#!/usr/bin/env python3 # -*- coding: utf-8 -*- # # Credit: # [1] Radially averaged power spectrum of 2D real-valued matrix # Evan Ruzanski # 'raPsd2d.m' # https://www.mathworks.com/matlabcentral/fileexchange/23636-radially-averaged-power-spectrum-of-2d-real-valued-matrix # # Aaron LI # Created: 2015-04-22 # Updated: 2016-04-28 # # Changelog: # 2016-04-28: # * Set default value for 'args.png' # * Rename from 'radialPSD2d.py' to 'calc_radial_psd.py' # 2016-04-26: # * Adjust plot function # * Update normalize argument; Add pixel argument # 2016-04-25: # * Update plot function # * Add command line scripting support # * Encapsulate the functions within class 'PSD' # * Update docs/comments # """ Compute the radially averaged power spectral density (i.e., power spectrum). """ __version__ = "0.3.2" __date__ = "2016-04-28" import sys import os import argparse import numpy as np from scipy import fftpack from astropy.io import fits import matplotlib.pyplot as plt from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas from matplotlib.figure import Figure plt.style.use("ggplot") class PSD: """ Computes the 2D power spectral density and the radially averaged power spectral density (i.e., 1D power spectrum). """ # 2D image data img = None # value and unit of 1 pixel for the input image pixel = (None, None) # whether to normalize the power spectral density by image size normalize = True # 2D power spectral density psd2d = None # 1D (radially averaged) power spectral density freqs = None psd1d = None psd1d_err = None def __init__(self, img, pixel=(1.0, "pixel"), normalize=True): self.img = img.astype(np.float) self.pixel = pixel self.normalize = normalize def calc_psd2d(self): """ Computes the 2D power spectral density of the given image. Note that the low frequency components are shifted to the center of the FFT'ed image. Return: 2D power spectral density, which is dimensionless if normalized, otherwise has unit ${pixel_unit}^2. """ rows, cols = self.img.shape ## Compute the power spectral density (i.e., power spectrum) imgf = fftpack.fftshift(fftpack.fft2(self.img)) if self.normalize: norm = rows * cols * self.pixel[0]**2 else: norm = 1.0 # Do not normalize self.psd2d = (np.abs(imgf) / norm) ** 2 return self.psd2d def calc_radial_psd1d(self, k_geometric=True, k_step=1.2): """ Computes the radially averaged power spectral density from the provided 2D power spectral density. XXX/TODO: Arguments: * k_geometric: whether the k (i.e., frequency) varies as geometric sequences (i.e., k, k*k_step, ...), otherwise, k varies as (k, k+k_step, ...) * k_step: the step ratio or step length for k Return: (freqs, radial_psd, radial_psd_err) freqs: spatial freqencies (unit: ${pixel_unit}^(-1)) if k_geometric=True, frequencies are taken as the geometric means. radial_psd: radially averaged power spectral density for each frequency radial_psd_err: standard deviations of each radial_psd """ psd2d = self.psd2d.copy() rows, cols = psd2d.shape ## Adjust the PSD array size dim_diff = np.abs(rows - cols) dim_max = max(rows, cols) # Pad the 2D PSD array to be sqaure if rows > cols: # pad columns if np.mod(dim_diff, 2) == 0: cols_left = np.zeros((rows, dim_diff/2)) cols_left[:] = np.nan cols_right = np.zeros((rows, dim_diff/2)) cols_right[:] = np.nan psd2d = np.hstack((cols_left, psd2d, cols_right)) else: cols_left = np.zeros((rows, np.floor(dim_diff/2))) cols_left[:] = np.nan cols_right = np.zeros((rows, np.floor(dim_diff/2)+1)) cols_right[:] = np.nan psd2d = np.hstack((cols_left, psd2d, cols_right)) elif rows < cols: # pad rows if np.mod(dim_diff, 2) == 0: rows_top = np.zeros((dim_diff/2, cols)) rows_top[:] = np.nan rows_bottom = np.zeros((dim_diff/2, cols)) rows_bottom[:] = np.nan psd2d = np.vstack((rows_top, psd2d, rows_bottom)) else: rows_top = np.zeros((np.floor(dim_diff/2), cols)) rows_top[:] = np.nan rows_bottom = np.zeros((np.floor(dim_diff/2)+1, cols)) rows_bottom[:] = np.nan psd2d = np.vstack((rows_top, psd2d, rows_bottom)) ## Compute radially average power spectrum px = np.arange(-dim_max/2, dim_max/2) x, y = np.meshgrid(px, px) rho, phi = self.cart2pol(x, y) rho = np.around(rho).astype(np.int) dim_half = int(np.floor(dim_max/2) + 1) radial_psd = np.zeros(dim_half) radial_psd_err = np.zeros(dim_half) # standard error for r in range(dim_half): # Get the indices of the elements satisfying rho[i,j]==r ii, jj = (rho == r).nonzero() # Calculate the mean value at a given radii data = psd2d[ii, jj] radial_psd[r] = np.nanmean(data) radial_psd_err[r] = np.nanstd(data) # Calculate frequencies f = fftpack.fftfreq(dim_max, d=1) # sample spacing: set to 1 pixel freqs = np.abs(f[:dim_half]) # self.freqs = freqs self.psd1d = radial_psd self.psd1d_err = radial_psd_err return (freqs, radial_psd, radial_psd_err) @staticmethod def cart2pol(x, y): """ Convert Cartesian coordinates to polar coordinates. """ rho = np.sqrt(x**2 + y**2) phi = np.arctan2(y, x) return (rho, phi) @staticmethod def pol2cart(rho, phi): """ Convert polar coordinates to Cartesian coordinates. """ x = rho * np.cos(phi) y = rho * np.sin(phi) return (x, y) def plot(self, ax=None, fig=None): """ Make a plot of the radial (1D) PSD with matplotlib. """ if ax is None: fig, ax = plt.subplots(1, 1) # xmin = self.freqs[1] / 1.2 # ignore the first 0 xmax = self.freqs[-1] ymin = np.nanmin(self.psd1d) / 10.0 ymax = np.nanmax(self.psd1d + self.psd1d_err) # eb = ax.errorbar(self.freqs, self.psd1d, yerr=self.psd1d_err, fmt="none") ax.plot(self.freqs, self.psd1d, "ko") ax.set_xscale("log") ax.set_yscale("log") ax.set_xlim(xmin, xmax) ax.set_ylim(ymin, ymax) ax.set_title("Radially Averaged Power Spectral Density") ax.set_xlabel(r"k (%s$^{-1}$)" % self.pixel[1]) if self.normalize: ax.set_ylabel("Power") else: ax.set_ylabel(r"Power (%s$^2$)" % self.pixel[1]) fig.tight_layout() return (fig, ax) def main(): parser = argparse.ArgumentParser( description="Compute the radially averaged power spectral density", epilog="Version: %s (%s)" % (__version__, __date__)) parser.add_argument("-V", "--version", action="version", version="%(prog)s " + "%s (%s)" % (__version__, __date__)) parser.add_argument("-i", "--infile", dest="infile", required=True, help="input image") parser.add_argument("-o", "--outfile", dest="outfile", required=True, help="output file to store the PSD data") parser.add_argument("-p", "--png", dest="png", help="plot the PSD and save (default: same basename as outfile)") parser.add_argument("-v", "--verbose", dest="verbose", action="store_true", help="show verbose information") parser.add_argument("-C", "--clobber", dest="clobber", action="store_true", help="overwrite the output files if already exist") args = parser.parse_args() if args.png == "": args.png = os.path.splitext(args.outfile)[0] + ".png" # Check output files whether already exists if (not args.clobber) and os.path.exists(args.outfile): raise ValueError("outfile '%s' already exists" % args.outfile) if (not args.clobber) and os.path.exists(args.png): raise ValueError("output png '%s' already exists" % args.png) # Load image data if args.verbose: print("Loading input image ...", file=sys.stderr) with fits.open(args.infile) as ffile: img = ffile[0].data psd = PSD(img, normalize=True) # Calculate the power spectral density if args.verbose: print("Calculate 2D power spectral density ...", file=sys.stderr) psd.calc_psd2d() if args.verbose: print("Calculate radially averaged (1D) power spectral density ...", file=sys.stderr) freqs, psd1d, psd1d_err = psd.calc_radial_psd1d() # Write out PSD results psd_data = np.column_stack((freqs, psd1d, psd1d_err)) np.savetxt(args.outfile, psd_data, header="freqs psd1d psd1d_err") # Make and save a plot fig = Figure(figsize=(10, 8)) canvas = FigureCanvas(fig) ax = fig.add_subplot(111) psd.plot(ax=ax, fig=fig) fig.savefig(args.png, format="png", dpi=150) if __name__ == "__main__": main()