def test_instantiate(deimos_flat_files, kast_blue_bias_files):
one_file = deimos_flat_files[0]
spectograph = load_spectrograph('keck_deimos')
# DEIMOS
deimos_flat = processrawimage.ProcessRawImage(one_file, spectograph, 3,
par)
# Test
assert isinstance(deimos_flat.image, np.ndarray)
assert deimos_flat.rawdatasec_img.shape == (4096, 2128)
# Kast blue
one_file = kast_blue_bias_files[0]
spectograph2 = load_spectrograph('shane_kast_blue')
kastb_bias = processrawimage.ProcessRawImage(one_file, spectograph2, 1,
par)
def test_instantiate_from_one(shane_kast_blue_sci_files):
"""
Run on a single science frame
"""
#
det = 1
# Load calibrations
pixelflat = load_kast_blue_masters(pixflat=True)[0]
bpm = kast_blue.empty_bpm(shane_kast_blue_sci_files[0], det)
# Process steps
bias = None
par = kast_par['scienceframe']['process']
process_steps = procimg.init_process_steps(bias, par)
process_steps += ['trim', 'apply_gain', 'orient']
process_steps += ['flatten']
process_steps += ['extras']
process_steps += ['crmask']
# Load
rawImage = rawimage.RawImage(shane_kast_blue_sci_files[0], kast_blue, det)
processRawImage = processrawimage.ProcessRawImage(rawImage,
kast_par['scienceframe']['process'])
pypeItImage = processRawImage.process(process_steps, pixel_flat=pixelflat)
# Do it
sciImg = scienceimage.ScienceImage(kast_blue, det, kast_par['scienceframe']['process'],
pypeItImage.image, pypeItImage.ivar, bpm)
def test_overscan_subtract(deimos_flat_files):
one_file = deimos_flat_files[0]
spectograph = load_spectrograph('keck_deimos')
# DEIMOS
deimos_flat = processrawimage.ProcessRawImage(one_file, spectograph, 3,
par)
# Bias subtract
pre_sub = deimos_flat.image.copy()
_ = deimos_flat.subtract_overscan()
oscan = np.median(pre_sub - deimos_flat.image)
assert np.isclose(oscan, 1001.2, rtol=0.01)
# Trim
_ = deimos_flat.trim()
# Test
assert deimos_flat.steps['subtract_overscan']
assert deimos_flat.steps['trim']
assert deimos_flat.image.shape == (4096, 2048)
def process_one(self,
filename,
process_steps,
bias,
pixel_flat=None,
illum_flat=None,
bpm=None):
"""
Process a single image
Args:
filename (str):
File to process
process_steps (list):
List of processing steps
bias (np.ndarray or None):
Bias image
pixel_flat (np.ndarray, optional):
Flat image
illum_flat (np.ndarray, optional):
Illumination image
bpm (np.ndarray, optional):
Bad pixel mask
Returns:
:class:`pypeit.images.pypeitimage.PypeItImage`:
"""
# Load raw image
rawImage = rawimage.RawImage(filename, self.spectrograph, self.det)
# Process
processrawImage = processrawimage.ProcessRawImage(rawImage,
self.par,
bpm=bpm)
processedImage = processrawImage.process(process_steps,
bias=bias,
pixel_flat=pixel_flat,
illum_flat=illum_flat)
# Return
return processedImage
def from_single_file(cls,
spectrograph,
det,
par,
bpm,
filename,
bias,
pixel_flat,
illum_flat=None):
"""
Instantiate from a single file
This will also generate the ivar, crmask, rn2img and mask
Args:
spectrograph (:class:`pypeit.spectrographs.spectrograph.Spectrograph`):
Spectrograph used to take the data.
det (:obj:`int`, optional):
The 1-indexed detector number to process.
par (:class:`pypeit.par.pypeitpar.ProcessImagesPar`):
Parameters that dictate the processing of the images. See
:class:`pypeit.par.pypeitpar.ProcessImagesPar` for the
defaults.
bpm (np.ndarray):
Bad pixel mask. Held in ImageMask
filename (str):
Filename
bias (np.ndarray or None):
Bias image
pixel_flat (np.ndarray):
Flat image
illum_flat (np.ndarray, optional):
Illumination image
Returns:
ScienceImage:
"""
slf = cls(spectrograph, det, par, bpm)
slf.files = [filename]
# Build up
prawImage = processrawimage.ProcessRawImage(filename, slf.spectrograph,
slf.det, slf.par)
# Save a bit
slf.filename = filename
slf.exptime = prawImage.exptime
# Process steps
process_steps = procimg.init_process_steps(bias, slf.par)
process_steps += ['trim', 'apply_gain', 'orient']
if (pixel_flat is not None) or (illum_flat is not None):
process_steps += ['flatten']
# Do it
slf.image = prawImage.process(process_steps,
pixel_flat=pixel_flat,
bias=bias,
illum_flat=illum_flat,
bpm=slf.bpm,
debug=True)
# Build the rest
slf.build_ivar()
slf.build_rn2img()
slf.build_crmask()
slf.build_mask(
saturation=slf.spectrograph.detector[slf.det - 1]['saturation'],
mincounts=slf.spectrograph.detector[slf.det - 1]['mincounts'])
# Return
return slf