plotastrodata 1.8.3__tar.gz → 1.8.4__tar.gz

{plotastrodata-1.8.3/plotastrodata.egg-info → plotastrodata-1.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.8.3
+Version: 1.8.4
 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-1.8.3 → plotastrodata-1.8.4}/plotastrodata/__init__.py

@@ -1,4 +1,4 @@
 import warnings
 
 warnings.simplefilter('ignore', FutureWarning)
-__version__ = '1.8.3'
+__version__ = '1.8.4'

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/analysis_utils.py

@@ -1,18 +1,18 @@
-import warnings
 import numpy as np
+import warnings
 from dataclasses import dataclass
 from scipy.interpolate import RegularGridInterpolator as RGI
 from scipy.optimize import curve_fit
 from scipy.signal import convolve
 
-from plotastrodata.coord_utils import coord2xy, xy2coord, rel2abs
-from plotastrodata.matrix_utils import Mfac, Mrot, dot2d
-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
+from plotastrodata.coord_utils import coord2xy, rel2abs, xy2coord
+from plotastrodata.fits_utils import data2fits, FitsData, Jy2K
 from plotastrodata.fitting_utils import EmceeCorner
+from plotastrodata.matrix_utils import dot2d, Mfac, Mrot
+from plotastrodata.noise_utils import estimate_rms
+from plotastrodata.other_utils import (gaussian2d, isdeg,
+                                       RGIxy, RGIxyv, to4dim, trim)
 
 
 def quadrantmean(data: np.ndarray, x: np.ndarray, y: np.ndarray,

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/coord_utils.py

@@ -1,6 +1,6 @@
 import numpy as np
-from astropy.coordinates import SkyCoord, FK5, FK4
 from astropy import units
+from astropy.coordinates import FK4, FK5, SkyCoord
 
 
 def _updateframe(frame: str) -> str:

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/fft_utils.py

@@ -1,8 +1,8 @@
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 
 from plotastrodata.fits_utils import fits2data
-from plotastrodata.plot_utils import set_rcparams
+from plotastrodata.other_utils import close_figure
 
 
 def shiftphase(F: np.ndarray, u: np.ndarray,
@@ -198,7 +198,9 @@ def zeropadding(f: np.ndarray, x: np.ndarray, y: np.ndarray,
 
 def fftfits(fitsimage: str, center: str | None = None, lam: float = 1,
             xlim: list | None = None, ylim: list | None = None,
-            plot: bool = False) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
+            savefig: dict | str | None = None,
+            show: bool = False,
+            ) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
     """FFT a fits image with the phase referring to a specific point.
 
     Args:
@@ -207,7 +209,8 @@ def fftfits(fitsimage: str, center: str | None = None, lam: float = 1,
         lam (float, optional): Return u * lam and v * lam. Defaults to 1.
         xlim (list, optional): Range of x for zero padding in arcsec.
         ylim (list, optional): Range of y for zero padding in arcsec.
-        plot (bool, optional): Check F through images.
+        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: (F, u, v). F is FFT of f in the unit of Jy. u and v are 1D arrays in the unit of lambda or meter if lam it not unity.
@@ -215,32 +218,26 @@ def fftfits(fitsimage: str, center: str | None = None, lam: float = 1,
     f, (x, y, v), _, _, _ = fits2data(fitsimage, center=center)
     if xlim is not None and ylim is not None:
         f, x, y = zeropadding(f, x, y, xlim, ylim)
+    f[np.isnan(f)] = 0
     arcsec = np.radians(1) / 3600.
     F, u, v = fftcentering2(f, x * arcsec, y * arcsec)
     u, v = u * lam, v * lam
-    if plot:
-        set_rcparams()
-        fig = plt.figure(figsize=(10, 8))
-        ax = fig.add_subplot(2, 2, 1)
-        m = ax.pcolormesh(u, v, np.real(F), shading='nearest', cmap='jet')
-        fig.colorbar(m, ax=ax, label='Real', format='%.1e')
-        ax.set_ylabel(r'v ($\lambda$)')
-        ax = fig.add_subplot(2, 2, 2)
-        m = ax.pcolormesh(u, v, np.imag(F), shading='nearest', cmap='jet')
-        fig.colorbar(m, ax=ax, label='Imaginary', format='%.1e')
-        ax = fig.add_subplot(2, 2, 3)
-        m = ax.pcolormesh(u, v, np.abs(F), shading='nearest', cmap='jet')
-        fig.colorbar(m, ax=ax, label='Amplitude', format='%.1e')
-        ax.set_xlabel(r'u ($\lambda$)')
-        ax.set_ylabel(r'v ($\lambda$)')
-        ax = fig.add_subplot(2, 2, 4)
-        m = ax.pcolormesh(u, v, np.angle(F) * np.degrees(1),
-                          shading='nearest', cmap='jet')
-        fig.colorbar(m, ax=ax, label='Phase (deg)', format='%.0f')
-        ax.set_xlabel(r'u ($\lambda$)')
-        fig.tight_layout()
-        plt.show()
-        plt.close()
+    if savefig is not None or show:
+        fig, ax = plt.subplots(2, 2, figsize=(10, 8))
+        m = ax[0, 0].pcolormesh(u, v, np.real(F), cmap='jet')
+        fig.colorbar(m, ax=ax[0, 0], label='Real', format='%.1e')
+        ax[0, 0].set_ylabel(r'v ($\lambda$)')
+        m = ax[0, 1].pcolormesh(u, v, np.imag(F), cmap='jet')
+        fig.colorbar(m, ax=ax[0, 1], label='Imaginary', format='%.1e')
+        m = ax[1, 0].pcolormesh(u, v, np.abs(F), cmap='jet')
+        fig.colorbar(m, ax=ax[1, 0], label='Amplitude', format='%.1e')
+        ax[1, 0].set_xlabel(r'u ($\lambda$)')
+        ax[1, 0].set_ylabel(r'v ($\lambda$)')
+        m = ax[1, 1].pcolormesh(u, v, np.angle(F) * np.degrees(1),
+                                cmap='jet')
+        fig.colorbar(m, ax=ax[1, 1], label='Phase (deg)', format='%.0f')
+        ax[1, 1].set_xlabel(r'u ($\lambda$)')
+        close_figure(fig, savefig, show)
     return F, u, v
 
 

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/fits_utils.py

@@ -1,12 +1,12 @@
 import numpy as np
-from astropy.io import fits
 from astropy import units, wcs
+from astropy.io import fits
 
+from plotastrodata import const_utils as cu
 from plotastrodata.coord_utils import coord2xy, xy2coord
 from plotastrodata.matrix_utils import dot2d
 from plotastrodata.noise_utils import estimate_rms
-from plotastrodata.other_utils import trim, isdeg, RGIxy
-from plotastrodata import const_utils as cu
+from plotastrodata.other_utils import isdeg, RGIxy, trim
 
 
 def Jy2K(header=None, bmaj: float | None = None, bmin: float | None = None,

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/fitting_utils.py

@@ -1,12 +1,14 @@
-import numpy as np
-import matplotlib.pyplot as plt
+import corner
 import emcee
+import matplotlib.pyplot as plt
+import numpy as np
 import ptemcee
-import corner
-from dynesty import DynamicNestedSampler as DNS
 import warnings
-from tqdm import tqdm
+from dynesty import DynamicNestedSampler as DNS
 from multiprocessing import Pool
+from tqdm import tqdm
+
+from plotastrodata.other_utils import close_figure
 
 
 global_bounds = None
@@ -109,9 +111,9 @@ class EmceeCorner():
         while np.max(GR) > 1.25 and i < ntry:
             i += 1
             if pos0 is None:
-                pos0 = np.random.rand(ntemps, nwalkers, self.dim) \
-                       * (self.bounds[:, 1] - self.bounds[:, 0]) \
-                       + self.bounds[:, 0]
+                pos0 = np.random.rand(ntemps, nwalkers, self.dim)
+                pos0 = pos0 * (self.bounds[:, 1] - self.bounds[:, 0])
+                pos0 = pos0 + self.bounds[:, 0]
                 if not pt:
                     pos0 = pos0[0]
             if pt:
@@ -176,17 +178,17 @@ class EmceeCorner():
         if global_progressbar:
             print('')
 
-    def plotcorner(self, show: bool = False,
-                   savefig: str | None = None,
-                   labels: list[str] | None = None,
-                   cornerrange: list[float] | None = None) -> None:
+    def plotcorner(self, labels: list[str] | None = None,
+                   cornerrange: list[float] | None = None,
+                   savefig: dict | str | None = None,
+                   show: bool = False) -> None:
         """Make the corner plot from self.samples.
 
         Args:
-            show (bool, optional): Whether to show the corner plot. Defaults to False.
-            savefig (str, optional): File name of the corner plot. Defaults to None.
             labels (list, optional): Labels for the corner plot. Defaults to None.
             cornerrange (list, optional): Range for the corner plot. 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.
         """
         if labels is None:
             labels = [f'Par {i:d}' for i in range(self.dim)]
@@ -198,21 +200,17 @@ class EmceeCorner():
                                  0.5,
                                  self.percent[1] / 100],
                       show_titles=True, labels=labels, range=cornerrange)
-        if savefig is not None:
-            plt.savefig(savefig)
-        if show:
-            plt.show()
-        plt.close()
+        close_figure(plt, savefig, show, tight=False)
 
-    def plotchain(self, show: bool = False, savefig: str = None,
-                  labels: list = None, ylim: list = None):
+    def plotchain(self, labels: list = None, ylim: list = None,
+                  savefig: dict | str = None, show: bool = False):
         """Plot parameters as a function of steps using self.samples. This method plots nine lines: percent[0], 50%, percent[1] percentiles (over the steps by 1% binning) of percent[0], 50%, percent[1] percentiles (over the walkers).
 
         Args:
-            show (bool, optional): Whether to show the chain plot. Defaults to False.
-            savefig (str, optional): File name of the chain plot. Defaults to None.
             labels (list, optional): Labels for the chain plot. Defaults to None.
             ylim (list, optional): Y-range for the chain plot. 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.
         """
         if labels is None:
             labels = [f'Par {i:d}' for i in range(self.dim)]
@@ -239,12 +237,7 @@ class EmceeCorner():
                 ax.set_xticks([])
             else:
                 ax.set_xlabel('Step')
-        fig.tight_layout()
-        if savefig is not None:
-            plt.savefig(savefig)
-        if show:
-            plt.show()
-        plt.close()
+        close_figure(fig, savefig, show)
 
     def posteriorongrid(self, ngrid: list[int] | int = 100,
                         log: list[bool] | bool = False, pcut: float = 0):
@@ -381,13 +374,7 @@ class EmceeCorner():
                         plt.setp(ax[k].get_xticklabels(), rotation=45)
                     else:
                         plt.setp(ax[k].get_xticklabels(), visible=False)
-        # fig.tight_layout()
-        if savefig is not None:
-            plt.savefig(savefig)
-        if show:
-            plt.show()
-        else:
-            plt.close()
+        close_figure(fig, savefig, show, tight=False)
 
     def getDNSevidence(self, **kwargs):
         """Calculate the Bayesian evidence for a model using dynamic nested sampling through dynesty.

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/matrix_utils.py

@@ -24,7 +24,7 @@ def Mrot(pa: float = 0) -> np.ndarray:
         np.ndarray: Matrix for the rotation.
     """
     p = np.radians(pa)
-    return np.array([[np.cos(p), -np.sin(p)], [np.sin(p),  np.cos(p)]])
+    return np.array([[np.cos(p), -np.sin(p)], [np.sin(p), np.cos(p)]])
 
 
 def dot2d(M: np.ndarray = [[1, 0], [0, 1]],

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/noise_utils.py

@@ -1,6 +1,6 @@
-import warnings
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+import warnings
 from scipy.special import erf
 
 from plotastrodata.fitting_utils import EmceeCorner
@@ -167,8 +167,7 @@ class Noise:
             savefig (dict or str, optional): For plt.figure().savefig(). Defaults to None.
             show (bool, optional): True means doing plt.show(). Defaults to False.
         """
-        fig = plt.figure()
-        ax = fig.add_subplot(1, 1, 1)
+        fig, ax = plt.subplots()
         ax.plot(self.hbin, self.hist, drawstyle='steps-mid')
         ax.plot(self.hbin, self.model, '-')
         ax.set_xlabel('(noise - m0) / s0')

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/other_utils.py

@@ -1,5 +1,5 @@
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 from scipy.interpolate import RegularGridInterpolator as RGI
 
 from plotastrodata.matrix_utils import Mrot, dot2d
@@ -209,18 +209,19 @@ def gaussian2d(xy: np.ndarray,
     return g
 
 
-def close_figure(fig: object,
-                 savefig: dict | str | None = None,
-                 show: bool = False) -> None:
+def close_figure(fig: object, savefig: dict | str | None = None,
+                 show: bool = False, tight: bool = True) -> None:
     """Save, show, and close the figure.
 
     Args:
         fig (object): 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.
+        tight (bool, optional): True means doing fig.tight_layout(). Defaults to False.
     """
     savefig0 = {'bbox_inches': 'tight', 'transparent': True}
-    fig.tight_layout()
+    if tight:
+        fig.tight_layout()
     if savefig is not None:
         s = {'fname': savefig} if type(savefig) is str else savefig
         savefig0.update(s)

{plotastrodata-1.8.3 → plotastrodata-1.8.4}/plotastrodata/plot_utils.py

@@ -1,14 +1,14 @@
-import warnings
-import numpy as np
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-from matplotlib.patches import Ellipse, Rectangle
+import numpy as np
+import warnings
 from dataclasses import dataclass
+from matplotlib.patches import Ellipse, Rectangle
 
+from plotastrodata.analysis_utils import AstroData, AstroFrame
 from plotastrodata.coord_utils import coord2xy, xy2coord
 from plotastrodata.noise_utils import estimate_rms
-from plotastrodata.other_utils import listing, close_figure
-from plotastrodata.analysis_utils import AstroData, AstroFrame
+from plotastrodata.other_utils import close_figure, listing
 
 
 plt.ioff()  # force to turn off interactive mode

{plotastrodata-1.8.3 → plotastrodata-1.8.4/plotastrodata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.8.3
+Version: 1.8.4
 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-1.8.3 → plotastrodata-1.8.4}/plotastrodata/ext_utils.py

@@ -1,6 +1,6 @@
-import subprocess
-import shlex
 import numpy as np
+import shlex
+import subprocess
 
 from plotastrodata import const_utils as cu