Python script to extract pixels (Fundamentals - Image Int. Primer Pt.2 @19:28)

Ivor Trueman

Would it be possible to get the python script mentioned in the Fundamentals - Image Integration Primer Pt.2 at approx. the 19min28sec mark?

I'm interested in extracting some (noise) values from my images, to look at their distribution...

Thanks
Ivor

BlockHead

I wrote this several years ago when learning Python... so forgive the amateurish code (it still is that way...just more complex).

#!python

#

#Usage:

#  Reads the value at a particular pixel from a set of images.

#  Generates a list of those values.

#  Outputs a CSV file

#  Also create a histogram graph

import numpy as np

from astropy.io import fits

import matplotlib.pyplot as plt

import glob 

import argparse 

def frange(start, stop, step):

    i = start

    while i < stop:

        yield i

        i += step

def main():

     

    #Creation of the command line options and arguments

    parser = argparse.ArgumentParser()

    parser.add_argument('filefilter',help ='Use a wildcard to capture desired data files in directory. e.g. *.csv',action='store')

       

    args = parser.parse_args()

    

    #The file list constraint of the command line to identify all FIT files

    filefilter = args.filefilter

    

    FileList = []

    for file in glob.glob(filefilter):  #create a list of files from directory from command line

        FileList.append(file)   

        

    pixelstack = []    

    bins = []

    

    for i in range(len(FileList)):

        ccd_image = fits.getdata(FileList[i])

        ccd_image = ccd_image.astype(np.float64)

        x = 2165

        y = 2276

        pixelvalue = ccd_image[y,x]

        pixelstack.append(pixelvalue)

       # print(FileList[i],pixelvalue)

        

    with open('pixelvalues.csv', 'w') as f:

        header = ('Filename,PixelValue\n')

        f.write(header)

        for i in range(len(FileList)):

            row = (str(FileList[i]) + ',' + str(pixelstack[i]) + '\n')

            print(FileList[i]+' '+ str(pixelstack[i]))

            f.write(row)

    f.close()  

    

    #font formatting for the chart   

    font = {'family' : 'DejaVu Sans',

        'weight' : 'regular',

        'size'   : 15}  

    plt.rc('font', **font)

    #setup figure

    plt.title('Histogram')

    plt.xlabel('Pixel Value')

    plt.ylabel('Frequency')

    

    print(min(pixelstack),max(pixelstack))

    

    for j in frange(min(pixelstack),max(pixelstack)+.03, 5):

        bins.append(j)  

        

   

    plt.hist(pixelstack,bins)

    plt.show()    

    

    

    return()           

    

# This is the standard boilerplate that calls the main() function.

if __name__ == '__main__':

  main() 

Ivor Trueman

Thanks Adam - that's really useful. I'm completely new to Python & Spyder, so it took me a while to figure out how to add 'astropy' & enter the file wildcards into the command line / modify the code for OSC fits, but it's working fine!

Many thanks
Ivor