Want to download/retrive DICOM files to my local file system.

[Manoj Solanki]

Thanks ORTHANC team for the valuable PACS server. 

I am very new to Medical terminologies and DICOM related task.

I have a requirement to download the DICOM images of ORTHANC server to my local machine file system from python. Currently, I am using one python library which is “pynetdicom3” but facing lots of issues. If you have any specific library or any sample code through which I can achieve my goal, please let me know.

Thanks in advance.

[John Roberts]

I've used python with the requests module to run Orthanc API requests against the server.

For example, you can request a particular study download as a zip archive:

            query = orthanc_url + '/studies/' + orthanc_study_id + '/archive'
            response_study = requests.get(query, verify=False, \
                                          auth=(orthanc_user, orthanc_password))
            if response_study.status_code != 200:
                print 'Problem retrieving study: ' + orthanc_study_id
                print response_study.status, response_study.reason
                continue
            print '   Retrieved: %s' % orthanc_study_id
            zip_content = response_study.content

I then use the io and zipfile modules to extract the DICOM:

            file_like_object = io.BytesIO(zip_content)
            zip_object = zipfile.ZipFile(file_like_object)
            for zip_name in zip_object.namelist():
                zip_object.extract(zip_name, some_destination_dir)

Note that the above snippets are cut/paste from working code.  I haven't confirmed that the above code works by itself.  Obviously, you need to define the variable values.  My Orthanc is behind an Apache proxy, so I have to use the auth option in requests to send a login and password.

John.

[Manoj Solanki]

Hi John,

Thanks for the help.

Actually, I need to connect with only "TCP/IP address" and "port number" as I may have many other PACS as well like "Conquest" etc. Currently, I am using following code snippets on "pynetdicom3" to fetch DICOM files but getting an error: "No accepted Presentation Context for 'dataset'". I am bit confused what should be the Presentation context for the Orthanc server.

Here is my code:

/**********************START******************************/

from pynetdicom3 import AE
from pydicom import read_file
from pydicom import Dataset
from pynetdicom3 import AE
from pynetdicom3 import StorageSOPClassList
from pynetdicom3 import QueryRetrieveSOPClassList
from pydicom.uid import UID

# The Verification SOP Class has a UID of 1.2.840.10008.1.1


# List of presentation context : http://dicom.nema.org/medical/dicom/2014c/output/chtml/part02/sect_F.4.2.2.4.html Which presentation context I should use?

ct_storage_uid = UID('1.2.840.10008.1.1')
ae = AE(scu_sop_class=[ct_storage_uid])

# Try and associate with the peer AE
#   Returns the Association thread
print('Requesting Association with the peer')
assoc = ae.associate("localhost", 4242)

print (assoc)

if assoc.is_established:
    print('Association accepted by the peer')

    # Creat a new DICOM dataset with the attributes to match against
    #   In this case match any patient's name at the PATIENT query
    #   level. See PS3.4 Annex C.6 for the complete list of possible
    #   attributes and query levels.
    dataset = Dataset()
    dataset.PatientID = '*'
    dataset.QueryRetrieveLevel = "PATIENT"

    # Send a DIMSE C-FIND request to the peer
    #   query_model is the Query/Retrieve Information Model to use
    #   and is one of 'W', 'P', 'S', 'O'
    #       'W' - Modality Worklist (1.2.840.10008.5.1.4.31)
    #       'P' - Patient Root (1.2.840.10008.5.1.4.1.2.1.1)
    #       'S' - Study Root (1.2.840.10008.5.1.4.1.2.2.1)
    #       'O' - Patient/Study Only (1.2.840.10008.5.1.4.1.2.3.1)
    responses = assoc.send_c_get(dataset, query_model='P')


    print ( responses)

    for (status, dataset) in responses:
        # While status is pending we should get the matching datasets
        if status == 'Pending':
            print(dataset)
        elif status == 'Success':
            print('C-FIND finished, releasing the association')
        elif status == 'Cancel':
            print('C-FIND cancelled, releasing the association')
        elif status == 'Failure':
            print('C-FIND failed, releasing the association')

    # Release the association
    assoc.release()

/***********************END********************************/

Thanks,

Manoj Solanki

[Alain Mazy]

This is not a pynetdicom support forum !

FYI, you're actually using send_c_get, not send_c_find.  C-GET is not supported by Orthanc.

--

Alain Mazy / CTO 
a...@osimis.io / +32 494 31 67 27

	OSIMIS S.A.  Rue bois Saint-Jean 15/1BE-4102 Seraing  www.osimis.io

[PS]

Hi Manoj, 

Were you able to solve your issue? I'm currently facing a similar problem

[Alain Mazy]

As mentioned in another thread, instead of send_c_get, you should use send_c_move.