[yt-users] yt-users Digest, Vol 72, Issue 26
Varadarajan Parthasarathy
varada at camk.edu.pl
Tue Feb 18 13:31:35 PST 2014
Hi,
pf = load("/../../testproblem/data.nnnn.dbl.h5"), as well as pf =
load("/../../testproblem/data.nnnn.dbl.h5", "r") gave-
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/yt/convenience.py", line 78,
in load
return output_type_registry[candidates[0]](*args, **kwargs)
File
"/usr/local/lib/python2.7/dist-packages/yt/frontends/pluto/data_structures.py",
line 182, in __init__
self.current_time = self._handle.attrs['time']
File "/usr/lib/python2.7/dist-packages/h5py/_hl/attrs.py", line 36, in
__getitem__
attr = h5a.open(self._id, self._e(name))
File "h5a.pyx", line 77, in h5py.h5a.open (h5py/h5a.c:1945)
KeyError: "can't open attribute (Attribute: Can't open object)"
the h5 files produced from PLUTO are having cell_coords (group),
node_coords(group) and vars(group), and this vars contain prs, rho, vx1,
vx2 and vx3, which are the data sets, but their attributes are not clear.
Cheers,
V.
On Tue, Feb 18, 2014 at 5:19 PM, <yt-users-request at lists.spacepope.org>wrote:
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> Today's Topics:
>
> 1. Re: strange error with StarMassMsun (Geoffrey So)
> 2. yt for PLUTO (Varadarajan Parthasarathy)
> 3. rainbow+white? (Stephanie Tonnesen)
> 4. Re: yt for PLUTO (Kacper Kowalik)
> 5. Re: rainbow+white? (Sam Skillman)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 17 Feb 2014 12:38:47 -0800
> From: Geoffrey So <gsiisg at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] strange error with StarMassMsun
> Message-ID: <C72AB831-6629-41B4-ADE4-2A9479CA96EA at gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Thanks, will give it a try and let you know.
>
> From
> G.S.
>
> Sent from my iPhone
>
> > On Feb 17, 2014, at 5:01 AM, John Wise <jwise at physics.gatech.edu> wrote:
> >
> > Hi Geoffrey,
> >
> > This pull request has been merged, so all you have to do is update your
> yt installation on Stampede now.
> >
> > Thanks,
> > John
> >
> >> On 02/16/2014 08:00 PM, John Wise wrote:
> >> Hi Geoffrey,
> >>
> >> This will happen if you're running with 32-bit precision in Enzo, and
> >> the particle fields except for position will be in 32-bit. However, the
> >> CICDeposit3 routine expects 64-bit floats as input. I've created a pull
> >> request that fixes this bug.
> >>
> >>
> https://bitbucket.org/yt_analysis/yt/pull-request/706/input-enzo-deposited-fields-should-be/diff
> >>
> >>
> >> You can go ahead and test it by pulling my changeset and recompiling.
> >>
> >> hg pull -r f9127d6 https://bitbucket.org/jwise77/yt
> >> hg up
> >>
> >> Please see if this works for you and comment on the PR page.
> >>
> >> Cheers,
> >> John
> >>
> >>> On 02/14/2014 05:12 PM, Geoffrey So wrote:
> >>> I'm getting a strange error when executing the command
> >>>
> >>> starmass = ell.quantities['TotalQuantity']('StarMassMsun')[0]
> >>>
> >>> This is on Stampede, and on my laptop running OSX I did not get the
> same
> >>> error. Has anyone else seen something similar?
> >>>
> >>> From
> >>> G.S.
> >>>
> >>> In [100]: ell.quantities['TotalQuantity']('StarMassMsun')
> >>>
> ---------------------------------------------------------------------------
> >>>
> >>> ValueError Traceback (most recent call
> >>> last)
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/scripts/iyt in <module>()
> >>> ----> 1 ell.quantities['TotalQuantity']('StarMassMsun')
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc
> >>>
> >>> in __call__(self, *args, **kwargs)
> >>> 80 self._data_source.pf.h.io
> >>> <http://data_source.pf.h.io>)
> >>> 81 if lazy_reader and not self.force_unlazy:
> >>> ---> 82 return self._call_func_lazy(args, kwargs)
> >>> 83 else:
> >>> 84 return self._call_func_unlazy(args, kwargs)
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc
> >>>
> >>> in _call_func_lazy(self, args, kwargs)
> >>> 87 self.retvals = [ [] for i in range(self.n_ret)]
> >>> 88 for gi,g in enumerate(self._get_grids()):
> >>> ---> 89 rv = self.func(GridChildMaskWrapper(g,
> >>> self._data_source), *args, **kwargs)
> >>> 90 if not iterable(rv): rv = (rv,)
> >>> 91 for i in range(self.n_ret):
> >>> self.retvals[i].append(rv[i])
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc
> >>>
> >>> in _TotalQuantity(data, fields)
> >>> 703 totals = []
> >>> 704 for field in fields:
> >>> --> 705 if data[field].size < 1:
> >>> 706 totals.append(0.0)
> >>> 707 continue
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/derived_quantities.pyc
> >>>
> >>> in __getitem__(self, item)
> >>> 48 def __getitem__(self, item):
> >>> 49 if item not in self.local_cache:
> >>> ---> 50 data =
> >>> self.data_source._get_data_from_grid(self.grid, item)
> >>> 51 self.local_cache[item] = data
> >>> 52 return self.local_cache[item]
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/data_containers.pyc
> >>>
> >>> in save_state(self, grid, field, *args, **kwargs)
> >>> 79 old_keys = grid.field_data.keys()
> >>> 80 grid.field_parameters = self.field_parameters
> >>> ---> 81 tr = func(self, grid, field, *args, **kwargs)
> >>> 82 grid.field_parameters = old_params
> >>> 83 grid.field_data = YTFieldData( [(k, grid.field_data[k])
> >>> for k in old_keys] )
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/data_containers.pyc
> >>>
> >>> in _get_data_from_grid(self, grid, field)
> >>> 2644 return np.array([f[i,:][pointI] for i in range(3)])
> >>> 2645 else:
> >>> -> 2646 tr = grid[field]
> >>> 2647 if tr.size == 1: # dx, dy, dz, cellvolume
> >>> 2648 tr = tr * np.ones(grid.ActiveDimensions,
> >>> dtype='float64')
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc
> in
> >>> __getitem__(self, key)
> >>> 145 """
> >>> 146 if key not in self.field_data:
> >>> --> 147 self.get_data(key)
> >>> 148 return self.field_data[key]
> >>> 149
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc
> in
> >>> get_data(self, field, convert)
> >>> 188 else: raise
> >>> 189 else:
> >>> --> 190 self._generate_field(field)
> >>> 191 return self.field_data[field]
> >>> 192
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc
> in
> >>> _generate_field(self, field)
> >>> 133 self[field] = temp_array[sl]
> >>> 134 else:
> >>> --> 135 self[field] = self.pf.field_info[field](self)
> >>> 136 else: # Can't find the field, try as it might
> >>> 137 raise exceptions.KeyError(field)
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/field_info_container.pyc
> >>>
> >>> in __call__(self, data)
> >>> 383 ii = self.check_available(data)
> >>> 384 original_fields = data.keys() # Copy
> >>> --> 385 dd = self._function(self, data)
> >>> 386 dd *= self._convert_function(data)
> >>> 387 for field_name in data.keys():
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/universal_fields.pyc
> >>>
> >>> in _StarMass(field, data)
> >>> 439
> >>> 440 def _StarMass(field,data):
> >>> --> 441 return data["star_density"] * data["CellVolume"]
> >>> 442 add_field("StarMassMsun", units=r"M_{\odot}",
> >>> 443 function=_StarMass,
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc
> in
> >>> __getitem__(self, key)
> >>> 145 """
> >>> 146 if key not in self.field_data:
> >>> --> 147 self.get_data(key)
> >>> 148 return self.field_data[key]
> >>> 149
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc
> in
> >>> get_data(self, field, convert)
> >>> 188 else: raise
> >>> 189 else:
> >>> --> 190 self._generate_field(field)
> >>> 191 return self.field_data[field]
> >>> 192
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/grid_patch.pyc
> in
> >>> _generate_field(self, field)
> >>> 133 self[field] = temp_array[sl]
> >>> 134 else:
> >>> --> 135 self[field] = self.pf.field_info[field](self)
> >>> 136 else: # Can't find the field, try as it might
> >>> 137 raise exceptions.KeyError(field)
> >>>
> >>>
> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/data_objects/field_info_container.pyc
> >>>
> >>> in __call__(self, data)
> >>> 383 ii = self.check_available(data)
> >>> 384 original_fields = data.keys() # Copy
> >>> --> 385 dd = self._function(self, data)
> >>> 386 dd *= self._convert_function(data)
> >>> 387 for field_name in data.keys():
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/frontends/enzo/fields.pyc in
> >>> _spdensity(field, data)
> >>> 360 blank,
> >>> np.array(data.LeftEdge).astype(np.float64),
> >>> 361
> >>> np.array(data.ActiveDimensions).astype(np.int32),
> >>> --> 362 np.float64(data['dx']))
> >>> 363 return blank
> >>> 364
> >>>
> >>> /home1/01041/tg802953/dev-yt/src/yt-hg/yt/utilities/lib/CICDeposit.so
> in
> >>> yt.utilities.lib.CICDeposit.CICDeposit_3
> >>> (yt/utilities/lib/CICDeposit.c:1643)()
> >>>
> >>> ValueError: Buffer dtype mismatch, expected 'float64_t' but got 'float'
> >>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users at lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> > --
> > John Wise
> > Assistant Professor of Physics
> > Center for Relativistic Astrophysics, Georgia Tech
> > http://cosmo.gatech.edu
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 17 Feb 2014 23:16:37 +0100
> From: Varadarajan Parthasarathy <varada at camk.edu.pl>
> To: yt-users at lists.spacepope.org
> Subject: [yt-users] yt for PLUTO
> Message-ID:
> <CAPFsH9fr6qTi5WNqt7wtQy092OapkfA96ZyZBhP1ELdo=
> CghxQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I read through the webpages of yt-project and came to know that
> PLUTO is partly supported for yt and there is still a scope for creating a
> new code front end. To that extent, I would like to inform with how much I
> could get into this:
>
> import h5py
> from yt.mods import *
>
> f = h5py.File("/.../.../testproblem/data.nnnn.dbl.h5", "r")
>
> print f.items()
> [(u'cell_coords', <HDF5 group "/cell_coords" (3 members)>),
> (u'node_coords', <HDF5 group "/node_coords" (3 members)>), (u'vars', <HDF5
> group "/vars" (5 members)>)]
>
> print f.keys()
> [u'cell_coords', u'node_coords', u'vars']
>
> where cell_coords and node_coords are X, Y, Z cell and node contain
> different values. 'vars' are 'prs', 'rho', 'vx1', 'vx2', 'vx3'.
>
> But after this I am not able to get the data into the dictionary and hence
> unable to produce plots. I did see through the PLUTO specified field list,
> but I am not able to make the way out. Also, the simulation was not run
> with Chombo refinement, but I hope it may not be a serious issue. Moreover,
> the procedure given in loading a generic array data for HDF5 files was a
> bit confusing with regard to,
>
> data_dir = ytcfg.get('yt','test_data_dir')
> f = h5py.File(data_dir+"/Unigriddata/....h5", "r")
>
> can anyone explain if this 'test_data_dir' is just the working directory
> and then 'f' consists of the file, else the procedure that I have followed
> directly is still correct.
>
> I will be really glad if I can get to do data analysis and other such stuff
> with yt.
>
> I hope to hear soon.
>
> Regards.,
> Varadarajan
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> ------------------------------
>
> Message: 3
> Date: Mon, 17 Feb 2014 20:27:07 -0500
> From: Stephanie Tonnesen <stonnes at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: [yt-users] rainbow+white?
> Message-ID:
> <
> CAE4JVxBRAT9ofEJGB0yLaOqRP2OMULrHHA2Y8CWq15JVETp2Rg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi yt-users,
>
> I am imagining that this is something silly, but I tried to use rainbow +
> white, and it seems to me that it is actually rainbow + black? Certainly
> on the colormaps page those two maps look identical:
>
> http://yt-project.org/docs/dev/visualizing/colormaps/index.html?highlight=cmap
> Is this actually the case? is there just some simple pointer that is
> messed up somewhere? Or can someone point me to the white in
> rainbow+white?
>
> Thanks!
>
> Stephanie
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> ------------------------------
>
> Message: 4
> Date: Tue, 18 Feb 2014 09:24:53 +0100
> From: Kacper Kowalik <xarthisius.kk at gmail.com>
> To: yt-users at lists.spacepope.org
> Subject: Re: [yt-users] yt for PLUTO
> Message-ID: <530318D5.1060103 at gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 02/17/2014 11:16 PM, Varadarajan Parthasarathy wrote:
> > Hi,
> >
> > I read through the webpages of yt-project and came to know that
> > PLUTO is partly supported for yt and there is still a scope for creating
> a
> > new code front end. To that extent, I would like to inform with how much
> I
> > could get into this:
> >
> > import h5py
> > from yt.mods import *
> >
> > f = h5py.File("/.../.../testproblem/data.nnnn.dbl.h5", "r")
>
> Hi Varadarajan,
> does yt's load method any sort of error? Could you try the following
> script:
>
> from yt.mods import *
> pf = load("/.../.../testproblem/data.nnnn.dbl.h5")
> slc = SlicePlot(pf, 'z', 'rho')
> slc.save()
>
> this should create an slice plot of gas density, but the most
> interesting part is load(). It should take care of reading and
> interpreting all data from hdf5 file.
> Best regards,
> Kacper
>
>
> > print f.items()
> > [(u'cell_coords', <HDF5 group "/cell_coords" (3 members)>),
> > (u'node_coords', <HDF5 group "/node_coords" (3 members)>), (u'vars',
> <HDF5
> > group "/vars" (5 members)>)]
> >
> > print f.keys()
> > [u'cell_coords', u'node_coords', u'vars']
> >
> > where cell_coords and node_coords are X, Y, Z cell and node contain
> > different values. 'vars' are 'prs', 'rho', 'vx1', 'vx2', 'vx3'.
> >
> > But after this I am not able to get the data into the dictionary and
> hence
> > unable to produce plots. I did see through the PLUTO specified field
> list,
> > but I am not able to make the way out. Also, the simulation was not run
> > with Chombo refinement, but I hope it may not be a serious issue.
> Moreover,
> > the procedure given in loading a generic array data for HDF5 files was a
> > bit confusing with regard to,
> >
> > data_dir = ytcfg.get('yt','test_data_dir')
> > f = h5py.File(data_dir+"/Unigriddata/....h5", "r")
> >
> > can anyone explain if this 'test_data_dir' is just the working directory
> > and then 'f' consists of the file, else the procedure that I have
> followed
> > directly is still correct.
> >
> > I will be really glad if I can get to do data analysis and other such
> stuff
> > with yt.
> >
> > I hope to hear soon.
> >
> > Regards.,
> > Varadarajan
> >
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
>
>
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> ------------------------------
>
> Message: 5
> Date: Tue, 18 Feb 2014 08:17:27 -0800
> From: Sam Skillman <samskillman at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] rainbow+white?
> Message-ID:
> <CAB4=1s15uFHog3=SWXH7mZ+CU0mncpBuXgMKHrNm5oZ02=
> SZxg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Stephanie,
>
> Hmm, it doesn't look like there is a messed up pointer in the
> yt/visualization/_colormap_data.py file to me, and looking at (random site
> found searching for idl maps)
> http://ham.space.umn.edu/johnd/ct/ct-names.html it seems like they have
> qualitatively the same colors for rainbow+white. If you want to try
> editing the _colormap_data.py entry for "idl39" you might have some luck.
> It seems from
>
> http://yt-project.org/docs/dev/_images/cmap_images__Projection_Rainbow_+_white_r.pngthat
> the white is being put at the max value (which gets put at the bottom
> for the _r) rather than the min value, which is I think what you want.
>
> Let us know if that helps.
> Sam
>
>
> On Mon, Feb 17, 2014 at 5:27 PM, Stephanie Tonnesen <stonnes at gmail.com
> >wrote:
>
> > Hi yt-users,
> >
> > I am imagining that this is something silly, but I tried to use rainbow +
> > white, and it seems to me that it is actually rainbow + black? Certainly
> > on the colormaps page those two maps look identical:
> >
> http://yt-project.org/docs/dev/visualizing/colormaps/index.html?highlight=cmap
> > Is this actually the case? is there just some simple pointer that is
> > messed up somewhere? Or can someone point me to the white in
> rainbow+white?
> >
> > Thanks!
> >
> > Stephanie
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
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>
> _______________________________________________
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> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> End of yt-users Digest, Vol 72, Issue 26
> ****************************************
>
>
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