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

Comments

• BlockHead

  June 2021

  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

  June 2021

  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