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