Merge pull request #303 from lsst/tickets/DM-20566-pipe_tasks

DM-20566: Replace afwGeom with geom where appropriate

examples/runRepair.py

@@ -25,7 +25,7 @@
 import sys
 
 import lsst.afw.image as afwImage
-import lsst.afw.geom as afwGeom
+import lsst.geom as geom
 import lsst.meas.algorithms as measAlg
 from lsst.pipe.tasks.repair import RepairTask
 
@@ -65,12 +65,12 @@ def addDefects(exp, nBadCols=10):
     for xi in numpy.random.randint(0, xsize, nBadCols):
         yi = numpy.random.randint(0, ysize)
         xi, yi = int(xi), int(yi)
-        bbox = afwGeom.Box2I(afwGeom.PointI(xi, 0), afwGeom.ExtentI(1, yi+1))
+        bbox = geom.Box2I(geom.PointI(xi, 0), geom.ExtentI(1, yi+1))
         subIm = afwImage.ImageF(img, bbox)
         subIm.set(1e7)
         defectList.append(bbox)
     # set a 15 pixel box of defects at the upper left corner to demonstrate fallbackValue
-    bbox = afwGeom.Box2I(afwGeom.PointI(0, ysize-15), afwGeom.ExtentI(15, 15))
+    bbox = geom.Box2I(geom.PointI(0, ysize-15), geom.ExtentI(15, 15))
     subIm = afwImage.ImageF(img, bbox)
     subIm.set(1e7)
     defectList.append(bbox)

python/lsst/pipe/tasks/assembleCoadd.py

@@ -24,6 +24,7 @@
 import warnings
 import lsst.pex.config as pexConfig
 import lsst.pex.exceptions as pexExceptions
+import lsst.geom as geom
 import lsst.afw.geom as afwGeom
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
@@ -789,7 +790,7 @@ def run(self, skyInfo, tempExpRefList, imageScalerList, weightList,
         self.assembleMetadata(coaddExposure, tempExpRefList, weightList)
         coaddMaskedImage = coaddExposure.getMaskedImage()
         subregionSizeArr = self.config.subregionSize
-        subregionSize = afwGeom.Extent2I(subregionSizeArr[0], subregionSizeArr[1])
+        subregionSize = geom.Extent2I(subregionSizeArr[0], subregionSizeArr[1])
         # if nImage is requested, create a zero one which can be passed to assembleSubregion
         if self.config.doNImage:
             nImage = afwImage.ImageU(skyInfo.bbox)
@@ -829,8 +830,8 @@ def assembleMetadata(self, coaddExposure, tempExpRefList, weightList):
         # (and we need more than just the PropertySet that contains the header), which is not possible
         # with the current butler (see #2777).
         tempExpList = [tempExpRef.get(tempExpName + "_sub",
-                                      bbox=afwGeom.Box2I(coaddExposure.getBBox().getMin(),
-                                                         afwGeom.Extent2I(1, 1)), immediate=True)
+                                      bbox=geom.Box2I(coaddExposure.getBBox().getMin(),
+                                                      geom.Extent2I(1, 1)), immediate=True)
                        for tempExpRef in tempExpRefList]
         numCcds = sum(len(tempExp.getInfo().getCoaddInputs().ccds) for tempExp in tempExpList)
 
@@ -882,7 +883,7 @@ def assembleSubregion(self, coaddExposure, bbox, tempExpRefList, imageScalerList
         ----------
         coaddExposure : `lsst.afw.image.Exposure`
             The target exposure for the coadd.
-        bbox : `lsst.afw.geom.Box`
+        bbox : `lsst.geom.Box`
             Sub-region to coadd.
         tempExpRefList : `list`
             List of data reference to tempExp.
@@ -1031,7 +1032,7 @@ def shrinkValidPolygons(self, coaddInputs):
             if polyOrig:
                 validPolygon = polyOrig.intersectionSingle(validPolyBBox)
             else:
-                validPolygon = afwGeom.polygon.Polygon(afwGeom.Box2D(validPolyBBox))
+                validPolygon = afwGeom.polygon.Polygon(geom.Box2D(validPolyBBox))
             ccd.setValidPolygon(validPolygon)
 
     def readBrightObjectMasks(self, dataRef):
@@ -1078,17 +1079,17 @@ def setBrightObjectMasks(self, exposure, dataId, brightObjectMasks):
         plateScale = wcs.getPixelScale().asArcseconds()
 
         for rec in brightObjectMasks:
-            center = afwGeom.PointI(wcs.skyToPixel(rec.getCoord()))
+            center = geom.PointI(wcs.skyToPixel(rec.getCoord()))
             if rec["type"] == "box":
                 assert rec["angle"] == 0.0, ("Angle != 0 for mask object %s" % rec["id"])
                 width = rec["width"].asArcseconds()/plateScale    # convert to pixels
                 height = rec["height"].asArcseconds()/plateScale  # convert to pixels
 
-                halfSize = afwGeom.ExtentI(0.5*width, 0.5*height)
-                bbox = afwGeom.Box2I(center - halfSize, center + halfSize)
+                halfSize = geom.ExtentI(0.5*width, 0.5*height)
+                bbox = geom.Box2I(center - halfSize, center + halfSize)
 
-                bbox = afwGeom.BoxI(afwGeom.PointI(int(center[0] - 0.5*width), int(center[1] - 0.5*height)),
-                                    afwGeom.PointI(int(center[0] + 0.5*width), int(center[1] + 0.5*height)))
+                bbox = geom.BoxI(geom.PointI(int(center[0] - 0.5*width), int(center[1] - 0.5*height)),
+                                 geom.PointI(int(center[0] + 0.5*width), int(center[1] + 0.5*height)))
                 spans = afwGeom.SpanSet(bbox)
             elif rec["type"] == "circle":
                 radius = int(rec["radius"].asArcseconds()/plateScale)   # convert to pixels
@@ -1138,14 +1139,14 @@ def _subBBoxIter(bbox, subregionSize):
 
         Parameters
         ----------
-        bbox : `lsst.afw.geom.Box2I`
+        bbox : `lsst.geom.Box2I`
             Bounding box over which to iterate.
-        subregionSize: `lsst.afw.geom.Extent2I`
+        subregionSize: `lsst.geom.Extent2I`
             Size of sub-bboxes.
 
         Yields
         ------
-        subBBox : `lsst.afw.geom.Box2I`
+        subBBox : `lsst.geom.Box2I`
             Next sub-bounding box of size ``subregionSize`` or smaller; each ``subBBox``
             is contained within ``bbox``, so it may be smaller than ``subregionSize`` at
             the edges of ``bbox``, but it will never be empty.
@@ -1157,7 +1158,7 @@ def _subBBoxIter(bbox, subregionSize):
 
         for rowShift in range(0, bbox.getHeight(), subregionSize[1]):
             for colShift in range(0, bbox.getWidth(), subregionSize[0]):
-                subBBox = afwGeom.Box2I(bbox.getMin() + afwGeom.Extent2I(colShift, rowShift), subregionSize)
+                subBBox = geom.Box2I(bbox.getMin() + geom.Extent2I(colShift, rowShift), subregionSize)
                 subBBox.clip(bbox)
                 if subBBox.isEmpty():
                     raise RuntimeError("Bug: empty bbox! bbox=%s, subregionSize=%s, "
@@ -1683,7 +1684,7 @@ def detectClipBig(self, clipList, clipFootprints, clipIndices, detectionFootprin
             Mask value of clipped pixels.
         maskDetValue
             Mask value of detected pixels.
-        coaddBBox : `lsst.afw.geom.Box`
+        coaddBBox : `lsst.geom.Box`
             BBox of the coadd and warps.
 
         Returns

python/lsst/pipe/tasks/coaddBase.py

@@ -20,6 +20,7 @@
 # see <http://www.lsstcorp.org/LegalNotices/>.
 #
 import lsst.pex.config as pexConfig
+import lsst.geom as geom
 import lsst.afw.geom as afwGeom
 import lsst.afw.image as afwImage
 import lsst.pipe.base as pipeBase
@@ -114,7 +115,7 @@ def selectExposures(self, patchRef, skyInfo=None, selectDataList=[]):
         """!
         @brief Select exposures to coadd
 
-        Get the corners of the bbox supplied in skyInfo using @ref afwGeom.Box2D and convert the pixel
+        Get the corners of the bbox supplied in skyInfo using @ref geom.Box2D and convert the pixel
         positions of the bbox corners to sky coordinates using @ref skyInfo.wcs.pixelToSky. Use the
         @ref WcsSelectImagesTask_ "WcsSelectImagesTask" to select exposures that lie inside the patch
         indicated by the dataRef.
@@ -126,7 +127,7 @@ def selectExposures(self, patchRef, skyInfo=None, selectDataList=[]):
         """
         if skyInfo is None:
             skyInfo = self.getSkyInfo(patchRef)
-        cornerPosList = afwGeom.Box2D(skyInfo.bbox).getCorners()
+        cornerPosList = geom.Box2D(skyInfo.bbox).getCorners()
         coordList = [skyInfo.wcs.pixelToSky(pos) for pos in cornerPosList]
         return self.select.runDataRef(patchRef, coordList, selectDataList=selectDataList).dataRefList
 
@@ -142,7 +143,7 @@ def getSkyInfo(self, patchRef):
         - tractInfo: information for chosen tract of sky map
         - patchInfo: information about chosen patch of tract
         - wcs: WCS of tract
-        - bbox: outer bbox of patch, as an afwGeom Box2I
+        - bbox: outer bbox of patch, as an geom Box2I
         """
         return getSkyInfo(coaddName=self.config.coaddName, patchRef=patchRef)
 
@@ -240,7 +241,7 @@ def getSkyInfo(coaddName, patchRef):
     - tractInfo: information for chosen tract of sky map
     - patchInfo: information about chosen patch of tract
     - wcs: WCS of tract
-    - bbox: outer bbox of patch, as an afwGeom Box2I
+    - bbox: outer bbox of patch, as an geom Box2I
     """
     skyMap = patchRef.get(coaddName + "Coadd_skyMap")
     return makeSkyInfo(skyMap, patchRef.dataId["tract"], patchRef.dataId["patch"])

python/lsst/pipe/tasks/dcrAssembleCoadd.py

@@ -23,7 +23,7 @@
 from math import ceil
 import numpy as np
 from scipy import ndimage
-import lsst.afw.geom as afwGeom
+import lsst.geom as geom
 import lsst.afw.image as afwImage
 import lsst.afw.table as afwTable
 import lsst.coadd.utils as coaddUtils
@@ -481,7 +481,7 @@ def run(self, skyInfo, warpRefList, imageScalerList, weightList,
         else:
             dcrNImages = None
 
-        subregionSize = afwGeom.Extent2I(*self.config.subregionSize)
+        subregionSize = geom.Extent2I(*self.config.subregionSize)
         nSubregions = (ceil(skyInfo.bbox.getHeight()/subregionSize[1]) *
                        ceil(skyInfo.bbox.getWidth()/subregionSize[0]))
         subIter = 0
@@ -490,7 +490,7 @@ def run(self, skyInfo, warpRefList, imageScalerList, weightList,
             subIter += 1
             self.log.info("Computing coadd over patch %s subregion %s of %s: %s",
                           skyInfo.patchInfo.getIndex(), subIter, nSubregions, subBBox)
-            dcrBBox = afwGeom.Box2I(subBBox)
+            dcrBBox = geom.Box2I(subBBox)
             dcrBBox.grow(self.bufferSize)
             dcrBBox.clip(dcrModels.bbox)
             modelWeights = self.calculateModelWeights(dcrModels, dcrBBox)
@@ -566,7 +566,7 @@ def calculateNImage(self, dcrModels, bbox, warpRefList, spanSetMaskList, statsCt
         ----------
         dcrModels : `lsst.pipe.tasks.DcrModel`
             Best fit model of the true sky after correcting chromatic effects.
-        bbox : `lsst.afw.geom.box.Box2I`
+        bbox : `lsst.geom.box.Box2I`
             Bounding box of the patch to coadd.
         warpRefList : `list` of `lsst.daf.persistence.ButlerDataRef`
             The data references to the input warped exposures.
@@ -637,9 +637,9 @@ def dcrAssembleSubregion(self, dcrModels, subExposures, bbox, dcrBBox, warpRefLi
             Best fit model of the true sky after correcting chromatic effects.
         subExposures : `dict` of `lsst.afw.image.ExposureF`
             The pre-loaded exposures for the current subregion.
-        bbox : `lsst.afw.geom.box.Box2I`
+        bbox : `lsst.geom.box.Box2I`
             Bounding box of the subregion to coadd.
-        dcrBBox : `lsst.afw.geom.box.Box2I`
+        dcrBBox : `lsst.geom.box.Box2I`
             Sub-region of the coadd which includes a buffer to allow for DCR.
         warpRefList : `list` of `lsst.daf.persistence.ButlerDataRef`
             The data references to the input warped exposures.
@@ -726,7 +726,7 @@ def newModelFromResidual(self, dcrModels, residualGeneratorList, dcrBBox, statsC
             Current model of the true sky after correcting chromatic effects.
         residualGeneratorList : `generator` of `numpy.ndarray`
             The residual image for the next subfilter, shifted for DCR.
-        dcrBBox : `lsst.afw.geom.box.Box2I`
+        dcrBBox : `lsst.geom.box.Box2I`
             Sub-region of the coadd which includes a buffer to allow for DCR.
         statsCtrl : `lsst.afw.math.StatisticsControl`
             Statistics control object for coadd
@@ -780,7 +780,7 @@ def calculateConvergence(self, dcrModels, subExposures, bbox, warpRefList, weigh
             Best fit model of the true sky after correcting chromatic effects.
         subExposures : `dict` of `lsst.afw.image.ExposureF`
             The pre-loaded exposures for the current subregion.
-        bbox : `lsst.afw.geom.box.Box2I`
+        bbox : `lsst.geom.box.Box2I`
             Sub-region to coadd
         warpRefList : `list` of `lsst.daf.persistence.ButlerDataRef`
             The data references to the input warped exposures.
@@ -1016,7 +1016,7 @@ def calculateModelWeights(self, dcrModels, dcrBBox):
         ----------
         dcrModels : `lsst.pipe.tasks.DcrModel`
             Best fit model of the true sky after correcting chromatic effects.
-        dcrBBox : `lsst.afw.geom.box.Box2I`
+        dcrBBox : `lsst.geom.box.Box2I`
             Sub-region of the coadd which includes a buffer to allow for DCR.
 
         Returns
@@ -1067,7 +1067,7 @@ def loadSubExposures(self, bbox, statsCtrl, warpRefList, imageScalerList, spanSe
 
         Parameters
         ----------
-        bbox : `lsst.afw.geom.box.Box2I`
+        bbox : `lsst.geom.box.Box2I`
             Sub-region to coadd
         statsCtrl : `lsst.afw.math.StatisticsControl`
             Statistics control object for coadd

python/lsst/pipe/tasks/imageDifference.py

@@ -26,7 +26,7 @@
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
 import lsst.daf.base as dafBase
-import lsst.afw.geom as afwGeom
+import lsst.geom as geom
 import lsst.afw.math as afwMath
 import lsst.afw.table as afwTable
 from lsst.meas.astrom import AstrometryConfig, AstrometryTask
@@ -426,7 +426,7 @@ def runDataRef(self, sensorRef, templateIdList=None):
                         # match exposure sources to template sources
                         mc = afwTable.MatchControl()
                         mc.findOnlyClosest = False
-                        matches = afwTable.matchRaDec(templateSources, selectSources, 1.0*afwGeom.arcseconds,
+                        matches = afwTable.matchRaDec(templateSources, selectSources, 1.0*geom.arcseconds,
                                                       mc)
                     else:
                         raise RuntimeError("doSelectSources=True and kernelSourcesFromRef=False,"
@@ -882,17 +882,17 @@ def __init__(self, **kwargs):
     def fitAstrometry(self, templateSources, templateExposure, selectSources):
         """Fit the relative astrometry between templateSources and selectSources"""
         if self.config.winter2013WcsShift > 0.0:
-            offset = afwGeom.Extent2D(self.config.winter2013WcsShift,
-                                      self.config.winter2013WcsShift)
+            offset = geom.Extent2D(self.config.winter2013WcsShift,
+                                   self.config.winter2013WcsShift)
             cKey = templateSources[0].getTable().getCentroidKey()
             for source in templateSources:
                 centroid = source.get(cKey)
                 source.set(cKey, centroid + offset)
         elif self.config.winter2013WcsRms > 0.0:
             cKey = templateSources[0].getTable().getCentroidKey()
             for source in templateSources:
-                offset = afwGeom.Extent2D(self.config.winter2013WcsRms*numpy.random.normal(),
-                                          self.config.winter2013WcsRms*numpy.random.normal())
+                offset = geom.Extent2D(self.config.winter2013WcsRms*numpy.random.normal(),
+                                       self.config.winter2013WcsRms*numpy.random.normal())
                 centroid = source.get(cKey)
                 source.set(cKey, centroid + offset)
 

python/lsst/pipe/tasks/insertFakes.py

@@ -25,7 +25,7 @@
 import galsim
 from astropy.table import Table
 
-import lsst.afw.geom as afwGeom
+import lsst.geom as geom
 import lsst.afw.image as afwImage
 import lsst.afw.math as afwMath
 import lsst.pex.config as pexConfig
@@ -264,7 +264,7 @@ def run(self, fakeCat, image, wcs, photoCalib):
                     The catalog of fake sources to be input
         image : `lsst.afw.image.exposure.exposure.ExposureF`
                     The image into which the fake sources should be added
-        wcs : `lsst.afw.geom.skyWcs.skyWcs.SkyWcs`
+        wcs : `lsst.afw.geom.SkyWcs`
                     WCS to use to add fake sources
         photoCalib : `lsst.afw.image.photoCalib.PhotoCalib`
                     Photometric calibration to be used to calibrate the fake sources
@@ -320,7 +320,7 @@ def addPixCoords(self, fakeCat, wcs):
         ----------
         fakeCat : `pandas.core.frame.DataFrame`
                     The catalog of fake sources to be input
-        wcs : `lsst.afw.geom.skyWcs.skyWcs.SkyWcs`
+        wcs : `lsst.afw.geom.SkyWcs`
                     WCS to use to add fake sources
 
         Returns
@@ -353,7 +353,7 @@ def trimFakeCat(self, fakeCat, image, wcs):
                     The catalog of fake sources to be input
         image : `lsst.afw.image.exposure.exposure.ExposureF`
                     The image into which the fake sources should be added
-        wcs : `lsst.afw.geom.skyWcs.skyWcs.SkyWcs`
+        wcs : `lsst.afw.geom.SkyWcs`
                     WCS to use to add fake sources
 
         Returns
@@ -392,7 +392,7 @@ def mkFakeGalsimGalaxies(self, fakeCat, band, photoCalib, pixelScale, psf, image
         -------
         galImages : `list`
                     A list of tuples of `lsst.afw.image.exposure.exposure.ExposureF` and
-                    `lsst.afw.geom.Point2D` of their locations.
+                    `lsst.geom.Point2D` of their locations.
 
         Notes
         -----
@@ -411,7 +411,7 @@ def mkFakeGalsimGalaxies(self, fakeCat, band, photoCalib, pixelScale, psf, image
         self.log.info("Making %d fake galaxy images" % len(fakeCat))
 
         for (index, row) in fakeCat.iterrows():
-            xy = afwGeom.Point2D(row["x"], row["y"])
+            xy = geom.Point2D(row["x"], row["y"])
 
             try:
                 # Due to the different radii used for calibration and measurement a correction factor is
@@ -470,16 +470,16 @@ def mkFakeStars(self, fakeCat, band, photoCalib, psf, image):
         Returns
         -------
         starImages : `list`
-                    A list of tuples of `lsst.afw.image.image.image.ImageF` of fake stars and
-                    `lsst.afw.geom.Point2D` of their locations.
+                    A list of tuples of `lsst.afw.image.ImageF` of fake stars and
+                    `lsst.geom.Point2D` of their locations.
         """
 
         starImages = []
 
         self.log.info("Making %d fake star images" % len(fakeCat))
 
         for (index, row) in fakeCat.iterrows():
-            xy = afwGeom.Point2D(row["x"], row["y"])
+            xy = geom.Point2D(row["x"], row["y"])
 
             try:
                 # Due to the different radii used for calibration and measurement a correction factor is
@@ -531,7 +531,7 @@ def addFakeSources(self, image, fakeImages, sourceType):
         image : `lsst.afw.image.exposure.exposure.ExposureF`
                     The image into which the fake sources should be added
         fakeImages : `list`
-                    A list of tuples of `lsst.afw.image.image.image.ImageF` and `lsst.afw.geom.Point2D,
+                    A list of tuples of `lsst.afw.image.ImageF` and `lsst.geom.Point2D,
                     the images and the locations they are to be inserted at.
         sourceType : `str`
                     The type (star/galaxy) of fake sources input