def process(self, input):
# Open the input data model
with rdm.open(input) as input_model:
# Get the name of the saturation reference file
self.ref_name = self.get_reference_file(input_model, 'saturation')
self.log.info('Using SATURATION reference file %s', self.ref_name)
# Check for a valid reference file
if self.ref_name == 'N/A':
self.log.warning('No SATURATION reference file found')
self.log.warning('Saturation step will be skipped')
result = input_model.copy()
result.meta.cal_step.saturation = 'SKIPPED'
return result
# Open the reference file data model
ref_model = SaturationRefModel(self.ref_name)
# Perform saturation check
sat = saturation.flag_saturation(input_model, ref_model)
# Close the reference file and update the step status
ref_model.close()
sat.meta.cal_step.saturation = 'COMPLETE'
return sat
def test_nans_in_mask(setup_wfi_datamodels):
'''Check that pixels in the reference files that have value NaN are not
flagged as saturated in the data and that in the PIXELDQ array the
pixel is set to NO_SAT_CHECK.'''
# Create inputs, and data and saturation models
ngroups = 5
nrows = 20
ncols = 20
data, satmap = setup_wfi_datamodels(ngroups, nrows, ncols)
# Add ramp values up to the saturation limit
data.data[0, 5, 5] = 10
data.data[1, 5, 5] = 20000
data.data[2, 5, 5] = 40000
data.data[3, 5, 5] = 60000
data.data[4, 5, 5] = 62000
# Set saturation value for pixel to NaN
satmap.data[5, 5] = np.nan
# Run the pipeline
output = flag_saturation(data, satmap)
# Check that output GROUPDQ is not flagged as saturated
assert np.all(output.groupdq[:, 5, 5] != dqflags.group['SATURATED'])
# Check that output PIXELDQ is set to NO_SAT_CHECK
assert output.pixeldq[5, 5] == dqflags.pixel['NO_SAT_CHECK']
def test_ad_floor_flagging(setup_wfi_datamodels):
"""Check that the ad_floor flag is set when a pixel value is zero or
negative."""
# Create inputs, and data and saturation models
ngroups = 5
nrows = 20
ncols = 20
satvalue = 60000
data, satmap = setup_wfi_datamodels(ngroups, nrows, ncols)
# Add ramp values up to the saturation limit
data.data[0, 5, 5] = 0 # Signal at bottom rail - low saturation
data.data[1, 5, 5] = 0 # Signal at bottom rail - low saturation
data.data[2, 5, 5] = 20
data.data[3, 5, 5] = 40
data.data[4, 5, 5] = 60
# frames that should be flagged as saturation (low)
satindxs = [0, 1]
# Set saturation value in the saturation model
satmap.data[5, 5] = satvalue
# Run the pipeline
output = flag_saturation(data, satmap)
# Check if the right frames are flagged as saturated
assert np.all(output.groupdq[satindxs, 5, 5] == dqflags.group['DO_NOT_USE']
| dqflags.group['AD_FLOOR'])
def test_all_groups_saturated(setup_wfi_datamodels):
'''Check case where all groups are saturated.'''
# Create inputs, and data and saturation models
ngroups = 5
nrows = 20
ncols = 20
satvalue = 60000
data, satmap = setup_wfi_datamodels(ngroups, nrows, ncols)
# Add ramp values at or above saturation limit
data.data[0, 5, 5] = 60000
data.data[1, 5, 5] = 62000
data.data[2, 5, 5] = 62000
data.data[3, 5, 5] = 60000
data.data[4, 5, 5] = 62000
# Set saturation value in the saturation model
satmap.data[5, 5] = satvalue
# Run the pipeline
output = flag_saturation(data, satmap)
# Make sure all groups are flagged
assert np.all(output.groupdq[:, 5, 5] == dqflags.group['SATURATED'])
def test_basic_saturation_flagging(setup_wfi_datamodels):
'''Check that the saturation flag is set when a pixel value is above the
threshold given by the reference file.'''
# Create inputs, and data and saturation models
ngroups = 5
nrows = 20
ncols = 20
satvalue = 60000
data, satmap = setup_wfi_datamodels(ngroups, nrows, ncols)
# Add ramp values up to the saturation limit
data.data[0, 5, 5] = 0
data.data[1, 5, 5] = 20000
data.data[2, 5, 5] = 40000
data.data[3, 5, 5] = 60000 # Signal reaches saturation limit
data.data[4, 5, 5] = 62000
# Set saturation value in the saturation model
satmap.data[5, 5] = satvalue
# Run the pipeline
output = flag_saturation(data, satmap)
# Make sure that groups with signal > saturation limit get flagged
satindex = np.argmax(output.data[:, 5, 5] == satvalue)
assert np.all(output.groupdq[satindex:, 5,
5] == dqflags.group['SATURATED'])
def test_signal_fluctuation_flagging(setup_wfi_datamodels):
'''Check that once a pixel is flagged as saturated in a group, all
subsequent groups should also be flagged as saturated, even if the
signal value drops back below saturation.'''
# Create inputs, and data and saturation models
ngroups = 5
nrows = 20
ncols = 20
satvalue = 60000
data, satmap = setup_wfi_datamodels(ngroups, nrows, ncols)
# Add ramp values up to the saturation limit
data.data[0, 5, 5] = 10
data.data[1, 5, 5] = 20000
data.data[2, 5, 5] = 40000
data.data[3, 5, 5] = 60000 # Signal reaches saturation limit
data.data[4, 5, 5] = 40000 # Signal drops below saturation limit
# Set saturation value in the saturation model
satmap.data[5, 5] = satvalue
# Run the pipeline
output = flag_saturation(data, satmap)
# Make sure that all groups after first saturated group are flagged
satindex = np.argmax(output.data[:, 5, 5] == satvalue)
assert np.all(output.groupdq[satindex:, 5,
5] == dqflags.group['SATURATED'])
def test_dq_propagation(setup_wfi_datamodels):
'''Check PIXELDQ propagation.'''
# Create inputs, data, and saturation maps
ngroups = 5
nrows = 20
ncols = 20
dqval1 = 5
dqval2 = 10
data, satmap = setup_wfi_datamodels(ngroups, nrows, ncols)
# Add DQ values to the data and reference file
data.pixeldq[5, 5] = dqval1
satmap.dq[5, 5] = dqval2
# Run the pipeline
output = flag_saturation(data, satmap)
# Make sure DQ values from data and reference file are added in the output
assert output.pixeldq[5, 5] == dqval1 + dqval2
def test_no_sat_check(setup_wfi_datamodels):
'''Check that pixels flagged with NO_SAT_CHECK in the reference file get
added to the DQ mask and are not flagged as saturated.'''
# Create inputs, and data and saturation models
ngroups = 5
nrows = 20
ncols = 20
satvalue = 60000
data, satmap = setup_wfi_datamodels(ngroups, nrows, ncols)
# Add ramp values up to the saturation limit
data.data[0, 5, 5] = 10
data.data[1, 5, 5] = 20000
data.data[2, 5, 5] = 40000
data.data[3, 5, 5] = 60000
data.data[4, 5, 5] = 62000 # Signal reaches saturation limit
# Set saturation value in the saturation model & DQ value for NO_SAT_CHECK
satmap.data[5, 5] = satvalue
satmap.dq[5, 5] = dqflags.pixel['NO_SAT_CHECK']
# Also set an existing DQ flag in input science data
data.pixeldq[5, 5] = dqflags.pixel['DO_NOT_USE']
# Run the pipeline
output = flag_saturation(data, satmap)
# Make sure output GROUPDQ does not get flagged as saturated
# Make sure PIXELDQ is set to NO_SAT_CHECK and original flag
assert np.all(output.groupdq[:, 5, 5] != dqflags.group['SATURATED'])
# Test that saturation bit is NOT set
assert np.all(output.groupdq[:, 5, 5]
& (1 << dqflags.group['SATURATED'].bit_length() - 1) == 0)
assert output.pixeldq[5, 5] == (dqflags.pixel['NO_SAT_CHECK'] +
dqflags.pixel['DO_NOT_USE'])
