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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": "8d48ca51-ba3b-412b-b5c1-8de044c96817",
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "#load required libraries\n",
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+ "import sys\n",
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+ "import os\n",
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+ "import SimpleITK\n",
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+ "import numpy\n",
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+ "import matplotlib.pyplot\n",
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+ "import chardet\n",
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+ "import json\n",
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+ "\n",
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+ "#you should get nixSuite via git clone https://git0.fmf.uni-lj.si/studen/nixSuite.git\n",
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+ "#if you don't put it to $HOME/software/src/, you should update the path\n",
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+ "nixSuite=os.path.join(os.path.expanduser('~'),'software','src','nixSuite')\n",
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+ "sys.path.append(os.path.join(nixSuite,'wrapper'))\n",
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+ "import nixWrapper\n",
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+ "nixWrapper.loadLibrary('labkeyInterface')\n",
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+ "import labkeyInterface\n",
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+ "import labkeyDatabaseBrowser\n",
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+ "import labkeyFileBrowser\n",
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+ "\n",
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+ "def connectDB(server):\n",
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+ " #check connectivity. This checks the configuration in $HOME/.labkey/network.json, \n",
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+ " #where paths to certificates are stored\n",
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+ " net=labkeyInterface.labkeyInterface()\n",
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+ " fconfig=os.path.join(os.path.expanduser('~'),'.labkey','{}.json'.format(server))\n",
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+ " net.init(fconfig)\n",
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+ " #this reports the certificate used\n",
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+ " try:\n",
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+ " print('Using: {}'.format(net.connectionConfig['SSL']['user']))\n",
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+ " except KeyError:\n",
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+ " pass\n",
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+ " #This gets a deafult CSRF code; It should report user name plus a long string of random hex numbers\n",
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+ " net.getCSRF()\n",
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+ " db=labkeyDatabaseBrowser.labkeyDB(net)\n",
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+ " fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
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+ " return db,fb"
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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": "1322d7a2-b34b-43ef-8c7a-74065d41b560",
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "db,fb=connectDB('onko-nix')\n",
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+ "imageDir='preprocessedImages'\n",
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+ "idFilter={'variable':'ParticipantId','value':'1057/18','oper':'eq'}\n",
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+ "project='limfomiPET/Study'\n",
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+ "ds=db.selectRows(project,'study','Imaging1',[idFilter])\n",
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+ "localDir=os.path.join(os.path.expanduser('~'),'temp','limfomiPET')\n",
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+ "if not os.path.isdir(localDir):\n",
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+ " os.mkdir(localDir)\n",
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+ "for r in ds['rows']:\n",
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+ " print(r)\n",
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+ " remotePath='/'.join([imageDir,r['patientCode'],r['visitCode'],r['ctResampled']])\n",
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+ " urlPath=fb.formatPathURL(project,remotePath)\n",
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+ " #print('{}'.format(fb.entryExists(urlPath)))\n",
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+ " localPath=os.path.join(localDir,r['ctResampled'])\n",
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+ " fb.readFileToFile(urlPath,localPath)\n",
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+ " "
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+ ]
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+ }
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+ ],
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+ "metadata": {
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+ "kernelspec": {
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+ "display_name": "Python 3 (ipykernel)",
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+ "language": "python",
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+ "name": "python3"
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+ },
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+ "language_info": {
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+ "codemirror_mode": {
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+ "name": "ipython",
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+ "version": 3
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+ },
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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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+ "nbconvert_exporter": "python",
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+ "pygments_lexer": "ipython3",
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+ "version": "3.10.6"
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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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