Create SimImage.py

2dfft_utils/misc/SimImage.py

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+'''
+    SimImage.py
+    A python class interface that collects many of the tasks needed to prepare simulated galaxy images
+    for 2DFFT and pitch angle measurement in one place.
+
+    To use this class, include this import statement (without quotes) in the header of your python script 
+    (or type it into your python shell of choice):
+        "from SimImage import SimImage"
+
+    Methods:    SimImage(filename, radius = None, center = (None,None)) - Constructor; can be passed a
+                    radius and a center tuple.
+                GetCenter() - Finds the image center with an IRAF (Pyraf) task.
+                GetRadius() - Finds the galaxy's radial extent using Astropy. Requires a defined center.
+                Crop() - Crops the image with an IRAF (Pyraf) task. Requires a defined radius and center.
+                ConvertText() - Converts the image to a .txt file with an IRAF (Pyraf) task.
+                ScriptString() - Returns a string formatted for the 2DFFT scripter's input.
+                ImgStats() - Returns a string containing the name, center, and radius of the image.
+
+    Methods include exception handling where relevant and return a Linux standard exit status (0 = success, 1 = error) 
+    where relevant. However, IRAF converts some errors into warnings which can't be caught by try-except. This is 
+    common when the name of an input file is entered incorrectly, so it is best to double-check filenames.
+
+    This class was designed and tested with a very specific set of disk-on simulation images in mind, so 
+    modification may be necessary to extend it to other simulations or real galaxy images.
+
+    Several methods are modified or copied from programs written by J.E. Berlanga Medina.
+
+    The methods GetCenter, Crop, and ConvertText use Pyraf; GetRadius uses Astropy.
+
+    Class written by E. Monson
+    Last edited June 22, 2015.
+
+TODO - make GetCenter work with filenames outside our convention.
+'''
+
+from pyraf import iraf
+from astropy.io import fits
+import numpy as np
+
+class SimImage():
+
+    #Constructor expects only the name of the image file, but can be passed
+    #the radius and center as well.
+    def __init__(self, filename, radius = None, center = (None,None)):
+        self.name = filename
+        self.radius = radius
+        self.center = center
+
+    #GetCenter uses the IRAF imcntr task to find the center of the image.
+    #Based on the size of the image, the first guess for center may need to be changed.
+    #cboxsize should be an odd number.
+    #See get_center.py (J. Berlanga) for the original implementation and documentation.
+    def GetCenter(self):
+        try:
+            center_string = iraf.imcntr(self.name,300,300,cboxsize=31, Stdout=1)
+            x_coord = int(round(float(center_string[0][19:26])))
+            y_coord = int(round(float(center_string[0][33:40])))
+            self.center = (x_coord,y_coord)
+            return 0
+        except IndexError:
+            print "IndexError: Image not found or incompatible."
+            return 1
+        except iraf.IrafError as e:
+            print "IRAF Error: " + e
+            return 1
+
+    #GetRadius uses the fits module from astropy to pull the pixel values of the image.
+    #Based on the size of the image and whether it has overlaid scales, the indices
+    #in the fourth line may need to be changed.
+    #Note that GetRadius requires that self.center be defined, e.g. by calling GetCenter().
+    #See get_radius.py (E. Monson) for the orignal implementation and documentation.
+    def GetRadius(self):
+        try:
+            img_data = fits.getdata(self.name, ignore_missing_end = True)
+            X_SIZE,Y_SIZE = img_data.shape
+            img_data[0:80,0:600] = img_data[520:600,0:600] = 0
+            radius = 1
+            for i in range(Y_SIZE):
+                for j in range(X_SIZE):
+                    if img_data[i][j] != 0:
+                        distance = int(np.ceil(np.sqrt((j-self.center[0])**2+(i-self.center[1])**2)))
+                        if distance > radius:
+                            radius = distance
+            self.radius = radius
+            status = 0
+        except TypeError:
+            print "TypeError: Image center not defined."
+            status = 1
+        except IOError:
+            print "IOError: Image not found or incompatible."
+            status = 1
+        finally:
+            return status
+
+    #Crop uses the IRAF imcopy task to crop a galaxy image to a square filled by the galaxy.
+    #Creates a new file name_crop.fit in the current directory.
+    #See auto_crop_fits.py (J. Berlanga) for the original implementation and documentation.
+    def Crop(self):
+        try:
+            iraf.imcopy(self.name+"["+str(int(self.center[0]-self.radius))+":"+str(int(self.center[0]+self.radius))+","+str(int(self.center[1]-self.radius))+":"+str(int(self.center[1]+self.radius))+"]",self.name[:-4]+"_crop.fit")
+            status = 0
+        except TypeError:
+            print "TypeError: Image center or radius not defined."
+            status = 1
+        except iraf.IrafError as e:
+            print "IRAF Error: " + e
+            status = 1
+        finally:
+            return status
+
+    #ConvertText uses the IRAF wtextimage task to convert images (usually cropped images) to text files.
+    #Creates a new file, name.txt, in the current directory.
+    #ConvertText is particularly susceptible to returning a misleading exit status due to the way that IRAF
+    #handles errors - if given an invalid filename, its exit status will remain 0 even though the process does not
+    #complete.
+    def ConvertText(self):
+        try:
+            iraf.wtextimage(self.name,self.name[:-4]+".txt",header='no',pixels='yes')
+            return 0
+        except iraf.IrafError as e:
+            print "IRAF Error: " + e
+            return 1
+
+    #ScriptString returns a string formatted for the 2DFFT scripter input.
+    def ScriptString(self):
+        return self.name[0:8]+"_crop.txt"+","+self.name[0:8]+","+str(int(self.radius-1))
+
+    #ImgStats returns a string containing the image keyword (i.e., the snapshot date),
+    #the center coordinates, and the radius, separated by tabs.
+    def ImgStats(self):
+        return self.name[0:8]+"\t"+str(self.center)+"\t"+str(self.radius)

2dfft_utils/misc/sim_prep.py

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+'''
+    sim_prep.py
+    A simple script using SimImage.py to prepare an entire sim batch at once.
+
+    Erik Monson
+    Last edited August 21, 2015
+'''
+
+#/usr/bin/env python
+import glob
+from SimImage import SimImage
+
+#------Begin program------
+all_fits = glob.glob("*.fit")
+sim_name = str(raw_input("Enter the name of this simulation (e.g. a1_lores): "))
+
+scripter_file = open("scripter_input-"+sim_name+".txt",'w')
+scripter_file.write('\n')
+
+for filename in all_fits:
+    image = SimImage(filename)
+    if not image.GetCenter():
+        image.GetRadius()
+        print image.ImgStats()
+        if not image.Crop():
+            crop_image = SimImage(image.name[:-4]+"_crop.fit")
+            crop_image.ConvertText()
+            del crop_image
+            scripter_file.write(image.ScriptString()+'\n')
+    del image
+
+scripter_file.write('\n')
+scripter_file.close()
+#-----End program-----