plotastrodata 1.8.0__tar.gz → 1.8.2__tar.gz

{plotastrodata-1.8.0/plotastrodata.egg-info → plotastrodata-1.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.8.0
+Version: 1.8.2
 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-1.8.0 → plotastrodata-1.8.2}/plotastrodata/__init__.py

@@ -1,4 +1,4 @@
 import warnings
 
 warnings.simplefilter('ignore', FutureWarning)
-__version__ = '1.8.0'
+__version__ = '1.8.2'

{plotastrodata-1.8.0 → plotastrodata-1.8.2}/plotastrodata/noise_utils.py

@@ -1,5 +1,6 @@
 import warnings
 import numpy as np
+import matplotlib.pyplot as plt
 from scipy.special import erf
 
 from plotastrodata.fitting_utils import EmceeCorner
@@ -100,23 +101,23 @@ def select_noise(data: np.ndarray, sigma: str) -> np.ndarray:
 
 
 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.
+    """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'.
-        """
+    Args:
+        data (np.ndarray): Original data array.
+        sigma (str): Methods above, like 'edge,neg,hist-pbcor'.
+    """
+    def __init__(self, data: np.ndarray, sigma: str):
         self.data = select_noise(data, sigma)
         self.sigma = sigma
         self.m0 = np.mean(self.data)
@@ -157,12 +158,36 @@ class Noise:
         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 N-D array.
-       When a float number or None is given, this function just outputs it.
+    """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.

{plotastrodata-1.8.0 → plotastrodata-1.8.2}/plotastrodata/plot_utils.py

@@ -88,7 +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
@@ -99,8 +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
 
@@ -271,6 +271,8 @@ def kwargs2AstroFrame(kw: dict) -> AstroFrame:
     for k in vars(f):
         if k in kw:
             tmp[k] = kw[k]
+            if k not in ['fitsimage', 'center']:
+                del kw[k]
     f = AstroFrame(**tmp)
     return f
 
@@ -1161,6 +1163,30 @@ class PlotAstroData(AstroFrame):
         return fig, self.ax[0]
 
 
+def close_figure(fig: object,
+                 savefig: dict | str | None = None,
+                 show: bool = False) -> tuple[object, object]:
+    """Save, show, and close the figure.
+
+    Args:
+        fig (optional): External plt.figure(). Defaults to None.
+        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.
+    """
+    savefig0 = {'bbox_inches': 'tight', 'transparent': True}
+    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 plotprofile(coords: list[str] | str = [],
                 xlist: list[float] = [], ylist: list[float] = [],
                 ellipse: list[float, float, float] | None = None,
@@ -1169,12 +1195,14 @@ def plotprofile(coords: list[str] | str = [],
                 gaussfit: bool = False, gauss_kwargs: dict = {},
                 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.
+    """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 must include the arguments of AstroFrame to specify the ranges and so on for plotting. kwargs can include the arguments of PlotAxes2D to adjust x and y axes.
 
     Args:
         coords (list, optional): Coordinates. Defaults to [].
@@ -1188,6 +1216,13 @@ 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.
+        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.
@@ -1196,13 +1231,10 @@ def plotprofile(coords: list[str] | str = [],
     _kw.update(kwargs)
     _kwgauss = {'drawstyle': 'default', 'color': 'g'}
     _kwgauss.update(gauss_kwargs)
-    savefig0 = {'bbox_inches': 'tight', 'transparent': True}
     if type(coords) is str:
         coords = [coords]
-    vmin, vmax = _kw['xlim'] if 'xlim' in _kw else [-1e10, 1e10]
-    f = AstroFrame(dist=dist, vsys=vsys, vmin=vmin, vmax=vmax)
+    f = kwargs2AstroFrame(_kw)
     d = kwargs2AstroData(_kw)
-    Tb = d.Tb
     f.read(d)
     d.binning([width, 1, 1])
     v, prof, gfitres = d.profile(coords=coords, xlist=xlist, ylist=ylist,
@@ -1211,7 +1243,7 @@ def plotprofile(coords: list[str] | str = [],
     nprof = len(prof)
     if 'ylabel' in _kw:
         ylabel = _kw['ylabel']
-    elif Tb:
+    elif d.Tb:
         ylabel = r'$T_b$ (K)'
     elif flux:
         ylabel = 'Flux (Jy)'
@@ -1237,7 +1269,7 @@ def plotprofile(coords: list[str] | str = [],
     if 'xlim' not in _kw:
         _kw['xlim'] = [v.min(), v.max()]
     _kw['samexy'] = False
-    pa2d = kwargs2PlotAxes2D(_kw)
+    pa2 = kwargs2PlotAxes2D(_kw)
     for i in range(nprof):
         sharex = None if i < nrows - 1 else ax[i - 1]
         ax[i] = fig.add_subplot(nrows, ncols, i + 1, sharex=sharex)
@@ -1246,7 +1278,7 @@ def plotprofile(coords: list[str] | str = [],
         ax[i].plot(v, prof[i], **_kw)
         ax[i].hlines([0], v.min(), v.max(), linestyle='dashed', color='k')
         ax[i].set_ylabel(ylabel[i])
-        pa2d.set_xyaxes(ax[i])
+        pa2.set_xyaxes(ax[i])
         if text is not None:
             ax[i].text(**text[i])
         if title is not None:
@@ -1257,59 +1289,51 @@ def plotprofile(coords: list[str] | str = [],
             plt.setp(ax[i].get_xticklabels(), visible=False)
     if getfigax:
         return fig, ax
-    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()
+
+    close_figure(fig, savefig, show)
 
 
 def plotslice(length: float, dx: float | None = None, pa: float = 0,
-              dist: float = 1, xoff: float = 0, yoff: float = 0,
-              xflip: bool = True, yflip: bool = False,
               txtfile: str | None = None,
               fig: object | None = None, ax: object | None = None,
               getfigax: bool = False,
               savefig: str | dict | None = None, show: bool = False,
-              **kwargs) -> None:
-    """Use Axes.plot of matplotlib to plot a 1D spatial slice in a 2D map. 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.
+              **kwargs) -> tuple[object, object]:
+    """Use Axes.plot of matplotlib to plot a 1D spatial slice in a 2D map. kwargs must include the arguments of AstroData to specify the data to be plotted. kwargs must include the arguments of AstroFrame to specify the ranges and so on for plotting. kwargs can include the arguments of PlotAxes2D to adjust x and y axes.
 
     Args:
         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.
+        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)
-    savefig0 = {'bbox_inches': 'tight', 'transparent': True}
-    center = _kw['center'] if 'center' in _kw else None
-    f = AstroFrame(rmax=length / 2, dist=dist, xoff=xoff, yoff=yoff,
-                   xflip=xflip, yflip=yflip, center=center)
+    _kw['rmax'] = length / 2
+    f = kwargs2AstroFrame(_kw)
     d = kwargs2AstroData(_kw)
-    Tb = d.Tb
     f.read(d)
     if np.ndim(d.data) > 2:
         print('Only 2D map is supported.')
         return
 
     r, z = d.slice(length=length, pa=pa, dx=dx)
-    xunit = 'arcsec' if dist == 1 else 'au'
-    yunit = 'K' if Tb else d.bunit
-    yquantity = 'Tb' if Tb else 'intensity'
+    xunit = 'arcsec' if f.dist == 1 else 'au'
+    yunit = 'K' if d.Tb else d.bunit
+    yquantity = r'$T_b$' if d.Tb else 'intensity'
 
     if txtfile is not None:
         np.savetxt(txtfile, np.c_[r, z],
                    header=f'x ({xunit}), {yquantity} ({yunit}); '
                    + f'positive x is pa={pa:.2f} deg.')
-    set_rcparams()
-    if fig is None:
-        fig = plt.figure()
-    if ax is None:
-        ax = fig.add_subplot(1, 1, 1)
     if 'xlabel' not in _kw:
         _kw['xlabel'] = f'Offset ({xunit})'
     if 'ylabel' not in _kw:
@@ -1317,21 +1341,20 @@ def plotslice(length: float, dx: float | None = None, pa: float = 0,
     if 'xlim' not in _kw:
         _kw['xlim'] = [r.min(), r.max()]
     _kw['samexy'] = False
-    pa2d = kwargs2PlotAxes2D(_kw)
+    set_rcparams()
+    if fig is None:
+        fig = plt.figure()
+    if ax is None:
+        ax = fig.add_subplot(1, 1, 1)
+    pa2 = kwargs2PlotAxes2D(_kw)
     ax.plot(r, z, **_kw)
     if d.sigma is not None:
         ax.plot(r, r * 0 + 3 * d.sigma, 'k--')
-    pa2d.set_xyaxes(ax)
+    pa2.set_xyaxes(ax)
     if getfigax:
         return fig, ax
-    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()
+
+    close_figure(fig, savefig, show)
 
 
 def plot3d(levels: list[float] = [3, 6, 12],

{plotastrodata-1.8.0 → plotastrodata-1.8.2/plotastrodata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.8.0
+Version: 1.8.2
 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