raacampbell

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

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of

raacampbell

function affineRotExample3D(thetaX, thetaY, thetaZ)
% Example of how to rotate an array of points in 3 using affine transformation
%
% function affineRotExample3D(thetaX, thetaY, thetaZ)
%
% Purpose
% Rotate a grid of points in three dimensions about its centre using affine transformation
%
% 
% By default:

raacampbell

#!/usr/local/bin/python3

# Make a 3d point cloud and fit a surface to it


import numpy as np
import scipy.linalg
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt

raacampbell

#!/usr/local/bin/python3

import numpy as np
import scipy.linalg
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt

# some 3-dim points
n=20
xx=np.linspace(-12,5,num=n)

raacampbell

## Multiple assignment
a=b=c=0 # all have the same value

a,b,c = 1,2,3 #a=1, b=2, c=3

a,*b,c = 1,11,22,33,44,2 #b contains all numbers >10


# Chaining comparison operators

raacampbell

function gitInfo=getGitInfo()
% Get information about the Git repository in the current directory, including: 
%          - branch name of the current Git Repo 
%          -Git SHA1 HASH of the most recent commit
%          -url of corresponding remote repository, if one exists
%
% The function first checks to see if a .git/ directory is present. If so it
% reads the .git/HEAD file to identify the branch name and then it looks up
% the corresponding commit.
%

raacampbell

function swipeTester

    % Test if BakingTray swipe moves are causing a failure

    % How large the swipe size should be. 
    swipeSize = 4;

    % Pull in BT object
    evalin('base','clear ans') %Because it sometimes makes a copy of BT in ans when it fails
    hBT=BakingTray.getObject(true);

raacampbell

import napari
import numpy as np
from skimage import data
from skimage.color import rgb2gray


# Convert the astronaut image to a grayscale
astro_im = rgb2gray(data.astronaut())

# Display the astronaut image and also display its negative in a new layer

raacampbell

function scanBeamPathDiagram
    % Generate a figure showing a scanned beam with scan and image field
    %
    % The path of a resonant-scanned focused beam over a sample. The beam moves
    % sinusoidally along the fast axis whilst being scanned up/down with a galvo.
    % The area over which the beam moves is known as the “scan field”. On the left and
    % right edges the beam slows and turns around. In these areas the potential for
    % photodamage is greatest, as the beam is travelling more slowly over the sample.
    % Thus the beam is “blanked” or disabled during these epochs. In a resonant scanning
    % microscope the beam is blanked about 30% of the time. The image field (red lines

raacampbell

function sectionInd = bake(obj,varargin)
    % Runs an automated anatomy acquisition using the currently attached parameter file
    %
    % function BT.bake('Param1',val1,'Param2',val2,...)
    %
    %
    % Inputs (optional param/val pairs)
    % 'leaveLaserOn' - If true, the laser is not switched off when acquisition finishes.
    %                  This setting can also be supplied by setting BT.leaveLaserOn. If
    %                  not supplied, this built-in value is used.