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Tickets/dm 10091 Patch up DM-9952 #210

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merged 3 commits into from
Apr 4, 2017
Merged

Tickets/dm 10091 Patch up DM-9952 #210

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6b91775
Catch a few occurrences of hdu==0 which I missed on DM-9952
RobertLuptonTheGood Apr 4, 2017
806b744
The previous code was incorrect, failing to use hdu==INT_MIN
RobertLuptonTheGood Apr 4, 2017
934d455
Use test in pipe_tasks's testProcessCcd.py to fix the hdu handling
RobertLuptonTheGood Apr 4, 2017
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7 changes: 6 additions & 1 deletion python/lsst/afw/math/backgroundList.py
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Original file line number Diff line number Diff line change
Expand Up @@ -152,7 +152,12 @@ def readFits(fileName, hdu=0, flags=0):

self = BackgroundList()

hdu -= 1 # we want to start at 0 (post RFC-304), but are about to increment
INT_MIN = -(1 << 31)
if hdu == INT_MIN:
hdu = -1
else:
hdu -= 1 # we want to start at 0 (post RFC-304), but are about to increment

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Code changes look fine although I don't understand the commit message and its relationship with pipe_tasks's testProcessCcd.py

while True:
hdu += 1

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11 changes: 2 additions & 9 deletions src/formatters/PropertyListFormatter.cc
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Expand Up @@ -77,19 +77,12 @@ void PropertyListFormatter::write(
}

namespace {
// I'd use a unique_ptr, except that PropertyList won't allow me to merge non-shared_ptrs
std::unique_ptr<daf::base::PropertyList>
readMetadataAsUniquePtr(std::string const & fileName, int hdu, bool strip)
{
auto metadata = std::unique_ptr<daf::base::PropertyList>(new lsst::daf::base::PropertyList);
//
// We need a shared_ptr to be able to call PropertyList.combine()
//
auto inheritedMetadata = std::shared_ptr<daf::base::PropertyList>(new daf::base::PropertyList);

fits::Fits fitsfile(fileName, "r", fits::Fits::AUTO_CLOSE | fits::Fits::AUTO_CHECK);
fitsfile.setHdu(hdu);
fitsfile.readMetadata(*inheritedMetadata, strip);

auto inheritedMetadata = fits::readMetadata(fileName, hdu, strip);
metadata->combine(inheritedMetadata);

return metadata;
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2 changes: 1 addition & 1 deletion src/formatters/TanWcsFormatter.cc
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Expand Up @@ -118,7 +118,7 @@ dafBase::Persistable* afwForm::TanWcsFormatter::read(
else if (typeid(*storage) == typeid(dafPersist::FitsStorage)) {
LOGL_DEBUG(_log, "TanWcsFormatter read FitsStorage");
dafPersist::FitsStorage* fits = dynamic_cast<dafPersist::FitsStorage*>(storage.get());
int hdu = additionalData->get<int>("hdu", 0);
int hdu = additionalData->get<int>("hdu", INT_MIN);
dafBase::PropertySet::Ptr md =
afw::fits::readMetadata(fits->getPath(), hdu);
afwImg::TanWcs* ip = new afwImg::TanWcs(md);
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2 changes: 1 addition & 1 deletion src/formatters/WcsFormatter.cc
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Expand Up @@ -120,7 +120,7 @@ dafBase::Persistable* afwForm::WcsFormatter::read(
else if (typeid(*storage) == typeid(dafPersist::FitsStorage)) {
LOGL_DEBUG(_log, "WcsFormatter read FitsStorage");
dafPersist::FitsStorage* fits = dynamic_cast<dafPersist::FitsStorage*>(storage.get());
int hdu = additionalData->get<int>("hdu", 0);
int hdu = additionalData->get<int>("hdu", INT_MIN);
dafBase::PropertySet::Ptr md =
afw::fits::readMetadata(fits->getPath(), hdu);
afwImg::Wcs* ip = new afwImg::Wcs(md);
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4 changes: 2 additions & 2 deletions tests/ramFitsIO.cc
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Expand Up @@ -108,7 +108,7 @@ void test6()

//Read FITS file from disk into an Image
PTR(dafBase::PropertySet) miMetadata(new dafBase::PropertySet);
PTR(ImageF) image(new ImageF(gFilename, 0, miMetadata));
PTR(ImageF) image(new ImageF(gFilename, INT_MIN, miMetadata));

//Write the Image to a RAM FITS file
image->writeFits(string(gFilenameStripped + "_imageOut.fit").c_str());
Expand All @@ -133,7 +133,7 @@ void test7()

//Read FITS file from disk into an Exposure
dafBase::PropertySet::Ptr miMetadata(new dafBase::PropertySet);
ImageF::Ptr image = ImageF::Ptr(new ImageF(gFilename, 0, miMetadata));
ImageF::Ptr image = ImageF::Ptr(new ImageF(gFilename, INT_MIN, miMetadata));
MaskedImageF maskedImage(image);
afwImage::Wcs::Ptr wcsFromFITS = afwImage::makeWcs(miMetadata);
ExposureF exposure(maskedImage, wcsFromFITS);
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6 changes: 3 additions & 3 deletions tests/testImage.py
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Expand Up @@ -588,9 +588,9 @@ def testReadFits(self):
"""Test reading FITS files"""

hdus = {}
hdus["img"] = 2 # an S16 fits HDU
hdus["msk"] = 3 # an U8 fits HDU
hdus["var"] = 4 # an F32 fits HDU
hdus["img"] = 1 # an S16 fits HDU
hdus["msk"] = 2 # an U8 fits HDU
hdus["var"] = 3 # an F32 fits HDU

imgU = afwImage.DecoratedImageU(self.fileForMetadata, hdus["img"]) # read as unsigned short
imgF = afwImage.DecoratedImageF(self.fileForMetadata, hdus["img"]) # read as float
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6 changes: 3 additions & 3 deletions tests/testImageIo1.py
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Expand Up @@ -79,10 +79,10 @@ def testS16(self):
@unittest.skipIf(dataDir is None, "afwdata not setup")
def testF32(self):
"""Test reading F32 image"""
im = afwImage.ImageD(os.path.join(dataDir, "871034p_1_MI.fits"), 4)
im = afwImage.ImageD(os.path.join(dataDir, "871034p_1_MI.fits"), 3)

col, row, val = 32, 1, 39.11672
self.assertAlmostEqual(im.get(col, row), val, 5)
self.assertAlmostEqual(im.get(col, row), val, 4)

@unittest.skipIf(dataDir is None, "afwdata not setup")
def testF64(self):
Expand All @@ -103,7 +103,7 @@ def testWriteReadF64(self):
@unittest.skipIf(dataDir is None, "afwdata not setup")
def testSubimage(self):
"""Test reading a subimage image"""
fileName, hdu = os.path.join(dataDir, "871034p_1_MI.fits"), 4
fileName, hdu = os.path.join(dataDir, "871034p_1_MI.fits"), 3
im = afwImage.ImageF(fileName, hdu)

bbox = afwGeom.Box2I(afwGeom.Point2I(110, 120), afwGeom.Extent2I(20, 15))
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6 changes: 3 additions & 3 deletions tests/testMask.py
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Expand Up @@ -222,21 +222,21 @@ def testSubmasks(self):
@unittest.skipIf(afwdataDir is None, "afwdata not setup")
def testReadFits(self):
nMaskPlanes0 = self.Mask.getNumPlanesUsed()
mask = self.Mask(self.maskFile, 3) # will shift any unrecognised mask planes into unused slots
mask = self.Mask(self.maskFile, hdu=2) # will shift any unrecognised mask planes into unused slots

self.assertMasksEqual(mask, self.expect << nMaskPlanes0)

@unittest.skipIf(afwdataDir is None, "afwdata not setup")
def testReadFitsConform(self):
hdu = 3
hdu = 2
mask = afwImage.MaskU(self.maskFile, hdu, None, afwGeom.Box2I(), afwImage.LOCAL, True)

self.assertMasksEqual(mask, self.expect)

@unittest.skipIf(afwdataDir is None, "afwdata not setup")
def testWriteFits(self):
nMaskPlanes0 = self.Mask.getNumPlanesUsed()
mask = self.Mask(self.maskFile, 3)
mask = self.Mask(self.maskFile, hdu=2)

self.assertMasksEqual(mask, self.expect << nMaskPlanes0)

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4 changes: 2 additions & 2 deletions tests/testMaskedImageIO.py
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Expand Up @@ -143,7 +143,7 @@ def testFitsReadConform(self):
def testFitsReadNoConform2(self):
"""Check that reading a mask doesn't invalidate the plane dictionary"""

testMask = afwImage.MaskU(self.fileName, 3)
testMask = afwImage.MaskU(self.fileName, hdu=2)

mask = self.mi.getMask()
mask |= testMask
Expand All @@ -152,7 +152,7 @@ def testFitsReadNoConform2(self):
def testFitsReadConform2(self):
"""Check that conforming a mask invalidates the plane dictionary"""

hdu, metadata, bbox, conformMasks = 3, None, afwGeom.Box2I(), True
hdu, metadata, bbox, conformMasks = 2, None, afwGeom.Box2I(), True
testMask = afwImage.MaskU(self.fileName,
hdu, metadata, bbox, afwImage.LOCAL, conformMasks)

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