[yt-users] question about transfer function colorbar

Fri May 23 08:06:26 PDT 2014

Sam, I looked at this in more detail.  The transfer function is setting
things up correctly.  As best as I can tell, the issue is in the vert_cbar
routine.  In particular, since the transfer function uses linspace, which
by default has endpoint=True, when we convert from indices into x values,
we should divide by self.alpha.x.size-1 instead of self.alpha.x.size.
 i.e., if I change the one line:

            val = x * (self.alpha.x[-1] - self.alpha.x[0]) /
(self.alpha.x.size) + self.alpha.x[0]

to

            val = x * (self.alpha.x[-1] - self.alpha.x[0]) /
(self.alpha.x.size-1) + self.alpha.x[0]

then I get the expected behavior.

I am a little confused as well why we do add the "+1"
in np.floor(self.alpha.x[-1]) + 1, 1) when defining xticks as well -- I
imagine that's a good thing if your are working with logs, but for my
purpose, where x ranges from -1.e7 to 1.e7, this doesn't seem needed, but I
can live with that.

Thoughts?

On Thu, May 22, 2014 at 8:32 AM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:

> I haven't explored this in any detail yet (still dealing with the end of
> the semester here)
>
>
> On Wed, May 21, 2014 at 8:38 PM, Sam Skillman <samskillman at gmail.com>wrote:
>
>> Hi Michael,
>>
>> That looks like a bug to me. I'll take a look at it in more detail
>> tomorrow.  If you have a fix that works, let us know...
>>
>> Sam
>>
>>
>> On Wed, May 21, 2014 at 8:17 AM, Michael Zingale <
>> michael.zingale at stonybrook.edu> wrote:
>>
>>> I looked at this some more.  It is this line in vert_cbar that adds the
>>> odd-valued colorbar label:
>>>
>>> xticks = np.append(visible[-1], xticks)
>>>
>>> in particular, that adds the "255" value into the xticks array.
>>>  Interestingly, xticks has a 256 value with the correct x_format() behavior
>>> (mapping to 1.e7, the upper limit of my transfer function), but that is
>>> ignored, since it is outside of the bounds of the color bar.
>>>
>>> So the question then is why when I setup a transfer function via:
>>>
>>>     tf =
>>>  yt.visualization.volume_rendering.api.ColorTransferFunction((mi, ma))
>>>
>>> with mi = -1.e7 and ma = 1.e7, does it map -1.e7 into index 0 in the
>>> palette and 1.e7 into 256 in the palette, instead of 255?
>>>
>>>
>>> On Sun, May 11, 2014 at 6:03 PM, Michael Zingale <
>>> michael.zingale at stonybrook.edu> wrote:
>>>
>>>> I poked around that code earlier but didn't see anything odd.  I'll
>>>> look some more at it tomorrow.
>>>>
>>>>
>>>> On Sat, May 10, 2014 at 11:31 AM, Chris Malone <
>>>> chris.m.malone at gmail.com> wrote:
>>>>
>>>>> Hi Mike,
>>>>>
>>>>> The number that is getting set (~9.92e6) is just one bin off from the
>>>>> maximum value (you have a range of 2e7 and the default is 256 bins).  The
>>>>> code that displays the colorbar, as best I can tell, occurs when you call
>>>>> save_annotated.  This method eventually calls
>>>>> ColorTransferFunction.vert_cbar where the ticks and limits are applied to
>>>>> the colorbar axes object.
>>>>>
>>>>> Looking over the logic in that code, it is not immediately obvious to
>>>>> me why the index is off.  I suspect is has something to do with how the
>>>>> `visible` variable is defined, but I'd need to play with a dataset and some
>>>>> print statements...
>>>>>
>>>>> Chris
>>>>>
>>>>>
>>>>> On Wed, May 7, 2014 at 8:17 PM, Michael Zingale <
>>>>> michael.zingale at stonybrook.edu> wrote:
>>>>>
>>>>>> I'm trying to show the transfer function on a volume render.
>>>>>>  Plotting a velocity component, I set the transfer function with 4
>>>>>> Gaussians all with the same width.  The range of the transfer function is
>>>>>> -1.e7 to 1.e7, but for some reason, when output, the upper label in the
>>>>>> colorbar is not 1.e7 but a bit lower (9.92e6).  I am not sure where the
>>>>>> code is that draws this, and I am confused why it is not setting the tick
>>>>>> at 1.e7. It gets the bottom tick right.
>>>>>> Here's an image:
>>>>>>
>>>>>> http://bender.astro.sunysb.edu/random/test_0000.png
>>>>>>
>>>>>> and the script:
>>>>>>
>>>>>> http://bender.astro.sunysb.edu/random/vol_rotate.py
>>>>>>
>>>>>> any pointers are appreciated.
>>>>>>
>>>>>> Mike
>>>>>> --
>>>>>> Michael Zingale
>>>>>> Associate Professor
>>>>>>
>>>>>> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook,
>>>>>> NY 11794-3800
>>>>>> *phone*:  631-632-8225
>>>>>> *e-mail*: Michael.Zingale at stonybrook.edu
>>>>>> *web*: http://www.astro.sunysb.edu/mzingale
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>
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>>>>>
>>>>
>>>>
>>>> --
>>>> Michael Zingale
>>>> Associate Professor
>>>>
>>>> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
>>>> 11794-3800
>>>> *phone*:  631-632-8225
>>>> *e-mail*: Michael.Zingale at stonybrook.edu
>>>> *web*: http://www.astro.sunysb.edu/mzingale
>>>>
>>>
>>>
>>>
>>> --
>>> Michael Zingale
>>> Associate Professor
>>>
>>> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
>>> 11794-3800
>>> *phone*:  631-632-8225
>>> *e-mail*: Michael.Zingale at stonybrook.edu
>>> *web*: http://www.astro.sunysb.edu/mzingale
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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>>
>
>
> --
> Michael Zingale
> Associate Professor
>
> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
> 11794-3800
> *phone*:  631-632-8225
> *e-mail*: Michael.Zingale at stonybrook.edu
> *web*: http://www.astro.sunysb.edu/mzingale
>

-- 
Michael Zingale
Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
11794-3800
*phone*:  631-632-8225
*e-mail*: Michael.Zingale at stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
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