[yt-svn] commit/yt: 6 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Sun Apr 13 01:14:23 PDT 2014
6 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/e8399e3fbeb7/
Changeset: e8399e3fbeb7
Branch: yt
User: xarthisius
Date: 2013-07-06 19:18:18
Summary: Merge fortran_utils from yt-3.0
Affected #: 1 file
diff -r 213d534593fb056814ce918c902e4fc3ea3360e9 -r e8399e3fbeb7e12671b8268586070f690af28085 yt/utilities/fortran_utils.py
--- /dev/null
+++ b/yt/utilities/fortran_utils.py
@@ -0,0 +1,243 @@
+"""
+Utilities for reading Fortran files.
+
+Author: Matthew Turk <matthewturk at gmail.com>
+Affiliation: Columbia University
+Homepage: http://yt.enzotools.org/
+License:
+ Copyright (C) 2012 Matthew Turk. All Rights Reserved.
+
+ This file is part of yt.
+
+ yt 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; either version 3 of the License, or
+ (at your option) any later version.
+
+ 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, see <http://www.gnu.org/licenses/>.
+"""
+
+import struct
+import numpy as np
+import os
+
+def read_attrs(f, attrs,endian='='):
+ r"""This function accepts a file pointer and reads from that file pointer
+ according to a definition of attributes, returning a dictionary.
+
+ Fortran unformatted files provide total bytesize at the beginning and end
+ of a record. By correlating the components of that record with attribute
+ names, we construct a dictionary that gets returned. Note that this
+ function is used for reading sequentially-written records. If you have
+ many written that were written simultaneously, see read_record.
+
+ Parameters
+ ----------
+ f : File object
+ An open file object. Should have been opened in mode rb.
+ attrs : iterable of iterables
+ This object should be an iterable of one of the formats:
+ [ (attr_name, count, struct type), ... ].
+ [ ((name1,name2,name3),count, vector type]
+ [ ((name1,name2,name3),count, 'type type type']
+ endian : str
+ '=' is native, '>' is big, '<' is little endian
+
+ Returns
+ -------
+ values : dict
+ This will return a dict of iterables of the components of the values in
+ the file.
+
+ Examples
+ --------
+
+ >>> header = [ ("ncpu", 1, "i"), ("nfiles", 2, "i") ]
+ >>> f = open("fort.3", "rb")
+ >>> rv = read_attrs(f, header)
+ """
+ vv = {}
+ net_format = endian
+ for a, n, t in attrs:
+ for end in '@=<>':
+ t = t.replace(end,'')
+ net_format += "".join(["I"] + ([t] * n) + ["I"])
+ size = struct.calcsize(net_format)
+ vals = list(struct.unpack(net_format, f.read(size)))
+ vv = {}
+ for a, n, t in attrs:
+ for end in '@=<>':
+ t = t.replace(end,'')
+ if type(a)==tuple:
+ n = len(a)
+ s1 = vals.pop(0)
+ v = [vals.pop(0) for i in range(n)]
+ s2 = vals.pop(0)
+ if s1 != s2:
+ size = struct.calcsize(endian + "I" + "".join(n*[t]) + "I")
+ assert(s1 == s2)
+ if n == 1: v = v[0]
+ if type(a)==tuple:
+ assert len(a) == len(v)
+ for k,val in zip(a,v):
+ vv[k]=val
+ else:
+ vv[a] = v
+ return vv
+
+def read_vector(f, d, endian='='):
+ r"""This function accepts a file pointer and reads from that file pointer
+ a vector of values.
+
+ Parameters
+ ----------
+ f : File object
+ An open file object. Should have been opened in mode rb.
+ d : data type
+ This is the datatype (from the struct module) that we should read.
+ endian : str
+ '=' is native, '>' is big, '<' is little endian
+
+ Returns
+ -------
+ tr : numpy.ndarray
+ This is the vector of values read from the file.
+
+ Examples
+ --------
+
+ >>> f = open("fort.3", "rb")
+ >>> rv = read_vector(f, 'd')
+ """
+ pad_fmt = "%sI" % (endian)
+ pad_size = struct.calcsize(pad_fmt)
+ vec_len = struct.unpack(pad_fmt,f.read(pad_size))[0] # bytes
+ vec_fmt = "%s%s" % (endian, d)
+ vec_size = struct.calcsize(vec_fmt)
+ if vec_len % vec_size != 0:
+ print "fmt = '%s' ; length = %s ; size= %s" % (fmt, length, size)
+ raise RuntimeError
+ vec_num = vec_len / vec_size
+ if isinstance(f, file): # Needs to be explicitly a file
+ tr = np.fromfile(f, vec_fmt, count=vec_num)
+ else:
+ tr = np.fromstring(f.read(vec_len), vec_fmt, count=vec_num)
+ vec_len2 = struct.unpack(pad_fmt,f.read(pad_size))[0]
+ assert(vec_len == vec_len2)
+ return tr
+
+def skip(f, n=1, endian='='):
+ r"""This function accepts a file pointer and skips a Fortran unformatted
+ record. Optionally check that the skip was done correctly by checking
+ the pad bytes.
+
+ Parameters
+ ----------
+ f : File object
+ An open file object. Should have been opened in mode rb.
+ n : int
+ Number of records to skip.
+ check : bool
+ Assert that the pad bytes are equal
+ endian : str
+ '=' is native, '>' is big, '<' is little endian
+
+ Returns
+ -------
+ skipped: The number of elements in the skipped array
+
+ Examples
+ --------
+
+ >>> f = open("fort.3", "rb")
+ >>> skip(f, 3)
+ """
+ skipped = 0
+ pos = f.tell()
+ for i in range(n):
+ fmt = endian+"I"
+ size = f.read(struct.calcsize(fmt))
+ s1= struct.unpack(fmt, size)[0]
+ f.seek(s1+ struct.calcsize(fmt), os.SEEK_CUR)
+ s2= struct.unpack(fmt, size)[0]
+ assert s1==s2
+ skipped += s1/struct.calcsize(fmt)
+ return skipped
+
+def peek_record_size(f,endian='='):
+ r""" This function accept the file handle and returns
+ the size of the next record and then rewinds the file
+ to the previous position.
+
+ Parameters
+ ----------
+ f : File object
+ An open file object. Should have been opened in mode rb.
+ endian : str
+ '=' is native, '>' is big, '<' is little endian
+
+ Returns
+ -------
+ Number of bytes in the next record
+ """
+ pos = f.tell()
+ s = struct.unpack('>i', f.read(struct.calcsize('>i')))
+ f.seek(pos)
+ return s[0]
+
+def read_record(f, rspec, endian='='):
+ r"""This function accepts a file pointer and reads from that file pointer
+ a single "record" with different components.
+
+ Fortran unformatted files provide total bytesize at the beginning and end
+ of a record. By correlating the components of that record with attribute
+ names, we construct a dictionary that gets returned.
+
+ Parameters
+ ----------
+ f : File object
+ An open file object. Should have been opened in mode rb.
+ rspec : iterable of iterables
+ This object should be an iterable of the format [ (attr_name, count,
+ struct type), ... ].
+ endian : str
+ '=' is native, '>' is big, '<' is little endian
+
+ Returns
+ -------
+ values : dict
+ This will return a dict of iterables of the components of the values in
+ the file.
+
+ Examples
+ --------
+
+ >>> header = [ ("ncpu", 1, "i"), ("nfiles", 2, "i") ]
+ >>> f = open("fort.3", "rb")
+ >>> rv = read_record(f, header)
+ """
+ vv = {}
+ net_format = endian + "I"
+ for a, n, t in rspec:
+ t = t if len(t)==1 else t[-1]
+ net_format += "%s%s"%(n, t)
+ net_format += "I"
+ size = struct.calcsize(net_format)
+ vals = list(struct.unpack(net_format, f.read(size)))
+ vvv = vals[:]
+ s1, s2 = vals.pop(0), vals.pop(-1)
+ if s1 != s2:
+ print "S1 = %s ; S2 = %s ; SIZE = %s"
+ raise RuntimeError
+ pos = 0
+ for a, n, t in rspec:
+ vv[a] = vals[pos:pos+n]
+ pos += n
+ return vv
+
https://bitbucket.org/yt_analysis/yt/commits/0afb2e5f6290/
Changeset: 0afb2e5f6290
Branch: yt
User: xarthisius
Date: 2013-09-10 18:01:55
Summary: merging
Affected #: 401 files
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 COPYING.txt
--- /dev/null
+++ b/COPYING.txt
@@ -0,0 +1,81 @@
+===============================
+ The yt project licensing terms
+===============================
+
+yt is licensed under the terms of the Modified BSD License (also known as New
+or Revised BSD), as follows:
+
+Copyright (c) 2013-, yt Development Team
+Copyright (c) 2006-2013, Matthew Turk <matthewturk at gmail.com>
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+Neither the name of the yt Development Team nor the names of its
+contributors may be used to endorse or promote products derived from this
+software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+About the yt Development Team
+-----------------------------
+
+Matthew Turk began yt in 2006 and remains the project lead. Over time yt has
+grown to include contributions from a large number of individuals from many
+diverse institutions, scientific, and technical backgrounds.
+
+Until the fall of 2013, yt was licensed under the GPLv3. However, with consent
+from all developers and on a public mailing list, yt has been relicensed under
+the BSD 3-clause under a shared copyright model. For more information, see:
+http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-July/003239.html
+All versions of yt prior to this licensing change are available under the
+GPLv3; all subsequent versions are available under the BSD 3-clause license.
+
+The yt Development Team is the set of all contributors to the yt project. This
+includes all of the yt subprojects.
+
+The core team that coordinates development on BitBucket can be found here:
+http://bitbucket.org/yt_analysis/
+
+
+Our Copyright Policy
+--------------------
+
+yt uses a shared copyright model. Each contributor maintains copyright
+over their contributions to yt. But, it is important to note that these
+contributions are typically only changes to the repositories. Thus, the yt
+source code, in its entirety is not the copyright of any single person or
+institution. Instead, it is the collective copyright of the entire yt
+Development Team. If individual contributors want to maintain a record of what
+changes/contributions they have specific copyright on, they should indicate
+their copyright in the commit message of the change, when they commit the
+change to one of the yt repositories.
+
+With this in mind, the following banner should be used in any source code file
+to indicate the copyright and license terms:
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 CREDITS
--- a/CREDITS
+++ b/CREDITS
@@ -1,51 +1,55 @@
-YT is a group effort.
+yt is a group effort.
-Contributors: Tom Abel (tabel at stanford.edu)
- David Collins (dcollins at physics.ucsd.edu)
- Brian Crosby (crosby.bd at gmail.com)
- Andrew Cunningham (ajcunn at gmail.com)
- Nathan Goldbaum (goldbaum at ucolick.org)
- Markus Haider (markus.haider at uibk.ac.at)
- Cameron Hummels (chummels at gmail.com)
- Christian Karch (chiffre at posteo.de)
- Ji-hoon Kim (me at jihoonkim.org)
- Steffen Klemer (sklemer at phys.uni-goettingen.de)
- Kacper Kowalik (xarthisius.kk at gmail.com)
- Michael Kuhlen (mqk at astro.berkeley.edu)
- Eve Lee (elee at cita.utoronto.ca)
- Yuan Li (yuan at astro.columbia.edu)
- Chris Malone (chris.m.malone at gmail.com)
- Josh Maloney (joshua.moloney at colorado.edu)
- Chris Moody (cemoody at ucsc.edu)
- Andrew Myers (atmyers at astro.berkeley.edu)
- Jeff Oishi (jsoishi at gmail.com)
- Jean-Claude Passy (jcpassy at uvic.ca)
- Mark Richardson (Mark.L.Richardson at asu.edu)
- Thomas Robitaille (thomas.robitaille at gmail.com)
- Anna Rosen (rosen at ucolick.org)
- Anthony Scopatz (scopatz at gmail.com)
- Devin Silvia (devin.silvia at colorado.edu)
- Sam Skillman (samskillman at gmail.com)
- Stephen Skory (s at skory.us)
- Britton Smith (brittonsmith at gmail.com)
- Geoffrey So (gsiisg at gmail.com)
- Casey Stark (caseywstark at gmail.com)
- Elizabeth Tasker (tasker at astro1.sci.hokudai.ac.jp)
- Stephanie Tonnesen (stonnes at gmail.com)
- Matthew Turk (matthewturk at gmail.com)
- Rich Wagner (rwagner at physics.ucsd.edu)
- John Wise (jwise at physics.gatech.edu)
- John ZuHone (jzuhone at gmail.com)
+Contributors:
+ Tom Abel (tabel at stanford.edu)
+ David Collins (dcollins at physics.ucsd.edu)
+ Brian Crosby (crosby.bd at gmail.com)
+ Andrew Cunningham (ajcunn at gmail.com)
+ Hilary Egan (hilaryye at gmail.com)
+ John Forces (jforbes at ucolick.org)
+ Nathan Goldbaum (goldbaum at ucolick.org)
+ Markus Haider (markus.haider at uibk.ac.at)
+ Cameron Hummels (chummels at gmail.com)
+ Christian Karch (chiffre at posteo.de)
+ Ji-hoon Kim (me at jihoonkim.org)
+ Steffen Klemer (sklemer at phys.uni-goettingen.de)
+ Kacper Kowalik (xarthisius.kk at gmail.com)
+ Michael Kuhlen (mqk at astro.berkeley.edu)
+ Eve Lee (elee at cita.utoronto.ca)
+ Sam Leitner (sam.leitner at gmail.com)
+ Yuan Li (yuan at astro.columbia.edu)
+ Chris Malone (chris.m.malone at gmail.com)
+ Josh Maloney (joshua.moloney at colorado.edu)
+ Chris Moody (cemoody at ucsc.edu)
+ Andrew Myers (atmyers at astro.berkeley.edu)
+ Jill Naiman (jnaiman at ucolick.org)
+ Kaylea Nelson (kaylea.nelson at yale.edu)
+ Jeff Oishi (jsoishi at gmail.com)
+ Jean-Claude Passy (jcpassy at uvic.ca)
+ Mark Richardson (Mark.L.Richardson at asu.edu)
+ Thomas Robitaille (thomas.robitaille at gmail.com)
+ Anna Rosen (rosen at ucolick.org)
+ Douglas Rudd (drudd at uchicago.edu)
+ Anthony Scopatz (scopatz at gmail.com)
+ Noel Scudder (noel.scudder at stonybrook.edu)
+ Devin Silvia (devin.silvia at colorado.edu)
+ Sam Skillman (samskillman at gmail.com)
+ Stephen Skory (s at skory.us)
+ Britton Smith (brittonsmith at gmail.com)
+ Geoffrey So (gsiisg at gmail.com)
+ Casey Stark (caseywstark at gmail.com)
+ Elizabeth Tasker (tasker at astro1.sci.hokudai.ac.jp)
+ Stephanie Tonnesen (stonnes at gmail.com)
+ Matthew Turk (matthewturk at gmail.com)
+ Rich Wagner (rwagner at physics.ucsd.edu)
+ Andrew Wetzel (andrew.wetzel at yale.edu)
+ John Wise (jwise at physics.gatech.edu)
+ John ZuHone (jzuhone at gmail.com)
-We also include the Delaunay Triangulation module written by Robert Kern of
-Enthought, the cmdln.py module by Trent Mick, and the progressbar module by
+Several items included in the yt/extern directory were written by other
+individuals and may bear their own license, including the progressbar module by
Nilton Volpato. The PasteBin interface code (as well as the PasteBin itself)
-was written by the Pocoo collective (pocoo.org). The RamsesRead++ library was
-developed by Oliver Hahn. yt also includes a slightly-modified version of
-libconfig (http://www.hyperrealm.com/libconfig/) and an unmodified version of
-several routines from HEALpix (http://healpix.jpl.nasa.gov/).
-
-Large parts of development of yt were guided by discussions with Tom Abel, Ralf
-Kaehler, Mike Norman and Greg Bryan.
+was written by the Pocoo collective (pocoo.org).
+developed by Oliver Hahn.
Thanks to everyone for all your contributions!
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 FUNDING
--- a/FUNDING
+++ /dev/null
@@ -1,35 +0,0 @@
-The development of yt has benefited from funding from many different sources
-and institutions. Here is an incomplete list of these sources:
-
- * NSF grant OCI-1048505
- * NSF grant AST-0239709
- * NSF grant AST-0707474
- * NSF grant AST-0708960
- * NSF grant AST-0808184
- * NSF grant AST-0807215
- * NSF grant AST-0807312
- * NSF grant AST-0807075
- * NSF grant AST-0908199
- * NSF grant AST-0908553
- * NASA grant ATFP NNX08-AH26G
- * NASA grant ATFP NNX09-AD80G
- * NASA grant ATFP NNZ07-AG77G
- * DOE Computational Science Graduate Fellowship under grant number DE-FG02-97ER25308
-
-Additionally, development of yt has benefited from the hospitality and hosting
-of the following institutions:
-
- * Columbia University
- * Harvard-Smithsonian Center for Astrophysics
- * Institute for Advanced Study
- * Kavli Institute for Particle Astrophysics and Cosmology
- * Kavli Institute for Theoretical Physics
- * Los Alamos National Lab
- * Michigan State University
- * Princeton University
- * Stanford University
- * University of California High-Performance Astro-Computing Center
- * University of California at Berkeley
- * University of California at San Diego
- * University of California at Santa Cruz
- * University of Colorado at Boulder
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 LICENSE.txt
--- a/LICENSE.txt
+++ /dev/null
@@ -1,674 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works. By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users. We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors. You can apply it to
-your programs, too.
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- When we speak of free software, we are referring to freedom, not
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-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
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-
- The GNU General Public License does not permit incorporating your program
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diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 doc/how_to_develop_yt.txt
--- a/doc/how_to_develop_yt.txt
+++ b/doc/how_to_develop_yt.txt
@@ -25,7 +25,7 @@
Licenses
--------
-All code in yt should be under the GPL-3 (preferred) or a compatible license.
+All code in yt should be under the BSD 3-clause license.
How To Get The Source Code
--------------------------
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 setup.py
--- a/setup.py
+++ b/setup.py
@@ -248,7 +248,7 @@
classifiers=["Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Intended Audience :: Science/Research",
- "License :: OSI Approved :: GNU General Public License (GPL)",
+ "License :: OSI Approved :: BSD License",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: AIX",
"Operating System :: POSIX :: Linux",
@@ -269,7 +269,7 @@
author="Matthew J. Turk",
author_email="matthewturk at gmail.com",
url="http://yt-project.org/",
- license="GPL-3",
+ license="BSD",
configuration=configuration,
zip_safe=False,
data_files=REASON_FILES,
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/__init__.py
--- a/yt/__init__.py
+++ b/yt/__init__.py
@@ -60,27 +60,20 @@
All broadly useful code that doesn't clearly fit in one of the other
categories goes here.
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2007-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
__version__ = "2.5-dev"
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/absorption_spectrum/__init__.py
--- a/yt/analysis_modules/absorption_spectrum/__init__.py
+++ b/yt/analysis_modules/absorption_spectrum/__init__.py
@@ -1,24 +1,17 @@
"""
Import stuff for light cone generator.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/absorption_spectrum/absorption_line.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_line.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_line.py
@@ -1,27 +1,20 @@
"""
Absorption line generating functions.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
@@ -1,27 +1,20 @@
"""
AbsorptionSpectrum class and member functions.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import h5py
import numpy as np
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/absorption_spectrum/api.py
--- a/yt/analysis_modules/absorption_spectrum/api.py
+++ b/yt/analysis_modules/absorption_spectrum/api.py
@@ -1,33 +1,23 @@
"""
API for absorption_spectrum
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * J.S. Oishi
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .absorption_spectrum import \
AbsorptionSpectrum
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -1,33 +1,23 @@
"""
API for yt.analysis_modules
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * J.S. Oishi
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .absorption_spectrum.api import \
AbsorptionSpectrum
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/coordinate_transformation/api.py
--- a/yt/analysis_modules/coordinate_transformation/api.py
+++ b/yt/analysis_modules/coordinate_transformation/api.py
@@ -1,32 +1,22 @@
"""
API for coordinate_transformation
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * J.S. Oishi
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .transforms import \
spherical_regrid
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/coordinate_transformation/transforms.py
--- a/yt/analysis_modules/coordinate_transformation/transforms.py
+++ b/yt/analysis_modules/coordinate_transformation/transforms.py
@@ -1,29 +1,21 @@
"""
Transformations between coordinate systems
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: JS Oishi <jsoishi at astro.berkeley.edu>
-Organization: UC Berkeley
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2007-2011 Matthew Turk, J. S. Oishi. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * JS Oishi
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
from yt.funcs import *
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/api.py
--- a/yt/analysis_modules/cosmological_observation/api.py
+++ b/yt/analysis_modules/cosmological_observation/api.py
@@ -1,29 +1,21 @@
"""
API for cosmology analysis.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .cosmology_splice import \
CosmologySplice
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/cosmology_splice.py
--- a/yt/analysis_modules/cosmological_observation/cosmology_splice.py
+++ b/yt/analysis_modules/cosmological_observation/cosmology_splice.py
@@ -1,27 +1,20 @@
"""
CosmologyTimeSeries class and member functions.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2012 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_cone/__init__.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/__init__.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/__init__.py
@@ -1,24 +1,17 @@
"""
Import stuff for light cone generator.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_cone/api.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/api.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/api.py
@@ -1,33 +1,23 @@
"""
API for lightcone
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * J.S. Oishi
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .light_cone import \
LightCone
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_cone/common_n_volume.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/common_n_volume.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/common_n_volume.py
@@ -2,27 +2,20 @@
Function to calculate volume in common between two n-cubes, with optional
periodic boundary conditions.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_cone/halo_mask.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/halo_mask.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/halo_mask.py
@@ -1,27 +1,20 @@
"""
Light cone halo mask functions.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import copy
import h5py
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
@@ -1,27 +1,20 @@
"""
LightCone class and member functions.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2012 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import copy
import h5py
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_cone/light_cone_projection.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/light_cone_projection.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/light_cone_projection.py
@@ -1,27 +1,20 @@
"""
Create randomly centered, tiled projections to be used in light cones.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
import copy
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_cone/unique_solution.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/unique_solution.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/unique_solution.py
@@ -1,27 +1,20 @@
"""
Functions to generate unique light cone solutions.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import copy
import numpy as np
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_ray/api.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/api.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/api.py
@@ -1,32 +1,22 @@
"""
API for light_ray
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * J.S. Oishi
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .light_ray import \
LightRay
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
@@ -1,27 +1,20 @@
"""
LightRay class and member functions.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2012 Britton Smith. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import copy
import h5py
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/halo_finding/api.py
--- a/yt/analysis_modules/halo_finding/api.py
+++ b/yt/analysis_modules/halo_finding/api.py
@@ -1,33 +1,23 @@
"""
API for halo_finding
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * J.S. Oishi
+ * Britton Smith
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from halo_objects import \
Halo, \
HOPHalo, \
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/halo_finding/fof/EnzoFOF.c
--- a/yt/analysis_modules/halo_finding/fof/EnzoFOF.c
+++ b/yt/analysis_modules/halo_finding/fof/EnzoFOF.c
@@ -1,22 +1,10 @@
-/************************************************************************
-* Copyright (C) 2008-2011 Matthew Turk. All Rights Reserved.
-*
-* This file is part of yt.
-*
-* yt 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; either version 3 of the License, or
-* (at your option) any later version.
-*
-* 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, see <http://www.gnu.org/licenses/>.
-*
-************************************************************************/
+/*******************************************************************************
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+*******************************************************************************/
//
// EnzoFOF
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -1,31 +1,22 @@
"""
HOP-output data handling
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Stephen Skory <s at skory.us>
-Affiliation: UCSD Physics/CASS
-Author: Geoffrey So <gsiisg at gmail.com> (Ellipsoidal functions)
-Affiliation: UCSD Physics/CASS
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
+ * Stephen Skory
+ * Geoffrey So
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import gc
import h5py
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/halo_finding/hop/EnzoHop.c
--- a/yt/analysis_modules/halo_finding/hop/EnzoHop.c
+++ b/yt/analysis_modules/halo_finding/hop/EnzoHop.c
@@ -1,22 +1,10 @@
-/************************************************************************
-* Copyright (C) 2008-2011 Matthew Turk. All Rights Reserved.
-*
-* This file is part of yt.
-*
-* yt 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; either version 3 of the License, or
-* (at your option) any later version.
-*
-* 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, see <http://www.gnu.org/licenses/>.
-*
-************************************************************************/
+/*******************************************************************************
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+*******************************************************************************/
//
// EnzoHop
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
--- a/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
+++ b/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py
@@ -1,27 +1,20 @@
"""
A implementation of the HOP algorithm that runs in parallel.
-Author: Stephen Skory <s at skory.us>
-Affiliation: UCSD/CASS
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Stephen Skory. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Stephen Skory
- yt 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; either version 3 of the License, or
- (at your option) any later version.
- 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, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
from collections import defaultdict
import itertools, sys
diff -r 9651b830f049931de6fa3813eb2ee2e15bfdb17c -r 0afb2e5f62909ee58c7da90503e1874bc90140e4 yt/analysis_modules/halo_finding/rockstar/api.py
--- a/yt/analysis_modules/halo_finding/rockstar/api.py
+++ b/yt/analysis_modules/halo_finding/rockstar/api.py
@@ -1,27 +1,19 @@
"""
API for Rockstar halo finding
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: Columbia
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
+Authors:
+ * Matthew Turk
- yt 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; either version 3 of the License, or
- (at your option) any later version.
-
- 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, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .rockstar import RockstarHaloFinder
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt/commits/f9d93f525115/
Changeset: f9d93f525115
Branch: yt
User: xarthisius
Date: 2013-09-29 11:17:44
Summary: merging
Affected #: 1 file
https://bitbucket.org/yt_analysis/yt/commits/0cddfb9d6650/
Changeset: 0cddfb9d6650
Branch: yt
User: xarthisius
Date: 2013-10-07 18:12:43
Summary: merging
Affected #: 25 files
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -103,5 +103,8 @@
TwoPointFunctions, \
FcnSet
+from .sunyaev_zeldovich.api import SZProjection
+
from .radmc3d_export.api import \
RadMC3DWriter
+
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -21,4 +21,5 @@
config.add_subpackage("star_analysis")
config.add_subpackage("two_point_functions")
config.add_subpackage("radmc3d_export")
+ config.add_subpackage("sunyaev_zeldovich")
return config
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/analysis_modules/sunyaev_zeldovich/api.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/api.py
@@ -0,0 +1,12 @@
+"""
+API for sunyaev_zeldovich
+"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from projection import SZProjection
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/analysis_modules/sunyaev_zeldovich/projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -0,0 +1,349 @@
+"""
+Projection class for the Sunyaev-Zeldovich effect. Requires SZpack (at least
+version 1.1.1) to be downloaded and installed:
+
+http://www.chluba.de/SZpack/
+
+For details on the computations involved please refer to the following references:
+
+Chluba, Nagai, Sazonov, Nelson, MNRAS, 2012, arXiv:1205.5778
+Chluba, Switzer, Nagai, Nelson, MNRAS, 2012, arXiv:1211.3206
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.utilities.physical_constants import sigma_thompson, clight, hcgs, kboltz, mh, Tcmb
+from yt.data_objects.image_array import ImageArray
+from yt.data_objects.field_info_container import add_field
+from yt.funcs import fix_axis, mylog, iterable, get_pbar
+from yt.utilities.definitions import inv_axis_names
+from yt.visualization.image_writer import write_fits, write_projection
+from yt.visualization.volume_rendering.camera import off_axis_projection
+from yt.utilities.parallel_tools.parallel_analysis_interface import \
+ communication_system, parallel_root_only
+import numpy as np
+
+I0 = 2*(kboltz*Tcmb)**3/((hcgs*clight)**2)*1.0e17
+
+try:
+ import SZpack
+except:
+ raise ImportError("SZpack not installed. It can be obtained from from http://www.chluba.de/SZpack/.")
+
+vlist = "xyz"
+
+def _t_squared(field, data):
+ return data["Density"]*data["TempkeV"]*data["TempkeV"]
+add_field("TSquared", function=_t_squared)
+
+def _beta_perp_squared(field, data):
+ return data["Density"]*data["VelocityMagnitude"]**2/clight/clight - data["BetaParSquared"]
+add_field("BetaPerpSquared", function=_beta_perp_squared)
+
+def _beta_par_squared(field, data):
+ return data["BetaPar"]**2/data["Density"]
+add_field("BetaParSquared", function=_beta_par_squared)
+
+def _t_beta_par(field, data):
+ return data["TempkeV"]*data["BetaPar"]
+add_field("TBetaPar", function=_t_beta_par)
+
+def _t_sz(field, data):
+ return data["Density"]*data["TempkeV"]
+add_field("TeSZ", function=_t_sz)
+
+class SZProjection(object):
+ r""" Initialize a SZProjection object.
+
+ Parameters
+ ----------
+ pf : parameter_file
+ The parameter file.
+ freqs : array_like
+ The frequencies (in GHz) at which to compute the SZ spectral distortion.
+ mue : float, optional
+ Mean molecular weight for determining the electron number density.
+ high_order : boolean, optional
+ Should we calculate high-order moments of velocity and temperature?
+
+ Examples
+ --------
+ >>> freqs = [90., 180., 240.]
+ >>> szprj = SZProjection(pf, freqs, high_order=True)
+ """
+ def __init__(self, pf, freqs, mue=1.143, high_order=False):
+
+ self.pf = pf
+ self.num_freqs = len(freqs)
+ self.high_order = high_order
+ self.freqs = np.array(freqs)
+ self.mueinv = 1./mue
+ self.xinit = hcgs*self.freqs*1.0e9/(kboltz*Tcmb)
+ self.freq_fields = ["%d_GHz" % (int(freq)) for freq in freqs]
+ self.data = {}
+
+ self.units = {}
+ self.units["TeSZ"] = r"$\mathrm{keV}$"
+ self.units["Tau"] = None
+
+ self.display_names = {}
+ self.display_names["TeSZ"] = r"$\mathrm{T_e}$"
+ self.display_names["Tau"] = r"$\mathrm{\tau}$"
+
+ for f, field in zip(self.freqs, self.freq_fields):
+ self.units[field] = r"$\mathrm{MJy\ sr^{-1}}$"
+ self.display_names[field] = r"$\mathrm{\Delta{I}_{%d\ GHz}}$" % (int(f))
+
+ def on_axis(self, axis, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an on-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ axis : integer or string
+ The axis of the simulation domain along which to make the SZprojection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+
+ Examples
+ --------
+ >>> szprj.on_axis("y", center="max", width=(1.0, "mpc"), source=my_sphere)
+ """
+ axis = fix_axis(axis)
+
+ def _beta_par(field, data):
+ axis = data.get_field_parameter("axis")
+ vpar = data["Density"]*data["%s-velocity" % (vlist[axis])]
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ proj = self.pf.h.proj(axis, "Density", source=source)
+ proj.set_field_parameter("axis", axis)
+ frb = proj.to_frb(width, nx)
+ dens = frb["Density"]
+ Te = frb["TeSZ"]/dens
+ bpar = frb["BetaPar"]/dens
+ omega1 = frb["TSquared"]/dens/(Te*Te) - 1.
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ if self.high_order:
+ bperp2 = frb["BetaPerpSquared"]/dens
+ sigma1 = frb["TBetaPar"]/dens/Te - bpar
+ kappa1 = frb["BetaParSquared"]/dens - bpar*bpar
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ nx,ny = frb.buff_size
+ self.bounds = frb.bounds
+ self.dx = (frb.bounds[1]-frb.bounds[0])/nx
+ self.dy = (frb.bounds[3]-frb.bounds[2])/ny
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def off_axis(self, L, center="c", width=(1, "unitary"), nx=800, source=None):
+ r""" Make an off-axis projection of the SZ signal.
+
+ Parameters
+ ----------
+ L : array_like
+ The normal vector of the projection.
+ center : array_like or string, optional
+ The center of the projection.
+ width : float or tuple
+ The width of the projection.
+ nx : integer, optional
+ The dimensions on a side of the projection image.
+ source : yt.data_objects.api.AMRData, optional
+ If specified, this will be the data source used for selecting regions to project.
+ Currently unsupported in yt 2.x.
+
+ Examples
+ --------
+ >>> L = np.array([0.5, 1.0, 0.75])
+ >>> szprj.off_axis(L, center="c", width=(2.0, "mpc"))
+ """
+ if iterable(width):
+ w = width[0]/self.pf.units[width[1]]
+ else:
+ w = width
+ if center == "c":
+ ctr = self.pf.domain_center
+ elif center == "max":
+ ctr = self.pf.h.find_max("Density")
+ else:
+ ctr = center
+
+ if source is not None:
+ mylog.error("Source argument is not currently supported for off-axis S-Z projections.")
+ raise NotImplementedError
+
+ def _beta_par(field, data):
+ vpar = data["Density"]*(data["x-velocity"]*L[0]+
+ data["y-velocity"]*L[1]+
+ data["z-velocity"]*L[2])
+ return vpar/clight
+ add_field("BetaPar", function=_beta_par)
+
+ dens = off_axis_projection(self.pf, ctr, L, w, nx, "Density")
+ Te = off_axis_projection(self.pf, ctr, L, w, nx, "TeSZ")/dens
+ bpar = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPar")/dens
+ omega1 = off_axis_projection(self.pf, ctr, L, w, nx, "TSquared")/dens
+ omega1 = omega1/(Te*Te) - 1.
+ if self.high_order:
+ bperp2 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaPerpSquared")/dens
+ sigma1 = off_axis_projection(self.pf, ctr, L, w, nx, "TBetaPar")/dens
+ sigma1 = sigma1/Te - bpar
+ kappa1 = off_axis_projection(self.pf, ctr, L, w, nx, "BetaParSquared")/dens
+ kappa1 -= bpar
+ else:
+ bperp2 = np.zeros((nx,nx))
+ sigma1 = np.zeros((nx,nx))
+ kappa1 = np.zeros((nx,nx))
+ tau = sigma_thompson*dens*self.mueinv/mh
+
+ self.bounds = np.array([-0.5*w, 0.5*w, -0.5*w, 0.5*w])
+ self.dx = w/nx
+ self.dy = w/nx
+ self.nx = nx
+
+ self._compute_intensity(tau, Te, bpar, omega1, sigma1, kappa1, bperp2)
+
+ def _compute_intensity(self, tau, Te, bpar, omega1, sigma1, kappa1, bperp2):
+
+ # Bad hack, but we get NaNs if we don't do something like this
+ small_beta = np.abs(bpar) < 1.0e-20
+ bpar[small_beta] = 1.0e-20
+
+ comm = communication_system.communicators[-1]
+
+ nx, ny = self.nx,self.nx
+ signal = np.zeros((self.num_freqs,nx,ny))
+ xo = np.zeros((self.num_freqs))
+
+ k = int(0)
+
+ start_i = comm.rank*nx/comm.size
+ end_i = (comm.rank+1)*nx/comm.size
+
+ pbar = get_pbar("Computing SZ signal.", nx*nx)
+
+ for i in xrange(start_i, end_i):
+ for j in xrange(ny):
+ xo[:] = self.xinit[:]
+ SZpack.compute_combo_means(xo, tau[i,j], Te[i,j],
+ bpar[i,j], omega1[i,j],
+ sigma1[i,j], kappa1[i,j], bperp2[i,j])
+ signal[:,i,j] = xo[:]
+ pbar.update(k)
+ k += 1
+
+ signal = comm.mpi_allreduce(signal)
+
+ pbar.finish()
+
+ for i, field in enumerate(self.freq_fields):
+ self.data[field] = ImageArray(I0*self.xinit[i]**3*signal[i,:,:])
+ self.data["Tau"] = ImageArray(tau)
+ self.data["TeSZ"] = ImageArray(Te)
+
+ @parallel_root_only
+ def write_fits(self, filename_prefix, clobber=True):
+ r""" Export images to a FITS file. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the FITS filename.
+ clobber : boolean, optional
+ If the file already exists, do we overwrite?
+
+ Examples
+ --------
+ >>> szprj.write_fits("SZbullet", clobber=False)
+ """
+ coords = {}
+ coords["dx"] = self.dx*self.pf.units["kpc"]
+ coords["dy"] = self.dy*self.pf.units["kpc"]
+ coords["xctr"] = 0.0
+ coords["yctr"] = 0.0
+ coords["units"] = "kpc"
+ other_keys = {"Time" : self.pf.current_time}
+ write_fits(self.data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=other_keys)
+
+ @parallel_root_only
+ def write_png(self, filename_prefix):
+ r""" Export images to PNG files. Writes the SZ distortion in all
+ specified frequencies as well as the mass-weighted temperature and the
+ optical depth. Distance units are in kpc.
+
+ Parameters
+ ----------
+ filename_prefix : string
+ The prefix of the image filenames.
+
+ Examples
+ --------
+ >>> szprj.write_png("SZsloshing")
+ """
+ extent = tuple([bound*self.pf.units["kpc"] for bound in self.bounds])
+ for field, image in self.items():
+ filename=filename_prefix+"_"+field+".png"
+ label = self.display_names[field]
+ if self.units[field] is not None:
+ label += " ("+self.units[field]+")"
+ write_projection(image, filename, colorbar_label=label, take_log=False,
+ extent=extent, xlabel=r"$\mathrm{x\ (kpc)}$",
+ ylabel=r"$\mathrm{y\ (kpc)}$")
+
+ @parallel_root_only
+ def write_hdf5(self, filename):
+ r"""Export the set of S-Z fields to a set of HDF5 datasets.
+
+ Parameters
+ ----------
+ filename : string
+ This file will be opened in "write" mode.
+
+ Examples
+ --------
+ >>> szprj.write_hdf5("SZsloshing.h5")
+ """
+ import h5py
+ f = h5py.File(filename, "w")
+ for field, data in self.items():
+ f.create_dataset(field,data=data)
+ f.close()
+
+ def keys(self):
+ return self.data.keys()
+
+ def items(self):
+ return self.data.items()
+
+ def values(self):
+ return self.data.values()
+
+ def has_key(self, key):
+ return key in self.data.keys()
+
+ def __getitem__(self, key):
+ return self.data[key]
+
+ @property
+ def shape(self):
+ return (self.nx,self.nx)
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/analysis_modules/sunyaev_zeldovich/setup.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/setup.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+import setuptools
+import os
+import sys
+import os.path
+
+
+def configuration(parent_package='', top_path=None):
+ from numpy.distutils.misc_util import Configuration
+ config = Configuration('sunyaev_zeldovich', parent_package, top_path)
+ config.add_subpackage("tests")
+ config.make_config_py() # installs __config__.py
+ #config.make_svn_version_py()
+ return config
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- /dev/null
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -0,0 +1,139 @@
+"""
+Unit test the sunyaev_zeldovich analysis module.
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.frontends.stream.api import load_uniform_grid
+from yt.funcs import get_pbar, mylog
+from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
+ mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
+from yt.testing import *
+from yt.utilities.answer_testing.framework import requires_pf, \
+ GenericArrayTest, data_dir_load, GenericImageTest
+try:
+ from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
+except ImportError:
+ pass
+import numpy as np
+try:
+ import SZpack
+except ImportError:
+ pass
+
+mue = 1./0.88
+freqs = np.array([30., 90., 240.])
+
+def setup():
+ """Test specific setup."""
+ from yt.config import ytcfg
+ ytcfg["yt", "__withintesting"] = "True"
+
+def full_szpack3d(pf, xo):
+ data = pf.h.grids[0]
+ dz = pf.h.get_smallest_dx()*pf.units["cm"]
+ nx,ny,nz = data["Density"].shape
+ dn = np.zeros((nx,ny,nz))
+ Dtau = sigma_thompson*data["Density"]/(mh*mue)*dz
+ Te = data["Temperature"]/K_per_keV
+ betac = data["z-velocity"]/clight
+ pbar = get_pbar("Computing 3-D cell-by-cell S-Z signal for comparison.", nx)
+ for i in xrange(nx):
+ pbar.update(i)
+ for j in xrange(ny):
+ for k in xrange(nz):
+ dn[i,j,k] = SZpack.compute_3d(xo, Dtau[i,j,k],
+ Te[i,j,k], betac[i,j,k],
+ 1.0, 0.0, 0.0, 1.0e-5)
+ pbar.finish()
+ return I0*xo**3*np.sum(dn, axis=2)
+
+def setup_cluster():
+
+ R = 1000.
+ r_c = 100.
+ rho_c = 1.673e-26
+ beta = 1.
+ T0 = 4.
+ nx,ny,nz = 16,16,16
+ c = 0.17
+ a_c = 30.
+ a = 200.
+ v0 = 300.*cm_per_km
+ ddims = (nx,ny,nz)
+
+ x, y, z = np.mgrid[-R:R:nx*1j,
+ -R:R:ny*1j,
+ -R:R:nz*1j]
+
+ r = np.sqrt(x**2+y**2+z**2)
+
+ dens = np.zeros(ddims)
+ dens = rho_c*(1.+(r/r_c)**2)**(-1.5*beta)
+ temp = T0*K_per_keV/(1.+r/a)*(c+r/a_c)/(1.+r/a_c)
+ velz = v0*temp/(T0*K_per_keV)
+
+ data = {}
+ data["Density"] = dens
+ data["Temperature"] = temp
+ data["x-velocity"] = np.zeros(ddims)
+ data["y-velocity"] = np.zeros(ddims)
+ data["z-velocity"] = velz
+
+ bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]])
+
+ L = 2*R*cm_per_kpc
+ dl = L/nz
+
+ pf = load_uniform_grid(data, ddims, L, bbox=bbox)
+
+ return pf
+
+ at requires_module("SZpack")
+def test_projection():
+ pf = setup_cluster()
+ nx,ny,nz = pf.domain_dimensions
+ xinit = 1.0e9*hcgs*freqs/(kboltz*Tcmb)
+ szprj = SZProjection(pf, freqs, mue=mue, high_order=True)
+ szprj.on_axis(2, nx=nx)
+ deltaI = np.zeros((3,nx,ny))
+ for i in xrange(3):
+ deltaI[i,:,:] = full_szpack3d(pf, xinit[i])
+ yield assert_almost_equal, deltaI[i,:,:], szprj["%d_GHz" % int(freqs[i])], 6
+
+M7 = "DD0010/moving7_0010"
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_onaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.on_axis(2, nx=100)
+ def onaxis_array_func():
+ return szprj.data
+ def onaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ for test in [GenericArrayTest(pf, onaxis_array_func),
+ GenericImageTest(pf, onaxis_image_func, 3)]:
+ test_M7_onaxis.__name__ = test.description
+ yield test
+
+ at requires_module("SZpack")
+ at requires_pf(M7)
+def test_M7_offaxis():
+ pf = data_dir_load(M7)
+ szprj = SZProjection(pf, freqs)
+ szprj.off_axis(np.array([0.1,-0.2,0.4]), nx=100)
+ def offaxis_array_func():
+ return szprj.data
+ def offaxis_image_func(filename_prefix):
+ szprj.write_png(filename_prefix)
+ for test in [GenericArrayTest(pf, offaxis_array_func),
+ GenericImageTest(pf, offaxis_image_func, 3)]:
+ test_M7_offaxis.__name__ = test.description
+ yield test
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -499,7 +499,7 @@
points[:, 2] = points[:, 2] / self.period[2]
fKD.qv_many = points.T
fKD.nn_tags = np.asfortranarray(np.empty((1, points.shape[0]), dtype='int64'))
- find_many_nn_nearest_neighbors()
+ fKD.find_many_nn_nearest_neighbors()
# The -1 is for fortran counting.
n = fKD.nn_tags[0,:] - 1
return n
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/data_objects/tests/test_fields.py
--- a/yt/data_objects/tests/test_fields.py
+++ b/yt/data_objects/tests/test_fields.py
@@ -86,6 +86,9 @@
if field.startswith("particle"): continue
if field.startswith("CIC"): continue
if field.startswith("WeakLensingConvergence"): continue
+ if field.startswith("BetaPar"): continue
+ if field.startswith("TBetaPar"): continue
+ if field.startswith("BetaPerp"): continue
if FieldInfo[field].particle_type: continue
for nproc in [1, 4, 8]:
yield TestFieldAccess(field, nproc)
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/frontends/chombo/tests/test_outputs.py
--- a/yt/frontends/chombo/tests/test_outputs.py
+++ b/yt/frontends/chombo/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(gc)
yield assert_equal, str(pf), "data.0077.3d.hdf5"
for test in small_patch_amr(gc, _fields):
+ test_gc.__name__ = test.description
yield test
tb = "TurbBoxLowRes/data.0005.3d.hdf5"
@@ -37,4 +38,5 @@
pf = data_dir_load(tb)
yield assert_equal, str(pf), "data.0005.3d.hdf5"
for test in small_patch_amr(tb, _fields):
+ test_tb.__name__ = test.description
yield test
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/frontends/enzo/tests/test_outputs.py
--- a/yt/frontends/enzo/tests/test_outputs.py
+++ b/yt/frontends/enzo/tests/test_outputs.py
@@ -30,6 +30,7 @@
pf = data_dir_load(m7)
yield assert_equal, str(pf), "moving7_0010"
for test in small_patch_amr(m7, _fields):
+ test_moving7.__name__ = test.description
yield test
g30 = "IsolatedGalaxy/galaxy0030/galaxy0030"
@@ -38,4 +39,5 @@
pf = data_dir_load(g30)
yield assert_equal, str(pf), "galaxy0030"
for test in big_patch_amr(g30, _fields):
+ test_galaxy0030.__name__ = test.description
yield test
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/frontends/flash/tests/test_outputs.py
--- a/yt/frontends/flash/tests/test_outputs.py
+++ b/yt/frontends/flash/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(sloshing)
yield assert_equal, str(pf), "sloshing_low_res_hdf5_plt_cnt_0300"
for test in small_patch_amr(sloshing, _fields):
+ test_sloshing.__name__ = test.description
yield test
_fields_2d = ("Temperature", "Density")
@@ -39,4 +40,5 @@
pf = data_dir_load(wt)
yield assert_equal, str(pf), "windtunnel_4lev_hdf5_plt_cnt_0030"
for test in small_patch_amr(wt, _fields_2d):
+ test_wind_tunnel.__name__ = test.description
yield test
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/frontends/orion/tests/test_outputs.py
--- a/yt/frontends/orion/tests/test_outputs.py
+++ b/yt/frontends/orion/tests/test_outputs.py
@@ -29,6 +29,7 @@
pf = data_dir_load(radadvect)
yield assert_equal, str(pf), "plt00000"
for test in small_patch_amr(radadvect, _fields):
+ test_radadvect.__name__ = test.description
yield test
rt = "RadTube/plt00500"
@@ -37,4 +38,5 @@
pf = data_dir_load(rt)
yield assert_equal, str(pf), "plt00500"
for test in small_patch_amr(rt, _fields):
+ test_radtube.__name__ = test.description
yield test
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/gui/reason/extdirect_router.py
--- a/yt/gui/reason/extdirect_router.py
+++ b/yt/gui/reason/extdirect_router.py
@@ -9,6 +9,13 @@
This code was released under the BSD License.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import inspect
class DirectException(Exception):
@@ -186,12 +193,4 @@
-"""
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -14,6 +14,7 @@
import itertools as it
import numpy as np
+import importlib
from yt.funcs import *
from numpy.testing import assert_array_equal, assert_almost_equal, \
assert_approx_equal, assert_array_almost_equal, assert_equal, \
@@ -251,3 +252,23 @@
list_of_kwarg_dicts[i][key] = keywords[key][0]
return list_of_kwarg_dicts
+
+def requires_module(module):
+ """
+ Decorator that takes a module name as an argument and tries to import it.
+ If the module imports without issue, the function is returned, but if not,
+ a null function is returned. This is so tests that depend on certain modules
+ being imported will not fail if the module is not installed on the testing
+ platform.
+ """
+ def ffalse(func):
+ return lambda: None
+ def ftrue(func):
+ return func
+ try:
+ importlib.import_module(module)
+ except ImportError:
+ return ffalse
+ else:
+ return ftrue
+
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -24,6 +24,7 @@
import shelve
import zlib
import tempfile
+import glob
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -576,6 +577,16 @@
for newc, oldc in zip(new_result["children"], old_result["children"]):
assert(newp == oldp)
+def compare_image_lists(new_result, old_result, decimals):
+ fns = ['old.png', 'new.png']
+ num_images = len(old_result)
+ assert(num_images > 0)
+ for i in xrange(num_images):
+ mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[i])))
+ mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[i])))
+ assert compare_images(fns[0], fns[1], 10**(decimals)) == None
+ for fn in fns: os.remove(fn)
+
class PlotWindowAttributeTest(AnswerTestingTest):
_type_name = "PlotWindowAttribute"
_attrs = ('plot_type', 'plot_field', 'plot_axis', 'attr_name', 'attr_args')
@@ -603,12 +614,71 @@
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
- fns = ['old.png', 'new.png']
- mpimg.imsave(fns[0], np.loads(zlib.decompress(old_result[0])))
- mpimg.imsave(fns[1], np.loads(zlib.decompress(new_result[0])))
- assert compare_images(fns[0], fns[1], 10**(-self.decimals)) == None
- for fn in fns: os.remove(fn)
+ compare_image_lists(new_result, old_result, self.decimals)
+
+class GenericArrayTest(AnswerTestingTest):
+ _type_name = "GenericArray"
+ _attrs = ('array_func_name','args','kwargs')
+ def __init__(self, pf_fn, array_func, args=None, kwargs=None, decimals=None):
+ super(GenericArrayTest, self).__init__(pf_fn)
+ self.array_func = array_func
+ self.array_func_name = array_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ return self.array_func(*args, **kwargs)
+ def compare(self, new_result, old_result):
+ assert_equal(len(new_result), len(old_result),
+ err_msg="Number of outputs not equal.",
+ verbose=True)
+ for k in new_result:
+ if self.decimals is None:
+ assert_equal(new_result[k], old_result[k])
+ else:
+ assert_allclose(new_result[k], old_result[k], 10**(-self.decimals))
+class GenericImageTest(AnswerTestingTest):
+ _type_name = "GenericImage"
+ _attrs = ('image_func_name','args','kwargs')
+ def __init__(self, pf_fn, image_func, decimals, args=None, kwargs=None):
+ super(GenericImageTest, self).__init__(pf_fn)
+ self.image_func = image_func
+ self.image_func_name = image_func.func_name
+ self.args = args
+ self.kwargs = kwargs
+ self.decimals = decimals
+ def run(self):
+ if self.args is None:
+ args = []
+ else:
+ args = self.args
+ if self.kwargs is None:
+ kwargs = {}
+ else:
+ kwargs = self.kwargs
+ comp_imgs = []
+ tmpdir = tempfile.mkdtemp()
+ image_prefix = os.path.join(tmpdir,"test_img")
+ self.image_func(image_prefix, *args, **kwargs)
+ imgs = glob.glob(image_prefix+"*")
+ assert(len(imgs) > 0)
+ for img in imgs:
+ img_data = mpimg.imread(img)
+ os.remove(img)
+ comp_imgs.append(zlib.compress(img_data.dumps()))
+ return comp_imgs
+ def compare(self, new_result, old_result):
+ compare_image_lists(new_result, old_result, self.decimals)
+
def requires_pf(pf_fn, big_data = False):
def ffalse(func):
return lambda: None
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/utilities/physical_constants.py
--- a/yt/utilities/physical_constants.py
+++ b/yt/utilities/physical_constants.py
@@ -84,6 +84,7 @@
erg_per_keV = erg_per_eV * 1.0e3
K_per_keV = erg_per_keV / boltzmann_constant_cgs
keV_per_K = 1.0 / K_per_keV
+Tcmb = 2.726 # Current CMB temperature
#Short cuts
G = gravitational_constant_cgs
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -19,6 +19,7 @@
y_dict, \
axis_names
from .volume_rendering.api import off_axis_projection
+from image_writer import write_fits
from yt.data_objects.image_array import ImageArray
import _MPL
import numpy as np
@@ -263,8 +264,8 @@
output.create_dataset(field,data=self[field])
output.close()
- def export_fits(self, filename_prefix, fields = None, clobber=False,
- other_keys=None, gzip_file=False, units="1"):
+ def export_fits(self, filename_prefix, fields=None, clobber=False,
+ other_keys=None, units="cm", sky_center=(0.0,0.0), D_A=None):
"""
This will export a set of FITS images of either the fields specified
@@ -273,106 +274,80 @@
existing FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also
+ part of AstroPy.
"""
r"""Export a set of pixelized fields to a FITS file.
This will export a set of FITS images of either the fields specified
- or all the fields already in the object. The output filename is the
- the specified prefix.
+ or all the fields already in the object.
Parameters
----------
filename_prefix : string
- This prefix will be prepended to every FITS file name.
+ This prefix will be prepended to the FITS file name.
fields : list of strings
These fields will be pixelized and output.
clobber : boolean
If the file exists, this governs whether we will overwrite.
other_keys : dictionary, optional
A set of header keys and values to write into the FITS header.
- gzip_file : boolean, optional
- gzip the file after writing, default False
units : string, optional
- the length units that the coordinates are written in, default '1'
+ the length units that the coordinates are written in, default 'cm'
+ If units are set to "deg" then assume that sky coordinates are
+ requested.
+ sky_center : array_like, optional
+ Center of the image in (ra,dec) in degrees if sky coordinates
+ (units="deg") are requested.
+ D_A : float or tuple, optional
+ Angular diameter distance, given in code units as a float or
+ a tuple containing the value and the length unit. Required if
+ using sky coordinates.
"""
-
- import pyfits
- from os import system
-
+
+ if units == "deg" and D_A is None:
+ mylog.error("Sky coordinates require an angular diameter distance. Please specify D_A.")
+ if iterable(D_A):
+ dist = D_A[0]/self.pf.units[D_A[1]]
+ else:
+ dist = D_A
+
+ if other_keys is None:
+ hdu_keys = {}
+ else:
+ hdu_keys = other_keys
+
extra_fields = ['x','y','z','px','py','pz','pdx','pdy','pdz','weight_field']
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
if fields is None:
fields = [field for field in self.data_source.fields
if field not in extra_fields]
+ coords = {}
nx, ny = self.buff_size
- dx = (self.bounds[1]-self.bounds[0])/nx*self.pf[units]
- dy = (self.bounds[3]-self.bounds[2])/ny*self.pf[units]
- xmin = self.bounds[0]*self.pf[units]
- ymin = self.bounds[2]*self.pf[units]
- simtime = self.pf.current_time
+ dx = (self.bounds[1]-self.bounds[0])/nx
+ dy = (self.bounds[3]-self.bounds[2])/ny
+ if units == "deg":
+ coords["dx"] = -np.rad2deg(dx/dist)
+ coords["dy"] = np.rad2deg(dy/dist)
+ coords["xctr"] = sky_center[0]
+ coords["yctr"] = sky_center[1]
+ hdu_keys["MTYPE1"] = "EQPOS"
+ hdu_keys["MFORM1"] = "RA,DEC"
+ hdu_keys["CTYPE1"] = "RA---TAN"
+ hdu_keys["CTYPE2"] = "DEC--TAN"
+ else:
+ coords["dx"] = dx*self.pf.units[units]
+ coords["dy"] = dy*self.pf.units[units]
+ coords["xctr"] = 0.5*(self.bounds[0]+self.bounds[1])*self.pf.units[units]
+ coords["yctr"] = 0.5*(self.bounds[2]+self.bounds[3])*self.pf.units[units]
+ coords["units"] = units
+
+ hdu_keys["Time"] = self.pf.current_time
- hdus = []
-
- first = True
-
- for field in fields:
-
- if (first) :
- hdu = pyfits.PrimaryHDU(self[field])
- first = False
- else :
- hdu = pyfits.ImageHDU(self[field])
+ data = dict([(field,self[field]) for field in fields])
+ write_fits(data, filename_prefix, clobber=clobber, coords=coords,
+ other_keys=hdu_keys)
- if self.data_source.has_key('weight_field'):
- weightname = self.data_source._weight
- if weightname is None: weightname = 'None'
- field = field +'_'+weightname
-
- hdu.header.update("Field", field)
- hdu.header.update("Time", simtime)
-
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', xmin)
- hdu.header.update('CRVAL2P', ymin)
- hdu.header.update('CDELT1P', dx)
- hdu.header.update('CDELT2P', dy)
-
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', units)
- hdu.header.update('CUNIT2', units)
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', xmin)
- hdu.header.update('CRVAL2', ymin)
- hdu.header.update('CDELT1', dx)
- hdu.header.update('CDELT2', dy)
-
- if (other_keys is not None) :
-
- for k,v in other_keys.items() :
-
- hdu.header.update(k,v)
-
- hdus.append(hdu)
-
- del hdu
-
- hdulist = pyfits.HDUList(hdus)
-
- hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
-
- if (gzip_file) :
- clob = ""
- if (clobber) : clob = "-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
-
def open_in_ds9(self, field, take_log=True):
"""
This will open a given field in the DS9 viewer.
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/visualization/image_writer.py
--- a/yt/visualization/image_writer.py
+++ b/yt/visualization/image_writer.py
@@ -333,7 +333,8 @@
def write_projection(data, filename, colorbar=True, colorbar_label=None,
title=None, limits=None, take_log=True, figsize=(8,6),
- dpi=100, cmap_name='algae'):
+ dpi=100, cmap_name='algae', extent=None, xlabel=None,
+ ylabel=None):
r"""Write a projection or volume rendering to disk with a variety of
pretty parameters such as limits, title, colorbar, etc. write_projection
uses the standard matplotlib interface to create the figure. N.B. This code
@@ -392,16 +393,22 @@
# Create the figure and paint the data on
fig = matplotlib.figure.Figure(figsize=figsize)
ax = fig.add_subplot(111)
- fig.tight_layout()
-
- cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm, cmap=cmap_name)
+
+ cax = ax.imshow(data, vmin=limits[0], vmax=limits[1], norm=norm,
+ extent=extent, cmap=cmap_name)
if title:
ax.set_title(title)
+ if xlabel:
+ ax.set_xlabel(xlabel)
+ if ylabel:
+ ax.set_ylabel(ylabel)
+
# Suppress the x and y pixel counts
- ax.set_xticks(())
- ax.set_yticks(())
+ if extent is None:
+ ax.set_xticks(())
+ ax.set_yticks(())
# Add a color bar and label if requested
if colorbar:
@@ -409,6 +416,8 @@
if colorbar_label:
cbar.ax.set_ylabel(colorbar_label)
+ fig.tight_layout()
+
suffix = get_image_suffix(filename)
if suffix == '':
@@ -429,70 +438,89 @@
return filename
-def write_fits(image, filename_prefix, clobber=True, coords=None, gzip_file=False) :
+def write_fits(image, filename_prefix, clobber=True, coords=None,
+ other_keys=None):
"""
This will export a FITS image of a floating point array. The output filename is
*filename_prefix*. If clobber is set to True, this will overwrite any existing
FITS file.
This requires the *pyfits* module, which is a standalone module
- provided by STSci to interface with FITS-format files.
+ provided by STSci to interface with FITS-format files, and is also part of
+ AstroPy.
"""
- r"""Write out a floating point array directly to a FITS file, optionally
- adding coordinates.
+ r"""Write out floating point arrays directly to a FITS file, optionally
+ adding coordinates and header keywords.
Parameters
----------
- image : array_like
- This is an (unscaled) array of floating point values, shape (N,N,) to save
- in a FITS file.
+ image : array_like, or dict of array_like objects
+ This is either an (unscaled) array of floating point values, or a dict of
+ such arrays, shape (N,N,) to save in a FITS file.
filename_prefix : string
This prefix will be prepended to every FITS file name.
clobber : boolean
If the file exists, this governs whether we will overwrite.
coords : dictionary, optional
A set of header keys and values to write to the FITS header to set up
- a coordinate system.
- gzip_file : boolean, optional
- gzip the file after writing, default False
+ a coordinate system, which is assumed to be linear unless specified otherwise
+ in *other_keys*
+ "units": the length units
+ "xctr","yctr": the center of the image
+ "dx","dy": the pixel width in each direction
+ other_keys : dictionary, optional
+ A set of header keys and values to write into the FITS header.
"""
+
+ try:
+ import pyfits
+ except ImportError:
+ try:
+ import astropy.io.fits as pyfits
+ except:
+ raise ImportError("You don't have pyFITS or AstroPy installed.")
- import pyfits
from os import system
- if filename_prefix.endswith('.fits'): filename_prefix=filename_prefix[:-5]
-
- hdu = pyfits.PrimaryHDU(image)
+ try:
+ image.keys()
+ image_dict = image
+ except:
+ image_dict = dict(yt_data=image)
- if (coords is not None) :
+ hdulist = [pyfits.PrimaryHDU()]
- hdu.header.update('WCSNAMEP', "PHYSICAL")
- hdu.header.update('CTYPE1P', "LINEAR")
- hdu.header.update('CTYPE2P', "LINEAR")
- hdu.header.update('CRPIX1P', 0.5)
- hdu.header.update('CRPIX2P', 0.5)
- hdu.header.update('CRVAL1P', coords["xmin"])
- hdu.header.update('CRVAL2P', coords["ymin"])
- hdu.header.update('CDELT1P', coords["dx"])
- hdu.header.update('CDELT2P', coords["dy"])
+ for key in image_dict.keys():
+
+ mylog.info("Writing image block \"%s\"" % (key))
+ hdu = pyfits.ImageHDU(image_dict[key])
+ hdu.update_ext_name(key)
- hdu.header.update('CTYPE1', "LINEAR")
- hdu.header.update('CTYPE2', "LINEAR")
- hdu.header.update('CUNIT1', coords["units"])
- hdu.header.update('CUNIT2', coords["units"])
- hdu.header.update('CRPIX1', 0.5)
- hdu.header.update('CRPIX2', 0.5)
- hdu.header.update('CRVAL1', coords["xmin"])
- hdu.header.update('CRVAL2', coords["ymin"])
- hdu.header.update('CDELT1', coords["dx"])
- hdu.header.update('CDELT2', coords["dy"])
+ if coords is not None:
- hdu.writeto("%s.fits" % (filename_prefix), clobber=clobber)
+ nx, ny = image_dict[key].shape
- if (gzip_file) :
- clob = ""
- if (clobber) : clob="-f"
- system("gzip "+clob+" %s.fits" % (filename_prefix))
+ hdu.header.update('CUNIT1', coords["units"])
+ hdu.header.update('CUNIT2', coords["units"])
+ hdu.header.update('CRPIX1', 0.5*(nx+1))
+ hdu.header.update('CRPIX2', 0.5*(ny+1))
+ hdu.header.update('CRVAL1', coords["xctr"])
+ hdu.header.update('CRVAL2', coords["yctr"])
+ hdu.header.update('CDELT1', coords["dx"])
+ hdu.header.update('CDELT2', coords["dy"])
+ # These are the defaults, but will get overwritten if
+ # the caller has specified them
+ hdu.header.update('CTYPE1', "LINEAR")
+ hdu.header.update('CTYPE2', "LINEAR")
+
+ if other_keys is not None:
+ for k,v in other_keys.items():
+ hdu.header.update(k,v)
+
+ hdulist.append(hdu)
+
+ hdulist = pyfits.HDUList(hdulist)
+ hdulist.writeto("%s.fits" % (filename_prefix), clobber=clobber)
def display_in_notebook(image, max_val=None):
"""
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -94,8 +94,10 @@
for ax in 'xyz':
for attr_name in ATTR_ARGS.keys():
for args in ATTR_ARGS[attr_name]:
- yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
- args, decimals)
+ test = PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
+ args, decimals)
+ test_attributes.__name__ = test.description
+ yield test
@requires_pf(WT)
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -72,6 +72,9 @@
cubical, but if not, it is left/right, top/bottom, front/back.
resolution : int or list of ints
The number of pixels in each direction.
+ transfer_function : `yt.visualization.volume_rendering.TransferFunction`
+ The transfer function used to map values to colors in an image. If
+ not specified, defaults to a ProjectionTransferFunction.
north_vector : array_like, optional
The 'up' direction for the plane of rays. If not specific, calculated
automatically.
@@ -184,7 +187,7 @@
_tf_figure = None
_render_figure = None
def __init__(self, center, normal_vector, width,
- resolution, transfer_function,
+ resolution, transfer_function = None,
north_vector = None, steady_north=False,
volume = None, fields = None,
log_fields = None,
@@ -1465,7 +1468,7 @@
class MosaicCamera(Camera):
def __init__(self, center, normal_vector, width,
- resolution, transfer_function,
+ resolution, transfer_function = None,
north_vector = None, steady_north=False,
volume = None, fields = None,
log_fields = None,
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/visualization/volume_rendering/multi_texture.py
--- a/yt/visualization/volume_rendering/multi_texture.py
+++ b/yt/visualization/volume_rendering/multi_texture.py
@@ -35,6 +35,14 @@
I hope this helps,
Almar
"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
from yt.mods import *
from yt.funcs import *
@@ -300,14 +308,3 @@
ax.Draw()
return mtex, ax
-
-
-"""
-
-#-----------------------------------------------------------------------------
-# Copyright (c) 2013, yt Development Team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file COPYING.txt, distributed with this software.
-#-----------------------------------------------------------------------------
diff -r f9d93f52511598519293a34920d466cad6082bb5 -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae yt/visualization/volume_rendering/transfer_function_helper.py
--- /dev/null
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -0,0 +1,211 @@
+"""
+A helper class to build, display, and modify transfer functions for volume
+rendering.
+
+
+
+"""
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+from yt.funcs import mylog
+from yt.data_objects.profiles import BinnedProfile1D
+from yt.visualization.volume_rendering.api import ColorTransferFunction
+from yt.visualization._mpl_imports import FigureCanvasAgg
+from matplotlib.figure import Figure
+from IPython.core.display import Image
+import cStringIO
+import numpy as np
+
+
+class TransferFunctionHelper(object):
+
+ profiles = None
+
+ def __init__(self, pf):
+ r"""A transfer function helper.
+
+ This attempts to help set up a good transfer function by finding
+ bounds, handling linear/log options, and displaying the transfer
+ function combined with 1D profiles of rendering quantity.
+
+ Parameters
+ ----------
+ pf: A StaticOutput instance
+ A static output that is currently being rendered. This is used to
+ help set up data bounds.
+
+ Notes
+ -----
+ """
+ self.pf = pf
+ self.field = None
+ self.log = False
+ self.tf = None
+ self.bounds = None
+ self.grey_opacity = True
+ self.profiles = {}
+
+ def set_bounds(self, bounds=None):
+ """
+ Set the bounds of the transfer function.
+
+ Parameters
+ ----------
+ bounds: array-like, length 2, optional
+ A length 2 list/array in the form [min, max]. These should be the
+ raw values and not the logarithm of the min and max. If bounds is
+ None, the bounds of the data are calculated from all of the data
+ in the dataset. This can be slow for very large datasets.
+ """
+ if bounds is None:
+ bounds = self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+ self.bounds = bounds
+
+ # Do some error checking.
+ assert(len(self.bounds) == 2)
+ if self.log:
+ assert(self.bounds[0] > 0.0)
+ assert(self.bounds[1] > 0.0)
+ return
+
+ def set_field(self, field):
+ """
+ Set the field to be rendered
+
+ Parameters
+ ----------
+ field: string
+ The field to be rendered.
+ """
+ self.field = field
+
+ def set_log(self, log):
+ """
+ Set whether or not the transfer function should be in log or linear
+ space. Also modifies the pf.field_info[field].take_log attribute to
+ stay in sync with this setting.
+
+ Parameters
+ ----------
+ log: boolean
+ Sets whether the transfer function should use log or linear space.
+ """
+ self.log = log
+ self.pf.h
+ self.pf.field_info[self.field].take_log = log
+
+ def build_transfer_function(self):
+ """
+ Builds the transfer function according to the current state of the
+ TransferFunctionHelper.
+
+ Parameters
+ ----------
+ None
+
+ Returns
+ -------
+
+ A ColorTransferFunction object.
+
+ """
+ if self.bounds is None:
+ mylog.info('Calculating data bounds. This may take a while.' +
+ ' Set the .bounds to avoid this.')
+ self.set_bounds()
+
+ if self.log:
+ mi, ma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ mi, ma = self.bounds
+ self.tf = ColorTransferFunction((mi, ma),
+ grey_opacity=self.grey_opacity,
+ nbins=512)
+ return self.tf
+
+ def plot(self, fn=None, profile_field=None, profile_weight=None):
+ """
+ Save the current transfer function to a bitmap, or display
+ it inline.
+
+ Parameters
+ ----------
+ fn: string, optional
+ Filename to save the image to. If None, the returns an image
+ to an IPython session.
+
+ Returns
+ -------
+
+ If fn is None, will return an image to an IPython notebook.
+
+ """
+ if self.tf is None:
+ self.build_transfer_function()
+ tf = self.tf
+ if self.log:
+ xfunc = np.logspace
+ xmi, xma = np.log10(self.bounds[0]), np.log10(self.bounds[1])
+ else:
+ xfunc = np.linspace
+ xmi, xma = self.bounds
+
+ x = xfunc(xmi, xma, tf.nbins)
+ y = tf.funcs[3].y
+ w = np.append(x[1:]-x[:-1], x[-1]-x[-2])
+ colors = np.array([tf.funcs[0].y, tf.funcs[1].y, tf.funcs[2].y,
+ np.ones_like(x)]).T
+
+ fig = Figure(figsize=[6, 3])
+ canvas = FigureCanvasAgg(fig)
+ ax = fig.add_axes([0.2, 0.2, 0.75, 0.75])
+ ax.bar(x, tf.funcs[3].y, w, edgecolor=[0.0, 0.0, 0.0, 0.0],
+ log=True, color=colors, bottom=[0])
+
+ if profile_field is not None:
+ try:
+ prof = self.profiles[self.field]
+ except KeyError:
+ self.setup_profile(profile_field, profile_weight)
+ prof = self.profiles[self.field]
+ if profile_field not in prof.keys():
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='w', linewidth=3)
+ ax.plot(prof[self.field], prof[profile_field]*tf.funcs[3].y.max() /
+ prof[profile_field].max(), color='k')
+
+ ax.set_xscale({True: 'log', False: 'linear'}[self.log])
+ ax.set_xlim(x.min(), x.max())
+ ax.set_xlabel(self.pf.field_info[self.field].get_label())
+ ax.set_ylabel(r'$\mathrm{alpha}$')
+ ax.set_ylim(y.max()*1.0e-3, y.max()*2)
+
+ if fn is None:
+ f = cStringIO.StringIO()
+ canvas.print_figure(f)
+ f.seek(0)
+ img = f.read()
+ return Image(img)
+ else:
+ fig.savefig(fn)
+
+ def setup_profile(self, profile_field=None, profile_weight=None):
+ if profile_field is None:
+ profile_field = 'CellVolume'
+ prof = BinnedProfile1D(self.pf.h.all_data(), 128, self.field,
+ self.bounds[0], self.bounds[1],
+ log_space=self.log,
+ lazy_reader=False, end_collect=False)
+ prof.add_fields([profile_field], fractional=False,
+ weight=profile_weight)
+ self.profiles[self.field] = prof
+ return
https://bitbucket.org/yt_analysis/yt/commits/d0f22c945ecf/
Changeset: d0f22c945ecf
Branch: yt
User: xarthisius
Date: 2013-10-12 12:37:42
Summary: mergin
Affected #: 2 files
diff -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae -r d0f22c945ecf1824654f4250f511466599742bcd doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -918,6 +918,8 @@
do_setup_py $SYMPY
[ $INST_PYX -eq 1 ] && do_setup_py $PYX
+( ${DEST_DIR}/bin/pip install jinja2 2>&1 ) 1>> ${LOG_FILE}
+
# Now we build Rockstar and set its environment variable.
if [ $INST_ROCKSTAR -eq 1 ]
then
diff -r 0cddfb9d6650bbac4b7cf75667b759b328cba9ae -r d0f22c945ecf1824654f4250f511466599742bcd yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -33,8 +33,8 @@
try:
import SZpack
-except:
- raise ImportError("SZpack not installed. It can be obtained from from http://www.chluba.de/SZpack/.")
+except ImportError:
+ pass
vlist = "xyz"
https://bitbucket.org/yt_analysis/yt/commits/ec265cad745a/
Changeset: ec265cad745a
Branch: yt-3.0
User: xarthisius
Date: 2014-04-13 10:12:52
Summary: Add short paragraph concerning manual installation. Fixes #790
Affected #: 1 file
diff -r cc6b873a4471e049b6fef33146e92615c72f1243 -r ec265cad745a200dd7bacdf45194e00f5bcacd4c doc/source/installing.rst
--- a/doc/source/installing.rst
+++ b/doc/source/installing.rst
@@ -12,7 +12,7 @@
computation engine, Matplotlib for some visualization tasks and Mercurial for
version control. Because installation of all of these interlocking parts can
be time-consuming, yt provides an installation script which downloads and builds
-a fully-isolated Python + Numpy + Matplotlib + HDF5 + Mercurial installation.
+a fully-isolated Python + NumPy + Matplotlib + HDF5 + Mercurial installation.
yt supports Linux and OSX deployment, with the possibility of deployment on
other Unix-like systems (XSEDE resources, clusters, etc.). Windows is not
supported.
@@ -86,16 +86,41 @@
Alternative Installation Methods
--------------------------------
-If you want to forego the use of the install script, you need to make sure
-you have yt's dependencies installed on your system. These include: a C compiler,
-``HDF5``, ``Freetype``, ``libpng``, ``python``, ``cython``, ``numpy``, and
-``matplotlib``. From here, you can use ``pip`` (which comes with ``Python``)
-to install yt as:
+If you want to forego the use of the install script, you need to make sure you
+have yt's dependencies installed on your system. These include: a C compiler,
+``HDF5``, ``Freetype``, ``libpng``, ``python``, ``cython``, ``NumPy``, and
+``matplotlib``. From here, you can use ``pip`` (which comes with ``Python``) to
+install yt as:
.. code-block:: bash
$ pip install yt
+The source code for yt may be found at the Bitbucket project site and can also be
+utilized for installation. If you prefer to use it instead of relying on external
+tools, you will need ``mercurial`` to clone the official repo:
+
+.. code-block:: bash
+
+ $ hg clone https://bitbucket.org/yt_analysis/yt
+ $ cd yt
+ $ hg update yt
+ $ python setup.py install --user
+
+It will install yt into ``$HOME/.local/lib64/python2.7/site-packages``.
+Please refer to ``setuptools`` documentation for the additional options.
+
+Provided that the required dependencies are in a predictable location, yt should
+be able to find them automatically. However, you can manually specify prefix used
+for installation of ``HDF5``, ``Freetype`` and ``libpng`` by using ``hdf5.cfg``,
+``freetype.cfg``, ``png.cfg`` or setting ``HDF5_DIR``, ``FTYPE_DIR``, ``PNG_DIR``
+environmental variables respectively, e.g.
+
+.. code-block:: bash
+
+ $ echo '/usr/local' > hdf5.cfg
+ $ export FTYPE_DIR=/opt/freetype
+
If you choose this installation method, you do not need to run the activation
script as it is unnecessary.
Repository URL: https://bitbucket.org/yt_analysis/yt/
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