# Read MCNP Output

### Reads the output from the MCNP simulation and analyzes the data.

``````

In [17]:

#Imports
from math import *
import cmath
import numpy as np
import scipy as sp
import scipy.special
import matplotlib as mpl
import matplotlib.pyplot as plt
import seaborn as sns
import IPython.display as IPdisplay
import sys
import os

#Import custom modules
from physics import *

sns.set(font_scale=2.0)
sns.set_style("darkgrid")
sns.set_palette(palette='deep')
sns.set_color_codes(palette='deep')

%matplotlib notebook

``````
``````

/home/drake/.anaconda3/lib/python3.4/site-packages/matplotlib/__init__.py:872: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
warnings.warn(self.msg_depr % (key, alt_key))

``````

## Defined functions for the espec

``````

In [2]:

B0 = 2136.0 #Magnetic field strength in Gauss
B0 = B0/10**4
yM = 0.5*.0254

def Radius(KE):
'''Radius of electron orbit in m given KE in keV'''
return me*c/(q*B0)*np.sqrt(1-(1/(KE*1000*q/(me*c**2)+1))**2)*(KE*1000*q/(me*c**2)+1)

def AngleIncidence(KE):
R = Radius(KE)
return np.arcsin((R-yM)/R)

``````

## Create array of kinetic energies and angles

``````

In [3]:

KEstepsize = 0.01
KEsim = np.arange(0.15,3.00+KEstepsize,KEstepsize)
CosThetaSim = np.cos(AngleIncidence(KEsim*1000))
#CosThetaSim = np.cos(np.zeros(len(KEsim))) #Normal incidence

``````

## Read MCNP output files and add the energy deposited in the active layer into an array along with its associated error

``````

In [4]:

mass = 2.95680*10**-2 #mass of active layer in g
Nsegments = 101 #number of segments
segmentmass = mass/Nsegments #mass of each segment in g
phosphorthickness = 81.*10**-6 #thickness of active layer in m
Eabsorbed = []
EabsorbedError = []
FractionAbsorbed = []
MCNP_Directory = '/home/drake/Documents/Physics/Research/Python/MCNP_Code'
for i in range(len(KEsim)):
#Directory of the input files
directory = MCNP_Directory + '/MCNP_Decks/Output/2136Gauss_Oblique_Incidence/Out_{KE}MeV_{Theta}Degrees'\
.format(KE=str(round(KEsim[i],3)),Theta=str(round(np.arccos(CosThetaSim[i])*360/(2*pi),1)))

printflag = False
with open(directory) as searchfile:
for line in searchfile:
left,sep,right = line.partition('whole cell')
if printflag:
Eabs_per_g = float(line[17:28])
Eabs_per_g_Error = float(line[29:35])
Eabsorbed.append(Eabs_per_g*mass)
EabsorbedError.append(Eabs_per_g_Error*mass)
FractionAbsorbed.append(Eabs_per_g*mass/KEsim[i])
printflag = False
if sep: # True iff 'whole cell' in line
printflag = True

``````

## Read MCNP output files and add the energy deposited in the photoactive CCD layer into an array along with its associated error

``````

In [5]:

EphAbsorbedCCD = [] #x-rays
EphAbsorbedCCDError = []
EelAbsorbedCCD = [] #electrons
EelAbsorbedCCDError = []
CCDmass = 2.09610*10**-4 #mass of photoactive layer of CCD
for i in range(len(KEsim)):
#Directory of the input files
directory = MCNP_Directory + '/MCNP_Decks/Output/2136Gauss_Oblique_Incidence/Out_{KE}MeV_{Theta}Degrees'\
.format(KE=str(round(KEsim[i],3)),Theta=str(round(np.arccos(CosThetaSim[i])*360/(2*pi),1)))

printflag = False
with open(directory) as searchfile:
firstoccurence = False
for line in searchfile:
left,sep,right = line.partition('cell  6')
if printflag:
Eabs_per_g = float(line[17:28])
Eabs_per_g_Error = float(line[29:35])
if firstoccurence:
EphAbsorbedCCD.append(Eabs_per_g*CCDmass)
EphAbsorbedCCDError.append(Eabs_per_g_Error*CCDmass)
else:
EelAbsorbedCCD.append(Eabs_per_g*CCDmass)
EelAbsorbedCCDError.append(Eabs_per_g_Error*CCDmass)
printflag = False
if sep: # True iff 'cell  6' in line
printflag = True
firstoccurence = not firstoccurence

``````

## No lanex case

``````

In [7]:

# EphAbsorbedCCD_No_Lanex = [] #x-rays
# EphAbsorbedCCDError_No_Lanex = []
# EelAbsorbedCCD_No_Lanex = [] #electrons
# EelAbsorbedCCDError_No_Lanex = []
# CCDmass = 2.09610*10**-4 #mass of photoactive layer of CCD
# for i in range(len(KEsim)):
#     #Directory of the input files
#     directory = '/home/drake/Desktop/Physics/Research/Python/MCNP_Code/MCNP_Decks/Output/1.5um_CCD_No_Lanex_Output/Out_{KE}MeV_{Theta}Degrees'\
#     .format(KE=str(round(KEsim[i],3)),Theta=str(round(np.arccos(CosThetaSim[i])*360/(2*pi),1)))

#     printflag = False
#     with open(directory) as searchfile:
#         firstoccurence = False
#         for line in searchfile:
#             left,sep,right = line.partition('cell  2')
#             if printflag:
#                 Eabs_per_g = float(line[17:28])
#                 Eabs_per_g_Error = float(line[29:35])
#                 if firstoccurence:
#                     EphAbsorbedCCD_No_Lanex.append(Eabs_per_g*CCDmass)
#                     EphAbsorbedCCDError_No_Lanex.append(Eabs_per_g_Error*CCDmass)
#                 else:
#                     EelAbsorbedCCD_No_Lanex.append(Eabs_per_g*CCDmass)
#                     EelAbsorbedCCDError_No_Lanex.append(Eabs_per_g_Error*CCDmass)
#                 printflag = False
#             if sep: # True iff 'cell  6' in line
#                 printflag = True
#                 firstoccurence = not firstoccurence

``````

## Read MCNP output files and add the energy deposited in each segment of the phosphor layer into an array along with its associated error

``````

In [8]:

deptharray= []
Eabsorbed_Segments = []
Eabsorbed_Segments_Error = []
for i in range(len(KEsim)):
deptharray.append([])
Eabsorbed_Segments.append([])
Eabsorbed_Segments_Error.append([])

#Directory of the input files
directory = MCNP_Directory + '/MCNP_Decks/Output/2136Gauss_Oblique_Incidence/Out_{KE}MeV_{Theta}Degrees'\
.format(KE=str(round(KEsim[i],3)),Theta=str(round(np.arccos(CosThetaSim[i])*360/(2*pi),1)))

for segmentnumber in range(Nsegments-1):
segment = segmentnumber+100 #segment number
deptharray[i].append(segmentnumber*phosphorthickness/Nsegments) #depth for each segment in microns
printflag = False
with open(directory) as searchfile:
for line in searchfile:
left,sep,right = line.partition('       -{segmentlabel}  '.format(segmentlabel=str(segment)))
if printflag:
Eabs_per_g = float(line[17:28])
Eabs_per_g_Error = float(line[29:35])
Eabsorbed_Segments[i].append(Eabs_per_g*segmentmass)
Eabsorbed_Segments_Error[i].append(Eabs_per_g_Error*segmentmass)
printflag = False
if sep:
printflag = True

``````

## Calculate number of photons that reach the CCD

``````

In [9]:

scatteringlength = 2.84*10**-6 #photon scattering length in Gd2O2S in m
conversionefficiency = 0.16 #electron energy to light energy conversion efficiency
emissionwavelength = 545*10**-9 #lanex emission wavelength in m
emissionenergy = hbar*2*pi*c/emissionwavelength
photonNumberArray = []
for i in range(len(KEsim)):
photonNumber = 0
for j in range(len(deptharray[i])):
photonNumber += conversionefficiency*Eabsorbed_Segments[i][j]*10**6*q/emissionenergy\
*(j+0.5)/Nsegments # Nabs = Nexc*(Distance from top of lanex)/(Phosphor thickness)
#where Distance from top of lanex = (SegmentNumber+0.5)/(Nsegments)*(Phosphor thickness)

photonNumberArray.append(photonNumber)

``````

## Plot total energy absorbed in the phosphor layer

``````

In [19]:

plt.subplots(figsize=(12,6))
plt.plot(np.multiply(KEsim,10**3),np.multiply(Eabsorbed,10**3),linewidth=3)
plt.xlim(150,3000)
plt.ylim(0)
plt.xlabel('Kinetic Energy (keV)')
plt.ylabel('Energy Absorbed by Active Layer (keV)')
plt.tight_layout()

``````
``````

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mpl.figure.prototype._make_on_message_function = function(fig) {
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fig.waiting = false;
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// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas
mpl.findpos = function(e) {
//this section is from http://www.quirksmode.org/js/events_properties.html
var targ;
if (!e)
e = window.event;
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mpl.figure.prototype.mouse_event = function(event, name) {
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this.canvas_div.focus();
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var x = canvas_pos.x;
var y = canvas_pos.y;

this.send_message(name, {x: x, y: y, button: event.button,
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value += 'k';
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this._key_event_extra(event, name);

this.send_message(name, {key: value,
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mpl.figure.prototype.toolbar_button_onclick = function(name) {
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this.handle_save(this, null);
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this.send_message("toolbar_button", {name: name});
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mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {
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mpl.extensions = ["eps", "jpeg", "pdf", "png", "ps", "raw", "svg", "tif"];

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};
ws.send = function(m) {
//console.log('sending', m);
comm.send(m);
};
// Register the callback with on_msg.
comm.on_msg(function(msg) {
//console.log('receiving', msg['content']['data'], msg);
// Pass the mpl event to the overriden (by mpl) onmessage function.
ws.onmessage(msg['content']['data'])
});
return ws;
}

mpl.mpl_figure_comm = function(comm, msg) {
// This is the function which gets called when the mpl process
// starts-up an IPython Comm through the "matplotlib" channel.

var id = msg.content.data.id;
// Get hold of the div created by the display call when the Comm
// socket was opened in Python.
var element = \$("#" + id);
var ws_proxy = comm_websocket_adapter(comm)

function ondownload(figure, format) {
window.open(figure.imageObj.src);
}

var fig = new mpl.figure(id, ws_proxy,
ondownload,
element.get(0));

// Call onopen now - mpl needs it, as it is assuming we've passed it a real
// web socket which is closed, not our websocket->open comm proxy.
ws_proxy.onopen();

fig.parent_element = element.get(0);
fig.cell_info = mpl.find_output_cell("<div id='" + id + "'></div>");
if (!fig.cell_info) {
console.error("Failed to find cell for figure", id, fig);
return;
}

var output_index = fig.cell_info[2]
var cell = fig.cell_info[0];

};

mpl.figure.prototype.handle_close = function(fig, msg) {
fig.root.unbind('remove')

// Update the output cell to use the data from the current canvas.
fig.push_to_output();
var dataURL = fig.canvas.toDataURL();
// Re-enable the keyboard manager in IPython - without this line, in FF,
// the notebook keyboard shortcuts fail.
IPython.keyboard_manager.enable()
\$(fig.parent_element).html('<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">');
fig.close_ws(fig, msg);
}

mpl.figure.prototype.close_ws = function(fig, msg){
fig.send_message('closing', msg);
// fig.ws.close()
}

mpl.figure.prototype.push_to_output = function(remove_interactive) {
// Turn the data on the canvas into data in the output cell.
var dataURL = this.canvas.toDataURL();
this.cell_info[1]['text/html'] = '<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">';
}

mpl.figure.prototype.updated_canvas_event = function() {
// Tell IPython that the notebook contents must change.
IPython.notebook.set_dirty(true);
this.send_message("ack", {});
var fig = this;
// Wait a second, then push the new image to the DOM so
// that it is saved nicely (might be nice to debounce this).
setTimeout(function () { fig.push_to_output() }, 1000);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items){
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) { continue; };

var button = \$('<button class="btn btn-default" href="#" title="' + name + '"><i class="fa ' + image + ' fa-lg"></i></button>');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);
nav_element.append(button);
}

// Add the status bar.
var status_bar = \$('<span class="mpl-message" style="text-align:right; float: right;"/>');
nav_element.append(status_bar);
this.message = status_bar[0];

// Add the close button to the window.
var buttongrp = \$('<div class="btn-group inline pull-right"></div>');
var button = \$('<button class="btn btn-mini btn-primary" href="#" title="Stop Interaction"><i class="fa fa-power-off icon-remove icon-large"></i></button>');
button.click(function (evt) { fig.handle_close(fig, {}); } );
button.mouseover('Stop Interaction', toolbar_mouse_event);
buttongrp.append(button);
var titlebar = this.root.find(\$('.ui-dialog-titlebar'));
titlebar.prepend(buttongrp);
}

mpl.figure.prototype._root_extra_style = function(el){
var fig = this
el.on("remove", function(){
fig.close_ws(fig, {});
});
}

mpl.figure.prototype._canvas_extra_style = function(el){
// this is important to make the div 'focusable
el.attr('tabindex', 0)
// reach out to IPython and tell the keyboard manager to turn it's self
// off when our div gets focus

// location in version 3
if (IPython.notebook.keyboard_manager) {
IPython.notebook.keyboard_manager.register_events(el);
}
else {
// location in version 2
IPython.keyboard_manager.register_events(el);
}

}

mpl.figure.prototype._key_event_extra = function(event, name) {
var manager = IPython.notebook.keyboard_manager;
if (!manager)
manager = IPython.keyboard_manager;

// Check for shift+enter
if (event.shiftKey && event.which == 13) {
this.canvas_div.blur();
event.shiftKey = false;
// Send a "J" for go to next cell
event.which = 74;
event.keyCode = 74;
manager.command_mode();
manager.handle_keydown(event);
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
fig.ondownload(fig, null);
}

mpl.find_output_cell = function(html_output) {
// Return the cell and output element which can be found *uniquely* in the notebook.
// Note - this is a bit hacky, but it is done because the "notebook_saving.Notebook"
// IPython event is triggered only after the cells have been serialised, which for
// our purposes (turning an active figure into a static one), is too late.
var cells = IPython.notebook.get_cells();
var ncells = cells.length;
for (var i=0; i<ncells; i++) {
var cell = cells[i];
if (cell.cell_type === 'code'){
for (var j=0; j<cell.output_area.outputs.length; j++) {
var data = cell.output_area.outputs[j];
if (data.data) {
// IPython >= 3 moved mimebundle to data attribute of output
data = data.data;
}
if (data['text/html'] == html_output) {
return [cell, data, j];
}
}
}
}
}

// Register the function which deals with the matplotlib target/channel.
// The kernel may be null if the page has been refreshed.
if (IPython.notebook.kernel != null) {
IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);
}

``````

## Plot energy absorbed by each segment of the phoshpor layer for various energies

``````

In [13]:

plt.subplots(figsize=(12,6))
SegmentThickness = phosphorthickness/Nsegments*10**6 #Segment thickness in meters
Eabs_Seg_Smoothed_10 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[10][1:]),11,3),10**3/SegmentThickness)
Eabs_Seg_Smoothed_15 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[15][1:]),11,3),10**3/SegmentThickness)
Eabs_Seg_Smoothed_20 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[20][1:]),11,3),10**3/SegmentThickness)
Eabs_Seg_Smoothed_25 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[25][1:]),11,3),10**3/SegmentThickness)
Eabs_Seg_Smoothed_30 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[30][1:]),11,3),10**3/SegmentThickness)
Eabs_Seg_Smoothed_40 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[40][1:]),11,3),10**3/SegmentThickness)
Eabs_Seg_Smoothed_50 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[50][1:]),11,3),10**3/SegmentThickness)
#Eabs_Seg_Smoothed_290 = np.multiply(savitzky_golay(np.array(Eabsorbed_Segments[290][1:]),11,3),10**3/SegmentThickness)

plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_10,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[10]))
plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_15,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[15]))
plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_20,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[20]))
plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_25,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[25]))
plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_30,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[30]))
plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_40,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[40]))
plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_50,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[50]),color='orange')
#plt.plot(np.multiply(deptharray[0][1:],10**6),Eabs_Seg_Smoothed_290,linewidth=3,label='{KE:.2f}'.format(KE=KEsim[224]),color='k')
plt.xlabel('Depth (' +  u'\u03bcm)')
plt.ylabel('Energy Absorbed (keV/'+ u'\u03bcm)')
plt.xlim(0)
plt.ylim(0)
plt.subplots_adjust(left=0.12,bottom=0.15) #Adjust spacing to prevent clipping of x and y labels
plt.legend(title='{:<} \n {:<}'.format('Incident','Energy (MeV)'))
plt.show()

``````
``````

/home/drake/.anaconda3/lib/python3.4/site-packages/matplotlib/__init__.py:872: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
warnings.warn(self.msg_depr % (key, alt_key))

var element = \$('#73a4ba19-60ba-4911-860a-8206df891178');
/* Put everything inside the global mpl namespace */
window.mpl = {};

mpl.get_websocket_type = function() {
if (typeof(WebSocket) !== 'undefined') {
return WebSocket;
} else if (typeof(MozWebSocket) !== 'undefined') {
return MozWebSocket;
} else {
alert('Your browser does not have WebSocket support.' +
'Please try Chrome, Safari or Firefox ≥ 6. ' +
'Firefox 4 and 5 are also supported but you ' +
'have to enable WebSockets in about:config.');
};
}

mpl.figure = function(figure_id, websocket, ondownload, parent_element) {
this.id = figure_id;

this.ws = websocket;

this.supports_binary = (this.ws.binaryType != undefined);

if (!this.supports_binary) {
var warnings = document.getElementById("mpl-warnings");
if (warnings) {
warnings.style.display = 'block';
warnings.textContent = (
"This browser does not support binary websocket messages. " +
"Performance may be slow.");
}
}

this.imageObj = new Image();

this.context = undefined;
this.message = undefined;
this.canvas = undefined;
this.rubberband_canvas = undefined;
this.rubberband_context = undefined;
this.format_dropdown = undefined;

this.image_mode = 'full';

this.root = \$('<div/>');
this._root_extra_style(this.root)
this.root.attr('style', 'display: inline-block');

\$(parent_element).append(this.root);

this._init_header(this);
this._init_canvas(this);
this._init_toolbar(this);

var fig = this;

this.waiting = false;

this.ws.onopen =  function () {
fig.send_message("supports_binary", {value: fig.supports_binary});
fig.send_message("send_image_mode", {});
fig.send_message("refresh", {});
}

this.imageObj.onload = function() {
if (fig.image_mode == 'full') {
// Full images could contain transparency (where diff images
// almost always do), so we need to clear the canvas so that
// there is no ghosting.
fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);
}
fig.context.drawImage(fig.imageObj, 0, 0);
};

this.imageObj.onunload = function() {
this.ws.close();
}

this.ws.onmessage = this._make_on_message_function(this);

this.ondownload = ondownload;
}

mpl.figure.prototype._init_header = function() {
var titlebar = \$(
'<div class="ui-dialog-titlebar ui-widget-header ui-corner-all ' +
'ui-helper-clearfix"/>');
var titletext = \$(
'<div class="ui-dialog-title" style="width: 100%; ' +
'text-align: center; padding: 3px;"/>');
titlebar.append(titletext)
this.root.append(titlebar);
this.header = titletext[0];
}

mpl.figure.prototype._canvas_extra_style = function(canvas_div) {

}

mpl.figure.prototype._root_extra_style = function(canvas_div) {

}

mpl.figure.prototype._init_canvas = function() {
var fig = this;

var canvas_div = \$('<div/>');

canvas_div.attr('style', 'position: relative; clear: both; outline: 0');

function canvas_keyboard_event(event) {
return fig.key_event(event, event['data']);
}

canvas_div.keydown('key_press', canvas_keyboard_event);
canvas_div.keyup('key_release', canvas_keyboard_event);
this.canvas_div = canvas_div
this._canvas_extra_style(canvas_div)
this.root.append(canvas_div);

var canvas = \$('<canvas/>');
canvas.addClass('mpl-canvas');
canvas.attr('style', "left: 0; top: 0; z-index: 0; outline: 0")

this.canvas = canvas[0];
this.context = canvas[0].getContext("2d");

var rubberband = \$('<canvas/>');
rubberband.attr('style', "position: absolute; left: 0; top: 0; z-index: 1;")

var pass_mouse_events = true;

canvas_div.resizable({
start: function(event, ui) {
pass_mouse_events = false;
},
resize: function(event, ui) {
fig.request_resize(ui.size.width, ui.size.height);
},
stop: function(event, ui) {
pass_mouse_events = true;
fig.request_resize(ui.size.width, ui.size.height);
},
});

function mouse_event_fn(event) {
if (pass_mouse_events)
return fig.mouse_event(event, event['data']);
}

rubberband.mousedown('button_press', mouse_event_fn);
rubberband.mouseup('button_release', mouse_event_fn);
// Throttle sequential mouse events to 1 every 20ms.
rubberband.mousemove('motion_notify', mouse_event_fn);

rubberband.mouseenter('figure_enter', mouse_event_fn);
rubberband.mouseleave('figure_leave', mouse_event_fn);

canvas_div.on("wheel", function (event) {
event = event.originalEvent;
event['data'] = 'scroll'
if (event.deltaY < 0) {
event.step = 1;
} else {
event.step = -1;
}
mouse_event_fn(event);
});

canvas_div.append(canvas);
canvas_div.append(rubberband);

this.rubberband = rubberband;
this.rubberband_canvas = rubberband[0];
this.rubberband_context = rubberband[0].getContext("2d");
this.rubberband_context.strokeStyle = "#000000";

this._resize_canvas = function(width, height) {
// Keep the size of the canvas, canvas container, and rubber band
// canvas in synch.
canvas_div.css('width', width)
canvas_div.css('height', height)

canvas.attr('width', width);
canvas.attr('height', height);

rubberband.attr('width', width);
rubberband.attr('height', height);
}

// Set the figure to an initial 600x600px, this will subsequently be updated
// upon first draw.
this._resize_canvas(600, 600);

// Disable right mouse context menu.
\$(this.rubberband_canvas).bind("contextmenu",function(e){
return false;
});

function set_focus () {
canvas.focus();
canvas_div.focus();
}

window.setTimeout(set_focus, 100);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items) {
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) {
// put a spacer in here.
continue;
}
var button = \$('<button/>');
button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +
'ui-button-icon-only');
button.attr('role', 'button');
button.attr('aria-disabled', 'false');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);

var icon_img = \$('<span/>');
icon_img.addClass('ui-button-icon-primary ui-icon');
icon_img.addClass(image);
icon_img.addClass('ui-corner-all');

var tooltip_span = \$('<span/>');
tooltip_span.addClass('ui-button-text');
tooltip_span.html(tooltip);

button.append(icon_img);
button.append(tooltip_span);

nav_element.append(button);
}

var fmt_picker_span = \$('<span/>');

var fmt_picker = \$('<select/>');
fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');
fmt_picker_span.append(fmt_picker);
nav_element.append(fmt_picker_span);
this.format_dropdown = fmt_picker[0];

for (var ind in mpl.extensions) {
var fmt = mpl.extensions[ind];
var option = \$(
'<option/>', {selected: fmt === mpl.default_extension}).html(fmt);
fmt_picker.append(option)
}

// Add hover states to the ui-buttons
\$( ".ui-button" ).hover(
function() { \$(this).addClass("ui-state-hover");},
function() { \$(this).removeClass("ui-state-hover");}
);

var status_bar = \$('<span class="mpl-message"/>');
nav_element.append(status_bar);
this.message = status_bar[0];
}

mpl.figure.prototype.request_resize = function(x_pixels, y_pixels) {
// Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,
// which will in turn request a refresh of the image.
this.send_message('resize', {'width': x_pixels, 'height': y_pixels});
}

mpl.figure.prototype.send_message = function(type, properties) {
properties['type'] = type;
properties['figure_id'] = this.id;
this.ws.send(JSON.stringify(properties));
}

mpl.figure.prototype.send_draw_message = function() {
if (!this.waiting) {
this.waiting = true;
this.ws.send(JSON.stringify({type: "draw", figure_id: this.id}));
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
var format_dropdown = fig.format_dropdown;
var format = format_dropdown.options[format_dropdown.selectedIndex].value;
fig.ondownload(fig, format);
}

mpl.figure.prototype.handle_resize = function(fig, msg) {
var size = msg['size'];
if (size[0] != fig.canvas.width || size[1] != fig.canvas.height) {
fig._resize_canvas(size[0], size[1]);
fig.send_message("refresh", {});
};
}

mpl.figure.prototype.handle_rubberband = function(fig, msg) {
var x0 = msg['x0'];
var y0 = fig.canvas.height - msg['y0'];
var x1 = msg['x1'];
var y1 = fig.canvas.height - msg['y1'];
x0 = Math.floor(x0) + 0.5;
y0 = Math.floor(y0) + 0.5;
x1 = Math.floor(x1) + 0.5;
y1 = Math.floor(y1) + 0.5;
var min_x = Math.min(x0, x1);
var min_y = Math.min(y0, y1);
var width = Math.abs(x1 - x0);
var height = Math.abs(y1 - y0);

fig.rubberband_context.clearRect(
0, 0, fig.canvas.width, fig.canvas.height);

fig.rubberband_context.strokeRect(min_x, min_y, width, height);
}

mpl.figure.prototype.handle_figure_label = function(fig, msg) {
// Updates the figure title.
fig.header.textContent = msg['label'];
}

mpl.figure.prototype.handle_cursor = function(fig, msg) {
var cursor = msg['cursor'];
switch(cursor)
{
case 0:
cursor = 'pointer';
break;
case 1:
cursor = 'default';
break;
case 2:
cursor = 'crosshair';
break;
case 3:
cursor = 'move';
break;
}
fig.rubberband_canvas.style.cursor = cursor;
}

mpl.figure.prototype.handle_message = function(fig, msg) {
fig.message.textContent = msg['message'];
}

mpl.figure.prototype.handle_draw = function(fig, msg) {
// Request the server to send over a new figure.
fig.send_draw_message();
}

mpl.figure.prototype.handle_image_mode = function(fig, msg) {
fig.image_mode = msg['mode'];
}

mpl.figure.prototype.updated_canvas_event = function() {
// Called whenever the canvas gets updated.
this.send_message("ack", {});
}

// A function to construct a web socket function for onmessage handling.
// Called in the figure constructor.
mpl.figure.prototype._make_on_message_function = function(fig) {
return function socket_on_message(evt) {
if (evt.data instanceof Blob) {
/* FIXME: We get "Resource interpreted as Image but
* transferred with MIME type text/plain:" errors on
* Chrome.  But how to set the MIME type?  It doesn't seem
* to be part of the websocket stream */
evt.data.type = "image/png";

/* Free the memory for the previous frames */
if (fig.imageObj.src) {
(window.URL || window.webkitURL).revokeObjectURL(
fig.imageObj.src);
}

fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(
evt.data);
fig.updated_canvas_event();
fig.waiting = false;
return;
}
else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == "data:image/png;base64") {
fig.imageObj.src = evt.data;
fig.updated_canvas_event();
fig.waiting = false;
return;
}

var msg = JSON.parse(evt.data);
var msg_type = msg['type'];

// Call the  "handle_{type}" callback, which takes
// the figure and JSON message as its only arguments.
try {
var callback = fig["handle_" + msg_type];
} catch (e) {
console.log("No handler for the '" + msg_type + "' message type: ", msg);
return;
}

if (callback) {
try {
// console.log("Handling '" + msg_type + "' message: ", msg);
callback(fig, msg);
} catch (e) {
console.log("Exception inside the 'handler_" + msg_type + "' callback:", e, e.stack, msg);
}
}
};
}

// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas
mpl.findpos = function(e) {
//this section is from http://www.quirksmode.org/js/events_properties.html
var targ;
if (!e)
e = window.event;
if (e.target)
targ = e.target;
else if (e.srcElement)
targ = e.srcElement;
if (targ.nodeType == 3) // defeat Safari bug
targ = targ.parentNode;

// jQuery normalizes the pageX and pageY
// pageX,Y are the mouse positions relative to the document
// offset() returns the position of the element relative to the document
var x = e.pageX - \$(targ).offset().left;
var y = e.pageY - \$(targ).offset().top;

return {"x": x, "y": y};
};

/*
* return a copy of an object with only non-object keys
* we need this to avoid circular references
* http://stackoverflow.com/a/24161582/3208463
*/
function simpleKeys (original) {
return Object.keys(original).reduce(function (obj, key) {
if (typeof original[key] !== 'object')
obj[key] = original[key]
return obj;
}, {});
}

mpl.figure.prototype.mouse_event = function(event, name) {
var canvas_pos = mpl.findpos(event)

if (name === 'button_press')
{
this.canvas.focus();
this.canvas_div.focus();
}

var x = canvas_pos.x;
var y = canvas_pos.y;

this.send_message(name, {x: x, y: y, button: event.button,
step: event.step,
guiEvent: simpleKeys(event)});

/* This prevents the web browser from automatically changing to
* the text insertion cursor when the button is pressed.  We want
* to control all of the cursor setting manually through the
* 'cursor' event from matplotlib */
event.preventDefault();
return false;
}

mpl.figure.prototype._key_event_extra = function(event, name) {
// Handle any extra behaviour associated with a key event
}

mpl.figure.prototype.key_event = function(event, name) {

// Prevent repeat events
if (name == 'key_press')
{
if (event.which === this._key)
return;
else
this._key = event.which;
}
if (name == 'key_release')
this._key = null;

var value = '';
if (event.ctrlKey && event.which != 17)
value += "ctrl+";
if (event.altKey && event.which != 18)
value += "alt+";
if (event.shiftKey && event.which != 16)
value += "shift+";

value += 'k';
value += event.which.toString();

this._key_event_extra(event, name);

this.send_message(name, {key: value,
guiEvent: simpleKeys(event)});
return false;
}

mpl.figure.prototype.toolbar_button_onclick = function(name) {
if (name == 'download') {
this.handle_save(this, null);
} else {
this.send_message("toolbar_button", {name: name});
}
};

mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {
this.message.textContent = tooltip;
};
mpl.toolbar_items = [["Home", "Reset original view", "fa fa-home icon-home", "home"], ["Back", "Back to  previous view", "fa fa-arrow-left icon-arrow-left", "back"], ["Forward", "Forward to next view", "fa fa-arrow-right icon-arrow-right", "forward"], ["", "", "", ""], ["Pan", "Pan axes with left mouse, zoom with right", "fa fa-arrows icon-move", "pan"], ["Zoom", "Zoom to rectangle", "fa fa-square-o icon-check-empty", "zoom"], ["", "", "", ""], ["Download", "Download plot", "fa fa-floppy-o icon-save", "download"]];

mpl.extensions = ["eps", "jpeg", "pdf", "png", "ps", "raw", "svg", "tif"];

mpl.default_extension = "png";var comm_websocket_adapter = function(comm) {
// Create a "websocket"-like object which calls the given IPython comm
// object with the appropriate methods. Currently this is a non binary
// socket, so there is still some room for performance tuning.
var ws = {};

ws.close = function() {
comm.close()
};
ws.send = function(m) {
//console.log('sending', m);
comm.send(m);
};
// Register the callback with on_msg.
comm.on_msg(function(msg) {
//console.log('receiving', msg['content']['data'], msg);
// Pass the mpl event to the overriden (by mpl) onmessage function.
ws.onmessage(msg['content']['data'])
});
return ws;
}

mpl.mpl_figure_comm = function(comm, msg) {
// This is the function which gets called when the mpl process
// starts-up an IPython Comm through the "matplotlib" channel.

var id = msg.content.data.id;
// Get hold of the div created by the display call when the Comm
// socket was opened in Python.
var element = \$("#" + id);
var ws_proxy = comm_websocket_adapter(comm)

function ondownload(figure, format) {
window.open(figure.imageObj.src);
}

var fig = new mpl.figure(id, ws_proxy,
ondownload,
element.get(0));

// Call onopen now - mpl needs it, as it is assuming we've passed it a real
// web socket which is closed, not our websocket->open comm proxy.
ws_proxy.onopen();

fig.parent_element = element.get(0);
fig.cell_info = mpl.find_output_cell("<div id='" + id + "'></div>");
if (!fig.cell_info) {
console.error("Failed to find cell for figure", id, fig);
return;
}

var output_index = fig.cell_info[2]
var cell = fig.cell_info[0];

};

mpl.figure.prototype.handle_close = function(fig, msg) {
fig.root.unbind('remove')

// Update the output cell to use the data from the current canvas.
fig.push_to_output();
var dataURL = fig.canvas.toDataURL();
// Re-enable the keyboard manager in IPython - without this line, in FF,
// the notebook keyboard shortcuts fail.
IPython.keyboard_manager.enable()
\$(fig.parent_element).html('<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">');
fig.close_ws(fig, msg);
}

mpl.figure.prototype.close_ws = function(fig, msg){
fig.send_message('closing', msg);
// fig.ws.close()
}

mpl.figure.prototype.push_to_output = function(remove_interactive) {
// Turn the data on the canvas into data in the output cell.
var dataURL = this.canvas.toDataURL();
this.cell_info[1]['text/html'] = '<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">';
}

mpl.figure.prototype.updated_canvas_event = function() {
// Tell IPython that the notebook contents must change.
IPython.notebook.set_dirty(true);
this.send_message("ack", {});
var fig = this;
// Wait a second, then push the new image to the DOM so
// that it is saved nicely (might be nice to debounce this).
setTimeout(function () { fig.push_to_output() }, 1000);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items){
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) { continue; };

var button = \$('<button class="btn btn-default" href="#" title="' + name + '"><i class="fa ' + image + ' fa-lg"></i></button>');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);
nav_element.append(button);
}

// Add the status bar.
var status_bar = \$('<span class="mpl-message" style="text-align:right; float: right;"/>');
nav_element.append(status_bar);
this.message = status_bar[0];

// Add the close button to the window.
var buttongrp = \$('<div class="btn-group inline pull-right"></div>');
var button = \$('<button class="btn btn-mini btn-primary" href="#" title="Stop Interaction"><i class="fa fa-power-off icon-remove icon-large"></i></button>');
button.click(function (evt) { fig.handle_close(fig, {}); } );
button.mouseover('Stop Interaction', toolbar_mouse_event);
buttongrp.append(button);
var titlebar = this.root.find(\$('.ui-dialog-titlebar'));
titlebar.prepend(buttongrp);
}

mpl.figure.prototype._root_extra_style = function(el){
var fig = this
el.on("remove", function(){
fig.close_ws(fig, {});
});
}

mpl.figure.prototype._canvas_extra_style = function(el){
// this is important to make the div 'focusable
el.attr('tabindex', 0)
// reach out to IPython and tell the keyboard manager to turn it's self
// off when our div gets focus

// location in version 3
if (IPython.notebook.keyboard_manager) {
IPython.notebook.keyboard_manager.register_events(el);
}
else {
// location in version 2
IPython.keyboard_manager.register_events(el);
}

}

mpl.figure.prototype._key_event_extra = function(event, name) {
var manager = IPython.notebook.keyboard_manager;
if (!manager)
manager = IPython.keyboard_manager;

// Check for shift+enter
if (event.shiftKey && event.which == 13) {
this.canvas_div.blur();
event.shiftKey = false;
// Send a "J" for go to next cell
event.which = 74;
event.keyCode = 74;
manager.command_mode();
manager.handle_keydown(event);
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
fig.ondownload(fig, null);
}

mpl.find_output_cell = function(html_output) {
// Return the cell and output element which can be found *uniquely* in the notebook.
// Note - this is a bit hacky, but it is done because the "notebook_saving.Notebook"
// IPython event is triggered only after the cells have been serialised, which for
// our purposes (turning an active figure into a static one), is too late.
var cells = IPython.notebook.get_cells();
var ncells = cells.length;
for (var i=0; i<ncells; i++) {
var cell = cells[i];
if (cell.cell_type === 'code'){
for (var j=0; j<cell.output_area.outputs.length; j++) {
var data = cell.output_area.outputs[j];
if (data.data) {
// IPython >= 3 moved mimebundle to data attribute of output
data = data.data;
}
if (data['text/html'] == html_output) {
return [cell, data, j];
}
}
}
}
}

// Register the function which deals with the matplotlib target/channel.
// The kernel may be null if the page has been refreshed.
if (IPython.notebook.kernel != null) {
IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);
}

``````

## Plot number of photons absorbed by the CCD

``````

In [16]:

plt.subplots(figsize=(12,6))
plt.plot(np.multiply(KEsim,10**3),np.multiply(Eabsorbed,conversionefficiency*10**6*q/emissionenergy/2),linewidth=3,color='r',label='Without Diffusion')
plt.plot(np.multiply(KEsim,10**3),photonNumberArray,linewidth=3,color='b',label='With Diffusion')
plt.xlabel('Electron Kinetic Energy (keV)')
plt.ylabel('Number of Photons')
plt.xlim(150,3000)
plt.title('Number of photons absorbed by CCD due to single electron',y=1.03)
plt.legend(loc=1)
plt.tight_layout()

``````
``````

var element = \$('#2820e997-3d51-4de3-913c-29e08bf134ee');
/* Put everything inside the global mpl namespace */
window.mpl = {};

mpl.get_websocket_type = function() {
if (typeof(WebSocket) !== 'undefined') {
return WebSocket;
} else if (typeof(MozWebSocket) !== 'undefined') {
return MozWebSocket;
} else {
alert('Your browser does not have WebSocket support.' +
'Please try Chrome, Safari or Firefox ≥ 6. ' +
'Firefox 4 and 5 are also supported but you ' +
'have to enable WebSockets in about:config.');
};
}

mpl.figure = function(figure_id, websocket, ondownload, parent_element) {
this.id = figure_id;

this.ws = websocket;

this.supports_binary = (this.ws.binaryType != undefined);

if (!this.supports_binary) {
var warnings = document.getElementById("mpl-warnings");
if (warnings) {
warnings.style.display = 'block';
warnings.textContent = (
"This browser does not support binary websocket messages. " +
"Performance may be slow.");
}
}

this.imageObj = new Image();

this.context = undefined;
this.message = undefined;
this.canvas = undefined;
this.rubberband_canvas = undefined;
this.rubberband_context = undefined;
this.format_dropdown = undefined;

this.image_mode = 'full';

this.root = \$('<div/>');
this._root_extra_style(this.root)
this.root.attr('style', 'display: inline-block');

\$(parent_element).append(this.root);

this._init_header(this);
this._init_canvas(this);
this._init_toolbar(this);

var fig = this;

this.waiting = false;

this.ws.onopen =  function () {
fig.send_message("supports_binary", {value: fig.supports_binary});
fig.send_message("send_image_mode", {});
fig.send_message("refresh", {});
}

this.imageObj.onload = function() {
if (fig.image_mode == 'full') {
// Full images could contain transparency (where diff images
// almost always do), so we need to clear the canvas so that
// there is no ghosting.
fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);
}
fig.context.drawImage(fig.imageObj, 0, 0);
};

this.imageObj.onunload = function() {
this.ws.close();
}

this.ws.onmessage = this._make_on_message_function(this);

this.ondownload = ondownload;
}

mpl.figure.prototype._init_header = function() {
var titlebar = \$(
'<div class="ui-dialog-titlebar ui-widget-header ui-corner-all ' +
'ui-helper-clearfix"/>');
var titletext = \$(
'<div class="ui-dialog-title" style="width: 100%; ' +
'text-align: center; padding: 3px;"/>');
titlebar.append(titletext)
this.root.append(titlebar);
this.header = titletext[0];
}

mpl.figure.prototype._canvas_extra_style = function(canvas_div) {

}

mpl.figure.prototype._root_extra_style = function(canvas_div) {

}

mpl.figure.prototype._init_canvas = function() {
var fig = this;

var canvas_div = \$('<div/>');

canvas_div.attr('style', 'position: relative; clear: both; outline: 0');

function canvas_keyboard_event(event) {
return fig.key_event(event, event['data']);
}

canvas_div.keydown('key_press', canvas_keyboard_event);
canvas_div.keyup('key_release', canvas_keyboard_event);
this.canvas_div = canvas_div
this._canvas_extra_style(canvas_div)
this.root.append(canvas_div);

var canvas = \$('<canvas/>');
canvas.addClass('mpl-canvas');
canvas.attr('style', "left: 0; top: 0; z-index: 0; outline: 0")

this.canvas = canvas[0];
this.context = canvas[0].getContext("2d");

var rubberband = \$('<canvas/>');
rubberband.attr('style', "position: absolute; left: 0; top: 0; z-index: 1;")

var pass_mouse_events = true;

canvas_div.resizable({
start: function(event, ui) {
pass_mouse_events = false;
},
resize: function(event, ui) {
fig.request_resize(ui.size.width, ui.size.height);
},
stop: function(event, ui) {
pass_mouse_events = true;
fig.request_resize(ui.size.width, ui.size.height);
},
});

function mouse_event_fn(event) {
if (pass_mouse_events)
return fig.mouse_event(event, event['data']);
}

rubberband.mousedown('button_press', mouse_event_fn);
rubberband.mouseup('button_release', mouse_event_fn);
// Throttle sequential mouse events to 1 every 20ms.
rubberband.mousemove('motion_notify', mouse_event_fn);

rubberband.mouseenter('figure_enter', mouse_event_fn);
rubberband.mouseleave('figure_leave', mouse_event_fn);

canvas_div.on("wheel", function (event) {
event = event.originalEvent;
event['data'] = 'scroll'
if (event.deltaY < 0) {
event.step = 1;
} else {
event.step = -1;
}
mouse_event_fn(event);
});

canvas_div.append(canvas);
canvas_div.append(rubberband);

this.rubberband = rubberband;
this.rubberband_canvas = rubberband[0];
this.rubberband_context = rubberband[0].getContext("2d");
this.rubberband_context.strokeStyle = "#000000";

this._resize_canvas = function(width, height) {
// Keep the size of the canvas, canvas container, and rubber band
// canvas in synch.
canvas_div.css('width', width)
canvas_div.css('height', height)

canvas.attr('width', width);
canvas.attr('height', height);

rubberband.attr('width', width);
rubberband.attr('height', height);
}

// Set the figure to an initial 600x600px, this will subsequently be updated
// upon first draw.
this._resize_canvas(600, 600);

// Disable right mouse context menu.
\$(this.rubberband_canvas).bind("contextmenu",function(e){
return false;
});

function set_focus () {
canvas.focus();
canvas_div.focus();
}

window.setTimeout(set_focus, 100);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items) {
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) {
// put a spacer in here.
continue;
}
var button = \$('<button/>');
button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +
'ui-button-icon-only');
button.attr('role', 'button');
button.attr('aria-disabled', 'false');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);

var icon_img = \$('<span/>');
icon_img.addClass('ui-button-icon-primary ui-icon');
icon_img.addClass(image);
icon_img.addClass('ui-corner-all');

var tooltip_span = \$('<span/>');
tooltip_span.addClass('ui-button-text');
tooltip_span.html(tooltip);

button.append(icon_img);
button.append(tooltip_span);

nav_element.append(button);
}

var fmt_picker_span = \$('<span/>');

var fmt_picker = \$('<select/>');
fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');
fmt_picker_span.append(fmt_picker);
nav_element.append(fmt_picker_span);
this.format_dropdown = fmt_picker[0];

for (var ind in mpl.extensions) {
var fmt = mpl.extensions[ind];
var option = \$(
'<option/>', {selected: fmt === mpl.default_extension}).html(fmt);
fmt_picker.append(option)
}

// Add hover states to the ui-buttons
\$( ".ui-button" ).hover(
function() { \$(this).addClass("ui-state-hover");},
function() { \$(this).removeClass("ui-state-hover");}
);

var status_bar = \$('<span class="mpl-message"/>');
nav_element.append(status_bar);
this.message = status_bar[0];
}

mpl.figure.prototype.request_resize = function(x_pixels, y_pixels) {
// Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,
// which will in turn request a refresh of the image.
this.send_message('resize', {'width': x_pixels, 'height': y_pixels});
}

mpl.figure.prototype.send_message = function(type, properties) {
properties['type'] = type;
properties['figure_id'] = this.id;
this.ws.send(JSON.stringify(properties));
}

mpl.figure.prototype.send_draw_message = function() {
if (!this.waiting) {
this.waiting = true;
this.ws.send(JSON.stringify({type: "draw", figure_id: this.id}));
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
var format_dropdown = fig.format_dropdown;
var format = format_dropdown.options[format_dropdown.selectedIndex].value;
fig.ondownload(fig, format);
}

mpl.figure.prototype.handle_resize = function(fig, msg) {
var size = msg['size'];
if (size[0] != fig.canvas.width || size[1] != fig.canvas.height) {
fig._resize_canvas(size[0], size[1]);
fig.send_message("refresh", {});
};
}

mpl.figure.prototype.handle_rubberband = function(fig, msg) {
var x0 = msg['x0'];
var y0 = fig.canvas.height - msg['y0'];
var x1 = msg['x1'];
var y1 = fig.canvas.height - msg['y1'];
x0 = Math.floor(x0) + 0.5;
y0 = Math.floor(y0) + 0.5;
x1 = Math.floor(x1) + 0.5;
y1 = Math.floor(y1) + 0.5;
var min_x = Math.min(x0, x1);
var min_y = Math.min(y0, y1);
var width = Math.abs(x1 - x0);
var height = Math.abs(y1 - y0);

fig.rubberband_context.clearRect(
0, 0, fig.canvas.width, fig.canvas.height);

fig.rubberband_context.strokeRect(min_x, min_y, width, height);
}

mpl.figure.prototype.handle_figure_label = function(fig, msg) {
// Updates the figure title.
fig.header.textContent = msg['label'];
}

mpl.figure.prototype.handle_cursor = function(fig, msg) {
var cursor = msg['cursor'];
switch(cursor)
{
case 0:
cursor = 'pointer';
break;
case 1:
cursor = 'default';
break;
case 2:
cursor = 'crosshair';
break;
case 3:
cursor = 'move';
break;
}
fig.rubberband_canvas.style.cursor = cursor;
}

mpl.figure.prototype.handle_message = function(fig, msg) {
fig.message.textContent = msg['message'];
}

mpl.figure.prototype.handle_draw = function(fig, msg) {
// Request the server to send over a new figure.
fig.send_draw_message();
}

mpl.figure.prototype.handle_image_mode = function(fig, msg) {
fig.image_mode = msg['mode'];
}

mpl.figure.prototype.updated_canvas_event = function() {
// Called whenever the canvas gets updated.
this.send_message("ack", {});
}

// A function to construct a web socket function for onmessage handling.
// Called in the figure constructor.
mpl.figure.prototype._make_on_message_function = function(fig) {
return function socket_on_message(evt) {
if (evt.data instanceof Blob) {
/* FIXME: We get "Resource interpreted as Image but
* transferred with MIME type text/plain:" errors on
* Chrome.  But how to set the MIME type?  It doesn't seem
* to be part of the websocket stream */
evt.data.type = "image/png";

/* Free the memory for the previous frames */
if (fig.imageObj.src) {
(window.URL || window.webkitURL).revokeObjectURL(
fig.imageObj.src);
}

fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(
evt.data);
fig.updated_canvas_event();
fig.waiting = false;
return;
}
else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == "data:image/png;base64") {
fig.imageObj.src = evt.data;
fig.updated_canvas_event();
fig.waiting = false;
return;
}

var msg = JSON.parse(evt.data);
var msg_type = msg['type'];

// Call the  "handle_{type}" callback, which takes
// the figure and JSON message as its only arguments.
try {
var callback = fig["handle_" + msg_type];
} catch (e) {
console.log("No handler for the '" + msg_type + "' message type: ", msg);
return;
}

if (callback) {
try {
// console.log("Handling '" + msg_type + "' message: ", msg);
callback(fig, msg);
} catch (e) {
console.log("Exception inside the 'handler_" + msg_type + "' callback:", e, e.stack, msg);
}
}
};
}

// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas
mpl.findpos = function(e) {
//this section is from http://www.quirksmode.org/js/events_properties.html
var targ;
if (!e)
e = window.event;
if (e.target)
targ = e.target;
else if (e.srcElement)
targ = e.srcElement;
if (targ.nodeType == 3) // defeat Safari bug
targ = targ.parentNode;

// jQuery normalizes the pageX and pageY
// pageX,Y are the mouse positions relative to the document
// offset() returns the position of the element relative to the document
var x = e.pageX - \$(targ).offset().left;
var y = e.pageY - \$(targ).offset().top;

return {"x": x, "y": y};
};

/*
* return a copy of an object with only non-object keys
* we need this to avoid circular references
* http://stackoverflow.com/a/24161582/3208463
*/
function simpleKeys (original) {
return Object.keys(original).reduce(function (obj, key) {
if (typeof original[key] !== 'object')
obj[key] = original[key]
return obj;
}, {});
}

mpl.figure.prototype.mouse_event = function(event, name) {
var canvas_pos = mpl.findpos(event)

if (name === 'button_press')
{
this.canvas.focus();
this.canvas_div.focus();
}

var x = canvas_pos.x;
var y = canvas_pos.y;

this.send_message(name, {x: x, y: y, button: event.button,
step: event.step,
guiEvent: simpleKeys(event)});

/* This prevents the web browser from automatically changing to
* the text insertion cursor when the button is pressed.  We want
* to control all of the cursor setting manually through the
* 'cursor' event from matplotlib */
event.preventDefault();
return false;
}

mpl.figure.prototype._key_event_extra = function(event, name) {
// Handle any extra behaviour associated with a key event
}

mpl.figure.prototype.key_event = function(event, name) {

// Prevent repeat events
if (name == 'key_press')
{
if (event.which === this._key)
return;
else
this._key = event.which;
}
if (name == 'key_release')
this._key = null;

var value = '';
if (event.ctrlKey && event.which != 17)
value += "ctrl+";
if (event.altKey && event.which != 18)
value += "alt+";
if (event.shiftKey && event.which != 16)
value += "shift+";

value += 'k';
value += event.which.toString();

this._key_event_extra(event, name);

this.send_message(name, {key: value,
guiEvent: simpleKeys(event)});
return false;
}

mpl.figure.prototype.toolbar_button_onclick = function(name) {
if (name == 'download') {
this.handle_save(this, null);
} else {
this.send_message("toolbar_button", {name: name});
}
};

mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {
this.message.textContent = tooltip;
};
mpl.toolbar_items = [["Home", "Reset original view", "fa fa-home icon-home", "home"], ["Back", "Back to  previous view", "fa fa-arrow-left icon-arrow-left", "back"], ["Forward", "Forward to next view", "fa fa-arrow-right icon-arrow-right", "forward"], ["", "", "", ""], ["Pan", "Pan axes with left mouse, zoom with right", "fa fa-arrows icon-move", "pan"], ["Zoom", "Zoom to rectangle", "fa fa-square-o icon-check-empty", "zoom"], ["", "", "", ""], ["Download", "Download plot", "fa fa-floppy-o icon-save", "download"]];

mpl.extensions = ["eps", "jpeg", "pdf", "png", "ps", "raw", "svg", "tif"];

mpl.default_extension = "png";var comm_websocket_adapter = function(comm) {
// Create a "websocket"-like object which calls the given IPython comm
// object with the appropriate methods. Currently this is a non binary
// socket, so there is still some room for performance tuning.
var ws = {};

ws.close = function() {
comm.close()
};
ws.send = function(m) {
//console.log('sending', m);
comm.send(m);
};
// Register the callback with on_msg.
comm.on_msg(function(msg) {
//console.log('receiving', msg['content']['data'], msg);
// Pass the mpl event to the overriden (by mpl) onmessage function.
ws.onmessage(msg['content']['data'])
});
return ws;
}

mpl.mpl_figure_comm = function(comm, msg) {
// This is the function which gets called when the mpl process
// starts-up an IPython Comm through the "matplotlib" channel.

var id = msg.content.data.id;
// Get hold of the div created by the display call when the Comm
// socket was opened in Python.
var element = \$("#" + id);
var ws_proxy = comm_websocket_adapter(comm)

function ondownload(figure, format) {
window.open(figure.imageObj.src);
}

var fig = new mpl.figure(id, ws_proxy,
ondownload,
element.get(0));

// Call onopen now - mpl needs it, as it is assuming we've passed it a real
// web socket which is closed, not our websocket->open comm proxy.
ws_proxy.onopen();

fig.parent_element = element.get(0);
fig.cell_info = mpl.find_output_cell("<div id='" + id + "'></div>");
if (!fig.cell_info) {
console.error("Failed to find cell for figure", id, fig);
return;
}

var output_index = fig.cell_info[2]
var cell = fig.cell_info[0];

};

mpl.figure.prototype.handle_close = function(fig, msg) {
fig.root.unbind('remove')

// Update the output cell to use the data from the current canvas.
fig.push_to_output();
var dataURL = fig.canvas.toDataURL();
// Re-enable the keyboard manager in IPython - without this line, in FF,
// the notebook keyboard shortcuts fail.
IPython.keyboard_manager.enable()
\$(fig.parent_element).html('<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">');
fig.close_ws(fig, msg);
}

mpl.figure.prototype.close_ws = function(fig, msg){
fig.send_message('closing', msg);
// fig.ws.close()
}

mpl.figure.prototype.push_to_output = function(remove_interactive) {
// Turn the data on the canvas into data in the output cell.
var dataURL = this.canvas.toDataURL();
this.cell_info[1]['text/html'] = '<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">';
}

mpl.figure.prototype.updated_canvas_event = function() {
// Tell IPython that the notebook contents must change.
IPython.notebook.set_dirty(true);
this.send_message("ack", {});
var fig = this;
// Wait a second, then push the new image to the DOM so
// that it is saved nicely (might be nice to debounce this).
setTimeout(function () { fig.push_to_output() }, 1000);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items){
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) { continue; };

var button = \$('<button class="btn btn-default" href="#" title="' + name + '"><i class="fa ' + image + ' fa-lg"></i></button>');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);
nav_element.append(button);
}

// Add the status bar.
var status_bar = \$('<span class="mpl-message" style="text-align:right; float: right;"/>');
nav_element.append(status_bar);
this.message = status_bar[0];

// Add the close button to the window.
var buttongrp = \$('<div class="btn-group inline pull-right"></div>');
var button = \$('<button class="btn btn-mini btn-primary" href="#" title="Stop Interaction"><i class="fa fa-power-off icon-remove icon-large"></i></button>');
button.click(function (evt) { fig.handle_close(fig, {}); } );
button.mouseover('Stop Interaction', toolbar_mouse_event);
buttongrp.append(button);
var titlebar = this.root.find(\$('.ui-dialog-titlebar'));
titlebar.prepend(buttongrp);
}

mpl.figure.prototype._root_extra_style = function(el){
var fig = this
el.on("remove", function(){
fig.close_ws(fig, {});
});
}

mpl.figure.prototype._canvas_extra_style = function(el){
// this is important to make the div 'focusable
el.attr('tabindex', 0)
// reach out to IPython and tell the keyboard manager to turn it's self
// off when our div gets focus

// location in version 3
if (IPython.notebook.keyboard_manager) {
IPython.notebook.keyboard_manager.register_events(el);
}
else {
// location in version 2
IPython.keyboard_manager.register_events(el);
}

}

mpl.figure.prototype._key_event_extra = function(event, name) {
var manager = IPython.notebook.keyboard_manager;
if (!manager)
manager = IPython.keyboard_manager;

// Check for shift+enter
if (event.shiftKey && event.which == 13) {
this.canvas_div.blur();
event.shiftKey = false;
// Send a "J" for go to next cell
event.which = 74;
event.keyCode = 74;
manager.command_mode();
manager.handle_keydown(event);
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
fig.ondownload(fig, null);
}

mpl.find_output_cell = function(html_output) {
// Return the cell and output element which can be found *uniquely* in the notebook.
// Note - this is a bit hacky, but it is done because the "notebook_saving.Notebook"
// IPython event is triggered only after the cells have been serialised, which for
// our purposes (turning an active figure into a static one), is too late.
var cells = IPython.notebook.get_cells();
var ncells = cells.length;
for (var i=0; i<ncells; i++) {
var cell = cells[i];
if (cell.cell_type === 'code'){
for (var j=0; j<cell.output_area.outputs.length; j++) {
var data = cell.output_area.outputs[j];
if (data.data) {
// IPython >= 3 moved mimebundle to data attribute of output
data = data.data;
}
if (data['text/html'] == html_output) {
return [cell, data, j];
}
}
}
}
}

// Register the function which deals with the matplotlib target/channel.
// The kernel may be null if the page has been refreshed.
if (IPython.notebook.kernel != null) {
IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);
}

``````

## Plot electron and x-ray energy deposited in photoactive layer of CCD

``````

In [20]:

plt.subplots(figsize=(12,6))
plt.plot(np.multiply(KEsim,10**3),np.multiply(EelAbsorbedCCD,10**3),linewidth=3,color='r')
plt.plot(np.multiply(KEsim,10**3),np.multiply(EphAbsorbedCCD,10**3),linewidth=3,color='g')
plt.xlabel('Kinetic Energy (keV)')
plt.ylabel('Energy (keV)')
plt.xlim(150,3000)
plt.title('Energy deposited in photoactive layer of CCD due to single electron')
plt.tight_layout()

``````
``````

var element = \$('#559face4-0ba3-4194-9d93-6233d407ffb0');
/* Put everything inside the global mpl namespace */
window.mpl = {};

mpl.get_websocket_type = function() {
if (typeof(WebSocket) !== 'undefined') {
return WebSocket;
} else if (typeof(MozWebSocket) !== 'undefined') {
return MozWebSocket;
} else {
alert('Your browser does not have WebSocket support.' +
'Please try Chrome, Safari or Firefox ≥ 6. ' +
'Firefox 4 and 5 are also supported but you ' +
'have to enable WebSockets in about:config.');
};
}

mpl.figure = function(figure_id, websocket, ondownload, parent_element) {
this.id = figure_id;

this.ws = websocket;

this.supports_binary = (this.ws.binaryType != undefined);

if (!this.supports_binary) {
var warnings = document.getElementById("mpl-warnings");
if (warnings) {
warnings.style.display = 'block';
warnings.textContent = (
"This browser does not support binary websocket messages. " +
"Performance may be slow.");
}
}

this.imageObj = new Image();

this.context = undefined;
this.message = undefined;
this.canvas = undefined;
this.rubberband_canvas = undefined;
this.rubberband_context = undefined;
this.format_dropdown = undefined;

this.image_mode = 'full';

this.root = \$('<div/>');
this._root_extra_style(this.root)
this.root.attr('style', 'display: inline-block');

\$(parent_element).append(this.root);

this._init_header(this);
this._init_canvas(this);
this._init_toolbar(this);

var fig = this;

this.waiting = false;

this.ws.onopen =  function () {
fig.send_message("supports_binary", {value: fig.supports_binary});
fig.send_message("send_image_mode", {});
fig.send_message("refresh", {});
}

this.imageObj.onload = function() {
if (fig.image_mode == 'full') {
// Full images could contain transparency (where diff images
// almost always do), so we need to clear the canvas so that
// there is no ghosting.
fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);
}
fig.context.drawImage(fig.imageObj, 0, 0);
};

this.imageObj.onunload = function() {
this.ws.close();
}

this.ws.onmessage = this._make_on_message_function(this);

this.ondownload = ondownload;
}

mpl.figure.prototype._init_header = function() {
var titlebar = \$(
'<div class="ui-dialog-titlebar ui-widget-header ui-corner-all ' +
'ui-helper-clearfix"/>');
var titletext = \$(
'<div class="ui-dialog-title" style="width: 100%; ' +
'text-align: center; padding: 3px;"/>');
titlebar.append(titletext)
this.root.append(titlebar);
this.header = titletext[0];
}

mpl.figure.prototype._canvas_extra_style = function(canvas_div) {

}

mpl.figure.prototype._root_extra_style = function(canvas_div) {

}

mpl.figure.prototype._init_canvas = function() {
var fig = this;

var canvas_div = \$('<div/>');

canvas_div.attr('style', 'position: relative; clear: both; outline: 0');

function canvas_keyboard_event(event) {
return fig.key_event(event, event['data']);
}

canvas_div.keydown('key_press', canvas_keyboard_event);
canvas_div.keyup('key_release', canvas_keyboard_event);
this.canvas_div = canvas_div
this._canvas_extra_style(canvas_div)
this.root.append(canvas_div);

var canvas = \$('<canvas/>');
canvas.addClass('mpl-canvas');
canvas.attr('style', "left: 0; top: 0; z-index: 0; outline: 0")

this.canvas = canvas[0];
this.context = canvas[0].getContext("2d");

var rubberband = \$('<canvas/>');
rubberband.attr('style', "position: absolute; left: 0; top: 0; z-index: 1;")

var pass_mouse_events = true;

canvas_div.resizable({
start: function(event, ui) {
pass_mouse_events = false;
},
resize: function(event, ui) {
fig.request_resize(ui.size.width, ui.size.height);
},
stop: function(event, ui) {
pass_mouse_events = true;
fig.request_resize(ui.size.width, ui.size.height);
},
});

function mouse_event_fn(event) {
if (pass_mouse_events)
return fig.mouse_event(event, event['data']);
}

rubberband.mousedown('button_press', mouse_event_fn);
rubberband.mouseup('button_release', mouse_event_fn);
// Throttle sequential mouse events to 1 every 20ms.
rubberband.mousemove('motion_notify', mouse_event_fn);

rubberband.mouseenter('figure_enter', mouse_event_fn);
rubberband.mouseleave('figure_leave', mouse_event_fn);

canvas_div.on("wheel", function (event) {
event = event.originalEvent;
event['data'] = 'scroll'
if (event.deltaY < 0) {
event.step = 1;
} else {
event.step = -1;
}
mouse_event_fn(event);
});

canvas_div.append(canvas);
canvas_div.append(rubberband);

this.rubberband = rubberband;
this.rubberband_canvas = rubberband[0];
this.rubberband_context = rubberband[0].getContext("2d");
this.rubberband_context.strokeStyle = "#000000";

this._resize_canvas = function(width, height) {
// Keep the size of the canvas, canvas container, and rubber band
// canvas in synch.
canvas_div.css('width', width)
canvas_div.css('height', height)

canvas.attr('width', width);
canvas.attr('height', height);

rubberband.attr('width', width);
rubberband.attr('height', height);
}

// Set the figure to an initial 600x600px, this will subsequently be updated
// upon first draw.
this._resize_canvas(600, 600);

// Disable right mouse context menu.
\$(this.rubberband_canvas).bind("contextmenu",function(e){
return false;
});

function set_focus () {
canvas.focus();
canvas_div.focus();
}

window.setTimeout(set_focus, 100);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items) {
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) {
// put a spacer in here.
continue;
}
var button = \$('<button/>');
button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +
'ui-button-icon-only');
button.attr('role', 'button');
button.attr('aria-disabled', 'false');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);

var icon_img = \$('<span/>');
icon_img.addClass('ui-button-icon-primary ui-icon');
icon_img.addClass(image);
icon_img.addClass('ui-corner-all');

var tooltip_span = \$('<span/>');
tooltip_span.addClass('ui-button-text');
tooltip_span.html(tooltip);

button.append(icon_img);
button.append(tooltip_span);

nav_element.append(button);
}

var fmt_picker_span = \$('<span/>');

var fmt_picker = \$('<select/>');
fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');
fmt_picker_span.append(fmt_picker);
nav_element.append(fmt_picker_span);
this.format_dropdown = fmt_picker[0];

for (var ind in mpl.extensions) {
var fmt = mpl.extensions[ind];
var option = \$(
'<option/>', {selected: fmt === mpl.default_extension}).html(fmt);
fmt_picker.append(option)
}

// Add hover states to the ui-buttons
\$( ".ui-button" ).hover(
function() { \$(this).addClass("ui-state-hover");},
function() { \$(this).removeClass("ui-state-hover");}
);

var status_bar = \$('<span class="mpl-message"/>');
nav_element.append(status_bar);
this.message = status_bar[0];
}

mpl.figure.prototype.request_resize = function(x_pixels, y_pixels) {
// Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,
// which will in turn request a refresh of the image.
this.send_message('resize', {'width': x_pixels, 'height': y_pixels});
}

mpl.figure.prototype.send_message = function(type, properties) {
properties['type'] = type;
properties['figure_id'] = this.id;
this.ws.send(JSON.stringify(properties));
}

mpl.figure.prototype.send_draw_message = function() {
if (!this.waiting) {
this.waiting = true;
this.ws.send(JSON.stringify({type: "draw", figure_id: this.id}));
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
var format_dropdown = fig.format_dropdown;
var format = format_dropdown.options[format_dropdown.selectedIndex].value;
fig.ondownload(fig, format);
}

mpl.figure.prototype.handle_resize = function(fig, msg) {
var size = msg['size'];
if (size[0] != fig.canvas.width || size[1] != fig.canvas.height) {
fig._resize_canvas(size[0], size[1]);
fig.send_message("refresh", {});
};
}

mpl.figure.prototype.handle_rubberband = function(fig, msg) {
var x0 = msg['x0'];
var y0 = fig.canvas.height - msg['y0'];
var x1 = msg['x1'];
var y1 = fig.canvas.height - msg['y1'];
x0 = Math.floor(x0) + 0.5;
y0 = Math.floor(y0) + 0.5;
x1 = Math.floor(x1) + 0.5;
y1 = Math.floor(y1) + 0.5;
var min_x = Math.min(x0, x1);
var min_y = Math.min(y0, y1);
var width = Math.abs(x1 - x0);
var height = Math.abs(y1 - y0);

fig.rubberband_context.clearRect(
0, 0, fig.canvas.width, fig.canvas.height);

fig.rubberband_context.strokeRect(min_x, min_y, width, height);
}

mpl.figure.prototype.handle_figure_label = function(fig, msg) {
// Updates the figure title.
fig.header.textContent = msg['label'];
}

mpl.figure.prototype.handle_cursor = function(fig, msg) {
var cursor = msg['cursor'];
switch(cursor)
{
case 0:
cursor = 'pointer';
break;
case 1:
cursor = 'default';
break;
case 2:
cursor = 'crosshair';
break;
case 3:
cursor = 'move';
break;
}
fig.rubberband_canvas.style.cursor = cursor;
}

mpl.figure.prototype.handle_message = function(fig, msg) {
fig.message.textContent = msg['message'];
}

mpl.figure.prototype.handle_draw = function(fig, msg) {
// Request the server to send over a new figure.
fig.send_draw_message();
}

mpl.figure.prototype.handle_image_mode = function(fig, msg) {
fig.image_mode = msg['mode'];
}

mpl.figure.prototype.updated_canvas_event = function() {
// Called whenever the canvas gets updated.
this.send_message("ack", {});
}

// A function to construct a web socket function for onmessage handling.
// Called in the figure constructor.
mpl.figure.prototype._make_on_message_function = function(fig) {
return function socket_on_message(evt) {
if (evt.data instanceof Blob) {
/* FIXME: We get "Resource interpreted as Image but
* transferred with MIME type text/plain:" errors on
* Chrome.  But how to set the MIME type?  It doesn't seem
* to be part of the websocket stream */
evt.data.type = "image/png";

/* Free the memory for the previous frames */
if (fig.imageObj.src) {
(window.URL || window.webkitURL).revokeObjectURL(
fig.imageObj.src);
}

fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(
evt.data);
fig.updated_canvas_event();
fig.waiting = false;
return;
}
else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == "data:image/png;base64") {
fig.imageObj.src = evt.data;
fig.updated_canvas_event();
fig.waiting = false;
return;
}

var msg = JSON.parse(evt.data);
var msg_type = msg['type'];

// Call the  "handle_{type}" callback, which takes
// the figure and JSON message as its only arguments.
try {
var callback = fig["handle_" + msg_type];
} catch (e) {
console.log("No handler for the '" + msg_type + "' message type: ", msg);
return;
}

if (callback) {
try {
// console.log("Handling '" + msg_type + "' message: ", msg);
callback(fig, msg);
} catch (e) {
console.log("Exception inside the 'handler_" + msg_type + "' callback:", e, e.stack, msg);
}
}
};
}

// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas
mpl.findpos = function(e) {
//this section is from http://www.quirksmode.org/js/events_properties.html
var targ;
if (!e)
e = window.event;
if (e.target)
targ = e.target;
else if (e.srcElement)
targ = e.srcElement;
if (targ.nodeType == 3) // defeat Safari bug
targ = targ.parentNode;

// jQuery normalizes the pageX and pageY
// pageX,Y are the mouse positions relative to the document
// offset() returns the position of the element relative to the document
var x = e.pageX - \$(targ).offset().left;
var y = e.pageY - \$(targ).offset().top;

return {"x": x, "y": y};
};

/*
* return a copy of an object with only non-object keys
* we need this to avoid circular references
* http://stackoverflow.com/a/24161582/3208463
*/
function simpleKeys (original) {
return Object.keys(original).reduce(function (obj, key) {
if (typeof original[key] !== 'object')
obj[key] = original[key]
return obj;
}, {});
}

mpl.figure.prototype.mouse_event = function(event, name) {
var canvas_pos = mpl.findpos(event)

if (name === 'button_press')
{
this.canvas.focus();
this.canvas_div.focus();
}

var x = canvas_pos.x;
var y = canvas_pos.y;

this.send_message(name, {x: x, y: y, button: event.button,
step: event.step,
guiEvent: simpleKeys(event)});

/* This prevents the web browser from automatically changing to
* the text insertion cursor when the button is pressed.  We want
* to control all of the cursor setting manually through the
* 'cursor' event from matplotlib */
event.preventDefault();
return false;
}

mpl.figure.prototype._key_event_extra = function(event, name) {
// Handle any extra behaviour associated with a key event
}

mpl.figure.prototype.key_event = function(event, name) {

// Prevent repeat events
if (name == 'key_press')
{
if (event.which === this._key)
return;
else
this._key = event.which;
}
if (name == 'key_release')
this._key = null;

var value = '';
if (event.ctrlKey && event.which != 17)
value += "ctrl+";
if (event.altKey && event.which != 18)
value += "alt+";
if (event.shiftKey && event.which != 16)
value += "shift+";

value += 'k';
value += event.which.toString();

this._key_event_extra(event, name);

this.send_message(name, {key: value,
guiEvent: simpleKeys(event)});
return false;
}

mpl.figure.prototype.toolbar_button_onclick = function(name) {
if (name == 'download') {
this.handle_save(this, null);
} else {
this.send_message("toolbar_button", {name: name});
}
};

mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {
this.message.textContent = tooltip;
};
mpl.toolbar_items = [["Home", "Reset original view", "fa fa-home icon-home", "home"], ["Back", "Back to  previous view", "fa fa-arrow-left icon-arrow-left", "back"], ["Forward", "Forward to next view", "fa fa-arrow-right icon-arrow-right", "forward"], ["", "", "", ""], ["Pan", "Pan axes with left mouse, zoom with right", "fa fa-arrows icon-move", "pan"], ["Zoom", "Zoom to rectangle", "fa fa-square-o icon-check-empty", "zoom"], ["", "", "", ""], ["Download", "Download plot", "fa fa-floppy-o icon-save", "download"]];

mpl.extensions = ["eps", "jpeg", "pdf", "png", "ps", "raw", "svg", "tif"];

mpl.default_extension = "png";var comm_websocket_adapter = function(comm) {
// Create a "websocket"-like object which calls the given IPython comm
// object with the appropriate methods. Currently this is a non binary
// socket, so there is still some room for performance tuning.
var ws = {};

ws.close = function() {
comm.close()
};
ws.send = function(m) {
//console.log('sending', m);
comm.send(m);
};
// Register the callback with on_msg.
comm.on_msg(function(msg) {
//console.log('receiving', msg['content']['data'], msg);
// Pass the mpl event to the overriden (by mpl) onmessage function.
ws.onmessage(msg['content']['data'])
});
return ws;
}

mpl.mpl_figure_comm = function(comm, msg) {
// This is the function which gets called when the mpl process
// starts-up an IPython Comm through the "matplotlib" channel.

var id = msg.content.data.id;
// Get hold of the div created by the display call when the Comm
// socket was opened in Python.
var element = \$("#" + id);
var ws_proxy = comm_websocket_adapter(comm)

function ondownload(figure, format) {
window.open(figure.imageObj.src);
}

var fig = new mpl.figure(id, ws_proxy,
ondownload,
element.get(0));

// Call onopen now - mpl needs it, as it is assuming we've passed it a real
// web socket which is closed, not our websocket->open comm proxy.
ws_proxy.onopen();

fig.parent_element = element.get(0);
fig.cell_info = mpl.find_output_cell("<div id='" + id + "'></div>");
if (!fig.cell_info) {
console.error("Failed to find cell for figure", id, fig);
return;
}

var output_index = fig.cell_info[2]
var cell = fig.cell_info[0];

};

mpl.figure.prototype.handle_close = function(fig, msg) {
fig.root.unbind('remove')

// Update the output cell to use the data from the current canvas.
fig.push_to_output();
var dataURL = fig.canvas.toDataURL();
// Re-enable the keyboard manager in IPython - without this line, in FF,
// the notebook keyboard shortcuts fail.
IPython.keyboard_manager.enable()
\$(fig.parent_element).html('<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">');
fig.close_ws(fig, msg);
}

mpl.figure.prototype.close_ws = function(fig, msg){
fig.send_message('closing', msg);
// fig.ws.close()
}

mpl.figure.prototype.push_to_output = function(remove_interactive) {
// Turn the data on the canvas into data in the output cell.
var dataURL = this.canvas.toDataURL();
this.cell_info[1]['text/html'] = '<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">';
}

mpl.figure.prototype.updated_canvas_event = function() {
// Tell IPython that the notebook contents must change.
IPython.notebook.set_dirty(true);
this.send_message("ack", {});
var fig = this;
// Wait a second, then push the new image to the DOM so
// that it is saved nicely (might be nice to debounce this).
setTimeout(function () { fig.push_to_output() }, 1000);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items){
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) { continue; };

var button = \$('<button class="btn btn-default" href="#" title="' + name + '"><i class="fa ' + image + ' fa-lg"></i></button>');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);
nav_element.append(button);
}

// Add the status bar.
var status_bar = \$('<span class="mpl-message" style="text-align:right; float: right;"/>');
nav_element.append(status_bar);
this.message = status_bar[0];

// Add the close button to the window.
var buttongrp = \$('<div class="btn-group inline pull-right"></div>');
var button = \$('<button class="btn btn-mini btn-primary" href="#" title="Stop Interaction"><i class="fa fa-power-off icon-remove icon-large"></i></button>');
button.click(function (evt) { fig.handle_close(fig, {}); } );
button.mouseover('Stop Interaction', toolbar_mouse_event);
buttongrp.append(button);
var titlebar = this.root.find(\$('.ui-dialog-titlebar'));
titlebar.prepend(buttongrp);
}

mpl.figure.prototype._root_extra_style = function(el){
var fig = this
el.on("remove", function(){
fig.close_ws(fig, {});
});
}

mpl.figure.prototype._canvas_extra_style = function(el){
// this is important to make the div 'focusable
el.attr('tabindex', 0)
// reach out to IPython and tell the keyboard manager to turn it's self
// off when our div gets focus

// location in version 3
if (IPython.notebook.keyboard_manager) {
IPython.notebook.keyboard_manager.register_events(el);
}
else {
// location in version 2
IPython.keyboard_manager.register_events(el);
}

}

mpl.figure.prototype._key_event_extra = function(event, name) {
var manager = IPython.notebook.keyboard_manager;
if (!manager)
manager = IPython.keyboard_manager;

// Check for shift+enter
if (event.shiftKey && event.which == 13) {
this.canvas_div.blur();
event.shiftKey = false;
// Send a "J" for go to next cell
event.which = 74;
event.keyCode = 74;
manager.command_mode();
manager.handle_keydown(event);
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
fig.ondownload(fig, null);
}

mpl.find_output_cell = function(html_output) {
// Return the cell and output element which can be found *uniquely* in the notebook.
// Note - this is a bit hacky, but it is done because the "notebook_saving.Notebook"
// IPython event is triggered only after the cells have been serialised, which for
// our purposes (turning an active figure into a static one), is too late.
var cells = IPython.notebook.get_cells();
var ncells = cells.length;
for (var i=0; i<ncells; i++) {
var cell = cells[i];
if (cell.cell_type === 'code'){
for (var j=0; j<cell.output_area.outputs.length; j++) {
var data = cell.output_area.outputs[j];
if (data.data) {
// IPython >= 3 moved mimebundle to data attribute of output
data = data.data;
}
if (data['text/html'] == html_output) {
return [cell, data, j];
}
}
}
}
}

// Register the function which deals with the matplotlib target/channel.
// The kernel may be null if the page has been refreshed.
if (IPython.notebook.kernel != null) {
IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);
}

``````

## No lanex case

``````

In [21]:

# plt.subplots(figsize=(12,6))
# plt.plot(np.multiply(KEsim,10**3),np.multiply(EelAbsorbedCCD_No_Lanex,10**3),linewidth=3,color='r')
# plt.plot(np.multiply(KEsim,10**3),np.multiply(EphAbsorbedCCD_No_Lanex,10**3),linewidth=3,color='g')
# plt.xlabel('Kinetic Energy (keV)')
# plt.ylabel('Energy (keV)')
# plt.title('Energy deposited in photoactive layer of CCD due to single electron')
# plt.subplots_adjust(left=0.12,bottom=0.14) #Adjust spacing to prevent clipping of x and y labels
# plt.show()

``````

## Plot CCD signal due to photons and electrons

``````

In [23]:

sns.set(context='poster',font_scale=1.5)
sns.set_style("darkgrid")
sns.set_palette(palette='deep')
sns.set_color_codes(palette='deep')

Qph = 0.4 #Quantum efficiency for 545 nm photons
Energy_eh_pair = 3.65 #Energy needed to generate electron-hole pair in Si in eV
Total_Signal = np.multiply(photonNumberArray,Qph) + np.multiply(EelAbsorbedCCD,10**6/Energy_eh_pair) + \
np.multiply(EphAbsorbedCCD,10**6/Energy_eh_pair)
Total_Relative_Signal = Total_Signal/np.max(Total_Signal)
KEarray = np.multiply(KEsim,1.0)
EspecCalibration = np.vstack((KEarray,Total_Relative_Signal))

plt.subplots(figsize=(8,6))

plt.plot(np.multiply(KEsim,1.0),np.multiply(photonNumberArray,Qph),linewidth=2,color='b',label='Photons')
plt.plot(np.multiply(KEsim,1.0),np.multiply(EelAbsorbedCCD,10**6/Energy_eh_pair),linewidth=2,color='r',label='Electrons')
#plt.plot(np.multiply(KEsim,10**3),np.multiply(EphAbsorbedCCD,10**6/Energy_eh_pair),linewidth=2,color='g',label='X-rays')
plt.plot(EspecCalibration[0],np.multiply(np.max(Total_Signal),EspecCalibration[1]),linewidth=2,color='k',label='Total')
#plt.plot(np.multiply(KEsim,1.0),np.multiply(EelAbsorbedCCD_No_Lanex,10**6/Energy_eh_pair),linewidth=2,color='g',label='No Lanex')

plt.xlabel('Electron Energy (MeV)')
plt.ylabel('Number of Electron-Hole Pairs')
plt.xlim(0,3.0)
plt.ticklabel_format(style='sci', axis='y', scilimits=(0,0))
plt.title('Mean CCD signal from\nsingle incident electron')
#plt.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
plt.legend(loc=4)
plt.tight_layout()

``````
``````

/home/drake/.anaconda3/lib/python3.4/site-packages/matplotlib/__init__.py:872: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
warnings.warn(self.msg_depr % (key, alt_key))

var element = \$('#91f112eb-5096-4b5e-803f-ce2fdee4ffce');
/* Put everything inside the global mpl namespace */
window.mpl = {};

mpl.get_websocket_type = function() {
if (typeof(WebSocket) !== 'undefined') {
return WebSocket;
} else if (typeof(MozWebSocket) !== 'undefined') {
return MozWebSocket;
} else {
alert('Your browser does not have WebSocket support.' +
'Please try Chrome, Safari or Firefox ≥ 6. ' +
'Firefox 4 and 5 are also supported but you ' +
'have to enable WebSockets in about:config.');
};
}

mpl.figure = function(figure_id, websocket, ondownload, parent_element) {
this.id = figure_id;

this.ws = websocket;

this.supports_binary = (this.ws.binaryType != undefined);

if (!this.supports_binary) {
var warnings = document.getElementById("mpl-warnings");
if (warnings) {
warnings.style.display = 'block';
warnings.textContent = (
"This browser does not support binary websocket messages. " +
"Performance may be slow.");
}
}

this.imageObj = new Image();

this.context = undefined;
this.message = undefined;
this.canvas = undefined;
this.rubberband_canvas = undefined;
this.rubberband_context = undefined;
this.format_dropdown = undefined;

this.image_mode = 'full';

this.root = \$('<div/>');
this._root_extra_style(this.root)
this.root.attr('style', 'display: inline-block');

\$(parent_element).append(this.root);

this._init_header(this);
this._init_canvas(this);
this._init_toolbar(this);

var fig = this;

this.waiting = false;

this.ws.onopen =  function () {
fig.send_message("supports_binary", {value: fig.supports_binary});
fig.send_message("send_image_mode", {});
fig.send_message("refresh", {});
}

this.imageObj.onload = function() {
if (fig.image_mode == 'full') {
// Full images could contain transparency (where diff images
// almost always do), so we need to clear the canvas so that
// there is no ghosting.
fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);
}
fig.context.drawImage(fig.imageObj, 0, 0);
};

this.imageObj.onunload = function() {
this.ws.close();
}

this.ws.onmessage = this._make_on_message_function(this);

this.ondownload = ondownload;
}

mpl.figure.prototype._init_header = function() {
var titlebar = \$(
'<div class="ui-dialog-titlebar ui-widget-header ui-corner-all ' +
'ui-helper-clearfix"/>');
var titletext = \$(
'<div class="ui-dialog-title" style="width: 100%; ' +
'text-align: center; padding: 3px;"/>');
titlebar.append(titletext)
this.root.append(titlebar);
this.header = titletext[0];
}

mpl.figure.prototype._canvas_extra_style = function(canvas_div) {

}

mpl.figure.prototype._root_extra_style = function(canvas_div) {

}

mpl.figure.prototype._init_canvas = function() {
var fig = this;

var canvas_div = \$('<div/>');

canvas_div.attr('style', 'position: relative; clear: both; outline: 0');

function canvas_keyboard_event(event) {
return fig.key_event(event, event['data']);
}

canvas_div.keydown('key_press', canvas_keyboard_event);
canvas_div.keyup('key_release', canvas_keyboard_event);
this.canvas_div = canvas_div
this._canvas_extra_style(canvas_div)
this.root.append(canvas_div);

var canvas = \$('<canvas/>');
canvas.addClass('mpl-canvas');
canvas.attr('style', "left: 0; top: 0; z-index: 0; outline: 0")

this.canvas = canvas[0];
this.context = canvas[0].getContext("2d");

var rubberband = \$('<canvas/>');
rubberband.attr('style', "position: absolute; left: 0; top: 0; z-index: 1;")

var pass_mouse_events = true;

canvas_div.resizable({
start: function(event, ui) {
pass_mouse_events = false;
},
resize: function(event, ui) {
fig.request_resize(ui.size.width, ui.size.height);
},
stop: function(event, ui) {
pass_mouse_events = true;
fig.request_resize(ui.size.width, ui.size.height);
},
});

function mouse_event_fn(event) {
if (pass_mouse_events)
return fig.mouse_event(event, event['data']);
}

rubberband.mousedown('button_press', mouse_event_fn);
rubberband.mouseup('button_release', mouse_event_fn);
// Throttle sequential mouse events to 1 every 20ms.
rubberband.mousemove('motion_notify', mouse_event_fn);

rubberband.mouseenter('figure_enter', mouse_event_fn);
rubberband.mouseleave('figure_leave', mouse_event_fn);

canvas_div.on("wheel", function (event) {
event = event.originalEvent;
event['data'] = 'scroll'
if (event.deltaY < 0) {
event.step = 1;
} else {
event.step = -1;
}
mouse_event_fn(event);
});

canvas_div.append(canvas);
canvas_div.append(rubberband);

this.rubberband = rubberband;
this.rubberband_canvas = rubberband[0];
this.rubberband_context = rubberband[0].getContext("2d");
this.rubberband_context.strokeStyle = "#000000";

this._resize_canvas = function(width, height) {
// Keep the size of the canvas, canvas container, and rubber band
// canvas in synch.
canvas_div.css('width', width)
canvas_div.css('height', height)

canvas.attr('width', width);
canvas.attr('height', height);

rubberband.attr('width', width);
rubberband.attr('height', height);
}

// Set the figure to an initial 600x600px, this will subsequently be updated
// upon first draw.
this._resize_canvas(600, 600);

// Disable right mouse context menu.
\$(this.rubberband_canvas).bind("contextmenu",function(e){
return false;
});

function set_focus () {
canvas.focus();
canvas_div.focus();
}

window.setTimeout(set_focus, 100);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items) {
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) {
// put a spacer in here.
continue;
}
var button = \$('<button/>');
button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +
'ui-button-icon-only');
button.attr('role', 'button');
button.attr('aria-disabled', 'false');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);

var icon_img = \$('<span/>');
icon_img.addClass('ui-button-icon-primary ui-icon');
icon_img.addClass(image);
icon_img.addClass('ui-corner-all');

var tooltip_span = \$('<span/>');
tooltip_span.addClass('ui-button-text');
tooltip_span.html(tooltip);

button.append(icon_img);
button.append(tooltip_span);

nav_element.append(button);
}

var fmt_picker_span = \$('<span/>');

var fmt_picker = \$('<select/>');
fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');
fmt_picker_span.append(fmt_picker);
nav_element.append(fmt_picker_span);
this.format_dropdown = fmt_picker[0];

for (var ind in mpl.extensions) {
var fmt = mpl.extensions[ind];
var option = \$(
'<option/>', {selected: fmt === mpl.default_extension}).html(fmt);
fmt_picker.append(option)
}

// Add hover states to the ui-buttons
\$( ".ui-button" ).hover(
function() { \$(this).addClass("ui-state-hover");},
function() { \$(this).removeClass("ui-state-hover");}
);

var status_bar = \$('<span class="mpl-message"/>');
nav_element.append(status_bar);
this.message = status_bar[0];
}

mpl.figure.prototype.request_resize = function(x_pixels, y_pixels) {
// Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,
// which will in turn request a refresh of the image.
this.send_message('resize', {'width': x_pixels, 'height': y_pixels});
}

mpl.figure.prototype.send_message = function(type, properties) {
properties['type'] = type;
properties['figure_id'] = this.id;
this.ws.send(JSON.stringify(properties));
}

mpl.figure.prototype.send_draw_message = function() {
if (!this.waiting) {
this.waiting = true;
this.ws.send(JSON.stringify({type: "draw", figure_id: this.id}));
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
var format_dropdown = fig.format_dropdown;
var format = format_dropdown.options[format_dropdown.selectedIndex].value;
fig.ondownload(fig, format);
}

mpl.figure.prototype.handle_resize = function(fig, msg) {
var size = msg['size'];
if (size[0] != fig.canvas.width || size[1] != fig.canvas.height) {
fig._resize_canvas(size[0], size[1]);
fig.send_message("refresh", {});
};
}

mpl.figure.prototype.handle_rubberband = function(fig, msg) {
var x0 = msg['x0'];
var y0 = fig.canvas.height - msg['y0'];
var x1 = msg['x1'];
var y1 = fig.canvas.height - msg['y1'];
x0 = Math.floor(x0) + 0.5;
y0 = Math.floor(y0) + 0.5;
x1 = Math.floor(x1) + 0.5;
y1 = Math.floor(y1) + 0.5;
var min_x = Math.min(x0, x1);
var min_y = Math.min(y0, y1);
var width = Math.abs(x1 - x0);
var height = Math.abs(y1 - y0);

fig.rubberband_context.clearRect(
0, 0, fig.canvas.width, fig.canvas.height);

fig.rubberband_context.strokeRect(min_x, min_y, width, height);
}

mpl.figure.prototype.handle_figure_label = function(fig, msg) {
// Updates the figure title.
fig.header.textContent = msg['label'];
}

mpl.figure.prototype.handle_cursor = function(fig, msg) {
var cursor = msg['cursor'];
switch(cursor)
{
case 0:
cursor = 'pointer';
break;
case 1:
cursor = 'default';
break;
case 2:
cursor = 'crosshair';
break;
case 3:
cursor = 'move';
break;
}
fig.rubberband_canvas.style.cursor = cursor;
}

mpl.figure.prototype.handle_message = function(fig, msg) {
fig.message.textContent = msg['message'];
}

mpl.figure.prototype.handle_draw = function(fig, msg) {
// Request the server to send over a new figure.
fig.send_draw_message();
}

mpl.figure.prototype.handle_image_mode = function(fig, msg) {
fig.image_mode = msg['mode'];
}

mpl.figure.prototype.updated_canvas_event = function() {
// Called whenever the canvas gets updated.
this.send_message("ack", {});
}

// A function to construct a web socket function for onmessage handling.
// Called in the figure constructor.
mpl.figure.prototype._make_on_message_function = function(fig) {
return function socket_on_message(evt) {
if (evt.data instanceof Blob) {
/* FIXME: We get "Resource interpreted as Image but
* transferred with MIME type text/plain:" errors on
* Chrome.  But how to set the MIME type?  It doesn't seem
* to be part of the websocket stream */
evt.data.type = "image/png";

/* Free the memory for the previous frames */
if (fig.imageObj.src) {
(window.URL || window.webkitURL).revokeObjectURL(
fig.imageObj.src);
}

fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(
evt.data);
fig.updated_canvas_event();
fig.waiting = false;
return;
}
else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == "data:image/png;base64") {
fig.imageObj.src = evt.data;
fig.updated_canvas_event();
fig.waiting = false;
return;
}

var msg = JSON.parse(evt.data);
var msg_type = msg['type'];

// Call the  "handle_{type}" callback, which takes
// the figure and JSON message as its only arguments.
try {
var callback = fig["handle_" + msg_type];
} catch (e) {
console.log("No handler for the '" + msg_type + "' message type: ", msg);
return;
}

if (callback) {
try {
// console.log("Handling '" + msg_type + "' message: ", msg);
callback(fig, msg);
} catch (e) {
console.log("Exception inside the 'handler_" + msg_type + "' callback:", e, e.stack, msg);
}
}
};
}

// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas
mpl.findpos = function(e) {
//this section is from http://www.quirksmode.org/js/events_properties.html
var targ;
if (!e)
e = window.event;
if (e.target)
targ = e.target;
else if (e.srcElement)
targ = e.srcElement;
if (targ.nodeType == 3) // defeat Safari bug
targ = targ.parentNode;

// jQuery normalizes the pageX and pageY
// pageX,Y are the mouse positions relative to the document
// offset() returns the position of the element relative to the document
var x = e.pageX - \$(targ).offset().left;
var y = e.pageY - \$(targ).offset().top;

return {"x": x, "y": y};
};

/*
* return a copy of an object with only non-object keys
* we need this to avoid circular references
* http://stackoverflow.com/a/24161582/3208463
*/
function simpleKeys (original) {
return Object.keys(original).reduce(function (obj, key) {
if (typeof original[key] !== 'object')
obj[key] = original[key]
return obj;
}, {});
}

mpl.figure.prototype.mouse_event = function(event, name) {
var canvas_pos = mpl.findpos(event)

if (name === 'button_press')
{
this.canvas.focus();
this.canvas_div.focus();
}

var x = canvas_pos.x;
var y = canvas_pos.y;

this.send_message(name, {x: x, y: y, button: event.button,
step: event.step,
guiEvent: simpleKeys(event)});

/* This prevents the web browser from automatically changing to
* the text insertion cursor when the button is pressed.  We want
* to control all of the cursor setting manually through the
* 'cursor' event from matplotlib */
event.preventDefault();
return false;
}

mpl.figure.prototype._key_event_extra = function(event, name) {
// Handle any extra behaviour associated with a key event
}

mpl.figure.prototype.key_event = function(event, name) {

// Prevent repeat events
if (name == 'key_press')
{
if (event.which === this._key)
return;
else
this._key = event.which;
}
if (name == 'key_release')
this._key = null;

var value = '';
if (event.ctrlKey && event.which != 17)
value += "ctrl+";
if (event.altKey && event.which != 18)
value += "alt+";
if (event.shiftKey && event.which != 16)
value += "shift+";

value += 'k';
value += event.which.toString();

this._key_event_extra(event, name);

this.send_message(name, {key: value,
guiEvent: simpleKeys(event)});
return false;
}

mpl.figure.prototype.toolbar_button_onclick = function(name) {
if (name == 'download') {
this.handle_save(this, null);
} else {
this.send_message("toolbar_button", {name: name});
}
};

mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {
this.message.textContent = tooltip;
};
mpl.toolbar_items = [["Home", "Reset original view", "fa fa-home icon-home", "home"], ["Back", "Back to  previous view", "fa fa-arrow-left icon-arrow-left", "back"], ["Forward", "Forward to next view", "fa fa-arrow-right icon-arrow-right", "forward"], ["", "", "", ""], ["Pan", "Pan axes with left mouse, zoom with right", "fa fa-arrows icon-move", "pan"], ["Zoom", "Zoom to rectangle", "fa fa-square-o icon-check-empty", "zoom"], ["", "", "", ""], ["Download", "Download plot", "fa fa-floppy-o icon-save", "download"]];

mpl.extensions = ["eps", "jpeg", "pdf", "png", "ps", "raw", "svg", "tif"];

mpl.default_extension = "png";var comm_websocket_adapter = function(comm) {
// Create a "websocket"-like object which calls the given IPython comm
// object with the appropriate methods. Currently this is a non binary
// socket, so there is still some room for performance tuning.
var ws = {};

ws.close = function() {
comm.close()
};
ws.send = function(m) {
//console.log('sending', m);
comm.send(m);
};
// Register the callback with on_msg.
comm.on_msg(function(msg) {
//console.log('receiving', msg['content']['data'], msg);
// Pass the mpl event to the overriden (by mpl) onmessage function.
ws.onmessage(msg['content']['data'])
});
return ws;
}

mpl.mpl_figure_comm = function(comm, msg) {
// This is the function which gets called when the mpl process
// starts-up an IPython Comm through the "matplotlib" channel.

var id = msg.content.data.id;
// Get hold of the div created by the display call when the Comm
// socket was opened in Python.
var element = \$("#" + id);
var ws_proxy = comm_websocket_adapter(comm)

function ondownload(figure, format) {
window.open(figure.imageObj.src);
}

var fig = new mpl.figure(id, ws_proxy,
ondownload,
element.get(0));

// Call onopen now - mpl needs it, as it is assuming we've passed it a real
// web socket which is closed, not our websocket->open comm proxy.
ws_proxy.onopen();

fig.parent_element = element.get(0);
fig.cell_info = mpl.find_output_cell("<div id='" + id + "'></div>");
if (!fig.cell_info) {
console.error("Failed to find cell for figure", id, fig);
return;
}

var output_index = fig.cell_info[2]
var cell = fig.cell_info[0];

};

mpl.figure.prototype.handle_close = function(fig, msg) {
fig.root.unbind('remove')

// Update the output cell to use the data from the current canvas.
fig.push_to_output();
var dataURL = fig.canvas.toDataURL();
// Re-enable the keyboard manager in IPython - without this line, in FF,
// the notebook keyboard shortcuts fail.
IPython.keyboard_manager.enable()
\$(fig.parent_element).html('<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">');
fig.close_ws(fig, msg);
}

mpl.figure.prototype.close_ws = function(fig, msg){
fig.send_message('closing', msg);
// fig.ws.close()
}

mpl.figure.prototype.push_to_output = function(remove_interactive) {
// Turn the data on the canvas into data in the output cell.
var dataURL = this.canvas.toDataURL();
this.cell_info[1]['text/html'] = '<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">';
}

mpl.figure.prototype.updated_canvas_event = function() {
// Tell IPython that the notebook contents must change.
IPython.notebook.set_dirty(true);
this.send_message("ack", {});
var fig = this;
// Wait a second, then push the new image to the DOM so
// that it is saved nicely (might be nice to debounce this).
setTimeout(function () { fig.push_to_output() }, 1000);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items){
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) { continue; };

var button = \$('<button class="btn btn-default" href="#" title="' + name + '"><i class="fa ' + image + ' fa-lg"></i></button>');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);
nav_element.append(button);
}

// Add the status bar.
var status_bar = \$('<span class="mpl-message" style="text-align:right; float: right;"/>');
nav_element.append(status_bar);
this.message = status_bar[0];

// Add the close button to the window.
var buttongrp = \$('<div class="btn-group inline pull-right"></div>');
var button = \$('<button class="btn btn-mini btn-primary" href="#" title="Stop Interaction"><i class="fa fa-power-off icon-remove icon-large"></i></button>');
button.click(function (evt) { fig.handle_close(fig, {}); } );
button.mouseover('Stop Interaction', toolbar_mouse_event);
buttongrp.append(button);
var titlebar = this.root.find(\$('.ui-dialog-titlebar'));
titlebar.prepend(buttongrp);
}

mpl.figure.prototype._root_extra_style = function(el){
var fig = this
el.on("remove", function(){
fig.close_ws(fig, {});
});
}

mpl.figure.prototype._canvas_extra_style = function(el){
// this is important to make the div 'focusable
el.attr('tabindex', 0)
// reach out to IPython and tell the keyboard manager to turn it's self
// off when our div gets focus

// location in version 3
if (IPython.notebook.keyboard_manager) {
IPython.notebook.keyboard_manager.register_events(el);
}
else {
// location in version 2
IPython.keyboard_manager.register_events(el);
}

}

mpl.figure.prototype._key_event_extra = function(event, name) {
var manager = IPython.notebook.keyboard_manager;
if (!manager)
manager = IPython.keyboard_manager;

// Check for shift+enter
if (event.shiftKey && event.which == 13) {
this.canvas_div.blur();
event.shiftKey = false;
// Send a "J" for go to next cell
event.which = 74;
event.keyCode = 74;
manager.command_mode();
manager.handle_keydown(event);
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
fig.ondownload(fig, null);
}

mpl.find_output_cell = function(html_output) {
// Return the cell and output element which can be found *uniquely* in the notebook.
// Note - this is a bit hacky, but it is done because the "notebook_saving.Notebook"
// IPython event is triggered only after the cells have been serialised, which for
// our purposes (turning an active figure into a static one), is too late.
var cells = IPython.notebook.get_cells();
var ncells = cells.length;
for (var i=0; i<ncells; i++) {
var cell = cells[i];
if (cell.cell_type === 'code'){
for (var j=0; j<cell.output_area.outputs.length; j++) {
var data = cell.output_area.outputs[j];
if (data.data) {
// IPython >= 3 moved mimebundle to data attribute of output
data = data.data;
}
if (data['text/html'] == html_output) {
return [cell, data, j];
}
}
}
}
}

// Register the function which deals with the matplotlib target/channel.
// The kernel may be null if the page has been refreshed.
if (IPython.notebook.kernel != null) {
IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);
}

``````

## Plot total relative CCD signal due to visible photons, electrons, and x-rays

``````

In [24]:

sns.set(context='poster',font_scale=1.5)
sns.set_style("darkgrid")
sns.set_palette(palette='deep')
sns.set_color_codes(palette='deep')

Total_Signal = np.multiply(photonNumberArray,Qph) + np.multiply(EelAbsorbedCCD,10**6/Energy_eh_pair) + \
np.multiply(EphAbsorbedCCD,10**6/Energy_eh_pair)

plt.subplots(figsize=(12,6))
#plt.plot(np.multiply(KEsim,10**3),Total_Signal/np.max(Total_Signal),linewidth=3,color='k')
plt.plot(np.multiply(KEsim,10**3),Total_Signal,linewidth=3,color='k')
plt.xlabel('Electron Kinetic Energy (keV)')
plt.ylabel('CCD Signal')
plt.title('Total Relative CCD Signal')
plt.xlim(0,3000)
plt.tight_layout()

``````
``````

/home/drake/.anaconda3/lib/python3.4/site-packages/matplotlib/__init__.py:872: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
warnings.warn(self.msg_depr % (key, alt_key))

var element = \$('#be3ec58f-466e-45db-a77f-58a98f6c6bb1');
/* Put everything inside the global mpl namespace */
window.mpl = {};

mpl.get_websocket_type = function() {
if (typeof(WebSocket) !== 'undefined') {
return WebSocket;
} else if (typeof(MozWebSocket) !== 'undefined') {
return MozWebSocket;
} else {
alert('Your browser does not have WebSocket support.' +
'Please try Chrome, Safari or Firefox ≥ 6. ' +
'Firefox 4 and 5 are also supported but you ' +
'have to enable WebSockets in about:config.');
};
}

mpl.figure = function(figure_id, websocket, ondownload, parent_element) {
this.id = figure_id;

this.ws = websocket;

this.supports_binary = (this.ws.binaryType != undefined);

if (!this.supports_binary) {
var warnings = document.getElementById("mpl-warnings");
if (warnings) {
warnings.style.display = 'block';
warnings.textContent = (
"This browser does not support binary websocket messages. " +
"Performance may be slow.");
}
}

this.imageObj = new Image();

this.context = undefined;
this.message = undefined;
this.canvas = undefined;
this.rubberband_canvas = undefined;
this.rubberband_context = undefined;
this.format_dropdown = undefined;

this.image_mode = 'full';

this.root = \$('<div/>');
this._root_extra_style(this.root)
this.root.attr('style', 'display: inline-block');

\$(parent_element).append(this.root);

this._init_header(this);
this._init_canvas(this);
this._init_toolbar(this);

var fig = this;

this.waiting = false;

this.ws.onopen =  function () {
fig.send_message("supports_binary", {value: fig.supports_binary});
fig.send_message("send_image_mode", {});
fig.send_message("refresh", {});
}

this.imageObj.onload = function() {
if (fig.image_mode == 'full') {
// Full images could contain transparency (where diff images
// almost always do), so we need to clear the canvas so that
// there is no ghosting.
fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);
}
fig.context.drawImage(fig.imageObj, 0, 0);
};

this.imageObj.onunload = function() {
this.ws.close();
}

this.ws.onmessage = this._make_on_message_function(this);

this.ondownload = ondownload;
}

mpl.figure.prototype._init_header = function() {
var titlebar = \$(
'<div class="ui-dialog-titlebar ui-widget-header ui-corner-all ' +
'ui-helper-clearfix"/>');
var titletext = \$(
'<div class="ui-dialog-title" style="width: 100%; ' +
'text-align: center; padding: 3px;"/>');
titlebar.append(titletext)
this.root.append(titlebar);
this.header = titletext[0];
}

mpl.figure.prototype._canvas_extra_style = function(canvas_div) {

}

mpl.figure.prototype._root_extra_style = function(canvas_div) {

}

mpl.figure.prototype._init_canvas = function() {
var fig = this;

var canvas_div = \$('<div/>');

canvas_div.attr('style', 'position: relative; clear: both; outline: 0');

function canvas_keyboard_event(event) {
return fig.key_event(event, event['data']);
}

canvas_div.keydown('key_press', canvas_keyboard_event);
canvas_div.keyup('key_release', canvas_keyboard_event);
this.canvas_div = canvas_div
this._canvas_extra_style(canvas_div)
this.root.append(canvas_div);

var canvas = \$('<canvas/>');
canvas.addClass('mpl-canvas');
canvas.attr('style', "left: 0; top: 0; z-index: 0; outline: 0")

this.canvas = canvas[0];
this.context = canvas[0].getContext("2d");

var rubberband = \$('<canvas/>');
rubberband.attr('style', "position: absolute; left: 0; top: 0; z-index: 1;")

var pass_mouse_events = true;

canvas_div.resizable({
start: function(event, ui) {
pass_mouse_events = false;
},
resize: function(event, ui) {
fig.request_resize(ui.size.width, ui.size.height);
},
stop: function(event, ui) {
pass_mouse_events = true;
fig.request_resize(ui.size.width, ui.size.height);
},
});

function mouse_event_fn(event) {
if (pass_mouse_events)
return fig.mouse_event(event, event['data']);
}

rubberband.mousedown('button_press', mouse_event_fn);
rubberband.mouseup('button_release', mouse_event_fn);
// Throttle sequential mouse events to 1 every 20ms.
rubberband.mousemove('motion_notify', mouse_event_fn);

rubberband.mouseenter('figure_enter', mouse_event_fn);
rubberband.mouseleave('figure_leave', mouse_event_fn);

canvas_div.on("wheel", function (event) {
event = event.originalEvent;
event['data'] = 'scroll'
if (event.deltaY < 0) {
event.step = 1;
} else {
event.step = -1;
}
mouse_event_fn(event);
});

canvas_div.append(canvas);
canvas_div.append(rubberband);

this.rubberband = rubberband;
this.rubberband_canvas = rubberband[0];
this.rubberband_context = rubberband[0].getContext("2d");
this.rubberband_context.strokeStyle = "#000000";

this._resize_canvas = function(width, height) {
// Keep the size of the canvas, canvas container, and rubber band
// canvas in synch.
canvas_div.css('width', width)
canvas_div.css('height', height)

canvas.attr('width', width);
canvas.attr('height', height);

rubberband.attr('width', width);
rubberband.attr('height', height);
}

// Set the figure to an initial 600x600px, this will subsequently be updated
// upon first draw.
this._resize_canvas(600, 600);

// Disable right mouse context menu.
\$(this.rubberband_canvas).bind("contextmenu",function(e){
return false;
});

function set_focus () {
canvas.focus();
canvas_div.focus();
}

window.setTimeout(set_focus, 100);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items) {
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) {
// put a spacer in here.
continue;
}
var button = \$('<button/>');
button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +
'ui-button-icon-only');
button.attr('role', 'button');
button.attr('aria-disabled', 'false');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);

var icon_img = \$('<span/>');
icon_img.addClass('ui-button-icon-primary ui-icon');
icon_img.addClass(image);
icon_img.addClass('ui-corner-all');

var tooltip_span = \$('<span/>');
tooltip_span.addClass('ui-button-text');
tooltip_span.html(tooltip);

button.append(icon_img);
button.append(tooltip_span);

nav_element.append(button);
}

var fmt_picker_span = \$('<span/>');

var fmt_picker = \$('<select/>');
fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');
fmt_picker_span.append(fmt_picker);
nav_element.append(fmt_picker_span);
this.format_dropdown = fmt_picker[0];

for (var ind in mpl.extensions) {
var fmt = mpl.extensions[ind];
var option = \$(
'<option/>', {selected: fmt === mpl.default_extension}).html(fmt);
fmt_picker.append(option)
}

// Add hover states to the ui-buttons
\$( ".ui-button" ).hover(
function() { \$(this).addClass("ui-state-hover");},
function() { \$(this).removeClass("ui-state-hover");}
);

var status_bar = \$('<span class="mpl-message"/>');
nav_element.append(status_bar);
this.message = status_bar[0];
}

mpl.figure.prototype.request_resize = function(x_pixels, y_pixels) {
// Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,
// which will in turn request a refresh of the image.
this.send_message('resize', {'width': x_pixels, 'height': y_pixels});
}

mpl.figure.prototype.send_message = function(type, properties) {
properties['type'] = type;
properties['figure_id'] = this.id;
this.ws.send(JSON.stringify(properties));
}

mpl.figure.prototype.send_draw_message = function() {
if (!this.waiting) {
this.waiting = true;
this.ws.send(JSON.stringify({type: "draw", figure_id: this.id}));
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
var format_dropdown = fig.format_dropdown;
var format = format_dropdown.options[format_dropdown.selectedIndex].value;
fig.ondownload(fig, format);
}

mpl.figure.prototype.handle_resize = function(fig, msg) {
var size = msg['size'];
if (size[0] != fig.canvas.width || size[1] != fig.canvas.height) {
fig._resize_canvas(size[0], size[1]);
fig.send_message("refresh", {});
};
}

mpl.figure.prototype.handle_rubberband = function(fig, msg) {
var x0 = msg['x0'];
var y0 = fig.canvas.height - msg['y0'];
var x1 = msg['x1'];
var y1 = fig.canvas.height - msg['y1'];
x0 = Math.floor(x0) + 0.5;
y0 = Math.floor(y0) + 0.5;
x1 = Math.floor(x1) + 0.5;
y1 = Math.floor(y1) + 0.5;
var min_x = Math.min(x0, x1);
var min_y = Math.min(y0, y1);
var width = Math.abs(x1 - x0);
var height = Math.abs(y1 - y0);

fig.rubberband_context.clearRect(
0, 0, fig.canvas.width, fig.canvas.height);

fig.rubberband_context.strokeRect(min_x, min_y, width, height);
}

mpl.figure.prototype.handle_figure_label = function(fig, msg) {
// Updates the figure title.
fig.header.textContent = msg['label'];
}

mpl.figure.prototype.handle_cursor = function(fig, msg) {
var cursor = msg['cursor'];
switch(cursor)
{
case 0:
cursor = 'pointer';
break;
case 1:
cursor = 'default';
break;
case 2:
cursor = 'crosshair';
break;
case 3:
cursor = 'move';
break;
}
fig.rubberband_canvas.style.cursor = cursor;
}

mpl.figure.prototype.handle_message = function(fig, msg) {
fig.message.textContent = msg['message'];
}

mpl.figure.prototype.handle_draw = function(fig, msg) {
// Request the server to send over a new figure.
fig.send_draw_message();
}

mpl.figure.prototype.handle_image_mode = function(fig, msg) {
fig.image_mode = msg['mode'];
}

mpl.figure.prototype.updated_canvas_event = function() {
// Called whenever the canvas gets updated.
this.send_message("ack", {});
}

// A function to construct a web socket function for onmessage handling.
// Called in the figure constructor.
mpl.figure.prototype._make_on_message_function = function(fig) {
return function socket_on_message(evt) {
if (evt.data instanceof Blob) {
/* FIXME: We get "Resource interpreted as Image but
* transferred with MIME type text/plain:" errors on
* Chrome.  But how to set the MIME type?  It doesn't seem
* to be part of the websocket stream */
evt.data.type = "image/png";

/* Free the memory for the previous frames */
if (fig.imageObj.src) {
(window.URL || window.webkitURL).revokeObjectURL(
fig.imageObj.src);
}

fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(
evt.data);
fig.updated_canvas_event();
fig.waiting = false;
return;
}
else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == "data:image/png;base64") {
fig.imageObj.src = evt.data;
fig.updated_canvas_event();
fig.waiting = false;
return;
}

var msg = JSON.parse(evt.data);
var msg_type = msg['type'];

// Call the  "handle_{type}" callback, which takes
// the figure and JSON message as its only arguments.
try {
var callback = fig["handle_" + msg_type];
} catch (e) {
console.log("No handler for the '" + msg_type + "' message type: ", msg);
return;
}

if (callback) {
try {
// console.log("Handling '" + msg_type + "' message: ", msg);
callback(fig, msg);
} catch (e) {
console.log("Exception inside the 'handler_" + msg_type + "' callback:", e, e.stack, msg);
}
}
};
}

// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas
mpl.findpos = function(e) {
//this section is from http://www.quirksmode.org/js/events_properties.html
var targ;
if (!e)
e = window.event;
if (e.target)
targ = e.target;
else if (e.srcElement)
targ = e.srcElement;
if (targ.nodeType == 3) // defeat Safari bug
targ = targ.parentNode;

// jQuery normalizes the pageX and pageY
// pageX,Y are the mouse positions relative to the document
// offset() returns the position of the element relative to the document
var x = e.pageX - \$(targ).offset().left;
var y = e.pageY - \$(targ).offset().top;

return {"x": x, "y": y};
};

/*
* return a copy of an object with only non-object keys
* we need this to avoid circular references
* http://stackoverflow.com/a/24161582/3208463
*/
function simpleKeys (original) {
return Object.keys(original).reduce(function (obj, key) {
if (typeof original[key] !== 'object')
obj[key] = original[key]
return obj;
}, {});
}

mpl.figure.prototype.mouse_event = function(event, name) {
var canvas_pos = mpl.findpos(event)

if (name === 'button_press')
{
this.canvas.focus();
this.canvas_div.focus();
}

var x = canvas_pos.x;
var y = canvas_pos.y;

this.send_message(name, {x: x, y: y, button: event.button,
step: event.step,
guiEvent: simpleKeys(event)});

/* This prevents the web browser from automatically changing to
* the text insertion cursor when the button is pressed.  We want
* to control all of the cursor setting manually through the
* 'cursor' event from matplotlib */
event.preventDefault();
return false;
}

mpl.figure.prototype._key_event_extra = function(event, name) {
// Handle any extra behaviour associated with a key event
}

mpl.figure.prototype.key_event = function(event, name) {

// Prevent repeat events
if (name == 'key_press')
{
if (event.which === this._key)
return;
else
this._key = event.which;
}
if (name == 'key_release')
this._key = null;

var value = '';
if (event.ctrlKey && event.which != 17)
value += "ctrl+";
if (event.altKey && event.which != 18)
value += "alt+";
if (event.shiftKey && event.which != 16)
value += "shift+";

value += 'k';
value += event.which.toString();

this._key_event_extra(event, name);

this.send_message(name, {key: value,
guiEvent: simpleKeys(event)});
return false;
}

mpl.figure.prototype.toolbar_button_onclick = function(name) {
if (name == 'download') {
this.handle_save(this, null);
} else {
this.send_message("toolbar_button", {name: name});
}
};

mpl.figure.prototype.toolbar_button_onmouseover = function(tooltip) {
this.message.textContent = tooltip;
};
mpl.toolbar_items = [["Home", "Reset original view", "fa fa-home icon-home", "home"], ["Back", "Back to  previous view", "fa fa-arrow-left icon-arrow-left", "back"], ["Forward", "Forward to next view", "fa fa-arrow-right icon-arrow-right", "forward"], ["", "", "", ""], ["Pan", "Pan axes with left mouse, zoom with right", "fa fa-arrows icon-move", "pan"], ["Zoom", "Zoom to rectangle", "fa fa-square-o icon-check-empty", "zoom"], ["", "", "", ""], ["Download", "Download plot", "fa fa-floppy-o icon-save", "download"]];

mpl.extensions = ["eps", "jpeg", "pdf", "png", "ps", "raw", "svg", "tif"];

mpl.default_extension = "png";var comm_websocket_adapter = function(comm) {
// Create a "websocket"-like object which calls the given IPython comm
// object with the appropriate methods. Currently this is a non binary
// socket, so there is still some room for performance tuning.
var ws = {};

ws.close = function() {
comm.close()
};
ws.send = function(m) {
//console.log('sending', m);
comm.send(m);
};
// Register the callback with on_msg.
comm.on_msg(function(msg) {
//console.log('receiving', msg['content']['data'], msg);
// Pass the mpl event to the overriden (by mpl) onmessage function.
ws.onmessage(msg['content']['data'])
});
return ws;
}

mpl.mpl_figure_comm = function(comm, msg) {
// This is the function which gets called when the mpl process
// starts-up an IPython Comm through the "matplotlib" channel.

var id = msg.content.data.id;
// Get hold of the div created by the display call when the Comm
// socket was opened in Python.
var element = \$("#" + id);
var ws_proxy = comm_websocket_adapter(comm)

function ondownload(figure, format) {
window.open(figure.imageObj.src);
}

var fig = new mpl.figure(id, ws_proxy,
ondownload,
element.get(0));

// Call onopen now - mpl needs it, as it is assuming we've passed it a real
// web socket which is closed, not our websocket->open comm proxy.
ws_proxy.onopen();

fig.parent_element = element.get(0);
fig.cell_info = mpl.find_output_cell("<div id='" + id + "'></div>");
if (!fig.cell_info) {
console.error("Failed to find cell for figure", id, fig);
return;
}

var output_index = fig.cell_info[2]
var cell = fig.cell_info[0];

};

mpl.figure.prototype.handle_close = function(fig, msg) {
fig.root.unbind('remove')

// Update the output cell to use the data from the current canvas.
fig.push_to_output();
var dataURL = fig.canvas.toDataURL();
// Re-enable the keyboard manager in IPython - without this line, in FF,
// the notebook keyboard shortcuts fail.
IPython.keyboard_manager.enable()
\$(fig.parent_element).html('<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">');
fig.close_ws(fig, msg);
}

mpl.figure.prototype.close_ws = function(fig, msg){
fig.send_message('closing', msg);
// fig.ws.close()
}

mpl.figure.prototype.push_to_output = function(remove_interactive) {
// Turn the data on the canvas into data in the output cell.
var dataURL = this.canvas.toDataURL();
this.cell_info[1]['text/html'] = '<amp-img layout="responsive" width="500" height="300" src="' + dataURL + '">';
}

mpl.figure.prototype.updated_canvas_event = function() {
// Tell IPython that the notebook contents must change.
IPython.notebook.set_dirty(true);
this.send_message("ack", {});
var fig = this;
// Wait a second, then push the new image to the DOM so
// that it is saved nicely (might be nice to debounce this).
setTimeout(function () { fig.push_to_output() }, 1000);
}

mpl.figure.prototype._init_toolbar = function() {
var fig = this;

var nav_element = \$('<div/>')
nav_element.attr('style', 'width: 100%');
this.root.append(nav_element);

// Define a callback function for later on.
function toolbar_event(event) {
return fig.toolbar_button_onclick(event['data']);
}
function toolbar_mouse_event(event) {
return fig.toolbar_button_onmouseover(event['data']);
}

for(var toolbar_ind in mpl.toolbar_items){
var name = mpl.toolbar_items[toolbar_ind][0];
var tooltip = mpl.toolbar_items[toolbar_ind][1];
var image = mpl.toolbar_items[toolbar_ind][2];
var method_name = mpl.toolbar_items[toolbar_ind][3];

if (!name) { continue; };

var button = \$('<button class="btn btn-default" href="#" title="' + name + '"><i class="fa ' + image + ' fa-lg"></i></button>');
button.click(method_name, toolbar_event);
button.mouseover(tooltip, toolbar_mouse_event);
nav_element.append(button);
}

// Add the status bar.
var status_bar = \$('<span class="mpl-message" style="text-align:right; float: right;"/>');
nav_element.append(status_bar);
this.message = status_bar[0];

// Add the close button to the window.
var buttongrp = \$('<div class="btn-group inline pull-right"></div>');
var button = \$('<button class="btn btn-mini btn-primary" href="#" title="Stop Interaction"><i class="fa fa-power-off icon-remove icon-large"></i></button>');
button.click(function (evt) { fig.handle_close(fig, {}); } );
button.mouseover('Stop Interaction', toolbar_mouse_event);
buttongrp.append(button);
var titlebar = this.root.find(\$('.ui-dialog-titlebar'));
titlebar.prepend(buttongrp);
}

mpl.figure.prototype._root_extra_style = function(el){
var fig = this
el.on("remove", function(){
fig.close_ws(fig, {});
});
}

mpl.figure.prototype._canvas_extra_style = function(el){
// this is important to make the div 'focusable
el.attr('tabindex', 0)
// reach out to IPython and tell the keyboard manager to turn it's self
// off when our div gets focus

// location in version 3
if (IPython.notebook.keyboard_manager) {
IPython.notebook.keyboard_manager.register_events(el);
}
else {
// location in version 2
IPython.keyboard_manager.register_events(el);
}

}

mpl.figure.prototype._key_event_extra = function(event, name) {
var manager = IPython.notebook.keyboard_manager;
if (!manager)
manager = IPython.keyboard_manager;

// Check for shift+enter
if (event.shiftKey && event.which == 13) {
this.canvas_div.blur();
event.shiftKey = false;
// Send a "J" for go to next cell
event.which = 74;
event.keyCode = 74;
manager.command_mode();
manager.handle_keydown(event);
}
}

mpl.figure.prototype.handle_save = function(fig, msg) {
fig.ondownload(fig, null);
}

mpl.find_output_cell = function(html_output) {
// Return the cell and output element which can be found *uniquely* in the notebook.
// Note - this is a bit hacky, but it is done because the "notebook_saving.Notebook"
// IPython event is triggered only after the cells have been serialised, which for
// our purposes (turning an active figure into a static one), is too late.
var cells = IPython.notebook.get_cells();
var ncells = cells.length;
for (var i=0; i<ncells; i++) {
var cell = cells[i];
if (cell.cell_type === 'code'){
for (var j=0; j<cell.output_area.outputs.length; j++) {
var data = cell.output_area.outputs[j];
if (data.data) {
// IPython >= 3 moved mimebundle to data attribute of output
data = data.data;
}
if (data['text/html'] == html_output) {
return [cell, data, j];
}
}
}
}
}

// Register the function which deals with the matplotlib target/channel.
// The kernel may be null if the page has been refreshed.
if (IPython.notebook.kernel != null) {
IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);
}

``````

## Write to csv

``````

In [26]:

Total_Relative_Signal = Total_Signal/np.max(Total_Signal)
KEarray = np.multiply(KEsim,10**3)
EspecCalibration = np.vstack((KEarray,Total_Relative_Signal))

#np.savetxt('Total_Relative_CCD_Signal_vs_Energy_(keV)_Normal_Incidence.csv',np.transpose(EspecCalibration),delimiter=',')

``````