First commit

.gitignore

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+# Compiled python modules.
+*.pyc
+
+# Setuptools distribution folder.
+/dist/
+
+# Python egg metadata, regenerated from source files by setuptools.
+/*.egg-info
+/*.egg

MANIFEST.in

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+include README.rst

bin/ptk-echo

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+#!/usr/bin/env python
+#                                                            _
+# Pacs ToolKit Find wrapper
+#
+# (c) 2016 Fetal-Neonatal Neuroimaging & Developmental Science Center
+#                   Boston Children's Hospital
+#
+#              http://childrenshospital.org/FNNDSC/
+#                        [email protected]
+#
+
+# FOR DEV PURPOSE
+import sys, os
+sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+
+import ptk
+import argparse
+
+parser = argparse.ArgumentParser(description='Echo PACS')
+
+# PACS settings
+parser.add_argument('--aet', action='store', dest='aet', type=str, default='CHRIS-ULTRON-AET', help='aet')
+parser.add_argument('--aec', action='store', dest='aec', type=str, default='CHRIS-ULTRON-AEC', help='aec')
+parser.add_argument('--serverIP', action='store', dest='server_ip', type=str, default='192.168.1.110', help='PACS server IP')
+parser.add_argument('--serverPort', action='store', dest='server_port', type=str, default='4242', help='PACS server port')
+
+opts = parser.parse_args()
+output = ptk.echo(vars(opts))
+print(output)

bin/ptk-find

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+#!/usr/bin/env python
+#                                                            _
+# Pacs ToolKit Find wrapper
+#
+# (c) 2016 Fetal-Neonatal Neuroimaging & Developmental Science Center
+#                   Boston Children's Hospital
+#
+#              http://childrenshospital.org/FNNDSC/
+#                        [email protected]
+#
+
+# FOR DEV PURPOSE
+import sys, os
+sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+
+import ptk
+import argparse
+
+parser = argparse.ArgumentParser(description='Find PACS')
+
+# PACS settings
+parser.add_argument('--aet', action='store', dest='aet', type=str, default='CHRIS-ULTRON-AET', help='aet')
+parser.add_argument('--aec', action='store', dest='aec', type=str, default='CHRIS-ULTRON-AEC', help='aec')
+parser.add_argument('--serverIP', action='store', dest='server_ip', type=str, default='192.168.1.110', help='PACS server IP')
+parser.add_argument('--serverPort', action='store', dest='server_port', type=str, default='4242', help='PACS server port')
+
+# Query settings
+parser.add_argument('--patientID', action='store', dest='PatientID', type=str, default='2175', help='Patient ID')
+parser.add_argument('--patientName', action='store', dest='PatientName', type=str, default='', help='Patient name')
+parser.add_argument('--patientSex', action='store', dest='PatientSex', type=str, default='', help='Patient sex')
+parser.add_argument('--studyDate', action='store', dest='StudyDate', type=str, default='', help='Study date (YYYY/MM/DD)')
+parser.add_argument('--modalitiesInStudy', action='store', dest='ModalitiesInStudy', type=str, default='', help='Modalities in study')
+parser.add_argument('--performedStationAETitle', action='store', dest='PerformedStationAETitle', type=str, default='', help='Performed station aet')
+parser.add_argument('--studyDescription', action='store', dest='StudyDescription', type=str, default='', help='Study description')
+parser.add_argument('--seriesDescription', action='store', dest='SeriesDescription', type=str, default='', help='Series Description')
+
+opts = parser.parse_args()
+output = ptk.find(vars(opts))
+print(output)

bin/ptk-listen

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+#!/usr/bin/env python
+#                                                            _
+# Pacs ToolKit Listener
+#
+# (c) 2016 Fetal-Neonatal Neuroimaging & Developmental Science Center
+#                   Boston Children's Hospital
+#
+#              http://childrenshospital.org/FNNDSC/
+#                        [email protected]
+#
+
+# FOR DEV PURPOSE
+import sys, os
+sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+
+import argparse
+import ptk
+
+parser = argparse.ArgumentParser(description='DICOM Listener script (based on DCMTK and PyDicom)')
+parser.add_argument('-t', '--tmpdir', action='store', dest='tmp_directory', required=True, type=str, help='Directory to store temporary files.')
+parser.add_argument('-l', '--logdir', action='store', dest='log_directory', required=True, type=str, help='Directory to store log files.')
+parser.add_argument('-d', '--datadir', action='store', dest='data_directory', required=True, type=str, help='Directory to store DICOM files.')
+
+opts = parser.parse_args()
+ptk.listen(vars(opts))

doc/listener/README.rst

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+## pre-requisites
+```
+dcmtk
+pydicom
+```
+
+## configuration
+In `xinetd` or in `launchd`, the dicom listener scripts requires the following arguments to be provided:
+```
+   -t: temporary directory
+   -l: log directory
+   -d: data directory
+
+```
+## service
+In `/etc/services` add: 
+```
+   chris-ultron    10401/tcp   # chris ultron dicom listener
+   chris-ultron    10401/udp   # chris ultron dicom listener
+```
+
+## launchd
+Add `org.babymri.chris-ultron.plist` in `/Library/LaunchDaemons`.
+
+Load: `sudo launchctl load -w org.babymri.chris-ultron.plist`
+
+Unload: `sudo launchctl unload org.babymri.chris-ultron.plist`
+
+Test: `nc localhost 10401` (must hang)

doc/listener/listener.plist

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+    <key>UserName</key>
+    <string>nico</string>
+    <key>Label</key>
+    <string>org.babymri.chris-ultron</string>
+    <key>ProgramArguments</key>
+    <array>
+        <string>/Users/nico/work/gitroot/chris-ultron-backend/chris_backend/plugins/services/pacslistener/pacslistener.py</string>
+    	<string>-t</string>
+    	<string>/tmp</string>
+    	<string>-l</string>
+    	<string>/tmp/log</string>
+    	<string>-d</string>
+    	<string>/tmp/data</string>
+    </array>
+    <key>inetdCompatibility</key>
+    <dict>
+        <key>Wait</key>
+        <false/>
+    </dict>
+    <key>Sockets</key>
+    <dict>
+        <key>Listeners</key>
+        <dict>
+            <key>SockServiceName</key>
+            <string>chris-ultron</string>
+            <key>SockType</key>
+            <string>stream</string>
+        </dict>
+    </dict>
+</dict>
+</plist>

ptk/.gitignore

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+# Compiled python modules.
+*.pyc
+
+# Setuptools distribution folder.
+/dist/
+
+# Python egg metadata, regenerated from source files by setuptools.
+/*.egg-info

ptk/__init__.py

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+from .echo   import Echo
+from .find   import Find
+from .listen import Listen
+from .move   import Move
+
+def echo(opt={}):
+    return Echo(opt).run()
+
+def find(opt={}):
+    return Find(opt).run(opt)
+
+def listen(opt={}):
+    return Listen(opt).run()
+
+def move(opt={}):
+    return Move(opt).run(opt)

ptk/echo.py

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+import subprocess
+import ptk.utils
+
+class Echo():
+    """docstring for Echo."""
+    def __init__(self, arg):
+        ptk.utils.init(self, arg)
+        self.executable = 'echoscu'
+
+    def command(self):
+        command = ' --timeout 5' #5s timeout
+
+        return self.executable + ' ' + command + ' ' + self.command_suffix
+
+    def run(self):
+        response = subprocess.run(self.command(), stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
+        result = self.handle(response)
+        return result
+
+    def handle(self, echo_response):
+        std = echo_response.stdout.decode('ascii')
+        response = {
+            'status': 'success',
+            'data': '',
+            'command': echo_response.args
+        }
+        if std != '':
+            response['status'] = 'error'
+            response['data'] = std
+
+        return response

ptk/find.py

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+import subprocess, re
+import ptk.utils
+
+class Find():
+    """docstring for Find."""
+    def __init__(self, arg):
+
+        ptk.utils.init(self, arg)
+        self.executable = 'findscu'
+        # to be moved out
+        self.postfilter_parameters = {
+            'PatientSex': '',
+            'PerformedStationAETitle': '',
+            'StudyDescription': '',
+            'SeriesDescription': ''
+        }
+
+    def buildCommand(self, opt={}):
+        parameters = {
+            'PatientID': '',                     # PATIENT INFORMATION
+            'PatientName': '',
+            'PatientBirthDate': '',
+            'PatientSex': '',
+            'StudyDate': '',                     # STUDY INFORMATION
+            'StudyDescription': '',
+            'StudyInstanceUID': '',
+            'ModalitiesInStudy': '',
+            'PerformedStationAETitle': '',
+            'NumberOfSeriesRelatedInstances': '', # SERIES INFORMATION
+            'InstanceNumber': '',
+            'SeriesDate': '',
+            'SeriesDescription': '',
+            'SeriesInstanceUID': '',
+            'QueryRetrieveLevel': 'SERIES'
+        }
+
+        # build query
+        command = ' -xi'
+        command += ' -S'
+
+        return self.commandWrap(command, parameters, opt)
+
+    def commandWrap(self, command, parameters, opt={}):
+        for key, value in parameters.items():
+            # update value if provided
+            if key in opt:
+                value = opt[key]
+            # update command
+            if value != '':
+                command += ' -k "' + key + '=' + value + '"'
+            else:
+                command += ' -k ' + key
+
+        print(command)
+
+        return self.executable + ' ' + command + ' ' + self.command_suffix
+
+    def preparePostFilter(self):
+        print('prepare post filter')
+        # $post_filter['PatientSex'] = $patientsex;
+        # $post_filter['PerformedStationAETitle'] = $station;
+        # $post_filter['StudyDescription'] = $studydescription;
+        # $post_filter['SeriesDescription'] = $seriesdescription;
+
+    def run(self, opt={}):
+        print('run Find')
+        print(opt)
+        #
+        #
+        # find data
+        response = subprocess.run(self.buildCommand(opt), stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
+        # format response
+        return self.formatResponse(response)
+
+    def checkResponse(self, response):
+        stdSplit = response.split('\n')
+        infoCount = 0
+        errorCount = 0
+        for line in stdSplit:
+            if line.startswith('I: '):
+                infoCount += 1
+            elif line.startswith('E: '):
+                errorCount += 1
+
+        status = 'error'
+        if errorCount == 0:
+            status = 'success'
+
+        return status
+
+    def parseResponse(self, response):
+        data = []
+
+        uid = 0
+        stdSplit = response.split('\n')
+
+        for line in stdSplit:
+            if line.startswith('I: ---------------------------'):
+                data.append({})
+                data[-1]['uid'] = {}
+                data[-1]['uid']['tag'] = 0
+                data[-1]['uid']['value'] = uid
+                data[-1]['uid']['label'] = 'uid'
+                uid +=1
+
+            elif line.startswith('I: '):
+                lineSplit = line.split()
+                if len(lineSplit) >= 8 and re.search('\((.*?)\)', lineSplit[1]) != None:
+                    # extract DICOM tag
+                    tag = re.search('\((.*?)\)', lineSplit[1]).group(0)[1:-1].strip().replace('\x00', '')
+
+                    # extract value
+                    value = re.search('\[(.*?)\]', line)
+                    if value != None:
+                        value = value.group(0)[1:-1].strip().replace('\x00', '')
+                    else:
+                        value = 'no value provided'
+
+                    # extract label
+                    label = lineSplit[-1].strip()
+
+                    data[-1][label] = {}
+                    data[-1][label]['tag'] = tag
+                    data[-1][label]['value'] = value
+                    data[-1][label]['label'] = label
+
+        return data
+
+    def formatResponse(self, response):
+        std = response.stdout.decode('ascii')
+        response = {
+            'status': 'success',
+            'data': '',
+            'command': response.args
+        }
+
+        status = self.checkResponse(std)
+        if status == 'error':
+            response['status'] = 'error'
+            response['data'] = std
+        else:
+            response['status'] = 'success'
+            response['data'] = self.parseResponse(std)
+
+        return response