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code cleanup
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Simon Torres committed Aug 29, 2019
1 parent e5c9aed commit 627e2f3
Showing 1 changed file with 14 additions and 54 deletions.
68 changes: 14 additions & 54 deletions goodman_pipeline/core/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -508,7 +508,6 @@ def create_master_flats(flat_files,

log.info('Creating Master Flat')
for flat_file in flat_files:
# print(f_file)
image_full_path = os.path.join(raw_data, flat_file)
ccd = read_fits(image_full_path, technique=technique)
log.debug('Loading flat image: ' + image_full_path)
Expand Down Expand Up @@ -560,7 +559,6 @@ def create_master_flats(flat_files,

log.info('Created Master Flat: ' + master_flat_name)
return master_flat, master_flat_name
# print(master_flat_name)
else:
log.error('Empty flat list. Check that they do not exceed the '
'saturation limit.')
Expand Down Expand Up @@ -835,9 +833,6 @@ def combine_data(image_list, dest_path, prefix=None, output_name=None,
field)

combined_base_name += "{:s}_".format(value)

# print(combined_base_name)

number = len(glob.glob(
os.path.join(dest_path,
combined_base_name + "*.fits")))
Expand Down Expand Up @@ -936,8 +931,6 @@ def dcr_cosmicray_rejection(data_path, in_file, prefix, dcr_par_dir,

log.debug('DCR command:')
log.debug(command)
# print(command.split(' '))

# get the current working directory to go back to it later in case the
# the pipeline has not been called from the same data directory.
cwd = os.getcwd()
Expand Down Expand Up @@ -1201,10 +1194,6 @@ def extract_fractional_pixel(ccd, target_trace, target_fwhm, extraction_width,
# this defines the extraction limit for every column
low_limit = trace_points[i] - 0.5 * extraction_width * target_fwhm
high_limit = trace_points[i] + 0.5 * extraction_width * target_fwhm
# print(trace_points[i], extraction_width, target_stddev)

# low_limits_list.append(low_limit)
# high_limits_list.append(high_limit)

if apnum1 is None:
# TODO (simon): add secondary targets
Expand Down Expand Up @@ -1245,12 +1234,10 @@ def extract_fractional_pixel(ccd, target_trace, target_fwhm, extraction_width,
# low_background_zone
high_1 = low_limit - background_spacing * target_fwhm
low_1 = high_1 - background_width
# print(low_1,high_1)

# High background zone
low_2 = high_limit + background_spacing * target_fwhm
high_2 = low_2 + background_width
# print(low_1, ' to ', high_1, ':', low_2, ' to ', high_2,)

# validate background subtraction zones
background_1 = None
Expand All @@ -1268,15 +1255,15 @@ def extract_fractional_pixel(ccd, target_trace, target_fwhm, extraction_width,
low_limit=low_1,
high_limit=high_1)
else:
print("Invalid Zone 1")
log.error("Invalid Zone 1: [{}:{}]".format(low_1, high_1))

if high_2 < spat_length and neighbouring_target_condition:
background_2 = fractional_sum(data=ccd.data,
index=i,
low_limit=low_2,
high_limit=high_2)
else:
print("Invalid Zone 2")
log.error("Invalid Zone 2: [{}:{}]".format(low_2, high_2))

# background = 0
if background_1 is not None and background_2 is None:
Expand Down Expand Up @@ -1412,7 +1399,6 @@ def fractional_sum(data, index, low_limit, high_limit):
data[int(low_integer), index] * low_fraction + \
data[int(high_integer), index] * high_fraction

# print(low_limit, high_limit, column_sum)
return column_sum


Expand Down Expand Up @@ -1516,7 +1502,6 @@ def get_lines_in_lamp(ccd, plots=False):
"""
if isinstance(ccd, CCDData):
# print(ccddata_lamp.data.shape)
lamp_data = ccd.data
lamp_header = ccd.header
raw_pixel_axis = range(len(lamp_data))
Expand Down Expand Up @@ -1545,7 +1530,6 @@ def get_lines_in_lamp(ccd, plots=False):
new_order = int(round(float(slit_size) / (0.15 * serial_binning)))
log.debug('New Order: {:d}'.format(new_order))

# print(round(new_order))
peaks = signal.argrelmax(filtered_data, axis=0, order=new_order)[0]

if slit_size >= 5.:
Expand All @@ -1559,10 +1543,8 @@ def get_lines_in_lamp(ccd, plots=False):
lines_center = recenter_lines(no_nan_lamp_data, peaks)

if plots: # pragma: no cover
# print(new_order, slit_size, )
plt.close('all')
fig, ax = plt.subplots()
# ax = fig.add_subplot(111)
fig.canvas.set_window_title('Lines Detected')

mng = plt.get_current_fig_manager()
Expand Down Expand Up @@ -2136,15 +2118,11 @@ def linearize_spectrum(data, wavelength_solution, plots=False):
and the smoothed linearized data itself.
"""
# for data_point in data:
# print(data_point)
# print('data ', data)
pixel_axis = range(len(data))
if any(np.isnan(data)):
log.error("there are nans")
sys.exit(0)

# print(pixel_axis)
if wavelength_solution is not None:
x_axis = wavelength_solution(pixel_axis)
try:
Expand All @@ -2159,7 +2137,6 @@ def linearize_spectrum(data, wavelength_solution, plots=False):
der=0)

smoothed_linearized_data = signal.medfilt(linearized_data)
# print('sl ', smoothed_linearized_data)
if plots: # pragma: no cover
fig6 = plt.figure(6)
plt.xlabel('Wavelength (Angstrom)')
Expand Down Expand Up @@ -2258,8 +2235,6 @@ def name_master_flats(header,

date_obs = datetime.datetime.strptime(header['DATE-OBS'],
"%Y-%m-%dT%H:%M:%S.%f")
# print(sunset, date_obs, evening_twilight)
# print(' ')
if target_name != '':
target_name = '_' + target_name
if not get:
Expand Down Expand Up @@ -2854,7 +2829,6 @@ def search_comp_group(object_group, comp_groups, reference_data):
(comp_group['filter2'] == object_confs.iloc[0]['filter2']
)).all():
if reference_data.check_comp_group(comp_group) is not None:
# print(comp_group)
log.debug('Found a matching comparison lamp group')
return comp_group

Expand Down Expand Up @@ -2994,28 +2968,24 @@ def trace(ccd,
lower_limit_list.append(lower_limit)
upper_limit_list.append(upper_limit)

# print(sample_center, nsigmas, model_fwhm, lower_limit, upper_limit)

sample = ccd.data[lower_limit:upper_limit, point:point + sampling_step]
sample_median = np.median(sample, axis=1)

try:
sample_peak = np.argmax(sample_median)
# print(sample_peak + lower_limit)
except ValueError: # pragma: no cover
# plt.plot(model(range(spatial_length)))
# plt.plot(ccd.data[:,point])
# plt.show()
print('Nfwhm ', nfwhm)
print('Model Stddev ', model_fwhm)
print('sample_center ', sample_center)
print('sample ', sample)
print('sample_median ', sample_median)
print('lower_limit ', lower_limit)
print('upper_limit ', upper_limit)
print('point ', point)
print('point + sampling_step ', point + sampling_step)
print(spatial_length, dispersion_length)
log.error('Nfwhm {}'.format(nfwhm))
log.error('Model Stddev {}'.format(model_fwhm))
log.error('sample_center {}'.format(sample_center))
log.error('sample {}'.format(sample))
log.error('sample_median {}'.format(sample_median))
log.error('lower_limit {}'.format(lower_limit))
log.error('upper_limit {}'.format(upper_limit))
log.error('point {}'.format(point))
log.error('point + sampling_step {}'.format(point + sampling_step))
log.error("Spatial length: {}, Dispersion length {}".format(
spatial_length,
dispersion_length))
sys.exit()

sample_values.append(sample_peak + lower_limit)
Expand Down Expand Up @@ -3194,8 +3164,6 @@ def trace_targets(ccd, target_list, sampling_step=5, pol_deg=2, nfwhm=5,
sampling_step=sampling_step,
nfwhm=nfwhm,
plots=plots)
# print(single_trace)
# print(trace_rms)

if 0 < single_trace.c0.value < ccd.shape[0]:
log.debug('Adding trace to list')
Expand Down Expand Up @@ -3449,7 +3417,6 @@ def __repr__(self):
self.full_path,
self.instrument,
self.technique))
# print(class_info)

if all([self.gain, self.rdnoise, self.roi]):
class_info += str("\nGain: {:.2f}\n"
Expand Down Expand Up @@ -3622,7 +3589,6 @@ def add_spec_group(self, spec_group):
self.is_empty = False
comp_group = spec_group[spec_group.obstype == 'COMP']
self.add_comp_group(comp_group=comp_group)
# print(comp_group)

def set_sun_times(self, sun_set, sun_rise):
"""Sets values for sunset and sunrise
Expand Down Expand Up @@ -3708,7 +3674,6 @@ def __init__(self, reference_dir):
self.reference_dir = reference_dir
reference_collection = ccdproc.ImageFileCollection(self.reference_dir)
self.ref_lamp_collection = reference_collection.summary.to_pandas()
# print(self.ref_lamp_collection)
self.lines_pixel = None
self.lines_angstrom = None
self._ccd = None
Expand Down Expand Up @@ -3866,7 +3831,6 @@ def check_comp_group(self, comp_group):
(comp_group['lamp_ar'] == lamps.iloc[i]['lamp_ar']) &
(comp_group['lamp_fe'] == lamps.iloc[i]['lamp_fe']) &
(comp_group['lamp_cu'] == lamps.iloc[i]['lamp_cu'])]
# print(new_group.file)
return new_group
else:
self.log.warning("The target's comparison lamps do not have "
Expand Down Expand Up @@ -4102,7 +4066,6 @@ def __call__(self,
camera_targ = str(header['cam_targ'])
grating_targ = str(header['grt_targ'])
blocking_filter = str(header['filter2'])
# print(grating, camera_targ, grating_targ, blocking_filter)

return self.get_mode(grating=grating,
camera_targ=camera_targ,
Expand Down Expand Up @@ -4136,8 +4099,6 @@ def get_mode(self, grating, camera_targ, grating_targ, blocking_filter):
string that defines the wavelength mode used
"""

# print(grating, camera_targ, grating_targ)
if any(grat == grating for grat in ('1800', '2100', '2400')):
central_wavelength = get_central_wavelength(grating=grating,
grt_ang=grating_targ,
Expand Down Expand Up @@ -4696,7 +4657,6 @@ def _fit_gaussian(fitter,

ax.plot(spatial_profile, color='k', label='Median Profile')
for profile in profile_model:
# print(profile_model)
ax.plot(profile(range(len(spatial_profile))),
label=profile.name)

Expand Down

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