Dev

.readthedocs.yaml

@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: requirements.txt

INSTALL.rst

@@ -28,7 +28,6 @@ The latest tagged version of **zCluster** can be installed using ``pip``:
 
    pip install zCluster
 
-Note that you will need to have ``cython`` and ``numpy`` installed already (for the moment).
 Other dependencies will be installed by ``pip``.
 
 You may also install using the standard ``setup.py`` script, e.g., as root:

bin/zCluster

@@ -445,7 +445,7 @@ def makeParser():
     parser.add_argument("-Z", "--z-prior-max", dest="zPriorMax", help="Set maximum redshift of prior.",
                         default = None)
     parser.add_argument("-b", "--brighter-absmag-cut", dest="absMagCut", help="Set bright absolute magnitude cut.",
-                        default = -24.)
+                        default = -24., type = float)
     parser.add_argument("-n", "--name", dest="name", help="Find photo-z of only the named cluster in the catalog.")
     parser.add_argument("-t", "--templates-directory", dest="templatesDir", help="Specify a directory containing\
                         a custom set of spectral templates.",  default = None)

pyproject.toml

@@ -1,2 +1,2 @@
 [build-system]
-requires = ["numpy", "setuptools", "wheel", "cython"]
+requires = ["numpy", "setuptools", "wheel"] #, "cython"]

setup.py

@@ -6,12 +6,12 @@
 from setuptools import Extension
 from setuptools.command.install import install
 import stat
-from Cython.Distutils import build_ext
+#from Cython.Distutils import build_ext
 import numpy
 import versioneer
 
 cmdclass=versioneer.get_cmdclass()
-cmdclass['build_ext']=build_ext
+#cmdclass['build_ext']=build_ext
 
 setup(name='zCluster',
       version=versioneer.get_version(),
@@ -27,12 +27,12 @@
       package_data={'zCluster': ['data/*', 'SED/CWW/*', 'SED/BR07/*', 'SED/EAZY_v1.0/*', 
                                  'passbands/*']},
       scripts=['bin/zCluster', 'bin/zField', 'bin/zClusterBCG', 'bin/zClusterComparisonPlot'],
-      ext_modules=[Extension("zClusterCython", ["zCluster/zClusterCython.pyx"], include_dirs=[numpy.get_include()])],
+      #ext_modules=[Extension("zClusterCython", ["zCluster/zClusterCython.pyx"], include_dirs=[numpy.get_include()])],
       install_requires=["astropy >= 4.0",
                         "numpy >= 1.19",
                         "matplotlib >= 2.0",
                         "astLib >= 0.11.7",
                         "scipy >= 1.0",
-                        "cython",
+                        #"cython",
                         "requests"]
 )

zCluster/PhotoRedshiftEngine.py

@@ -28,8 +28,10 @@ def __init__(self, absMagCut, passbandSet = 'SDSS+Ks', zMin = 0.01, zMax = 3.0,
         """Sets up the stuff we would otherwise calculate every time, i.e., the templates.
 
         """
-
-        # Redshift grid on which to calculate p(z)
+
+        if zStep < 0:
+            print("... WARNING: zStep was negative - forced to be positive")
+            zStep=abs(zStep)
         self.zRange=np.linspace(zMin, zMax, int(((zMax+zStep)-zMin)/zStep))
 
         # Set up passbands
@@ -423,8 +425,12 @@ def estimateStellarMasses(self, galaxyCatalog, stellarMassModelDir, z = None):
             mags=[]
             magErrs=[]
             for band in self.bands:
-                mags.append(objDict[band])
-                magErrs.append(objDict[band+"Err"])
+                if band in list(objDict.keys()):
+                    mags.append(objDict[band])
+                    magErrs.append(objDict[band+"Err"])
+                else:
+                    mags.append(99)
+                    magErrs.append(99)
             obsSEDDict=astSED.mags2SEDDict(mags, magErrs, self.passbandsList)
             distNorm=4*np.pi*np.power(DL*3.08567758e24, 2)
             fitResult=sm.fitSEDDictAndCalcStellarMass(obsSEDDict, modelSEDDictList, distNorm)

zCluster/clusters.py

@@ -16,7 +16,6 @@
 from astropy.coordinates import match_coordinates_sky
 from PIL import Image
 from PIL import ImageDraw
-import zClusterCython
 import pylab as plt
 
 #------------------------------------------------------------------------------------------------------------
@@ -42,6 +41,66 @@ def getPixelAreaDeg2Map(mapData, wcs):
 
     return pixAreasDeg2Map   
 
+#---------------------------------------------------------------------------------------------------
+def makeDegreesDistanceMap(degreesMap, wcs, RADeg, decDeg, maxDistDegrees):
+    """Fills (in place) the 2d array degreesMap with distance in degrees from the given position,
+    out to some user-specified maximum distance.
+
+    Args:
+        degreesMap (:obj:`np.ndarray`): Map (2d array) that will be filled with angular distance
+            from the given coordinates. Probably you should feed in an array set to some extreme
+            initial value (e.g., 1e6 everywhere) to make it easy to filter for pixels near the
+            object coords afterwards.
+        wcs (:obj:`astWCS.WCS`): WCS corresponding to degreesMap.
+        RADeg (float): RA in decimal degrees of position of interest (e.g., object location).
+        decDeg (float): Declination in decimal degrees of position of interest (e.g., object
+            location).
+        maxDistDegrees: The maximum radius out to which distance will be calculated.
+
+    Returns:
+        A map (2d array) of distance in degrees from the given position,
+        (min x, max x) pixel coords corresponding to maxDistDegrees box,
+        (min y, max y) pixel coords corresponding to maxDistDegrees box
+
+    Note:
+        This routine measures the pixel scale local to the given position, then assumes that it
+        does not change. So, this routine may only be accurate close to the given position,
+        depending upon the WCS projection used.
+
+    """
+
+    x0, y0=wcs.wcs2pix(RADeg, decDeg)
+    ra0, dec0=RADeg, decDeg
+    ra1, dec1=wcs.pix2wcs(x0+1, y0+1)
+    xPixScale=astCoords.calcAngSepDeg(ra0, dec0, ra1, dec0)
+    yPixScale=astCoords.calcAngSepDeg(ra0, dec0, ra0, dec1)
+
+    xDistPix=int(round((maxDistDegrees)/xPixScale))
+    yDistPix=int(round((maxDistDegrees)/yPixScale))
+
+    Y=degreesMap.shape[0]
+    X=degreesMap.shape[1]
+
+    minX=int(round(x0))-xDistPix
+    maxX=int(round(x0))+xDistPix
+    minY=int(round(y0))-yDistPix
+    maxY=int(round(y0))+yDistPix
+    if minX < 0:
+        minX=0
+    if maxX > X:
+        maxX=X
+    if minY < 0:
+        minY=0
+    if maxY > Y:
+        maxY=Y
+
+    xDeg=(np.arange(degreesMap.shape[1])-x0)*xPixScale
+    yDeg=(np.arange(degreesMap.shape[0])-y0)*yPixScale
+    for i in range(minY, maxY):
+        degreesMap[i][minX:maxX]=np.sqrt(yDeg[i]**2+xDeg[minX:maxX]**2)
+
+    return degreesMap, [minX, maxX], [minY, maxY]
+
 #------------------------------------------------------------------------------------------------------------
 def makeBlankMap(RADeg, decDeg, sizePix, sizeDeg):
     """Makes a square blank map with a WCS.
@@ -301,7 +360,7 @@ def makeWeightedNz(RADeg, decDeg, catalog, zPriorMax, weightsType, minDistanceMp
     else:
         areaMap=getPixelAreaDeg2Map(areaMask, wcs)
         rDegMap=np.zeros(areaMask.shape)
-        rDegMap, xRange, yRange=zClusterCython.makeDegreesDistanceMap(rDegMap, wcs, RADeg, decDeg, 2.0)
+        rDegMap, xRange, yRange=makeDegreesDistanceMap(rDegMap, wcs, RADeg, decDeg, 2.0)
         rDegMap=rDegMap[yRange[0]:yRange[1], xRange[0]:xRange[1]]
         areaMap=areaMask[yRange[0]:yRange[1], xRange[0]:xRange[1]]*areaMap[yRange[0]:yRange[1], xRange[0]:xRange[1]]
         areaMpc2=[]

zCluster/retrievers.py

@@ -113,7 +113,7 @@ def getRetriever(database, maxMagError = 0.2):
         retrieverOptions={'maxMagError': maxMagError}
     elif database.find("DECaLS") != -1:
         if database == "DECaLS":
-            raise Exception("Specify either 'DECaLSDR8' or 'DECaLSDR9' instead of DECaLS")
+            raise Exception("Specify either 'DECaLSDR8', 'DECaLSDR9', or 'DECaLSDR10' instead of DECaLS")
         if database == 'DECaLSDR8':
             DR="DR8"
             retriever=DECaLSDR8Retriever
@@ -123,6 +123,8 @@ def getRetriever(database, maxMagError = 0.2):
         elif database == "DECaLSDR10":
             DR="DR10"
             retriever=DECaLSDR10Retriever
+        else:
+            raise Exception("Didn't understand DECaLS database choice")
         passbandSet='DECaLS'
         # For DECaLS, need the bricks files that define survey on the sky
         # These were previously included in zCluster, but now we fetch over web and cache