img prep utils

2dfft_utils/misc/fits_to_text.py

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+'''
+    fitstotext.py
+    Purpose: Converts .fit files to .txt, replacing IRAF cl script.
+    Input: FITS image files. The string in line 16 can be modified to reflect your needs and file
+    naming conventions.
+    Output: .txt files with the pixel values for the corresponding image and the same basename.
+    Author: Erik Monson
+
+    Last modified May 29, 2015
+'''
+
+import glob
+from pyraf import iraf
+
+#Get filenames of all the suitable fits files in working directory
+fits_list_all = glob.glob("*crop.fit")
+
+if (len(fits_list_all) == 0):
+    print "ERROR: No fits files matching search string were found.\nCheck directory or search string."
+else:
+    #Convert the .fit files to .txt
+    for i in range(0,len(fits_list_all)):
+        basename = fits_list_all[i][0:(len(fits_list_all[i])-4)]
+        iraf.wtextimage(fits_list_all[i],basename+".txt",header='no',pixels='yes')
+#End program

2dfft_utils/misc/get_radius.py

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+'''
+    get_radius.py
+    Purpose: Automates the process of finding the radii of simulation images. Uses numpy and astropy.
+    Inputs:  all_centers.txt (the output from get_center.py) and all FITS images in the working directory
+    Outputs: r_max.txt, a list of the galaxies' radii in the same order as all_centers.txt
+    Notes: Line 28 in the Radius function removes the scales superimposed on the image from the calculation.
+           You may need to modify the slice indices, depending on whether or not your image has scales and 
+           where they are located.
+           It is best to run this script from a directory containing a complete set of simulation images (0.000 - 3.000 Gyr).
+           Otherwise, the entries in r_max.txt will not line up with those in all_centers.txt
+           It is not strictly necessary to loop over the entire image; assuming symmetry and looping over a smaller part 
+           would increase program speed.
+    Author: Erik Monson
+
+    Last modified July 10, 2015
+'''
+#!/usr/bin/env/ python
+import numpy as np
+from astropy.io import fits
+import glob
+import sys
+
+# Begin subroutine Radius
+def Radius(filename, CENTER_X, CENTER_Y):
+    img_data = fits.getdata(filename, ignore_missing_end = True) #Grab the pixel values from the image
+    X_SIZE,Y_SIZE = img_data.shape
+    img_data[0:80,0:600] = img_data[520:600,0:600] = 0 #Get rid of the scales at the top and bottom of the image
+    radius = 1
+    for i in range(Y_SIZE):
+        for j in range(X_SIZE):
+            if img_data[i][j] != 0: #If the pixel at (j,i) isn't black ...
+                distance = int(np.ceil(np.sqrt((j-CENTER_X)**2+(i-CENTER_Y)**2))) #find the distance from the center to the pixel at (j,i) ...
+                if distance > radius: #and if it's greater than the current record ...
+                    radius = distance #set the distance as the new record.
+    return radius
+# End subroutine
+
+# Begin main program
+imgs = glob.glob("*.fit") #Grab all the FITS files in the working directory
+if len(imgs) == 0:
+    print "There are no FITS files (.fit) in this directory\n"
+    sys.exit()
+names = np.loadtxt("all_centers.txt", dtype ='S', usecols = (0,)) #Grab the base names of the images to compare with the files in the directory
+centers = np.loadtxt("all_centers.txt",usecols = (1,2)) #Grab the x and y coords for the center from all_centers.txt
+outfile = open("r_max.txt","w")
+
+for i in range(len(names)):
+    if (names[i]+".fit") in imgs: #Make sure that the image is in the working directory
+        if len(names) > 1:
+            center_x = centers[i][0]
+            center_y = centers[i][1]
+        else:
+            center_x = centers[0]
+            center_y = centers[1]
+        radius = Radius(names[i]+".fit",center_x,center_y)
+        outfile.write(str(radius))
+        outfile.write('\n')
+        print names[i] + ' ' + str(radius) #This line can be commented
+outfile.close()
+# End main program