moved example datasets and config files to their own directory

examples/example_observation/example_observation.py

@@ -0,0 +1,111 @@
+#!/usr/bin/env python
+#+
+#   VIDE -- Void IDentification and Examination -- ./python_tools/void_pipeline/datasets/example_observation.py
+#   Copyright (C) 2010-2014 Guilhem Lavaux
+#   Copyright (C) 2011-2014 P. M. Sutter
+#
+#   This program is free software; you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation; version 2 of the License.
+#
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU General Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program; if not, write to the Free Software Foundation, Inc.,
+#   51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#+
+
+import os
+import numpy as np
+from vide.backend.classes import *
+
+# if True, will scan log files for last known completed state and run from there
+continueRun = False
+
+# stages:
+#   1 : extract redshift slices from data
+#   2 : void extraction using zobov
+#   3 : removal of small voids and voids near the edge
+startCatalogStage = 1
+endCatalogStage   = 3
+
+basePath = os.path.dirname(os.path.abspath(__file__))
+basePath = os.path.abspath(os.path.join(basePath,"..","..","..","examples"))
+
+# directory for input data files
+inputDataDir = basePath
+
+# void catalog output directory
+workDir = os.path.join(basePath,"example_observation")
+
+# output directory for log files
+logDir = os.path.join(basePath,"logs","example_observation")
+
+# output directory for figures
+figDir = os.path.join(basePath,"figs","example_observation")
+
+# optimization: maximum number of parallel threads to use
+numZobovThreads = 2
+
+# optimization: number of subdivisions of the box
+numZobovDivisions = 2
+
+# Maximum density for merging voids
+#   0 (equivalent to infinitely large value) -> Merge everything (no threshold)
+#   1e-9 (or smaller != 0) -> Do not merge anything
+mergingThreshold = 1e-9
+
+# don't change this
+dataSampleList = []
+
+# define your volume-limited samples
+newSample = Sample(
+                   # path to galaxy file is inputDataDir+dataFile
+                   dataFile = "example_observation.dat",
+
+                   # full name for this sample
+                   fullName = "example_observation",
+
+                   # a convenient nickname
+                   nickName = "exobs",
+
+                   # don't change this
+                   dataType = "observation",
+
+                   # assume sample is volume-limited?
+                   volumeLimited = True,
+
+                   # HEALpix mask file
+                   maskFile = inputDataDir+"/example_observation_mask.fits",
+
+                   # radial selection function (if not volume limited)
+                   selFunFile = None,
+
+                   # max and min redshifts of galaxies in your sample
+                   zBoundary = (0.0, 0.15),
+
+                   # max and min redshifts where you want to find voids
+                   zRange = (0.1, 0.15),
+
+                   # leave this at -1 for mean particle separation,
+                   # or specify your own in Mpc/h
+                   minVoidRadius = -1,
+
+                   # density of mock particles in cubic Mpc/h
+                   # (make this as high as you can afford)
+                   fakeDensity = 0.05,
+
+                   # if true, convert to comoving space using LCDM cosmology
+                   useComoving = True,
+
+                   # cosmology
+                   omegaM = 0.3,
+
+                   )
+dataSampleList.append(newSample)
+
+# repeat the above block for any other samples