ADN Informatique

#!/usr/bin/python2.2  # Title: CDs.py # Descr: Retrieve images from IMAGEM PACS (Oracle/FTP) #        build up a dicomdir file # Author: Jean-Luc Cyr # License: (C)2005 Jean-Luc Cyr / Les systèmes médicaux IMAGEM # Created: 2005-04-08 # # Require: DCMTK utilities (dcmdjpeg, dcmconv, dcmgpdir)   # Oracle connection settings db_user = "ris_pacs" db_pass = "password" db_host = "rpdev" # FTP retrieve connection settings ftp_user = "robin" ftp_pass = "blitzkrieg" ftp_host = "192.168.2.70"  # Imports and defs ftp = "ftp://%s:%s@%s" % (ftp_user, ftp_pass, ftp_host) import cx_Oracle as db from urllib import urlretrieve import commands from os import stat  #program start HERE  #Ask for a patient id to fetch study list for patid = raw_input("Enter Pat ID:")  #Connect to db con = db.connect(db_user, db_pass, db_host) cur = con.cursor()  #Fetch study list for this patient cur.execute("select STU_DATE, STU_DESC, STU_INSTANCE_UID from study where stu_pat_id='%s' order by stu_date desc" % patid)  study = cur.fetchall()  for row in range(0,study.__len__()):     (date,desc,stuuid) = study[row]     print "%s - %s - %s" % (row+1,date,desc)  #Ask for studies to burn (index from returned list) studylist = raw_input("Enter Study (comma separated):")  stunolist = studylist.split(",") stulist="" for stuno in stunolist:     #stulist.insert(1,study[int(stuno)][2])     if stulist.__len__()>0:         stulist = "%s,'%s'" % (stulist,study[int(stuno)-1][2])     else:         stulist = "'%s'" % study[int(stuno)-1][2];  #Fetch image list (for all studies) select = "select MFS_MOUNT_POINT,COI_STUDY_INSTANCE_UID,COI_SERIES_INSTANCE_UID,COI_SOP_INSTANCE_UID from composite_object_instance,media_file_set where coi_study_instance_uid in (%s) and coi_sto_media_fset_uid = mfs_uid" % (stulist) cur.execute(select) coi = cur.fetchall()  #clean up last dicomdir and files op = commands.getoutput("rm *dcm") op = commands.getoutput("rm DICOMDIR") op = commands.getoutput("rm image.iso")  #Fetch images, convert them to the good uncompressed format #and build up the DICOMDIR file imlist=[] for row in range(0, coi.__len__()):     print "=== %s de %s ===" % (int(row)+1,coi.__len__())     (mfsuid,stuuid,seruid,coiuid) = coi[row]     url = "%s/%s/%s/%s/%s.dcm" % (ftp,mfsuid,stuuid,seruid,coiuid)     fileName = "%sdcm" % (row)     imlist.insert(1,"%s.dcm" % (coiuid))     print "*Retrieving %s" % coiuid     try:         urlretrieve(url,fileName);     except IOError:         print "Can't retrieve file"     else:         path = "/home/jlcyr/old_home/Devel/CDs";          print '*Uncompressing'             op = commands.getoutput("dcmdjpeg +te %s %s" % (fileName,fileName))         if op!="":             print op          print '*Converting to LittleEndianExplicit'         op = commands.getoutput("dcmconv +te %s %s" % (fileName,fileName))         if op!="":             print op          try:             stat("DICOMDIR")         except OSError:#file doesn't exist             print '*Creating DICOMDIR'             op = commands.getoutput("dcmgpdir +m +D DICOMDIR %s" % (fileName))             if op!="":                 print op                 op = commands.getoutput("rm %s" % (fileName))         else:             print '*Adding to DICOMDIR'                         op = commands.getoutput("dcmgpdir +A +m +D DICOMDIR %s" % (fileName))             if op!="":                 print op                 op = commands.getoutput("rm %s" % (fileName))  #Now burn the CD! print "==== Making ISO image ====" op = commands.getoutput("mkisofs *dcm DICOMDIR >image.iso") print op 

#!/usr/bin/python2.3 # # Script to download a worklist file # and fetch each enumerated file # # author: Jean-Luc Cyr # created on : 2005-06-16 # for: Les systemes medicaux IMAGEM inc #   from urllib import urlopen, urlretrieve from os import makedirs, stat  #Variables globales method = "http://" listserver = "192.168.2.21" path = "/worklist/" inst = "CHUL" fileserver = "ftp://robin:blitzkrieg@192.168.2.70/" rootdir = "/home/jlcyr/dl/"  #Fonction pour downloader la liste de travail a partir du web def fetchlistweb():     print 'Retrieving worklist'     url = method + listserver + path + "worklist.php?INST_ID=" + inst     #print url     try:         page = urlopen(url).read()     except IOError:         print "Can't connect to server"         page = "Can't connect to server"     return page;  #Fonction pour downloader la liste de travail a partir de la db def fetchlistdb():     import cx_Oracle     list = "<PRE>#Liste de travail pour: CHUL\n"     destination='CHUL'     conn2 = cx_Oracle.connect('ris_pacs','password','rpdev')     cur2 = conn2.cursor()     select = "SELECT /*+ INDEX(c IDX_COI_STUDY_UID) */ DISTINCT a.AR_START_DOWNLOAD, c.COI_PAT_ID, c.COI_DATE, m.MFS_MOUNT_POINT,a.AR_STU_INSTANCE_UID, c.COI_SERIES_INSTANCE_UID, c.COI_SOP_INSTANCE_UID || '.dcm', s.STU_DESC FROM AUTO_ROUTING a, COMPOSITE_OBJECT_INSTANCE c, MEDIA_FILE_SET m, STUDY s WHERE COI_STUDY_INSTANCE_UID = AR_STU_INSTANCE_UID AND  COI_STO_MEDIA_FSET_UID = MFS_UID AND AR_STATUS = 'CREATED' AND  AR_DESTINATION = '%s' AND COI_TYPE = 'IMAGE'  AND AR_START_DOWNLOAD <= SYSDATE AND COI_STUDY_INSTANCE_UID = STU_INSTANCE_UID UNION SELECT /*+ INDEX(c1 IDX_COI_STUDY_UID) */ DISTINCT a.AR_START_DOWNLOAD, c2.COI_PAT_ID, c2.COI_DATE, m.MFS_MOUNT_POINT, c2.COI_STUDY_INSTANCE_UID, c2.COI_SERIES_INSTANCE_UID, c2.COI_SOP_INSTANCE_UID || '.dcm', s2.STU_DESC FROM AUTO_ROUTING a, COMPOSITE_OBJECT_INSTANCE c1, STUDY s1, HISTORICAL_IMAGES h, STUDY s2, COMPOSITE_OBJECT_INSTANCE c2, MEDIA_FILE_SET m WHERE a.AR_STATUS = 'CREATED' AND  a.AR_DESTINATION = '%s' AND a.AR_START_DOWNLOAD <= SYSDATE AND c1.COI_STUDY_INSTANCE_UID = a.AR_STU_INSTANCE_UID AND c1.COI_TYPE = 'IMAGE' AND a.AR_STU_INSTANCE_UID = s1.STU_INSTANCE_UID AND s1.STU_OTHER_NUMBER = h.HI_REF_EXAMCODE AND h.HI_EXAMCODE = s2.STU_OTHER_NUMBER AND s1.STU_PAT_ID = s2.STU_PAT_ID AND s1.STU_INSTANCE_UID != s2.STU_INSTANCE_UID AND s2.STU_INSTANCE_UID = c2.COI_STUDY_INSTANCE_UID AND c2.COI_TYPE = 'IMAGE' AND  c2.COI_STO_MEDIA_FSET_UID = m.MFS_UID ORDER BY 1  asc, 2, 3 desc" % (destination, destination)     items = 8     cur2.execute(select)     res2 = cur2.fetchall()     result={}     study = ""     for item in range(1,cur2.rowcount):         for cnt in range(0,items):             result[cur2.description[cnt][0]] = res2[item][cnt]         if (study!=result['AR_STU_INSTANCE_UID']):             if (study!=""):                 list += "End of Study:  "                 list += study                 list += "\n"             study=result['AR_STU_INSTANCE_UID']             list += "Start of Study:  "             list += study             list += "\n"         list += "%s/%s/%s/%s\n" % (result['MFS_MOUNT_POINT'],result['AR_STU_INSTANCE_UID'],result['COI_SERIES_INSTANCE_UID'],result["C.COI_SOP_INSTANCE_UID||'.DCM'"])     if (study!=""):         list += "End of Study:  "         list += study         list += "\n"     list += "</PRE>"     return list  #Fonction mettre des entrees dans la liste de travail def makedb():     print "Generation d'une liste de travail"     import cx_Oracle     conn2 = cx_Oracle.connect('ris_pacs','password','rpdev')     cur2 = conn2.cursor()     select = "update AUTO_ROUTING set AR_STATUS='CREATED'"     cur2.execute(select)     select = "commit"     cur2.execute(select)  #Fonction pour updater la liste de travail quand une etude est downloade def updatelist(study):     print "Updating worklist for study %s " % ( study )     url = method + listserver + path + "update_worklist.php?STU_INSTANCE_UID=" + study     #print url     try:         page = urlopen(url).read()     except IOError:         print "Can't connect to server"         page = "Can't connect to server"     print "response:%s" % ( page )  #Fonction pour downloader une image, verifier les directory etc def download(full,stu,ser,file):     url = fileserver+full     try:         stat(rootdir+stu+"/"+ser)     except OSError:         print "Local directory doesn't exist, creating it (%s)" % (rootdir+stu+"/"+ser)         makedirs(rootdir+stu+"/"+ser)      print "Retrieving object %s" % (file)     fileName= "%s%s/%s/%s" % ( rootdir, stu, ser, file )     try:         urlretrieve(url,fileName);     except IOError:         print "Can't connect to server"             print 'Done'  #Fonction pour executer une liste de travail (downloader les images et updater a chaque etude) def parse(page):     print 'Parsing worklist'     lines = page.split("\n")     for line in lines:         #print line         compo = line.split('/')                 if line[0]=='/':             download(line,compo[3],compo[4],compo[5])         else:             if (line[0:3]=="End"):                 compo = line.split(':  ')                 print line                 updatelist(compo[1])             if (line[0:5]=="Start"):                 print line  #Programme principal makedb() print 'Starting download' #parse(fetchlistweb()) parse(fetchlistdb()) print 'All work done'