diff --git a/include/pfs/drp/stella/FiberTrace.h b/include/pfs/drp/stella/FiberTrace.h index 23649696a..707e9a55d 100644 --- a/include/pfs/drp/stella/FiberTrace.h +++ b/include/pfs/drp/stella/FiberTrace.h @@ -127,7 +127,7 @@ class FiberTrace { ndarray::Array const& profiles, ndarray::Array const& good, ndarray::Array const& centers, - ndarray::Array const& norm=ndarray::Array() + ndarray::Array const& norm=ndarray::Array() ); private: diff --git a/include/pfs/drp/stella/Spectrum.h b/include/pfs/drp/stella/Spectrum.h index e2083c21c..3e77ea7a4 100644 --- a/include/pfs/drp/stella/Spectrum.h +++ b/include/pfs/drp/stella/Spectrum.h @@ -13,8 +13,8 @@ namespace pfs { namespace drp { namespace stella { */ class Spectrum { public: - using ImageT = double; - using VarianceT = double; + using ImageT = float; + using VarianceT = float; using Mask = lsst::afw::image::Mask; using ImageArray = ndarray::Array; using ConstImageArray = ndarray::Array; diff --git a/include/pfs/drp/stella/SpectrumSet.h b/include/pfs/drp/stella/SpectrumSet.h index a3905e64a..b58221f7d 100644 --- a/include/pfs/drp/stella/SpectrumSet.h +++ b/include/pfs/drp/stella/SpectrumSet.h @@ -20,8 +20,8 @@ class SpectrumSet { using SpectrumPtr = std::shared_ptr; using ConstSpectrumPtr = std::shared_ptr; using Collection = std::vector; - using ImageArray = ndarray::Array; - using CovarianceArray = ndarray::Array; + using ImageArray = ndarray::Array; + using CovarianceArray = ndarray::Array; using MaskArray = ndarray::Array; using WavelengthArray = ndarray::Array; using iterator = Collection::iterator; diff --git a/python/pfs/drp/stella/fiberProfile.py b/python/pfs/drp/stella/fiberProfile.py index 9df34d8ef..4bf4f4d0b 100644 --- a/python/pfs/drp/stella/fiberProfile.py +++ b/python/pfs/drp/stella/fiberProfile.py @@ -27,7 +27,7 @@ class FiberProfile: profiles : array_like of `float`, shape ``(N, M)`` Profiles for each swath, each of width ``M = 2*(radius + 1)*oversample + 1``. - norm : array_like of `float`, optional + norm : array_like of `np.float32`, optional Normalisation for each spectral pixel. """ def __init__(self, radius, oversample, rows, profiles, norm=None): @@ -220,7 +220,8 @@ def makeFiberTraceFromDetectorMap(self, detectorMap, fiberId): """ return FiberTrace.fromProfile(fiberId, detectorMap.bbox.getDimensions(), self.radius, self.oversample, self.rows, self.profiles, ~self.profiles.mask, - detectorMap.getXCenter(fiberId), self.norm) + detectorMap.getXCenter(fiberId), + self.norm.astype(np.float32) if self.norm is not None else None) def makeFiberTrace(self, dimensions, centerFunc, fiberId): """Make a FiberTrace object @@ -244,7 +245,8 @@ def makeFiberTrace(self, dimensions, centerFunc, fiberId): """ rows = np.arange(dimensions.getY(), dtype=float) return FiberTrace.fromProfile(fiberId, dimensions, self.radius, self.oversample, self.rows, - self.profiles, ~self.profiles.mask, centerFunc(rows), self.norm) + self.profiles, ~self.profiles.mask, centerFunc(rows), + self.norm.astype(np.float32) if self.norm is not None else None) def extractSpectrum(self, maskedImage, detectorMap, fiberId): """Extract a single spectrum from an image diff --git a/python/pfs/drp/stella/findLines.py b/python/pfs/drp/stella/findLines.py index 9fb57cda1..1fa4bb377 100644 --- a/python/pfs/drp/stella/findLines.py +++ b/python/pfs/drp/stella/findLines.py @@ -125,7 +125,7 @@ def convolve(self, spectrum, continuum=None): size = 2*halfSize + 1 xx = np.arange(size, dtype=float) - halfSize sigma = self.config.width - kernel = np.exp(-0.5*xx**2/sigma**2)/sigma/np.sqrt(2.0*np.pi) + kernel = (np.exp(-0.5*xx**2/sigma**2)/sigma/np.sqrt(2.0*np.pi)).astype(spectrum.flux.dtype) flux = np.convolve(spectrum.normFlux if continuum is None else spectrum.normFlux - continuum, kernel, mode="same") diff --git a/python/pfs/drp/stella/fitContinuum.py b/python/pfs/drp/stella/fitContinuum.py index d8fa58565..bdf5e4948 100644 --- a/python/pfs/drp/stella/fitContinuum.py +++ b/python/pfs/drp/stella/fitContinuum.py @@ -141,13 +141,13 @@ def _fitContinuumImpl(self, values, good): fit : `numpy.ndarray`, floating-point Fit array. """ - indices = np.arange(len(values), dtype=float) + indices = np.arange(len(values), dtype=values.dtype) knots, binned = binData(indices, values, good, self.config.numKnots) use = np.isfinite(knots) & np.isfinite(binned) if not np.any(use): raise FitContinuumError("No finite knots when fitting continuum") interp = makeInterpolate(knots[use], binned[use], self.fitType) - fit = np.array(interp.interpolate(indices)) + fit = np.array(interp.interpolate(indices)).astype(values.dtype) if lsstDebug.Info(__name__).plot: import matplotlib.pyplot as plt @@ -285,4 +285,4 @@ def binData(xx, yy, good, numBins): select = good[low:high] xBinned[ii] = np.median(xx[low:high][select]) if np.any(select) else np.nan yBinned[ii] = np.median(yy[low:high][select]) if np.any(select) else np.nan - return xBinned, yBinned + return xBinned.astype(xx.dtype), yBinned.astype(yy.dtype) diff --git a/python/pfs/drp/stella/fitLine.cc b/python/pfs/drp/stella/fitLine.cc index df08a6f13..bfdb36486 100644 --- a/python/pfs/drp/stella/fitLine.cc +++ b/python/pfs/drp/stella/fitLine.cc @@ -36,9 +36,10 @@ PYBIND11_PLUGIN(fitLine) { lsst::utils::python::addOutputOp(cls, "__repr__"); mod.def("fitLine", - py::overload_cast const&, + py::overload_cast const&, ndarray::Array const&, - float, float, lsst::afw::image::MaskPixel, std::size_t>(&fitLine), + float, float, lsst::afw::image::MaskPixel, + std::size_t>(&fitLine), "flux"_a, "mask"_a, "peakPosition"_a, "rmsSize"_a, "badBitMask"_a, "fittingHalfSize"_a=0); diff --git a/python/pfs/drp/stella/mergeArms.py b/python/pfs/drp/stella/mergeArms.py index 26861dddd..67ab8ea5b 100644 --- a/python/pfs/drp/stella/mergeArms.py +++ b/python/pfs/drp/stella/mergeArms.py @@ -328,7 +328,7 @@ def normalizeSpectra(self, spectra): assert all(np.all(ss.fiberId == fiberId) for ss in spectra) # Consistent fibers # Collect normalisations from each arm, interpolated to common wavelength sampling - norm = np.zeros((fiberId.size, wavelength.size)) + norm = np.zeros((fiberId.size, wavelength.size), dtype=np.float32) for ss in spectra: badBitmask = ss.flags.get(*self.config.mask) for ii in range(len(ss)): diff --git a/src/FiberTrace.cc b/src/FiberTrace.cc index e1fd62c17..ba2fca83e 100644 --- a/src/FiberTrace.cc +++ b/src/FiberTrace.cc @@ -82,7 +82,7 @@ FiberTrace FiberTrace::fromP ndarray::Array const& profiles, ndarray::Array const& good, ndarray::Array const& centers, - ndarray::Array const& norm + ndarray::Array const& norm ) { int const width = dims.getX(); std::size_t const height = dims.getY(); diff --git a/tests/test_PfsArm.py b/tests/test_PfsArm.py index a1bf0b586..3146423aa 100644 --- a/tests/test_PfsArm.py +++ b/tests/test_PfsArm.py @@ -30,11 +30,11 @@ def setUp(self): self.identity = Identity(self.visit, self.arm, self.spectrograph, self.pfsDesignId) self.fiberId = self.synthConfig.fiberId self.wavelength = np.vstack([np.linspace(600, 900, self.synthConfig.height)]*num) - self.flux = self.rng.uniform(size=shape) - self.mask = self.rng.uniform(high=2**31, size=shape).astype(np.int32) - self.sky = self.rng.uniform(size=shape) - self.norm = self.rng.uniform(size=shape) - self.covar = self.rng.uniform(size=(num, 3, self.synthConfig.height)) + self.flux = self.rng.uniform(size=shape).astype(np.float32) + self.mask = self.rng.uniform(high=2**31, size=shape).astype(np.uint32) + self.sky = self.rng.uniform(size=shape).astype(np.float32) + self.norm = self.rng.uniform(size=shape).astype(np.float32) + self.covar = self.rng.uniform(size=(num, 3, self.synthConfig.height)).astype(np.float32) self.flags = MaskHelper() self.metadata = dict(FOO=12345, BAR=0.9876) # FITS keywords get capitalised @@ -48,9 +48,9 @@ def makeSpectra(self): def assertSpectra(self, spectra): """Check that the spectra match what's expected""" for name in ("visit", "arm", "spectrograph", "pfsDesignId"): - self.assertEqual(getattr(spectra.identity, name), getattr(self, name)) + self.assertEqual(getattr(spectra.identity, name), getattr(self, name), msg=name) for name in ("fiberId", "wavelength", "flux", "mask", "sky", "norm", "covar"): - self.assertFloatsEqual(getattr(spectra, name), getattr(self, name)) + self.assertFloatsEqual(getattr(spectra, name), getattr(self, name), msg=name) self.assertDictEqual(spectra.flags.flags, self.flags.flags) self.assertDictEqual({**self.metadata, **spectra.metadata}, spectra.metadata) diff --git a/tests/test_Spectrum.py b/tests/test_Spectrum.py index de7281b63..ed5417d26 100644 --- a/tests/test_Spectrum.py +++ b/tests/test_Spectrum.py @@ -23,12 +23,12 @@ def setUp(self): # Spectrum self.length = 123 self.fiberId = 456 - self.image = self.rng.uniform(size=self.length).astype(float) + self.image = self.rng.uniform(size=self.length).astype(np.float32) self.mask = lsst.afw.image.Mask(self.length, 1) self.mask.array[:] = self.rng.randint(0, 2**30, self.length).astype(np.int32) - self.background = self.rng.uniform(size=self.length).astype(float) - self.norm = self.rng.uniform(size=self.length).astype(float) - self.covariance = self.rng.uniform(size=(3, self.length)).astype(float) + self.background = self.rng.uniform(size=self.length).astype(np.float32) + self.norm = self.rng.uniform(size=self.length).astype(np.float32) + self.covariance = self.rng.uniform(size=(3, self.length)).astype(np.float32) self.wavelengthArray = np.arange(1, self.length + 1, dtype=float) def makeSpectrum(self): @@ -145,7 +145,7 @@ def testBasics(self): # Set the variance and ensure it changes the covariance spectrum.covariance[:] = self.covariance self.assertFloatsEqual(spectrum.covariance, self.covariance) - variance = self.rng.uniform(size=self.length) + variance = self.rng.uniform(size=self.length).astype(np.float32) spectrum.variance = variance self.covariance[0] = variance self.assertFloatsEqual(spectrum.covariance, self.covariance) diff --git a/tests/test_SpectrumSet.py b/tests/test_SpectrumSet.py index 84ecbddbe..0c2154ec5 100644 --- a/tests/test_SpectrumSet.py +++ b/tests/test_SpectrumSet.py @@ -21,12 +21,12 @@ def setUp(self): # Spectrum self.length = 123 self.fiberId = 456 - self.image = self.rng.uniform(size=self.length).astype(float) + self.image = self.rng.uniform(size=self.length).astype(np.float32) self.mask = lsst.afw.image.Mask(self.length, 1) self.mask.array[:] = self.rng.randint(0, 2**30, self.length).astype(np.int32) - self.background = self.rng.uniform(size=self.length).astype(float) - self.norm = self.rng.uniform(size=self.length).astype(float) - self.covariance = self.rng.uniform(size=(3, self.length)).astype(float) + self.background = self.rng.uniform(size=self.length).astype(np.float32) + self.norm = self.rng.uniform(size=self.length).astype(np.float32) + self.covariance = self.rng.uniform(size=(3, self.length)).astype(np.float32) self.wavelengthArray = np.arange(1, self.length + 1, dtype=float) def makeSpectrum(self): diff --git a/tests/test_extractSpectra.py b/tests/test_extractSpectra.py index aaa10f46e..0ad1c4506 100644 --- a/tests/test_extractSpectra.py +++ b/tests/test_extractSpectra.py @@ -37,7 +37,7 @@ def setUp(self): lsst.afw.image.makeExposure(self.image), detectorMap=self.detMap ).profiles for fiberId in self.fiberProfiles: - self.fiberProfiles[fiberId].norm = np.full(self.synthConfig.height, self.flux, dtype=float) + self.fiberProfiles[fiberId].norm = np.full(self.synthConfig.height, self.flux, dtype=np.float32) self.fiberTraces = self.fiberProfiles.makeFiberTracesFromDetectorMap(self.detMap) self.assertEqual(len(self.fiberTraces), self.synthConfig.numFibers) @@ -78,7 +78,7 @@ def assertSpectra(self, spectra, flux=None, mask=None): expectMask = 0 bbox = ft.trace.getBBox() - expectNorm = np.zeros(self.synthConfig.height, dtype=float) + expectNorm = np.zeros(self.synthConfig.height, dtype=np.float32) expectNorm[bbox.getMinY():bbox.getMaxY() + 1] = ft.trace.image.array.sum(axis=1) self.assertEqual(ss.fiberId, ft.fiberId) @@ -127,7 +127,7 @@ def testUndersizedFiberTrace(self): newTrace = type(trace)(trace.trace.Factory(trace.trace, newBox), trace.fiberId) self.fiberTraces[index] = newTrace spectra = self.fiberTraces.extractSpectra(self.image) - expectFlux = np.zeros(self.synthConfig.height, dtype=float) + expectFlux = np.zeros(self.synthConfig.height, dtype=np.float32) expectFlux[middle:] = self.flux expectMask = np.zeros(self.synthConfig.height, dtype=np.int32) expectMask[:middle] = trace.trace.mask.getPlaneBitMask("NO_DATA") @@ -138,7 +138,7 @@ def testUndersizedFiberTrace(self): newTrace = type(trace)(trace.trace.Factory(trace.trace, newBox), trace.fiberId) self.fiberTraces[index] = newTrace spectra = self.fiberTraces.extractSpectra(self.image) - expectFlux = np.zeros(self.synthConfig.height, dtype=float) + expectFlux = np.zeros(self.synthConfig.height, dtype=np.float32) expectFlux[:middle] = self.flux expectMask = np.zeros(self.synthConfig.height, dtype=np.int32) expectMask[middle:] = trace.trace.mask.getPlaneBitMask("NO_DATA") @@ -155,7 +155,7 @@ def testSingular(self): index = self.synthConfig.numFibers//2 row = self.synthConfig.height//2 fiberId = self.synthConfig.fiberId[index] - expectFlux = np.full(self.synthConfig.height, self.flux, dtype=float) + expectFlux = np.full(self.synthConfig.height, self.flux, dtype=np.float32) expectMask = np.zeros(self.synthConfig.height, dtype=np.int32) expectFlux[row] = 0.0 expectMask[row] = self.image.mask.getPlaneBitMask(["BAD_FIBERTRACE", "NO_DATA"]) diff --git a/tests/test_fitLine.py b/tests/test_fitLine.py index 1c71f5878..8e8499aef 100644 --- a/tests/test_fitLine.py +++ b/tests/test_fitLine.py @@ -61,7 +61,7 @@ def makeSpectrum(length, center, amplitude, rmsSize, bgConst=0.0, bgSlope=0.0): return spectrum -class FindLinesTestCase(lsst.utils.tests.TestCase): +class FitLinesTestCase(lsst.utils.tests.TestCase): def setUp(self): self.length = 256 self.center = 123.45 diff --git a/tests/test_profileNorm.py b/tests/test_profileNorm.py index a3707c585..3d5ab2cba 100644 --- a/tests/test_profileNorm.py +++ b/tests/test_profileNorm.py @@ -59,7 +59,7 @@ def testProfileNorm(self): newSpectra = traces.extractSpectra(image) for new, old in zip(newSpectra, spectra): self.assertFloatsAlmostEqual(new.norm, old.normFlux, rtol=1.0e-7) - self.assertFloatsAlmostEqual(new.normFlux, 1.0, atol=1.0e-7) + self.assertFloatsAlmostEqual(new.normFlux, 1.0, atol=1.0e-6) class TestMemory(lsst.utils.tests.MemoryTestCase):