E' + exaid
elif int(exaid)>1:
suj += '_E' + exaid
# if len(ds.SeriesDescription==0):
# ser = 'S%02d' % ds.SeriesNumber + '_'
# else:
ser = 'S%02d' % ds.SeriesNumber + '_' + alpha_num_str(ds.SeriesDescription)
return(exa,suj,ser)
def get_exam_suj_ser_from_dicom_dataset_new(self,ds):
exa = alpha_num_str(ds.StudyDescription)
str_date = ds.StudyDate
str_date = ds.SeriesDate
str_date = str_date[0:4]+'_'+str_date[4:6] + '_' + str_date[6:8]
suj = str_date + '_' + alpha_num_str(ds.PatientName)
exaid = ds.StudyID
if len(exaid)>1 : #Service patient has strange Eid
suj += '_E' + exaid
elif int(exaid)>1:
suj += '_E' + exaid
ser = 'S%02d' % ds.SeriesNumber + '_' + alpha_num_str(ds.SeriesDescription)
# d = Dataset()
# d.PatientID = ""
# d.StudyInstanceUID = ds.StudyInstanceUID
# d.QueryRetrieveLevel = "IMAGE"; #"INSTANCE"
# d.SeriesInstanceUID=ds.SeriesInstanceUID
# d.ImageType=""
#
# img = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
#
# toto
return(exa,suj,ser)
def check_send_dicom_from_remoteAE(self,assoc):
d = Dataset()
d.PatientsName = self.patient_search
d.QueryRetrieveLevel = "PATIENT"
d.PatientID = "*"
patients = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
self.log.info("Checking %d Exams ",len(patients))
# loop on patients
for pp in patients:
if pp.PatientName=="Service Patient":
print "skiping Service Patient"
continue
#self.log.info("Checking %s ",pp.PatientName)
# find studies
d = Dataset()
d.PatientID = pp.PatientID
d.QueryRetrieveLevel = "STUDY"
d.PatientName = ""
d.StudyInstanceUID = ""
d.StudyDate = ""
d.StudyTime = ""
d.StudyID = ""
d.ModalitiesInStudy = ""
d.StudyDescription = ""
d.NumberOfStudyRelatedInstances=""
studies = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
# loop on studies
for st in studies:
#print " %s - %s %s ||| %s " % (st.StudyDescription, st.StudyDate, st.StudyTime,st.NumberOfStudyRelatedInstances)
d = Dataset()
d.QueryRetrieveLevel = "SERIES"
d.StudyInstanceUID = st.StudyInstanceUID
d.PatientID = "" # st.PatientID #rrr
d.StudyDescription = ""
d.StudyDate = ""
d.PatientName = ""
d.StudyID = ""
d.AcquisitionDate = ""
d.SeriesInstanceUID = ""
d.InstanceNumber = ""
d.Modality = ""
d.SeriesNumber = ""
d.SeriesDescription = ""
d.SeriesDate = ""
d.SeriesTime = ""
d.SeriesID = ""
d.NumberOfSeriesRelatedInstances = ""
series = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
# print series uid and number of instances
for se in series:
if se.NumberOfSeriesRelatedInstances==0 :
log.info('Empyt Serie in %s_%s',se.StudyDescription,se.PatientName)
else:
(exa,suj,ser) = self.get_exam_suj_ser_from_dicom_dataset(se)
dic_dir = os.path.join(self.rootdir,exa,suj,ser)
if not os.path.isdir(dic_dir):
dic_dir+='_phase'
if not os.path.isdir(dic_dir):
(exa,suj,ser) = self.get_exam_suj_ser_from_dicom_dataset_new(se)
dic_dir = os.path.join(self.rootdir,exa,suj,ser)
if not os.path.isdir(dic_dir):
# i can not ask image instance level so do not kwon about IMAGETYPE so I check i _phase exist
dic_dir_p = os.path.join(self.rootdir,exa,suj,ser+'_phase')
if os.path.isdir(dic_dir_p):
dic_dir=dic_dir_p
if os.path.isdir(dic_dir) :
nbdic = glob.glob(os.path.join(dic_dir,"*dic"))
#print "nbd %d nbi %s" %(len(nbdic),se.NumberOfSeriesRelatedInstances)
if len(nbdic) != se.NumberOfSeriesRelatedInstances:
self.log.warning(" MISSING DICOMS found %d instead of %s in %s",len(nbdic),se.NumberOfSeriesRelatedInstances,dic_dir)
else :
self.log.warning(" MISSING SERIES : %s",dic_dir)
#print " %5s - %10s - %35s - %5s" % (se.SeriesNumber, se.Modality, se.SeriesDescription, se.NumberOfSeriesRelatedInstances)
#print "%s | %s |%s | %s | %s" % (se.StudyDescription, se.StudyDate, se.PatientName, se.SeriesNumber, se.SeriesDescription)
#print "%s | %s | %s" %(exa,suj,ser)
# print "%s | %s | %s | %s" % (se.StudyDescription, se.PatientName, se.SeriesNumber, se.SeriesDescription)
def check_send_dicom(self):
ts = [ ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian ]
# create application entity with Find and Move SOP classes as SCU and
# Storage SOP class as SCP
MyAE = AE("DCMTK",9999, [PatientRootFindSOPClass, PatientRootMoveSOPClass, VerificationSOPClass], [StorageSOPClass], ts)
MyAE.OnAssociateResponse = OnAssociateResponse
MyAE.OnAssociateRequest = OnAssociateRequest
MyAE.OnReceiveStore = OnReceiveStore
MyAE.start()
# remote application entity
PrismaAE = dict(Address="134.157.205.1", Port=104, AET="AN_MRC35181")
# create association with remote AE
self.log.info("Request association on PRISMA")
assoc = MyAE.RequestAssociation(PrismaAE)
# perform a DICOM ECHO
st = assoc.VerificationSOPClass.SCU(1)
self.log.info('DICOM Echo done with status "%s"', st)
try :
self.check_send_dicom_from_remoteAE(assoc)
except Exception as e:
self.log.warning('CODE ERROR because of %s',e)
assoc.Release(0)
# AGAIN with VERIO
VerioAE = dict(Address="134.157.205.51", Port=104, AET="MRC40527")
# create association with remote AE
self.log.info("Request association on VERIO")
assoc = MyAE.RequestAssociation(VerioAE)
# perform a DICOM ECHO
st = assoc.VerificationSOPClass.SCU(1)
self.log.info('DICOM Echo done with status "%s"', st)
#try :
self.check_send_dicom_from_remoteAE(assoc)
#except Exception as e:
# self.log.warning('CODE ERROR because of %s',e)
assoc.Release(0)
MyAE.Quit()
def create_dicom_tar(self,in_dir):
for suj in in_dir:
ser_dir= c.get_subdir_regex(suj,'.*')
cmde = 'cd ' + suj
for ser in ser_dir:
commandline = cmde + '; tar -czf ' + ser + '.tar.gz'
print commandline
# try:
# outvalue=call(commandline)
# except OSError:
# print " XX ERROR: unable to find executable "+commandline[0]
# return -1
#
if __name__ == '__main__':
doit = do_common.doit()
log = doit.get_log()
options = doit.get_option('results_db')
RES = Results_DB(log=log,opt=options)
if options.check_send:
RES.check_send_dicom()
sys.exit()
if options.create_tar:
in_dir= c.get_subdir_regex(options.rootdir,[options.proto_reg,options.suj_reg])
RES.create_dicom_tar(in_dir)
sys.exit()
if options.set_results:
RES.set_results_DB()