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{"repo": "glue-viz/glue", "pull_number": 99, "instance_id": "glue-viz__glue-99", "issue_numbers": "", "base_commit": "8b026e8681873d0b4408eba96360576ef37b56a9", "patch": "diff --git a/glue/core/coordinates.py b/glue/core/coordinates.py\n--- a/glue/core/coordinates.py\n+++ b/glue/core/coordinates.py\n@@ -1,10 +1,7 @@\n import logging\n \n-import pywcs\n import numpy as np\n \n-import pyfits.core\n-\n __all__ = ['Coordinates', 'WCSCoordinates', 'WCSCube']\n \n \n@@ -43,12 +40,14 @@ class WCSCoordinates(Coordinates):\n def __init__(self, header):\n super(WCSCoordinates, self).__init__()\n self._header = header\n- self._wcs = pywcs.WCS(header)\n+ from astropy import wcs\n+ self._wcs = wcs.WCS(header)\n \n def __setstate__(self, state):\n self.__dict__ = state\n # wcs object doesn't seem to unpickle properly. reconstruct it\n- self._wcs = pywcs.WCS(self._header)\n+ from astropy import wcs\n+ self._wcs = wcs.WCS(self._header)\n \n def pixel2world(self, xpix, ypix):\n '''\n@@ -145,8 +144,9 @@ class WCSCubeCoordinates(WCSCoordinates):\n \n def __init__(self, header):\n super(WCSCubeCoordinates, self).__init__(header)\n- if not isinstance(header, pyfits.core.Header):\n- raise TypeError(\"Header must by a pyfits header instance\")\n+ from astropy.io import fits\n+ if not isinstance(header, fits.Header):\n+ raise TypeError(\"Header must by an astropy.io.fits.Header instance\")\n \n if 'NAXIS' not in header or header['NAXIS'] != 3:\n raise AttributeError(\"Header must describe a 3D array\")\n@@ -173,10 +173,12 @@ def __init__(self, header):\n \"%s = %s\" %\n (k, header[k]))\n self._fix_header_for_2d()\n- self._wcs = pywcs.WCS(header)\n+\n+ from astropy import wcs\n+ self._wcs = wcs.WCS(header)\n \n def _fix_header_for_2d(self):\n- #workaround for pywcs -- need to remove 3D header keywords\n+ #workaround for astropy.wcs -- need to remove 3D header keywords\n self._header['NAXIS'] = 2\n for tag in ['NAXIS3', 'CDELT3', 'CD3_3', 'CRPIX3', 'CRVAL3', 'CTYPE3']:\n if tag in self._header:\n@@ -208,7 +210,7 @@ def coordinates_from_header(header):\n \"\"\" Convert a FITS header into a glue Coordinates object\n \n :param header: Header to convert\n- :type header: :class:`pyfits.Header`\n+ :type header: :class:`astropy.io.fits.Header`\n \n :rtype: :class:`~glue.core.coordinates.Coordinates`\n \"\"\"\ndiff --git a/glue/core/data.py b/glue/core/data.py\n--- a/glue/core/data.py\n+++ b/glue/core/data.py\n@@ -2,7 +2,6 @@\n import logging\n \n import numpy as np\n-import pyfits\n \n from .io import extract_data_fits, extract_data_hdf5\n from .coordinates import Coordinates, coordinates_from_header\n@@ -673,8 +672,9 @@ def read_data(self, filename, format='auto', **kwargs):\n \n # Read in the data\n if format in ['fits', 'fit']:\n+ from astropy.io import fits\n arrays = extract_data_fits(filename, **kwargs)\n- header = pyfits.open(filename, memmap=True)[0].header\n+ header = fits.open(filename, memmap=True)[0].header\n self.coords = coordinates_from_header(header)\n elif format in ['hdf', 'hdf5', 'h5']:\n arrays = extract_data_hdf5(filename, **kwargs)\ndiff --git a/glue/core/io.py b/glue/core/io.py\n--- a/glue/core/io.py\n+++ b/glue/core/io.py\n@@ -7,10 +7,10 @@ def extract_data_fits(filename, use_hdu='all'):\n Exception is raised.\n '''\n \n- import pyfits\n+ from astropy.io import fits\n \n # Read in all HDUs\n- hdulist = pyfits.open(filename, memmap=True)\n+ hdulist = fits.open(filename, memmap=True)\n \n # If only a subset are requested, extract those\n if use_hdu != 'all':\n@@ -18,8 +18,8 @@ def extract_data_fits(filename, use_hdu='all'):\n \n # Now only keep HDUs that are not tables\n for hdu in hdulist:\n- if not isinstance(hdu, pyfits.PrimaryHDU) and \\\n- not isinstance(hdu, pyfits.ImageHDU):\n+ if not isinstance(hdu, fits.PrimaryHDU) and \\\n+ not isinstance(hdu, fits.ImageHDU):\n hdulist.remove(hdu)\n \n # Check that dimensions of all HDU are the same\ndiff --git a/glue/core/subset.py b/glue/core/subset.py\n--- a/glue/core/subset.py\n+++ b/glue/core/subset.py\n@@ -1,6 +1,5 @@\n import operator\n import numpy as np\n-import pyfits\n \n from .visual import VisualAttributes, RED\n from .decorators import memoize_attr_check\n@@ -194,13 +193,15 @@ def write_mask(self, file_name, format=\"fits\"):\n \"\"\"\n mask = np.short(self.to_mask())\n if format == 'fits':\n- pyfits.writeto(file_name, mask, clobber=True)\n+ from astropy.io import fits\n+ fits.writeto(file_name, mask, clobber=True)\n else:\n raise AttributeError(\"format not supported: %s\" % format)\n \n def read_mask(self, file_name):\n try:\n- mask = pyfits.open(file_name)[0].data\n+ from astropy.io import fits\n+ mask = fits.open(file_name)[0].data\n except IOError:\n raise IOError(\"Could not read %s (not a fits file?)\" % file_name)\n ind = np.where(mask.flat)[0]\n", "test_patch": "diff --git a/glue/core/tests/test_coordinates.py b/glue/core/tests/test_coordinates.py\n--- a/glue/core/tests/test_coordinates.py\n+++ b/glue/core/tests/test_coordinates.py\n@@ -1,7 +1,6 @@\n #pylint: disable=I0011,W0613,W0201,W0212,E1101,E1103\n import pytest\n \n-from pyfits import Header, Card\n from mock import patch\n import numpy as np\n from numpy.testing import assert_almost_equal\n@@ -12,7 +11,8 @@\n class TestWcsCoordinates(object):\n \n def default_header(self):\n- hdr = Header()\n+ from astropy.io import fits\n+ hdr = fits.Header()\n hdr.update('NAXIS', 2)\n hdr.update('CRVAL1', 0)\n hdr.update('CRVAL2', 5)\n@@ -235,6 +235,7 @@ def test_attribute_error(self):\n \n \n def header_from_string(string):\n+ from astropy.io import fits\n cards = []\n for s in string.splitlines():\n try:\n@@ -247,8 +248,8 @@ def header_from_string(string):\n pass\n except ValueError:\n continue\n- cards.append(Card(key, value))\n- return Header(cards)\n+ cards.append(fits.Card(key, value))\n+ return fits.Header(cards)\n \n \n @pytest.mark.parametrize(('hdr'), (HDR_2D_VALID, HDR_3D_VALID_NOWCS))\ndiff --git a/glue/core/tests/test_subset.py b/glue/core/tests/test_subset.py\n--- a/glue/core/tests/test_subset.py\n+++ b/glue/core/tests/test_subset.py\n@@ -5,7 +5,6 @@\n import pytest\n import numpy as np\n from mock import MagicMock\n-import pyfits\n \n from ..data import Data, ComponentID, Component\n from ..subset import Subset, SubsetState, ElementSubsetState\n@@ -308,7 +307,8 @@ def setup_method(self, method):\n def test_write(self):\n with tempfile.NamedTemporaryFile() as tmp:\n self.subset.write_mask(tmp.name)\n- data = pyfits.open(tmp.name)[0].data\n+ from astropy.io import fits\n+ data = fits.open(tmp.name)[0].data\n expected = np.array([[0, 1, 1, 1],\n [0, 0, 0, 0],\n [0, 0, 0, 0],\n", "problem_statement": "", "hints_text": "", "created_at": "2012-09-23T15:03:37Z"}
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