plotastrodata 1.7.14__tar.gz → 1.8.1__tar.gz

{plotastrodata-1.7.14/plotastrodata.egg-info → plotastrodata-1.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.7.14
+Version: 1.8.1
 Summary: plotastrodata is a tool for astronomers to create figures from FITS files and perform fundamental data analyses with ease.
 Home-page: https://github.com/yusukeaso-astron/plotastrodata
 Download-URL: https://github.com/yusukeaso-astron/plotastrodata

{plotastrodata-1.7.14 → plotastrodata-1.8.1}/plotastrodata/__init__.py

@@ -1,4 +1,4 @@
 import warnings
 
 warnings.simplefilter('ignore', FutureWarning)
-__version__ = '1.7.14'
+__version__ = '1.8.1'

{plotastrodata-1.7.14 → plotastrodata-1.8.1}/plotastrodata/analysis_utils.py

@@ -7,8 +7,8 @@ from scipy.signal import convolve
 
 from plotastrodata.coord_utils import coord2xy, xy2coord, rel2abs
 from plotastrodata.matrix_utils import Mfac, Mrot, dot2d
-from plotastrodata.other_utils import (estimate_rms, trim,
-                                       gaussian2d, isdeg,
+from plotastrodata.noise_utils import estimate_rms
+from plotastrodata.other_utils import (trim, gaussian2d, isdeg,
                                        RGIxy, RGIxyv, to4dim)
 from plotastrodata.fits_utils import FitsData, data2fits, Jy2K
 from plotastrodata import const_utils as cu

{plotastrodata-1.7.14 → plotastrodata-1.8.1}/plotastrodata/fits_utils.py

@@ -4,8 +4,8 @@ from astropy import units, wcs
 
 from plotastrodata.coord_utils import coord2xy, xy2coord
 from plotastrodata.matrix_utils import dot2d
-from plotastrodata.other_utils import (estimate_rms, trim, isdeg,
-                                       RGIxy)
+from plotastrodata.noise_utils import estimate_rms
+from plotastrodata.other_utils import trim, isdeg, RGIxy
 from plotastrodata import const_utils as cu
 
 

plotastrodata-1.8.1/plotastrodata/noise_utils.py

@@ -0,0 +1,222 @@
+import warnings
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy.special import erf
+
+from plotastrodata.fitting_utils import EmceeCorner
+
+
+def normalize(range: tuple = (-3.5, 3.5), bins: int = 100):
+    """Decorator factory to normalize a function over the given range."""
+    def decorator(f):
+        h = np.linspace(*range, bins + 1)
+        h = (h[1:] + h[:-1]) / 2
+        dh = (range[1] - range[0]) / 100
+
+        def wrapper(x, *args):
+            area = np.sum(f(h, *args)) * dh
+            if area == 0:
+                p = np.where(np.abs(x - args[1]) < dh / 2, 1 / dh, 0)
+            else:
+                p = f(x, *args) / area
+            return p
+
+        return wrapper
+    return decorator
+
+
+def gauss(x: np.ndarray, s: float, m: float) -> np.ndarray:
+    """Probability density of Gaussian noise.
+
+    Args:
+        x (np.ndarray): Intensity. The variable of the probability density.
+        s (float): Standard deviation of the Gaussian noise.
+        m (float): Mean of the Gaussian noise.
+
+    Returns:
+        np.ndarray: Probability density.
+    """
+    x1 = (x - m) / np.sqrt(2) / s
+    p = np.exp(-x1**2)
+    p = p / (np.sqrt(2 * np.pi) * s)
+    return p
+
+
+def gauss_pbcor(x: np.ndarray, s: float, m: float, R: float
+                ) -> np.ndarray:
+    """Probability density of Gaussian noise after primary-beam correction.
+
+    Args:
+        x (np.ndarray): Intensity. The variable of the probability density.
+        s (float): Standard deviation of the Gaussian noise.
+        m (float): Mean of the Gaussian noise.
+        R (float): The maximum radius scaled by the FWHM of the primary beam.
+
+    Returns:
+        np.ndarray: Probability density.
+    """
+    x1 = (x - m) / np.sqrt(2) / s
+    x0 = (x * 2**(-R**2) - m) / np.sqrt(2) / s
+    p = erf(x1) - erf(x0)
+    p = p / (2 * np.log(2) * x * R**2)
+    return p
+
+
+def select_noise(data: np.ndarray, sigma: str) -> np.ndarray:
+    """Select data pixels to be used for noise estimation.
+
+    Args:
+        data (np.ndarray): Original data array.
+        sigma (str): Selection methods. Multiple options are possible. 'edge', 'out', 'neg', or 'iter'.
+
+    Returns:
+        np.ndarray: 1D array that includes only the selected pixels.
+    """
+    n = data * 1
+    if 'edge' in sigma:
+        if np.ndim(n) <= 2:
+            print('\'edge\' is ignored because ndim <= 2.')
+        else:
+            n = n[::len(n) - 1]
+    if 'out' in sigma and 'pbcor' in sigma:
+        print('\'out\' is ignored because of \'pbcor\'.')
+    elif 'out' in sigma:
+        nx = np.shape(n)[-1]
+        ny = np.shape(n)[-2]
+        ntmp = np.moveaxis(n, [-2, -1], [0, 1])
+        ntmp[ny // 5: ny * 4 // 5, nx // 5: nx * 4 // 5] = np.nan
+        if np.all(np.isnan(ntmp)):
+            print('\'out\' is ignored because'
+                  + ' the outer region is filled with nan.')
+        else:
+            n = ntmp
+    n = n[~np.isnan(n)]
+    if 'neg' in sigma:
+        n = n[n < 0]
+        n = np.r_[n, -n]
+    if 'iter' in sigma:
+        for _ in range(5):
+            n = n[np.abs(n - np.mean(n)) < 3.5 * np.std(n)]
+    return n.ravel()
+
+
+class Noise:
+    def __init__(self, data: np.ndarray, sigma: str):
+        """This class holds the data selected as noise, histogram, and best-fit function.
+           The following methods are acceptable for data selection. Multiple options are possible.
+           'edge': use data[0] and data[-1].
+           'out': exclude inner 60% about axes=-2 and -1.
+           'neg': use only negative values.
+           'iter': exclude outliers.
+           The following methods are acceptable for noise estimation. Only single option is possible.
+           'med': calculate rms from the median of data^2 assuming Gaussian.
+           'hist': fit histgram with Gaussian.
+           'hist-pbcor': fit histgram with PB-corrected Gaussian.
+           '(no string)': calculate the mean and standard deviation.
+
+        Args:
+            data (np.ndarray): Original data array.
+            sigma (str): Methods above, like 'edge,neg,hist-pbcor'.
+        """
+        self.data = select_noise(data, sigma)
+        self.sigma = sigma
+        self.m0 = np.mean(self.data)
+        self.s0 = np.std(self.data)
+
+    def gen_histogram(self, **kwargs):
+        """Generage a pair of histogram and bins using numpy.histogram. The data values are shifted and scaled by the mean and standard deviation, respectively, to generate the histogram. The mean and standard deviation are stored as self.m0 and self.s0, respectively.
+        """
+        _kw = {'bins': 100, 'range': (-3.5, 3.5), 'density': True}
+        _kw.update(kwargs)
+        self.bins = _kw['bins']
+        self.range = _kw['range']
+        n = (self.data - self.m0) / self.s0
+        hist, hbin = np.histogram(n, **_kw)
+        hbin = (hbin[:-1] + hbin[1:]) / 2
+        self.hist = hist
+        self.hbin = hbin
+
+    def fit_histogram(self, **kwargs):
+        """kwargs is for plotastrodata.fitting_utils.EmceeCorner.
+        """
+        _kw = {'nwalkersperdim': 4, 'nsteps': 200, 'nburnin': 0}
+        _kw.update(kwargs)
+        f = gauss_pbcor if 'pbcor' in self.sigma else gauss
+        model = normalize(range=self.range, bins=self.bins)(f)
+        bounds = [[0.1, 2], [-2, 2]]
+        if 'pbcor' in self.sigma:
+            bounds.append([0.1, 2])
+        # curve_fit does not work for this fitting.
+        # 0.01 in sigma is set only to search the best-fit parameters.
+        # Thus, this sigma does not justify the parameter errors.
+        fitter = EmceeCorner(bounds=bounds, model=model,
+                             xdata=self.hbin, ydata=self.hist,
+                             sigma=np.max(self.hist) * 0.01)
+        fitter.fit(**_kw)
+        self.popt = fitter.popt
+        self.mean = float(self.popt[1] * self.s0 + self.m0)
+        self.std = float(self.popt[0] * self.s0)
+        self.model = model(self.hbin, *self.popt)
+
+    def plot_histogram(self, savefig: dict | str | None = None,
+                       show: bool = False):
+        """Make a simple figure of the histogram and model.
+
+        Args:
+            savefig (dict or str, optional): For plt.figure().savefig(). Defaults to None.
+            show (bool, optional): True means doing plt.show(). Defaults to False.
+        """
+        savefig0 = {'bbox_inches': 'tight', 'transparent': True}
+        fig = plt.figure()
+        ax = fig.add_subplot(1, 1, 1)
+        ax.plot(self.hbin, self.hist, drawstyle='steps-mid')
+        ax.plot(self.hbin, self.model, '-')
+        ax.set_xlabel('(noise - m0) / s0')
+        ax.set_ylabel('Probability density')
+        fig.tight_layout()
+        if savefig is not None:
+            s = {'fname': savefig} if type(savefig) is str else savefig
+            savefig0.update(s)
+            fig.savefig(**savefig0)
+        if show:
+            plt.show()
+        plt.close()
+
+
+def estimate_rms(data: np.ndarray,
+                 sigma: float | str | None = 'hist'
+                 ) -> float:
+    """Estimate a noise level of a data array.
+       When a float number or None is given as sigma, this function just outputs it.
+
+    Args:
+        data (np.ndarray): Data array whose noise is estimated.
+        sigma (float or str): Methods for the Noise class, like 'edge,neg,hist-pbcor'. Defaults to 'hist'.
+
+    Returns:
+        float: The estimated standard deviation of noise.
+    """
+    nums = [float, int, np.float64, np.int64, np.float32, np.int32]
+    if sigma is None or type(sigma) in nums:
+        return sigma
+
+    if np.ndim(np.squeeze(data)) == 0:
+        print('sigma cannot be estimated from only one pixel.')
+        return 0.0
+
+    n = Noise(data, sigma)
+    if 'hist' in sigma:
+        n.gen_histogram()
+        n.fit_histogram()
+        ave = n.mean
+        noise = n.std
+    elif 'med' in sigma:
+        ave = 0
+        noise = np.sqrt(np.median(n.data**2) / 0.454936)
+    else:
+        ave = n.m0
+        noise = n.s0
+    if np.abs(ave) > 0.2 * noise:
+        s = 'Mean > 0.2 x standard deviation.'
+        warnings.warn(s, UserWarning)
+    return noise

{plotastrodata-1.7.14 → plotastrodata-1.8.1}/plotastrodata/other_utils.py

@@ -1,9 +1,6 @@
-import warnings
 import numpy as np
-from scipy.special import erf
 from scipy.interpolate import RegularGridInterpolator as RGI
 
-from plotastrodata.fitting_utils import EmceeCorner
 from plotastrodata.matrix_utils import Mrot, dot2d
 
 
@@ -37,127 +34,6 @@ def isdeg(s: str) -> bool:
         return False
 
 
-def _estimate_rms_hist(data: np.ndarray, sigma: str) -> tuple:
-    h_range = (-3.5, 3.5)
-    h = np.linspace(*h_range, 101)
-    dh = 0.07
-    m0 = np.mean(data)
-    s0 = np.std(data)
-    hist, hbin = np.histogram((data - m0) / s0, bins=100,
-                              density=True, range=h_range)
-    hbin = (hbin[:-1] + hbin[1:]) / 2
-    
-    def normalize(f):
-        """Decorator to normalize a function over h_range."""
-        def wrapper(x, *args):
-            area = np.sum(f(h, *args)) * dh
-            if area == 0:
-                p = np.where(np.abs(x - args[1]) < dh / 2, 1 / dh, 0)
-            else:
-                p = f(x, *args) / area
-            return p
-        return wrapper
-
-    if 'pbcor' in sigma:
-        @normalize
-        def model(x, *args):
-            s, m, R = args
-            x1 = (x - m) / np.sqrt(2) / s
-            x0 = (x * 2**(-R**2) - m) / np.sqrt(2) / s
-            p = erf(x1) - erf(x0)
-            p = p / (2 * np.log(2) * x * R**2)
-            return p
-        bounds = [[0.1, 2], [-2, 2], [0.1, 2]]
-    else:
-        @normalize
-        def model(x, *args):
-            s, m = args
-            x1 = (x - m) / np.sqrt(2) / s
-            p = np.exp(-x1**2)
-            p = p / (np.sqrt(2 * np.pi) * s)
-            return p
-        bounds = [[0.1, 2], [-2, 2]]
-    # curve_fit does not work for this fitting.
-    fitter = EmceeCorner(bounds=bounds, sigma=np.max(hist) * 0.01,
-                         model=model, xdata=hbin, ydata=hist)
-    fitter.fit(nwalkersperdim=4, nsteps=200, nburnin=0)
-    popt = fitter.popt
-    ave = popt[1] * s0 + m0
-    noise = popt[0] * s0
-    return ave, noise
-
-
-def estimate_rms(data: np.ndarray, sigma: float | str | None = 'hist'
-                 ) -> float:
-    """Estimate a noise level of a N-D array.
-       When a float number or None is given, this function just outputs it.
-       The following methods are acceptable for data selection. Multiple options are possible.
-       'edge': use data[0] and data[-1].
-       'out': exclude inner 60% about axes=-2 and -1.
-       'neg': use only negative values.
-       'iter': exclude outliers.
-       The following methods are acceptable for noise estimation. Only single option is possible.
-       'med': calculate rms from the median of data^2 assuming Gaussian.
-       'hist': fit histgram with Gaussian.
-       'hist-pbcor': fit histgram with PB-corrected Gaussian.
-       '(no string)': calculate the mean and standard deviation.
-
-    Args:
-        data (np.ndarray): N-D array.
-        sigma (float or str): Methods above, like 'edge,neg,hist-pbcor'. Defaults to 'hist'.
-
-    Returns:
-        float: The estimated standard deviation of noise.
-    """
-    nums = [float, int, np.float64, np.int64, np.float32, np.int32]
-    if sigma is None or type(sigma) in nums:
-        return sigma
-
-    if np.ndim(np.squeeze(data)) == 0:
-        print('sigma cannot be estimated from only one pixel.')
-        return 0.0
-
-    # Selection
-    n = data * 1
-    if 'edge' in sigma:
-        if np.ndim(n) <= 2:
-            print('\'edge\' is ignored because ndim <= 2.')
-        else:
-            n = n[::len(n) - 1]
-    if 'out' in sigma and 'pbcor' in sigma:
-        print('\'out\' is ignored because of \'pbcor\'.')
-    elif 'out' in sigma:
-        nx = np.shape(n)[-1]
-        ny = np.shape(n)[-2]
-        ntmp = np.moveaxis(n, [-2, -1], [0, 1])
-        ntmp[ny // 5 : ny * 4 // 5, nx // 5 : nx * 4 // 5] = np.nan
-        if np.all(np.isnan(ntmp)):
-            print('\'out\' is ignored because'
-                  + ' the outer region is filled with nan.')
-        else:
-            n = ntmp
-    n = n[~np.isnan(n)]
-    if 'neg' in sigma:
-        n = n[n < 0]
-        n = np.r_[n, -n]
-    if 'iter' in sigma:
-        for _ in range(5):
-            n = n[np.abs(n - np.mean(n)) < 3.5 * np.std(n)]
-    # Estimation
-    if 'hist' in sigma:
-        ave, noise = _estimate_rms_hist(n, sigma)
-    elif 'med' in sigma:
-        ave = 0
-        noise = np.sqrt(np.median(n**2) / 0.454936)
-    else:
-        ave = np.mean(n)
-        noise = np.std(n)
-    if np.abs(ave) > 0.2 * noise:
-        s = 'The intensity offset is larger than 0.2 sigma.'
-        warnings.warn(s, UserWarning)
-    return noise
-
-
 def trim(data: np.ndarray | None = None, x: np.ndarray | None = None,
          y: np.ndarray | None = None, v: np.ndarray | None = None,
          xlim: list[float, float] | None = None,

{plotastrodata-1.7.14 → plotastrodata-1.8.1}/plotastrodata/plot_utils.py

@@ -6,7 +6,8 @@ from matplotlib.patches import Ellipse, Rectangle
 from dataclasses import dataclass
 
 from plotastrodata.coord_utils import coord2xy, xy2coord
-from plotastrodata.other_utils import listing, estimate_rms
+from plotastrodata.noise_utils import estimate_rms
+from plotastrodata.other_utils import listing
 from plotastrodata.analysis_utils import AstroData, AstroFrame
 
 
@@ -87,7 +88,7 @@ class PlotAxes2D():
         aspect (dict or float, optional): Defaults to None.
     """
     samexy: bool = True
-    loglog: bool | None = None
+    loglog: float | None = None
     xscale: str = 'linear'
     yscale: str = 'linear'
     xlim: list | None = None
@@ -98,8 +99,8 @@ class PlotAxes2D():
     yticks: list | None = None
     xticklabels: list | None = None
     yticklabels: list | None = None
-    xticksminor: list | int = None
-    yticksminor: list | int = None
+    xticksminor: list | int | None = None
+    yticksminor: list | int | None = None
     grid: dict | None = None
     aspect: dict | float | None = None
 
@@ -1169,9 +1170,12 @@ def plotprofile(coords: list[str] | str = [],
                 title: list[str] | None = None,
                 text: list[str] | None = None,
                 dist: float = 1., vsys: float = 0.,
-                nrows: int = 0, ncols: int = 1, fig=None, ax=None,
+                nrows: int = 0, ncols: int = 1,
+                fig: object | None = None,
+                ax: object | None = None,
                 getfigax: bool = False,
-                savefig: dict = None, show: bool = True,
+                savefig: dict | str | None = None,
+                show: bool = False,
                 **kwargs) -> tuple[object, object]:
     """Use Axes.plot of matplotlib to plot line profiles at given coordinates. kwargs must include the arguments of AstroData to specify the data to be plotted. kwargs can include the arguments of PlotAxes2D to adjust x and y axes.
 
@@ -1187,6 +1191,15 @@ def plotprofile(coords: list[str] | str = [],
         gauss_kwargs (dict, optional): Kwargs for Axes.plot. Defaults to {}.
         title (list, optional): For each plot. Defaults to None.
         text (list, optional): For each plot. Defaults to None.
+        dist (float, optional): Change x and y in arcsec to au. Defaults to 1..
+        vsys (float, optional): Each channel shows v-vsys. Defaults to 0..
+        nrows (int, optional): Used for channel maps. Defaults to 0.
+        ncols (int, optional): Used for channel maps. Defaults to 1.
+        fig (optional): External plt.figure(). Defaults to None.
+        ax (optional): External fig.add_subplot(). Defaults to None.
+        getfigax (bool, optional): Defaults to False.
+        savefig (dict or str, optional): For plt.figure().savefig(). Defaults to None.
+        show (bool, optional): True means doing plt.show(). Defaults to False.
 
     Returns:
         tuple: (fig, ax), where ax is a list, if getfigax=True. Otherwise, no return.
@@ -1280,7 +1293,20 @@ def plotslice(length: float, dx: float | None = None, pa: float = 0,
         length (float): Slice length.
         dx (float, optional): Grid increment. Defaults to None.
         pa (float, optional): Degree. Position angle. Defaults to 0.
-        fitsimage to show: same as in PlotAstroData.
+        dist (float, optional): For AstroFrame. Defaults to 1.
+        xoff (float, optional): For AstroFrame. Defaults to 0.
+        yoff (float, optional): For AstroFrame. Defaults to 0.
+        xflip (bool, optional): For AstroFrame. Defaults to True.
+        yflip (bool, optional): For AstroFrame. Defaults to False.
+        txtfile (str, optional): File name for numpy.savetxt(). Defaults to None.
+        fig (optional): External plt.figure(). Defaults to None.
+        ax (optional): External fig.add_subplot(). Defaults to None.
+        getfigax (bool, optional): Defaults to False.
+        savefig (dict or str, optional): For plt.figure().savefig(). Defaults to None.
+        show (bool, optional): True means doing plt.show(). Defaults to False.
+
+    Returns:
+        tuple: (fig, ax), where ax is a list, if getfigax=True. Otherwise, no return.
     """
     _kw = {'linestyle': '-', 'marker': 'o'}
     _kw.update(kwargs)

{plotastrodata-1.7.14 → plotastrodata-1.8.1/plotastrodata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.7.14
+Version: 1.8.1
 Summary: plotastrodata is a tool for astronomers to create figures from FITS files and perform fundamental data analyses with ease.
 Home-page: https://github.com/yusukeaso-astron/plotastrodata
 Download-URL: https://github.com/yusukeaso-astron/plotastrodata

{plotastrodata-1.7.14 → plotastrodata-1.8.1}/plotastrodata.egg-info/SOURCES.txt

@@ -13,6 +13,7 @@ plotastrodata/fits_utils.py
 plotastrodata/fitting_utils.py
 plotastrodata/los_utils.py
 plotastrodata/matrix_utils.py
+plotastrodata/noise_utils.py
 plotastrodata/other_utils.py
 plotastrodata/plot_utils.py
 plotastrodata.egg-info/PKG-INFO