def show_trace(specobjs, det, viewer, ch):
if specobjs is None:
return
in_det = np.where(specobjs.DET == det)[0]
for kk in in_det:
trace = specobjs[kk]['TRACE_SPAT']
obj_id = specobjs[kk].NAME
display.show_trace(viewer, ch, trace, obj_id,
color='orange') #hdu.name)
def show_trace(specobjs, det, viewer, ch):
if specobjs is None:
return
in_det = np.where(specobjs.DET == det)[0]
for kk in in_det:
trace = specobjs[kk]['TRACE_SPAT']
obj_id = specobjs[kk].NAME
maskdef_objname = specobjs[kk].MASKDEF_OBJNAME
if maskdef_objname is not None:
trc_name = '{} OBJNAME:{}'.format(obj_id, maskdef_objname)
else:
trc_name = obj_id
display.show_trace(viewer, ch, trace, trc_name,
color='orange') #hdu.name)
def show_alignment(alignframe, align_traces=None, slits=None, clear=False):
"""
Show one of the class internals
Parameters
----------
alignframe : `numpy.ndarray`_
Image to be plotted (i.e. the master align frame)
align_traces : list, optional
The align traces
slits : :class:`pypeit.slittrace.SlitTraceSet`, optional
properties of the slits, including traces.
clear : bool, optional
Clear the plotting window in ginga?
Returns
-------
"""
display.connect_to_ginga(raise_err=True, allow_new=True)
ch_name = 'alignment'
viewer, channel = display.show_image(alignframe,
chname=ch_name,
clear=clear,
wcs_match=False)
# Display the slit edges
if slits is not None and viewer is not None:
left, right, mask = slits.select_edges()
display.show_slits(viewer, channel, left, right)
# Display the alignment traces
if align_traces is not None and viewer is not None:
for bar in range(align_traces.shape[1]):
for slt in range(align_traces.shape[2]):
# Alternate the colors of the slits
color = 'orange'
if slt % 2 == 0:
color = 'magenta'
# Display the trace
display.show_trace(viewer,
channel,
align_traces[:, bar, slt],
trc_name="",
color=color)
def show_trace(specobjs, det, viewer, ch):
"""
Overplot the extracted object traces for this detector in the provided ginga
channel.
Args:
specobjs (:class:`~pypeit.specobjs.SpecObjs`):
Object holding the 1D spectral extractions. If None, the function
doesn't do anything.
det (:obj:`str`):
The string identifier for the detector or mosaic used to select the
extractions to show.
viewer (?):
ch (?):
"""
if specobjs is None:
return
in_det = np.where(specobjs.DET == det)[0]
for kk in in_det:
trace = specobjs[kk]['TRACE_SPAT']
obj_id = specobjs[kk].NAME
maskdef_objname = specobjs[kk].MASKDEF_OBJNAME
maskdef_extr_flag = specobjs[kk].MASKDEF_EXTRACT
manual_extr_flag = specobjs[kk].hand_extract_flag
if maskdef_objname is not None:
trc_name = '{} OBJNAME:{}'.format(obj_id, maskdef_objname)
else:
trc_name = obj_id
if maskdef_extr_flag is not None and maskdef_extr_flag is True:
display.show_trace(viewer, ch, trace, trc_name,
color='#f0e442') #hdu.name)
elif manual_extr_flag is True:
display.show_trace(viewer, ch, trace, trc_name,
color='#33ccff') #hdu.name)
else:
display.show_trace(viewer, ch, trace, trc_name,
color='orange') #hdu.name)
def show(self, attr, image=None, showmask=False, sobjs=None,
chname=None, slits=False,clear=False):
"""
Show one of the internal images
.. todo::
Should probably put some of these in ProcessImages
Parameters
----------
attr : str
global -- Sky model (global)
sci -- Processed science image
rawvar -- Raw variance image
modelvar -- Model variance image
crmasked -- Science image with CRs set to 0
skysub -- Science image with global sky subtracted
image -- Input image
display : str, optional
image : ndarray, optional
User supplied image to display
"""
if showmask:
mask_in = self.sciImg.fullmask
bitmask_in = self.sciImg.bitmask
else:
mask_in = None
bitmask_in = None
img_gpm = self.sciImg.select_flag(invert=True)
detname = self.spectrograph.get_det_name(self.det)
# TODO Do we still need this here?
if attr == 'global' and all([a is not None for a in [self.sciImg.image, self.global_sky, self.sciImg.fullmask]]):
# global sky subtraction
# sky subtracted image
image = (self.sciImg.image - self.global_sky) * img_gpm.astype(float)
mean, med, sigma = stats.sigma_clipped_stats(image[img_gpm], sigma_lower=5.0,
sigma_upper=5.0)
cut_min = mean - 1.0 * sigma
cut_max = mean + 4.0 * sigma
ch_name = chname if chname is not None else f'global_sky_{detname}'
viewer, ch = display.show_image(image, chname=ch_name, bitmask=bitmask_in,
mask=mask_in, clear=clear, wcs_match=True)
#, cuts=(cut_min, cut_max))
elif attr == 'local' and all([a is not None for a in [self.sciImg.image, self.skymodel, self.sciImg.fullmask]]):
# local sky subtraction
# sky subtracted image
image = (self.sciImg.image - self.skymodel) * img_gpm.astype(float)
mean, med, sigma = stats.sigma_clipped_stats(image[img_gpm], sigma_lower=5.0,
sigma_upper=5.0)
cut_min = mean - 1.0 * sigma
cut_max = mean + 4.0 * sigma
ch_name = chname if chname is not None else f'local_sky_{detname}'
viewer, ch = display.show_image(image, chname=ch_name, bitmask=bitmask_in,
mask=mask_in, clear=clear, wcs_match=True)
#, cuts=(cut_min, cut_max))
elif attr == 'sky_resid' and all([a is not None for a in [self.sciImg.image, self.skymodel, self.objmodel,
self.ivarmodel, self.sciImg.fullmask]]):
# sky residual map with object included
image = (self.sciImg.image - self.skymodel) * np.sqrt(self.ivarmodel)
image *= img_gpm.astype(float)
ch_name = chname if chname is not None else f'sky_resid_{detname}'
viewer, ch = display.show_image(image, chname=ch_name, cuts=(-5.0, 5.0),
bitmask=bitmask_in, mask=mask_in, clear=clear,
wcs_match=True)
elif attr == 'resid' and all([a is not None for a in [self.sciImg.image, self.skymodel, self.objmodel,
self.ivarmodel, self.sciImg.fullmask]]):
# full residual map with object model subtractede
# full model residual map
image = (self.sciImg.image - self.skymodel - self.objmodel) * np.sqrt(self.ivarmodel)
image *= img_gpm.astype(float)
ch_name = chname if chname is not None else f'resid_{detname}'
viewer, ch = display.show_image(image, chname=ch_name, cuts=(-5.0, 5.0),
bitmask=bitmask_in, mask=mask_in, clear=clear,
wcs_match=True)
elif attr == 'image':
ch_name = chname if chname is not None else 'image'
viewer, ch = display.show_image(image, chname=ch_name, clear=clear, wcs_match=True)
else:
msgs.warn("Not an option for show")
if sobjs is not None:
for spec in sobjs:
color = 'magenta' if spec.hand_extract_flag else 'orange'
display.show_trace(viewer, ch, spec.TRACE_SPAT, spec.NAME, color=color)
if slits and self.slits_left is not None:
display.show_slits(viewer, ch, self.slits_left, self.slits_right)