This utility makes use of user provided XiO access credentials along with a patient ID and then returns the cutout X and Y coords along with applicator, energy, and server filepath for each plan found for that ID on the server.
An example of using this object can be found at the bottom of this notebook.
Copyright © 2015 Simon Biggs
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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import spur
import numpy as np
import shutil
import re
import os
import paramiko
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# client = paramiko.client
# client.load_system_host_keys()
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class XiO_Utility(object):
def __init__(self, **kwargs):
self.patientID = str(kwargs['patientID'])
self.hostname = kwargs['hostname']
self.username = kwargs['username']
self.password = kwargs['password']
self.find_tel_files()
self.sftp_tempfile_copy()
self.parse_tel_file()
self.remove_local_tel_files()
def ssh_shell(self):
return spur.SshShell(hostname=self.hostname,
username=self.username,
password=self.password)
def find_tel_files(self):
shell = self.ssh_shell()
result = shell.run(["find", "/FOCUS/rtp1/", "-regex", "^/.*"+self.patientID+".*.tel.1$"])
self.rtp1TelFilepaths = result.output.splitlines()
shell = self.ssh_shell()
result = shell.run(["find", "/FOCUS/rtp2/", "-regex", "^/.*"+self.patientID+".*.tel.1$"])
self.rtp2TelFilepaths = result.output.splitlines()
self.XiOTelFilepaths = self.rtp1TelFilepaths + self.rtp2TelFilepaths
def sftp_tempfile_copy(self):
self.localTelFilepaths = [0,] * len(self.XiOTelFilepaths)
for i in range(len(self.XiOTelFilepaths)):
self.localTelFilepaths[i] = "tempImportedPlan_"+str(i)
for i, filepath in enumerate(self.XiOTelFilepaths):
shell = self.ssh_shell()
with shell.open(filepath, "r") as remote_file:
with open(self.localTelFilepaths[i], "w") as local_file:
shutil.copyfileobj(remote_file, local_file)
def parse_tel_file(self):
self.XCoords = []
self.YCoords = []
self.info = []
for i, filepath in enumerate(self.localTelFilepaths):
with open(filepath, "r") as file:
telFileContents = np.array(file.read().splitlines())
electronPlanIndex = []
electronPlanEnergy = []
for j, item in enumerate(telFileContents):
if re.search('.*MeVSynergy.*', item):
electronPlanIndex += [j]
electronPlanEnergy += [item]
for j, index in enumerate(electronPlanIndex):
cutoutCoordsSection = telFileContents[index+41::]
cutoutCoordsStop = np.where(cutoutCoordsSection=='0')[0][0]
cutoutCoords = cutoutCoordsSection[:cutoutCoordsStop]
singleStringCoords = ",".join(list(cutoutCoords))
coordAsArray = np.fromstring(singleStringCoords, dtype=float, count=-1, sep=',')
XCoords = coordAsArray[0::2]/10
YCoords = coordAsArray[1::2]/10
applicator = float(telFileContents[index+7].split('x')[0])/10
appString = "%dcm Applicator" %(applicator,)
collatedInfo = np.concatenate([[self.XiOTelFilepaths[i]],
[electronPlanEnergy[j]],
[appString]])
self.XCoords += [XCoords]
self.YCoords += [YCoords]
self.info += [collatedInfo]
def remove_local_tel_files(self):
for filepath in self.localTelFilepaths:
os.remove(filepath)
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'stop nbimport'
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import matplotlib.pyplot as plt
%matplotlib inline
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hostname = 'hostname'
username = 'username'
password = 'password'
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patientID = 'number_goes_here'
example = XiO_Utility(patientID=patientID,
hostname=hostname,
username=username,
password=password)
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example.info[0][1::]
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plt.plot(example.XCoords[0], example.YCoords[0])
plt.axis("equal")