[yt-users] Why the two figures have different resolutions?

Nathan Goldbaum nathan12343 at gmail.com
Thu May 18 11:38:48 PDT 2017 

On Thu, May 18, 2017 at 1:24 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi,
>
> I looked into this, and one thing I thought would fix it (adding a
> _block_reorder attribute to ParticleOctreeSubset) didn't fix it, which
> surprised me.  But, transposing the return value rv in
> OctreeSubsetBlockSlicePosition did.  I thought that doing the copy in a
> different order would be sufficient, since we don't use memoryviews
> internal to the VR.
>
> I'm not ready yet to submit a PR for this yet, until I understand where
> it's coming from.  Nathan, wasn't there a recent change to the i,j,k loop
> order in the smoothing?
>

Not that I remember, but I could be forgetting something.


> Are we sure this behavior has been around for a long time?
>

I have no idea, I haven't tried testing on an old version of yt.


>
> -Matt
>
> On Thu, May 18, 2017 at 9:41 AM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Hi Dan,
>>
>> Thanks for the info. I was able to reproduce the behavior you're seeing.
>> Your script wasn't quite runnable (it still used set_size_inches, and you
>> also forgot to save the first image). I also noticed that the difference is
>> visible at yt's default resolution and with the ('gas', 'density') field,
>> so in the interest of making the script simpler I used those:
>>
>> http://paste.yt-project.org/show/7150/
>>
>> For anyone following along, here are the two images this script produces:
>>
>> axis-aligned projection: http://i.imgur.com/ddKkxaC.png
>>
>> off-axis projection: http://i.imgur.com/mhWR2NL.png
>>
>> The problem gets worse when I increase over_refine_factor to 2 and set
>> index_ptype='PartType0':
>>
>> axis-aligned projection: http://i.imgur.com/fctKRSO.png
>>
>> off-axis projection: http://i.imgur.com/eAz9BNt.png
>>
>> I'm not sure offhand why the results are different, in principle they
>> should be the same, although as I mentioned earlier the images are produced
>> using very different algorithms. It's possible there's a bug in how the
>> volume renderer is dealing with SPH particle data. The fact that the
>> problem gets worse when the resolution of the octree increases indicates to
>> me that this is likely a bug. I know we've had other issues in the past
>> using the volume rendering infrastructure with SPH data.
>>
>> Sorry to not have a more satisfactory answer. I think at this point we
>> should probably open an issue on github to track this, I think we have good
>> evidence that there are artifacts in SPH off-axis projections.
>>
>> I'm currently actively working on improving yt's support for particle
>> data of all kinds and SPH data in particular. See this page for more
>> details: https://bitbucket.org/ngoldbaum/ytep/src/2a754cae8a
>> 5825109bad00aa9a5607abbcc4f095/source/YTEPs/YTEP-0031.rst?
>> at=default&fileviewer=file-view-default
>>
>> Part of this will include writing a new particle-centric volume renderer
>> which will hopefully fix this. That's definitely a more long term goal
>> which will hopefully be done in the next few months. In the meantime
>> someone will need to try to figure out what's introducing these artifacts
>> we're seeing and optimally fix them somehow :)
>>
>> -Nathan
>>
>> On Thu, May 18, 2017 at 12:54 AM, bazhaoyu_sjtu <
>> hudan_bazhaoyu at sjtu.edu.cn> wrote:
>>
>>> Hi Nathan,
>>>
>>> I'm so sorry that I haven't expressed clearly.
>>>
>>> I learned your code, and replotted two images. The complete script:
>>> http://paste.yt-project.org/show/7146/
>>> where the 'surface brightness' is a derived field by myself.
>>>
>>> And my data 'snap_206.hdf5':  http://use.yt/upload/c7c0d617
>>>
>>> Here's the two images:
>>> regular projection:   https://1drv.ms/i/s!Aq__4QGcEmxvh06ErW9t_0BK-LQR
>>> off-axis projection:   https://1drv.ms/i/s!Aq__4QGcEmxvh09ajn0UdatFjIil
>>>
>>> The off-axis one is still blockier. So How can I fix it? I want to have
>>> same resolution of two figures.
>>> Thanks for you help!
>>>
>>>
>>> Regards,
>>> Dan
>>>
>>>
>>>
>>> On 05/16/2017 08:39 PM, Nathan Goldbaum wrote:
>>>
>>>
>>> On Tue, May 16, 2017 at 6:38 AM bazhaoyu_sjtu <
>>> <hudan_bazhaoyu at sjtu.edu.cn>hudan_bazhaoyu at sjtu.edu.cn> wrote:
>>>
>>>> Hi Nathan,
>>>>
>>>> Thank you for your prompt reply!
>>>>
>>>> I also have two questions:
>>>>
>>>> 1.  When I tried your new script, the bug are presented below:
>>>> ------------------------------------------------------------
>>>> -------------------------------------
>>>> pz.set_size_inches(10)
>>>> AttributeError: 'ProjectionPlot' object has no attribute
>>>> 'set_size_inches'
>>>>
>>>
>>> Oops, that should have been pz.set_figure_size(10). I thought I fixed
>>> that it I guess I forgot to update the email. Sorry for the confusion.
>>>
>>>
>>>> ------------------------------------------------------------
>>>> -------------------------------------
>>>>
>>>> 2.  For your two images, I also found that figure's resolution of the
>>>> 'off-axis projection' is worse than the 'regular projection', for example,
>>>> the 'off-axis projection' figure has more obvious grid point.
>>>> Is there any difference between two projection ways? Because I supposed
>>>> it should be same.
>>>>
>>>
>>> They are generated using very different algorithms. The axis-aligned
>>> projection is calculated based on an adaptive quadtree while the off-axis
>>> projection is calculated using a ray-casting volume renderer.
>>>
>>> I agree with you that in principle they should come out with
>>> identical-looking results for the script you provided. It's possible that
>>> you're data is exposing a corner case that somehow makes the off-axis
>>> projection appear blockier. It's hard to say without more info. Please see
>>> the last paragraph of my last message about this, if you share an example
>>> dataset that triggers this behavior or share the images you are seeing it
>>> will make it easier to speak intelligently about what you are seeing.
>>>
>>>
>>>>
>>>> Thank you again!
>>>>
>>>> Regards,
>>>> Dan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 05/15/2017 09:56 PM, Nathan Goldbaum wrote:
>>>>
>>>> Hi Dan,
>>>>
>>>> I adapted your script to use a public dataset from yt-project.org/data.
>>>> I also don't have a definition for a surface_brightness field in my copy of
>>>> yt, so I guess you defined that elsewhere? I used 'density'. Here's the
>>>> script I ended up coming up with:
>>>>
>>>> http://paste.yt-project.org/show/7142/
>>>>
>>>> (note that you can upload scripts with the "yt pastebin" command line
>>>> tool, e.g. "yt pastebin my_script.py")
>>>>
>>>> And indeed, in that case I get two images that aren't the desired high
>>>> resolution you're looking for (although both images have the same
>>>> resolution). The issue is that yt is saving the figure to disk through
>>>> matplotlib. To control the image size in pixels through matplotlib you need
>>>> to know the figure size in inches and the dpi (e.g. the number of pixels
>>>> per inch of figure). Here's a revised version of the script above which
>>>> saves to disk two images with the desired 3200x3200 resolution:
>>>>
>>>> http://paste.yt-project.org/show/7145/
>>>>
>>>> It also hides the axes and colorbar, since that makes it easier to
>>>> guess ahead of time what the final image resolution will be. Here are the
>>>> two images:
>>>>
>>>> regular projection: http://i.imgur.com/ialfYC4.png
>>>> off-axis projection: http://i.imgur.com/PcvPZ9f.png
>>>>
>>>> You can share images you make using yt using the "yt upload_image"
>>>> command, which will upload an image stored locally to imgur. We usually
>>>> suggest using that to share images or alternatively something like a
>>>> Jupyter notebook on gist.github.com to avoid clogging people's e-mail
>>>> with high resolution images.
>>>>
>>>> Finally, if you don't want to mess with matplotlib and just want the
>>>> underlying images, you can get those via the frb attribute of the plot
>>>> object. Something like:
>>>>
>>>>     plot = yt.ProjectionPlot(ds, 'z', ('gas', 'density'))
>>>>     plot.set_buff_size((3200, 3200))
>>>>
>>>>     # image will be a 3200x3200 numpy array
>>>>     image = plot.frb['gas', 'density']
>>>>
>>>> I hope that helps clear things up. If you are still having issues it
>>>> would help if you could share the exact yt version you are using as well as
>>>> a runnable test script that demonstrates the issue. If you can't trigger
>>>> the issue using one of the public SPH datasets on yt-project.org/data,
>>>> you can share one of your datasets using the yt curldrop:
>>>> https://docs.hub.yt/services.html#curldrop
>>>>
>>>> -Nathan
>>>>
>>>> On Mon, May 15, 2017 at 4:40 AM, bazhaoyu_sjtu <
>>>> <hudan_bazhaoyu at sjtu.edu.cn>hudan_bazhaoyu at sjtu.edu.cn> wrote:
>>>>
>>>>> Hi yt-users:
>>>>>
>>>>> I want to ask you a question about the figures' resolution, I handled
>>>>> Gadget file -- hdf5.
>>>>>
>>>>> I used the 'ProjectionPlot' to plot the surface brightness map which
>>>>> is integrated along the 'z' axis, please see the figure 1; And I plot
>>>>> another surface brightness map by 'OffAxisProjectionPlot' with the
>>>>> normal_vector is [0, 0, 1], please see the figure 2.
>>>>>
>>>>> # I can't upload attachments ??? #
>>>>>
>>>>> Comparing two figures, we can find the structures of them is same, but
>>>>> the resolution is different! The 'OffAxisProjectionPlot' is obviously worse
>>>>> than 'ProjectionPlot', I don't know why!
>>>>>
>>>>> Below are the process I created two figures:
>>>>>
>>>>> ======================================================================
>>>>> import yt
>>>>> import numpy as np
>>>>> import yt.units as units
>>>>> import pylab
>>>>>
>>>>> fname = "snap_206.hdf5"
>>>>> unit_base = {'UnitLength_in_cm' : 3.08568e+21,
>>>>> 'UnitMass_in_g' : 1.989e+43,
>>>>> 'UnitVelocity_in_cm_per_s' : 100000}
>>>>> bbox_lim = 1e5 # kpc
>>>>> bbox = [[-bbox_lim,bbox_lim],
>>>>> [-bbox_lim,bbox_lim],
>>>>> [-bbox_lim,bbox_lim]]
>>>>> ds = yt.load(fname,unit_base=unit_base,bounding_box=bbox)
>>>>> ds.index
>>>>> ad= ds.all_data()
>>>>>
>>>>>
>>>>> ## For 'ProjectionPlot' ##
>>>>> pz = yt.ProjectionPlot(ds, 'z', ('gas', 'surface_brightness'), 'max',
>>>>> width=(0.4,'Mpc'))
>>>>>
>>>>>
>>>>> ## For 'OffAxisProjectionPlot' ##
>>>>> L = [0,0,1]
>>>>> north_vector = [0,1,0]
>>>>> pz = yt.OffAxisProjectionPlot(ds, L, ('gas', 'surface_brightness'),
>>>>> 'max', north_vector = north_vector, width=(0.4,'Mpc'))
>>>>>
>>>>>
>>>>> pz.set_buff_size((3200,3200))
>>>>> pz.save()
>>>>> ============================================================
>>>>> =============
>>>>>
>>>>> What can i do to fix this difference of resolution between two plot
>>>>> ways?
>>>>> Thanks a lot!
>>>>>
>>>>> Regards,
>>>>> Dan
>>>>>
>>>>>
>>>>> ==================================
>>>>> Department of Physics, Shanghai Jiao Tong University
>>>>> 800 Dongchuan Road, Minhang, Shanghai 200240, PRC
>>>>> E-mail : hudan_bazhaoyu at 163.com
>>>>> hudan_bazhaoyu at sjtu.edu.cn
>>>>> ==================================
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>>>>
>>>>
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