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+{
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+ "cells": [
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "id": "704c900c-9af8-4a68-95e5-10a13a749a22",
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+ "metadata": {},
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+ "outputs": [
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "importDicom ver: 1.0.2\n",
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+ "loadDicom ver: 1.0.0\n",
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+ "loadPatient.load ver: 1.0.3\n",
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+ "User: andrej studen CSRF: 014d1d34b354fe0645d621f760feec80\n",
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+ "\n",
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+ "Adding series 1 f=http://onko-nix.onko-i.si:8080/labkey/_webdav/Test/Transfer/%40files/dicom/1.2.840.113704.1.1762661776.985.1253733606.8/2.16.840.1.114337.23840299283.22957.20190906170313.0/2.16.840.1.114337.23840299283.22957.20190906170313.0.0\n",
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+ "...................................................................................................Got 1 series\n",
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+ "Got 1 series\n",
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+ "....................................................................................................Added 100 files\n"
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+ ]
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+ },
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+ {
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+ "name": "stderr",
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+ "output_type": "stream",
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+ "text": [
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+ "C:\\Users\\studen\\AppData\\Local\\NA-MIC\\Slicer 4.11.20200930\\lib\\Python\\Lib\\site-packages\\urllib3\\connection.py:395: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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+ " SubjectAltNameWarning,\n"
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "User: andrej studen CSRF: a2559dbbd284436b12f91b98557e3fdf\n",
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+ "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
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+ ]
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+ },
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+ {
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+ "name": "stderr",
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+ "output_type": "stream",
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+ "text": [
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+ "C:\\Users\\studen\\AppData\\Local\\NA-MIC\\Slicer 4.11.20200930\\lib\\Python\\Lib\\site-packages\\urllib3\\connection.py:395: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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+ " SubjectAltNameWarning,\n"
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
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+ ]
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+ },
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+ {
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+ "name": "stderr",
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+ "output_type": "stream",
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+ "text": [
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+ "C:\\Users\\studen\\AppData\\Local\\NA-MIC\\Slicer 4.11.20200930\\lib\\Python\\Lib\\site-packages\\urllib3\\connection.py:395: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
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+ " SubjectAltNameWarning,\n"
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "xxxxxxxx"
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+ ]
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+ }
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+ ],
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+ "source": [
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+ "import sys\n",
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+ "import os\n",
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+ "import json\n",
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+ "import pydicom\n",
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+ "import importlib\n",
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+ "import numpy\n",
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+ "import Elastix \n",
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+ "import vtk\n",
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+ "import DicomRtImportExportPlugin\n",
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+ "import glob\n",
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+ "import zipfile\n",
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+ "\n",
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+ "#just load nix suite\n",
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+ "sys.path.append(os.path.join(os.path.expanduser('~'),'software','src','nixSuite','wrapper'))\n",
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+ "import nixWrapper\n",
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+ "\n",
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+ "nixWrapper.loadLibrary('labkeyInterface')\n",
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+ "import labkeyInterface\n",
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+ "\n",
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+ "#DB access at ONKO-NIX\n",
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+ "net=labkeyInterface.labkeyInterface()\n",
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+ "fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')\n",
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+ "net.init(fconfig)\n",
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+ "\n",
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+ "#DMR are at merlin\n",
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+ "netDMR=labkeyInterface.labkeyInterface()\n",
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+ "fconfigDMR=os.path.join(os.path.expanduser('~'),'.labkey','merlin.json')\n",
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+ "netDMR.init(fconfigDMR)\n",
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+ "\n",
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+ "import labkeyDatabaseBrowser\n",
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+ "db=labkeyDatabaseBrowser.labkeyDB(net)\n",
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+ "\n",
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+ "import labkeyFileBrowser\n",
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+ "fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
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+ "fbDMR=labkeyFileBrowser.labkeyFileBrowser(netDMR)\n",
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+ "\n",
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+ "#dicom tools\n",
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+ "nixWrapper.loadLibrary('DICOMtools')\n",
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+ "try:\n",
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+ " importlib.reload(importDicom)\n",
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+ "except NameError:\n",
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+ " import importDicom\n",
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+ " \n",
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+ "try:\n",
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+ " importlib.reload(loadDicom)\n",
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+ "except NameError:\n",
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+ " import loadDicom\n",
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+ "\n",
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+ " \n",
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+ "nixWrapper.loadLibrary('EMBRACE')\n",
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+ "try:\n",
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+ " importlib.reload(loadPatient)\n",
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+ "except NameError:\n",
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+ " import loadPatient\n",
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+ "\n",
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+ "project='EMBRACE/studija'\n",
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+ "iDicom=importDicom.importDicom()\n",
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+ "lDicom=loadDicom.loadDicom()\n",
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+ "\n",
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+ "try:\n",
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+ " del elastix\n",
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+ "except NameError:\n",
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+ " pass\n",
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+ "\n",
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+ "elastix = Elastix.ElastixLogic()\n",
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+ "\n",
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+ "registrationIndex = 29 #targeted EMBRACE\n",
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+ "registrationIndex = 30 #rigid EMBRACE\n",
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+ "RegistrationPresets_ParameterFilenames = 5\n",
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+ "parameterFilenames = elastix.getRegistrationPresets()[registrationIndex]\\\n",
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+ " [RegistrationPresets_ParameterFilenames]\n",
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+ "\n",
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+ "ids=range(1,87)\n",
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+ "ids=range(6,7)\n",
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+ "\n",
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+ "shn = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)\n",
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+ "baseDir=os.path.join('z:\\\\','EMBRACE')\n",
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+ "if not os.path.isdir(baseDir):\n",
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+ " os.makedirs(baseDir)\n",
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+ "\n",
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+ "transformLogic = slicer.vtkSlicerTransformLogic()\n",
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+ "\n",
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+ "exporter = DicomRtImportExportPlugin.DicomRtImportExportPluginClass()\n",
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+ "\n",
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+ "for id in ids:\n",
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+ "\n",
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+ " label = 'LJU'+'{:03d}'.format(id)\n",
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+ " loadDicom.clearNodes()\n",
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+ " \n",
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+ " nodes=loadPatient.load(db,fb,fbDMR,iDicom,lDicom,project,label)\n",
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+ " print('Segmentations: {}'.format(len(slicer.util.getNodesByClass(\"vtkMRMLSegmentationNode\"))))\n",
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+ " \n",
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+ " #debug \n",
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+ " #seg=nodes['CTRS'].GetSegmentation()\n",
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+ " #n=seg.GetNumberOfSegments()\n",
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+ " #for i in numpy.arange(n):\n",
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+ " # sId=seg.GetNthSegmentID(int(i))\n",
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+ " # print(sId)\n",
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+ " #continue\n",
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+ "\n",
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+ " try:\n",
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+ " fixedVolumeNode = nodes['DMR']\n",
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+ " movingVolumeNode = nodes['CT']\n",
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+ " except KeyError:\n",
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+ " continue\n",
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+ "\n",
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+ " transformNodeName = label+'_T2_DF'\n",
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+ " #\n",
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+ " transformNode=slicer.vtkMRMLGridTransformNode()\n",
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+ " transformNode.SetName(transformNodeName)\n",
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+ " slicer.mrmlScene.AddNode(transformNode)\n",
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+ " \n",
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+ " elastix.registerVolumes(fixedVolumeNode, movingVolumeNode, \\\n",
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+ " parameterFilenames = parameterFilenames, outputVolumeNode = None, \n",
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+ " outputTransformNode = transformNode, \\\n",
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+ " fixedVolumeMaskNode = None, movingVolumeMaskNode = None, \n",
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+ " forceDisplacementFieldOutputTransform = True)\n",
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+ "\n",
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+ " \n",
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+ " #dataManager.export(network, 'EMBRACE/Studija', patientID)\n",
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+ " #create output dicom with MRI and migrated CTRS\n",
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+ " oDir=os.path.join(baseDir,label)\n",
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+ " if not os.path.isdir(oDir):\n",
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+ " os.makedirs(oDir)\n",
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+ " #transformNode=slicer.util.loadTransform(os.path.join(oDir,'Transform_R.h5'))\n",
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+ " \n",
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+ " \n",
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+ " #remove all prior dicom files\n",
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+ " dcmList=glob.glob(os.path.join(oDir,'*.dcm'))\n",
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+ " for f in dcmList:\n",
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+ " os.remove(f)\n",
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+ " \n",
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+ " for mode in ['CT','DMR']:\n",
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+ " slicer.util.saveNode(nodes[mode],os.path.join(oDir,label+'_'+mode+'.nrrd'))\n",
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+ " slicer.util.saveNode(transformNode,os.path.join(oDir,label+'_DF.nrrd'))\n",
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+ " seg=nodes['CTRS'].GetSegmentation()\n",
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+ " n=seg.GetNumberOfSegments()\n",
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+ " \n",
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+ " nodes['CTRS'].SetAndObserveTransformNodeID(transformNode.GetID())\n",
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+ " \n",
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+ " #transformLogic.hardenTransform(nodes['CTRS'])\n",
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+ " for i in numpy.arange(n):\n",
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+ " sId=seg.GetNthSegmentID(int(i))\n",
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+ " print(sId)\n",
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+ " seg.GetSegment(sId)\n",
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+ " fname=os.path.join(oDir,label+'_{}.nrrd'.format(sId))\n",
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+ " labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')\n",
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+ " \n",
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+ " idArray = vtk.vtkStringArray()\n",
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+ " idArray.InsertNextValue(sId)\n",
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+ " slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(\n",
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+ " nodes['CTRS'], idArray, labelmapVolumeNode, nodes['DMR'])\n",
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+ " slicer.util.saveNode(labelmapVolumeNode, fname)\n",
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+ " \n",
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+ " exportables=[]\n",
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+ " for mode in ['CTRS','DMR']:\n",
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+ " itemId=shn.GetItemByDataNode(nodes[mode])\n",
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+ " exportables.extend(exporter.examineForExport(itemId))\n",
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+ " \n",
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+ " for exp in exportables:\n",
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+ " exp.directory=oDir\n",
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+ " exp.setTag('PatientID',label)\n",
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+ " exp.setTag('PatientName',label)\n",
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+ " exp.setTag('StudyDescription','contoursAligned')\n",
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+ " exp.setTag('PatientID',label)\n",
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+ " if exp.tag('Modality')=='CT':\n",
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+ " exp.setTag('Modality','MR')\n",
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+ " exp.setTag('ScanningSequence',nodes['metadataDMR']['scanningSequence'])\n",
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+ " exp.setTag('SequenceVariant',nodes['metadataDMR']['sequenceVariant'])\n",
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+ " \n",
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+ " \n",
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+ " exporter.export(exportables)\n",
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+ " "
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 22,
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+ "id": "f2399104-5f88-4151-80fa-59ab4446a69e",
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "ids=range(3,5)\n",
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+ "for id in ids:\n",
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+ " label = 'LJU'+'{:03d}'.format(id)\n",
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+ " oDir=os.path.join(baseDir,label)\n",
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+ " dcmList=glob.glob(os.path.join(oDir,'*.dcm'))\n",
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+ " ozip=os.path.join(baseDir,label+'.zip')\n",
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+ " with zipfile.ZipFile(ozip, 'w') as zf:\n",
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+ " for f in dcmList:\n",
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+ " zf.write(f)\n",
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+ "\n",
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+ " rDir=fb.buildPathURL(project,[label])\n",
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+ " rZip='{}/{}.zip'.format(rDir,label)\n",
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+ " fb.writeFileToFile(ozip,rZip)"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "id": "3943dc9d-3070-4cdb-90e8-c79e2100745b",
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+ "metadata": {},
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+ "outputs": [],
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+ "source": []
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+ }
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+ ],
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+ "metadata": {
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+ "kernelspec": {
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+ "display_name": "Slicer 4.11",
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+ "language": "python",
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+ "name": "slicer-4.11"
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+ },
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+ "language_info": {
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+ "file_extension": ".py",
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+ "mimetype": "text/x-python",
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+ "name": "python",
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+ "version": "3.6.7"
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+ }
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+ },
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+ "nbformat": 4,
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+ "nbformat_minor": 5
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+}
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