In : from mpdaf.obj import Cube In : from mpdaf.drs import PixTable
All of the examples in the MPDAF web pages are shown being typed into
an interactive IPython shell. This shell is the origin of the prompts
In : in the above example. The examples can also be entered
in other shells, such as the native Python shell.
Loading your first MUSE datacube¶
MUSE datacubes are generally loaded from FITS files. In these files the fluxes and variances are stored in separate FITS extensions. For example:
# data and variance arrays are read from DATA and STAT extensions of the file In : cube = Cube('obj/CUBE.fits') In : cube.info() [INFO] 1595 x 10 x 20 Cube (obj/CUBE.fits) [INFO] .data(1595 x 10 x 20) (1e-40 erg / (Angstrom cm2 s)), .var(1595 x 10 x 20) [INFO] center:(-30:00:00.4494,01:20:00.4376) size:(2.000",4.000") step:(0.200",0.200") rot:-0.0 deg frame:FK5 [INFO] wavelength: min:7300.00 max:9292.50 step:1.25 Angstrom
The listed dimensions of the cube, 1595 x 10 x 20, indicate that the cube has 1595 spectral pixels and 10 x 20 spatial pixels. The order in which these dimensions are listed, follows the indexing conventions used by Python to handle 3D arrays (see Spectrum, Image and Cube format for more information).
Let’s compute the reconstructed white-light image and display it. The white-light image is obtained by summing each spatial pixel of the cube along the wavelength axis. This converts the 3D cube into a 2D image.
In : ima = cube.sum(axis=0) In : type(ima) Out: mpdaf.obj.image.Image In : plt.figure() Out: <Figure size 640x480 with 0 Axes> In : ima.plot(scale='arcsinh', colorbar='v') Out: <matplotlib.image.AxesImage at 0x7f80d2b45a50>
Let’s now compute the overall spectrum of the cube by taking the cube and summing along the X and Y axes of the image plane. This yields the total flux per spectral pixel.
In : sp = cube.sum(axis=(1,2)) In : type(sp) Out: mpdaf.obj.spectrum.Spectrum In : plt.figure() Out: <Figure size 640x480 with 0 Axes> In : sp.plot()
Because different sub-packages have very different functionality,
further suggestions for getting started are provided in the online
documentation of these sub-packages. For example, click on Cube object,
Image object, or Spectrum object for help with the 3 main classes of
Alternatively, if you use the IPython interactive python shell, then you can
look at the docstrings of classes, objects and functions by following them with
? of IPython. Examples of this are shown below. A more general
way to see these docstrings, which works in all Python shells, is to use the
In : Cube.median? Signature: Cube.median(self, axis=None) Docstring: Return the median over a given axis. Beware that if the pixels of the cube have associated variances, these are discarded by this function, because there is no way to estimate the effects of a median on the variance. Parameters ---------- axis : None or int or tuple of ints The axis or axes along which a median is performed. The default (axis = None) performs a median over all the dimensions of the cube and returns a float. axis = 0 performs a median over the wavelength dimension and returns an image. axis = (1,2) performs a median over the (X,Y) axes and returns a spectrum. File: ~/checkouts/readthedocs.org/user_builds/mpdaf/conda/latest/lib/python2.7/site-packages/mpdaf-3.0.dev2677-py2.7-linux-x86_64.egg/mpdaf/obj/cube.py Type: instancemethod
In : help(ima.plot) Help on method plot in module mpdaf.obj.image: plot(self, title=None, scale='linear', vmin=None, vmax=None, zscale=False, colorbar=None, var=False, show_xlabel=True, show_ylabel=True, ax=None, unit=Unit("deg"), use_wcs=False, **kwargs) method of mpdaf.obj.image.Image instance Plot the image with axes labeled in pixels. If either axis has just one pixel, plot a line instead of an image. Colors are assigned to each pixel value as follows. First each pixel value, ``pv``, is normalized over the range ``vmin`` to ``vmax``, to have a value ``nv``, that goes from 0 to 1, as follows:: nv = (pv - vmin) / (vmax - vmin) This value is then mapped to another number between 0 and 1 which determines a position along the colorbar, and thus the color to give the displayed pixel. The mapping from normalized values to colorbar position, color, can be chosen using the scale argument, from the following options: - 'linear': ``color = nv`` - 'log': ``color = log(1000 * nv + 1) / log(1000 + 1)`` - 'sqrt': ``color = sqrt(nv)`` - 'arcsinh': ``color = arcsinh(10*nv) / arcsinh(10.0)`` A colorbar can optionally be drawn. If the colorbar argument is given the value 'h', then a colorbar is drawn horizontally, above the plot. If it is 'v', the colorbar is drawn vertically, to the right of the plot. By default the image is displayed in its own plot. Alternatively to make it a subplot of a larger figure, a suitable ``matplotlib.axes.Axes`` object can be passed via the ``ax`` argument. Note that unless matplotlib interative mode has previously been enabled by calling ``matplotlib.pyplot.ion()``, the plot window will not appear until the next time that ``matplotlib.pyplot.show()`` is called. So to arrange that a new window appears as soon as ``Image.plot()`` is called, do the following before the first call to ``Image.plot()``:: import matplotlib.pyplot as plt plt.ion() Parameters ---------- title : str An optional title for the figure (None by default). scale : 'linear' | 'log' | 'sqrt' | 'arcsinh' The stretch function to use mapping pixel values to colors (The default is 'linear'). The pixel values are first normalized to range from 0 for values <= vmin, to 1 for values >= vmax, then the stretch algorithm maps these normalized values, nv, to a position p from 0 to 1 along the colorbar, as follows: linear: p = nv log: p = log(1000 * nv + 1) / log(1000 + 1) sqrt: p = sqrt(nv) arcsinh: p = arcsinh(10*nv) / arcsinh(10.0) vmin : float Pixels that have values <= vmin are given the color at the dark end of the color bar. Pixel values between vmin and vmax are given colors along the colorbar according to the mapping algorithm specified by the scale argument. vmax : float Pixels that have values >= vmax are given the color at the bright end of the color bar. If None, vmax is set to the maximum pixel value in the image. zscale : bool If True, vmin and vmax are automatically computed using the IRAF zscale algorithm. colorbar : str If 'h', a horizontal colorbar is drawn above the image. If 'v', a vertical colorbar is drawn to the right of the image. If None (the default), no colorbar is drawn. var : bool If true variance array is shown in place of data array ax : matplotlib.axes.Axes An optional Axes instance in which to draw the image, or None to have one created using ``matplotlib.pyplot.gca()``. unit : `astropy.units.Unit` The units to use for displaying world coordinates (degrees by default). In the interactive plot, when the mouse pointer is over a pixel in the image the coordinates of the pixel are shown using these units, along with the pixel value. use_wcs : bool If True, use `astropy.visualization.wcsaxes` to get axes with world coordinates. kwargs : matplotlib.artist.Artist Optional extra keyword/value arguments to be passed to the ``ax.imshow()`` function. Returns ------- out : matplotlib AxesImage