def determine_imageOverlap(f1,
f2,
plotsave=False,
verbose=False,
debugmode=False,
quietmode=False):
''' Determine the max number of pixels in AXIS1 and AXIS2 of the input fits images, print to screen unless suppressed. Plot up the footprint if -p option is on. Right now, only takes in 2 fits images (YOLO).'''
# Read in f1,f2
d1, h1 = fits.getdata(f1, header=True)
d2, h2 = fits.getdata(f2, header=True)
w1 = wcs.WCS(h1)
w2 = wcs.WCS(h2)
# Get the RA and DEC coordinates of the four corners of each image
four_corners_RADECs1 = get_cornerRADECs(f1)
four_corners_RADECs2 = get_cornerRADECs(f2)
# Get polygon of each image corners
poly1 = Polygon(four_corners_RADECs1)
poly2 = Polygon(four_corners_RADECs2)
# Get intersection polygon
poly_intersect = poly1.intersection(poly2)
# Get RA DEC of corners of the intersection (overlapping) polygon
x_intersect, y2_intersect = poly_intersect.exterior.xy
# Get intersection RA and DEC.
# Note that the last coordinate is a repeat of the first, so remove it.
corner_RADECs_intersect = np.transpose(
np.array([x_intersect[0:-1], y2_intersect[0:-1]]))
# Do pixel scale checks: are pixels square, are pixel scales of two images similar enough
# Exits if input images found to be outside what this is coded for; Prints warnings if in debugmode but not exiting.
perform_pixelscaleChecks(w1, w2, verbose=verbose, debugmode=debugmode)
# Get XLEN and YLEN- Diff pix scales give diff XLEN, YLEN for same RA,DEC range
# Get the average XLEN and YLEN for the two input image pixscales
XLEN1, YLEN1 = get_imagesize(corner_RADECs_intersect, w1)
XLEN2, YLEN2 = get_imagesize(corner_RADECs_intersect, w2)
if verbose:
print(f'XLEN1,YLEN1: {XLEN1},{YLEN1}')
print(f'XLEN2,YLEN2: {XLEN2},{YLEN2}')
#XLEN = int(np.average([XLEN1,XLEN2])) # auto floor
#YLEN = int(np.average([YLEN1,YLEN2])) # auto floor
XLEN = min([XLEN1, XLEN2]) # Take the smallest
YLEN = min([YLEN1, YLEN2]) # Take the smallest
# Print information if not quiet mode, or if verbose
if not quietmode and not verbose:
print(f'-IMAGE_SIZE option in SWarp can be set to: {XLEN},{YLEN}')
printme = f'SWarp Command to align two images: swarp {f1} {f2} -SUBTRACT_BACK N -RESAMEPLE Y -COMBINE N -CENTER_TYPE MOST -IMAGE_SIZE {XLEN},{YLEN} -RESAMPLE_DIR ./'
print_verbose_string(printme, verbose=verbose)
# If plotsave, plot and save.
if plotsave:
plot_polygonOverlap(poly1, poly2, quietmode=quietmode)
return XLEN, YLEN
def test_spectralnorm():
cube = SpectralCube(data, wcs.WCS(h),
mask=BooleanArrayMask(mask, wcs=wcs.WCS(h)))
noiseobj = noise.Noise(cube)
noiseobj.estimate_noise()
expected = np.array([ 1.14898322, 0.71345272, 1.21989125])
assert np.allclose(noiseobj.spectral_norm, expected)
def test_spatialnorm():
cube = SpectralCube(data, wcs.WCS(h),
mask=BooleanArrayMask(mask, wcs=wcs.WCS(h)))
noiseobj = noise.Noise(cube)
noiseobj.estimate_noise()
print noiseobj.spatial_norm
expected = np.array([[ 0.04430196, 0.78314449, 0.07475047, 0.5494684 , 0.05790756],
[ 0.32931213, 0.76450342, 1.33944507, 1.06416389, 0.27999452],
[ 0.65174339, 0.24128143, 0.27692018, 0.0244925 , 0.11167775],
[ 0.60682872, 0.42536813, 0.20018275, 0.78523107, 0.95516435]])
assert np.allclose(noiseobj.spatial_norm, expected)
def mask_file(regionfile, infile, outfile, negate=False):
"""
Created a masked version of file, using a region.
Parameters
----------
regionfile : str
A file which can be loaded as a :class:`AegeanTools.regions.Region`.
The image will be masked according to this region.
infile : str
Input FITS image.
outfile : str
Output FITS image.
negate : bool
If True then pixels *outside* the region are masked.
Default = False.
See Also
--------
:func:`AegeanTools.MIMAS.mask_plane`
"""
# Check that the input file is accessible and then open it
if not os.path.exists(infile):
raise AssertionError("Cannot locate fits file {0}".format(infile))
im = pyfits.open(infile)
if not os.path.exists(regionfile):
raise AssertionError(
"Cannot locate region file {0}".format(regionfile))
region = Region.load(regionfile)
try:
wcs = pywcs.WCS(im[0].header, naxis=2)
except: # TODO: figure out what error is being thrown
wcs = pywcs.WCS(str(im[0].header), naxis=2)
if len(im[0].data.shape) > 2:
data = np.squeeze(im[0].data)
else:
data = im[0].data
print(data.shape)
if len(data.shape) == 3:
for plane in range(data.shape[0]):
mask_plane(data[plane], wcs, region, negate)
else:
mask_plane(data, wcs, region, negate)
im[0].data = data
im.writeto(outfile, overwrite=True)
logging.info("Wrote {0}".format(outfile))
return
def add_plot(fn: Path, cm, ax, alpha=1):
"""Astrometry.net makes file ".new" with the image and the WCS SIP 2-D polynomial fit coefficients in the FITS header
We use DECL as "x" and RA as "y".
pcolormesh() is used as it handles arbitrary pixel shapes.
Note that pcolormesh() cannot tolerate NaN in X or Y (NaN in C is OK).
This is handled in https://github.com/scivision/pcolormesh_nan.py.
"""
with fits.open(fn, mode='readonly', memmap=False) as f:
img = f[0].data
yPix, xPix = f[0].shape[-2:]
x, y = np.meshgrid(range(xPix), range(yPix)) # pixel indices to find RA/dec of
xy = np.column_stack((x.ravel(order='C'), y.ravel(order='C')))
radec = wcs.WCS(f[0].header).all_pix2world(xy, 0)
ra = radec[:, 0].reshape((yPix, xPix), order='C')
dec = radec[:, 1].reshape((yPix, xPix), order='C')
ax.set_title(fn.name)
ax.pcolormesh(ra, dec, img, alpha=alpha, cmap=cm, norm=LogNorm())
ax.set_ylabel('Right Ascension [deg.]')
ax.set_xlabel('Declination [deg.]')
def test_header_parse():
from astropy.io import fits
with get_pkg_data_fileobj('data/header_newlines.fits',
encoding='binary') as test_file:
hdulist = fits.open(test_file)
w = wcs.WCS(hdulist[0].header)
assert w.wcs.ctype[0] == 'RA---TAN-SIP'
def format_coord(x, y):
x = int(x + 0.5)
y = int(y + 0.5)
if x < 0 or y < 0: return " "
try:
self.img
try:
hdr = self.hdr
mywcs = wcs.WCS(hdr)
pixcrd = np.array([[x, y]])
world = mywcs.wcs_pix2world(pixcrd, 1)
try:
object = self.hdr['object']
except:
object = None
return "[x,y]=[%4d, %4d] val=%8.5g [%s %s]=[%10.6f,%10.6f] OBJECT: %s" % (
x, y, self.img[y, x], mywcs.wcs.ctype[0],
mywcs.wcs.ctype[1], world[0, 0], world[0, 1], object)
except:
mywcs = None
try:
return "[x,y]\n [%4i, %4i] val=%8.5g OBJECT: %s" % (
x, y, self.img[y, x], object)
except IndexError:
return ""
except:
return " [%4i, %4i]" % (x, y)
def test_sub_segfault():
# Issue #1960
header = fits.Header.fromtextfile(
get_pkg_data_filename('data/sub-segfault.hdr'))
w = wcs.WCS(header)
sub = w.sub([wcs.WCSSUB_CELESTIAL])
gc.collect()
def get_cornerRADECs(f):
d,h = fits.getdata(f,header=True)
w = wcs.WCS(h)
lenx,leny = np.shape(d)
four_corners_pixels = [[0,0],[0,lenx-1],[leny-1,lenx-1],[leny-1,0]]
four_corners_RADEC = w.all_pix2world(four_corners_pixels,0)
return four_corners_RADEC
def build_a_plane_position(plane):
from astropy.io import fits
from astropy.wcs import wcs
from caom2 import SegmentType, Point, Vertex, Position, shape
logging.error('do i get here?')
try:
z = fits.open('/usr/src/app/draogmims2caom2/draogmims2caom2/tests'
'/data/gmims_HBN_Fan.fits')
w = wcs.WCS(z[0].header)
points = []
vertices = []
segment_type = SegmentType['MOVE']
for x, y in ([0, 0], [1, 0], [1, 1], [0, 1]):
v = w.all_pix2world(x * z[0].header['naxis1'],
y * z[0].header['naxis2'], 1, 1)
points.append(Point(float(v[0]), float(v[1])))
vertices.append(Vertex(float(v[0]), float(v[1]), segment_type))
segment_type = SegmentType['LINE']
vertices.append(
Vertex(points[0].cval1, points[0].cval2, SegmentType['CLOSE']))
polygon = shape.Polygon(points=points,
samples=shape.MultiPolygon(vertices))
position = Position(time_dependent=False, bounds=polygon)
plane.position = position
except Exception as e:
logging.error('wtf {}'.format(e))
def test_iteration():
world = np.array(
[[-0.58995335, -0.5], [0.00664326, -0.5], [-0.58995335, -0.25],
[0.00664326, -0.25], [-0.58995335, 0.], [0.00664326, 0.],
[-0.58995335, 0.25], [0.00664326, 0.25], [-0.58995335, 0.5],
[0.00664326, 0.5]], float)
w = wcs.WCS()
w.wcs.ctype = ['GLON-CAR', 'GLAT-CAR']
w.wcs.cdelt = [-0.006666666828, 0.006666666828]
w.wcs.crpix = [75.907, 74.8485]
x = w.wcs_world2pix(world, 1)
expected = np.array(
[[1.64400000e+02, -1.51498185e-01], [7.49105110e+01, -1.51498185e-01],
[1.64400000e+02, 3.73485009e+01], [7.49105110e+01, 3.73485009e+01],
[1.64400000e+02, 7.48485000e+01], [7.49105110e+01, 7.48485000e+01],
[1.64400000e+02, 1.12348499e+02], [7.49105110e+01, 1.12348499e+02],
[1.64400000e+02, 1.49848498e+02], [7.49105110e+01, 1.49848498e+02]],
float)
assert_array_almost_equal(x, expected)
w2 = w.wcs_pix2world(x, 1)
world[:, 0] %= 360.
assert_array_almost_equal(w2, world)
def HDU_to_NDData(hdu):
"""
Create an N-dimensional dataset from an HDU component.
Parameters
----------
hdu : HDU object
HDU to transform into an N-dimensional dataset.
Returns
-------
result: astropy.nddata.NDDataRef with data from the HDU object.
"""
hdu.verify("fix")
data=hdu.data
meta=hdu.header
mask=np.isnan(data)
# Hack to correct wrong uppercased units generated by CASA
try:
bscale=meta['BSCALE']
except KeyError:
bscale=1.0
try:
bzero=meta['BZERO']
except KeyError:
bzero=0.0
try:
bsu=meta['BUNIT']
bsu=bsu.lower()
bsu=bsu.replace("jy","Jy")
bunit=u.Unit(bsu,format="fits")
except KeyError:
bunit=u.Unit("u.Jy/u.beam")
rem_list=[]
for i in meta.items():
if i[0].startswith('PC00'):
rem_list.append(i[0])
for e in rem_list:
meta.remove(e)
mywcs=wcs.WCS(meta)
# Create astropy units
if len(data.shape) == 4:
# Put data in physically-meaninful values, and remove stokes
# TODO: Stokes is removed by summing (is this correct? maybe is averaging?)
log.info("4D data detected: assuming RA-DEC-FREQ-STOKES (like CASA-generated ones), and dropping STOKES")
data=data.sum(axis=0)*bscale+bzero
mask = np.logical_and.reduce(mask,axis=0)
mywcs=mywcs.dropaxis(3)
elif len(data.shape) == 3:
log.info("3D data detected: assuming RA-DEC-FREQ")
data=data*bscale+bzero
elif len(data.shape) == 2:
log.info("2D data detected: assuming RA-DEC")
data=data*bscale+bzero
else:
log.error("Only 3D data allowed (or 4D in case of polarization)")
raise TypeError
return ndd.NDDataRef(data, uncertainty=None, mask=mask,wcs=mywcs, meta=meta, unit=bunit)
def test_unit3():
w = wcs.WCS()
for idx in (2, -3):
with pytest.raises(IndexError):
w.wcs.cunit[idx]
with pytest.raises(IndexError):
w.wcs.cunit[idx] = u.m
with pytest.raises(ValueError):
w.wcs.cunit = [u.m, u.m, u.m]
def __init__(
self,
data=None,
spec_axis=None,
pyorder=True,
hdr=None,
wcs=None,
casa_cs=None,
):
# If we have another cube object, then copy it
if isinstance(data, Cube):
self.init_from_cube(data)
# If we have a string then read a file
if type(data) == type("file.fits"):
if (data[-4:]).upper() == "FITS":
# ... if it ends in FITS call astropy
self.from_fits_file(data)
else:
# ... else call CASA
self.from_casa_image(data, transpose=pyorder)
# If we have an array, save it
if type(data) == type(np.array([1, 1])):
self.data = data
# Allow the user to force/supply attributes but note that
# these may already be set by the file reader. If so, respect
# that.
if spec_axis != None and self.spec_axis == None:
self.spec_axis = spec_axis
if hdr != None and self.hdr == None:
self.hdr == hdr
if wcs != None and self.astropy_wcs == None:
self.astropy_wcs == wcs
if casa_cs != None and self.casa_cs == None:
self.casa_cs == wcs
if self.pyorder == None:
self.pyorder = pyorder
# Some filling-out logic
if self.astropy_wcs == None and self.hdr != None:
if astropy_ok:
self.astropy_wcs = wcs.WCS(self.hdr)
if self.spec_axis == None:
self.find_spec_axis()
def __init__(self, file_path, build_cdf=True):
"""Constructor.
"""
logger.info('Reading FITS image from %s...' % file_path)
self.hdu_list = fits.open(file_path)
self.hdu_list.info()
self.wcs = wcs.WCS(self.hdu_list['PRIMARY'].header)
self.data = self.hdu_list['PRIMARY'].data.transpose()
self.vmin = None
self.vmax = None
if build_cdf:
self.build_cdf()
def fits2radec(
fitsfn: Path, WCSfn: Path = None, solve: bool = False, args: str = None
) -> xarray.Dataset:
fitsfn = Path(fitsfn).expanduser()
if WCSfn is None:
if fitsfn.suffix in (".fits", ".new"):
# using .wcs will also work but gives a spurious warning
WCSfn = fitsfn.with_suffix(".wcs")
elif fitsfn.suffix == ".wcs":
WCSfn = fitsfn
else:
raise ValueError(f"please convert {fitsfn} to GRAYSCALE .fits")
if solve:
if not doSolve(fitsfn, args):
logging.error(f"{fitsfn} was not solved")
return None
if not WCSfn.is_file():
WCSfn = WCSfn.parent / (WCSfn.stem + "_stack.wcs")
if not WCSfn.is_file():
logging.error(f"it appears {fitsfn} was not solved as {WCSfn} is not found")
return None
with fits.open(fitsfn, mode="readonly") as f:
yPix, xPix = f[0].shape[-2:]
x, y = meshgrid(range(xPix), range(yPix)) # pixel indices to find RA/dec of
xy = column_stack((x.ravel(order="C"), y.ravel(order="C")))
# %% use astropy.wcs to register pixels to RA/DEC
"""
http://docs.astropy.org/en/stable/api/astropy.wcs.WCS.html#astropy.wcs.WCS
naxis=[0,1] is to take x,y axes in case a color photo was input e.g. to astrometry.net cloud solver
"""
with fits.open(WCSfn, mode="readonly") as f:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
radec = wcs.WCS(f[0].header).all_pix2world(xy, 0)
# radec = wcs.WCS(hdul[0].header,naxis=[0,1]).all_pix2world(xy, 0)
ra = radec[:, 0].reshape((yPix, xPix), order="C")
dec = radec[:, 1].reshape((yPix, xPix), order="C")
# %% collect output
radec = xarray.Dataset(
{"ra": (("y", "x"), ra), "dec": (("y", "x"), dec)},
{"x": range(xPix), "y": range(yPix)},
attrs={"filename": str(fitsfn)},
)
return radec
def get_wcs(fits_filename):
""" Finds and returns the WCS for an image. If Primary Header WCS no good, searches each index until a good one
is found. If none found, raises a ValueError
"""
# Try just opening the initial header
wcs_init = wcs.WCS(fits_filename)
ra, dec = wcs_init.axis_type_names
if ra.upper() == "RA" and dec.upper() == "DEC":
return wcs_init
else:
hdu_list = fits.open(fits_filename)
for n in hdu_list:
try:
wcs_slice = wcs.WCS(n.header)
ra, dec = wcs_slice.axis_type_names
if ra.upper() == "RA" and dec.upper() == "DEC":
return wcs_slice
except:
continue
hdu_list.close()
raise ValueError
def test_against_wcslib(inp):
w = wcs.WCS()
crval = [202.4823228, 47.17511893]
w.wcs.crval = crval
w.wcs.ctype = ['RA---TAN', 'DEC--TAN']
lonpole = 180
tan = models.Pix2Sky_TAN()
n2c = models.RotateNative2Celestial(crval[0], crval[1], lonpole)
c2n = models.RotateCelestial2Native(crval[0], crval[1], lonpole)
m = tan | n2c
minv = c2n | tan.inverse
radec = w.wcs_pix2world(inp[0], inp[1], 1)
xy = w.wcs_world2pix(radec[0], radec[1], 1)
assert_allclose(m(*inp), radec, atol=1e-12)
assert_allclose(minv(*radec), xy, atol=1e-12)
def read_fits(fits_filename):
"""
Function to read the FITS file and store the image array and WCS
Inputs:
fits_filename: Name of the FITS filename
Outputs:
wcs_info: WCS of the FITS image
image_array: Array of the FITS image
"""
list_of_hdu = fits.open(fits_filename)
# Get the image array
image_array = fits.getdata(fits_filename)
image_array = image_array[0][0]
# Get the WCS of the image
wcs_info = wcs.WCS(list_of_hdu[0].header, list_of_hdu).celestial
return image_array, wcs_info
def load_fits(filepath):
hdulist = fits.open(filepath)
hduobject = hdulist[0]
hduobject.verify("fix")
bscale = 1.0
bunit = units.Unit('u.Jy/u.beam')
bzero = 0.0
mask = numpy.isnan(hduobject.data)
if 'BSCALE' in hduobject.header:
bscale = hduobject.header['BSCALE']
if 'BZERO' in hduobject.header:
bzero = hduobject.header['BZERO']
if 'BUNIT' in hduobject.header:
unit = hduobject.header['BUNIT'].lower().replace('jy', 'Jy')
bunit = units.Unit(unit, format='fits')
for item in hduobject.header.items():
if item[0].startswith('PC00'):
hduobject.header.remove(item[0])
coordinateSystem = wcs.WCS(hduobject.header)
if len(hduobject.data.shape) == 4:
log.info(
'4D Detected: Assuming RA-DEC-FREQ-STOKES, and dropping STOKES')
coordinateSystem = coordinateSystem.dropaxis(3)
hduobject.data = hduobject.data.sum(axis=0) * bscale + bzero
mask = numpy.logical_and.reduce(mask, axis=0)
elif len(hduobject.data.shape) == 3:
log.info('3D Detected: Assuming RA-DEC-FREQ')
hduobject.data = (hduobject.data * bscale) + bzero
elif len(hduobject.data.shape) == 2:
log.info('2D Detected: Assuming RA-DEC')
hduobject.data = (hduobject.data * bscale) + bzero
else:
log.error('Only 2-4D data allowed')
raise TypeError('Only 2-4D data allowed')
hdulist.close()
return astropy.nddata.NDDataRef(hduobject.data,
uncertainty=None,
mask=mask,
wcs=coordinateSystem,
meta=hduobject.header,
unit=bunit)
def fits2radec(fitsfn: Path, solve: bool=False, args: str=None) -> xarray.Dataset:
fitsfn = Path(fitsfn).expanduser()
if fitsfn.suffix == '.fits':
WCSfn = fitsfn.with_suffix('.wcs') # using .wcs will also work but gives a spurious warning
elif fitsfn.suffix == '.wcs':
WCSfn = fitsfn
else:
raise ValueError(f'please convert {fitsfn} to GRAYSCALE .fits e.g. with ImageJ or ImageMagick')
if solve:
doSolve(fitsfn, args)
with fits.open(fitsfn, mode='readonly') as f:
yPix, xPix = f[0].shape[-2:]
x, y = meshgrid(range(xPix), range(yPix)) # pixel indices to find RA/dec of
xy = column_stack((x.ravel(order='C'), y.ravel(order='C')))
# %% use astropy.wcs to register pixels to RA/DEC
"""
http://docs.astropy.org/en/stable/api/astropy.wcs.WCS.html#astropy.wcs.WCS
naxis=[0,1] is to take x,y axes in case a color photo was input e.g. to astrometry.net cloud solver
"""
try:
with fits.open(WCSfn, mode='readonly') as f:
# radec = wcs.WCS(hdul[0].header,naxis=[0,1]).all_pix2world(xy, 0)
radec = wcs.WCS(f[0].header).all_pix2world(xy, 0)
except OSError:
raise OSError(f'It appears the WCS solution is not present, was the FITS image solved? looking for: {WCSfn}')
ra = radec[:, 0].reshape((yPix, xPix), order='C')
dec = radec[:, 1].reshape((yPix, xPix), order='C')
# %% collect output
radec = xarray.Dataset({'ra': (('y', 'x'), ra),
'dec': (('y', 'x'), dec), },
{'x': range(xPix), 'y': range(yPix)},
attrs={'filename': fitsfn})
return radec
def mask2mim(maskfile, mimfile, threshold=1.0, maxdepth=8):
"""
Use a fits file as a mask to create a region file.
Pixels in mask file that are equal or above the threshold will be included in the reigon,
while those that are below the threshold will not.
Parameters
----------
maskfile : str
Input file in fits format.
mimfile : str
Output filename
threshold : float
threshold value for separating include/exclude values
maxdepth : int
Maximum depth (resolution) of the healpix pixels
"""
hdu = pyfits.open(maskfile)
wcs = pywcs.WCS(hdu[0].header)
x, y = np.where(hdu[0].data >= threshold)
ra, dec = wcs.all_pix2world(y, x, 0)
sky = np.radians(Region.radec2sky(ra, dec))
vec = Region.sky2vec(sky)
x, y, z = np.transpose(vec)
pix = hp.vec2pix(2**maxdepth, x, y, z, nest=True)
region = Region(maxdepth=maxdepth)
region.add_pixels(pix, depth=maxdepth)
region._renorm()
save_region(region, mimfile)
logging.info("Converted {0} -> {1}".format(maskfile, mimfile))
return
def from_fits_file(self,
filename=None,
skipdata=False,
skipvalid=False,
skiphdr=False):
"""
Read in a cube from a FITS file using astropy.
"""
# Require astropy to be loaded.
if astropy_ok == False:
print "Cannot read FITS files without astropy."
return
# ... record the filename
self.filename = filename
# ... open the file
hdulist = fits.open(filename)
# ... read the data - assume first extension
if skipdata == False:
self.data = hdulist[0].data
# ... note where data is valid
if skipvalid == False:
self.valid = np.isfinite(self.data)
# ... astropy always reads in pyorder
self.pyorder = True
# ... note the header and WCS information
if skiphdr == False:
self.astropy_wcs = wcs.WCS(hdulist[0].header)
self.hdr = hdulist[0].header
# ... figure out the spectral axis
self.find_spec_axis()
def test_scalegen():
cube = SpectralCube(data, wcs.WCS(h),
mask=BooleanArrayMask(mask, wcs=wcs.WCS(h)))
noiseobj = noise.Noise(cube)
assert np.isclose(noiseobj.scale, 1.1382529312849043)
def plot_fits_map(data,
header,
stretch='auto',
exponent=2,
scaleFrac=0.9,
cmapName='gist_heat',
zMin=None,
zMax=None,
annEllipseLst=[],
annPolyLst=[],
bunit=None,
lw=1.0,
interpolation='Nearest',
fig=None,
dpi=100,
doColbar=True):
"""
Plot a colourscale image of a FITS map.
annEllipseLst is a list of lists:
annEllipseLst[0][i] = x_deg
annEllipseLst[1][i] = y_deg
annEllipseLst[2][i] = minor_deg
annEllipseLst[3][i] = major_deg
annEllipseLst[4][i] = pa_deg
annEllipseLst[5][i] = colour ... optional, default to 'g'
annPolyLst is also a list of lists:
annPolyLst[0][i] = list of polygon coords = [[x1,y1], [x2, y2] ...]
annPolyLst[1][i] = colour of polygon e.g., 'w'
"""
# Strip unused dimensions from the array
data, header = strip_fits_dims(data, header, 2, 5)
# Parse the WCS information
w = mkWCSDict(header)
wcs = pw.WCS(w['header2D'])
# Calculate the image vmin and vmax by measuring the range in the inner
# 'scale_frac' of the image
s = data.shape
boxMaxX = int(s[-1] / 2.0 + s[-1] * scaleFrac / 2.0 + 1.0)
boxMinX = int(s[-1] / 2.0 - s[-1] * scaleFrac / 2.0 + 1.0)
boxMaxY = int(s[-2] / 2.0 + s[-2] * scaleFrac / 2.0 + 1.0)
boxMinY = int(s[-2] / 2.0 - s[-2] * scaleFrac / 2.0 + 1.0)
dataSample = data[boxMinY:boxMaxY, boxMinX:boxMaxX]
measures = calc_stats(dataSample)
sigma = abs(measures['max'] / measures['madfm'])
if stretch == 'auto':
if sigma <= 20:
vMin = measures['madfm'] * (-1.5)
vMax = measures['madfm'] * 10.0
stretch = 'linear'
elif sigma > 20:
vMin = measures['madfm'] * (-3.0)
vMax = measures['madfm'] * 40.0
stretch = 'linear'
elif sigma > 500:
vMin = measures['madfm'] * (-7.0)
vMax = measures['madfm'] * 200.0
stretch = 'sqrt'
if not zMax is None:
vMax = max(zMax, measures['max'])
if not zMax is None:
vMin = zMin
# Set the colourscale using an normalizer object
normalizer = APLpyNormalize(stretch=stretch,
exponent=exponent,
vmin=vMin,
vmax=vMax)
# Setup the figure
if fig is None:
fig = plt.figure(facecolor='w', figsize=(9.5, 8))
ax = fig.add_axes([0.1, 0.08, 0.9, 0.87])
if w['coord_type'] == 'EQU':
ax.set_xlabel('Right Ascension')
ax.set_ylabel('Declination')
elif w['coord_type'] == 'GAL':
ax.set_xlabel('Galactic Longitude (deg)')
ax.set_ylabel('Galactic Latitude (deg)')
else:
ax.set_xlabel('Unknown')
ax.set_ylabel('Unknown')
cosY = m.cos(m.radians(w['ycent']))
aspect = abs(w['ydelt'] / (w['xdelt'] * cosY))
# Set the format of the major tick mark and labels
if w['coord_type'] == 'EQU':
f = 15.0
majorFormatterX = FuncFormatter(label_format_hms)
minorFormatterX = None
majorFormatterY = FuncFormatter(label_format_dms)
minorFormattery = None
else:
f = 1.0
majorFormatterX = FuncFormatter(label_format_deg)
minorFormatterX = None
majorFormatterY = FuncFormatter(label_format_deg)
minorFormattery = None
ax.xaxis.set_major_formatter(majorFormatterX)
ax.yaxis.set_major_formatter(majorFormatterY)
# Set the location of the the major tick marks
#xrangeArcmin = abs(w['xmax']-w['xmin'])*(60.0*f)
#xmultiple = m.ceil(xrangeArcmin/3.0)/(60.0*f)
#yrangeArcmin = abs(w['ymax']-w['ymin'])*60.0
#ymultiple = m.ceil(yrangeArcmin/3.0)/60.0
#majorLocatorX = MultipleLocator(xmultiple)
#ax.xaxis.set_major_locator(majorLocatorX)
#majorLocatorY = MultipleLocator(ymultiple)
#ax.yaxis.set_major_locator(majorLocatorY)
ax.xaxis.set_major_locator(MaxNLocator(5))
ax.yaxis.set_major_locator(MaxNLocator(5))
# Print the image to the axis
im = ax.imshow(data,
interpolation=interpolation,
origin='lower',
aspect=aspect,
extent=[w['xmax'], w['xmin'], w['ymin'], w['ymax']],
cmap=plt.get_cmap(cmapName),
norm=normalizer)
# Add the colorbar
if doColbar:
cbar = fig.colorbar(im, pad=0.0)
if 'BUNIT' in header:
cbar.set_label(header['BUNIT'])
else:
cbar.set_label('Unknown')
if not bunit is None:
cbar.set_label(bunit)
# Format the colourbar labels - TODO
# Set white ticks
ax.tick_params(pad=5)
for line in ax.xaxis.get_ticklines() + ax.get_yticklines():
line.set_markeredgewidth(1)
line.set_color('w')
# Create the ellipse source annotations
if len(annEllipseLst) > 0:
if len(annEllipseLst) >= 5:
srcXLst = np.array(annEllipseLst[0])
srcYLst = np.array(annEllipseLst[1])
srcMinLst = np.array(annEllipseLst[2])
srcMajLst = np.array(annEllipseLst[3])
srcPALst = np.array(annEllipseLst[4])
if len(annEllipseLst) >= 6:
if type(annEllipseLst[5]) is str:
srcEColLst = [annEllipseLst[5]] * len(srcXLst)
elif type(annEllipseLst[5]) is list:
srcEColLst = annEllipseLst[5]
else:
rcEColLst = ['g'] * len(srcXLst)
else:
srcEColLst = ['g'] * len(srcXLst)
for i in range(len(srcXLst)):
try:
el = Ellipse((srcXLst[i], srcYLst[i]),
srcMinLst[i],
srcMajLst[i],
angle=180.0 - srcPALst[i],
edgecolor=srcEColLst[i],
linewidth=lw,
facecolor='none')
ax.add_artist(el)
except Exception:
pass
# Create the polygon source annotations
if len(annPolyLst) > 0:
annPolyCoordLst = annPolyLst[0]
if len(annPolyLst) > 1:
if type(annPolyLst[1]) is str:
annPolyColorLst = [annPolyLst[1]] * len(annPolyCoordLst)
elif type(annPolyLst[1]) is list:
annPolyColorLst = annPolyLst[1]
else:
annPolyColorLst = ['g'] * len(annPolyCoordLst)
else:
annPolyColorLst = ['g'] * len(annPolyCoordLst)
for i in range(len(annPolyCoordLst)):
cpoly = Polygon(annPolyCoordLst[i], animated=False, linewidth=lw)
cpoly.set_edgecolor(annPolyColorLst[i])
cpoly.set_facecolor('none')
ax.add_patch(cpoly)
return fig
starnames = a['name'].data
radecstrs = []
for k in range(len(a)):
cstr = '{}h{}m{}s {}d{}m{}s'.format(a['rah'][k], a['ram'][k],
a['ras'][k], a['decd'][k],
a['decm'][k], a['decs'][k])
radecstrs.append(cstr)
print(starnames)
print(radecstrs)
# get the large fits file and wcs info
filename = 'F475W_mosaic.fits.gz'
cband = 'F475W'
hdulist = fits.open(filename)
image_wcs = wcs.WCS(hdulist[0].header)
image = hdulist[0].data
# size to extract in (ra, dec) arcsec
size = (10., 10.)
for k, cradec in enumerate(radecstrs):
pimage = get_postage_stamp(cradec, size, image, image_wcs)
if pimage is not None:
print(pimage.wcs)
ohdu = fits.PrimaryHDU(pimage.data, header=pimage.wcs.to_header())
ohdul = fits.HDUList([ohdu])
ohdul.writeto('%s_%s_pstamp.fits' % (starnames[k], cband),
overwrite=True)
def test_unit2():
w = wcs.WCS()
myunit = u.Unit("FOOBAR", parse_strict="warn")
w.wcs.cunit[0] = myunit
def test_unit():
w = wcs.WCS()
w.wcs.cunit[0] = u.erg
assert w.wcs.cunit[0] == u.erg
assert repr(w.wcs.cunit) == "['erg', '']"
if phot_band == "radio":
sep_pattern = [400, 400]
corner_coord = cent_coord.directional_offset_by(
pa_pattern * u.deg, sep_pattern * u.arcsec)
else:
sep_pattern = [300, 300]
corner_coord = cent_coord.directional_offset_by(
pa_pattern * u.deg, sep_pattern * u.arcsec)
# Name the section based on Source_Name and phot_band
crop_img_name = BASE_OUT + "/" + prefilt_out["Source_Name"][
ii] + "_" + phot_band + ".fits"
img_to_crop = img_dict[phot_band]
if not os.path.exists(crop_img_name):
hdul = fits.open(img_to_crop)
img_wcs = wcs.WCS(hdul[0].header, hdul).celestial
print(crop_img_name)
xc, yc = img_wcs.all_world2pix(corner_coord.ra, corner_coord.dec,
0)
xc = np.sort(xc)
yc = np.sort(yc)
xr = slice(int(np.round(xc[0])), int(np.floor(xc[1])))
yr = slice(int(np.round(yc[0])), int(np.floor(yc[1])))
if phot_band != "radio":
crop_write_fits(hdul, img_wcs, hdul[0].data, xr, yr,
crop_img_name)
else:
def match_crop_fits(filename_indx):
"""
Use the funtions defined previously to find the overlapping
region between two images and crop both the images to the
overlapping image.
This assumes that the WCS information in the FITS header
is accurate.
Parameters:
-----------
filename_indx : The index into the list of filenames to
select the file that needs to be processed
"""
wht_img = wht_list[filename_indx]
coadd_img = coadd_list[filename_indx]
print("Matching " + coadd_img)
# Open wht image and store image data and WCS information
wht_hdu = fits.open(wht_img)
wht_wcs = wcs.WCS(wht_hdu[wcs_hext].header, wht_hdu).celestial
wht_data = wht_hdu[img_hext].data
# Open the image and store image data and WCS information
coadd_hdu = fits.open(coadd_img)
coadd_wcs = wcs.WCS(coadd_hdu[wcs_hext].header, coadd_hdu).celestial
coadd_data = coadd_hdu[img_hext].data
img_c_ra, img_c_dec = world_extent(coadd_wcs, coadd_hdu[wcs_hext].header)
wht_c_ra, wht_c_dec = world_extent(wht_wcs, wht_hdu[wcs_hext].header)
# Compute the corners of the ectangle that define the
# overlapping region from the images
ov_ra = np.zeros(4)
ov_dec = np.zeros(4)
# The left corners
ov_ra[0:2] = np.min([img_c_ra[0:2], wht_c_ra[0:2]], axis=0)
ov_dec[0:2] = np.max([img_c_dec[0:2], wht_c_dec[0:2]], axis=0)
ov_ra[2:] = np.max([img_c_ra[2:], wht_c_ra[2:]], axis=0)
ov_dec[2:] = np.min([img_c_dec[2:], wht_c_dec[2:]], axis=0)
# Compute the pixel (x,y) coordinates at these overlapping
# world coordinates
img_ovx, img_ovy = coadd_wcs.all_world2pix(ov_ra, ov_dec, 1)
wht_ovx, wht_ovy = wht_wcs.all_world2pix(ov_ra, ov_dec, 1)
# Define the range of the x and y-axis of overlapping region
# and check that they are of the same size
wht_xr = np.round(np.array([wht_ovx[1], wht_ovx[2]])).astype(int)
img_xr = np.round(np.array([img_ovx[1], img_ovx[2]])).astype(int)
wht_yr = np.round(np.array([wht_ovy[0], wht_ovy[2]])).astype(int)
img_yr = np.round(np.array([img_ovy[0], img_ovy[2]])).astype(int)
# Now check that the area of the overlapping images
# will be the same
check_imsize(wht_xr, wht_yr, img_xr, img_yr)
# Write the cropped, overlapping images to file
crop_write_fits(coadd_hdu, coadd_wcs, coadd_data, img_xr, img_yr,
coadd_outlist[filename_indx])
crop_write_fits(wht_hdu, wht_wcs, wht_data, wht_xr, wht_yr,
wht_outlist[filename_indx])
return