plotastrodata 1.8.12__tar.gz → 1.8.14__tar.gz

{plotastrodata-1.8.12/plotastrodata.egg-info → plotastrodata-1.8.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.8.12
+Version: 1.8.14
 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-1.8.12 → plotastrodata-1.8.14}/plotastrodata/__init__.py

@@ -1,4 +1,4 @@
 import warnings
 
 warnings.simplefilter('ignore', FutureWarning)
-__version__ = '1.8.12'
+__version__ = '1.8.14'

{plotastrodata-1.8.12 → plotastrodata-1.8.14}/plotastrodata/analysis_utils.py

@@ -438,15 +438,15 @@ class AstroData():
             print('Data must be 3D with the v, y, and x axes.')
             return
 
-        if len(coords) > 0:
-            xlist, ylist = coord2xy(coords, self.center) * 3600.
-        nprof = len(xlist)
         v = self.v
         data, xf, yf = filled2d(self.data, self.x, self.y, ninterp)
         x, y = np.meshgrid(xf, yf)
+        if len(coords) > 0:
+            xlist, ylist = coord2xy(coords, self.center) * 3600.
+        nprof = len(xlist)
         prof = np.empty((nprof, len(v)))
-        if ellipse is None:
-            ellipse = [[0, 0, 0]] * nprof
+        ellipse = ellipse or [[0, 0, 0]] * nprof
+        calc = np.sum if flux else np.mean
         for i, (xc, yc, e) in enumerate(zip(xlist, ylist, ellipse)):
             major, minor, pa = e
             z = dot2d(Mrot(-pa), [y - yc, x - xc])
@@ -455,11 +455,8 @@ class AstroData():
                 idx = np.unravel_index(np.argmin(r), np.shape(r))
                 prof[i] = [d[idx] for d in data]
             else:
-                r = np.hypot(*dot2d(Mfac(2/major, 2/minor), z))
-                if flux:
-                    prof[i] = [np.sum(d[r <= 1]) for d in data]
-                else:
-                    prof[i] = [np.mean(d[r <= 1]) for d in data]
+                r = np.hypot(*dot2d(Mfac(2 / major, 2 / minor), z))
+                prof[i] = [calc(d[r <= 1]) for d in data]
         if flux:
             if None in self.beam or None in [self.dx, self.dy]:
                 print('None in beam, dx, or dy. Flux is not converted.')

{plotastrodata-1.8.12 → plotastrodata-1.8.14}/plotastrodata/fitting_utils.py

@@ -438,7 +438,8 @@ def gaussfit1d(xdata: np.ndarray, ydata: np.ndarray,
     plow = fitter.plow
     phigh = fitter.phigh
     perr = (phigh - plow) / 2
+    pars = 'peak, center, FWHM' + (', lnsigma' if sigma is None else '')
     if show:
-        print('Gauss (peak, center, FWHM):', popt)
+        print(f'Gauss ({pars}):', popt)
         print('Gauss uncertainties:', perr)
     return {'popt': popt, 'perr': perr}

{plotastrodata-1.8.12 → plotastrodata-1.8.14}/plotastrodata/plot_utils.py

@@ -4,6 +4,7 @@ import numpy as np
 import warnings
 from dataclasses import dataclass
 from matplotlib.patches import Ellipse, Rectangle
+from typing import TypeVar
 
 from plotastrodata.analysis_utils import AstroData, AstroFrame
 from plotastrodata.coord_utils import coord2xy, xy2coord
@@ -13,6 +14,8 @@ from plotastrodata.other_utils import close_figure, listing
 
 plt.ioff()  # force to turn off interactive mode
 
+T = TypeVar('T')
+
 
 def set_rcparams(fontsize: int = 18, nancolor: str = 'w',
                  dpi: int = 256) -> None:
@@ -98,7 +101,7 @@ def logcbticks(vmin: float = 1e-3, vmax: float = 1e3
 
 @dataclass
 class Stretcher():
-    """Get the stretched values.
+    """Arguments and methods related to the stretch in PlotAstroData.add_color() and add_rgb().
 
         Args:
             stretch (str, optional): 'log', 'asinh', 'power', or 'linear'. Any other means 'linear'. 'log' means the mapped data are logarithmic. 'asinh' means the mapped data are arc sin hyperbolic. 'power' means the mapped data are power-law (see also stretchpower). Defaults to 'linear'.
@@ -202,6 +205,37 @@ class Stretcher():
         return dataout, vminout, vmaxout
 
 
+class Beam():
+    """Arguments for PlotAstroData.add_beam().
+
+        Args:
+            show_beam (bool, optional): Defaults to True.
+            beam (list, optional): [bmaj, bmin, bpa]. This may be a list of list. Defaults to [None, None, None].
+            beamcolor (str, optional): matplotlib color. This may be a list of str. Defaults to 'gray'.
+            beampos (list, optional): Relative position. This may be a list of list or a list of None. Defaults to None.
+            beam_kwargs (dict, optional): Additional arguments for matplotlib.patches. Defaults to {}.
+    """
+    def __init__(self,
+                 show_beam: bool = True,
+                 beam: list[float | None] = [None] * 3,
+                 beamcolor: str = 'gray',
+                 beampos: list[float] | None = None,
+                 beam_kwargs: dict = {}):
+        self.show_beam = show_beam
+        self.beam = beam
+        self.beamcolor = beamcolor
+        self.beampos = beampos
+        self.beam_kwargs = beam_kwargs
+
+    def todict(self):
+        tmp = {'show_beam': self.show_beam,
+               'beam': self.beam,
+               'beamcolor': self.beamcolor,
+               'beampos': self.beampos}
+        tmp.update(self.beam_kwargs)
+        return tmp
+
+
 @dataclass
 class PlotAxes2D():
     """Use Axes.set_* to adjust x and y axes.
@@ -305,81 +339,29 @@ class PlotAxes2D():
                 ax.set_aspect(self.aspect)
 
 
-def kwargs2AstroData(kw: dict) -> AstroData:
-    """Get AstroData and remove its arguments from kwargs.
-
-    Args:
-        kw (dict): Parameters to make AstroData.
-
-    Returns:
-        AstroData: AstroData made from the parameters in kwargs.
-    """
-    tmp = {}
-    d = AstroData(data=np.zeros((2, 2)))
-    for k in vars(d):
-        if k in kw:
-            tmp[k] = kw.pop(k)
-    if tmp == {}:
-        print('No argument given.')
-        return None
-    else:
-        d = AstroData(**tmp)
-        return d
-
-
-def kwargs2AstroFrame(kw: dict) -> AstroFrame:
-    """Get AstroFrame from kwargs.
-
-    Args:
-        kw (dict): Parameters to make AstroFrame.
-
-    Returns:
-        AstroFrame: AstroFrame made from the parameters in kwargs.
-    """
-    tmp = {}
-    f = 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
-
-
-def kwargs2PlotAxes2D(kw: dict) -> PlotAxes2D:
-    """Get PlotAxes2D and remove its arguments from kwargs.
+def kwargs2instance(cls: type[T], kw: dict) -> T:
+    """Get an instance and remove its arguments from kwargs.
 
     Args:
-        kw (dict): Parameters to make PlotAxes2D.
+        cls (class): Class to make the instance.
+        kw (dict): Parameters to make Stretcher.
 
     Returns:
-        PlotAxes2D: PlotAxes2D made from the parameters in kwargs.
+        instance: an instance of cls made from the parameters in kwargs.
     """
-    tmp = {}
-    d = PlotAxes2D()
-    for k in vars(d):
-        if k in kw:
-            tmp[k] = kw.pop(k)
-    d = PlotAxes2D(**tmp)
-    return d
-
-
-def kwargs2beamargs(kw: dict) -> dict:
-    """Get arguments for add_beam() from kwargs.
-
-    Args:
-        kw (dict): Parameters to make beam.
-
-    Returns:
-        dict: Arguments for add_beam().
-    """
-    tmp = {}
-    for k in ['show_beam', 'beamcolor', 'beampos']:
-        if k in kw:
-            tmp[k] = kw.pop(k)
-    tmp.update(kw.pop('beam_kwargs', {}))
-    return tmp
+    kw0 = {}
+    if cls == AstroData:
+        kw0 = {'data': np.zeros((2, 2))}
+    exkeys = {}
+    if cls == AstroFrame:
+        exkeys = {'fitsimage', 'center'}
+    elif cls == Stretcher:
+        exkeys = {'vmin', 'vmax'}
+    keys = vars(cls(**kw0)).keys()
+    tmp = {k: kw[k] for k in keys if k in kw}
+    for k in keys - exkeys:
+        kw.pop(k, None)
+    return cls(**tmp)
 
 
 class PlotAstroData(AstroFrame):
@@ -563,17 +545,21 @@ class PlotAstroData(AstroFrame):
         Returns:
             tuple: Data and parameters used in each method.
         """
-        beam_kwargs = kwargs2beamargs(kw)
+        b = kwargs2instance(Beam, kw)
         self._kw.update(kw)
         xskip = self._kw.pop('xskip', 1)
         yskip = self._kw.pop('yskip', 1)
-        d = kwargs2AstroData(self._kw)
+        d = kwargs2instance(AstroData, self._kw)
         self.read(d, xskip, yskip)
-        self.beam = d.beam
         self.sigma = d.sigma
         singlepix = d.dx is None or d.dy is None
-        return (d.data, d.x, d.y, d.v, d.beam, d.sigma, d.bunit,
-                self._kw, beam_kwargs, singlepix)
+        if len(d.beam) == 4:
+            b.beam = self.beam = next(b for b in d.beam if None not in b)
+        else:
+            b.beam = self.beam = d.beam
+        self.add_beam(**b.todict())
+        return (d.data, d.x, d.y, d.v, d.sigma, d.bunit,
+                self._kw, singlepix)
 
     def add_region(self, patch: str = 'ellipse',
                    poslist: list[str | list[float, float]] = [],
@@ -622,7 +608,7 @@ class PlotAstroData(AstroFrame):
                 axnow.add_patch(p)
 
     def add_beam(self, show_beam: bool = True,
-                 beam: list[float | None, float | None, float | None] = [None, None, None],
+                 beam: list[float | None] = [None] * 3,
                  beamcolor: str = 'gray',
                  beampos: list[float, float] | None = None,
                  **kwargs) -> None:
@@ -853,21 +839,15 @@ class PlotAstroData(AstroFrame):
         self._kw = {'cmap': 'cubehelix', 'alpha': 1,
                     'edgecolors': 'none', 'zorder': 1,
                     'vmin': None, 'vmax': None}
-        c, x, y, v, beam, sigma, bunit, _kw, beam_kwargs, singlepix \
-            = self._map_init(kwargs)
+        c, x, y, v, sigma, bunit, _kw, singlepix = self._map_init(kwargs)
         if singlepix:
             print('No pixel size. Skip add_color.')
             return
 
-        if cblabel is None:
-            cblabel = bunit
+        cblabel = bunit if cblabel is None else cblabel
 
-        stretch_params = {}
-        for k in ['stretch', 'stretchscale', 'stretchpower']:
-            if k in _kw:
-                stretch_params[k] = _kw.pop(k)
-        st = Stretcher(vmin=_kw['vmin'], vmax=_kw['vmax'],
-                       sigma=sigma, **stretch_params)
+        _kw['sigma'] = sigma
+        st = kwargs2instance(Stretcher, _kw)
         c, cmin, cmax = st.set_minmax(c)
         _kw['vmin'] = cmin
         _kw['vmax'] = cmax
@@ -882,7 +862,6 @@ class PlotAstroData(AstroFrame):
         for ch in self.bottomleft:
             self._set_colorbar(p, ch, show_cbar, cblabel, cbformat,
                                cbticks, cbticklabels, cblocation, st)
-        self.add_beam(beam=beam, **beam_kwargs)
 
     def add_contour(self,
                     levels: list[float] = [-12, -6, -3, 3, 6, 12, 24, 48, 96, 192, 384],
@@ -893,8 +872,7 @@ class PlotAstroData(AstroFrame):
             levels (list, optional): Contour levels in the unit of sigma. Defaults to [-12,-6,-3,3,6,12,24,48,96,192,384].
         """
         self._kw = {'colors': 'gray', 'linewidths': 1.0, 'zorder': 2}
-        c, x, y, v, beam, sigma, _, _kw, beam_kwargs, singlepix \
-            = self._map_init(kwargs)
+        c, x, y, v, sigma, _, _kw, singlepix = self._map_init(kwargs)
         if singlepix:
             print('No pixel size. Skip add_contour.')
             return
@@ -904,7 +882,6 @@ class PlotAstroData(AstroFrame):
             c = [c[self.channelnumber]]
         for axnow, cnow in zip(self.ax, c):
             axnow.contour(x, y, cnow, np.sort(levels) * sigma, **_kw)
-        self.add_beam(beam=beam, **beam_kwargs)
 
     def add_segment(self,
                     ampfits: str = None, angfits: str = None,
@@ -938,16 +915,13 @@ class PlotAstroData(AstroFrame):
                     'headaxislength': 0, 'width': 0.007, 'zorder': 3,
                     'fitsimage': [ampfits, angfits, Ufits, Qfits],
                     'data': [amp, ang, stU, stQ]}
-        c, x, y, v, beam, sigma, _, _kw, beam_kwargs, singlepix \
-            = self._map_init(kwargs)
+        c, x, y, v, sigma, _, _kw, singlepix = self._map_init(kwargs)
         if singlepix:
             print('No pixel size. Skip add_segment.')
             return
 
         amp, ang, stU, stQ = c
         sigmaU, sigmaQ = sigma[2:]
-        beam = [beam[i] for i in range(4) if beam[i][0] is not None][0]
-        self.beam = beam
         if stU is not None and stQ is not None:
             self.sigma = sigma = (sigmaU + sigmaQ) / 2.
             ang = np.degrees(np.arctan2(stU, stQ) / 2.)
@@ -968,12 +942,11 @@ class PlotAstroData(AstroFrame):
         _kw['scale'] = 1. / np.abs(x[1] - x[0])
         for axnow, unow, vnow in zip(self.ax, U, V):
             axnow.quiver(x, y, unow, vnow, **_kw)
-        self.add_beam(beam=beam, **beam_kwargs)
 
     def add_rgb(self,
-                stretch: list[str, str, str] = ['linear'] * 3,
-                stretchscale: list[float | None, float | None, float | None] = [None] * 3,
-                stretchpower: list[float, float, float] = [0.5, 0.5, 0.5],
+                stretch: list[str] = ['linear'] * 3,
+                stretchscale: list[float | None] = [None] * 3,
+                stretchpower: list[float] = [0.5] * 3,
                 **kwargs) -> None:
         """Use PIL.Image and imshow of matplotlib. kwargs must include the arguments of AstroData to specify the data to be plotted. A three-element array ([red, green, blue]) is supposed for all arguments, except for xskip, yskip and show_beam, including vmax and vmin. kwargs may include the arguments for Stretcher (stretch, stretchscale, and stretchpower; three-element array for each) to specify the stretch parameters. kwargs may include arguments for add_beam() and a dict of beam_kwargs to specify the beam patch in more detail. kwargs may include xskiip and yskip.
 
@@ -984,9 +957,10 @@ class PlotAstroData(AstroFrame):
         """
         from PIL import Image
 
-        self._kw = {'vmin': [None] * 3, 'vmax': [None] * 3}
-        c, x, y, v, beam, sigma, _, _kw, beam_kwargs, singlepix \
-            = self._map_init(kwargs)
+        self._kw = {'vmin': [None] * 3, 'vmax': [None] * 3,
+                    'stretch': stretch, 'stretchscale': stretchscale,
+                    'stretchpower': stretchpower}
+        c, x, y, v, _, _, _kw, singlepix = self._map_init(kwargs)
         if singlepix:
             print('No pixel size. Skip add_rgb.')
             return
@@ -995,8 +969,7 @@ class PlotAstroData(AstroFrame):
             print('RGB shapes mismatch. Skip add_rgb.')
             return
 
-        st = Stretcher(stretch, stretchscale, stretchpower,
-                       _kw['vmin'], _kw['vmax'], sigma)
+        st = kwargs2instance(Stretcher, _kw)
         c, cmin, cmax = st.set_minmax(c)
         for i in range(st.n):
             if cmax[i] > cmin[i]:
@@ -1012,7 +985,6 @@ class PlotAstroData(AstroFrame):
                     im.putpixel((i, j), value)
             axnow.imshow(im, extent=[x[0], x[-1], y[0], y[-1]])
             axnow.set_aspect(np.abs((x[-1]-x[0]) / (y[-1]-y[0])))
-        self.add_beam(beam=beam, **beam_kwargs)
 
     def _set_axis_shared(self, pa2: PlotAxes2D, title: dict | str | None):
         """Internal method used in set_axis() and set_axis_radec().
@@ -1072,7 +1044,7 @@ class PlotAstroData(AstroFrame):
             _kw['xlim'] = self.Xlim
         if 'ylim' not in _kw:
             _kw['ylim'] = self.Ylim
-        pa2 = kwargs2PlotAxes2D(_kw)
+        pa2 = kwargs2instance(PlotAxes2D, _kw)
         self._set_axis_shared(pa2=pa2, title=title)
 
     def set_axis_radec(self, center: str | None = None,
@@ -1265,8 +1237,8 @@ def plotprofile(coords: list[str] | str = [],
     _kwgauss.update(gauss_kwargs)
     if type(coords) is str:
         coords = [coords]
-    f = kwargs2AstroFrame(_kw)
-    d = kwargs2AstroData(_kw)
+    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,
@@ -1301,7 +1273,7 @@ def plotprofile(coords: list[str] | str = [],
     if 'xlim' not in _kw:
         _kw['xlim'] = [v.min(), v.max()]
     _kw['samexy'] = False
-    pa2 = kwargs2PlotAxes2D(_kw)
+    pa2 = kwargs2instance(PlotAxes2D, _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)
@@ -1350,8 +1322,8 @@ def plotslice(length: float, dx: float | None = None, pa: float = 0,
     _kw = {'linestyle': '-', 'marker': 'o'}
     _kw.update(kwargs)
     _kw['rmax'] = length / 2
-    f = kwargs2AstroFrame(_kw)
-    d = kwargs2AstroData(_kw)
+    f = kwargs2instance(AstroFrame, _kw)
+    d = kwargs2instance(AstroData, _kw)
     f.read(d)
     if np.ndim(d.data) > 2:
         print('Only 2D map is supported.')
@@ -1378,7 +1350,7 @@ def plotslice(length: float, dx: float | None = None, pa: float = 0,
         fig = plt.figure()
     if ax is None:
         ax = fig.add_subplot(1, 1, 1)
-    pa2 = kwargs2PlotAxes2D(_kw)
+    pa2 = kwargs2instance(PlotAxes2D, _kw)
     ax.plot(r, z, **_kw)
     if d.sigma is not None:
         ax.plot(r, r * 0 + 3 * d.sigma, 'k--')
@@ -1431,8 +1403,8 @@ def plot3d(levels: list[float] = [3, 6, 12],
     import plotly.graph_objs as go
     from skimage import measure
 
-    f = kwargs2AstroFrame(kwargs)
-    d = kwargs2AstroData(kwargs)
+    f = kwargs2instance(AstroFrame, kwargs)
+    d = kwargs2instance(AstroData, kwargs)
     f.read(d, xskip, yskip)
     volume, x, y, v, sigma = d.data, d.x, d.y, d.v, d.sigma
     dx, dy, dv = d.dx, d.dy, d.dv

{plotastrodata-1.8.12 → plotastrodata-1.8.14/plotastrodata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plotastrodata
-Version: 1.8.12
+Version: 1.8.14
 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