pydicomsend.py

#!/usr/bin/env python
# coding: utf-8

# In[28]:


# Coded version of DICOM file 'app11he.dcm'
# Produced by pydicom codify utility script
import pydicom
from pydicom.dataset import Dataset, FileMetaDataset
from pydicom.sequence import Sequence
from PIL import Image
import numpy as np
import glob
from datetime import datetime
import random
import xmltodict
from pynetdicom import AE, debug_logger, StoragePresentationContexts
from pynetdicom.sop_class import CTImageStorage
import io
from pydicom.encaps import encapsulate
import requests
import psycopg2

file = open("allImageMetadata.xml", "r")

xml = file.read()


#Establishing the connection
conn = psycopg2.connect(
   database="postgres", user='postgres', password='postgres', host='127.0.0.1', port= '5432'
)
#Setting auto commit false
conn.autocommit = True

cursor = conn.cursor()

metadata = xmltodict.parse(xml)

# pynetdicom stuff
#debug_logger()

# Initialise the Application Entity
ae = AE()

# Add a requested presentation context
ae.requested_contexts = StoragePresentationContexts

# Associate with peer AE at IP 127.0.0.1 and port 104
assoc = ae.associate("127.0.0.1", 104)


if assoc.is_established:


   for img in metadata['HistoImages']['image']:
       
       
       # Read JPG and convert to Byte Array
       jpg_image = Image.open(img['@src'])
       
       description = img['description'].replace(" ", "^")

       # Create unique SOPInstanceUID
       now = datetime.now()
       SOPInstanceUID = "1.2.826.10.1.3680043.8.654.10.2010." + now.strftime("X%d.X%m.X%Y.X%H.X%M.X%S").replace('X0','X').replace('X','') + "." + str(random.randint(1, 999999))

       print(SOPInstanceUID)
       
       # direkt mit DICOM Send an Server

       # File meta info data elements
       file_meta = FileMetaDataset()
       file_meta.FileMetaInformationGroupLength = 178
       file_meta.FileMetaInformationVersion = b'\x00\x01'
       file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.7'
       file_meta.MediaStorageSOPInstanceUID = SOPInstanceUID
       file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
       file_meta.ImplementationClassUID = '1.2.40.0.13.1.1'
       file_meta.ImplementationVersionName = 'dcm4che-2.0'

       # Main data elements
       ds = Dataset()
       ds.SpecificCharacterSet = 'ISO_IR 100'
       ds.InstanceCreationDate = '20100303'
       ds.InstanceCreationTime = '152750.242'
       ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.7'
       ds.SOPInstanceUID = SOPInstanceUID
       ds.StudyDate = '20100303'
       ds.StudyTime = '1815'
       ds.AccessionNumber = ''
       ds.Modality = 'OT'
       ds.ConversionType = 'SI'
       ds.Manufacturer = ''
       ds.ReferringPhysicianName = 'House^Gregory'
       ds.StudyDescription = 'Duennschnittstudien'
       ds.PatientName = 'Telvis^Test'
       ds.PatientID = '424243'
       ds.PatientBirthDate = '19700101'
       ds.PatientSex = 'M'
       ds.StudyInstanceUID = '1.2.826.0.1.3680043.8.654.10.2010'
       ds.SeriesInstanceUID = '1.2.826.0.1.3680043.8.654.20.2010'
       ds.StudyID = '0000100'
       ds.SeriesNumber = '1'
       ds.InstanceNumber = '1'
       ds.ImageComments = description
       ds.SamplesPerPixel = 3
       ds.PhotometricInterpretation = 'RGB'
       ds.PlanarConfiguration = 0
       ds.Rows = jpg_image.height
       ds.Columns = jpg_image.width
       ds.BitsAllocated = 8
       ds.BitsStored = 8
       ds.HighBit = 7
       ds.PixelRepresentation = 0

       ds.file_meta = file_meta
       ds.is_implicit_VR = False
       ds.is_little_endian = True
       
       print(jpg_image.mode)
       
       if jpg_image.mode == 'RGBA' or jpg_image.mode == 'RGB':

           np_image = np.array(jpg_image.getdata(), dtype=np.uint8)[:,:3]
           ds.Rows = jpg_image.height
           ds.Columns = jpg_image.width
           ds.PhotometricInterpretation = "RGB"
           ds.SamplesPerPixel = 3
           ds.BitsStored = 8
           ds.BitsAllocated = 8
           ds.HighBit = 7
           ds.PixelRepresentation = 0
           ds.PixelData = np_image.tobytes()
           
       if jpg_image.mode == 'L':
      
           np_image = np.array(jpg_image.getdata(),dtype=np.uint8)
           ds.Rows = jpg_image.height
           ds.Columns = jpg_image.width
           ds.PhotometricInterpretation = "MONOCHROME1"
           ds.SamplesPerPixel = 1
           ds.BitsStored = 8
           ds.BitsAllocated = 8
           ds.HighBit = 7
           ds.PixelRepresentation = 0
           ds.PixelData = np_image.tobytes()

       #np_image = np.array(jpg_image.getdata(), dtype=np.uint8)[:,:3]
       #ds.PixelData = np_image.tobytes()
       #ds.save_as('result_rgb.dcm')

       ## POST REQUEST (Sascha)
       #post_data = {
       #'sopInstanceUID':SOPInstanceUID,
       #'description':description,
       #}
       #headers = {"Authorization": "Bearer eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJCanRLSkdOYlF1REY5M28zNjRyZFVGbXh5SWdfMWJzcWM4UFRYUFZaOWRFIn0.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.obzRE8RHXagilXy87BMeMKQiG7qqJZmQtuEzhuuoAuOIqDLwg4_8fr4dlRpZKnCg6kiwwWUBMHDMmEsF3H_A7gs-jKuBYELhg5JugVz10StDpF0uLvhWp7IIRdm4mq5b_VYmAbLzAH-y5WWRjMDcpgdGLbawwKoYwR9PD38sRh1GI4wGKUAc8_rhwt3PhjjDIgfq8D5yQndojorAFBXHxRHVwye5dbdr1hq9hc-82nKwdQd00IYTabl85v0C4vI5KaPz3OXYn30mUOicGc2OG7gXwp-ubEDnKjRNo9gI9e182PyPfh5XjFRSzkZfbVLuisCjwl3QiKubNzdTECSGfw"}
       #r = requests.post(url = "https://v000561.fhnw.ch/spithub-api/api/images", json = post_data, headers=headers)
       #print(r.text)
       cursor.execute("INSERT INTO images (comment, description, sop_instanceuid, image_name, hue,saturation,brightness) VALUES (%s,%s,%s, %s,0,0,0)",( "", description,SOPInstanceUID,img['@src']))
       conn.commit()

       try:
           image = Image.open(img['@src'])
           image.thumbnail((100, 100))
           image.save('/srv/spithub/static-content/thumbnails/'+img['@src'])
       except IOError:
           pass

       # Use the C-STORE service to send the dataset
       # returns the response status as a pydicom Dataset
       status = assoc.send_c_store(ds)
       
       # Check the status of the storage request
       if status:
           # If the storage request succeeded this will be 0x0000
           print('C-STORE request status: 0x{0:04x}'.format(status.Status))
       else:
           print('Connection timed out, was aborted or received invalid response')

       #ds.save_as(r'app11he_from_codify.dcm', write_like_original=False)
       
       
   conn.close()
   # Release the association
   assoc.release()
       
else:
   print('Association rejected, aborted or never connected')