Implemented (yet another) new boundary handling scheme, whereby we scan radially along survey edge while flagging nearest galaxies. The prepObservation routine was significantly cleaned up to accommodate this, but it was ultimately implemented in python (surveyTools.py) for ease of prototyping, with the intent to move it back into C later.

Some general housekeeping, making sure some new parameters are passed around correctly, and removing the storage of some unused files.

This update is considered HIGHLY UNSTABLE. It will almost certainly break somewhere for simulations.

Still under active development.

examples/example_observation/example_observation.py

@@ -30,7 +30,7 @@ continueRun = False
 #   1 : extract redshift slices from data
 #   2 : void extraction using zobov
 #   3 : removal of small voids and voids near the edge
-startCatalogStage = 1
+startCatalogStage = 2
 endCatalogStage   = 3
 
 basePath = os.path.dirname(os.path.abspath(__file__))
@@ -50,7 +50,7 @@ figDir = os.path.join(workDir,"figs","example_observation")
 # optimization: maximum number of parallel threads to use
 numZobovThreads = 2
 
-# optimization: number of subdivisions of the box
+# optimization: number of subdivisions of the volume
 numZobovDivisions = 2
 
 # Maximum density for merging voids
@@ -65,7 +65,7 @@ boundaryTolerance = 1.0
 # don't change this
 dataSampleList = []
 
-# define your volume-limited samples
+# define your data samples
 newSample = Sample(
                    # path to galaxy file is inputDataDir+dataFile
                    dataFile = "example_observation.dat",
@@ -76,19 +76,22 @@ newSample = Sample(
                    # a convenient nickname
                    nickName = "exobs",
 
-                   # don't change this
+                   # don't change this or nothing will make sense
                    dataType = "observation",
 
                    # assume sample is volume-limited?
                    volumeLimited = True,
 
                    # HEALpix mask file - set to None to auto-compute
+                   # NOTE: auto-computed masks are pretty terrible, so
+                   #       only do that if you have no other options
                    #maskFile = "",
                    maskFile = inputDataDir+"/example_observation_mask.fits",
 
-                   # if maskFile blank, desired resolution for HEALpix
-                   # mask mapping, otherwise pulled from maskFile
-                   nsideForMask = 128,
+                   # resolution for HEALpix mapping of survey edge contours
+                   #   Set to -1 to use nside from given fits file
+                   #   MUST be set if auto-computing mask
+                   nsideForContour = 128,
 
                    # radial selection function (if not volume limited)
                    selFunFile = None,
@@ -109,6 +112,7 @@ newSample = Sample(
 
                    # density of mock particles in cubic Mpc/h
                    # (make this as high as you can afford)
+                   ### DEPRECATED
                    fakeDensity = 0.05,
 
                    # if true, convert to comoving space using LCDM cosmology