plotastrodata 1.6.4__tar.gz → 1.7.0__tar.gz

{plotastrodata-1.6.4 → plotastrodata-1.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.6.4
+Version: 1.7.0
 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
@@ -8,10 +8,10 @@ Author: yusukeaso-astron
 License: GNU General Public License Version 3
 Keywords: astronomy,FITS,plot
 Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: astropy
+Requires-Dist: astropy>=7.2
 Requires-Dist: corner
 Requires-Dist: dynesty
 Requires-Dist: emcee

plotastrodata-1.7.0/plotastrodata/__init__.py

@@ -0,0 +1,4 @@
+import warnings
+
+warnings.simplefilter('ignore', FutureWarning)
+__version__ = '1.7.0'

{plotastrodata-1.6.4 → plotastrodata-1.7.0}/plotastrodata/other_utils.py

@@ -1,5 +1,6 @@
+import warnings
 import numpy as np
-from scipy.optimize import curve_fit
+from scipy.optimize import curve_fit, OptimizeWarning
 from scipy.special import erf
 from scipy.interpolate import RegularGridInterpolator as RGI
 
@@ -59,6 +60,11 @@ def estimate_rms(data: np.ndarray, sigma: float | str | None = 'hist'
     if sigma is None:
         return None
 
+    def warning_offset(ave, noise):
+        if np.abs(ave) > 0.2 * noise:
+            s = 'The intensity offset is larger than 0.2 sigma.'
+            warnings.warn(s, UserWarning)
+
     nums = [float, int, np.float64, np.int64, np.float32, np.int32]
     if type(sigma) in nums:
         noise = sigma
@@ -68,8 +74,7 @@ def estimate_rms(data: np.ndarray, sigma: float | str | None = 'hist'
     elif sigma == 'edge':
         ave = np.nanmean(data[::len(data) - 1])
         noise = np.nanstd(data[::len(data) - 1])
-        if np.abs(ave) > 0.2 * noise:
-            print('Warning: The intensity offset is larger than 0.2 sigma.')
+        warning_offset(ave, noise)
     elif sigma == 'neg':
         noise = np.sqrt(np.nanmean(data[data < 0]**2))
     elif sigma == 'med':
@@ -82,8 +87,7 @@ def estimate_rms(data: np.ndarray, sigma: float | str | None = 'hist'
             n = n[np.abs(n) < 3.5 * sig]
         ave = np.nanmean(n)
         noise = np.nanstd(n)
-        if np.abs(ave) > 0.2 * noise:
-            print('Warning: The intensity offset is larger than 0.2 sigma.')
+        warning_offset(ave, noise)
     elif sigma == 'out':
         n, n0, n1 = data.copy(), len(data), len(data[0])
         n = np.moveaxis(n, [-2, -1], [0, 1])
@@ -95,8 +99,7 @@ def estimate_rms(data: np.ndarray, sigma: float | str | None = 'hist'
         else:
             ave = np.nanmean(n)
             noise = np.nanstd(n)
-            if np.abs(ave) > 0.2 * noise:
-                print('Warning: The intensity offset is larger than 0.2 sigma.')
+            warning_offset(ave, noise)
     elif sigma[:4] == 'hist':
         m0, s0 = np.nanmean(data), np.nanstd(data)
         hist, hbin = np.histogram(data[~np.isnan(data)],
@@ -108,13 +111,15 @@ def estimate_rms(data: np.ndarray, sigma: float | str | None = 'hist'
                 xn = (x - c) / np.sqrt(2) / s
                 return (erf(xn) - erf(xn * np.exp(-R**2))) / (2 * (x-c) * R**2)
         else:
-            def g(x, s, c, R):
-                return np.exp(-((x-c)/s)**2 / 2) / np.sqrt(2*np.pi) / s
-        popt, _ = curve_fit(g, hbin, hist, p0=[1, 0, 1])
+            def g(x, s, c, _):
+                xn = (x - c) / np.sqrt(2) / s
+                return np.exp(-xn**2) / np.sqrt(2 * np.pi) / s
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore', OptimizeWarning)
+            popt, _ = curve_fit(g, hbin, hist, p0=[1, 0, 1])
         ave = popt[1]
         noise = popt[0]
-        if np.abs(ave) > 0.2 * noise:
-            print('Warning: The intensity offset is larger than 0.2 sigma.')
+        warning_offset(ave, noise)
         noise = noise * s0
     return noise
 

{plotastrodata-1.6.4 → plotastrodata-1.7.0}/plotastrodata/plot_utils.py

@@ -1,3 +1,4 @@
+import warnings
 import numpy as np
 import matplotlib as mpl
 import matplotlib.pyplot as plt
@@ -408,7 +409,7 @@ class PlotAstroData(AstroFrame):
                 figsize = (ncols * 2 / sqrt_a, max(nrows*2, 3) * sqrt_a)
         for ch in range(nchan):
             n, i, j = ch2nij(ch)
-            if internalfig:
+            if internalfig and n not in plt.get_fignums():
                 fig = plt.figure(n, figsize=figsize)
             sharex = ax[nij2ch(n, i - 1, j)] if i > 0 else None
             sharey = ax[nij2ch(n, i, j - 1)] if j > 0 else None
@@ -431,8 +432,11 @@ class PlotAstroData(AstroFrame):
         self.allchan = np.arange(nv)
         self.bottomleft = nij2ch(np.arange(npages), nrows - 1, 0)
         self.channelnumber = channelnumber
+        self.v = v
 
-        def vskipfill(c: np.ndarray, v_in: np.ndarray = None) -> np.ndarray:
+        def vskipfill(c: np.ndarray,
+                      v_in: np.ndarray | None = None
+                      ) -> np.ndarray:
             """Skip and fill channels with nan.
 
             Args:
@@ -442,20 +446,41 @@ class PlotAstroData(AstroFrame):
             Returns:
                 np.ndarray: 3D arrays skipped and filled with nan.
             """
-            if np.ndim(c) == 3:
+            if np.ndim(c) == 2:
+                d = np.full((nv, *np.shape(c)), c)
+            elif np.ndim(c) == 3:
                 if v_in is not None:
-                    if (k0 := np.argmin(np.abs(v - v_in[0]))) > 0:
-                        prenan = np.full((k0, *np.shape(c)[1:]), np.nan)
-                        d = np.append(prenan, c, axis=0)
-                    else:
+                    dv_org = self.v[1] - self.v[0]
+                    dv_in = (v_in[1] - v_in[0]) * vskip
+                    k0 = np.argmin(np.abs(self.v - v_in[0]))
+                    k1 = np.argmin(np.abs(self.v - v_in[-1]))
+                    if np.abs(dv_in - dv_org) / dv_org < 0.01:
                         d = c
+                    else:
+                        s = 'Velocity resolution mismatch (>1%).' \
+                            + ' The cube needs to be regridded' \
+                            + ' outside plotastrodata.'
+                        warnings.warn(s, UserWarning)
+                        n_valid = k1 - k0
+                        d = [None] * n_valid
+                        for k in range(n_valid):
+                            k_tmp = np.argmin(np.abs(v_in - self.v[k]))
+                            diffvel = np.abs(v_in[k_tmp] - self.v[k])
+                            nearby = diffvel < dv_org * 0.5
+                            d[k] = c[k_tmp] if nearby else c[0] * np.nan
+                        d = np.array(d)
+                    if k0 > 0:
+                        prenan = np.full((k0, *np.shape(d)[1:]), np.nan)
+                        d = np.append(prenan, d, axis=0)
                 d = d[::vskip]
             else:
-                d = np.full((nv, *np.shape(c)), c)
+                print('c must be 2D or 3D.')
+                return
             n = nchan if channelnumber is None else nv
             shape = (n - len(d), len(d[0]), len(d[0, 0]))
-            dnan = np.full(shape, d[0] * np.nan)
-            return np.concatenate((d, dnan), axis=0)
+            postnan = np.full(shape, d[0] * np.nan)
+            d = np.append(d, postnan, axis=0)
+            return d
         self.vskipfill = vskipfill
 
     def _map_init(self, kw: dict) -> tuple:
@@ -746,8 +771,11 @@ class PlotAstroData(AstroFrame):
         c = self.vskipfill(c, v)
         if type(self.channelnumber) is int:
             c = [c[self.channelnumber]]
-        for axnow, cnow in zip(self.ax, c):
-            p = axnow.pcolormesh(x, y, cnow, **_kw)
+        p = [None] * len(self.ax)
+        for ch, (axnow, cnow) in enumerate(zip(self.ax, c)):
+            pnow = axnow.pcolormesh(x, y, cnow, **_kw)
+            if ch in self.bottomleft:
+                p[ch] = pnow
         for ch in self.bottomleft:
             if not show_cbar:
                 break
@@ -758,24 +786,28 @@ class PlotAstroData(AstroFrame):
             else:
                 fig = self.fig
             if len(self.ax) == 1:
-                ax = self.ax[0]
-                cb = fig.colorbar(p, ax=ax, label=cblabel,
+                ax = self.ax[ch]
+                cb = fig.colorbar(p[ch], ax=ax, label=cblabel,
                                   format=cbformat, location=cblocation)
             else:
                 cax = plt.axes([0.88, 0.105, 0.015, 0.77])
-                cb = fig.colorbar(p, cax=cax, label=cblabel, format=cbformat)
+                cb = fig.colorbar(p[ch], cax=cax, label=cblabel,
+                                  format=cbformat)
             cb.ax.tick_params(labelsize=14)
             font = mpl.font_manager.FontProperties(size=16)
             cb.ax.yaxis.label.set_font_properties(font)
+            if cbticks is not None and ch // self.rowcol == 0:
+                cbticks = np.array(cbticks)
+                match stretch:
+                    case 'log':
+                        cbticks = np.log10(cbticks)
+                    case 'asinh':
+                        cbticks = np.arcsinh(cbticks / stretchscale)
+                    case 'power':
+                        p = 1 - stretchpower
+                        cbticks = (cbticks / cmin_org)**p - 1
+                        cbticks = cbticks / p / np.log(10)
             if cbticks is not None:
-                if stretch == 'log':
-                    cbticks = np.log10(cbticks)
-                elif stretch == 'asinh':
-                    cbticks = np.arcsinh(np.array(cbticks) / stretchscale)
-                elif stretch == 'power':
-                    cbticks = np.array(cbticks)
-                    p = 1 - stretchpower
-                    cbticks = ((cbticks / cmin_org)**p - 1) / p / np.log(10)
                 cb.set_ticks(cbticks)
             if cbticklabels is not None:
                 cb.set_ticklabels(cbticklabels)
@@ -1112,7 +1144,7 @@ class PlotAstroData(AstroFrame):
                 fig.savefig(fname, **_kw)
         if show:
             plt.show()
-        plt.close()
+        plt.close('all')
 
     def get_figax(self) -> tuple[object, object]:
         """Output the external fig and ax after plotting.

{plotastrodata-1.6.4 → plotastrodata-1.7.0}/plotastrodata.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.6.4
+Version: 1.7.0
 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
@@ -8,10 +8,10 @@ Author: yusukeaso-astron
 License: GNU General Public License Version 3
 Keywords: astronomy,FITS,plot
 Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: astropy
+Requires-Dist: astropy>=7.2
 Requires-Dist: corner
 Requires-Dist: dynesty
 Requires-Dist: emcee

{plotastrodata-1.6.4 → plotastrodata-1.7.0}/plotastrodata.egg-info/requires.txt

@@ -1,4 +1,4 @@
-astropy
+astropy>=7.2
 corner
 dynesty
 emcee

{plotastrodata-1.6.4 → plotastrodata-1.7.0}/setup.cfg

@@ -14,9 +14,9 @@ classifiers = Programming Language :: Python :: 3
 [options]
 packages = find:
 zip_safe = False
-python_requires = >=3.10
+python_requires = >=3.12
 install_requires = 
-	astropy
+	astropy >= 7.2
 	corner
 	dynesty
 	emcee

plotastrodata-1.6.4/plotastrodata/__init__.py

@@ -1,4 +0,0 @@
-import warnings
-
-warnings.simplefilter('ignore', UserWarning)
-__version__ = '1.6.4'