Example shape parameterisation

In [1]:

    

import re

import numpy as np
import dicom

import matplotlib.pyplot as plt
%matplotlib inline

from electroninserts import (
    parameterise_single_insert, display_parameterisation)

print("All modules and functions successfully imported.")


    

    




All modules and functions successfully imported.

In [2]:

    

# !pip install --upgrade version_information
# %load_ext version_information
# %version_information dicom, electroninserts, re, numpy, matplotlib, version_information


    

    




Requirement already up-to-date: version_information in c:\users\sbiggs\appdata\local\continuum\anaconda3\envs\electroninserts\lib\site-packages






    
Out[2]:




Software
Version
Python
3.5.2 64bit [MSC v.1900 64 bit (AMD64)]
IPython
5.0.0
OS
Windows 7 6.1.7601 SP1
dicom
0.9.9
electroninserts
0.1.0
re
2.2.1
numpy
1.11.1
matplotlib
1.5.1
version_information
1.0.3
Fri Aug 05 15:04:23 2016 AUS Eastern Standard Time

In [3]:

    

x = [0.99, -0.14, -1.0, -1.73, -2.56, -3.17, -3.49, -3.57, -3.17, -2.52, -1.76,
    -1.04, -0.17, 0.77, 1.63, 2.36, 2.79, 2.91, 3.04, 3.22, 3.34, 3.37, 3.08, 2.54,
    1.88, 1.02, 0.99]
y = [5.05, 4.98, 4.42, 3.24, 1.68, 0.6, -0.64, -1.48, -2.38, -3.77, -4.81,
    -5.26, -5.51, -5.58, -5.23, -4.64, -3.77, -2.77, -1.68, -0.29, 1.23, 2.68, 3.8,
    4.6, 5.01, 5.08, 5.05]

width, length, poi = parameterise_single_insert(x, y)
print("Width = {0:0.2f} cm\nLength = {1:0.2f} cm".format(width, length))

display_parameterisation(x, y, width, length, poi)


    

    




Width = 6.53 cm
Length = 10.99 cm






    

In [4]:

    

# Change this name to match the dicom file located in the same directory
# as this notebook.
dicom_filename = "example_dicom_file.dcm"  

dcm = dicom.read_file(dicom_filename, force=True)
applicator_string = dcm.BeamSequence[0].ApplicatorSequence[0].ApplicatorID
energy_string = dcm.BeamSequence[0].ControlPointSequence[0].NominalBeamEnergy
ssd_string = dcm.BeamSequence[0].ControlPointSequence[0].SourceToSurfaceDistance

print("Applicator = {} (identifier name)".format(applicator_string))
print("Energy = {} (nominal)".format(energy_string))
print("SSD = {} (dicom units)\n".format(ssd_string))

block_data = np.array(dcm.BeamSequence[0].BlockSequence[0].BlockData)
x = np.array(block_data[0::2]).astype(float)/10
y = np.array(block_data[1::2]).astype(float)/10

width, length, poi = parameterise_single_insert(x, y)
print("Width = {0:0.2f} cm".format(width))
print("Length = {0:0.2f} cm".format(length))

display_parameterisation(x, y, width, length, poi)


    

    




Applicator = 10X10 (identifier name)
Energy = 12.0 (nominal)
SSD = 1001.0 (dicom units)

Width = 4.11 cm
Length = 9.52 cm






    

In [5]:

    

# patientID = '00000'.zfill(6)
# string_search_pattern = r'\\MONACODA\FocalData\YOURDIRECTORYHERE\1~Clinical\*{}\plan\*\*tel.1'.format(patientID)
# string_search_pattern


    

In [ ]:

    

# filepath_list = glob(string_search_pattern)
# filepath_list


    

In [6]:

    

telfilepath = "example_monaco510_telfile"
electronmodel_regex = "YourMachineName - \d+MeV"  # \d+ stands for any positive integer

with open(telfilepath, "r") as file:
    telfilecontents = np.array(file.read().splitlines())

electronmodel_index = []
for i, item in enumerate(telfilecontents):
    if re.search(electronmodel_regex, item):
        electronmodel_index += [i]

print("Located applicator and energy strings for plans within telfile:")
applicator_tel_string = [
    telfilecontents[i+12]  # applicator string is located 12 lines below electron model name
    for i in electronmodel_index]
print(applicator_tel_string)

energy_tel_string = [
    telfilecontents[i]
    for i in electronmodel_index]
print(energy_tel_string)


    

    




Located applicator and energy strings for plans within telfile:
['14X14']
['YourMachineName - 15MeV']

In [7]:

    

for i, index in enumerate(electronmodel_index):
    print("Applicator = {}".format(applicator_tel_string[i]))
    print("Energy = {}\n".format(energy_tel_string[i]))
    
    insert_inital_range = telfilecontents[
        index + 51::]  # coords start 51 lines after electron model name
    insert_stop = np.where(
        insert_inital_range=='0')[0][0]  # coords stop right before a line containing 0
    
    insert_coords_string = insert_inital_range[:insert_stop]
    insert_coords = np.fromstring(','.join(insert_coords_string), sep=',')
    x = insert_coords[0::2]/10
    y = insert_coords[1::2]/10
    
    width, length, poi = parameterise_single_insert(x, y)
    print("Width = {0:0.2f} cm".format(width))
    print("Length = {0:0.2f} cm".format(length))
    display_parameterisation(x, y, width, length, poi)


    

    




Applicator = 14X14
Energy = YourMachineName - 15MeV

Width = 8.76 cm
Length = 14.00 cm