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

# # A utility for the importing of patient cutouts from XiO
# 
# 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](#Example).

# ## Copyright information
# 
# 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/.

# ## Required modules

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import spur
import numpy as np
import shutil
import re
import os
import paramiko


# In[ ]:


# client = paramiko.client
# client.load_system_host_keys()


# ## The XiO utility object

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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)


# ## Execute no further if being imported
# 
# Don't want to waste time running the example if this notebook is just being imported. The following cell triggers the notebook import to stop.

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'stop nbimport'


# ## Example

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import matplotlib.pyplot as plt
get_ipython().run_line_magic('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")