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Tickets/DM-4820 Improvement of raw data handling in DecamMapper #14

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Jan 16, 2016
Merged

Tickets/DM-4820 Improvement of raw data handling in DecamMapper #14

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eee5b2c
DecamMapper: Correct metadata copying of raw and calibration data
Dec 23, 2015
e61bf68
Improve the conversion of defects
Jan 13, 2016
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25 changes: 11 additions & 14 deletions python/lsst/obs/decam/decamMapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,9 +178,8 @@ def std_raw(self, item, dataId):
"""Standardize a raw dataset by converting it to an Exposure.

Raw images are MEF files with one HDU for each detector.
Some useful header keywords, such as EXPTIME and MJD-OBS,
exist only in the zeroth extensionr. Here information in
the zeroth header are copied to metadata.
Header keywords EXPTIME and MJD-OBS exist only in the zeroth
extension and are copied to metadata.

@param item: The image read by the butler
@param dataId: Data identifier
Expand All @@ -191,8 +190,8 @@ def std_raw(self, item, dataId):
rawPath = self.map_raw(dataId).getLocations()[0]
headerPath = re.sub(r'[\[](\d+)[\]]$', "[0]", rawPath)
md0 = afwImage.readMetadata(headerPath)
for kw in md0.paramNames():
if kw not in md.paramNames():
for kw in ('EXPTIME', 'MJD-OBS'):
if kw in md0.paramNames() and kw not in md.paramNames():
md.add(kw, md0.get(kw))
return self._standardizeExposure(self.exposures['raw'], exp, dataId,
trimmed=False)
Expand All @@ -216,8 +215,9 @@ def _standardizeMasterCal(self, datasetType, item, dataId, setFilter=False):
masterCalPath = masterCalMap(dataId).getLocations()[0]
headerPath = re.sub(r'[\[](\d+)[\]]$', "[0]", masterCalPath)
md0 = afwImage.readMetadata(headerPath)
for kw in md0.paramNames():
if kw not in md.paramNames():
for kw in ('CTYPE1', 'CTYPE2', 'CRVAL1', 'CRVAL2', 'CUNIT1', 'CUNIT2',
'CD1_1', 'CD1_2', 'CD2_1', 'CD2_2'):
if kw in md0.paramNames() and kw not in md.paramNames():
md.add(kw, md0.get(kw))
wcs = afwImage.makeWcs(md, True)
exp = afwImage.makeExposure(mi, wcs)
Expand Down Expand Up @@ -257,13 +257,10 @@ def bypass_defects(self, datasetType, pythonType, butlerLocation, dataId):
"""
bpmFitsPath = butlerLocation.locationList[0]
bpmImg = afwImage.ImageU(bpmFitsPath)
bpmArr = bpmImg.getArray()
idxBad = np.nonzero(bpmArr)
workImg = afwImage.ImageU(bpmImg.getDimensions())
workImg.getArray()[idxBad] = 1
ds = afwDetection.FootprintSet(workImg, afwDetection.Threshold(0.5))
fpList = ds.getFootprints()
return isr.defectListFromFootprintList(fpList, growFootprints=0)
idxBad = np.nonzero(bpmImg.getArray())
mim = afwImage.MaskedImageU(bpmImg.getDimensions())
mim.getMask().getArray()[idxBad] |= mim.getMask().getPlaneBitMask("BAD")
return isr.getDefectListFromMask(mim, "BAD", growFootprints=0)

def std_defects(self, item, dataId):
"""Return the defect list as it is.
Expand Down
12 changes: 12 additions & 0 deletions tests/getRaw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ def setUp(self):
self.size = (2160, 4146)
self.dataId = {'visit': 229388, 'ccdnum': 1}
self.filter = "z"
self.exptime = 200.0

def tearDown(self):
del self.butler
Expand All @@ -69,6 +70,14 @@ def testRaw(self):
self.assertEqual(exp.getHeight(), self.size[1])
self.assertEqual(exp.getDetector().getId(), self.dataId["ccdnum"])
self.assertEqual(exp.getFilter().getFilterProperty().getName(), self.filter)
self.assertTrue(exp.hasWcs())

# Metadata which should have been copied from zeroth extension.
self.assertIn("MJD-OBS", exp.getMetadata().paramNames())
self.assertEqual(exp.getCalib().getExptime(), self.exptime)

# Example of metadata which should *not* have been copied from zeroth extension.
self.assertNotIn("PROPOSER", exp.getMetadata().paramNames())

def testRawMetadata(self):
"""Test retrieval of metadata"""
Expand All @@ -84,6 +93,7 @@ def testBias(self):
print("dataId: %s" % self.dataId)
print("detector id: %s" % exp.getDetector().getId())
self.assertEqual(exp.getDetector().getId(), self.dataId["ccdnum"])
self.assertTrue(exp.hasWcs())

def testFlat(self):
"""Test retrieval of flat image"""
Expand All @@ -93,6 +103,7 @@ def testFlat(self):
print("filter: %s" % self.filter)
self.assertEqual(exp.getDetector().getId(), self.dataId["ccdnum"])
self.assertEqual(exp.getFilter().getFilterProperty().getName(), self.filter)
self.assertTrue(exp.hasWcs())

def testFringe(self):
"""Test retrieval of fringe image"""
Expand All @@ -106,6 +117,7 @@ def testFringe(self):
def testDefect(self):
"""Test retrieval of defect list"""
defectList = self.butler.get("defects", self.dataId)
self.assertEqual(len(defectList), 9)
for d in defectList:
self.assertIsInstance(d, afwImage.DefectBase)

Expand Down