CnrLwlss

simDSLogistic=function(K,r,N0){
  # Unusually, for this model, we know the number of events a priori
  eventNo=K-N0
  # So we can just generate all required random numbers (quickly) in one go
  unifs=runif(eventNo)
  # Every event produces one cell and consumes one unit of nutrients
  clist=(N0+1):K
  # Simulate time between events by generating 
  # exponential random numbers using the inversion method
  dts=-log(1-unifs)/(r*clist*(1-clist/K))

CnrLwlss

import numpy as np

def simDSLogistic(K,r,N0):
    '''Discrete stochastic logistic model simulation.  Carrying capacity K,
intrinsic growth rate r, initial population size (inoculum) N0.  Returns an
array with a (continuous) time column and a (discrete) population size column.'''
    # Unusually, for this model, we know the number of events a priori
    eventNo=K-N0
    # So we can just generate all required random numbers (quickly) in one go
    unifs=np.random.uniform(size=eventNo)

CnrLwlss

###########
# Optimum circle packing in R
###########

# Function closure, sets up list of possible combinations
# and returns objective function
createObj<-function(N,W,H){

print("Generating combinations...")
# Generate all possible circle pairings

CnrLwlss

library(DEoptim)
library(rgenoud)
library(snow)

# CirclePacking.R from https://gist.github.com/4571810
source("CirclePacking.R")

# Number of circles and dimensions of bounding rectangle 
N=100; W=10; H=10
root="N64_100"

CnrLwlss

import random, numpy

def genGuess(N,W,H):
    '''Generate sensible initial guess vector (random circle coordinates and radii)'''
    z=numpy.zeros(3*N)
    for i in xrange(0,N):
        z[i*3]=random.random()*W
        z[i*3+1]=random.random()*H
        z[i*3+2]=0.001*min(W,H)+random.random()*(0.009*min(W,H))
    return(z)

CnrLwlss

# Simulating n steps of a biased random walk
# starting from x0 and with decreasing steps 
# occurring with probability theta
randomWalk=function(n=100,x0=0,theta=0.5){
	x=x0
	res=array(x0,dim=n+1)
	unifs=runif(n)
	for(i in 0:(n-1)){
		if (unifs[i+1]<=theta){x=x-1}else{x=x+1}
		res[i+2]=x	

CnrLwlss

simCellsHybrid=function(K,r,N0,NSwitch,detpts=100){
  # Every event produces one cell and consumes one unit of nutrients
  if(NSwitch>N0){
    # Unusually, for this model, we know the number of events a priori
    eventNo=NSwitch-N0
    # So we can just generate all required random numbers (quickly) in one go
    unifs=runif(eventNo)
    clist=(N0+1):NSwitch
    # Time between events
    dts=-log(1-unifs)/(r*clist*(1-clist/K))

CnrLwlss

from colonyzer2 import *
import time, sys

def main(fmt="384"):
    # Lydall lab file naming convention
    # First 15 characters in filename identify unique plates
    # Remaining charaters can be used to store date, time etc.
    barcRange=(0,15)
    if len(sys.argv)>1:
        fmt=sys.argv[1]

CnrLwlss

import pygame, os, sys
from pygame.locals import *

# Runs through all jpgs in current directory
# Opens each in turn, allowing user to click on image features
# Left clicking draws a red dot, right-clicking draws a yellow dot
# Press q or esc to move to next image
# Once an image is finished, a version with click locations overlaid is saved to file
# Numbers of left and right clicks are embedded into filename

CnrLwlss

import winsound, time, Tkinter

slides=[]
cells=[0,0,0]
labels=["G1","S","G2/M"]
print "Slide: %02d"%(len(slides)+1)

def key(event):
    if event.char=="g":
        cells[0]+=1