plotter/prepper.py at main · sglanger/plotter · GitHub

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#!/usr/bin/python3

#################################### prepper.py
# Purpose: take a files dropped into /pipeline/input,
#	maake sure it is a SR, if so fetch related priors and
#	pass to the next link in the pipeline
#
# Author: SG Langer
# Date : July 2021
##################################

import time, os, sys
import pydicom

def checkDICOM(path):
#############################
# Purpose: see if DICOM, if yes dispatch prefetch
# tasks, else delete.
############################

  try :
    ds = pydicom.dcmread(path)
    tags = getDemog(ds)
    tmpDir = mkTmpDir (tags, path)
    fetchSR(tmpDir, tags)
    moveToPending(tmpDir)
  except :
    print('not dicom, deleting it and exiting')
    os.system('rm ' + path)
    sys.exit(1)

  return


def getDemog(file):
############################
# Purpose: get Patient ID and
#  exam info
###########################
  tags = []

  for tag in file:
    #print (tag)
    if 'Study Description' in str(tag): tags.append(str(tag))
    if 'Patient\s Name' in str(tag): tags.append(str(tag))
    if 'Patient ID' in str(tag): tags.append(str(tag))
    if 'SOP Class UID' in str(tag): tags.append(str(tag))

  #  this not working
  #tags.append(file.PatientsName)
  #tags.append(file.SOPClassUID)
  #tags.append(file.PatientID)
  #tags.append(file.StudyDescription)

  #print (tags)
  return tags

def moveToPending(path):
################################
#
#
#
################################

  root = os.getcwd()
  root = root + '/pipeline/pending'
  cmdStr = 'mv -f ' + path + ' ' + root
  try :
    print (cmdStr)
    os.system(cmdStr)
  except:
    os.system('rm -Rf /pipeline/pending/* ')
    os.system(cmdStr)

  return


def mkTmpDir(list, file):
############################
# Purpose: use PatId to make
#  a temp Dir
###########################

  for i in list:
    #print (i)
    if 'Patient ID' in str(i):
      PatID=i[i.index('LO:') +5 : -1]

  tmpDir = os.getcwd() + '/tmp/'  + PatID
  print (tmpDir)

  try:
    # make tmp folder for this patient
    os.system('mkdir ' +tmpDir)
    os.system('mkdir ' +tmpDir +'/priors')
    # and now move DICOM from input to /tmp/patID
    #print (file)
    os.system('mv ' + file +' ' + tmpDir)
  except:
    print('could not make  folder ' + tmpDir)
    pass

  return tmpDir

def fetchSR(path, list):
##########################################
# Purpose: find relevent prios based on PatID and studyType
# Ref: https://support.dcmtk.org/docs/findscu.html
# caller: chkDICOM
#########################################

  # on board VNA info
  # SGL 31 Jul; echoscu to this is failing, why? Orthanc is up
  AET= 'orthanc'
  PORT = '4242'
  PEER = '127.0.0.1'

  for i in list:
    #print (i)
    if 'Patient ID' in str(i):
      PatID=i[i.index('LO:') +5 : -1]
    if 'Description' in str(i):
      stdyDescrip=i[i.index('LO:') +5 : -1]

  cmdStr = 'findscu -P -k PatientID=\"' + PatID  + '\" -k StudyDescription=\"' + stdyDescrip + '\" '  \
    + PEER + ' ' + PORT

  try:
    print (cmdStr)
    os.system(cmdStr)
    # once the C-FIND finds studies, filter on SR objects, then C-Move them to
    # /tmp/patID/priors
  except :
    print ('C-FIND blew up')

  return


if __name__ == "__main__":
#############################################################
# Purpose: be called by fwatcher.py, create a /patID folder
#  in /tmp, stuff it with priors if any, then move whole
#  /patID to pipeline/pending
#
# Advice, this does not need to be a class
############################################################
  #os.system('clear')
  print ('in prepper')

  # use cmd line arg to locate projectDir
  if len(sys.argv ) != 2 :
    print ("Incorrect Usage: Must include -input file path- ")
    print (">./prepper.py file_path ")
    sys.exit(1)

  checkDICOM(sys.argv[1])

  sys.exit()