Merge pull request #75 from DESI-UR/periodic

Documentation corrections

doc/paper.md

@@ -10,7 +10,7 @@ authors:
   - name: Kelly A. Douglass
     orcid: 0000-0002-9540-546X
     affiliation: 1
-  - name: Dylan Veyrat
+  - name: Dahlia Veyrat
     orcid: 0000-0001-8101-2836
     affiliation: 1
   - name: Stephen W. O'Neill, Jr.

doc/source/Vsquared_functions.rst

@@ -64,6 +64,13 @@ V\ :sup:`2` API
 
 
 
+``util.getBuff``
+=============
+
+.. autofunction:: vast.vsquared.util.getBuff
+
+
+
 ``util.wCen``
 =============
 

doc/source/Vsquared_intro.rst

@@ -12,7 +12,8 @@ Introduction
 voids based on the ZOBOV (ZOnes Bordering On Voidness) algorithm by 
 `Neyrinck (2008) <https://arxiv.org/abs/0712.3049>`_, which uses the gradient of 
 the volume of adjacent voronoi cells to flow multiple cells into larger void 
-regions.
+regions. Voids can be found both in observational surveys and simulations with 
+periodic boundary conditions.
 
 **VAST** contains the package, as well as an example script for automatically 
 running all steps of the algorithm. To import the main void-finding class of 

doc/source/conf.py

@@ -16,8 +16,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'VAST'
-copyright = "2022, Kelly A. Douglass, D. Veyrat, Stephen W. O'Neill Jr., Segev BenZvi, Fatima Zaidouni, Michaela Guzzetti"
-author = "Kelly A. Douglass, D. Veyrat, Stephen W. O'Neill Jr., Segev BenZvi, Fatima Zaidouni, Michaela Guzzetti"
+copyright = "2022, Kelly A. Douglass, Dahlia Veyrat, Stephen W. O'Neill Jr., Segev BenZvi, Fatima Zaidouni, Michaela Guzzetti"
+author = "Kelly A. Douglass, Dahlia Veyrat, Stephen W. O'Neill Jr., Segev BenZvi, Fatima Zaidouni, Michaela Guzzetti"
 
 # The short X.Y version
 version = re.match(r"v?(\d+\.\d+)", vast._version.__version__).group(1)

example_scripts/DR7_config.ini

@@ -21,3 +21,12 @@ radius_min    = 10.0
 nside         = 32
 #Step size for comoving-distance-to-redshift lookup table
 redshift_step = 5e-5
+#Periodic limits (Mpc/h)
+x_min         = -50.
+y_min         = -50.
+z_min         = -50.
+x_max         = 50.
+y_max         = 50.
+z_max         = 50.
+#Periodic buffer shell width (Mpc/h)
+buffer        = 5.

example_scripts/Gadget_VoidFinder_periodic.py

@@ -13,7 +13,7 @@
 #-------------------------------------------------------------------------------
 import numpy as np
 
-from vast.voidfinder import find_voids
+from vast.voidfinder import find_voids, wall_field_separation
 
 from vast.voidfinder.preprocessing import load_data_to_Table
 ################################################################################
@@ -54,20 +54,27 @@
 # Read in data
 #-------------------------------------------------------------------------------
 # Read in the simulated data
-wall_coords_xyz = load_data_to_Table(sim_filename)
+coords_xyz = load_data_to_Table(sim_filename)
 
 #-------------------------------------------------------------------------------
 # Restructure the data for the find_voids function
 #-------------------------------------------------------------------------------
-x = wall_coords_xyz['x']
-y = wall_coords_xyz['y']
-z = wall_coords_xyz['z']
+x = coords_xyz['x']
+y = coords_xyz['y']
+z = coords_xyz['z']
 
 num_gal = x.shape[0]
 
-wall_coords_xyz = np.concatenate((x.reshape(num_gal,1),
-                                  y.reshape(num_gal,1),
-                                  z.reshape(num_gal,1)), axis=1)
+coords_xyz = np.concatenate((x.reshape(num_gal,1),
+                             y.reshape(num_gal,1),
+                             z.reshape(num_gal,1)), axis=1)
+#-------------------------------------------------------------------------------
+
+
+#-------------------------------------------------------------------------------
+# Remove isolated galaxies
+#-------------------------------------------------------------------------------
+wall_coords_xyz, field_coords_xyz = wall_field_separation(coords_xyz)
 #-------------------------------------------------------------------------------
 ################################################################################
 

example_scripts/Gadget_VoidFinder_xyz.py

@@ -13,7 +13,7 @@
 #-------------------------------------------------------------------------------
 import numpy as np
 
-from vast.voidfinder import find_voids
+from vast.voidfinder import find_voids, wall_field_separation
 
 from vast.voidfinder.preprocessing import load_data_to_Table
 ################################################################################
@@ -54,20 +54,26 @@
 # Read in data
 #-------------------------------------------------------------------------------
 # Read in the simulated data
-wall_coords_xyz = load_data_to_Table(galaxies_filename)
+coords_xyz = load_data_to_Table(galaxies_filename)
 
 #-------------------------------------------------------------------------------
 # Restructure the data for the find_voids function
 #-------------------------------------------------------------------------------
-x = wall_coords_xyz['x']
-y = wall_coords_xyz['y']
-z = wall_coords_xyz['z']
+x = coords_xyz['x']
+y = coords_xyz['y']
+z = coords_xyz['z']
 
 num_gal = x.shape[0]
 
-wall_coords_xyz = np.concatenate((x.reshape(num_gal,1),
-                                  y.reshape(num_gal,1),
-                                  z.reshape(num_gal,1)), axis=1)
+coords_xyz = np.concatenate((x.reshape(num_gal,1),
+                             y.reshape(num_gal,1),
+                             z.reshape(num_gal,1)), axis=1)
+#-------------------------------------------------------------------------------
+
+#-------------------------------------------------------------------------------
+# Remove isolated galaxies
+#-------------------------------------------------------------------------------
+wall_coords_xyz, field_coords_xyz = wall_field_separation(coords_xyz)
 #-------------------------------------------------------------------------------
 ################################################################################
 

example_scripts/vsquared.py

@@ -16,6 +16,8 @@
                help='Enable void visualization.')
 p.add_argument('-w', '--save_intermediate', action='store_true', default=False,
                help='Save intermediate files in void calculation.')
+p.add_argument('-p', '--periodic', action='store_true', default=False,
+               help='Use periodic boundary contitions.')
 
 req = p.add_argument_group('required named arguments')
 req.add_argument('-c', '--config', dest='config_file', required=True, default="DR7_config.ini",
@@ -25,7 +27,8 @@
 
 newZobov = Zobov(args.config_file, args.method, 3,
                  save_intermediate=args.save_intermediate,
-                 visualize=args.visualize)
+                 visualize=args.visualize
+                 periodic=args.periodic)
 
 newZobov.sortVoids(method=args.method)