Get value from variable instead of command line in argparse

Question

I am using pynetdicom script to fetch the data from the dcm4chee. to run the script I need to pass the arguments from the command line. But I already have that value in some variable or in other object and I need to use from there but I am not getting how can I pass that value to the parser or Is it possible to do without parsing.

Please help me to know how can I pass the value using some variables instead of passing through the command line.

Script :

 #!/usr/bin/python

"""
For help on usage, 
python qrscu.py -h 

"""

import argparse
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

# parse commandline
parser = argparse.ArgumentParser(description='storage SCU example')
print "parser", parser
parser.add_argument('remotehost')
parser.add_argument('remoteport', type=int)
parser.add_argument('searchstring')
parser.add_argument('-p', help='local server port', type=int, default=9999)
parser.add_argument('-aet', help='calling AE title', default='PYNETDICOM')
parser.add_argument('-aec', help='called AE title', default='REMOTESCU')
parser.add_argument('-implicit', action='store_true', help='negociate implicit transfer syntax only', default=False)
parser.add_argument('-explicit', action='store_true', help='negociate explicit transfer syntax only', default=False)

args = parser.parse_args()
print "args :::: ", type(args), args

if args.implicit:
    ts = [ImplicitVRLittleEndian]
elif args.explicit:
    ts = [ExplicitVRLittleEndian]
else:
    ts = [
        ExplicitVRLittleEndian, 
        ImplicitVRLittleEndian, 
        ExplicitVRBigEndian
        ]

# 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

# create application entity with Find and Move SOP classes as SCU and
# Storage SOP class as SCP
MyAE = AE(args.aet, args.p, [PatientRootFindSOPClass,
                             PatientRootMoveSOPClass,
                             VerificationSOPClass], [StorageSOPClass], ts)
MyAE.OnAssociateResponse = OnAssociateResponse
MyAE.OnAssociateRequest = OnAssociateRequest
MyAE.OnReceiveStore = OnReceiveStore
MyAE.start()


# remote application entity
RemoteAE = dict(Address=args.remotehost, Port=args.remoteport, AET=args.aec)

# create association with remote AE
print "Request association"
assoc = MyAE.RequestAssociation(RemoteAE)

# perform a DICOM ECHO
print "DICOM Echo ... ",
if assoc:
    st = assoc.VerificationSOPClass.SCU(1)
    print 'done with status "%s"' % st

    print "DICOM FindSCU ... ",
    print "\n\n----------------------------------------------------------------------\n\n"
    d = Dataset()
    d.StudyDate = args.searchstring
    d.QueryRetrieveLevel = "STUDY"
    d.PatientID = "*"
    study = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
    print 'done with status "%s"' % st
    print "\n\n\n Cont...", study
    print "\n\n----------------------------------------------------------------------\n\n"
    # loop on patients
    for pp in study:
        print "\n\n----------------------Pateint Detals------------------------------------------------\n\n"
        print "%s - %s" % (pp.StudyDate, pp.PatientID)
        # 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 = ""
        studies = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
        # loop on studies
        for st in studies:
            print "\n study :: ", studies
            print "\n\n---------------------------Study---------------------------\n\n"
            print "    %s - %s %s" % (st.StudyDescription, st.StudyDate, st.StudyTime)
            d = Dataset()
            d.QueryRetrieveLevel = "SERIES"
            d.StudyInstanceUID = st.StudyInstanceUID
            d.SeriesInstanceUID = ""
            d.InstanceNumber = ""
            d.Modality = ""
            d.SeriesNumber = ""
            d.SeriesDescription = ""
            d.AccessionNumber = ""
            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
            if series:
                for se in series:
                    print "\n\n---------------------------Series---------------------------\n\n"
                    print "\n\n\n series", se
                    print " %15s - %10s - %35s - %5s" % (se.SeriesNumber, se.Modality, se.SeriesDescription, se.NumberOfSeriesRelatedInstances)

    print "Release association"
    assoc.Release(0)

    # done
    MyAE.Quit()
else:
    print "Failed to create Association."

# vim:expandtab:smartindent:tabstop=4:softtabstop=4:shiftwidth=4:

Answer 1

You can incorporate and use the script above in your own code by using the pyhton module subprocess. It will let you run the script with arguments that you define depending on your variables or objects.

Example: Let say that you have some variables your_arg_1...your_arg_n that can be consumed by grscu.py. Then you can pass these variables to the script with

 import subprocess
 r = subprocess.check_call(['grscu.py', your_arg_1, your_arg_2, ..., your_arg_n])

The "args = parser.parse_args()" in the script will grab the variables and pass them to the MyAE object. For more information about argparse, see link.

Answer 2

Put everything inside functions and call them wherever you like:

#!/usr/bin/python
"""
For help on usage, 
python qrscu.py -h 

"""
import os
import argparse
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

# 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 = os.path.join(tempfile.gettempdir(), DS.SOPInstanceUID + '%s.dcm')
        ds = FileDataset(filename, {}, file_meta=file_meta, preamble="\0" * 128)
        ds.update(DS)
        ds.save_as(filename)
        print "File %s written" % filename
    except Exception as e:
        print "Some exception occured", e 
    # must return appropriate status
    return SOPClass.Success

def print_data(remotehost, remoteport, searchstring, local_port=9999,
        calling_title='PYNETDICOM', called_title='REMOTESCU',
        ts=(ExplicitVRLittleEndian, ImplicitVRLittleEndian, ExplicitVRBigEndian)):
    # create application entity with Find and Move SOP classes as SCU and
    # Storage SOP class as SCP
    MyAE = AE(calling_title, local_port, [PatientRootFindSOPClass,
                                PatientRootMoveSOPClass,
                                VerificationSOPClass], [StorageSOPClass], ts)
    MyAE.OnAssociateResponse = OnAssociateResponse
    MyAE.OnAssociateRequest = OnAssociateRequest
    MyAE.OnReceiveStore = OnReceiveStore
    MyAE.start()

    # remote application entity
    RemoteAE = dict(Address=remotehost, Port=remoteport, AET=called_title)

    # create association with remote AE
    print "Request association"
    assoc = MyAE.RequestAssociation(RemoteAE)

    # perform a DICOM ECHO
    print "DICOM Echo ... ",
    if not assoc:
        print "Failed to create Association."
        return

    st = assoc.VerificationSOPClass.SCU(1)
    print 'done with status "%s"' % st

    print "DICOM FindSCU ... ",
    print "\n\n----------------------------------------------------------------------\n\n"
    d = Dataset()
    d.StudyDate = searchstring
    d.QueryRetrieveLevel = "STUDY"
    d.PatientID = "*"
    study = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
    print 'done with status "%s"' % st
    print "\n\n\n Cont...", study
    print "\n\n----------------------------------------------------------------------\n\n"
    # loop on patients
    for pp in study:
        print "\n\n----------------------Pateint Detals------------------------------------------------\n\n"
        print "%s - %s" % (pp.StudyDate, pp.PatientID)
        # 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 = ""
        studies = [x[1] for x in assoc.PatientRootFindSOPClass.SCU(d, 1)][:-1]
        # loop on studies
        for st in studies:
            print "\n study :: ", studies
            print "\n\n---------------------------Study---------------------------\n\n"
            print "    %s - %s %s" % (st.StudyDescription, st.StudyDate, st.StudyTime)
            d = Dataset()
            d.QueryRetrieveLevel = "SERIES"
            d.StudyInstanceUID = st.StudyInstanceUID
            d.SeriesInstanceUID = ""
            d.InstanceNumber = ""
            d.Modality = ""
            d.SeriesNumber = ""
            d.SeriesDescription = ""
            d.AccessionNumber = ""
            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:
                print "\n\n---------------------------Series---------------------------\n\n"
                print "\n\n\n series", se
                print " %15s - %10s - %35s - %5s" % (se.SeriesNumber, se.Modality, se.SeriesDescription, se.NumberOfSeriesRelatedInstances)

    print "Release association"
    assoc.Release(0)

    # done
    MyAE.Quit()

def parse_commandline():
    # parse commandline
    parser = argparse.ArgumentParser(description='storage SCU example')
    print "parser", parser
    parser.add_argument('remotehost')
    parser.add_argument('remoteport', type=int)
    parser.add_argument('searchstring')
    parser.add_argument('-p', help='local server port', type=int, default=9999)
    parser.add_argument('-aet', help='calling AE title', default='PYNETDICOM')
    parser.add_argument('-aec', help='called AE title', default='REMOTESCU')
    parser.add_argument('-implicit', action='store_true', help='negociate implicit transfer syntax only', default=False)
    parser.add_argument('-explicit', action='store_true', help='negociate explicit transfer syntax only', default=False)

    args = parser.parse_args()
    print "args :::: ", type(args), args

    if args.implicit:
        ts = [ImplicitVRLittleEndian]
    elif args.explicit:
        ts = [ExplicitVRLittleEndian]
    else:
        ts = [
            ExplicitVRLittleEndian, 
            ImplicitVRLittleEndian, 
            ExplicitVRBigEndian
            ]
    return args, ts

if __name__ == '__main__':
    args, ts = parse_commandline()
    print_data(args.remotehost, args.remoteport, args.searchstring, args.p, args.aet, args.aec, ts)

and use it like:

import your_module
your_module.print_data(remotehost, remoteport, searchstring)