def test_add_missing_slits():
# Load instrument
keck_deimos = load_spectrograph('keck_deimos')
par = keck_deimos.default_pypeit_par()
# working only on detector 1
det = 1
# Built trace image
traceImage = buildimage.buildimage_fromlist(
keck_deimos, det, par['calibrations']['traceframe'],
deimos_flat_files())
msbpm = keck_deimos.bpm(traceImage.files[0], det)
# load specific config parameters
par = keck_deimos.config_specific_par(traceImage.files[0])
trace_par = par['calibrations']['slitedges']
# Running the EdgeTraceSet steps (one-by-one)
# Initialize EdgeTraceSet
edges = EdgeTraceSet(traceImage,
keck_deimos,
trace_par,
bpm=msbpm,
auto=False,
debug=False,
show_stages=False,
qa_path=None)
# Perform the initial edge detection and trace identification
edges.initial_trace(bpm=msbpm)
# Initial trace can result in no edges found
if not edges.is_empty:
# Refine the locations of the trace using centroids of the
# features in the Sobel-filtered image.
edges.centroid_refine()
# Initial trace can result in no edges found, or centroid
# refinement could have removed all traces (via `check_traces`)
if not edges.is_empty:
# Fit the trace locations with a polynomial
edges.fit_refine(debug=False)
# Use the fits to determine if there are any discontinous
# trace centroid measurements that are actually components
# of the same slit edge
edges.merge_traces(debug=False)
# Check if the PCA decomposition is possible; this should catch
# long slits
if edges.par['auto_pca'] and edges.can_pca():
# Use a PCA decomposition to parameterize the trace
# functional forms
edges.pca_refine(debug=False)
# Use the results of the PCA decomposition to rectify and
# detect peaks/troughs in the spectrally collapsed
# Sobel-filtered image, then use those peaks to further
# refine the edge traces
edges.peak_refine(rebuild_pca=True, debug=False)
# Check the values of the traces that will be removed
# Two traces NOT from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :]
[8]) == 458, 'wrong left trace position'
assert round(edges.edge_fit[edges.pca.reference_row, :]
[-12]) == 1686, 'wrong right trace position'
# Two traces from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :]
[10]) == 496, 'wrong left trace position'
assert round(edges.edge_fit[edges.pca.reference_row, :]
[11]) == 561, 'wrong right trace position'
# Remove two left traces and two right traces
# NOT form the same slit
indx = np.zeros(edges.ntrace, dtype=bool)
indx[8] = True
indx[-12] = True
# Form the same slit
indx[10] = True
indx[11] = True
edges.remove_traces(edges.synced_selection(indx, mode='ignore'),
rebuild_pca=True)
# Run slitmask matching algorithm
edges.maskdesign_matching(debug=False)
# Sync left and right edges
edges.sync()
# Check the values of the traces that have been recovered
# Two traces NOT from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :]
[8]) == 459, 'left trace position not recovered'
assert round(edges.edge_fit[edges.pca.reference_row, :]
[-12]) == 1690, 'right trace position not recovered'
# Two traces from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :]
[10]) == 497, 'wrong left trace position'
assert round(edges.edge_fit[edges.pca.reference_row, :]
[11]) == 561, 'wrong right trace position'
def test_add_missing_slits():
instr_names = ['keck_deimos', 'keck_mosfire']
for name in instr_names:
# Load instrument
instrument = load_spectrograph(name)
par = instrument.default_pypeit_par()
# working only on detector 1
det = 1
# Built trace image
traceImage = buildimage.buildimage_fromlist(instrument, det,
par['calibrations']['traceframe'],
flat_files(instr=name))
# load specific config parameters
par = instrument.config_specific_par(traceImage.files[0])
trace_par = par['calibrations']['slitedges']
# Running the EdgeTraceSet steps (one-by-one)
# Initialize EdgeTraceSet
edges = EdgeTraceSet(traceImage, instrument, trace_par, auto=False, debug=False,
show_stages=False, qa_path=None)
# Perform the initial edge detection and trace identification
edges.initial_trace()
# Initial trace can result in no edges found
if not edges.is_empty:
# Refine the locations of the trace using centroids of the
# features in the Sobel-filtered image.
edges.centroid_refine()
# Initial trace can result in no edges found, or centroid
# refinement could have removed all traces (via `check_traces`)
if not edges.is_empty:
# Fit the trace locations with a polynomial
edges.fit_refine(debug=False)
# Use the fits to determine if there are any discontinous
# trace centroid measurements that are actually components
# of the same slit edge
edges.merge_traces(debug=False)
# Check if the PCA decomposition is possible; this should catch
# long slits
if edges.par['auto_pca'] and edges.can_pca():
# Use a PCA decomposition to parameterize the trace
# functional forms
edges.pca_refine(debug=False)
# Use the results of the PCA decomposition to rectify and
# detect peaks/troughs in the spectrally collapsed
# Sobel-filtered image, then use those peaks to further
# refine the edge traces
edges.peak_refine(rebuild_pca=True, debug=False)
# Check the values of the traces that will be removed
if name == 'keck_deimos':
# Two traces NOT from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][7]) == 458, \
'wrong DEIMOS left trace position'
assert round(edges.edge_fit[edges.pca.reference_row, :][-11]) == 1736, \
'wrong DEIMOS right trace position'
# Two traces from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][9]) == 496, \
'wrong DEIMOS left trace position'
assert round(edges.edge_fit[edges.pca.reference_row, :][10]) == 561, \
'wrong DEIMOS right trace position'
# Remove two left traces and two right traces
# NOT form the same slit
indx = np.zeros(edges.ntrace, dtype=bool)
indx[7] = True
indx[-11] = True
# Form the same slit
indx[9] = True
indx[10] = True
elif name == 'keck_mosfire':
# Two traces NOT from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][0]) == 349, \
'wrong MOSFIRE left trace position'
assert round(edges.edge_fit[edges.pca.reference_row, :][-1]) == 2032, \
'wrong MOSFIRE right trace position'
# Two traces from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][9]) == 973, \
'wrong MOSFIRE left trace position'
assert round(edges.edge_fit[edges.pca.reference_row, :][10]) == 1100, \
'wrong MOSFIRE right trace position'
# Remove two left traces and two right traces
# NOT form the same slit
indx = np.zeros(edges.ntrace, dtype=bool)
indx[0] = True
indx[-1] = True
# Form the same slit
indx[9] = True
indx[10] = True
edges.remove_traces(edges.synced_selection(indx, mode='ignore'), rebuild_pca=True)
# Run slitmask matching algorithm
edges.maskdesign_matching(debug=False)
# Sync left and right edges
edges.sync()
# Check the values of the traces that have been recovered
if name == 'keck_deimos':
# Two traces NOT from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][8]) == 459, \
'DEIMOS left trace position not recovered'
assert round(edges.edge_fit[edges.pca.reference_row, :][-11]) == 1737, \
'DEIMOS right trace position not recovered'
# Two traces from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][10]) == 497, \
'DEIMOS left trace position not recovered'
assert round(edges.edge_fit[edges.pca.reference_row, :][11]) == 561, \
'DEIMOS right trace position not recovered'
# These values are obtained by running PypeIt with the "adding missing traces" functionality.
# These are within a few pixels (max 4 pixels) from their original values. The correctness of these values
# was also tested by visual inspection of the EdgeTraceSet image.
elif name == 'keck_mosfire':
# Two traces NOT from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][1]) == 348, \
'MOSFIRE left trace position not recovered'
assert round(edges.edge_fit[edges.pca.reference_row, :][-1]) == 2032, \
'MOSFIRE right trace position not recovered'
# Two traces from the same slit
assert round(edges.edge_fit[edges.pca.reference_row, :][10]) == 973, \
'MOSFIRE left trace position not recovered'
assert round(edges.edge_fit[edges.pca.reference_row, :][11]) == 1101, \
'MOSFIRE right trace position not recovered'