plotastrodata 1.9.8__tar.gz → 1.9.9__tar.gz

{plotastrodata-1.9.8/plotastrodata.egg-info → plotastrodata-1.9.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.9.8
+Version: 1.9.9
 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-1.9.8 → plotastrodata-1.9.9}/plotastrodata/__init__.py

@@ -1,4 +1,4 @@
 import warnings
 
 warnings.simplefilter('ignore', FutureWarning)
-__version__ = '1.9.8'
+__version__ = '1.9.9'

{plotastrodata-1.9.8 → plotastrodata-1.9.9}/plotastrodata/plot_utils.py

@@ -8,6 +8,7 @@ from typing import TypeVar
 from plotastrodata.analysis_utils import AstroData, AstroFrame
 from plotastrodata.coord_utils import (coord2xy, xy2coord,
                                        get_hmdm, get_min, get_sec)
+from plotastrodata.fitting_utils import gaussian1d
 from plotastrodata.noise_utils import estimate_rms
 from plotastrodata.other_utils import (close_figure, listing,
                                        reform_grid, reform_data)
@@ -1199,6 +1200,55 @@ class PlotAstroData(AstroFrame):
         return fig, self.ax[0]
 
 
+def _get_ylabel_profile(_kw: dict, Tb: bool, flux: bool, bunit: str
+                        ) -> str:
+    if "ylabel" in _kw:
+        return _kw["ylabel"]
+    if Tb:
+        return r"$T_b$ (K)"
+    if flux:
+        return "Flux (Jy)"
+    return bunit
+
+
+def _prep_plotprofile(width: int, coords: list | str,
+                      xlist: list, ylist: list, ellipse: list,
+                      ninterp: int, flux: bool, gaussfit: bool,
+                      _kw: dict) -> tuple:
+    if isinstance(coords, str):
+        coords = [coords]
+    Tb = _kw.get("Tb", False)
+    f = kwargs2instance(AstroFrame, _kw)
+    d = kwargs2instance(AstroData, _kw)
+    f.read(d)
+    d.binning([width, 1, 1])
+    v, prof, gfitres = d.profile(coords=coords, xlist=xlist, ylist=ylist,
+                                 ellipse=ellipse, ninterp=ninterp,
+                                 flux=flux, gaussfit=gaussfit)
+    ylabel = _get_ylabel_profile(_kw, Tb, flux, d.bunit)
+    if isinstance(ylabel, str):
+        ylabel = [ylabel] * len(prof)
+    _kw.setdefault("xlim", [v.min(), v.max()])
+    pa2 = kwargs2instance(PlotAxes2D, _kw)
+    return v, prof, gfitres, pa2, ylabel
+
+
+def _set_figax_plotprofile(fig, ax, nrows: int, ncols: int,
+                           nprof: int) -> tuple:
+    if ncols == 1:
+        nrows = nprof
+    if fig is None:
+        fig = plt.figure(figsize=(6 * ncols, 3 * nrows))
+    if nprof > 1 and ax is not None:
+        print("External ax is supported only when len(coords)=1.")
+        ax = None
+    ax = np.empty(nprof, dtype=object) if ax is None else [ax]
+    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)
+    return fig, ax
+
+
 def plotprofile(coords: list[str] | str = [],
                 xlist: list[float] = [], ylist: list[float] = [],
                 ellipse: list[float, float, float] | None = None,
@@ -1208,11 +1258,9 @@ def plotprofile(coords: list[str] | str = [],
                 title: list[str] | None = None,
                 text: list[str] | None = None,
                 nrows: int = 0, ncols: int = 1,
-                fig: object | None = None,
-                ax: object | None = None,
+                fig: object | None = None, ax: object | None = None,
                 getfigax: bool = False,
-                savefig: dict | str | None = None,
-                show: bool = False,
+                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 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.
 
@@ -1239,63 +1287,29 @@ def plotprofile(coords: list[str] | str = [],
     Returns:
         tuple: (fig, ax), where ax is a list, if getfigax=True. Otherwise, no return.
     """
-    _kw = {'drawstyle': 'steps-mid', 'color': 'k'}
+    _kw = {"drawstyle": "steps-mid", "color": "k",
+           "xlabel": r"Velocity (km s$^{-1}$)", "samexy": False}
     _kw.update(kwargs)
     _kwgauss = {'drawstyle': 'default', 'color': 'g'}
     _kwgauss.update(gauss_kwargs)
-    if type(coords) is str:
-        coords = [coords]
-    f = kwargs2instance(AstroFrame, _kw)
-    d = kwargs2instance(AstroData, _kw)
-    f.read(d)
-    d.binning([width, 1, 1])
-    v, prof, gfitres = d.profile(coords=coords, xlist=xlist, ylist=ylist,
-                                 ellipse=ellipse, ninterp=ninterp,
-                                 flux=flux, gaussfit=gaussfit)
+    v, prof, gfitres, pa2, ylabel \
+        = _prep_plotprofile(width, coords, xlist, ylist, ellipse,
+                            ninterp, flux, gaussfit, _kw)
     nprof = len(prof)
-    if 'ylabel' in _kw:
-        ylabel = _kw['ylabel']
-    elif d.Tb:
-        ylabel = r'$T_b$ (K)'
-    elif flux:
-        ylabel = 'Flux (Jy)'
-    else:
-        ylabel = d.bunit
-    if type(ylabel) is str:
-        ylabel = [ylabel] * nprof
-
-    def gauss(x, p, c, w):
-        return p * np.exp(-4. * np.log(2.) * ((x - c) / w)**2)
-
-    set_rcparams(20, 'w')
-    if ncols == 1:
-        nrows = nprof
-    if fig is None:
-        fig = plt.figure(figsize=(6 * ncols, 3 * nrows))
-    if nprof > 1 and ax is not None:
-        print('External ax is supported only when len(coords)=1.')
-        ax = None
-    ax = np.empty(nprof, dtype='object') if ax is None else [ax]
-    if 'xlabel' not in _kw:
-        _kw['xlabel'] = 'Velocity (km s$^{-1}$)'
-    if 'xlim' not in _kw:
-        _kw['xlim'] = [v.min(), v.max()]
-    _kw['samexy'] = False
-    pa2 = kwargs2instance(PlotAxes2D, _kw)
+    set_rcparams(20, "w")
+    fig, ax = _set_figax_plotprofile(fig, ax, nrows, ncols, nprof)
     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)
         if gaussfit:
-            ax[i].plot(v, gauss(v, *gfitres['best'][i]), **_kwgauss)
+            ax[i].plot(v, gaussian1d(v, *gfitres["best"][i]), **_kwgauss)
         ax[i].plot(v, prof[i], **_kw)
-        ax[i].hlines([0], v.min(), v.max(), linestyle='dashed', color='k')
+        ax[i].hlines([0], v.min(), v.max(), linestyle="dashed", color="k")
         ax[i].set_ylabel(ylabel[i])
         pa2.set_xyaxes(ax[i])
         if text is not None:
             ax[i].text(**text[i])
         if title is not None:
-            if type(title[i]) is str:
-                title[i] = {'label': title[i]}
+            if isinstance(title[i], str):
+                title[i] = {"label": title[i]}
             ax[i].set_title(**title[i])
         if i <= nprof - ncols - 1:
             plt.setp(ax[i].get_xticklabels(), visible=False)
@@ -1369,8 +1383,69 @@ def plotslice(length: float, dx: float | None = None, pa: float = 0,
     close_figure(fig, savefig, show)
 
 
+def _plot_on_wall(d: AstroData, x: np.ndarray, y: np.ndarray, v: np.ndarray,
+                  measure: object, datalist: list,
+                  sign: int, axis: int, **kwargs):
+    dx, dy, dv = x[1] - x[0], y[1] - y[0], v[1] - v[0]
+    s, ds = [x, y, v], [dx, dy, dv]
+    if kwargs == {}:
+        return
+
+    match axis:
+        case 2:
+            shape = np.shape(d.data[:, :, 0])
+        case 1:
+            shape = np.shape(d.data[:, 0, :])
+        case 0:
+            shape = np.shape(d.data[0, :, :])
+    if np.shape(kwargs['data']) != shape:
+        print('The shape of the 2D data is inconsistent'
+              + ' with the shape of the 3D data.')
+        return
+
+    _kw = {'levels': [3, 6, 12, 24, 48, 96, 192, 384],
+           'sigma': 'hist', 'cmap': 'Jet', 'alpha': 0.3}
+    _kw.update(kwargs)
+    volume = _kw['data']
+    levels = _kw['levels']
+    cmap = _kw['cmap']
+    alpha = _kw['alpha']
+    sigma = estimate_rms(data=volume, sigma=_kw['sigma'])
+    volume[np.isnan(volume)] = 0
+    a = int(sign == -1)
+    b = int(sign == 1)
+    volume = np.moveaxis([volume * a, volume * b], 0, axis)
+    if d.dx < 0:
+        volume = volume[:, :, ::-1]
+    if d.dy < 0:
+        volume = volume[:, ::-1, :]
+    if d.dv < 0:
+        volume = volume[::-1, :, :]
+    for lev in levels:
+        if lev * sigma > np.max(volume):
+            continue
+        vertices, simplices, _, _ = measure.marching_cubes(volume, lev * sigma)
+        Xg, Yg, Zg = [t[0] + i * dt for t, i, dt
+                      in zip(s, vertices.T[::-1], ds)]
+        match axis:
+            case 2:
+                Xg = Xg * 0 + (x[-1] if sign == 1 else x[0])
+            case 1:
+                Yg = Yg * 0 + (y[-1] if sign == 1 else y[0])
+            case 0:
+                Zg = Zg * 0 + (v[-1] if sign == 1 else v[0])
+        i, j, k = simplices.T
+        mesh2d = dict(type='mesh3d', x=Xg, y=Yg, z=Zg,
+                      i=i, j=j, k=k,
+                      intensity=Zg * 0 + lev,
+                      colorscale=cmap, reversescale=False,
+                      cmin=np.min(levels), cmax=np.max(levels),
+                      opacity=alpha, name='', showscale=False)
+        datalist.append(mesh2d)
+
+
 def plot3d(levels: list[float] = [3, 6, 12],
-           cmap: str = 'Jet', alpha: float = 0.08,
+           cmap: str = 'jet', alpha: float = 0.08,
            xlabel: str = 'R.A. (arcsec)',
            ylabel: str = 'Dec. (arcsec)',
            vlabel: str = 'Velocity (km/s)',
@@ -1461,67 +1536,11 @@ def plot3d(levels: list[float] = [3, 6, 12],
                      name='', line=dict(color='rgb(0,0,0)', width=1))
         data.append(lines)
 
-    def plot_on_wall(sign: int, axis: int, **kwargs):
-        if kwargs == {}:
-            return
-
-        match axis:
-            case 2:
-                shape = np.shape(d.data[:, :, 0])
-            case 1:
-                shape = np.shape(d.data[:, 0, :])
-            case 0:
-                shape = np.shape(d.data[0, :, :])
-        if np.shape(kwargs['data']) != shape:
-            print('The shape of the 2D data is inconsistent'
-                  + ' with the shape of the 3D data.')
-            return
-
-        _kw = {'levels': [3, 6, 12, 24, 48, 96, 192, 384],
-               'sigma': 'hist', 'cmap': 'Jet', 'alpha': 0.3}
-        _kw.update(kwargs)
-        volume = _kw['data']
-        levels = _kw['levels']
-        cmap = _kw['cmap']
-        alpha = _kw['alpha']
-        sigma = estimate_rms(data=volume, sigma=_kw['sigma'])
-        volume[np.isnan(volume)] = 0
-        a = int(sign == -1)
-        b = int(sign == 1)
-        volume = np.moveaxis([volume * a, volume * b], 0, axis)
-        if d.dx < 0:
-            volume = volume[:, :, ::-1]
-        if d.dy < 0:
-            volume = volume[:, ::-1, :]
-        if d.dv < 0:
-            volume = volume[::-1, :, :]
-        for lev in levels:
-            if lev * sigma > np.max(volume):
-                continue
-            vertices, simplices, _, _ = measure.marching_cubes(volume, lev * sigma)
-            Xg, Yg, Zg = [t[0] + i * dt for t, i, dt
-                          in zip(s, vertices.T[::-1], ds)]
-            match axis:
-                case 2:
-                    Xg = Xg * 0 + (x[-1] if sign == 1 else x[0])
-                case 1:
-                    Yg = Yg * 0 + (y[-1] if sign == 1 else y[0])
-                case 0:
-                    Zg = Zg * 0 + (v[-1] if sign == 1 else v[0])
-            i, j, k = simplices.T
-            mesh2d = dict(type='mesh3d', x=Xg, y=Yg, z=Zg,
-                          i=i, j=j, k=k,
-                          intensity=Zg * 0 + lev,
-                          colorscale=cmap, reversescale=False,
-                          cmin=np.min(levels), cmax=np.max(levels),
-                          opacity=alpha, name='', showscale=False)
-            data.append(mesh2d)
-
     klist = [xplus, xminus, yplus, yminus, vplus, vminus]
     slist = [1, -1, 1, -1, 1, -1]
     alist = [2, 2, 1, 1, 0, 0]
     for kw, sign, axis in zip(klist, slist, alist):
-        plot_on_wall(sign=sign, axis=axis, **kw)
+        _plot_on_wall(d, x, y, v, measure, data, sign, axis, **kw)
 
     if return_data_layout:
         return {'data': data, 'layout': layout}

{plotastrodata-1.9.8 → plotastrodata-1.9.9/plotastrodata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.9.8
+Version: 1.9.9
 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