import matplotlib.pyplot as plt
get_ipython().magic('matplotlib inline')
from bokeh.io import output_file
from electronfactors import generic_shape_convert, parameterise, create_report

input_dict = dict()

applicator = 10
energy = 12
ssd = 100


# In[3]:

key = '3cm circle'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9296

XCoords, YCoords = generic_shape_convert(3/0.95, 3/0.95, 'circle')
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd

plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[4]:

key = '5cm circle'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9705

XCoords, YCoords = generic_shape_convert(5/0.95, 5/0.95, 'circle')
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd

plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[5]:

key = '7cm circle'
input_dict[key] = dict()

input_dict[key]['factor'] = 1.0032

XCoords, YCoords = generic_shape_convert(7/0.95, 7/0.95, 'circle')
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd

plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[6]:

key = '9cm circle'
input_dict[key] = dict()

input_dict[key]['factor'] = 1.0084

XCoords, YCoords = generic_shape_convert(9/0.95, 9/0.95, 'circle')
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[7]:

key = '3x13cm ellipse'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9530

XCoords, YCoords = generic_shape_convert(3/0.95, 13/0.95, 'ellipse')
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[8]:

key = '1st clinical insert'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9931

XCoords = [-3.04, -3.04, -3.04, -2.95, -2.48, -1.69, -1.31, -1.28, -1.25, -1.23,
    -1.23, -1.21, -1.18, -1.16, -1.16, -1.14, -1.12, -1.08, -1.08, -1.04, -1.01, -0.99,
    -0.99, -0.97, -0.95, -0.92, -0.92, -0.89, -0.87, -0.84, -0.82, -0.8, -0.77, -0.75,
    -0.73, -0.71, -0.67, -0.63, -0.6, -0.56, -0.53, -0.51, -0.48, -0.46, -0.43, -0.41,
    -0.39, -0.36, -0.32, -0.29, -0.26, -0.22, -0.19, -0.17, -0.15, -0.12, -0.12, -0.09,
    -0.07, -0.05, -0.02, 0.02, 0.05, 0.09, 0.09, 0.12, 0.12, 0.15, 0.15, 0.17, 0.17,
    0.19, 0.19, 0.22, 0.22, 0.24, 0.24, 0.26, 0.29, 0.29, 0.32, 0.34, 0.36, 0.39,
    0.39, 0.41, 0.43, 0.43, 0.51, 0.99, 2.05, 2.68, 3.24, 3.6, 3.75, 3.77, 3.65, 3.21,
    2.71, 2.68, 2.65, 2.63, 2.61, 2.59, 2.56, 2.54, 2.52, 2.48, 2.46, 2.46, 2.44,
    2.41, 2.39, 2.37, 2.35, 2.32, 2.29, 2.27, 2.24, 2.22, 2.2, 2.2, 2.18, 2.15, 2.13,
    2.11, 1.86, 1.83, 1.81, 1.79, 1.77, 1.74, 1.72, 1.69, 1.66, 1.64, 1.55, 1.55,
    1.55, 1.53, 1.47, 1.45, 1.42, 1.4, 1.38, 1.36, 1.33, 1.31, 1.28, 1.25, 1.23, 1.23,
    1.21, 1.18, 1.18, 1.16, 1.14, 1.12, 1.08, 1.06, 1.04, 1.01, 0.99, 0.97, 0.95,
    0.95, 0.92, 0.89, 0.87, 0.84, 0.82, 0.8, 0.77, 0.75, 0.73, 0.71, 0.67, 0.65, 0.63,
    0.6, 0.58, 0.56, 0.53, 0.53, 0.51, 0.48, 0.48, 0.46, 0.43, 0.41, 0.17, -0.51,
    -1.74, -2.13, -2.78, -3.04, -3.09, -3.04]
YCoords = [-0.58, 0.63, 1.62, 2.32, 3.12, 3.38, 3.23, 3.23, 3.23, 3.23, 3.21, 3.21,
    3.21, 3.21, 3.19, 3.19, 3.19, 3.19, 3.16, 3.16, 3.16, 3.14, 3.12, 3.12, 3.12,
    3.12, 3.09, 3.09, 3.04, 3.04, 3.04, 3.04, 3.04, 3.04, 3.04, 3.04, 3.04, 3.06,
    3.06, 3.09, 3.09, 3.12, 3.14, 3.14, 3.14, 3.14, 3.16, 3.16, 3.16, 3.16, 3.19,
    3.21, 3.21, 3.21, 3.21, 3.21, 3.23, 3.23, 3.23, 3.26, 3.26, 3.28, 3.28, 3.31,
    3.33, 3.33, 3.36, 3.36, 3.38, 3.38, 3.4, 3.43, 3.45, 3.45, 3.47, 3.47, 3.51, 3.53,
    3.55, 3.57, 3.57, 3.6, 3.62, 3.62, 3.64, 3.64, 3.64, 3.67, 3.67, 3.72, 3.64, 3.19,
    1.81, 0.92, -0.67, -2.05, -3.04, -3.69, -3.84, -3.84, -3.84, -3.84, -3.84, -3.84,
    -3.84, -3.84, -3.84, -3.84, -3.84, -3.81, -3.81, -3.81, -3.81, -3.81, -3.81, -3.81,
    -3.81, -3.79, -3.79, -3.79, -3.79, -3.77, -3.77, -3.77, -3.77, -3.77, -3.62, -3.62,
    -3.62, -3.6, -3.6, -3.6, -3.57, -3.57, -3.57, -3.57, -3.57, -3.55, -3.53, -3.53,
    -3.53, -3.53, -3.53, -3.53, -3.53, -3.51, -3.51, -3.51, -3.51, -3.51, -3.51, -3.47,
    -3.47, -3.47, -3.45, -3.45, -3.45, -3.45, -3.45, -3.45, -3.45, -3.45, -3.45, -3.45,
    -3.45, -3.47, -3.47, -3.47, -3.47, -3.47, -3.47, -3.47, -3.51, -3.51, -3.51, -3.51,
    -3.51, -3.53, -3.53, -3.53, -3.53, -3.53, -3.53, -3.55, -3.55, -3.55, -3.57, -3.57,
    -3.6, -3.6, -3.77, -3.74, -3.09, -2.11, -1.74, -1.35, -0.58, -0.58]
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[9]:

key = '2nd clinical insert'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9931

XCoords = [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]
YCoords = [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]
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[10]:

key = '3rd clinical insert'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9989

XCoords = [-3.26, -3.21, 3.11, 3.21, 3.32, 3.74, 4.05, 4.16, 4.26, 4.53, 4.53, 4.63,
    4.63, 4.84, 4.84, 4.95, 4.95, 5.05, 5.05, 5.16, 5.16, 5.26, 5.26, 5.37, 5.37,
    5.26, 5.26, 5.16, 5.16, 5.05, 5.05, 4.95, 4.95, 4.68, 4.58, 4.47, 4.19, -1.85,
    -2.05, -2.16, -2.26, -2.53, -2.53, -2.58, -2.79, -2.89, -3.0, -3.26, -3.26, -3.32,
    -3.74, -3.84, -3.95, -4.21, -4.21, -4.63, -4.63, -4.74, -4.74, -4.84, -4.84, -4.74,
    -4.74, -4.63, -4.63, -4.37, -4.26, -4.16, -3.74, -3.68, -3.68, -3.42, -3.32, -3.26]
YCoords = [3.11, 3.16, 3.16, 3.05, 3.05, 2.63, 2.63, 2.53, 2.53, 2.26, 2.16, 2.05,
    1.95, 1.74, 1.63, 1.53, 1.11, 1.0, 0.79, 0.68, 0.58, 0.47, 0.05, -0.05, -1.0,
    -1.11, -1.53, -1.63, -1.74, -1.84, -2.05, -2.16, -2.26, -2.53, -2.53, -2.63, -2.56,
    -2.56, -2.63, -2.53, -2.53, -2.26, -2.16, -2.11, -2.11, -2.0, -2.0, -1.74, -1.63,
    -1.58, -1.58, -1.47, -1.47, -1.21, -1.11, -0.68, -0.58, -0.47, -0.05, 0.05, 1.53,
    1.63, 2.05, 2.16, 2.26, 2.53, 2.53, 2.63, 2.63, 2.68, 2.79, 3.05, 3.05, 3.11]
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[11]:

key = '4th clinical insert'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9634

XCoords = [-1.05, -1.03, -1.01, -0.98, -0.96, -0.94, -0.88, -0.86, -0.83, -0.79,
    -0.76, -0.74, -0.72, -0.68, -0.66, -0.64, -0.61, -0.59, -0.57, -0.54, -0.52, -0.49,
    -0.46, -0.44, -0.42, -0.39, -0.37, -0.35, -0.32, -0.29, -0.29, -0.27, -0.27, -0.24,
    -0.24, -0.22, -0.2, -0.15, -0.15, -0.13, -0.09, -0.05, -0.02, 0.0, 0.05, 0.07,
    0.07, 0.09, 0.13, 0.15, 0.2, 0.2, 0.22, 0.24, 0.27, 0.29, 0.32, 0.37, 0.39, 0.42,
    0.44, 0.46, 0.49, 0.52, 0.57, 0.57, 0.59, 0.61, 0.64, 0.8, 1.29, 1.75, 2.02, 2.11,
    2.24, 2.28, 2.21, 2.11, 1.99, 1.82, 1.42, 1.08, 0.78, 0.34, -0.07, -0.72, -1.11,
    -1.63, -2.03, -2.08, -2.08, -2.08, -2.11, -2.14, -2.14, -2.14, -2.14, -2.16, -2.18,
    -2.21, -2.21, -2.23, -2.23, -2.25, -2.25, -2.25, -2.28, -2.31, -2.31, -2.31, -2.33,
    -2.33, -2.33, -2.36, -2.36, -2.38, -2.4, -2.4, -2.4, -2.43, -2.43, -2.45, -2.45,
    -2.45, -2.47, -2.47, -2.47, -2.51, -2.51, -2.51, -2.53, -2.53, -2.53, -2.55, -2.58,
    -2.58, -2.6, -2.6, -2.6, -2.62, -2.62, -2.62, -2.65, -2.67, -2.67, -2.67, -2.67,
    -2.67, -2.67, -2.67, -2.73, -2.73, -2.73, -2.73, -2.73, -2.73, -2.73, -2.73, -2.73,
    -2.73, -2.73, -2.75, -2.75, -2.75, -2.75, -2.75, -2.75, -2.75, -2.73, -2.73, -2.73,
    -2.73, -2.73, -2.69, -2.69, -2.69, -2.69, -2.69, -2.69, -2.67, -2.67, -2.67, -2.67,
    -2.67, -2.67, -2.65, -2.65, -2.65, -2.65, -2.62, -2.62, -2.6, -2.6, -2.6, -2.58,
    -2.58, -2.58, -2.55, -2.53, -2.51, -2.51, -2.47, -2.47, -2.45, -2.43, -2.43, -2.43,
    -2.4, -2.4, -2.38, -2.36, -2.36, -2.33, -2.31, -2.31, -2.28, -2.25, -2.25, -2.23,
    -2.23, -2.21, -2.21, -2.18, -2.18, -2.16, -2.16, -2.14, -2.14, -2.11, -2.11, -2.08,
    -2.06, -2.06, -2.03, -2.03, -2.01, -1.99, -1.99, -1.96, -1.96, -1.96, -1.94, -1.92,
    -1.88, -1.86, -1.86, -1.84, -1.81, -1.79, -1.79, -1.77, -1.77, -1.74, -1.74, -1.72,
    -1.72, -1.72, -1.69, -1.66, -1.64, -1.64, -1.62, -1.62, -1.59, -1.57, -1.55, -1.55,
    -1.52, -1.49, -1.49, -1.47, -1.47, -1.44, -1.42, -1.4, -1.37, -1.35, -1.33, -1.29,
    -1.27, -1.27, -1.25, -1.22, -1.2, -1.2, -1.18, -1.15, -1.13, -1.11, -1.07, -1.05]
YCoords = [2.18, 2.18, 2.18, 2.2, 2.2, 2.23, 2.23, 2.23, 2.25, 2.25, 2.25, 2.25,
    2.25, 2.25, 2.25, 2.25, 2.25, 2.25, 2.25, 2.25, 2.25, 2.25, 2.25, 2.25, 2.25,
    2.25, 2.25, 2.23, 2.23, 2.23, 2.2, 2.2, 2.18, 2.18, 2.16, 2.16, 2.14, 2.11, 2.08,
    2.08, 2.06, 2.06, 2.03, 2.03, 2.01, 1.99, 1.96, 1.96, 1.96, 1.94, 1.94, 1.92,
    1.88, 1.88, 1.88, 1.86, 1.86, 1.84, 1.84, 1.81, 1.81, 1.79, 1.79, 1.74, 1.74,
    1.72, 1.72, 1.69, 1.69, 1.58, 1.27, 0.93, 0.55, 0.26, -0.08, -0.48, -0.75, -1.14,
    -1.48, -1.84, -2.37, -2.61, -2.87, -3.0, -3.0, -2.82, -2.61, -2.03, -1.38, -1.29,
    -1.27, -1.25, -1.25, -1.25, -1.22, -1.2, -1.18, -1.18, -1.15, -1.15, -1.13, -1.13,
    -1.11, -1.11, -1.07, -1.05, -1.05, -1.03, -1.0, -0.98, -0.98, -0.96, -0.93, -0.91,
    -0.88, -0.88, -0.85, -0.83, -0.81, -0.78, -0.76, -0.76, -0.74, -0.72, -0.72, -0.68,
    -0.66, -0.64, -0.61, -0.59, -0.59, -0.57, -0.54, -0.52, -0.49, -0.46, -0.46, -0.44,
    -0.42, -0.42, -0.39, -0.37, -0.35, -0.32, -0.29, -0.27, -0.24, -0.22, -0.2, -0.17,
    -0.15, -0.13, -0.09, -0.07, -0.05, -0.02, 0.0, 0.02, 0.05, 0.07, 0.09, 0.09, 0.13,
    0.15, 0.17, 0.2, 0.22, 0.27, 0.27, 0.29, 0.32, 0.35, 0.37, 0.37, 0.39, 0.42, 0.44,
    0.46, 0.49, 0.49, 0.52, 0.54, 0.57, 0.59, 0.61, 0.64, 0.66, 0.68, 0.72, 0.72,
    0.74, 0.74, 0.76, 0.78, 0.81, 0.83, 0.85, 0.85, 0.88, 0.91, 0.93, 0.96, 0.98,
    1.0, 1.0, 1.03, 1.05, 1.05, 1.07, 1.13, 1.13, 1.15, 1.15, 1.2, 1.22, 1.22, 1.22,
    1.25, 1.27, 1.29, 1.29, 1.33, 1.33, 1.35, 1.35, 1.37, 1.37, 1.4, 1.4, 1.42, 1.42,
    1.44, 1.47, 1.47, 1.49, 1.49, 1.49, 1.52, 1.52, 1.55, 1.57, 1.57, 1.57, 1.59,
    1.62, 1.64, 1.64, 1.66, 1.66, 1.69, 1.72, 1.74, 1.74, 1.77, 1.77, 1.79, 1.81,
    1.81, 1.84, 1.84, 1.86, 1.86, 1.88, 1.88, 1.92, 1.92, 1.94, 1.94, 1.94, 1.96,
    1.96, 1.99, 1.99, 2.01, 2.01, 2.01, 2.03, 2.03, 2.03, 2.06, 2.08, 2.08, 2.08,
    2.08, 2.11, 2.11, 2.14, 2.16, 2.16, 2.16, 2.18]
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[12]:

key = '5th clinical insert'
input_dict[key] = dict()

input_dict[key]['factor'] = 0.9683

XCoords = [-0.32, -0.26, 0.79, 1.11, 1.21, 1.42, 1.53, 1.95, 2.05, 2.32, 2.32, 2.42,
    2.42, 2.53, 2.53, 2.42, 2.42, 2.32, 2.32, 2.21, 2.21, 2.11, 2.11, 2.0, 2.0, 1.68,
    1.68, 1.42, 1.11, 0.89, 0.05, -0.05, -1.0, -1.21, -1.42, -1.89, -1.89, -2.0, -2.0,
    -2.11, -2.11, -2.21, -2.21, -2.11, -2.11, -2.0, -2.0, -1.79, -1.79, -1.68, -1.68,
    -1.47, -1.47, -1.37, -1.37, -1.26, -1.26, -0.58, -0.47, -0.32]
YCoords = [3.0, 3.05, 3.05, 2.74, 2.74, 2.53, 2.53, 2.11, 2.11, 1.84, 1.53, 1.42,
    1.11, 1.0, -0.89, -1.0, -1.32, -1.42, -1.63, -1.74, -1.84, -1.95, -2.05, -2.16,
    -2.26, -2.58, -2.68, -2.95, -2.95, -3.16, -3.16, -3.05, -3.05, -2.84, -2.84, -2.37,
    -2.05, -1.95, -1.63, -1.53, -1.42, -1.32, -0.16, -0.05, 0.16, 0.26, 0.58, 0.79,
    1.0, 1.11, 1.42, 1.63, 1.74, 1.84, 1.95, 2.05, 2.16, 2.84, 2.84, 3.0]
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[13]:

key = '6th clinical insert'
input_dict[key] = dict()

input_dict[key]['factor'] = 1.0067

XCoords = [-2.32, -2.26, -1.74, -1.63, -1.53, -1.42, -1.32, -1.11, -0.68, -0.58,
    0.37, 0.47, 0.58, 0.95, 1.05, 1.11, 1.74, 2.11, 2.11, 2.16, 2.47, 2.58, 2.68,
    2.89, 3.32, 3.42, 3.84, 4.42, 4.42, 4.53, 4.53, 4.74, 4.74, 4.84, 4.84, 4.95,
    4.95, 5.05, 5.05, 5.16, 5.16, 5.26, 5.26, 5.37, 5.37, 5.21, 5.21, 5.26, 5.26,
    5.16, 5.16, 4.95, 4.95, 4.74, 4.74, 4.53, 4.53, 4.21, 4.21, 3.84, 3.74, 3.63,
    3.53, 3.42, 3.32, 3.21, 3.11, 3.0, 2.89, 2.79, 2.37, 2.26, 2.05, 1.95, 1.84, 1.74,
    1.42, 1.32, 0.58, 0.47, 0.26, 0.05, -1.0, -1.11, -1.21, -1.58, -1.58, -1.79, -1.79,
    -1.89, -1.89, -2.0, -2.0, -2.16, -2.47, -2.58, -2.68, -3.05, -3.05, -3.16, -3.16,
    -3.26, -3.26, -3.37, -3.37, -3.42, -3.95, -4.32, -4.32, -4.42, -4.42, -4.53, -4.53,
    -4.63, -4.63, -4.74, -4.74, -4.84, -4.84, -4.95, -4.95, -5.05, -5.05, -5.16, -5.16,
    -5.26, -5.26, -5.37, -5.37, -5.47, -5.47, -5.58, -5.58, -5.68, -5.68, -5.21, -5.11,
    -4.74, -4.74, -4.37, -4.26, -4.16, -4.05, -3.95, -3.53, -3.32, -3.21, -3.11, -2.37,
    -2.32]
YCoords = [5.21, 5.26, 5.26, 5.16, 5.16, 5.05, 5.05, 4.84, 4.84, 4.95, 4.95, 4.84,
    4.84, 4.47, 4.47, 4.53, 4.53, 4.16, 4.05, 4.0, 4.0, 3.89, 3.89, 3.68, 3.68, 3.58,
    3.58, 3.0, 2.89, 2.79, 2.68, 2.47, 2.37, 2.26, 2.16, 2.05, 1.95, 1.84, 1.63, 1.53,
    1.42, 1.32, 1.11, 1.0, 0.47, 0.32, 0.21, 0.16, -0.37, -0.47, -0.58, -0.79, -1.11,
    -1.32, -2.05, -2.26, -2.47, -2.79, -2.89, -3.26, -3.26, -3.37, -3.37, -3.47, -3.47,
    -3.58, -3.58, -3.68, -3.68, -3.79, -3.79, -3.89, -3.89, -4.0, -4.0, -4.11, -4.11,
    -4.21, -4.21, -4.11, -4.11, -3.89, -3.89, -3.79, -3.79, -3.42, -3.32, -3.11, -3.0,
    -2.89, -2.79, -2.68, -2.58, -2.42, -2.42, -2.32, -2.32, -1.95, -1.84, -1.74, -1.63,
    -1.53, -1.42, -1.32, -1.21, -1.16, -1.16, -0.79, -0.68, -0.58, -0.47, -0.37, -0.26,
    -0.16, -0.05, 0.05, 0.16, 0.26, 0.47, 0.58, 0.68, 0.79, 0.89, 1.0, 1.21, 1.32,
    1.53, 1.63, 1.74, 1.84, 2.05, 2.16, 2.47, 2.58, 3.21, 3.68, 3.68, 4.05, 4.26,
    4.63, 4.63, 4.74, 4.74, 4.84, 4.84, 5.05, 5.05, 5.16, 5.16, 5.21]
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])


# In[14]:

key = '7th clinical insert'
input_dict[key] = dict()

input_dict[key]['factor'] = 1.0052

XCoords = [1.63, 0.34, -1.05, -1.16, -1.16, -1.29, -1.29, -1.39, -1.44, -1.44, -1.48,
    -1.59, -1.59, -1.68, -1.78, -1.82, -1.93, -1.97, -2.06, -2.12, -2.16, -2.25, -2.25,
    -2.31, -2.36, -2.4, -2.45, -2.49, -2.55, -2.59, -2.59, -2.64, -2.74, -2.79, -2.83,
    -2.83, -2.88, -2.93, -2.98, -2.98, -2.98, -3.07, -3.17, -3.22, -3.36, -3.36, -3.41,
    -3.46, -3.51, -3.56, -3.56, -3.6, -3.65, -3.65, -3.69, -3.69, -3.75, -3.8, -3.84,
    -3.84, -3.84, -3.89, -3.89, -3.89, -3.89, -3.89, -3.94, -3.99, -3.99, -3.99, -3.99,
    -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03,
    -4.03, -4.03, -4.03, -4.08, -4.08, -4.08, -4.08, -4.08, -4.08, -4.08, -4.08, -4.08,
    -4.08, -4.08, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03, -4.03,
    -4.03, -4.03, -4.03, -4.03, -4.03, -3.99, -3.17, -2.12, -0.62, -0.58, -0.43, -0.34,
    -0.28, -0.15, 0.0, 0.05, 0.09, 0.19, 0.24, 0.28, 0.39, 0.39, 0.43, 0.53, 0.58,
    0.67, 0.72, 0.77, 3.51, 3.51, 3.6, 3.65, 3.65, 3.69, 3.69, 3.75, 3.75, 3.8, 3.8,
    4.08, 4.23, 3.51, 1.59, 1.63]
YCoords = [4.46, 4.71, 4.08, 3.94, 3.88, 3.79, 3.75, 3.69, 3.69, 3.65, 3.6, 3.51,
    3.45, 3.41, 3.32, 3.26, 3.22, 3.12, 3.07, 2.98, 2.93, 2.78, 2.74, 2.64, 2.59,
    2.55, 2.49, 2.45, 2.4, 2.4, 2.31, 2.25, 2.16, 2.06, 1.97, 1.92, 1.92, 1.87, 1.82,
    1.78, 1.73, 1.63, 1.54, 1.48, 1.35, 1.29, 1.25, 1.2, 1.15, 1.15, 1.05, 1.05, 1.01,
    0.96, 0.92, 0.86, 0.82, 0.72, 0.67, 0.58, 0.53, 0.43, 0.34, 0.28, 0.24, 0.19,
    0.09, 0.05, 0.0, -0.09, -0.15, -0.19, -0.34, -0.38, -0.43, -0.48, -0.53, -0.62,
    -0.67, -0.72, -0.77, -0.82, -0.86, -0.92, -1.01, -1.15, -1.2, -1.29, -1.39, -1.48,
    -1.54, -1.63, -1.73, -1.78, -1.82, -1.97, -2.02, -2.02, -2.06, -2.16, -2.25, -2.31,
    -2.35, -2.45, -2.49, -2.55, -2.68, -2.74, -2.78, -2.83, -2.88, -2.98, -3.36, -4.52,
    -4.95, -4.99, -4.99, -5.04, -4.99, -4.99, -4.89, -4.89, -4.89, -4.85, -4.75, -4.75,
    -4.71, -4.71, -4.65, -4.61, -4.56, -4.52, -4.52, -4.52, -4.52, -1.48, -1.39, -1.29,
    -1.15, -1.05, -0.96, -0.86, -0.86, -0.82, -0.72, -0.62, 0.34, 2.45, 3.84, 4.52,
    4.46]
input_dict[key]['XCoords'] = XCoords
input_dict[key]['YCoords'] = YCoords
input_dict[key]['applicator'] = applicator
input_dict[key]['energy'] = energy
input_dict[key]['ssd'] = ssd


plt.figure(figsize=(5,5))
plt.plot(XCoords, YCoords)
plt.xlim([-applicator/2 - 1, applicator/2 + 1])
plt.ylim([-applicator/2 - 1, applicator/2 + 1])

# ### Parameterising the shapes via equivalent ellipse
# 
# Before modelling the shapes need to be able to be parameterised. This is done as so:

# In[15]:

parameterised = parameterise(
    display=True, working_directory=None, optimise_position=True,
    input_dict=input_dict)

# ### Creating an interactive report
# 
# Once the data has been parameterised the model can be created. This is done so in the following cell. Of interest is that these interactive reports can be saved to a html file and placed on a shared drive. No python is required to use these interactive reports, only a modern web browser.
# 
# The table in the report can be sorted and items can be selected. These selections are mirrored in the plots. Portions of the plots / colourbar can be selected which is then mirrored in the remaining plots.

# In[16]:

output_file('example.html')

create_report(
    input_dict=parameterised, standard_output=False) 


# ## 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/>.