# Diffusion Validation I

#### This notebbok simulates a diffusion process in a homogenous background magnetic field. The diffusion tensor is anisotropic, meaning the parallel component is larger than the perpendicular component ($\kappa_\parallel = 10\cdot\kappa_\perp$).

Load modules and use jupyter inline magic to use interactive plots.



In [7]:

%matplotlib notebook

import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
from scipy.stats import chisquare
from crpropa import *

#figure settings
A4heigth = 29.7/2.54
A4width = 21./2.54

sns.set_palette("Set2")



Definition of the probability distribution function of the particle density in one dimension:
$\psi(R, t) = \frac{2}{\sqrt{4 \pi D t}} \cdot \exp{-\frac{R^2}{4 D t}}$
Here, $R=||\vec{R}||$ is the norm of the position.



In [2]:

def pdf(R, t, epsilon):
D = 1e24*epsilon
pdf = 2 * pow(4 * np.pi * D * t, -0.5) * np.exp(- R**2. / (4 * D * t))
return pdf



Simulation set-up
Using 10000 pseudo particle to trace the phase space.



In [3]:

N = 10000

#Number of Snapshots
n = 50.
step = 100*kpc / n

#magnetic field
ConstMagVec = Vector3d(0*nG,0*nG,1*nG)
BField = UniformMagneticField(ConstMagVec)

# step precision needed for Diffusion
precision = 1e-4
minStep = 0.1*pc
maxStep = 1*kpc
epsilon = .1

# source settings
source = Source()

#Output settings
Out = TextOutput('./Test.txt')
Out.disableAll()
Out.enable(Output.TrajectoryLengthColumn)
Out.enable(Output.CurrentPositionColumn)
Out.setLengthScale(kpc)
Out.setEnergyScale(TeV)

#Observer settings
Obs = Observer()
Obs.setDeactivateOnDetection(False)
Obs.onDetection(Out)

#Difffusion Module
# D_xx=D_yy= 1e24 m^2 / s, D_zz=10*D_xx
Dif = DiffusionSDE(BField, precision, minStep, maxStep, epsilon)
Dif.setScale(1./6.1)
Dif.setAlpha(0.)

#Boundary
maxTra = MaximumTrajectoryLength(100.0*kpc)
maxTra.onReject(Out)

# module list
sim = ModuleList()

sim.run(source, N, True)
print("Simulation finished")




Simulation finished





In [4]:

df['t'] = df.D * kpc / c_light #time in seconds
#groups = df.groupby(df.D)



#### Distribution in x, y and z

Plot the density distribution in all three coordinates.



In [26]:

fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(1.*A4width,A4heigth/4.))

coord = ['X', 'Y', 'Z']

for i, x_i in enumerate(coord):
L = [10, 50, 100]
for j, l in enumerate(L):
t = l*kpc/c_light
s = '%.2e' % t
df[df.D==l][x_i].hist(bins=np.linspace(-0.5, 0.5, 20), ax=axes[i], label='t = '+s+' s', zorder=3-j)
axes[i].set_title(x_i)
axes[i].set_xlim(-0.5, 0.5)
axes[i].legend(loc='best')
axes[i].set_xlabel('Distance [kpc]')
if i>0:
axes[i].set_yticklabels([])
else:
axes[i].set_ylabel("number density")

plt.tight_layout()
plt.savefig('Diffusion1.pdf')
plt.show()




var element = $('#da9f0c99-a8a3-4158-97f7-9323990a0251'); /* Put everything inside the global mpl namespace */ window.mpl = {}; mpl.get_websocket_type = function() { if (typeof(WebSocket) !== 'undefined') { return WebSocket; } else if (typeof(MozWebSocket) !== 'undefined') { return MozWebSocket; } else { alert('Your browser does not have WebSocket support.' + 'Please try Chrome, Safari or Firefox ≥ 6. ' + 'Firefox 4 and 5 are also supported but you ' + 'have to enable WebSockets in about:config.'); }; } mpl.figure = function(figure_id, websocket, ondownload, parent_element) { this.id = figure_id; this.ws = websocket; this.supports_binary = (this.ws.binaryType != undefined); if (!this.supports_binary) { var warnings = document.getElementById("mpl-warnings"); if (warnings) { warnings.style.display = 'block'; warnings.textContent = ( "This browser does not support binary websocket messages. " + "Performance may be slow."); } } this.imageObj = new Image(); this.context = undefined; this.message = undefined; this.canvas = undefined; this.rubberband_canvas = undefined; this.rubberband_context = undefined; this.format_dropdown = undefined; this.image_mode = 'full'; this.root =$('<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/>');

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;
}

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) {
}

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) {
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);
}

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) {
}

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);
}



${\mathrm{\bf Fig 1:}}$ Distribution of particles in three directions. Z-axis is parallel to the mean magnetic field. $\kappa_{par}=100*\kappa_{perp}$

#### Use the absolute distance from origin $|x|, |y|, |z|$ and compare to analytical expectations.



In [27]:

fig, axes = plt.subplots(nrows=1, ncols=3, figsize=(1.*A4width,A4heigth/4.))

coord = ['X', 'Y', 'Z']

ChiDict = {}

for i, x_i in enumerate(coord):
ChiDict[str(x_i)] = {}

L = [10, 50, 100]
colors = sns.color_palette()
for j, l in enumerate(L):
ChiDict[str(x_i)][str(l)] = {}
if i <2:
abs(df[df.D==l][x_i]).hist(bins=np.linspace(0, 0.1, 11), ax=axes[i], alpha=1., zorder=3-j, color=colors[j])
hist = np.histogram(abs(df[df.D==l][x_i]), bins=np.linspace(0,0.1,11))

PDF = np.zeros(len(hist[0]))
xP = np.zeros(len(hist[0]))
for k in range(len(PDF)):
a, b = hist[1][k]*kpc, hist[1][k+1]*kpc
xP[k] = (a+b)/2./kpc
PDF[k] = quad(pdf, a,b, args=(l*kpc/c_light, 0.1))[0]*N
t = l*kpc/c_light
s = '%.2e' % t
axes[i].plot(xP, PDF, color=colors[j], label='t = '+s+' s', zorder=10)
#axes[i].legend(loc='best')
axes[i].set_xlim(0., 0.1)
else:
abs(df[df.D==l][x_i]).hist(bins=np.linspace(0, 0.5, 11), ax=axes[i], alpha=1., zorder=3-j, color=colors[j])
hist = np.histogram(abs(df[df.D==l][x_i]), bins=np.linspace(0,0.5,11))
PDF = np.zeros(len(hist[0]))
xP = np.zeros(len(hist[0]))
for k in range(len(PDF)):
a, b = hist[1][k]*kpc, hist[1][k+1]*kpc
xP[k] = (a+b)/2./kpc
PDF[k] = quad(pdf, a,b, args=(l*kpc/c_light, 1.))[0]*N

axes[i].plot(xP, PDF, color=colors[j], label='t = '+s+' s', zorder=10)
axes[i].set_xlim(0., 0.5)
ChiDict[str(x_i)][str(l)]['Obs'] = hist[0]
ChiDict[str(x_i)][str(l)]['Exp'] = PDF

axes[i].set_xlabel('Distance [kpc]')
axes[i].legend(loc='best')
axes[i].set_title(x_i)
if i>0:
axes[i].set_yticklabels([])
else:
axes[i].set_ylabel("number density")

plt.legend()
plt.tight_layout()
plt.savefig('Diffusion2.pdf')
plt.show()




var element = $('#c4f376dd-2b2d-45ec-91c9-ad7a8056b769'); /* Put everything inside the global mpl namespace */ window.mpl = {}; mpl.get_websocket_type = function() { if (typeof(WebSocket) !== 'undefined') { return WebSocket; } else if (typeof(MozWebSocket) !== 'undefined') { return MozWebSocket; } else { alert('Your browser does not have WebSocket support.' + 'Please try Chrome, Safari or Firefox ≥ 6. ' + 'Firefox 4 and 5 are also supported but you ' + 'have to enable WebSockets in about:config.'); }; } mpl.figure = function(figure_id, websocket, ondownload, parent_element) { this.id = figure_id; this.ws = websocket; this.supports_binary = (this.ws.binaryType != undefined); if (!this.supports_binary) { var warnings = document.getElementById("mpl-warnings"); if (warnings) { warnings.style.display = 'block'; warnings.textContent = ( "This browser does not support binary websocket messages. " + "Performance may be slow."); } } this.imageObj = new Image(); this.context = undefined; this.message = undefined; this.canvas = undefined; this.rubberband_canvas = undefined; this.rubberband_context = undefined; this.format_dropdown = undefined; this.image_mode = 'full'; this.root =$('<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/>');

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;
}

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) {
}

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) {
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);
}

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) {
}

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);
}



${\mathrm{\bf Fig 2:}}$ The distance from the source position follows nicely the expected pdf.

#### Calculate the pValue of the $\chi^2$-test to prove the visual stattement from above.



In [98]:

C, Time, pValue = [], [], []
for c in coord:
for l in L:
C.append(c)
t = l*kpc/c_light
s = '%.2e' % t
Time.append(s)
pValue.append(chisquare(ChiDict[c][str(l)]['Obs'], ChiDict[c][str(l)]['Exp'])[1])
Chi = pd.DataFrame(pValue, index = [C, Time])
Chi.rename(columns = {0:"p-Value"}, inplace=True)
Chi.index.names = ["Coordinate", "Time [s]"]
Chi




Out[98]:

p-Value

Coordinate
Time [s]

X
1.03e+12
0.731448

5.15e+12
0.314612

1.03e+13
0.281603

Y
1.03e+12
0.556101

5.15e+12
0.525063

1.03e+13
0.710337

Z
1.03e+12
0.467526

5.15e+12
0.650786

1.03e+13
0.260655



${\mathrm{\bf Tab 1:}}$ The assumption that the two samles (observed and expected) are drawn from the same distribution cannot be rejected for any diretion.