def testRaw(self):
"""Test retrieval of raw image"""
frame = 0
for expId, mit in [(22657, True), (127073, False)]:
for ccdNum in [2, 5]:
butler = getButler(self.datadir, mit)
raw = butler.get("raw", visit=expId, ccd=ccdNum)
print "Visit: ", expId
print "MIT detector: ", mit
print "width: ", raw.getWidth()
print "height: ", raw.getHeight()
print "detector(amp) name: ", raw.getDetector().getId().getName()
self.assertEqual(raw.getWidth(), self.sizes[mit][0]) # untrimmed
self.assertEqual(raw.getHeight(), self.sizes[mit][1]) # untrimmed
self.assertEqual(raw.getFilter().getFilterProperty().getName(), "i")
self.assertEqual(raw.getDetector().getId().getName(), self.names[mit][ccdNum])
if display:
ccd = raw.getDetector()
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print ccd.getId(), amp.getId(), amp.getDataSec().toString(), \
amp.getBiasSec().toString(), amp.getElectronicParams().getGain()
cameraGeomUtils.showCcd(ccd, ccdImage=raw, frame=frame)
frame += 1
def assertExposure(self, exp, ccd, checkFilter=True):
print("dataId: ", self.dataId)
print("ccd: ", ccd)
print("width: ", exp.getWidth())
print("height: ", exp.getHeight())
print("detector name: ", exp.getDetector().getName())
print("filter name: ", exp.getFilter().getFilterProperty().getName())
self.assertEqual(exp.getWidth(), self.size[0])
self.assertEqual(exp.getHeight(), self.size[1])
self.assertEqual(exp.getDetector().getName(), "ccd%02d" % ccd)
if checkFilter:
self.assertEqual(exp.getFilter().getFilterProperty().getName(),
self.filter)
if display and ccd % 18 == 0:
global frame
frame += 1
ccd = cameraGeom.cast_Ccd(exp.getDetector())
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print(ccd.getId(), amp.getId(),
amp.getDataSec().toString(),
amp.getBiasSec().toString(),
amp.getElectronicParams().getGain())
cameraGeomUtils.showCcd(ccd, ccdImage=exp, frame=frame)
def testRaw(self):
"""Test retrieval of raw image"""
frame = 0
for expId, mit in [(22657, True), (127073, False)]:
for ccdNum in [2, 5]:
butler = getButler(self.datadir, mit)
raw = butler.get("raw", visit=expId, ccd=ccdNum)
print "Visit: ", expId
print "MIT detector: ", mit
print "width: ", raw.getWidth()
print "height: ", raw.getHeight()
print "detector(amp) name: ", raw.getDetector().getId(
).getName()
self.assertEqual(raw.getWidth(),
self.sizes[mit][0]) # untrimmed
self.assertEqual(raw.getHeight(),
self.sizes[mit][1]) # untrimmed
self.assertEqual(raw.getFilter().getFilterProperty().getName(),
"i")
self.assertEqual(raw.getDetector().getId().getName(),
self.names[mit][ccdNum])
if display:
ccd = raw.getDetector()
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print ccd.getId(), amp.getId(), amp.getDataSec().toString(), \
amp.getBiasSec().toString(), amp.getElectronicParams().getGain()
cameraGeomUtils.showCcd(ccd, ccdImage=raw, frame=frame)
frame += 1
def getAmp(exposure):
"""Get the Amp referred to by an exposure
@param exposure Exposure to inspect
@returns Amp
"""
det = exposure.getDetector()
amp = cameraGeom.cast_Amp(det) # None if detector is not an Amp
return amp
def detectorIsAmp(exposure):
"""Is the detector referred to by the exposure an Amp?
@param exposure Exposure to inspect
@returns True if exposure's detector is an Amp
"""
det = exposure.getDetector()
amp = cameraGeom.cast_Amp(det)
return False if amp is None else True
def getAmp(exposure):
"""Get the Amp referred to by an exposure
@param exposure Exposure to inspect
@returns Amp
"""
det = exposure.getDetector()
amp = cameraGeom.cast_Amp(det) # None if detector is not an Amp
return amp
def detectorIsAmp(exposure):
"""Is the detector referred to by the exposure an Amp?
@param exposure Exposure to inspect
@returns True if exposure's detector is an Amp
"""
det = exposure.getDetector()
amp = cameraGeom.cast_Amp(det)
return False if amp is None else True
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing Saturation correction.")
#grab exposure from clipboard
exposure = clipboard.get(self.policy.getString("inputKeys.exposure"))
exposure = ipIsr.convertImageForIsr(exposure)
fwhm = self.policy.getDouble("parameters.defaultFwhm")
amp = cameraGeom.cast_Amp(exposure.getDetector())
dataBbox = amp.getDataSec(True)
x = dataBbox.getMinX()
y = dataBbox.getMinY()
height = dataBbox.getMaxY() - dataBbox.getMinY()
width = dataBbox.getMaxY() - dataBbox.getMinX()
dl = measAlg.DefectListT()
defectList = cameraGeom.cast_Ccd(amp.getParent()).getDefects()
if amp.getId().getIndex()[1] == 1:
for d in defectList:
d1 = measAlg.Defect(d.getBBox())
d1.shift(-x, -y)
bbox = d1.getBBox()
if bbox.getMinX() - 4 > width or bbox.getMaxY() - 4 < 0 or \
height - bbox.getMinY() - 1 > height or height - bbox.getMaxY() - 1 < 0:
pass
else:
nd = measAlg.Defect(afwGeom.Box2I(
afwGeom.Point2I(bbox.getMinX() + 4, height - bbox.getMinY() + 1),
bbox.getDimensions()))
dl.append(nd)
else:
for d in defectList:
d1 = measAlg.Defect(d.getBBox())
d1.shift(-x, -y)
bbox = d1.getBBox()
if bbox.getMinX() - 4 > width or bbox.getMaxY() - 4 < 0 or \
bbox.getMinY() - 1 > height or bbox.getMaxY() - 1 < 0:
pass
else:
nd = measAlg.Defect(afwGeom.Box2I(
bbox.getMin() + afwGeom.Extent2I(4, 1),
bbox.getDimensions()))
dl.append(nd)
saturation = amp.getElectronicParams().getSaturationLevel()
ipIsr.maskBadPixelsDef(exposure, dl,
fwhm, interpolate=True, maskName='BAD')
ipIsr.saturationCorrection(exposure, int(saturation), fwhm,
growSaturated=False, interpolate=True)
#ds9.mtv(exposure, frame = 0, title = "my Amp")
#exposure.writeFits("Amp.fits")
#output products
clipboard.put(self.policy.get("outputKeys.saturationCorrectedExposure"),
exposure)
def haveAmp(exposure, amp):
"""Does the detector referred to by the exposure contain this particular amp?
@param exposure Exposure to inspect
@param amp Amp for comparison
@returns True if exposure contains this amp
"""
det = exposure.getDetector()
testAmp = cameraGeom.cast_Amp(det)
if testAmp is None:
# Exposure contains a CCD, which contains all its amps
return True
return True if testAmp.getId() == amp.getId() else False
def haveAmp(exposure, amp):
"""Does the detector referred to by the exposure contain this particular amp?
@param exposure Exposure to inspect
@param amp Amp for comparison
@returns True if exposure contains this amp
"""
det = exposure.getDetector()
testAmp = cameraGeom.cast_Amp(det)
if testAmp is None:
# Exposure contains a CCD, which contains all its amps
return True
return True if testAmp.getId() == amp.getId() else False
def __init__(self, figure, camera, rect=(0.08, 0.08, 0.84, 0.84)):
self.figure = figure
self.camera = camera
self.rect = rect
self.detectors = {}
self.amps = {}
# use same rect as figure.add_axes(rect) to avoid confusion
l, b, w, h = self.rect
self.fig_left = l
self.fig_bottom = b
self.fig_width = w
self.fig_height = h
l_cam, b_cam, r_cam, t_cam = 1.0e6, 1.0e6, -1.0e6, -1.0e6
for r in self.camera:
raft = camGeom.cast_Raft(r)
for c in raft:
ccd = camGeom.cast_Ccd(c)
serial = ccd.getId().getSerial()
self.detectors[serial] = ccd
cc = ccd.getCenter().getPixels(ccd.getPixelSize())
cxc, cyc = cc.getX(), cc.getY()
cbbox = ccd.getAllPixels(True)
cwidth = cbbox.getMaxX() - cbbox.getMinX()
cheight = cbbox.getMaxY() - cbbox.getMinY()
l_cam = min(l_cam, cxc - cwidth/2)
b_cam = min(b_cam, cyc - cheight/2)
r_cam = max(r_cam, cxc + cwidth/2)
t_cam = max(t_cam, cyc + cheight/2)
self.amps[serial] = []
for a in ccd:
amp = camGeom.cast_Amp(a)
self.amps[serial].append(amp)
self.camera_width = r_cam - l_cam
self.camera_height = t_cam - b_cam
extent = afwGeom.Extent2D(self.camera_width, self.camera_height)
self.camera_bbox = afwGeom.Box2D(afwGeom.Point2D(0.0, 0.0), extent)
#print "Camera", self.camera_bbox
self.axes = {}
def testRaw(self):
"""Test retrieval of raw image"""
for ccd in range(12):
raw = self.butler.get("raw", self.dataId, ccd=ccd)
self.assertExposure(raw, ccd)
if display:
ccd = cameraGeom.cast_Ccd(raw.getDetector())
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print ccd.getId(), amp.getId(), amp.getDataSec().toString(), \
amp.getBiasSec().toString(), amp.getElectronicParams().getGain()
cameraGeomUtils.showCcd(ccd, ccdImage=raw, frame=frame)
frame += 1
def testRaw(self):
"""Test retrieval of raw image"""
ccd = 'VIRGO1'
raw = self.butler.get("raw", self.dataId, ccd=ccd)
self.assertExposure(raw, ccd)
if display:
ccd = cameraGeom.cast_Ccd(raw.getDetector())
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print ccd.getId(), amp.getId(), amp.getDataSec().toString(), \
amp.getBiasSec().toString(), amp.getElectronicParams().getGain()
cameraGeomUtils.showCcd(ccd, ccdImage=raw, frame=frame)
frame += 1
def getCcd(exposure):
"""Get the Ccd referred to by an exposure
@param exposure Exposure to inspect
@returns Ccd
"""
det = exposure.getDetector()
ccd = cameraGeom.cast_Ccd(det)
if ccd is not None:
return ccd
amp = cameraGeom.cast_Amp(det)
if amp is not None:
det = amp.getParent()
ccd = cameraGeom.cast_Ccd(det)
return ccd
raise RuntimeError("Can't find Ccd from detector.")
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing CCD assembly.")
#grab exposure from clipboard
exposureList = clipboard.get(self.policy.getString("inputKeys.exposureList"))
rmKeys = self.policy.getArray("parameters.deleteFieldsList")
amp = cameraGeom.cast_Amp(exposureList[0].getDetector())
ccdId = amp.getParent().getId()
ccd = cameraGeom.cast_Ccd(amp.getParent())
exposure = ipIsr.ccdAssemble.assembleCcd(exposureList, ccd,
keysToRemove=rmKeys)
#output products
clipboard.put(self.policy.get("outputKeys.assembledCcdExposure"),
exposure)
def __init__(self, figure, camera, rect=(0.08, 0.08, 0.84, 0.84)):
self.figure = figure
self.camera = camera
self.rect = rect
self.detectors = {}
self.amps = {}
# use same rect as figure.add_axes(rect) to avoid confusion
l, b, w, h = self.rect
self.fig_left = l
self.fig_bottom = b
self.fig_width = w
self.fig_height = h
l_cam, b_cam, r_cam, t_cam = 1.0e6, 1.0e6, -1.0e6, -1.0e6
for r in self.camera:
raft = camGeom.cast_Raft(r)
for c in raft:
ccd = camGeom.cast_Ccd(c)
serial = ccd.getId().getSerial()
self.detectors[serial] = ccd
cc = ccd.getCenter().getPixels(ccd.getPixelSize())
cxc, cyc = cc.getX(), cc.getY()
cbbox = ccd.getAllPixels(True)
cwidth = cbbox.getMaxX() - cbbox.getMinX()
cheight = cbbox.getMaxY() - cbbox.getMinY()
l_cam = min(l_cam, cxc - cwidth / 2)
b_cam = min(b_cam, cyc - cheight / 2)
r_cam = max(r_cam, cxc + cwidth / 2)
t_cam = max(t_cam, cyc + cheight / 2)
self.amps[serial] = []
for a in ccd:
amp = camGeom.cast_Amp(a)
self.amps[serial].append(amp)
self.camera_width = r_cam - l_cam
self.camera_height = t_cam - b_cam
extent = afwGeom.Extent2D(self.camera_width, self.camera_height)
self.camera_bbox = afwGeom.Box2D(afwGeom.Point2D(0.0, 0.0), extent)
#print "Camera", self.camera_bbox
self.axes = {}
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing Saturation correction.")
#grab exposure from clipboard
exposure = clipboard.get(self.policy.getString("inputKeys.exposure"))
metadata = exposure.getMetadata()
exposure = ipIsr.convertImageForIsr(exposure)
fwhm = self.policy.getDouble("parameters.defaultFwhm")
amp = cameraGeom.cast_Amp(exposure.getDetector())
saturation = amp.getElectronicParams().getSaturationLevel()
bboxes = ipIsr.saturationDetection(exposure, int(saturation), doMask = True)
self.log.log(Log.INFO, "Found %i saturated regions."%(len(bboxes)))
#output products
clipboard.put(self.policy.get("outputKeys.saturationMaskedExposure"),
exposure)
def variance(self, exposure):
"""Set variance from gain
@param exposure Exposure to process
"""
assert exposure, "No exposure provided"
mi = exposure.getMaskedImage()
if pipUtil.detectorIsCcd(exposure):
ccd = pipUtil.getCcd(exposure)
MaskedImage = type(mi)
for amp in ccd:
miAmp = MaskedImage(mi, amp.getDataSec(True), afwImage.LOCAL)
self._varianceAmp(miAmp, amp)
else:
amp = cameraGeom.cast_Amp(exposure.getDetector())
self._varianceAmp(mi, amp)
return
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing CCD assembly.")
#grab exposure from clipboard
exposureList = clipboard.get(
self.policy.getString("inputKeys.exposureList"))
rmKeys = self.policy.getArray("parameters.deleteFieldsList")
amp = cameraGeom.cast_Amp(exposureList[0].getDetector())
ccdId = amp.getParent().getId()
ccd = cameraGeom.cast_Ccd(amp.getParent())
exposure = ipIsr.ccdAssemble.assembleCcd(exposureList,
ccd,
keysToRemove=rmKeys)
#output products
clipboard.put(self.policy.get("outputKeys.assembledCcdExposure"),
exposure)
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing Saturation correction.")
#grab exposure from clipboard
exposure = clipboard.get(self.policy.getString("inputKeys.exposure"))
metadata = exposure.getMetadata()
exposure = ipIsr.convertImageForIsr(exposure)
fwhm = self.policy.getDouble("parameters.defaultFwhm")
amp = cameraGeom.cast_Amp(exposure.getDetector())
saturation = amp.getElectronicParams().getSaturationLevel()
bboxes = ipIsr.saturationDetection(exposure,
int(saturation),
doMask=True)
self.log.log(Log.INFO, "Found %i saturated regions." % (len(bboxes)))
#output products
clipboard.put(self.policy.get("outputKeys.saturationMaskedExposure"),
exposure)
def testRaw(self):
"""Test retrieval of raw image"""
frame = 0
if display:
cameraGeomUtils.showCamera(self.butler.mapper.camera, frame=frame)
for side in ("N", "S"):
for ccd in range(1, 32, 1):
raw = self.butler.get("raw", self.dataId, side=side, ccd=ccd)
self.assertExposure(raw, side, ccd)
if display:
frame += 1
ccd = cameraGeom.cast_Ccd(raw.getDetector())
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print ccd.getId(), amp.getId(), amp.getDataSec().toString(), \
amp.getBiasSec().toString(), amp.getElectronicParams().getGain()
cameraGeomUtils.showCcd(ccd, ccdImage=raw, frame=frame)
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing overscan subtraction.")
#grab exposure and overscan bbox from clipboard
exposure = clipboard.get(self.policy.getString("inputKeys.exposure"))
fittype = self.policy.getString("parameters.overscanFitType")
amp = cameraGeom.cast_Amp(exposure.getDetector())
overscanBbox = amp.getDiskBiasSec()
dataBbox = amp.getDiskDataSec()
#It just so happens that this is an o.k. place to put the SDQA
#calculation because the ratings requested at the moment can all be
#calculated here. If, for example, an Amp rating an the flat fielded
#amp were requested, it would have to be calculated separately.
ipIsr.calculateSdqaAmpRatings(exposure, overscanBbox, dataBbox)
ipIsr.overscanCorrection(exposure, overscanBbox, fittype)
#TODO optionally trim
#output products
clipboard.put(self.policy.get("outputKeys.overscanCorrectedExposure"), exposure)
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing overscan subtraction.")
#grab exposure and overscan bbox from clipboard
exposure = clipboard.get(self.policy.getString("inputKeys.exposure"))
fittype = self.policy.getString("parameters.overscanFitType")
amp = cameraGeom.cast_Amp(exposure.getDetector())
overscanBbox = amp.getDiskBiasSec()
dataBbox = amp.getDiskDataSec()
#It just so happens that this is an o.k. place to put the SDQA
#calculation because the ratings requested at the moment can all be
#calculated here. If, for example, an Amp rating an the flat fielded
#amp were requested, it would have to be calculated separately.
ipIsr.calculateSdqaAmpRatings(exposure, overscanBbox, dataBbox)
ipIsr.overscanCorrection(exposure, overscanBbox, fittype)
#TODO optionally trim
#output products
clipboard.put(self.policy.get("outputKeys.overscanCorrectedExposure"),
exposure)
def getCcd(exposure, allowRaise=True):
"""Get the Ccd referred to by an exposure
@param exposure Exposure to inspect
@param allowRaise If False, return None if the CCD can't be found rather than raising an exception
@returns Ccd
"""
det = exposure.getDetector()
ccd = cameraGeom.cast_Ccd(det)
if ccd is not None:
return ccd
amp = cameraGeom.cast_Amp(det)
if amp is not None:
det = amp.getParent()
ccd = cameraGeom.cast_Ccd(det)
return ccd
if allowRaise:
raise RuntimeError("Can't find Ccd from detector.")
else:
return None
def trim(self, exposure):
"""Trim overscan out of exposure
@param exposure Exposure to process
"""
assert exposure, "No exposure provided"
mi = exposure.getMaskedImage()
MaskedImage = type(mi)
if pipUtil.detectorIsCcd(exposure):
# Effectively doing CCD assembly since we have all amplifiers
ccd = pipUtil.getCcd(exposure)
miCcd = MaskedImage(ccd.getAllPixels(True).getDimensions())
for amp in ccd:
diskDataSec = amp.getDiskDataSec()
trimDataSec = amp.getElectronicDataSec(True)
miTrim = MaskedImage(mi, diskDataSec, afwImage.LOCAL)
miTrim = MaskedImage(amp.prepareAmpData(miTrim.getImage()),
amp.prepareAmpData(miTrim.getMask()),
amp.prepareAmpData(miTrim.getVariance()))
miAmp = MaskedImage(miCcd, trimDataSec, afwImage.LOCAL)
self.log.log(
self.log.INFO, "Trimming amp %s: %s --> %s" %
(amp.getId(), diskDataSec, trimDataSec))
miAmp <<= miTrim
amp.setTrimmed(True)
exposure.setMaskedImage(miCcd)
else:
# AFW doesn't provide a useful target datasec, so we just make an image that has the useful pixels
amp = cameraGeom.cast_Amp(exposure.getDetector())
diskDataSec = amp.getDiskDataSec()
self.log.log(self.log.INFO,
"Trimming amp %s: %s" % (amp.getId(), diskDataSec))
miTrim = MaskedImage(mi, diskDataSec, afwImage.LOCAL)
amp.setTrimmed(True)
miAmp = MaskedImage(amp.prepareAmpData(miTrim.getImage()),
amp.prepareAmpData(miTrim.getMask()),
amp.prepareAmpData(miTrim.getVariance()))
exposure.setMaskedImage(miAmp)
return
def assertExposure(self, exp, ccd, checkFilter=True):
print "dataId: ", self.dataId
print "ccd: ", ccd
print "width: ", exp.getWidth()
print "height: ", exp.getHeight()
print "detector name: ", exp.getDetector().getName()
print "filter name: ", exp.getFilter().getFilterProperty().getName()
self.assertEqual(exp.getWidth(), self.size[0])
self.assertEqual(exp.getHeight(), self.size[1])
self.assertEqual(exp.getDetector().getName(), "ccd%02d" % ccd)
if checkFilter:
self.assertEqual(exp.getFilter().getFilterProperty().getName(), self.filter)
if display and ccd % 18 == 0:
global frame
frame += 1
ccd = cameraGeom.cast_Ccd(exp.getDetector())
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print ccd.getId(), amp.getId(), amp.getDataSec().toString(), \
amp.getBiasSec().toString(), amp.getElectronicParams().getGain()
cameraGeomUtils.showCcd(ccd, ccdImage=exp, frame=frame)
def main(infile, ccds=None, camera="hsc", cmap="copper", cols=[0,1],
nsig=3.0, percent=False, textcolor='k', out=None):
###########################
# build the camera
policy_file = {
'hsc': os.path.join(os.getenv("OBS_SUBARU_DIR"), "hsc", "hsc_geom.paf"),
'sc' : os.path.join(os.getenv("OBS_SUBARU_DIR"), "suprimecam", "Full_Suprimecam_geom.paf")
}
geomPolicy = afwCGU.getGeomPolicy(policy_file[camera.lower()])
camera = afwCGU.makeCamera(geomPolicy)
###########################
# load the data
data = {}
if infile:
load = numpy.loadtxt(infile)
vals = load[:,cols[1]]
for i in range(len(vals)):
ccd = int(load[i,cols[0]])
if len(cols) == 3:
amp = int(load[i,cols[2]])
else:
amp = 0
if ccd not in data:
data[ccd] = {}
data[ccd][amp] = vals[i]
else:
vals = []
for r in camera:
for c in afwCG.cast_Raft(r):
ccd = afwCG.cast_Ccd(c)
ccdId = ccd.getId().getSerial()
data[ccdId] = {}
val = 1.0
if ccdId > 103:
val = 0.8
for a in ccd:
amp = afwCG.cast_Amp(a)
ampId = amp.getId().getSerial() - 1
data[ccdId][ampId] = val
vals.append(val)
if len(data[ccdId]) == 0:
data[ccdId][0] = val
vals.append(val)
vals = numpy.array(vals)
mean = vals.mean()
med = numpy.median(vals)
std = vals.std()
vmin, vmax = med - nsig*std, med+nsig*std
###########################
# make the plot
fig = figure.Figure(figsize=(7,7))
canvas = FigCanvas(fig)
if infile:
rect = (0.06, 0.12, 0.76, 0.76)
else:
rect = (0.06, 0.06, 0.88, 0.88)
fpa_fig = hscUtil.FpaFigure(fig, camera, rect=rect)
for i_ccd, amplist in data.items():
hide = False
if ccds and (i_ccd not in ccds):
hide = True
ax = fpa_fig.getAxes(i_ccd)
fpa_fig.highlightAmp(i_ccd, 0)
nq = fpa_fig.detectors[i_ccd].getOrientation().getNQuarter()
nx, ny = 4, 8
if nq % 2:
ny, nx = nx, ny
firstAmp = sorted(amplist.keys())[0]
im = numpy.zeros((ny, nx)) + amplist[firstAmp]
print i_ccd
for amp, val in amplist.items():
useVal = val
if hide:
useVal = 0.0
if nq == 0:
im[:,amp] = useVal
if nq == 1 or nq == -3:
im[3-amp,:] = useVal
if nq == 2:
im[:,3-amp] = useVal
if nq == -1 or nq == 3:
im[amp,:] = useVal
im_ax = ax.imshow(im, cmap=cmap, vmax=vmax, vmin=vmin, interpolation='nearest')
fpa_fig.addLabel(i_ccd, [str(i_ccd)], color=textcolor)
#############################
# the colorbar
ylo, yhi = vmin, vmax
if infile:
rect = (0.91, 0.25, 0.02, 0.6)
# real units
cax = fig.add_axes(rect)
cax.get_yaxis().get_major_formatter().set_useOffset(False)
cax.set_ylim([ylo, yhi])
cax.get_xaxis().set_ticks([])
cbar = fig.colorbar(im_ax, cax=cax)
# mirror the values. std or in percent (fractional) if requested
caxp = cax.twinx()
caxp.get_xaxis().set_ticks([])
caxp.get_yaxis().get_major_formatter().set_useOffset(False)
if percent:
caxp.set_ylim([(med-ylo)/(yhi-ylo), (yhi-med)/(yhi-ylo)])
else:
caxp.set_ylim([-nsig*std, nsig*std])
for t in cax.get_yticklabels():
t.set_size('small')
for t in caxp.get_yticklabels():
t.set_size("small")
#################################
# add stats
if infile:
stats = {"Mean":mean, "Med":med, "Std":std, "Max":vals.max(), "Min":vals.min()}
order = ["Mean", "Med", "Std", "Min", "Max"]
i = 0
for k in order:
v = stats[k]
ax.text(0.8, 0.03+0.02*i, "%-10s %.3g"%(k+":",v), fontsize=9,
horizontalalignment='left', verticalalignment='center', transform=fig.transFigure)
i += 1
#################################
# title and write it
date = datetime.datetime.now().strftime("%Y-%m-%d_%H:%M:%S")
title = "File: %s Cols: %s %s" % (infile, ":".join([str(x+1) for x in cols]), date) if infile else ""
fig.suptitle(title)
outfile = out if out else "camview-%s.png" % infile
fig.savefig(outfile)
def run(self, sensorRefList, calibType):
"""Process a calibration frame.
@param sensorRef: sensor-level butler data reference
@return pipe_base Struct containing these fields:
- masterExpList: amp exposures of master calibration products
"""
referenceAmps = sensorRefList[0].subItems(level="channel")
masterExpList = []
dataIdList = []
expmeta = None
for amp in referenceAmps:
if amp.dataId['snap'] == 1:
continue
self.log.info("Amp: Processing %s", amp.dataId)
print "dataid %s" % (amp.dataId)
butler = amp.butlerSubset.butler
ampMIList = afwImage.vectorMaskedImageF()
for sRef in sensorRefList:
self.log.info("Sensor: Processing %s", sRef.dataId)
ampSnapMIList = afwImage.vectorMaskedImageF()
dataId = eval(amp.dataId.__repr__())
dataId['visit'] = sRef.dataId['visit']
for snap in (0, 1):
dataId['snap'] = snap
ampExposure = sRef.butlerSubset.butler.get('raw', dataId)
if expmeta is None:
expmeta = ampExposure.getMetadata()
expfilter = ampExposure.getFilter()
expcalib = ampExposure.getCalib()
ampDetector = cameraGeom.cast_Amp(
ampExposure.getDetector())
ampExposure = self.convertIntToFloat(ampExposure)
ampExpDataView = ampExposure.Factory(
ampExposure, ampDetector.getDiskDataSec())
self.saturationDetection(ampExposure, ampDetector)
self.overscanCorrection(ampExposure, ampDetector)
if calibType in ('flat', 'dark'):
self.biasCorrection(ampExpDataView, amp)
if False:
self.darkCorrection(ampExpDataView, amp)
self.updateVariance(ampExpDataView, ampDetector)
ampSnapMIList.append(ampExpDataView.getMaskedImage())
ampMIList.append(self.combineMIList(ampSnapMIList))
masterFrame = self.combineMIList(ampMIList)
# Fix saturation too???
self.fixDefectsAndSat(masterFrame, ampDetector)
exp = afwImage.ExposureF(masterFrame)
self.copyMetadata(exp, expmeta, calibType)
exp.setDetector(ampDetector)
exp.setWcs(afwImage.Wcs())
exp.setCalib(expcalib)
if calibType is 'flat':
exp.setFilter(expfilter)
if self.config.doWrite and calibType is not 'flat':
print "writing file %s" % dataId
butler.put(exp, calibType, dataId=amp.dataId)
masterExpList.append(exp)
dataIdList.append(amp.dataId)
if self.config.doWrite and calibType is 'flat':
self.normChipAmps(masterExpList)
for exp, dataId in zip(masterExpList, dataIdList):
print "writing flat file %s" % dataId
butler.put(exp, calibType, dataId)
return pipeBase.Struct(masterFrameList=masterExpList, )
def testRaw(self):
"""Test retrieval of raw image"""
frame = 1
for ccdNum, rotated in zip(self.ccdList, self.rotated):
butler = getButler(self.datadir)
raw = butler.get("raw", visit=self.expId, ccd=ccdNum)
ccd = raw.getDetector()
print "Visit: ", self.expId
print "width: ", raw.getWidth()
print "height: ", raw.getHeight()
ccdName = ccd.getId().getName()
print "detector name: ", ccdName
self.assertEqual(raw.getWidth(), self.untrimmedSize[0])
self.assertEqual(raw.getHeight(), self.untrimmedSize[1])
self.assertEqual(raw.getFilter().getFilterProperty().getName(), "g")
self.assertEqual(ccd.getId().getName(), "hsc%03d" % ccdNum)
# CCD size
trimmed = ccd.getAllPixelsNoRotation(True).getDimensions()
self.assertEqual(trimmed.getX(), self.trimmedSize[0])
self.assertEqual(trimmed.getY(), self.trimmedSize[1])
# Size in camera coordinates
camera = ccd.getAllPixels(True).getDimensions()
self.assertEqual(camera.getX(), self.trimmedSize[0] if not rotated else self.trimmedSize[1])
self.assertEqual(camera.getY(), self.trimmedSize[1] if not rotated else self.trimmedSize[0])
for i, amp in enumerate(ccd):
amp = cameraGeom.cast_Amp(amp)
print "amp: %s %i"%(amp.getId(), i)
# Amplifier on CCD
datasec = amp.getAllPixels(True)
self.assertEqual(datasec.getWidth(), self.ampSize[0] if not rotated else self.ampSize[1])
self.assertEqual(datasec.getHeight(), self.ampSize[1] if not rotated else self.ampSize[0])
self.assertEqual(datasec.getMinX(), i*self.ampSize[0] if not rotated else 0)
self.assertEqual(datasec.getMinY(), 0 if not rotated else i*self.ampSize[0])
# Amplifier on disk
datasec = amp.getRawDataBBox()
self.assertEqual(datasec.getWidth(), self.ampSize[0])
self.assertEqual(datasec.getHeight(), self.ampSize[1])
if display:
ds9.mtv(raw, frame=frame, title="Raw %s" % ccdName)
frame += 1
for amp in ccd:
amp = cameraGeom.cast_Amp(amp)
print ccd.getId(), amp.getId(), amp.getDataSec().toString(), \
amp.getBiasSec().toString(), amp.getElectronicParams().getGain()
ccdIm = afwMath.rotateImageBy90(raw.getMaskedImage().getImage(),
ccd.getOrientation().getNQuarter())
cameraGeomUtils.showCcd(ccd, ccdImage=ccdIm, frame=frame)
frame += 1
if assemble:
ccdIm = ca.assembleCcd([raw], ccd, reNorm=False, imageFactory=afwImage.ImageU)
if display:
cameraGeomUtils.showCcd(ccd, ccdImage=ccdIm, frame=frame)
frame += 1
# If you'd like the image in un-rotated coordinates...
rotCcdIm = afwMath.rotateImageBy90(ccdIm.getMaskedImage().getImage(),
-ccd.getOrientation().getNQuarter())
ds9.mtv(rotCcdIm, frame=frame, title="Assembled derotated %s" % ccdName)
frame += 1
def process(self, clipboard):
"""
"""
self.log.log(Log.INFO, "Doing Saturation correction.")
#grab exposure from clipboard
exposure = clipboard.get(self.policy.getString("inputKeys.exposure"))
exposure = ipIsr.convertImageForIsr(exposure)
fwhm = self.policy.getDouble("parameters.defaultFwhm")
amp = cameraGeom.cast_Amp(exposure.getDetector())
dataBbox = amp.getDataSec(True)
x = dataBbox.getMinX()
y = dataBbox.getMinY()
height = dataBbox.getMaxY() - dataBbox.getMinY()
width = dataBbox.getMaxY() - dataBbox.getMinX()
dl = measAlg.DefectListT()
defectList = cameraGeom.cast_Ccd(amp.getParent()).getDefects()
if amp.getId().getIndex()[1] == 1:
for d in defectList:
d1 = measAlg.Defect(d.getBBox())
d1.shift(-x, -y)
bbox = d1.getBBox()
if bbox.getMinX() - 4 > width or bbox.getMaxY() - 4 < 0 or \
height - bbox.getMinY() - 1 > height or height - bbox.getMaxY() - 1 < 0:
pass
else:
nd = measAlg.Defect(
afwGeom.Box2I(
afwGeom.Point2I(bbox.getMinX() + 4,
height - bbox.getMinY() + 1),
bbox.getDimensions()))
dl.append(nd)
else:
for d in defectList:
d1 = measAlg.Defect(d.getBBox())
d1.shift(-x, -y)
bbox = d1.getBBox()
if bbox.getMinX() - 4 > width or bbox.getMaxY() - 4 < 0 or \
bbox.getMinY() - 1 > height or bbox.getMaxY() - 1 < 0:
pass
else:
nd = measAlg.Defect(
afwGeom.Box2I(bbox.getMin() + afwGeom.Extent2I(4, 1),
bbox.getDimensions()))
dl.append(nd)
saturation = amp.getElectronicParams().getSaturationLevel()
ipIsr.maskBadPixelsDef(exposure,
dl,
fwhm,
interpolate=True,
maskName='BAD')
ipIsr.saturationCorrection(exposure,
int(saturation),
fwhm,
growSaturated=False,
interpolate=True)
#ds9.mtv(exposure, frame = 0, title = "my Amp")
#exposure.writeFits("Amp.fits")
#output products
clipboard.put(
self.policy.get("outputKeys.saturationCorrectedExposure"),
exposure)
def run(self, sensorRefList, calibType):
"""Process a calibration frame.
@param sensorRef: sensor-level butler data reference
@return pipe_base Struct containing these fields:
- masterExpList: amp exposures of master calibration products
"""
referenceAmps = sensorRefList[0].subItems(level="channel")
masterExpList = []
dataIdList = []
expmeta = None
for amp in referenceAmps:
if amp.dataId['snap'] == 1:
continue
self.log.log(self.log.INFO, "Amp: Processing %s" % (amp.dataId))
print "dataid %s"%(amp.dataId)
butler = amp.butlerSubset.butler
ampMIList = afwImage.vectorMaskedImageF()
for sRef in sensorRefList:
self.log.log(self.log.INFO, "Sensor: Processing %s" % (sRef.dataId))
ampSnapMIList = afwImage.vectorMaskedImageF()
dataId = eval(amp.dataId.__repr__())
dataId['visit'] = sRef.dataId['visit']
for snap in (0,1):
dataId['snap'] = snap
ampExposure = sRef.butlerSubset.butler.get('raw', dataId)
if expmeta is None:
expmeta = ampExposure.getMetadata()
expfilter = ampExposure.getFilter()
expcalib = ampExposure.getCalib()
ampDetector = cameraGeom.cast_Amp(ampExposure.getDetector())
ampExposure = self.convertIntToFloat(ampExposure)
ampExpDataView = ampExposure.Factory(ampExposure, ampDetector.getDiskDataSec())
self.saturationDetection(ampExposure, ampDetector)
self.overscanCorrection(ampExposure, ampDetector)
if calibType in ('flat', 'dark'):
self.biasCorrection(ampExpDataView, amp)
if False:
self.darkCorrection(ampExpDataView, amp)
self.updateVariance(ampExpDataView, ampDetector)
ampSnapMIList.append(ampExpDataView.getMaskedImage())
ampMIList.append(self.combineMIList(ampSnapMIList))
masterFrame = self.combineMIList(ampMIList)
#Fix saturation too???
self.fixDefectsAndSat(masterFrame, ampDetector)
exp = afwImage.ExposureF(masterFrame)
self.copyMetadata(exp, expmeta, calibType)
exp.setDetector(ampDetector)
exp.setWcs(afwImage.Wcs())
exp.setCalib(expcalib)
if calibType is 'flat':
exp.setFilter(expfilter)
if self.config.doWrite and calibType is not 'flat':
print "writing file %s"%dataId
butler.put(exp, calibType, dataId = amp.dataId)
masterExpList.append(exp)
dataIdList.append(amp.dataId)
if self.config.doWrite and calibType is 'flat':
self.normChipAmps(masterExpList)
for exp, dataId in zip(masterExpList, dataIdList):
print "writing flat file %s"%dataId
butler.put(exp, calibType, dataId)
return pipeBase.Struct(
masterFrameList = masterExpList,
)