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import os
import tempfile
import warnings
import numpy as np
import pytest
from .makedata import make_data, lorem_ipsum
from .checks import check_header, compare_headerlist_header
from ..fitslib import FITS, read_header, write
from ..header import FITSHDR
from ..hdu.base import INVALID_HDR_CHARS
from ..util import cfitsio_version
CFITSIO_VERSION = cfitsio_version(asfloat=True)
def test_free_form_string():
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with open(fname, 'w') as f:
s = (
"SIMPLE = T / Standard FITS " # noqa
+ "BITPIX = 16 / number of bits per data pixel " # noqa
+ "NAXIS = 0 / number of data axes " # noqa
+ "EXTEND = T / File contains extensions " # noqa
+ "PHOTREF = 'previous MegaCam' / Source: cum.photcat " # noqa
+ "EXTRA = 7 / need another line following PHOTREF " # noqa
+ "END " # noqa
)
f.write(s + ' ' * (2880 - len(s)))
hdr = read_header(fname)
assert hdr['PHOTREF'] == 'previous MegaCam'
def test_add_delete_and_update_records():
# Build a FITSHDR from a few records (no need to write on disk)
# Record names have to be in upper case to match with FITSHDR.add_record
recs = [
{'name': "First_record".upper(), 'value': 1, 'comment': "number 1"},
{'name': "Second_record".upper(), 'value': "2"},
{'name': "Third_record".upper(), 'value': "3"},
{'name': "Last_record".upper(), 'value': 4, 'comment': "number 4"},
]
hdr = FITSHDR(recs)
# Add a new record
hdr.add_record({'name': 'New_record'.upper(), 'value': 5})
# Delete number 2 and 4
hdr.delete('Second_record'.upper())
hdr.delete('Last_record'.upper())
# Update records : first and new one
hdr['First_record'] = 11
hdr['New_record'] = 3
# Do some checks : len and get value/comment
assert len(hdr) == 3
assert hdr['First_record'] == 11
assert hdr['New_record'] == 3
assert hdr['Third_record'] == '3'
assert hdr.get_comment('First_record') == 'number 1'
assert not hdr.get_comment('New_record')
def testHeaderCommentPreserved():
"""
Test that the comment is preserved after resetting the value
"""
l1 = 'KEY1 = 77 / My comment1'
l2 = 'KEY2 = 88 / My comment2'
hdr = FITSHDR()
hdr.add_record(l1)
hdr.add_record(l2)
hdr['key1'] = 99
assert hdr.get_comment('key1') == 'My comment1', 'comment not preserved'
def test_header_write_read():
"""
Test a basic header write and read
Note the other read/write tests also are checking header writing with
a list of dicts
"""
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
data = np.zeros(10)
header = {
'x': 35,
'y': 88.215,
'eval': 1.384123233e43,
'empty': '',
'funky': '35-8', # test old bug when strings look
# like expressions
'name': 'J. Smith',
'what': '89113e6', # test bug where converted to float
'und': None,
'binop': '25-3', # test string with binary operation in it
'unders': '1_000_000', # test string with underscore
'longs': lorem_ipsum,
}
if CFITSIO_VERSION > 4.02:
# force hierarch + continue
header["long_keyword_name"] = lorem_ipsum
fits.write_image(data, header=header)
rh = fits[0].read_header()
check_header(header, rh)
with FITS(fname) as fits:
rh = fits[0].read_header()
check_header(header, rh)
def test_header_delete():
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
data = np.zeros(10)
header1 = {'SCARD': 'one', 'ICARD': 1, 'FCARD': 1.0, 'LCARD': True}
fits.write_image(data, header=header1)
rh = fits[0].read_header()
check_header(header1, rh)
fits[0].delete_key("SCARD")
del header1["SCARD"]
rh = fits[0].read_header()
check_header(header1, rh)
fits[0].delete_keys(["ICARD", "FCARD"])
del header1["ICARD"]
del header1["FCARD"]
rh = fits[0].read_header()
check_header(header1, rh)
with FITS(fname) as fits:
rh = fits[0].read_header()
check_header(header1, rh)
def test_header_update():
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
data = np.zeros(10)
header1 = {'SCARD': 'one', 'ICARD': 1, 'FCARD': 1.0, 'LCARD': True}
header2 = {
'SCARD': 'two',
'ICARD': 2,
'FCARD': 2.0,
'LCARD': False,
'SNEW': 'two',
'INEW': 2,
'FNEW': 2.0,
'LNEW': False,
}
fits.write_image(data, header=header1)
rh = fits[0].read_header()
check_header(header1, rh)
# Update header
fits[0].write_keys(header2)
with FITS(fname) as fits:
rh = fits[0].read_header()
check_header(header2, rh)
def test_read_header_case():
"""
Test read_header with and without case sensitivity
The reason we need a special test for this is because
the read_header code is optimized for speed and has
a different code path
"""
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
data = np.zeros(10)
adata = make_data()
fits.write_image(data, header=adata['keys'], extname='First')
fits.write_image(data, header=adata['keys'], extname='second')
cases = [
('First', True),
('FIRST', False),
('second', True),
('seConD', False),
]
for ext, ci in cases:
h = read_header(fname, ext=ext, case_sensitive=ci)
compare_headerlist_header(adata['keys'], h)
def test_blank_key_comments():
"""
test a few different comments
"""
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
records = [
# empty should return empty
{'name': None, 'value': '', 'comment': ''},
# this will also return empty
{'name': None, 'value': '', 'comment': ' '},
# this will return exactly
{'name': None, 'value': '', 'comment': ' h'},
# this will return exactly
{'name': None, 'value': '', 'comment': '--- test comment ---'},
]
header = FITSHDR(records)
fits.write(None, header=header)
rh = fits[0].read_header()
rrecords = rh.records()
for i, ri in ((0, 6), (1, 7), (2, 8)):
rec = records[i]
rrec = rrecords[ri]
assert rec['name'] is None, 'checking name is None'
comment = rec['comment']
rcomment = rrec['comment']
if '' == comment.strip():
comment = ''
assert comment == rcomment, "check empty key comment"
def test_blank_key_comments_from_cards():
"""
test a few different comments
"""
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
records = [
' ', # noqa
' --- testing comment --- ', # noqa
' --- testing comment --- ', # noqa
"COMMENT testing ", # noqa
]
header = FITSHDR(records)
fits.write(None, header=header)
rh = fits[0].read_header()
rrecords = rh.records()
assert rrecords[6]['name'] is None, 'checking name is None'
assert rrecords[6]['comment'] == '', 'check empty key comment'
assert rrecords[7]['name'] is None, 'checking name is None'
assert rrecords[7]['comment'] == ' --- testing comment ---', (
"check empty key comment"
)
assert rrecords[8]['name'] is None, 'checking name is None'
assert rrecords[8]['comment'] == '--- testing comment ---', (
"check empty key comment"
)
assert rrecords[9]['name'] == 'COMMENT', 'checking name is COMMENT'
assert rrecords[9]['comment'] == 'testing', "check comment"
def test_header_from_cards():
"""
test generating a header from cards, writing it out and getting
back what we put in
"""
hdr_from_cards = FITSHDR(
[
"IVAL = 35 / integer value ", # noqa
"SHORTS = 'hello world' ", # noqa
"UND = ", # noqa
"LONGS = 'Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiu&'", # noqa
"CONTINUE 'smod tempor incididunt ut labore et dolore magna aliqua' ", # noqa
"DBL = 1.25 ", # noqa
]
)
header = [
{'name': 'ival', 'value': 35, 'comment': 'integer value'},
{'name': 'shorts', 'value': 'hello world'},
{'name': 'und', 'value': None},
{'name': 'longs', 'value': lorem_ipsum},
{'name': 'dbl', 'value': 1.25},
]
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
data = np.zeros(10)
fits.write_image(data, header=hdr_from_cards)
rh = fits[0].read_header()
compare_headerlist_header(header, rh)
with FITS(fname) as fits:
rh = fits[0].read_header()
compare_headerlist_header(header, rh)
def test_bad_header_write_raises():
"""
Test that an invalid header raises.
"""
for c in INVALID_HDR_CHARS:
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
try:
hdr = {'bla%sg' % c: 3}
data = np.zeros(10)
write(fname, data, header=hdr, clobber=True)
except Exception as e:
assert "header key 'BLA%sG' has" % c in str(e)
def test_header_template():
"""
test adding bunch of cards from a split template
"""
header_template = """SIMPLE = T /
BITPIX = 8 / bits per data value
NAXIS = 0 / number of axes
EXTEND = T / Extensions are permitted
ORIGIN = 'LSST DM Header Service'/ FITS file originator
---- Date, night and basic image information ----
DATE = / Creation Date and Time of File
DATE-OBS= / Date of the observation (image acquisition)
DATE-BEG= / Time at the start of integration
DATE-END= / end date of the observation
MJD = / Modified Julian Date that the file was written
MJD-OBS = / Modified Julian Date of observation
MJD-BEG = / Modified Julian Date derived from DATE-BEG
MJD-END = / Modified Julian Date derived from DATE-END
OBSID = / ImageName from Camera StartIntergration
GROUPID = / imageSequenceName from StartIntergration
OBSTYPE = / BIAS, DARK, FLAT, OBJECT
BUNIT = 'adu ' / Brightness units for pixel array
---- Telescope info, location, observer ----
TELESCOP= 'LSST AuxTelescope' / Telescope name
INSTRUME= 'LATISS' / Instrument used to obtain these data
OBSERVER= 'LSST' / Observer name(s)
OBS-LONG= -70.749417 / [deg] Observatory east longitude
OBS-LAT = -30.244639 / [deg] Observatory latitude
OBS-ELEV= 2663.0 / [m] Observatory elevation
OBSGEO-X= 1818938.94 / [m] X-axis Geocentric coordinate
OBSGEO-Y= -5208470.95 / [m] Y-axis Geocentric coordinate
OBSGEO-Z= -3195172.08 / [m] Z-axis Geocentric coordinate
---- Pointing info, etc. ----
DECTEL = / Telescope DEC of observation
ROTPATEL= / Telescope Rotation
ROTCOORD= 'sky' / Telescope Rotation Coordinates
RA = / RA of Target
DEC = / DEC of Target
ROTPA = / Rotation angle relative to the sky (deg)
HASTART = / [HH:MM:SS] Telescope hour angle at start
ELSTART = / [deg] Telescope zenith distance at start
AZSTART = / [deg] Telescope azimuth angle at start
AMSTART = / Airmass at start
HAEND = / [HH:MM:SS] Telescope hour angle at end
ELEND = / [deg] Telescope zenith distance at end
AZEND = / [deg] Telescope azimuth angle at end
AMEND = / Airmass at end
---- Image-identifying used to build OBS-ID ----
TELCODE = 'AT' / The code for the telecope
CONTRLLR= / The controller (e.g. O for OCS, C for CCS)
DAYOBS = / The observation day as defined by image name
SEQNUM = / The sequence number from the image name
GROUPID = /
---- Information from Camera
CCD_MANU= 'ITL' / CCD Manufacturer
CCD_TYPE= '3800C' / CCD Model Number
CCD_SERN= '20304' / Manufacturers? CCD Serial Number
LSST_NUM= 'ITL-3800C-098' / LSST Assigned CCD Number
SEQCKSUM= / Checksum of Sequencer
SEQNAME = / SequenceName from Camera StartIntergration
REBNAME = / Name of the REB
CONTNUM = / CCD Controller (WREB) Serial Number
IMAGETAG= / DAQ Image id
TEMP_SET= / Temperature set point (deg C)
CCDTEMP = / Measured temperature (deg C)
---- Geometry from Camera ----
DETSIZE = / Size of sensor
OVERH = / Over-scan pixels
OVERV = / Vert-overscan pix
PREH = / Pre-scan pixels
---- Filter/grating information ----
FILTER = / Name of the filter
FILTPOS = / Filter position
GRATING = / Name of the second disperser
GRATPOS = / disperser position
LINSPOS = / Linear Stage
---- Exposure-related information ----
EXPTIME = / Exposure time in seconds
SHUTTIME= / Shutter exposure time in seconds
DARKTIME= / Dark time in seconds
---- Header information ----
FILENAME= / Original file name
HEADVER = / Version of header
---- Checksums ----
CHECKSUM= / checksum for the current HDU
DATASUM = / checksum of the data records\n"""
lines = header_template.splitlines()
hdr = FITSHDR()
for line in lines:
hdr.add_record(line)
def test_corrupt_continue():
"""
test with corrupt continue, just make sure it doesn't crash
"""
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with warnings.catch_warnings(record=True) as _:
hdr_from_cards = FITSHDR(
[
"IVAL = 35 / integer value ", # noqa
"SHORTS = 'hello world' ", # noqa
"CONTINUE= ' ' / '&' / Current observing orogram ", # noqa
"UND = ", # noqa
"DBL = 1.25 ", # noqa
]
)
with FITS(fname, 'rw') as fits:
fits.write(None, header=hdr_from_cards)
read_header(fname)
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with warnings.catch_warnings(record=True) as _:
hdr_from_cards = FITSHDR(
[
"IVAL = 35 / integer value ", # noqa
"SHORTS = 'hello world' ", # noqa
"PROGRAM = 'Setting the Scale: Determining the Absolute Mass Normalization and &'", # noqa
"CONTINUE 'Scaling Relations for Clusters at z~0.1&' ", # noqa
"CONTINUE '&' / Current observing orogram ", # noqa
"UND = ", # noqa
"DBL = 1.25 ", # noqa
]
)
with FITS(fname, 'rw') as fits:
fits.write(None, header=hdr_from_cards)
read_header(fname)
def record_exists(header_records, key, value):
for rec in header_records:
if rec['name'] == key and rec['value'] == value:
return True
return False
def test_read_comment_history():
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
data = np.arange(100).reshape(10, 10)
fits.create_image_hdu(data)
hdu = fits[-1]
hdu.write_comment('A COMMENT 1')
hdu.write_comment('A COMMENT 2')
hdu.write_history('SOME HISTORY 1')
hdu.write_history('SOME HISTORY 2')
fits.close()
with FITS(fname, 'r') as fits:
hdu = fits[-1]
header = hdu.read_header()
records = header.records()
assert record_exists(records, 'COMMENT', 'A COMMENT 1')
assert record_exists(records, 'COMMENT', 'A COMMENT 2')
assert record_exists(records, 'HISTORY', 'SOME HISTORY 1')
assert record_exists(records, 'HISTORY', 'SOME HISTORY 2')
def test_write_key_dict():
"""
test that write_key works using a standard key dict
"""
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, 'test.fits')
with FITS(fname, 'rw') as fits:
im = np.zeros((10, 10), dtype='i2')
fits.write(im)
keydict = {
'name': 'test',
'value': 35,
'comment': 'keydict test',
}
fits[-1].write_key(**keydict)
h = fits[-1].read_header()
assert h['test'] == keydict['value']
assert h.get_comment('test') == keydict['comment']
@pytest.mark.parametrize("fname", ["test.fits", "mem://"])
def test_header_update_compressed_image_to_table(fname):
data = np.arange(10).reshape(5, 2).astype(np.float32)
fname = "test.fits"
with tempfile.TemporaryDirectory() as tmpdir:
if "mem://" not in fname:
fpth = os.path.join(tmpdir, fname)
else:
fpth = fname
with FITS(fpth, "rw") as fits:
fits.write(data, compress="RICE", qlevel=1, dither_seed=10)
hdr = fits[1].read_header()
info_before = fits[1].get_info()
for key in hdr.keys():
if key.startswith("Z"):
fits[1].delete_key(key)
for i in range(1000):
fits[1].write_key("test" + str(i), "blah")
fits[1].delete_key("test0")
fits.update_hdu_list()
info_after = fits[1].get_info()
assert info_after != info_before
assert fits[1].get_exttype() == "BINARY_TBL"
if __name__ == '__main__':
test_header_write_read()
|
