def plotcontrast(img):
"""
http://docs.astropy.org/en/stable/visualization/index.html
"""
vistypes = (None, LogNorm(), vis.AsinhStretch(),
vis.ContrastBiasStretch(1, 0.5), vis.HistEqStretch(img),
vis.LinearStretch(), vis.LogStretch(),
vis.PowerDistStretch(a=10.), vis.PowerStretch(a=10.),
vis.SinhStretch(), vis.SqrtStretch(), vis.SquaredStretch())
fg, ax = subplots(4, 3, figsize=(10, 10))
ax = ax.ravel()
for i, v in enumerate(vistypes):
#a = figure().gca()
a = ax[i]
if v and not isinstance(v, LogNorm):
norm = ImageNormalize(stretch=v)
a.set_title(str(v.__class__).split('.')[-1].split("'")[0])
else:
norm = v
a.set_title(str(v).split('.')[-1].split(" ")[0])
a.imshow(img, origin='lower', cmap='gray', norm=norm)
a.axis('off')
fg.suptitle('Matplotlib/AstroPy normalizations')
def normalizeImage(cls, image):
"""Normalizes the image data to the [0,1] domain, using histogram
equalization.
Parameters
----------
image : `np.array`
Image.
Returns
-------
norm : `np.array`
Normalized image.
"""
# TODO: make things like these configurable (also see resize in
# store_thumbnail)
stretch = aviz.HistEqStretch(image)
norm = aviz.ImageNormalize(image, stretch=stretch, clip=True)
return norm(image)
def plot_image(image,
ax=None,
scale='log',
cmap=None,
origin='lower',
xlabel=None,
ylabel=None,
cbar=None,
clabel='Flux ($e^{-}s^{-1}$)',
cbar_ticks=None,
cbar_ticklabels=None,
cbar_pad=None,
cbar_size='5%',
title=None,
percentile=95.0,
vmin=None,
vmax=None,
offset_axes=None,
color_bad='k',
**kwargs):
"""
Utility function to plot a 2D image.
Parameters:
image (2d array): Image data.
ax (matplotlib.pyplot.axes, optional): Axes in which to plot.
Default (None) is to use current active axes.
scale (str or :py:class:`astropy.visualization.ImageNormalize` object, optional):
Normalization used to stretch the colormap.
Options: ``'linear'``, ``'sqrt'``, ``'log'``, ``'asinh'``, ``'histeq'``, ``'sinh'``
and ``'squared'``.
Can also be a :py:class:`astropy.visualization.ImageNormalize` object.
Default is ``'log'``.
origin (str, optional): The origin of the coordinate system.
xlabel (str, optional): Label for the x-axis.
ylabel (str, optional): Label for the y-axis.
cbar (string, optional): Location of color bar.
Choises are ``'right'``, ``'left'``, ``'top'``, ``'bottom'``.
Default is not to create colorbar.
clabel (str, optional): Label for the color bar.
cbar_size (float, optional): Fractional size of colorbar compared to axes. Default=0.03.
cbar_pad (float, optional): Padding between axes and colorbar.
title (str or None, optional): Title for the plot.
percentile (float, optional): The fraction of pixels to keep in color-trim.
If single float given, the same fraction of pixels is eliminated from both ends.
If tuple of two floats is given, the two are used as the percentiles.
Default=95.
cmap (matplotlib colormap, optional): Colormap to use. Default is the ``Blues`` colormap.
vmin (float, optional): Lower limit to use for colormap.
vmax (float, optional): Upper limit to use for colormap.
color_bad (str, optional): Color to apply to bad pixels (NaN). Default is black.
kwargs (dict, optional): Keyword arguments to be passed to :py:func:`matplotlib.pyplot.imshow`.
Returns:
:py:class:`matplotlib.image.AxesImage`: Image from returned
by :py:func:`matplotlib.pyplot.imshow`.
.. codeauthor:: Rasmus Handberg <*****@*****.**>
"""
logger = logging.getLogger(__name__)
# Backward compatible settings:
make_cbar = kwargs.pop('make_cbar', None)
if make_cbar:
raise FutureWarning("'make_cbar' is deprecated. Use 'cbar' instead.")
if not cbar:
cbar = make_cbar
# Special treatment for boolean arrays:
if isinstance(image, np.ndarray) and image.dtype == 'bool':
if vmin is None: vmin = 0
if vmax is None: vmax = 1
if cbar_ticks is None: cbar_ticks = [0, 1]
if cbar_ticklabels is None: cbar_ticklabels = ['False', 'True']
# Calculate limits of color scaling:
interval = None
if vmin is None or vmax is None:
if allnan(image):
logger.warning("Image is all NaN")
vmin = 0
vmax = 1
if cbar_ticks is None:
cbar_ticks = []
if cbar_ticklabels is None:
cbar_ticklabels = []
elif isinstance(percentile, (list, tuple, np.ndarray)):
interval = viz.AsymmetricPercentileInterval(
percentile[0], percentile[1])
else:
interval = viz.PercentileInterval(percentile)
# Create ImageNormalize object with extracted limits:
if scale in ('log', 'linear', 'sqrt', 'asinh', 'histeq', 'sinh',
'squared'):
if scale == 'log':
stretch = viz.LogStretch()
elif scale == 'linear':
stretch = viz.LinearStretch()
elif scale == 'sqrt':
stretch = viz.SqrtStretch()
elif scale == 'asinh':
stretch = viz.AsinhStretch()
elif scale == 'histeq':
stretch = viz.HistEqStretch(image[np.isfinite(image)])
elif scale == 'sinh':
stretch = viz.SinhStretch()
elif scale == 'squared':
stretch = viz.SquaredStretch()
# Create ImageNormalize object. Very important to use clip=False if the image contains
# NaNs, otherwise NaN points will not be plotted correctly.
norm = viz.ImageNormalize(data=image[np.isfinite(image)],
interval=interval,
vmin=vmin,
vmax=vmax,
stretch=stretch,
clip=not anynan(image))
elif isinstance(scale, (viz.ImageNormalize, matplotlib.colors.Normalize)):
norm = scale
else:
raise ValueError("scale {} is not available.".format(scale))
if offset_axes:
extent = (offset_axes[0] - 0.5, offset_axes[0] + image.shape[1] - 0.5,
offset_axes[1] - 0.5, offset_axes[1] + image.shape[0] - 0.5)
else:
extent = (-0.5, image.shape[1] - 0.5, -0.5, image.shape[0] - 0.5)
if ax is None:
ax = plt.gca()
# Set up the colormap to use. If a bad color is defined,
# add it to the colormap:
if cmap is None:
cmap = copy.copy(plt.get_cmap('Blues'))
elif isinstance(cmap, str):
cmap = copy.copy(plt.get_cmap(cmap))
if color_bad:
cmap.set_bad(color_bad, 1.0)
# Plotting the image using all the settings set above:
im = ax.imshow(image,
cmap=cmap,
norm=norm,
origin=origin,
extent=extent,
interpolation='nearest',
**kwargs)
if xlabel is not None:
ax.set_xlabel(xlabel)
if ylabel is not None:
ax.set_ylabel(ylabel)
if title is not None:
ax.set_title(title)
ax.set_xlim([extent[0], extent[1]])
ax.set_ylim([extent[2], extent[3]])
if cbar:
colorbar(im,
ax=ax,
loc=cbar,
size=cbar_size,
pad=cbar_pad,
label=clabel,
ticks=cbar_ticks,
ticklabels=cbar_ticklabels)
# Settings for ticks:
integer_locator = MaxNLocator(nbins=10, integer=True)
ax.xaxis.set_major_locator(integer_locator)
ax.xaxis.set_minor_locator(integer_locator)
ax.yaxis.set_major_locator(integer_locator)
ax.yaxis.set_minor_locator(integer_locator)
ax.tick_params(which='both', direction='out', pad=5)
ax.xaxis.tick_bottom()
ax.yaxis.tick_left()
return im
def stretchModel(self):
if self._stretchModel is None:
print('Using default HistEqStretch stretch model')
return lambda target, header, data: astrovis.HistEqStretch(data)
return self._stretchModel
def set_normalization(self,
stretch=None,
interval=None,
stretchkwargs={},
intervalkwargs={},
perm_linear=None):
if stretch is None:
if self.stretch is None:
stretch = 'linear'
else:
stretch = self.stretch
if isinstance(stretch, str):
print(stretch,
' '.join([f'{k}={v}' for k, v in stretchkwargs.items()]))
if self.data is None: #can not calculate objects yet
self.stretch_kwargs = stretchkwargs
else:
kwargs = self.prepare_kwargs(
self.stretch_kws_defaults[stretch], self.stretch_kwargs,
stretchkwargs)
if perm_linear is not None:
perm_linear_kwargs = self.prepare_kwargs(
self.stretch_kws_defaults['linear'], perm_linear)
print(
'linear', ' '.join([
f'{k}={v}' for k, v in perm_linear_kwargs.items()
]))
if stretch == 'asinh': # arg: a=0.1
stretch = vis.CompositeStretch(
vis.LinearStretch(**perm_linear_kwargs),
vis.AsinhStretch(**kwargs))
elif stretch == 'contrastbias': # args: contrast, bias
stretch = vis.CompositeStretch(
vis.LinearStretch(**perm_linear_kwargs),
vis.ContrastBiasStretch(**kwargs))
elif stretch == 'histogram':
stretch = vis.CompositeStretch(
vis.HistEqStretch(self.data, **kwargs),
vis.LinearStretch(**perm_linear_kwargs))
elif stretch == 'log': # args: a=1000.0
stretch = vis.CompositeStretch(
vis.LogStretch(**kwargs),
vis.LinearStretch(**perm_linear_kwargs))
elif stretch == 'powerdist': # args: a=1000.0
stretch = vis.CompositeStretch(
vis.LinearStretch(**perm_linear_kwargs),
vis.PowerDistStretch(**kwargs))
elif stretch == 'power': # args: a
stretch = vis.CompositeStretch(
vis.PowerStretch(**kwargs),
vis.LinearStretch(**perm_linear_kwargs))
elif stretch == 'sinh': # args: a=0.33
stretch = vis.CompositeStretch(
vis.LinearStretch(**perm_linear_kwargs),
vis.SinhStretch(**kwargs))
elif stretch == 'sqrt':
stretch = vis.CompositeStretch(
vis.SqrtStretch(),
vis.LinearStretch(**perm_linear_kwargs))
elif stretch == 'square':
stretch = vis.CompositeStretch(
vis.LinearStretch(**perm_linear_kwargs),
vis.SquaredStretch())
else:
raise ValueError('Unknown stretch:' + stretch)
else:
if stretch == 'linear': # args: slope=1, intercept=0
stretch = vis.LinearStretch(**kwargs)
else:
raise ValueError('Unknown stretch:' + stretch)
self.stretch = stretch
if interval is None:
if self.interval is None:
interval = 'zscale'
else:
interval = self.interval
if isinstance(interval, str):
print(interval,
' '.join([f'{k}={v}' for k, v in intervalkwargs.items()]))
kwargs = self.prepare_kwargs(self.interval_kws_defaults[interval],
self.interval_kwargs, intervalkwargs)
if self.data is None:
self.interval_kwargs = intervalkwargs
else:
if interval == 'minmax':
interval = vis.MinMaxInterval()
elif interval == 'manual': # args: vmin, vmax
interval = vis.ManualInterval(**kwargs)
elif interval == 'percentile': # args: percentile, n_samples
interval = vis.PercentileInterval(**kwargs)
elif interval == 'asymetric': # args: lower_percentile, upper_percentile, n_samples
interval = vis.AsymmetricPercentileInterval(**kwargs)
elif interval == 'zscale': # args: nsamples=1000, contrast=0.25, max_reject=0.5, min_npixels=5, krej=2.5, max_iterations=5
interval = vis.ZScaleInterval(**kwargs)
else:
raise ValueError('Unknown interval:' + interval)
self.interval = interval
if self.img is not None:
self.img.set_norm(
vis.ImageNormalize(self.data,
interval=self.interval,
stretch=self.stretch,
clip=True))
def get_image(data, fmt='JPEG', norm='percentile', lo=None, hi=None,
zcontrast=0.25, nsamples=1000, krej=2.5, max_iterations=5,
stretch='linear', a=None, bias=0.5, contrast=1, cmap=None,
dpi=100, **kwargs):
u"""
Return a byte array containing image in the given format
Image scaling is done using `~astropy.visualization`. It includes
normalization of the input data (mapping to [0, 1]) and stretching -
optional non-linear mapping [0, 1] -> [0, 1] for contrast enhancement.
A colormap can be applied to the normalized data. Conversion to the target
image format is done by matplotlib or Pillow.
:param array_like data: input 2D image data
:param str fmt: output image format
:param str norm: data normalization mode::
"manual": lower and higher clipping limits are set explicitly
"minmax": limits are set to the minimum and maximum data values
"percentile" (default): limits are set based on the specified fraction
of pixels
"zscale": use IRAF ZScale algorithm
:param int | float lo::
for ``norm`` == "manual", lower data limit
for ``norm`` == "percentile", lower percentile clipping value,
defaulting to 10
for ``norm`` == "zscale", lower limit on the number of rejected pixels,
defaulting to 5
:param int | float hi::
for ``norm`` == "manual", upper data limit
for ``norm`` == "percentile", upper percentile clipping value,
defaulting to 98
for ``norm`` == "zscale", upper limit on the number of rejected pixels,
defaulting to data.size/2
:param float zcontrast: for ``norm`` == "zscale", the scaling factor,
0 < zcontrast < 1, defaulting to 0.25
:param int nsamples: for ``norm`` == "zscale", the number of points in
the input array for determining scale factors, defaulting to 1000
:param float krej: for ``norm`` == "zscale", the sigma clipping factor,
defaulting to 2.5
:param int max_iterations: for ``norm`` == "zscale", the maximum number
of rejection iterations, defaulting to 5
:param str stretch: [0, 1] → [0, 1] mapping mode::
"asinh": hyperbolic arcsine stretch y = asinh(x/a)/asinh(1/a)
"contrast": linear bias/contrast-based stretch
y = (x - bias)*contrast + 0.5
"exp": exponential stretch y = (a^x - 1)/(a - 1)
"histeq": histogram equalization stretch
"linear" (default): direct mapping
"log": logarithmic stretch y = log(ax + 1)/log(a + 1)
"power": power stretch y = x^a
"sinh": hyperbolic sine stretch y = sinh(x/a)/sinh(1/a)
"sqrt": square root stretch y = √x
"square": power stretch y = x^2
:param float a: non-linear stretch parameter::
for ``stretch`` == "asinh", the point of transition from linear to
logarithmic behavior, 0 < a <= 1, defaulting to 0.1
for ``stretch`` == "exp", base of the exponent, a != 1, defaulting to
1000
for ``stretch`` == "log", base of the logarithm minus 1, a > 0,
defaulting to 1000
for ``stretch`` == "power", the power index, defaulting to 3
for ``stretch`` == "sinh", a > 0, defaulting to 1/3
:param float bias: for ``stretch`` == "contrast", the bias parameter,
defaulting to 0.5
:param float contrast: for ``stretch`` == "contrast", the contrast
parameter, defaulting to 1
:param str cmap: optional matplotlib colormap name, defaulting
to grayscale; when a non-grayscale colormap is specified,
the conversion is always done by matplotlib, regardless of the
availability of Pillow; see https://matplotlib.org/users/colormaps.html
for more info on matplotlib colormaps and
[name for name in matplotlib.cd.cmap_d.keys()
if not name.endswith('_r')]
to list the available colormap names
:param int dpi: target image resolution in dots per inch
:param kwargs: optional format-specific keyword arguments passed to Pillow,
e.g. "quality" for JPEG; see
`https://pillow.readthedocs.io/en/stable/handbook/
image-file-formats.html`_
:return: a bytes object containing the image in the given format
:rtype: bytes
"""
data = asanyarray(data)
# Normalize image data
if norm == 'manual':
if lo is None:
raise ValueError(
'Missing lower clipping boundary for norm="manual"')
if hi is None:
raise ValueError(
'Missing upper clipping boundary for norm="manual"')
elif norm == 'minmax':
lo, hi = data.min(), data.max()
elif norm == 'percentile':
if lo is None:
lo = 10
elif not 0 <= lo <= 100:
raise ValueError(
'Lower clipping percentile must be in the [0,100] range')
if hi is None:
hi = 98
elif not 0 <= hi <= 100:
raise ValueError(
'Upper clipping percentile must be in the [0,100] range')
if hi < lo:
raise ValueError(
'Upper clipping percentile must be greater or equal to '
'lower percentile')
lo, hi = percentile(data, [lo, hi])
elif norm == 'zscale':
if lo is None:
lo = 5
if hi is None:
hi = 0.5
else:
hi /= data.size
lo, hi = apy_vis.ZScaleInterval(
nsamples, zcontrast, hi, lo, krej, max_iterations).get_limits(data)
else:
raise ValueError('Unknown normalization mode "{}"'.format(norm))
data = clip((data - lo)/(hi - lo), 0, 1)
# Stretch the data
if stretch == 'asinh':
if a is None:
a = 0.1
apy_vis.AsinhStretch(a)(data, out=data)
elif stretch == 'contrast':
if bias != 0.5 or contrast != 1:
apy_vis.ContrastBiasStretch(contrast, bias)(data, out=data)
elif stretch == 'exp':
if a is None:
a = 1000
apy_vis.PowerDistStretch(a)(data, out=data)
elif stretch == 'histeq':
apy_vis.HistEqStretch(data)(data, out=data)
elif stretch == 'linear':
pass
elif stretch == 'log':
if a is None:
a = 1000
apy_vis.LogStretch(a)(data, out=data)
elif stretch == 'power':
if a is None:
a = 3
apy_vis.PowerStretch(a)(data, out=data)
elif stretch == 'sinh':
if a is None:
a = 1/3
apy_vis.SinhStretch(a)(data, out=data)
elif stretch == 'sqrt':
apy_vis.SqrtStretch()(data, out=data)
elif stretch == 'square':
apy_vis.SquaredStretch()(data, out=data)
else:
raise ValueError('Unknown stretch mode "{}"'.format(stretch))
buf = BytesIO()
try:
# Choose the backend for making an image
if cmap is None:
cmap = 'gray'
if cmap == 'gray':
try:
# noinspection PyPackageRequirements,PyPep8Naming
from PIL import Image as pil_image
except ImportError:
pil_image = None
else:
pil_image = None
if pil_image is not None:
# Use Pillow for grayscale output if available; flip the image to
# match the bottom-to-top FITS convention and convert from [0,1] to
# unsigned byte
pil_image.fromarray(
(data[::-1]*255 + 0.5).astype(uint8),
).save(buf, fmt, dpi=(dpi, dpi), **kwargs)
else:
# Use matplotlib for non-grayscale colormaps or if PIL is not
# available
# noinspection PyPackageRequirements
from matplotlib import image as mpl_image
if fmt.lower() == 'png':
# PNG images are saved upside down by matplotlib, regardless of
# the origin parameter
data = data[::-1]
# noinspection PyTypeChecker
mpl_image.imsave(
buf, data, cmap=cmap, format=fmt, origin='lower', dpi=dpi)
return buf.getvalue()
finally:
buf.close()
def make_fov_image(fov, pngfn=None, **kwargs):
stretch = kwargs.get('stretch', 'linear')
interval = kwargs.get('interval', 'zscale')
imrange = kwargs.get('imrange')
contrast = kwargs.get('contrast', 0.25)
ccdplotorder = ['CCD2', 'CCD4', 'CCD1', 'CCD3']
if interval == 'rms':
try:
losig, hisig = imrange
except:
losig, hisig = (2.5, 5.0)
#
cmap = kwargs.get('cmap', 'viridis')
cmap = plt.get_cmap(cmap)
cmap.set_bad('w', 1.0)
w = 0.4575
h = 0.455
rc('text', usetex=False)
fig = plt.figure(figsize=(6, 6.5))
cax = fig.add_axes([0.1, 0.04, 0.8, 0.01])
ims = [fov[ccd]['im'] for ccd in ccdplotorder]
allpix = np.ma.array(ims).flatten()
stretch = {
'linear': vis.LinearStretch(),
'histeq': vis.HistEqStretch(allpix),
'asinh': vis.AsinhStretch(),
}[stretch]
if interval == 'zscale':
iv = vis.ZScaleInterval(contrast=contrast)
vmin, vmax = iv.get_limits(allpix)
elif interval == 'rms':
nsample = 1000 // nbin
background = sigma_clip(allpix[::nsample], iters=3, sigma=2.2)
m, s = background.mean(), background.std()
vmin, vmax = m - losig * s, m + hisig * s
elif interval == 'fixed':
vmin, vmax = imrange
else:
raise ValueError
norm = ImageNormalize(vmin=vmin, vmax=vmax, stretch=stretch)
for n, (im, ccd) in enumerate(zip(ims, ccdplotorder)):
if im.ndim == 3:
im = im.mean(axis=-1)
x = fov[ccd]['x']
y = fov[ccd]['y']
i = n % 2
j = n // 2
pos = [0.0225 + i * w + i * 0.04, 0.05 + j * h + j * 0.005, w, h]
ax = fig.add_axes(pos)
_im = ax.imshow(im,
origin='lower',
extent=[x[0, 0], x[0, -1], y[0, 0], y[-1, 0]],
norm=norm,
cmap=cmap,
interpolation=kwargs.get('interpolation', 'nearest'))
if fov['coordsys'] == 'sky':
ax.set_xlim(x.max(), x.min())
else:
ax.set_xlim(x.min(), x.max())
ax.set_ylim(y.min(), y.max())
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
if n == 0:
cb = fig.colorbar(_im, cax, orientation='horizontal')
cb.ax.tick_params(labelsize=9)
tstr = fov.get('file', '') + ' ' + fov.get('objname', '')
title = kwargs.get('title', tstr)
title = title[-60:]
fig.text(0.5, 0.99, title, ha='center', va='top', size=12)
if pngfn is not None:
plt.savefig(pngfn)
plt.close(fig)
