From 2a4f07ece389ab3454afeeeced8480a1c958f8f9 Mon Sep 17 00:00:00 2001 From: Aaron LI Date: Mon, 16 Oct 2017 10:57:51 +0800 Subject: Move python/calc_radial_psd.py to astro/calc_psd.py with some cleanup --- python/calc_radial_psd.py | 460 ---------------------------------------------- 1 file changed, 460 deletions(-) delete mode 100755 python/calc_radial_psd.py (limited to 'python') diff --git a/python/calc_radial_psd.py b/python/calc_radial_psd.py deleted file mode 100755 index b7d1743..0000000 --- a/python/calc_radial_psd.py +++ /dev/null @@ -1,460 +0,0 @@ -#!/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 -# -# XXX: -# * If the input image is NOT SQUARE; then are the horizontal frequencies -# the same as the vertical frequencies ?? -# -# Aaron LI -# Created: 2015-04-22 -# Updated: 2016-04-28 -# -# Changelog: -# 2016-04-28: -# * Fix wrong meshgrid with respect to the shift zero-frequency component -# * Use "numpy.fft" instead of "scipy.fftpack" -# * Split method "pad_square()" from "calc_radial_psd()" -# * Hide numpy warning when dividing by zero -# * Add method "AstroImage.fix_shapes()" -# * Add support for background subtraction and exposure correction -# * Show verbose information during calculation -# * Add class "AstroImage" -# * 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__ = "0.5.0" -__date__ = "2016-04-28" - - -import sys -import os -import argparse - -import numpy as np -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. - - NOTE: - The zero-frequency component is shifted to position of index (0-based) - (ceil((n-1) / 2), ceil((m-1) / 2)), - where (n, m) are the number of rows and columns of the image/psd2d. - - Return: - 2D power spectral density, which is dimensionless if normalized, - otherwise has unit ${pixel_unit}^2. - """ - print("Calculating 2D power spectral density ... ", end="", flush=True) - rows, cols = self.img.shape - # Compute the power spectral density (i.e., power spectrum) - imgf = np.fft.fftshift(np.fft.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 - print("DONE", flush=True) - return self.psd2d - - def calc_radial_psd1d(self): - """ - Computes the radially averaged power spectral density from the - provided 2D power spectral density. - - Return: - (freqs, radial_psd, radial_psd_err) - freqs: spatial freqencies (unit: ${pixel_unit}^(-1)) - radial_psd: radially averaged power spectral density for each - frequency - radial_psd_err: standard deviations of each radial_psd - """ - print("Calculating radial (1D) power spectral density ... ", - end="", flush=True) - print("padding ... ", end="", flush=True) - psd2d = self.pad_square(self.psd2d, value=np.nan) - dim = psd2d.shape[0] - dim_half = (dim+1) // 2 - # NOTE: - # The zero-frequency component is shifted to position of index - # (0-based): (ceil((n-1) / 2), ceil((m-1) / 2)) - px = np.arange(dim_half-dim, dim_half) - x, y = np.meshgrid(px, px) - rho, phi = self.cart2pol(x, y) - rho = np.around(rho).astype(np.int) - radial_psd = np.zeros(dim_half) - radial_psd_err = np.zeros(dim_half) - print("radially averaging ... ", end="", flush=True) - 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 = np.fft.fftfreq(dim, d=self.pixel[0]) - freqs = np.abs(f[:dim_half]) - # - self.freqs = freqs - self.psd1d = radial_psd - self.psd1d_err = radial_psd_err - print("DONE", flush=True) - 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) - - @staticmethod - def pad_square(data, value=np.nan): - """ - Symmetrically pad the supplied data matrix to make it square. - The padding rows are equally added to the top and bottom, - as well as the columns to the left and right sides. - The padded rows/columns are filled with the specified value. - """ - mat = data.copy() - rows, cols = mat.shape - dim_diff = abs(rows - cols) - dim_max = max(rows, cols) - if rows > cols: - # pad columns - if dim_diff // 2 == 0: - cols_left = np.zeros((rows, dim_diff/2)) - cols_left[:] = value - cols_right = np.zeros((rows, dim_diff/2)) - cols_right[:] = value - mat = np.hstack((cols_left, mat, cols_right)) - else: - cols_left = np.zeros((rows, np.floor(dim_diff/2))) - cols_left[:] = value - cols_right = np.zeros((rows, np.floor(dim_diff/2)+1)) - cols_right[:] = value - mat = np.hstack((cols_left, mat, cols_right)) - elif rows < cols: - # pad rows - if dim_diff // 2 == 0: - rows_top = np.zeros((dim_diff/2, cols)) - rows_top[:] = value - rows_bottom = np.zeros((dim_diff/2, cols)) - rows_bottom[:] = value - mat = np.vstack((rows_top, mat, rows_bottom)) - else: - rows_top = np.zeros((np.floor(dim_diff/2), cols)) - rows_top[:] = value - rows_bottom = np.zeros((np.floor(dim_diff/2)+1, cols)) - rows_bottom[:] = value - mat = np.vstack((rows_top, mat, rows_bottom)) - return mat - - 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) - - -class AstroImage: - """ - Manipulate the astronimcal counts image, as well as the corresponding - exposure map and background map. - """ - # input counts image - image = None - # exposure map with respect to the input counts image - expmap = None - # background map (e.g., stowed background) - bkgmap = None - # exposure time of the input image - exposure = None - # exposure time of the background map - exposure_bkg = None - - def __init__(self, image, expmap=None, bkgmap=None): - self.load_image(image) - self.load_expmap(expmap) - self.load_bkgmap(bkgmap) - - @staticmethod - def open_image(infile): - """ - Open the slice image and return its header and 2D image data. - - NOTE - ---- - The input slice image may have following dimensions: - * NAXIS=2: [Y, X] - * NAXIS=3: [FREQ=1, Y, X] - * NAXIS=4: [STOKES=1, FREQ=1, Y, X] - - NOTE - ---- - Only open slice image that has only ONE frequency and ONE Stokes - parameter. - - Returns - ------- - header : `~astropy.io.fits.Header` - image : 2D `~numpy.ndarray` - The 2D [Y, X] image part of the slice image. - """ - with fits.open(infile) as f: - header = f[0].header - data = f[0].data - if data.ndim == 2: - # NAXIS=2: [Y, X] - image = data - elif data.ndim == 3 and data.shape[0] == 1: - # NAXIS=3: [FREQ=1, Y, X] - image = data[0, :, :] - elif data.ndim == 4 and data.shape[0] == 1 and data.shape[1] == 1: - # NAXIS=4: [STOKES=1, FREQ=1, Y, X] - image = data[0, 0, :, :] - else: - raise ValueError("Slice '{0}' has invalid dimensions: {1}".format( - infile, data.shape)) - return (header, image) - - def load_image(self, image): - print("Loading image ... ", end="", flush=True) - self.header, self.image = self.open_image(image) - self.exposure = self.header.get("EXPOSURE") - print("DONE", flush=True) - - def load_expmap(self, expmap): - if expmap: - print("Loading exposure map ... ", end="", flush=True) - __, self.expmap = self.open_image(expmap) - print("DONE", flush=True) - - def load_bkgmap(self, bkgmap): - if bkgmap: - print("Loading background map ... ", end="", flush=True) - header, self.bkgmap = self.open_image(bkgmap) - self.exposure_bkg = header.get("EXPOSURE") - print("DONE", flush=True) - - def fix_shapes(self, tolerance=2): - """ - Fix the shapes of self.expmap and self.bkgmap to make them have - the same shape as the self.image. - - NOTE: - * if the image is bigger than the reference image, then its - columns on the right and rows on the botton are clipped; - * if the image is smaller than the reference image, then padding - columns on the right and rows on the botton are added. - * Original images are REPLACED! - - Arguments: - * tolerance: allow absolute difference between images - """ - def _fix_shape(img, ref, tol=tolerance): - if img.shape == ref.shape: - print("SKIPPED", flush=True) - return img - elif np.allclose(img.shape, ref.shape, atol=tol): - print(img.shape, "->", ref.shape, flush=True) - rows, cols = img.shape - rows_ref, cols_ref = ref.shape - # rows - if rows > rows_ref: - img_fixed = img[:rows_ref, :] - else: - img_fixed = np.row_stack((img, - np.zeros((rows_ref-rows, cols), dtype=img.dtype))) - # columns - if cols > cols_ref: - img_fixed = img_fixed[:, :cols_ref] - else: - img_fixed = np.column_stack((img_fixed, - np.zeros((rows_ref, cols_ref-cols), dtype=img.dtype))) - return img_fixed - else: - raise ValueError("shape difference exceeds tolerance: " + \ - "(%d, %d) vs. (%d, %d)" % (img.shape + ref.shape)) - # - if self.bkgmap is not None: - print("Fixing shape for bkgmap ... ", end="", flush=True) - self.bkgmap = _fix_shape(self.bkgmap, self.image) - if self.expmap is not None: - print("Fixing shape for expmap ... ", end="", flush=True) - self.expmap = _fix_shape(self.expmap, self.image) - - def subtract_bkg(self): - print("Subtracting background ... ", end="", flush=True) - self.image -= (self.bkgmap / self.exposure_bkg * self.exposure) - print("DONE", flush=True) - - def correct_exposure(self, cut=0.015): - """ - Correct the image for exposure by dividing by the expmap to - create the exposure-corrected image. - - Arguments: - * cut: the threshold percentage with respect to the maximum - exposure map value; and those pixels with lower values - than this threshold will be excluded/clipped (set to ZERO) - if set to None, then skip clipping image - """ - print("Correcting image for exposure ... ", end="", flush=True) - with np.errstate(divide="ignore", invalid="ignore"): - self.image /= self.expmap - # set invalid values to ZERO - self.image[ ~ np.isfinite(self.image) ] = 0.0 - print("DONE", flush=True) - if cut is not None: - # clip image according the exposure threshold - print("Clipping image (%s) ... " % cut, end="", flush=True) - threshold = cut * np.max(self.expmap) - self.image[ self.expmap < threshold ] = 0.0 - print("DONE", flush=True) - - -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("-C", "--clobber", dest="clobber", - action="store_true", - help="overwrite the output files if already exist") - parser.add_argument("-i", "--infile", dest="infile", - required=True, help="input image") - parser.add_argument("-b", "--bkgmap", dest="bkgmap", default=None, - help="background map (for background subtraction)") - parser.add_argument("-e", "--expmap", dest="expmap", default=None, - help="exposure map (for exposure correction)") - parser.add_argument("-o", "--outfile", dest="outfile", - required=True, help="output file to store the PSD data") - parser.add_argument("-p", "--png", dest="png", default=None, - help="plot the PSD and save (default: same basename as outfile)") - args = parser.parse_args() - - if args.png is None: - 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 - image = AstroImage(image=args.infile, expmap=args.expmap, - bkgmap=args.bkgmap) - image.fix_shapes() - if args.bkgmap: - image.subtract_bkg() - if args.expmap: - image.correct_exposure() - - # Calculate the power spectral density - psd = PSD(img=image.image, normalize=True) - psd.calc_psd2d() - 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() -- cgit v1.2.2