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eteq/spectralcube_to_specutils.ipynb

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spectralcube_to_specutils.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import sys\n",
"\n",
"sys.path.insert(0, '/Users/erik/src/specutils/build/lib')"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'0.7.dev1778'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import specutils\n",
"specutils.__version__"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'0.4.4'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import spectral_cube\n",
"spectral_cube.__version__"
]
},
{
"cell_type": "code",
"execution_count": 77,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Spectral cube example data "
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"import astropy.units as u\n",
"from astropy.utils import data\n",
"from spectral_cube import SpectralCube\n",
"\n",
"fn = data.get_pkg_data_filename('tests/data/adv.fits', 'spectral_cube')\n",
"cube = SpectralCube.read(fn)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"SpectralCube with shape=(4, 3, 2) and unit=K:\n",
" n_x: 2 type_x: RA---SIN unit_x: deg range: 24.062698 deg: 24.063349 deg\n",
" n_y: 3 type_y: DEC--SIN unit_y: deg range: 29.934094 deg: 29.935209 deg\n",
" n_s: 4 type_s: VOPT unit_s: km / s range: -321.215 km / s: -317.350 km / s\n"
]
}
],
"source": [
"print(cube)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(4, 3, 2)"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cube.shape"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [],
"source": [
"from astropy.io import fits\n",
"from astropy.wcs import wcs\n",
"from astropy.nddata import NDData\n",
"\n",
"hdu = fits.open(fn)[0]"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
"w = wcs.WCS(hdu.header)"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"ename": "InconsistentAxisTypesError",
"evalue": "ERROR 4 in wcs_types() at line 2703 of file cextern/wcslib/C/wcs.c:\nUnmatched celestial axes.\n",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mInconsistentAxisTypesError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-22-7611d6ce6ac3>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mspecutils\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSpectrum1D\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mw\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mflux\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mhdu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mUnit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhdu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mheader\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'BUNIT'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/src/specutils/build/lib/specutils/spectra/spectrum1d.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, flux, spectral_axis, wcs, velocity_convention, rest_value, redshift, radial_velocity, **kwargs)\u001b[0m\n\u001b[1;32m 92\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0mwcs\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 93\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0missubclass\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mWCSAdapter\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 94\u001b[0;31m \u001b[0mwcs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mWCSWrapper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 95\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 96\u001b[0m \u001b[0;31m# In the case where the arithmetic operation is being performed with\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/specutils/build/lib/specutils/wcs/wcs_wrapper.py\u001b[0m in \u001b[0;36m__new__\u001b[0;34m(cls, wcs, *args, **kwargs)\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 40\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0madapter_class\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 41\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0madapter_class\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 42\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 43\u001b[0m raise NotImplementedError(\"No such adapter for class \"\n",
"\u001b[0;32m~/src/specutils/build/lib/specutils/wcs/adapters/fitswcs_adapter.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, wcs)\u001b[0m\n\u001b[1;32m 34\u001b[0m \u001b[0;31m# Store a reference to all axes information within the wcs object\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 35\u001b[0m self.axes = WCSAxes(\n\u001b[0;32m---> 36\u001b[0;31m \u001b[0mlongitude\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mWCSSUB_LONGITUDE\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 37\u001b[0m \u001b[0mlatitude\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mWCSSUB_LATITUDE\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 38\u001b[0m \u001b[0mcubeface\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mWCSSUB_CUBEFACE\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda3/envs/astro38/lib/python3.8/site-packages/astropy/wcs/wcs.py\u001b[0m in \u001b[0;36msub\u001b[0;34m(self, axes)\u001b[0m\n\u001b[1;32m 574\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 575\u001b[0m \u001b[0;31m# Subset the WCS\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 576\u001b[0;31m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maxes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 577\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnaxis\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnaxis\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 578\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mInconsistentAxisTypesError\u001b[0m: ERROR 4 in wcs_types() at line 2703 of file cextern/wcslib/C/wcs.c:\nUnmatched celestial axes.\n"
]
}
],
"source": [
"specutils.Spectrum1D(wcs=w, flux=hdu.data*u.Unit(hdu.header['BUNIT']))"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"NDData([[[0.54671028, 0.18485446],\n",
" [0.96958463, 0.77513282],\n",
" [0.93949894, 0.89482735]],\n",
"\n",
" [[0.59789998, 0.92187424],\n",
" [0.0884925 , 0.19598286],\n",
" [0.04522729, 0.32533033]],\n",
"\n",
" [[0.38867729, 0.27134903],\n",
" [0.82873751, 0.35675333],\n",
" [0.28093451, 0.54269608]],\n",
"\n",
" [[0.14092422, 0.80219698],\n",
" [0.07455064, 0.98688694],\n",
" [0.77224477, 0.19871568]]])"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"NDData(wcs=w, data=hdu.data, unit=u.Unit(hdu.header['BUNIT']))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Switch to more JWST-like example data"
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {},
"outputs": [],
"source": [
"from urllib.request import urlretrieve\n",
"\n",
"url = 'http://data.sdss.org/sas/dr13/manga/spectro/redux/v1_5_4/7495/stack/manga-7495-12704-LOGCUBE.fits.gz'\n",
"fn = url.split('/')[-1]\n",
"urlretrieve(url, filename=fn);"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Filename: manga-7495-12704-LOGCUBE.fits.gz\n",
"No. Name Ver Type Cards Dimensions Format\n",
" 0 PRIMARY 1 PrimaryHDU 73 () \n",
" 1 FLUX 1 ImageHDU 99 (72, 72, 4563) float32 \n",
" 2 IVAR 1 ImageHDU 17 (72, 72, 4563) float32 \n",
" 3 MASK 1 ImageHDU 17 (72, 72, 4563) int32 \n",
" 4 WAVE 1 ImageHDU 9 (4563,) float64 \n",
" 5 SPECRES 1 ImageHDU 9 (4563,) float64 \n",
" 6 SPECRESD 1 ImageHDU 9 (4563,) float64 \n",
" 7 OBSINFO 1 BinTableHDU 144 12R x 63C [25A, 17A, 5A, J, I, 9A, E, E, E, E, E, E, J, J, I, J, E, 12A, J, 8A, E, E, E, E, E, E, E, E, E, E, E, E, E, E, E, E, E, E, E, 13A, E, E, E, E, D, D, D, D, E, E, J, J, J, E, E, E, E, J, J, E, E, E, E] \n",
" 8 GIMG 1 ImageHDU 28 (72, 72) float32 \n",
" 9 RIMG 1 ImageHDU 28 (72, 72) float32 \n",
" 10 IIMG 1 ImageHDU 28 (72, 72) float32 \n",
" 11 ZIMG 1 ImageHDU 28 (72, 72) float32 \n",
" 12 GPSF 1 ImageHDU 28 (72, 72) float32 \n",
" 13 RPSF 1 ImageHDU 28 (72, 72) float32 \n",
" 14 IPSF 1 ImageHDU 28 (72, 72) float32 \n",
" 15 ZPSF 1 ImageHDU 28 (72, 72) float32 \n"
]
}
],
"source": [
"f = fits.open(fn)\n",
"f.info()"
]
},
{
"cell_type": "code",
"execution_count": 49,
"metadata": {},
"outputs": [],
"source": [
"sc = spectral_cube.SpectralCube(f[1].data, wcs.WCS(f[1]))"
]
},
{
"cell_type": "code",
"execution_count": 73,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(4563, 72, 72)"
]
},
"execution_count": 73,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f[1].data.shape"
]
},
{
"cell_type": "code",
"execution_count": 74,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING: UnitsWarning: '1E-17 erg/s/cm^2/A' contains multiple slashes, which is discouraged by the FITS standard [astropy.units.format.generic]\n",
"WARNING:astropy:UnitsWarning: '1E-17 erg/s/cm^2/A' contains multiple slashes, which is discouraged by the FITS standard\n"
]
},
{
"ename": "InconsistentAxisTypesError",
"evalue": "ERROR 4 in wcs_types() at line 2703 of file cextern/wcslib/C/wcs.c:\nUnmatched celestial axes.\n",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mInconsistentAxisTypesError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-74-82e12ef19bb2>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0mfunit\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mUnit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mheader\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'BUNIT'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreplace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Ang'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'A'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreplace\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'/spaxel'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mspec\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mspecutils\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSpectrum1D\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mWCS\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mT\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mfunit\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/src/specutils/build/lib/specutils/spectra/spectrum1d.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, flux, spectral_axis, wcs, velocity_convention, rest_value, redshift, radial_velocity, **kwargs)\u001b[0m\n\u001b[1;32m 92\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0mwcs\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 93\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0missubclass\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mWCSAdapter\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 94\u001b[0;31m \u001b[0mwcs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mWCSWrapper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 95\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflux\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 96\u001b[0m \u001b[0;31m# In the case where the arithmetic operation is being performed with\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/specutils/build/lib/specutils/wcs/wcs_wrapper.py\u001b[0m in \u001b[0;36m__new__\u001b[0;34m(cls, wcs, *args, **kwargs)\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 40\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0madapter_class\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 41\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0madapter_class\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 42\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 43\u001b[0m raise NotImplementedError(\"No such adapter for class \"\n",
"\u001b[0;32m~/src/specutils/build/lib/specutils/wcs/adapters/fitswcs_adapter.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, wcs)\u001b[0m\n\u001b[1;32m 34\u001b[0m \u001b[0;31m# Store a reference to all axes information within the wcs object\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 35\u001b[0m self.axes = WCSAxes(\n\u001b[0;32m---> 36\u001b[0;31m \u001b[0mlongitude\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mWCSSUB_LONGITUDE\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 37\u001b[0m \u001b[0mlatitude\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mWCSSUB_LATITUDE\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 38\u001b[0m \u001b[0mcubeface\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mWCSSUB_CUBEFACE\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda3/envs/astro38/lib/python3.8/site-packages/astropy/wcs/wcs.py\u001b[0m in \u001b[0;36msub\u001b[0;34m(self, axes)\u001b[0m\n\u001b[1;32m 574\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 575\u001b[0m \u001b[0;31m# Subset the WCS\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 576\u001b[0;31m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msub\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maxes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 577\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnaxis\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcopy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnaxis\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 578\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mInconsistentAxisTypesError\u001b[0m: ERROR 4 in wcs_types() at line 2703 of file cextern/wcslib/C/wcs.c:\nUnmatched celestial axes.\n"
]
}
],
"source": [
"funit = u.Unit(f[1].header['BUNIT'].replace('Ang', 'A').replace('/spaxel', ''))\n",
"spec = specutils.Spectrum1D(wcs=wcs.WCS(f[1]), data=f[1].data.T*funit)"
]
},
{
"cell_type": "code",
"execution_count": 87,
"metadata": {},
"outputs": [],
"source": [
"wl = wcs.WCS(f[1]).pixel_to_world(*np.indices(f[1].data.shape))[-1]"
]
},
{
"cell_type": "code",
"execution_count": 91,
"metadata": {},
"outputs": [
{
"ename": "ValueError",
"evalue": "lookup_table should be an array with 1 dimensions.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-91-31bc80b02501>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mspec\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mspecutils\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSpectrum1D\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mspectral_axis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mwl\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mT\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mto\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mu\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mangstrom\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mT\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mfunit\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/src/specutils/build/lib/specutils/spectra/spectrum1d.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, flux, spectral_axis, wcs, velocity_convention, rest_value, redshift, radial_velocity, **kwargs)\u001b[0m\n\u001b[1;32m 89\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Spectral axis must be a `Quantity` object.\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 90\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 91\u001b[0;31m \u001b[0mwcs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mWCSWrapper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_array\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mspectral_axis\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 92\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0mwcs\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 93\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0missubclass\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwcs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mWCSAdapter\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/specutils/build/lib/specutils/wcs/wcs_wrapper.py\u001b[0m in \u001b[0;36mfrom_array\u001b[0;34m(array)\u001b[0m\n\u001b[1;32m 56\u001b[0m axes_order=(0,))\n\u001b[1;32m 57\u001b[0m \u001b[0mspec_frame\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSpectralFrame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxes_order\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 58\u001b[0;31m \u001b[0mforward_transform\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTabular1D\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0marray\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 59\u001b[0m \u001b[0mforward_transform\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minverse\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTabular1D\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 60\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda3/envs/astro38/lib/python3.8/site-packages/astropy/modeling/tabular.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, points, lookup_table, method, bounds_error, fill_value, **kwargs)\u001b[0m\n\u001b[1;32m 111\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlookup_table\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndim\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0mlookup_table\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndim\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 113\u001b[0;31m raise ValueError(\"lookup_table should be an array with \"\n\u001b[0m\u001b[1;32m 114\u001b[0m \"{0} dimensions.\".format(self.lookup_table.ndim))\n\u001b[1;32m 115\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mValueError\u001b[0m: lookup_table should be an array with 1 dimensions."
]
}
],
"source": [
"spec = specutils.Spectrum1D(spectral_axis=wl.T.to(u.angstrom), data=f[1].data.T*funit)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
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"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.0"
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},
"nbformat": 4,
"nbformat_minor": 4
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