[yt-users] MultiVariate volume rendering difficulties

Noel Scudder noel.scudder at stonybrook.edu
Fri Aug 2 08:05:51 PDT 2013 

Hi Stella and Cameron,

Great, this looks like an easy solution. I'll have to try this out soon.
Thanks for your feedback!

-Noel

On Thu, Aug 1, 2013 at 5:13 PM, Stella Offner <offner at gmail.com> wrote:

> Hi Noel,
>
> That sounds like a lot of fun! I've been making crude bivariate volume
> renderings simply by adding the snapshots together:
>
> vals = cam.snapshot()
> vals2 = cam2.snapshot()
> valssum = vals+vals2
> write_bitmap(valssum, imfile)
>
> This seems to work ok if the transfer functions are not overlapping too
> much. Sometimes some weighting is required in the addition to avoid
> changing the colors too much. The MultiVariateTransferFunction will be
> great improvement on this.
>
> Cheers,
> Stella
>
> On Thu, Aug 1, 2013 at 4:53 PM, Noel Scudder <noel.scudder at stonybrook.edu>wrote:
>
>> Hi all,
>>
>> Over the past few days I've been investigating the
>> MultiVariateTransferFunction and receiving feedback from Matt. Since it
>> needs some updating and the documentation is so vague, I thought I'd try to
>> outline the basic flow and idea of an MVTF (thanks to Matt for his
>> outline), address a couple problems that have been noticed, and give an
>> example script with images. Please feel free to correct my mistakes, ask
>> questions, and add your own knowledge!
>>
>> The code for the MVTF is
>> in yt/visualization/volume_rendering/transfer_functions.py . It's also
>> useful to check out the Planck and Color Transfer Functions in the same
>> file.
>>
>> With a CTF, you are limited to one field, which is linked identically to
>> each of the RGB color channels and an alpha channel. However, an MVTF
>> allows you to set up different fields that control each channel and each
>> channel's opacity through the use of standard Transfer Functions. For
>> instance, I could link the red color channel and the red alpha channel to
>> Density, the blue and blue alpha channels to Temperature, and the green and
>> green alpha channels to Kinetic Energy.
>> It is important to note that only *one* field (and associated transfer
>> function) may be linked to any channel. This limits the number of variables
>> one can conceivably include to three.
>>
>> When an MVTF is created, it sets up a few variables:
>>
>> n_field_tables
>> tables
>> field_ids
>> weight_field_ids
>> field_table_ids
>> weight_table_ids
>> grad_field
>> light_source_v
>>
>> The important ones here are tables, field_ids, weight_field_ids,
>> field_table_ids, and weight_table_ids.
>> After creating your MVTF, the first thing you must do is create a
>> TransferFunction, which has some range and number of bins. This can then be
>> added as a "table" to your MVTF using add_field_table, which accepts the
>> table, the field_id used for interpolating on the x-axis of this table, a
>> weight_field_id, and/or a weight_table id.
>> The field_id is *not* the field index you get from pf.h.field_indexes .
>> Here, the field_id actually specifies the index of a certain field in the
>> field list you supply to the camera object. For instance, if I gave the
>> camera
>>
>> fields=['density', 'Temp']
>>
>> I would have previously called add_field_table using a field_id of 0 for
>> the TransferFunctions I wanted for density, and using a field_id of 1 for
>> the TransferFunctions I wanted for temperature.
>> The same specification with the field_id goes for weight_field_id, which
>> is used if the field itself should be a weighting factor for the
>> emission/absorption (although this does not do scaling, so you will likely
>> need to supply a pre-scaled field).
>> By supplying a weight_table_id, you are taking the results of
>> interpolation along the x-axis to get a y value from *another* field table
>> and using that as a weight.
>>
>> *Apparently density is typically logged by default. If you want to use it
>> as a weight, you probably want it un-logged.
>>
>> At this point you have added all of your field tables. The second step is
>> to link the field tables to the channels you want. Right now, all you have
>> is a set of "tables," TransferFunctions that describe how to get a value
>> out as a combination of:
>>
>> 1) The y-value interpolated along the x-axis defined by the table
>> 2) The weighting from a given field
>> 3) The weighting from a given field_table (i.e., if you had some scaling
>> that was a function of temperature)
>>
>> On its own, a table will do nothing--you must link it to a channel. These
>> are, in order, RGB and aR, aG, aB. You use the link_channels function for
>> this purpose, for instance linking table 0 to channel 0 (R). When linking
>> channels, there are a couple things to keep in mind. The two arguments you
>> supply are the  table_id and the channel, both *integers *(seems like a
>> common theme for MVTF stuff :-) ). The channel can be integers 0-5,
>> assigned in the order above. The table_id is a bit more nebulous: a
>> table_id is assigned to a table when it is created, meaning that the first
>> table you create using add_field_table will have a table_id of 0, the next
>> will have a table_id of 1, and so on. Although you cannot link more than
>> one table to a channel, you can have more than one channel linked to a
>> single table--simply supply a list in place of an integer for the channel
>> argument.
>>
>> Finally, don't leave your TransferFunctions empty! Add some gaussians,
>> keeping in mind the channel and field each TF uses. After that your MVTF
>> will be ready, and you can supply it to the camera object like any other
>> transfer function and take a snapshot.
>>
>> Here's a example script: http://pastebin.com/NC4pHPR7
>>
>> Which creates this image: http://i.imgur.com/EKv943G.png
>>
>> The main problem I've been noticing is with the grey_opacity, which was
>> already discussed--apparently the MVTF was never updated after opaque
>> volume rendering was implemented. Although by default an MVTF doesn't have
>> a grey_opacity attribute and yt will complain about this, you can placate
>> the beast by supplying
>>
>> mv.grey_opacity=False
>>
>> anyway. If you set grey_opacity to True, however, odd things will happen,
>> which I suspect is simply due to the MVTF not having been updated for
>> opaque rendering yet: http://i.imgur.com/rrOnbgy.png
>> I think that about sums up my two cents on the MVTF.
>>
>>
>> Finally, my original desire was to have two different
>> ColorTransferFunctions with two different fields rendered by one camera at
>> once. In other words, simultaneously render two different colormaps applied
>> to two different fields. Right now this isn't possible in yt (although Matt
>> thinks it may be somewhat straightforward to implement), so I came up with
>> a makeshift way, where I render one TF for the first field without a
>> background and the second TF for the second field *with* a background,
>> and then overlay them using ImageMagick:
>>
>> im.write_png('transparent_temp.png', background=None)
>> ...
>> im2.write_png('dens_and_background.png')
>> os.system('composite transparent_temp.png dens_and_background.png
>> multi.png')
>>
>> However, it's expensive, and it goes outside yt. Does anyone know if
>> there's a way to combine these images without leaving yt?
>>
>> Thanks for reading!
>>
>> -Noel
>>
>> On Tue, Jul 30, 2013 at 1:03 PM, Sam Skillman <samskillman at gmail.com>wrote:
>>
>>> Hi all,
>>> The multivariate tf could use both some updating and documentation. I'm
>>> offline for the next few days but if it hasn't been fixed by next week I
>>> can take a look.
>>>
>>> Sam
>>> On Jul 30, 2013 8:40 AM, "Nathan Goldbaum" <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> Hi Noel,
>>>>
>>>> I believe this is a bug that needs to be fixed.  It seems
>>>> MultiVariateTransferFunction was never updated after opaque volume
>>>> rendering was added.
>>>>
>>>> Can you please open a new issue about this?
>>>>
>>>> Nathan
>>>>
>>>> On Tuesday, July 30, 2013, Noel Scudder wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I'm attempting to visualize multiple variables in the same volume
>>>>> rendering. For instance, I'd like to show some density surfaces of a star
>>>>> and then get temperature overlayed to show hotspots. I found the
>>>>> MultiVariateTransferFunction, but it is unfortunately not particularly well
>>>>> documented yet, and I'm being repeatedly thwarted. I'm not sure if I've set
>>>>> it up correctly, or how to go from the transfer function to an image.
>>>>> Here's my current script, using just one variable for now:
>>>>>
>>>>> #----------------------------------
>>>>> from yt.mods import *
>>>>> pf = load('plt00100')
>>>>>
>>>>> #<some constants>
>>>>>
>>>>> pf.h
>>>>> pf.field_info['density'].take_log=True
>>>>>
>>>>> mv = MultiVariateTransferFunction()
>>>>>
>>>>> tf = TransferFunction((mi-1, ma+1), nbins=1.0e6)
>>>>> tf.add_gaussian(np.log10(9.0e5), 0.01, 1.0)
>>>>>
>>>>> mv.add_field_table(tf, 0)
>>>>> mv.link_channels(0, [0,1,2,3])
>>>>>
>>>>> c = [5.0e9, 5.0e9, 5.0e9]
>>>>> L = [0.15, 1.0, 0.40]
>>>>> W = wi*0.7
>>>>> Nvec = 1024
>>>>>
>>>>> cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = mv,
>>>>>                              fields=['density'], pf=pf, no_ghost=True)
>>>>>
>>>>> im = cam.snapshot(num_threads=4)
>>>>>
>>>>> im.write_png('plt00100.png' )
>>>>> #----------------------------------
>>>>>
>>>>> I checked to make sure density is indeed my 0-index field. I get the
>>>>> following error after ray casting:
>>>>>
>>>>> Traceback (most recent call last):
>>>>>   File "<stdin>", line 1, in <module>
>>>>>   File "multivol.py", line 153, in <module>
>>>>>     im = cam.snapshot(num_threads=4)
>>>>>   File
>>>>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py",
>>>>> line 742, in snapshot
>>>>>     image, sampler),
>>>>>   File
>>>>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py",
>>>>> line 632, in _render
>>>>>     image = self.finalize_image(image)
>>>>>   File
>>>>> "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py",
>>>>> line 611, in finalize_image
>>>>>     if self.transfer_function.grey_opacity is False:
>>>>> AttributeError: 'MultiVariateTransferFunction' object has no attribute
>>>>> 'grey_opacity'
>>>>>
>>>>>
>>>>> Can I not use snapshot in this case, or is something else the matter
>>>>> entirely?
>>>>>
>>>>> Thanks,
>>>>> Noel Scudder
>>>>>
>>>>
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