Hi yt gurus,
I've been making projections of star_density from enzo output files
and they seem to be working out fine. However, wherever particles do not
exist the background remains white instead of following my chosen colormap.
Is there a way to paint these areas to follow the colormap?
thanks!
Munier
I've attached an image of what gets plotted, and the relevant bits of my
script are:
*from yt.mods import **
*
*
*fName = "DD0006/test_sim_0006"*
*var = "star_density"*
*axis = 0*
*
*
*pf = load(fName)*
*pf.h*
*
*
*pc = PlotCollection(pf)*
*p = pc.add_projection(var,axis)*
*#p.modify["particles"](1.0)*
*
*
*radius = .02;*
*
*
*pc.set_xlim(.5-radius,.5+radius)*
*pc.set_ylim(.5-radius,.5+radius)*
*
*
*pc.save(fName)*
--
Munier A. Salem // 845.489.6450
Is this behavior familiar to anyone? I've done this with a fresh
build and one from a few months ago.
The set was generated with the latest build of enzo. With a set
generated from an earlier enzo build, I can read the set just fine.
Thanks!
d.
>>> from yt.mods import *
>>> pf = load('/Users/dccollins/Enzo/unstable/run/GravitySolver/GravityTest/./DD0000/data0000')
>>> pf.h
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/dccollins/local2/src/yt-hg/yt/data_objects/static_output.py",
line 189, in hierarchy
self, data_style=self.data_style)
File "/Users/dccollins/local2/src/yt-hg/yt/frontends/enzo/data_structures.py",
line 218, in __init__
AMRHierarchy.__init__(self, pf, data_style)
File "/Users/dccollins/local2/src/yt-hg/yt/data_objects/hierarchy.py",
line 62, in __init__
self._count_grids()
File "/Users/dccollins/local2/src/yt-hg/yt/frontends/enzo/data_structures.py",
line 240, in _count_grids
self._guess_data_style(self.pf.dimensionality, test_grid, test_grid_id)
File "/Users/dccollins/local2/src/yt-hg/yt/frontends/enzo/data_structures.py",
line 243, in _guess_data_style
if test_grid[0] != os.path.sep:
TypeError: 'NoneType' object is not subscriptable
--
Sent from my computer.
Hey all,
I've been trying to stick yt on an opensuse box, and I've run into a kind of funky error when it attempts to install mercurial-2.2.2. I just wanted to see if perhaps anyone has hit this wall before?
user_base = getuserbase() # this will also set USER_BASE
File "/home/nearl/yt-x86_64/lib/python2.7/site.py", line 243, in getuserbase
USER_BASE = get_config_var('userbase')
File "/home/nearl/yt-x86_64/lib/python2.7/sysconfig.py", line 520, in get_config_var
return get_config_vars().get(name)
File "/home/nearl/yt-x86_64/lib/python2.7/sysconfig.py", line 419, in get_config_vars
_init_posix(_CONFIG_VARS)
File "/home/nearl/yt-x86_64/lib/python2.7/sysconfig.py", line 287, in _init_posix
raise IOError(msg)
IOError: invalid Python installation: unable to open /home/nearl/yt-x86_64/lib/python2.7/config/Makefile (No such file or directory)
The directory /config does not exist. I've attempted to install the python-devel package, along with the python-setuptools-devel package, but they didn't seem to help at all.
I haven't worked with opensuse before, so it's quite possible that this may be a platform-dependent issue. Any suggestions would be greatly appreciated!
Nick
Hi,
I gather that cylindrical geometries aren't supported. Is it possible to force yt to read in cylindrical coordinates as though they were cartesian?
When I try to load an athena vtk in cylindrical, I get:
In [32]: pf = load("cyl_disk.0001.vtk")
yt : [INFO ] 2012-11-15 15:31:26,443 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected automatically if it is not the case.
yt : [INFO ] 2012-11-15 15:31:26,445 Parameters: current_time = 0.001080635
yt : [INFO ] 2012-11-15 15:31:26,445 Parameters: domain_dimensions = [ -37 128 -2147483648]
yt : [INFO ] 2012-11-15 15:31:26,445 Parameters: domain_left_edge = [ 1. -1.570796 0. ]
yt : [INFO ] 2012-11-15 15:31:26,445 Parameters: domain_right_edge = [-1. 1.570796 -0. ]
yt : [INFO ] 2012-11-15 15:31:26,445 Parameters: cosmological_simulation = 0.0
This is a 256 by 128 grid, and the dimensions should be -pi/2, pi/2 and 1, 15.
Thanks,
Kaitlin
Hey all!
When I try to call my own added field magB I get a runtime error saying
that the cgs unitsystem is
unrecognized. When I insert pf["unitsystem"] == "cgs" directly before
the call where the traceback
starts, it returns true.
Best wishes,
Patrick
I add the field with:
def _magB(field,data):
return (na.sqrt(data["Bx"]**2 + data["By"]**2 + data["Bz"]**2))
add_field("magB", function=_magB, units=r"\rm{Gauss}")
and then call:
rad_profile.add_fields("magB")
Traceback:
File "rad_profile_magb.py", line 100, in <module>
rad_profile.add_fields("magB")
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py",
line 170, in add_fields
self._unlazy_add_fields(fields, weight, accumulation)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py",
line 151, in _unlazy_add_fields
accumulation, self._args, check_cut = False)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py",
line 55, in save_state
tr = func(*args, **kwargs)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py",
line 264, in _bin_field
source_data = self._get_field(source, field, check_cut)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/profiles.py",
line 204, in _get_field
data.append(source[field][pointI].ravel().astype('float64'))
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 328, in __getitem__
self.get_data(key)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 2593, in get_data
if self._generate_field(field):
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 358, in _generate_field
self[field] = self.pf.field_info[field](self)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py",
line 378, in __call__
dd = self._function(self, data)
File "/home/patrick/Auswertung/yt-bit/Plot/common_fields.py", line 7,
in _magB
return (na.sqrt(data["Bx"]**2 + data["By"]**2 + data["Bz"]**2))
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 328, in __getitem__
self.get_data(key)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 2593, in get_data
if self._generate_field(field):
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
line 358, in _generate_field
self[field] = self.pf.field_info[field](self)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py",
line 378, in __call__
dd = self._function(self, data)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/fields.py",
line 357, in _Bx
factor = GetMagRescalingFactor(data.pf)
File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/fields.py",
line 353, in GetMagRescalingFactor
"value %s is unrecognized" % pf['unitsystem'])
RuntimeError: Runtime parameter unitsystem withvalue cgs is unrecognized
Hey all,
So I still get some strange behaviour with the ProjectionPlot. If I use
the projection.set_width() with the clumps callback method I get the
real image shrinked inside the the plot window. Strange thing is, that
it grows with each step! Here is a demonstration how it looks (you have
to look closely as it doesn't grow that much each step):
http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/
If I don't use the set_width() then the image itself looks fine, but the
scale on the axis grows with each step. So it seems to be the same error
than with fixed width.
Best wishes,
Patrick
Here is the code that I am using:
# ID is just a list of tuples with clumps/their position in an array
# sim_files and clump_files is a list containing the filenames
# get_myclump() simply returns a specific clump
for j, series in enumerate(ID):
for i in series:
pf = load(sim_files[i[0]])
myclump = get_myclump(clump_files[i[0]], i[1])
pc = ProjectionPlot(pf, axis, my_field, center =
pf.domain_center, weight_field = my_wfield)
pc.set_width(28, "mpc")
pc.annotate_text([0.0,1.05], "Clump %s" % j)
if redshift:
pc.annotate_text([0.917,1.05], "z = %0.4f" %
pf.current_redshift)
if grid:
pc.annotate_grids()
if fix_scale:
pc.set_zlim(my_field,boundaries[0],boundaries[1])
pc.set_cmap("Density", "idl01")
pc.annotate_clumps(myclump)
pc.save('%s/Clump_%s_File_%s_Nr_%s_%s_Projection.png' %
(myBASEDIR, j, i[0], i[1], axis))
Hi all,
I am unable to access the derived fields written for Orion such as temperature, pressure, etc.
The definitions are these fields are located here: yt-x86_64/src/yt-hg/yt/frontends/orion/fields.py
This is the error that I get if I try to access temperature:
In [14]: mi,ma= dd.quantities["Extrema"]("Temperature")[0]
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-14-c8df716340ab> in <module>()
----> 1 mi,ma= dd.quantities["Extrema"]("Temperature")[0]
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in __call__(self, *args, **kwargs)
90 self._data_source.pf.h.io)
91 if lazy_reader and not self.force_unlazy:
---> 92 return self._call_func_lazy(args, kwargs)
93 else:
94 return self._call_func_unlazy(args, kwargs)
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in _call_func_lazy(self, args, kwargs)
97 self.retvals = [ [] for i in range(self.n_ret)]
98 for gi,g in enumerate(self._get_grids()):
---> 99 rv = self.func(GridChildMaskWrapper(g, self._data_source), *args, **kwargs)
100 if not iterable(rv): rv = (rv,)
101 for i in range(self.n_ret): self.retvals[i].append(rv[i])
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in _Extrema(data, fields, non_zero, filter)
586 mins, maxs = [], []
587 for field in fields:
--> 588 if data[field].size < 1:
589 mins.append(1e90)
590 maxs.append(-1e90)
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.pyc in __getitem__(self, item)
58 def __getitem__(self, item):
59 if item not in self.local_cache:
---> 60 data = self.data_source._get_data_from_grid(self.grid, item)
61 self.local_cache[item] = data
62 return self.local_cache[item]
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs)
89 old_keys = grid.field_data.keys()
90 grid.field_parameters = self.field_parameters
---> 91 tr = func(self, grid, field, *args, **kwargs)
92 grid.field_parameters = old_params
93 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] )
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field)
2555 return na.array([f[i,:][pointI] for i in range(3)])
2556 else:
-> 2557 tr = grid[field]
2558 if tr.size == 1: # dx, dy, dz, cellvolume
2559 tr = tr * na.ones(grid.ActiveDimensions, dtype='float64')
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in __getitem__(self, key)
155 """
156 if not self.field_data.has_key(key):
--> 157 self.get_data(key)
158 return self.field_data[key]
159
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in get_data(self, field, convert)
198 else: raise
199 else:
--> 200 self._generate_field(field)
201 return self.field_data[field]
202
/home1/arosen2/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.pyc in _generate_field(self, field)
145 self[field] = self.pf.field_info[field](self)
146 else: # Can't find the field, try as it might
--> 147 raise exceptions.KeyError(field)
148
149 def has_key(self, key):
KeyError: 'Temperature'
Thanks!
Anna Rosen
Graduate Student
UCSC, Astronomy & Astrophysics
rosen(a)ucolick.org
Hey all!
I got a problem when using the title callback in a plot collection. It
seems to restrict the plot only to the image and "cut off" the top,
where the title should be. When I use
pc.plots[0].modify["title"]("sometitle") applied and then saved with
pc.save("somename") nothing appears on the top, but the image remains as
if I never applied anything.
Here is an example (with the title callback applied, but it doesn't show
up):
http://www.flickr.com/photos/87912862@N05/8166752608/in/photostream
Best wishes,
Patrick
