def get_bpm(image, pipeline_context):
bpm_filename = dbs.get_bpm(image.telescope_id, image.ccdsum,
db_address=pipeline_context.db_address)
if bpm_filename is None:
bpm = None
image.header['L1IDMASK'] = ('', 'Id. of mask file used')
else:
bpm_hdu = fits_utils.open_fits_file(bpm_filename)
bpm_extensions = fits_utils.get_extensions_by_name(bpm_hdu, 'BPM')
if len(bpm_extensions) > 1:
extension_shape = bpm_extensions[0].data.shape
bpm_shape = (len(bpm_extensions), extension_shape[0], extension_shape[1])
bpm = np.zeros(bpm_shape, dtype=np.uint8)
for i, extension in enumerate(bpm_extensions):
bpm[i, :, :] = extension.data[:, :]
elif len(bpm_extensions) == 1:
bpm = np.array(bpm_extensions[0].data, dtype=np.uint8)
else:
bpm = np.array(bpm_hdu[0].data, dtype=np.uint8)
if not bpm_has_valid_size(bpm, image):
tags = logs.image_config_to_tags(image, None)
logs.add_tag(tags, 'filename', image.filename)
logger.error('BPM shape mismatch', extra=tags)
err_msg = 'BPM shape mismatch for {filename} ' \
'{site}/{instrument}'.format(filename=image.filename, site=image.site,
instrument=image.instrument)
raise ValueError(err_msg)
image.header['L1IDMASK'] = (os.path.basename(bpm_filename), 'Id. of mask file used')
return bpm
def test_get_sci_extensions():
hdulist = [fits.PrimaryHDU(header=fits.Header({'test': 'test'}))]
input_data = []
for i in range(4):
data = np.random.uniform(0, 1,
size=(101, 101)).astype(dtype=np.float32)
input_data.append(data)
# Build the fits header manually because of a bug in the latest stable version of astropy
# This should be
# header = fits.Header({'EXTNAME': 'SCI', 'EXTVER': i + 1})
header = fits.Header()
header['EXTNAME'] = 'SCI'
header['EXTVER'] = i + 1
hdulist.append(fits.ImageHDU(data=data, header=header))
bpm_header = fits.Header()
bpm_header['EXTNAME'] = 'BPM'
bpm_hdu = fits.ImageHDU(data=np.zeros((101, 101), dtype=np.uint8),
header=bpm_header)
hdulist.append(bpm_hdu)
hdulist = fits.HDUList(hdulist)
sci_extensions = fits_utils.get_extensions_by_name(hdulist, 'SCI')
assert len(sci_extensions) == 4
for i in range(4):
np.testing.assert_allclose(sci_extensions[i].data,
input_data[i],
atol=1e-5)
def test_get_sci_extensions():
hdulist = [fits.PrimaryHDU(header=fits.Header({'test': 'test'}))]
input_data = []
for i in range(4):
data = np.random.uniform(0, 1, size=(101, 101)).astype(dtype=np.float32)
input_data.append(data)
# Build the fits header manually because of a bug in the latest stable version of astropy
# This should be
# header = fits.Header({'EXTNAME': 'SCI', 'EXTVER': i + 1})
header = fits.Header()
header['EXTNAME'] = 'SCI'
header['EXTVER'] = i + 1
hdulist.append(fits.ImageHDU(data=data, header=header))
bpm_header = fits.Header()
bpm_header['EXTNAME'] = 'BPM'
bpm_hdu = fits.ImageHDU(data=np.zeros((101, 101), dtype=np.uint8), header=bpm_header)
hdulist.append(bpm_hdu)
hdulist = fits.HDUList(hdulist)
sci_extensions = fits_utils.get_extensions_by_name(hdulist, 'SCI')
assert len(sci_extensions) == 4
for i in range(4):
np.testing.assert_allclose(sci_extensions[i].data, input_data[i], atol=1e-5)
def get_bpm(image, pipeline_context):
bpm_filename = dbs.get_bpm(image.telescope_id,
image.ccdsum,
db_address=pipeline_context.db_address)
if bpm_filename is None:
bpm = None
image.header['L1IDMASK'] = ('', 'Id. of mask file used')
else:
bpm_hdu = fits_utils.open_fits_file(bpm_filename)
bpm_extensions = fits_utils.get_extensions_by_name(bpm_hdu, 'BPM')
if len(bpm_extensions) > 1:
extension_shape = bpm_extensions[0].data.shape
bpm_shape = (len(bpm_extensions), extension_shape[0],
extension_shape[1])
bpm = np.zeros(bpm_shape, dtype=np.uint8)
for i, extension in enumerate(bpm_extensions):
bpm[i, :, :] = extension.data[:, :]
elif len(bpm_extensions) == 1:
bpm = np.array(bpm_extensions[0].data, dtype=np.uint8)
else:
bpm = np.array(bpm_hdu[0].data, dtype=np.uint8)
if not bpm_has_valid_size(bpm, image):
tags = logs.image_config_to_tags(image, None)
logs.add_tag(tags, 'filename', image.filename)
logger.error('BPM shape mismatch', extra=tags)
err_msg = 'BPM shape mismatch for {filename} ' \
'{site}/{instrument}'.format(filename=image.filename, site=image.site,
instrument=image.instrument)
raise ValueError(err_msg)
image.header['L1IDMASK'] = (os.path.basename(bpm_filename),
'Id. of mask file used')
return bpm
def load_bpm(bpm_filename):
bpm_hdu = fits_utils.open_fits_file(bpm_filename)
bpm_extensions = fits_utils.get_extensions_by_name(bpm_hdu, 'BPM')
# Filter out BPM extensions without data
bpm_extensions = [
extension for extension in bpm_extensions if extension.data is not None
]
if len(bpm_extensions) > 1:
extension_shape = bpm_extensions[0].data.shape
bpm_shape = (len(bpm_extensions), extension_shape[0],
extension_shape[1])
bpm = np.zeros(bpm_shape, dtype=np.uint8)
for i, extension in enumerate(bpm_extensions):
bpm[i, :, :] = extension.data[:, :]
elif len(bpm_extensions) == 1:
bpm = np.array(bpm_extensions[0].data, dtype=np.uint8)
else:
bpm = np.array(bpm_hdu[0].data, dtype=np.uint8)
return bpm