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test_core.py
1477 lines (1187 loc) · 52.4 KB
/
test_core.py
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# Licensed under a 3-clause BSD style license - see PYFITS.rst
import errno
import gzip
import io
import mmap
import os
import pathlib
import shutil
import sys
import urllib.request
import zipfile
from unittest.mock import patch
import numpy as np
import pytest
from astropy.io import fits
from astropy.io.fits.convenience import _getext
from astropy.io.fits.diff import FITSDiff
from astropy.io.fits.file import GZIP_MAGIC, _File
from astropy.io.tests import safeio
from astropy.utils import data
from astropy.utils.compat.optional_deps import (
HAS_BZ2, # NOTE: Python can be built without bz2
)
from astropy.utils.data import conf
from astropy.utils.exceptions import AstropyDeprecationWarning, AstropyUserWarning
from astropy.utils.misc import _NOT_OVERWRITING_MSG_MATCH
from .conftest import FitsTestCase
if HAS_BZ2:
import bz2
class TestCore(FitsTestCase):
def test_missing_file(self):
with pytest.raises(OSError):
fits.open(self.temp("does-not-exist.fits"))
def test_naxisj_check(self):
with fits.open(self.data("o4sp040b0_raw.fits")) as hdulist:
hdulist[1].header["NAXIS3"] = 500
assert "NAXIS3" in hdulist[1].header
hdulist.verify("silentfix")
assert "NAXIS3" not in hdulist[1].header
def test_byteswap(self):
p = fits.PrimaryHDU()
lst = fits.HDUList()
n = np.array([1, 60000, 0], dtype="u2").astype("i2")
c = fits.Column(name="foo", format="i2", bscale=1, bzero=32768, array=n)
t = fits.BinTableHDU.from_columns([c])
lst.append(p)
lst.append(t)
lst.writeto(self.temp("test.fits"), overwrite=True)
with fits.open(self.temp("test.fits")) as p:
assert p[1].data[1]["foo"] == 60000.0
def test_fits_file_path_object(self):
"""
Testing when fits file is passed as pathlib.Path object #4412.
"""
fpath = pathlib.Path(self.data("tdim.fits"))
with fits.open(fpath) as hdulist:
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
with fits.open(self.data("tdim.fits")) as hdulist2:
assert FITSDiff(hdulist2, hdulist).identical is True
def test_fits_pathlike_object(self):
"""
Testing when fits file is passed as os.PathLike object #11579.
"""
class TPath(os.PathLike):
def __init__(self, path):
self.path = path
def __fspath__(self):
return str(self.path)
fpath = TPath(self.data("tdim.fits"))
with fits.open(fpath) as hdulist:
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
with fits.open(self.data("tdim.fits")) as hdulist2:
assert FITSDiff(hdulist2, hdulist).identical is True
def test_fits_file_bytes_object(self):
"""
Testing when fits file is passed as bytes.
"""
with fits.open(self.data("tdim.fits").encode()) as hdulist:
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
with fits.open(self.data("tdim.fits")) as hdulist2:
assert FITSDiff(hdulist2, hdulist).identical is True
def test_add_del_columns(self):
p = fits.ColDefs([])
p.add_col(fits.Column(name="FOO", format="3J"))
p.add_col(fits.Column(name="BAR", format="1I"))
assert p.names == ["FOO", "BAR"]
p.del_col("FOO")
assert p.names == ["BAR"]
def test_add_del_columns2(self):
hdulist = fits.open(self.data("tb.fits"))
table = hdulist[1]
assert table.data.dtype.names == ("c1", "c2", "c3", "c4")
assert table.columns.names == ["c1", "c2", "c3", "c4"]
table.columns.del_col("c1")
assert table.data.dtype.names == ("c2", "c3", "c4")
assert table.columns.names == ["c2", "c3", "c4"]
table.columns.del_col("c3")
assert table.data.dtype.names == ("c2", "c4")
assert table.columns.names == ["c2", "c4"]
table.columns.add_col(fits.Column("foo", "3J"))
assert table.data.dtype.names == ("c2", "c4", "foo")
assert table.columns.names == ["c2", "c4", "foo"]
hdulist.writeto(self.temp("test.fits"), overwrite=True)
hdulist.close()
# NOTE: If you see a warning, might be related to
# https://github.com/spacetelescope/PyFITS/issues/44
with fits.open(self.temp("test.fits")) as hdulist:
table = hdulist[1]
assert table.data.dtype.names == ("c2", "c4", "foo")
assert table.columns.names == ["c2", "c4", "foo"]
def test_update_header_card(self):
"""A very basic test for the Header.update method--I'd like to add a
few more cases to this at some point.
"""
header = fits.Header()
comment = "number of bits per data pixel"
header["BITPIX"] = (16, comment)
assert "BITPIX" in header
assert header["BITPIX"] == 16
assert header.comments["BITPIX"] == comment
header.update(BITPIX=32)
assert header["BITPIX"] == 32
assert header.comments["BITPIX"] == ""
def test_set_card_value(self):
"""Similar to test_update_header_card(), but tests the the
`header['FOO'] = 'bar'` method of updating card values.
"""
header = fits.Header()
comment = "number of bits per data pixel"
card = fits.Card.fromstring(f"BITPIX = 32 / {comment}")
header.append(card)
header["BITPIX"] = 32
assert "BITPIX" in header
assert header["BITPIX"] == 32
assert header.cards[0].keyword == "BITPIX"
assert header.cards[0].value == 32
assert header.cards[0].comment == comment
def test_uint(self):
filename = self.data("o4sp040b0_raw.fits")
with fits.open(filename, uint=False) as hdulist_f:
with fits.open(filename, uint=True) as hdulist_i:
assert hdulist_f[1].data.dtype == np.float32
assert hdulist_i[1].data.dtype == np.uint16
assert np.all(hdulist_f[1].data == hdulist_i[1].data)
def test_fix_missing_card_append(self):
hdu = fits.ImageHDU()
errs = hdu.req_cards("TESTKW", None, None, "foo", "silentfix", [])
assert len(errs) == 1
assert "TESTKW" in hdu.header
assert hdu.header["TESTKW"] == "foo"
assert hdu.header.cards[-1].keyword == "TESTKW"
def test_fix_invalid_keyword_value(self):
hdu = fits.ImageHDU()
hdu.header["TESTKW"] = "foo"
errs = hdu.req_cards("TESTKW", None, lambda v: v == "foo", "foo", "ignore", [])
assert len(errs) == 0
# Now try a test that will fail, and ensure that an error will be
# raised in 'exception' mode
errs = hdu.req_cards(
"TESTKW", None, lambda v: v == "bar", "bar", "exception", []
)
assert len(errs) == 1
assert errs[0][1] == "'TESTKW' card has invalid value 'foo'."
# See if fixing will work
hdu.req_cards("TESTKW", None, lambda v: v == "bar", "bar", "silentfix", [])
assert hdu.header["TESTKW"] == "bar"
def test_unfixable_missing_card(self):
class TestHDU(fits.hdu.base.NonstandardExtHDU):
def _verify(self, option="warn"):
errs = super()._verify(option)
hdu.req_cards("TESTKW", None, None, None, "fix", errs)
return errs
@classmethod
def match_header(cls, header):
# Since creating this HDU class adds it to the registry we
# don't want the file reader to possibly think any actual
# HDU from a file should be handled by this class
return False
hdu = TestHDU(header=fits.Header())
with pytest.raises(fits.VerifyError):
hdu.verify("fix")
def test_exception_on_verification_error(self):
hdu = fits.ImageHDU()
del hdu.header["XTENSION"]
with pytest.raises(fits.VerifyError):
hdu.verify("exception")
def test_ignore_verification_error(self):
hdu = fits.ImageHDU()
del hdu.header["NAXIS"]
# The default here would be to issue a warning; ensure that no warnings
# or exceptions are raised
hdu.verify("ignore")
# Make sure the error wasn't fixed either, silently or otherwise
assert "NAXIS" not in hdu.header
def test_unrecognized_verify_option(self):
hdu = fits.ImageHDU()
with pytest.raises(ValueError):
hdu.verify("foobarbaz")
def test_errlist_basic(self):
# Just some tests to make sure that _ErrList is setup correctly.
# No arguments
error_list = fits.verify._ErrList()
assert error_list == []
# Some contents - this is not actually working, it just makes sure they
# are kept.
error_list = fits.verify._ErrList([1, 2, 3])
assert error_list == [1, 2, 3]
def test_combined_verify_options(self):
"""
Test verify options like fix+ignore.
"""
def make_invalid_hdu():
hdu = fits.ImageHDU()
# Add one keyword to the header that contains a fixable defect, and one
# with an unfixable defect
c1 = fits.Card.fromstring("test = ' test'")
c2 = fits.Card.fromstring("P.I. = ' Hubble'")
hdu.header.append(c1)
hdu.header.append(c2)
return hdu
# silentfix+ignore should be completely silent
hdu = make_invalid_hdu()
hdu.verify("silentfix+ignore")
# silentfix+warn should be quiet about the fixed HDU and only warn
# about the unfixable one
hdu = make_invalid_hdu()
with pytest.warns(fits.verify.VerifyWarning) as w:
hdu.verify("silentfix+warn")
assert len(w) == 4
assert "Illegal keyword name 'P.I.'" in str(w.list[2].message)
# silentfix+exception should only mention the unfixable error in the
# exception
hdu = make_invalid_hdu()
with pytest.raises(fits.VerifyError, match=r"Illegal keyword name") as excinfo:
hdu.verify("silentfix+exception")
assert "not upper case" not in str(excinfo.value)
# fix+ignore is not too useful, but it should warn about the fixed
# problems while saying nothing about the unfixable problems
hdu = make_invalid_hdu()
with pytest.warns(fits.verify.VerifyWarning) as w:
hdu.verify("fix+ignore")
assert len(w) == 4
assert "not upper case" not in str(w.list[0].message)
# fix+warn
hdu = make_invalid_hdu()
with pytest.warns(AstropyUserWarning) as w:
hdu.verify("fix+warn")
assert len(w) == 6
assert "not upper case" in str(w[2].message)
assert "Illegal keyword name" in str(w[4].message)
# fix+exception
hdu = make_invalid_hdu()
with pytest.raises(fits.VerifyError, match=r"Illegal keyword name") as excinfo:
hdu.verify("fix+exception")
assert "not upper case" in str(excinfo.value)
def test_getext(self):
"""
Test the various different ways of specifying an extension header in
the convenience functions.
"""
filename = self.data("test0.fits")
hl, ext = _getext(filename, "readonly", 1)
assert ext == 1
hl.close()
pytest.raises(ValueError, _getext, filename, "readonly", 1, 2)
pytest.raises(ValueError, _getext, filename, "readonly", (1, 2))
pytest.raises(ValueError, _getext, filename, "readonly", "sci", "sci")
pytest.raises(TypeError, _getext, filename, "readonly", 1, 2, 3)
hl, ext = _getext(filename, "readonly", ext=1)
assert ext == 1
hl.close()
hl, ext = _getext(filename, "readonly", ext=("sci", 2))
assert ext == ("sci", 2)
hl.close()
pytest.raises(
TypeError, _getext, filename, "readonly", 1, ext=("sci", 2), extver=3
)
pytest.raises(
TypeError, _getext, filename, "readonly", ext=("sci", 2), extver=3
)
hl, ext = _getext(filename, "readonly", "sci")
assert ext == ("sci", 1)
hl.close()
hl, ext = _getext(filename, "readonly", "sci", 1)
assert ext == ("sci", 1)
hl.close()
hl, ext = _getext(filename, "readonly", ("sci", 1))
assert ext == ("sci", 1)
hl.close()
hl, ext = _getext(
filename, "readonly", "sci", extver=1, do_not_scale_image_data=True
)
assert ext == ("sci", 1)
hl.close()
pytest.raises(TypeError, _getext, filename, "readonly", "sci", ext=1)
pytest.raises(TypeError, _getext, filename, "readonly", "sci", 1, extver=2)
hl, ext = _getext(filename, "readonly", extname="sci")
assert ext == ("sci", 1)
hl.close()
hl, ext = _getext(filename, "readonly", extname="sci", extver=1)
assert ext == ("sci", 1)
hl.close()
pytest.raises(TypeError, _getext, filename, "readonly", extver=1)
def test_extension_name_case_sensitive(self):
"""
Tests that setting fits.conf.extension_name_case_sensitive at
runtime works.
"""
hdu = fits.ImageHDU()
hdu.name = "sCi"
assert hdu.name == "SCI"
assert hdu.header["EXTNAME"] == "SCI"
with fits.conf.set_temp("extension_name_case_sensitive", True):
hdu = fits.ImageHDU()
hdu.name = "sCi"
assert hdu.name == "sCi"
assert hdu.header["EXTNAME"] == "sCi"
hdu.name = "sCi"
assert hdu.name == "SCI"
assert hdu.header["EXTNAME"] == "SCI"
def test_hdu_fromstring(self):
"""
Tests creating a fully-formed HDU object from a string containing the
bytes of the HDU.
"""
infile = self.data("test0.fits")
outfile = self.temp("test.fits")
with open(infile, "rb") as fin:
dat = fin.read()
offset = 0
with fits.open(infile) as hdul:
hdulen = hdul[0]._data_offset + hdul[0]._data_size
hdu = fits.PrimaryHDU.fromstring(dat[:hdulen])
assert isinstance(hdu, fits.PrimaryHDU)
assert hdul[0].header == hdu.header
assert hdu.data is None
hdu.header["TEST"] = "TEST"
hdu.writeto(outfile)
with fits.open(outfile) as hdul:
assert isinstance(hdu, fits.PrimaryHDU)
assert hdul[0].header[:-1] == hdu.header[:-1]
assert hdul[0].header["TEST"] == "TEST"
assert hdu.data is None
with fits.open(infile) as hdul:
for ext_hdu in hdul[1:]:
offset += hdulen
hdulen = len(str(ext_hdu.header)) + ext_hdu._data_size
hdu = fits.ImageHDU.fromstring(dat[offset : offset + hdulen])
assert isinstance(hdu, fits.ImageHDU)
assert ext_hdu.header == hdu.header
assert (ext_hdu.data == hdu.data).all()
def test_nonstandard_hdu(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/157
Tests that "Nonstandard" HDUs with SIMPLE = F are read and written
without prepending a superfluous and unwanted standard primary HDU.
"""
data = np.arange(100, dtype=np.uint8)
hdu = fits.PrimaryHDU(data=data)
hdu.header["SIMPLE"] = False
hdu.writeto(self.temp("test.fits"))
info = [(0, "", 1, "NonstandardHDU", 5, (), "", "")]
with fits.open(self.temp("test.fits")) as hdul:
assert hdul.info(output=False) == info
# NonstandardHDUs just treat the data as an unspecified array of
# bytes. The first 100 bytes should match the original data we
# passed in...the rest should be zeros padding out the rest of the
# FITS block
assert (hdul[0].data[:100] == data).all()
assert (hdul[0].data[100:] == 0).all()
def test_extname(self):
"""Test getting/setting the EXTNAME of an HDU."""
h1 = fits.PrimaryHDU()
assert h1.name == "PRIMARY"
# Normally a PRIMARY HDU should not have an EXTNAME, though it should
# have a default .name attribute
assert "EXTNAME" not in h1.header
# The current version of the FITS standard does allow PRIMARY HDUs to
# have an EXTNAME, however.
h1.name = "NOTREAL"
assert h1.name == "NOTREAL"
assert h1.header.get("EXTNAME") == "NOTREAL"
# Updating the EXTNAME in the header should update the .name
h1.header["EXTNAME"] = "TOOREAL"
assert h1.name == "TOOREAL"
# If we delete an EXTNAME keyword from a PRIMARY HDU it should go back
# to the default
del h1.header["EXTNAME"]
assert h1.name == "PRIMARY"
# For extension HDUs the situation is a bit simpler:
h2 = fits.ImageHDU()
assert h2.name == ""
assert "EXTNAME" not in h2.header
h2.name = "HELLO"
assert h2.name == "HELLO"
assert h2.header.get("EXTNAME") == "HELLO"
h2.header["EXTNAME"] = "GOODBYE"
assert h2.name == "GOODBYE"
def test_extver_extlevel(self):
"""Test getting/setting the EXTVER and EXTLEVEL of and HDU."""
# EXTVER and EXTNAME work exactly the same; their semantics are, for
# now, to be inferred by the user. Although they should never be less
# than 1, the standard does not explicitly forbid any value so long as
# it's an integer
h1 = fits.PrimaryHDU()
assert h1.ver == 1
assert h1.level == 1
assert "EXTVER" not in h1.header
assert "EXTLEVEL" not in h1.header
h1.ver = 2
assert h1.header.get("EXTVER") == 2
h1.header["EXTVER"] = 3
assert h1.ver == 3
del h1.header["EXTVER"]
assert h1.ver == 1
h1.level = 2
assert h1.header.get("EXTLEVEL") == 2
h1.header["EXTLEVEL"] = 3
assert h1.level == 3
del h1.header["EXTLEVEL"]
assert h1.level == 1
pytest.raises(TypeError, setattr, h1, "ver", "FOO")
pytest.raises(TypeError, setattr, h1, "level", "BAR")
def test_consecutive_writeto(self):
"""
Regression test for an issue where calling writeto twice on the same
HDUList could write a corrupted file.
https://github.com/spacetelescope/PyFITS/issues/40 is actually a
particular instance of this problem, though isn't unique to sys.stdout.
"""
with fits.open(self.data("test0.fits")) as hdul1:
# Add a bunch of header keywords so that the data will be forced to
# new offsets within the file:
for idx in range(40):
hdul1[1].header[f"TEST{idx}"] = "test"
hdul1.writeto(self.temp("test1.fits"))
hdul1.writeto(self.temp("test2.fits"))
# Open a second handle to the original file and compare it to hdul1
# (We only compare part of the one header that was modified)
# Compare also with the second writeto output
with fits.open(self.data("test0.fits")) as hdul2:
with fits.open(self.temp("test2.fits")) as hdul3:
for hdul in (hdul1, hdul3):
for idx, hdus in enumerate(zip(hdul2, hdul)):
hdu2, hdu = hdus
if idx != 1:
assert hdu.header == hdu2.header
else:
assert hdu2.header == hdu.header[: len(hdu2.header)]
assert np.all(hdu.data == hdu2.data)
class TestConvenienceFunctions(FitsTestCase):
def test_writeto(self, home_is_temp):
"""
Simple test for writing a trivial header and some data to a file
with the `writeto()` convenience function.
"""
filename = self.temp("array.fits")
data = np.zeros((100, 100))
header = fits.Header()
fits.writeto(filename, data, header=header, overwrite=True)
with fits.open(filename) as hdul:
assert len(hdul) == 1
assert (data == hdul[0].data).all()
def test_writeto_2(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/107
Test of `writeto()` with a trivial header containing a single keyword.
"""
filename = self.temp("array.fits")
data = np.zeros((100, 100))
header = fits.Header()
header.set("CRPIX1", 1.0)
fits.writeto(
filename, data, header=header, overwrite=True, output_verify="silentfix"
)
with fits.open(filename) as hdul:
assert len(hdul) == 1
assert (data == hdul[0].data).all()
assert "CRPIX1" in hdul[0].header
assert hdul[0].header["CRPIX1"] == 1.0
def test_writeto_overwrite(self, home_is_temp):
"""
Ensure the `overwrite` keyword works as it should
"""
filename = self.temp("array.fits")
data = np.zeros((100, 100))
header = fits.Header()
fits.writeto(filename, data, header=header)
with pytest.raises(OSError, match=_NOT_OVERWRITING_MSG_MATCH):
fits.writeto(filename, data, header=header, overwrite=False)
fits.writeto(filename, data, header=header, overwrite=True)
with fits.open(filename) as hdul:
assert len(hdul) == 1
assert (data == hdul[0].data).all()
class TestFileFunctions(FitsTestCase):
"""
Tests various basic I/O operations, specifically in the
astropy.io.fits.file._File class.
"""
def test_open_nonexistent(self):
"""Test that trying to open a non-existent file results in an
OSError (and not some other arbitrary exception).
"""
with pytest.raises(OSError, match=r"No such file or directory"):
fits.open(self.temp("foobar.fits"))
# But opening in ostream or append mode should be okay, since they
# allow writing new files
for mode in ("ostream", "append"):
with fits.open(self.temp("foobar.fits"), mode=mode) as _:
pass
assert os.path.exists(self.temp("foobar.fits"))
os.remove(self.temp("foobar.fits"))
def test_open_file_handle(self):
# Make sure we can open a FITS file from an open file handle
with open(self.data("test0.fits"), "rb") as handle:
with fits.open(handle) as _:
pass
with open(self.temp("temp.fits"), "wb") as handle:
with fits.open(handle, mode="ostream") as _:
pass
# Opening without explicitly specifying binary mode should fail
with pytest.raises(ValueError):
with open(self.data("test0.fits")) as handle:
with fits.open(handle) as _:
pass
# All of these read modes should fail
for mode in ["r", "rt"]:
with pytest.raises(ValueError):
with open(self.data("test0.fits"), mode=mode) as handle:
with fits.open(handle) as _:
pass
# These update or write modes should fail as well
for mode in ["w", "wt", "w+", "wt+", "r+", "rt+", "a", "at", "a+", "at+"]:
with pytest.raises(ValueError):
with open(self.temp("temp.fits"), mode=mode) as handle:
with fits.open(handle) as _:
pass
def test_fits_file_handle_mode_combo(self):
# This should work fine since no mode is given
with open(self.data("test0.fits"), "rb") as handle:
with fits.open(handle) as _:
pass
# This should work fine since the modes are compatible
with open(self.data("test0.fits"), "rb") as handle:
with fits.open(handle, mode="readonly") as _:
pass
# This should not work since the modes conflict
with pytest.raises(ValueError):
with open(self.data("test0.fits"), "rb") as handle:
with fits.open(handle, mode="ostream") as _:
pass
def test_open_from_url(self):
file_url = "file:///" + self.data("test0.fits").lstrip("/")
with urllib.request.urlopen(file_url) as urlobj:
with fits.open(urlobj) as _:
pass
# It will not be possible to write to a file that is from a URL object
for mode in ("ostream", "append", "update"):
with pytest.raises(ValueError):
with urllib.request.urlopen(file_url) as urlobj:
with fits.open(urlobj, mode=mode) as _:
pass
@pytest.mark.remote_data(source="astropy")
def test_open_from_remote_url(self):
for dataurl in (conf.dataurl, conf.dataurl_mirror):
remote_url = f"{dataurl}/allsky/allsky_rosat.fits"
try:
with urllib.request.urlopen(remote_url) as urlobj:
with fits.open(urlobj) as fits_handle:
assert len(fits_handle) == 1
for mode in ("ostream", "append", "update"):
with pytest.raises(ValueError):
with urllib.request.urlopen(remote_url) as urlobj:
with fits.open(urlobj, mode=mode) as fits_handle:
assert len(fits_handle) == 1
except (urllib.error.HTTPError, urllib.error.URLError):
continue
else:
break
else:
raise Exception("Could not download file")
def test_open_gzipped(self):
gzip_file = self._make_gzip_file()
with fits.open(gzip_file) as fits_handle:
assert fits_handle._file.compression == "gzip"
assert len(fits_handle) == 5
with fits.open(gzip.GzipFile(gzip_file)) as fits_handle:
assert fits_handle._file.compression == "gzip"
assert len(fits_handle) == 5
def test_open_gzipped_from_handle(self):
with open(self._make_gzip_file(), "rb") as handle:
with fits.open(handle) as fits_handle:
assert fits_handle._file.compression == "gzip"
def test_detect_gzipped(self):
"""Test detection of a gzip file when the extension is not .gz."""
with fits.open(self._make_gzip_file("test0.fz")) as fits_handle:
assert fits_handle._file.compression == "gzip"
assert len(fits_handle) == 5
def test_writeto_append_mode_gzip(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/33
Check that a new GzipFile opened in append mode can be used to write
out a new FITS file.
"""
# Note: when opening a GzipFile the 'b+' is superfluous, but this was
# still how the original test case looked
# Note: with statement not supported on GzipFile in older Python
# versions
fileobj = gzip.GzipFile(self.temp("test.fits.gz"), "ab+")
h = fits.PrimaryHDU()
try:
h.writeto(fileobj)
finally:
fileobj.close()
with fits.open(self.temp("test.fits.gz")) as hdul:
assert hdul[0].header == h.header
def test_fits_update_mode_gzip(self):
"""Test updating a GZipped FITS file"""
with fits.open(self._make_gzip_file("update.gz"), mode="update") as fits_handle:
hdu = fits.ImageHDU(data=list(range(100)))
fits_handle.append(hdu)
with fits.open(self.temp("update.gz")) as new_handle:
assert len(new_handle) == 6
assert (new_handle[-1].data == list(range(100))).all()
def test_fits_append_mode_gzip(self):
"""Make sure that attempting to open an existing GZipped FITS file in
'append' mode raises an error"""
with pytest.raises(OSError):
with fits.open(self._make_gzip_file("append.gz"), mode="append") as _:
pass
@pytest.mark.skipif(not HAS_BZ2, reason="Python built without bz2 module")
def test_open_bzipped(self):
bzip_file = self._make_bzip2_file()
with fits.open(bzip_file) as fits_handle:
assert fits_handle._file.compression == "bzip2"
assert len(fits_handle) == 5
with fits.open(bz2.BZ2File(bzip_file)) as fits_handle:
assert fits_handle._file.compression == "bzip2"
assert len(fits_handle) == 5
@pytest.mark.skipif(not HAS_BZ2, reason="Python built without bz2 module")
def test_open_bzipped_from_handle(self):
with open(self._make_bzip2_file(), "rb") as handle:
with fits.open(handle) as fits_handle:
assert fits_handle._file.compression == "bzip2"
assert len(fits_handle) == 5
@pytest.mark.skipif(not HAS_BZ2, reason="Python built without bz2 module")
def test_detect_bzipped(self):
"""Test detection of a bzip2 file when the extension is not .bz2."""
with fits.open(self._make_bzip2_file("test0.xx")) as fits_handle:
assert fits_handle._file.compression == "bzip2"
assert len(fits_handle) == 5
@pytest.mark.skipif(not HAS_BZ2, reason="Python built without bz2 module")
def test_writeto_bzip2_fileobj(self):
"""Test writing to a bz2.BZ2File file like object"""
fileobj = bz2.BZ2File(self.temp("test.fits.bz2"), "w")
h = fits.PrimaryHDU()
try:
h.writeto(fileobj)
finally:
fileobj.close()
with fits.open(self.temp("test.fits.bz2")) as hdul:
assert hdul[0].header == h.header
@pytest.mark.skipif(not HAS_BZ2, reason="Python built without bz2 module")
def test_writeto_bzip2_filename(self):
"""Test writing to a bzip2 file by name"""
filename = self.temp("testname.fits.bz2")
h = fits.PrimaryHDU()
h.writeto(filename)
with fits.open(self.temp("testname.fits.bz2")) as hdul:
assert hdul[0].header == h.header
def test_open_zipped(self):
zip_file = self._make_zip_file()
with fits.open(zip_file) as fits_handle:
assert fits_handle._file.compression == "zip"
assert len(fits_handle) == 5
with fits.open(zipfile.ZipFile(zip_file)) as fits_handle:
assert fits_handle._file.compression == "zip"
assert len(fits_handle) == 5
def test_open_zipped_from_handle(self):
with open(self._make_zip_file(), "rb") as handle:
with fits.open(handle) as fits_handle:
assert fits_handle._file.compression == "zip"
assert len(fits_handle) == 5
def test_detect_zipped(self):
"""Test detection of a zip file when the extension is not .zip."""
zf = self._make_zip_file(filename="test0.fz")
with fits.open(zf) as fits_handle:
assert len(fits_handle) == 5
def test_open_zipped_writeable(self):
"""Opening zipped files in a writeable mode should fail."""
zf = self._make_zip_file()
pytest.raises(OSError, fits.open, zf, "update")
pytest.raises(OSError, fits.open, zf, "append")
zf = zipfile.ZipFile(zf, "a")
pytest.raises(OSError, fits.open, zf, "update")
pytest.raises(OSError, fits.open, zf, "append")
def test_read_open_astropy_gzip_file(self):
"""
Regression test for https://github.com/astropy/astropy/issues/2774
This tests reading from a ``GzipFile`` object from Astropy's
compatibility copy of the ``gzip`` module.
"""
gf = gzip.GzipFile(self._make_gzip_file())
try:
assert len(fits.open(gf)) == 5
finally:
gf.close()
def test_open_multiple_member_zipfile(self):
"""
Opening zip files containing more than one member files should fail
as there's no obvious way to specify which file is the FITS file to
read.
"""
zfile = zipfile.ZipFile(self.temp("test0.zip"), "w")
zfile.write(self.data("test0.fits"))
zfile.writestr("foo", "bar")
zfile.close()
with pytest.raises(OSError):
fits.open(zfile.filename)
def test_read_open_file(self):
"""Read from an existing file object."""
with open(self.data("test0.fits"), "rb") as f:
assert len(fits.open(f)) == 5
def test_read_closed_file(self):
"""Read from an existing file object that's been closed."""
f = open(self.data("test0.fits"), "rb")
f.close()
with fits.open(f) as f2:
assert len(f2) == 5
def test_read_open_gzip_file(self):
"""Read from an open gzip file object."""
gf = gzip.GzipFile(self._make_gzip_file())
try:
assert len(fits.open(gf)) == 5
finally:
gf.close()
def test_open_gzip_file_for_writing(self):
"""Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/195."""
gf = self._make_gzip_file()
with fits.open(gf, mode="update") as h:
h[0].header["EXPFLAG"] = "ABNORMAL"
h[1].data[0, 0] = 1
with fits.open(gf) as h:
# Just to make sure the update worked; if updates work
# normal writes should work too...
assert h[0].header["EXPFLAG"] == "ABNORMAL"
assert h[1].data[0, 0] == 1
def test_write_read_gzip_file(self, home_is_temp):
"""
Regression test for https://github.com/astropy/astropy/issues/2794
Ensure files written through gzip are readable.
"""
data = np.arange(100)
hdu = fits.PrimaryHDU(data=data)
hdu.writeto(self.temp("test.fits.gz"))
with open(os.path.expanduser(self.temp("test.fits.gz")), "rb") as f:
assert f.read(3) == GZIP_MAGIC
with fits.open(self.temp("test.fits.gz")) as hdul:
assert np.all(hdul[0].data == data)
@pytest.mark.parametrize("ext", ["gz", "bz2", "zip"])
def test_compressed_ext_but_not_compressed(self, ext):
testfile = self.temp(f"test0.fits.{ext}")
shutil.copy(self.data("test0.fits"), testfile)
with fits.open(testfile) as hdul:
assert len(hdul) == 5
fits.append(testfile, np.arange(5))
with fits.open(testfile) as hdul:
assert len(hdul) == 6
def test_read_file_like_object(self):
"""Test reading a FITS file from a file-like object."""
filelike = io.BytesIO()
with open(self.data("test0.fits"), "rb") as f:
filelike.write(f.read())
filelike.seek(0)
assert len(fits.open(filelike)) == 5
def test_updated_file_permissions(self):
"""
Regression test for https://aeon.stsci.edu/ssb/trac/pyfits/ticket/79
Tests that when a FITS file is modified in update mode, the file
permissions are preserved.
"""
filename = self.temp("test.fits")
hdul = [fits.PrimaryHDU(), fits.ImageHDU()]
hdul = fits.HDUList(hdul)
hdul.writeto(filename)
old_mode = os.stat(filename).st_mode
hdul = fits.open(filename, mode="update")
hdul.insert(1, fits.ImageHDU())
hdul.flush()
hdul.close()
assert old_mode == os.stat(filename).st_mode
def test_fileobj_mode_guessing(self):
"""Tests whether a file opened without a specified io.fits mode
('readonly', etc.) is opened in a mode appropriate for the given file
object.
"""
self.copy_file("test0.fits")
# Opening in text mode should outright fail
for mode in ("r", "w", "a"):
with open(self.temp("test0.fits"), mode) as f:
pytest.raises(ValueError, fits.HDUList.fromfile, f)
# Need to re-copy the file since opening it in 'w' mode blew it away
self.copy_file("test0.fits")
with open(self.temp("test0.fits"), "rb") as f:
with fits.HDUList.fromfile(f) as h:
assert h.fileinfo(0)["filemode"] == "readonly"
for mode in ("wb", "ab"):
with open(self.temp("test0.fits"), mode) as f: