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Merge pull request #757 from desihub/ql_countbins
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Adjust Calibration Exposure QA Specifications
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@rkehoe
rkehoe authored Jan 25, 2019
2 parents 5cd4452 + 931fc5f commit 719c332
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Showing 4 changed files with 56 additions and 55 deletions.
10 changes: 5 additions & 5 deletions py/desispec/data/quicklook/qlconfig_arc.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,19 +24,19 @@ Algorithms:
Get_RMS:
PARAMS: {PERCENTILES: [68.2,95.4,99.7], NOISE_AMP_NORMAL_RANGE: [-1.5, 1.5], NOISE_AMP_WARN_RANGE: [-2.0, 2.0],NOISE_AMP_REF:[2.6,2.6,2.6,2.6]}
Count_Pixels:
PARAMS: {CUTPIX: 5, LITFRAC_AMP_NORMAL_RANGE: [-0.15, 0.15], LITFRAC_AMP_WARN_RANGE: [-0.2, 0.2],LITFRAC_AMP_REF:[0.01,0.01,0.01,0.01]}
PARAMS: {CUTPIX: 5, LITFRAC_AMP_NORMAL_RANGE: [-0.12, 0.12], LITFRAC_AMP_WARN_RANGE: [-0.16, 0.16],LITFRAC_AMP_REF:[0.05,0.05,0.05,0.05]}
Calc_XWSigma:
PARAMS: {B_PEAKS: [4047.7,4078.8,4359.6,4801.2,5087.2,5426.2],
R_PEAKS: [6144.7,6404.0,6508.3,6931.4,7034.3,7247.1],
Z_PEAKS: [8302.6,8379.9,8497.7,8856.3,9151.1,9668.0],
PIXEL_RANGE: 7,
MAX_SIGMA: 10,
XWSIGMA_NORMAL_RANGE: [-0.9, 0.9],
XWSIGMA_WARN_RANGE: [-1.2, 1.2],XWSIGMA_REF:[1.2,1.2]}
XWSIGMA_NORMAL_RANGE: [-0.45, 0.45],
XWSIGMA_WARN_RANGE: [-0.6, 0.6],XWSIGMA_REF:[1.1,1.2]}
Flexure:
QA:
Trace_Shifts:
PARAMS: {XYSHIFTS_NORMAL_RANGE: [-0.2,0.2], XYSHIFTS_WARN_RANGE: [-0.3,0.3],XYSHIFTS_REF:[0.0,0.0]}
PARAMS: {XYSHIFTS_NORMAL_RANGE: [-0.21,0.21], XYSHIFTS_WARN_RANGE: [-0.28,0.28],XYSHIFTS_REF:[-0.07,-0.07]}
Extract_QP:
wavelength: {
b: [3570,5730,0.8],
Expand All @@ -50,4 +50,4 @@ Algorithms:
NBINS: 5
QA:
Check_Resolution:
PARAMS: {CHECKARC_NORMAL_RANGE: [-30.0,30.0], CHECKARC_WARN_RANGE: [-40.0,40.0],CHECKARC_REF:[500]}
PARAMS: {CHECKARC_NORMAL_RANGE: [-30.0,30.0], CHECKARC_WARN_RANGE: [-40.0,40.0],CHECKARC_REF:[480]}
6 changes: 3 additions & 3 deletions py/desispec/data/quicklook/qlconfig_flat.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,11 @@ Algorithms:
Get_RMS:
PARAMS: {PERCENTILES: [68.2,95.4,99.7], NOISE_AMP_NORMAL_RANGE: [-1.5, 1.5], NOISE_AMP_WARN_RANGE: [-2.0, 2.0],NOISE_AMP_REF:[2.6,2.6,2.6,2.6]}
Count_Pixels:
PARAMS: {CUTPIX: 5, LITFRAC_AMP_NORMAL_RANGE: [-0.15, 0.15], LITFRAC_AMP_WARN_RANGE: [-0.2, 0.2],LITFRAC_AMP_REF:[0.8,0.8,0.8,0.8]}
PARAMS: {CUTPIX: 5, LITFRAC_AMP_NORMAL_RANGE: [-0.3, 0.3], LITFRAC_AMP_WARN_RANGE: [-0.4, 0.4],LITFRAC_AMP_REF:[0.78,0.78,0.78,0.78]}
Flexure:
QA:
Trace_Shifts:
PARAMS: {XYSHIFTS_NORMAL_RANGE: [-0.2,0.2], XYSHIFTS_WARN_RANGE: [-0.3,0.3],XYSHIFTS_REF:[0.0,0.0]}
PARAMS: {XYSHIFTS_NORMAL_RANGE: [-0.6,0.6], XYSHIFTS_WARN_RANGE: [-0.8,0.8],XYSHIFTS_REF:[0.0,0.0]}
Extract_QP:
wavelength: {
b: [3570,5730,0.8],
Expand All @@ -40,4 +40,4 @@ Algorithms:
ComputeFiberflat_QP:
QA:
Check_FiberFlat:
PARAMS: {CHECKFLAT_NORMAL_RANGE:[-0.3,0.3], CHECKFLAT_WARN_RANGE:[-0.4,0.4],CHECKFLAT_REF:[1.0]}
PARAMS: {CHECKFLAT_NORMAL_RANGE:[-0.01,0.01], CHECKFLAT_WARN_RANGE:[-0.02,0.02],CHECKFLAT_REF:[1.0]}
83 changes: 42 additions & 41 deletions py/desispec/qa/qa_quicklook.py
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Original file line number Diff line number Diff line change
Expand Up @@ -350,8 +350,8 @@ def run_qa(self,image,inputs):
retval["PARAMS"]=param

#get_outputs(qafile,qafig,retval,'plot_traceshifts')
outfile = qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# outfile = qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
return retval

def get_default_config(self):
Expand Down Expand Up @@ -475,9 +475,9 @@ def run_qa(self,image,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_bias_overscan(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -693,9 +693,9 @@ def run_qa(self,image,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_RMS(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -930,9 +930,9 @@ def run_qa(self,image,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_XWSigma(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -1040,9 +1040,9 @@ def run_qa(self,image,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_countpix(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -1147,8 +1147,9 @@ def run_qa(self,frame,inputs):
threshold=[param['CUTBINS']*ii for ii in rdnoise_fib]
#- compare the flux sum to threshold

passfibers=np.where(frame.flux.sum(axis=1)>threshold)[0]
ngoodfibers=passfibers.shape[0] - param["N_KNOWN_BROKEN_FIBERS"]
totcounts=frame.flux.sum(axis=1)
passfibers=np.where(totcounts>threshold)[0]
ngoodfibers=passfibers.shape[0]
good_fibers=np.array([0]*frame.nspec)
good_fibers[passfibers]=1 #- assign 1 for good fiber

Expand All @@ -1166,17 +1167,17 @@ def run_qa(self,frame,inputs):
retval["BOTTOM_MAX_WAVE_INDEX"]=int(bottommax)
retval["TOP_MIN_WAVE_INDEX"]=int(topmin)

retval["METRICS"]={"NGOODFIB": ngoodfibers, "GOOD_FIBERS": good_fibers}
retval["METRICS"]={"NGOODFIB": ngoodfibers, "GOOD_FIBERS": good_fibers, "TOTCOUNT_FIB": totcounts}

###############################################################
# This section is for adding QA metrics for plotting purposes #
###############################################################

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_countspectralbins(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -1281,9 +1282,9 @@ def run_qa(self,frame,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_sky_continuum(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -1427,9 +1428,9 @@ def run_qa(self,frame,inputs):
zerorband=0.
retval["METRICS"]={"SKYRBAND_FIB":zerospec,"SKYRBAND":zerorband}

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))

return retval

Expand Down Expand Up @@ -1535,9 +1536,9 @@ def run_qa(self,frame,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_sky_peaks(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -1644,9 +1645,9 @@ def run_qa(self,frame,skymodel,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_residuals(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -1871,9 +1872,9 @@ def run_qa(self,frame,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_integral(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -1994,9 +1995,9 @@ def run_qa(self,frame,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_SNR(retval,qafig,objlist,fitsnr,rescut,sigmacut,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down Expand Up @@ -2116,9 +2117,9 @@ def run_qa(self,file_psf,inputs):

###############################################################

if qafile is not None:
outfile=qa.write_qa_ql(qafile,retval)
log.debug("Output QA data is in {}".format(outfile))
# if qafile is not None:
# outfile=qa.write_qa_ql(qafile,retval)
# log.debug("Output QA data is in {}".format(outfile))
if qafig is not None:
fig.plot_lpolyhist(retval,qafig,plotconf=plotconf,hardplots=hardplots)
log.debug("Output QA fig {}".format(qafig))
Expand Down
12 changes: 6 additions & 6 deletions py/desispec/quicklook/qlconfig.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -248,19 +248,19 @@ def dump_qa(self):
Name and default locations of files are handled by desispec.io.meta.findfile
"""
#- QA level outputs
qa_outfile = {}
#qa_outfile = {}
qa_outfig = {}
for PA in self.palist:
for QA in self.qalist[PA]:
qa_outfile[QA] = self.io_qa(QA)[0]
#qa_outfile[QA] = self.io_qa(QA)[0]
qa_outfig[QA] = self.io_qa(QA)[1]

#- make path if needed
path = os.path.normpath(os.path.dirname(qa_outfile[QA]))
path = os.path.normpath(os.path.dirname(qa_outfig[QA]))
if not os.path.exists(path):
os.makedirs(path)

return (qa_outfile,qa_outfig)
return (qa_outfig)
# return ((qa_outfile,qa_outfig),(qa_pa_outfile,qa_pa_outfig))

@property
Expand All @@ -273,8 +273,8 @@ def qaargs(self):
params=self._qaparams(qa)
qaopts[qa]={'night' : self.night, 'expid' : self.expid,
'camera': self.camera, 'paname': PA, 'PSFFile': self.psf_filename,
'amps': self.amps, 'qafile': self.dump_qa()[0][qa],
'qafig': self.dump_qa()[1][qa], 'FiberMap': self.fibermap,
'amps': self.amps, #'qafile': self.dump_qa()[0][qa],
'qafig': self.dump_qa()[qa], 'FiberMap': self.fibermap,
'param': params, 'refKey':self._qaRefKeys[qa],
'singleqa' : self.singqa,
'plotconf':self.plotconf, 'hardplots': self.hardplots
Expand Down

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