[yt-users] Making a Multiplot using Ramses data
Matthew Turk
matthewturk at gmail.com
Wed Nov 13 05:26:47 PST 2013
Hi Kearn,
Huh, weird. So in 3 we switched the order of projection arguments. Try
swapping 0 and "Density".
Sorry this has been such a pain!!
Matt
On Nov 13, 2013 8:23 AM, <k.grisdale at surrey.ac.uk> wrote:
> Hi Matt,
>
> Thanks for that yt now loads in Ramses data but I get new errors.
>
>
> If I use:
> p1 = load("output_00001/info_00001.txt")
> pr1 = ProjectionPlot(p1,'z','Density',center=cen)
>
> I get:
>
>
> You are running with the wrong number of fields.
> Please specify these in the load command.
> We are looking for 6 fields.
> The last set of field sizes was: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> 2, 2, 1, 1, 16, 16, 16, 16, 16, 16]
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
> line 1441, in __init__
> field_parameters = field_parameters)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
> line 234, in __init__
> self.get_data(field)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
> line 278, in get_data
> chunk_fields, "io")):
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
> line 434, in parallel_objects
> for obj_id, obj in oiter:
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 453, in chunks
> self.get_data(fields)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 531, in get_data
> fluids, self, self._current_chunk)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py",
> line 520, in _read_fluid_fields
> chunk_size)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/io.py", line
> 41, in _read_fluid_selection
> rv = subset.fill(content, fields, selector)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py",
> line 304, in fill
> for level, offset in enumerate(self.domain.hydro_offset):
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py",
> line 102, in hydro_offset
> hvals = fpu.read_attrs(f, header, "=")
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py",
> line 74, in read_attrs
> assert(s1 == s2)
> AssertionError
>
> If I use the multi plot script that we have been discussing I get this
> error:
>
> Traceback (most recent call last):
> File "plotterm3.py", line 20, in <module>
> proj1 = p1.h.proj(0, "Density", center=cen)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
> line 234, in __init__
> self.get_data(field)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
> line 266, in get_data
> fields = self._determine_fields(ensure_list(fields))
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 396, in _determine_fields
> finfo = self.pf._get_field_info("unknown", fname)
> File
> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",
> line 331, in _get_field_info
> raise YTFieldNotFound((ftype, fname), self)
> yt.utilities.exceptions.YTFieldNotFound: Could not find field '('gas', 0)'
> in info_00001.
>
> Ideas what I’ve done?
>
> Thanks
>
> Kearn
>
> PS: As far as I know I am running yt 3. is there a way to check which
> version I have?
>
> On 13 Nov 2013, at 13:08, Matthew Turk <matthewturk at gmail.com> wrote:
>
> Hi Kearn,
>
> Looks like you got back onto the yt-2.X branch. I of course screwed
> up and should have realized that you were on 3.0! :) (You were,
> right?) My fault completely. Give a shot at this:
>
> hg pull http://bitbucket.org/yt_analysis/yt-3.0
> hg up -C tip
> python2.7 setup.py build_ext -i -f
>
> That should get you back running.
>
> -Matt
>
> On Wed, Nov 13, 2013 at 5:23 AM, <k.grisdale at surrey.ac.uk> wrote:
>
> Hi Matt,
>
> I have just applied the pull request using the command:
>
> cd $YT_DEST/src/yt-hg
> hg pull && hg update yt
>
> But now when i tried to load RAMSES data into the YT I get the following
> error:
>
> yt : [ERROR ] 2013-11-13 10:22:49,486 Couldn't figure out output type
> for
> output_00001/info_00001.txt
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line
> 90, in load
> raise YTOutputNotIdentified(args, kwargs)
> yt.utilities.exceptions.YTOutputNotIdentified: Supplied
> ('output_00001/info_00001.txt',) {}, but could not load!
>
> Any idea what has happened?
>
> Thanks
>
> Kearn
>
>
> Traceback (most recent call last):
> File "plotterm3.py", line 7, in <module>
> p1 = load("output_00001/info_00001.txt")
> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line
> 90, in load
> raise YTOutputNotIdentified(args, kwargs)
> yt.utilities.exceptions.YTOutputNotIdentified: Supplied
> ('output_00001/info_00001.txt',) {}, but could not load!
>
>
> On 12 Nov 2013, at 14:57, Matthew Turk <matthewturk at gmail.com> wrote:
>
> Hi Kearn,
>
>
> On Tue, Nov 12, 2013 at 9:47 AM, <k.grisdale at surrey.ac.uk> wrote:
>
>
> Dear Matt,
>
> Thanks again. The normalize command was just what I needed.
>
> Does the projection plot used in the multi-plot work differently to the
> normal ProjectionPlot?
>
>
> I ask because with the code below I get the image below, while using the
> same centre and width with the multi plot I get the image I sent in my last
> email. I have tried playing around with different centres, and projection
> radii but this only moves the image around or makes the square that it does
> plot different sizes(this is still the case even after changing to a linear
> scale). Both plots are using the same data set so i am explicating the same
> plot.
>
>
>
> They sort of work the same. What you're doing with the FRBs is much
> lower-level, though, even though it's what the ProjectionPlot uses. I
> think
> the issue you're running into is that the FixedResolutionBuffer is *not*
> periodic by default, and to_frb() doesn't turn it on. I've issued a pull
> request that adds this functionality to the to_frb() command, as I think it
> is a problem not to have it!
>
>
> https://bitbucket.org/yt_analysis/yt/pull-request/639/adding-periodic-default-false-to-to_frb
>
> -Matt
>
>
>
> Thanks Kearn
>
>
> from yt.mods import *
> p6 = load("output_00006/info_00006.txt")
> cen = [0,0,0]
> pr6 = ProjectionPlot(p6,'z','Density',center=cen)
> pr6.set_cmap('Density','YlOrRd')
> pr6.set_zlim('Density', 0.0,0.35)
> pr6.save("p6")
>
>
> <p6_Projection_z_Density.png>
>
> On 12 Nov 2013, at 11:33, Matthew Turk <matthewturk at gmail.com> wrote:
>
> Hi Kearn,
>
>
> On Tue, Nov 12, 2013 at 3:46 AM, <k.grisdale at surrey.ac.uk> wrote:
>
>
> Hi Matt.
>
> The Script you sent me has been of great help! I have now managed to get
> yt to plot projections for my data.
>
> However I am still having small trouble. Firstly script only plots the 1
> quarter of each projection(I can change which quarter), [Graph below] and
> secondly I would like to set the colorbar to be linear for my data. How can
> I go about that?
>
>
>
> If you change LogNorm to Normalize (and change the import) it should
> change to linear. You can probably then just remove the LogLocator ticker.
> To change the FOV, the 0.25 "unitary" is what I set, and you should be able
> to change it to whatever you like. Just be sure to also change the center
> value to be the center of the domain! :)
>
> -Matt
>
>
>
> Thanks
>
> Kearn
>
> <Screen Shot 2013-11-12 at 08.46.03.png>
> On 11 Nov 2013, at 22:39, Matthew Turk <matthewturk at gmail.com> wrote:
>
> Hi Kearn,
>
> Oops, I guess my reply was less than helpful! Sorry about that --
> been one of those days.
>
> On Mon, Nov 11, 2013 at 3:30 PM, <k.grisdale at surrey.ac.uk> wrote:
>
> Hi Matt,
>
> Thanks for the reply. The code that I used below is my attempt at
> adapting
> the script on the yt pages explaining how to use Multi-Plot Slice and
> Projections. As I couldn’t figure out how make multi-plots of yt
> Projections
> I thought I’d try the adapting route. Which means there bits there I
> don’t
> get but have included as I thought they where needed for the multi plot.
>
>
> I've spent a bit of time looking at this and I've been able to make a
> multi plot that I think matches what you're looking for. I've put the
> script here, and I've also tried to note where there might be issues
> with it that could be important when you adapt it to your data.
>
> http://paste.yt-project.org/show/4047/
>
> Let me know if that helps out, or if I can help in any other way.
>
> -Matt
>
> Thanks again
>
> Kearn
>
>
>
> On 11 Nov 2013, at 20:13, Matthew Turk <matthewturk at gmail.com> wrote:
>
> Hi Kearn,
>
>
> On Mon, Nov 11, 2013 at 10:18 AM, <k.grisdale at surrey.ac.uk> wrote:
>
>
> Hi everyone
>
> I am trying to make a multi plot using data from Ramses. I have outputs
> from Ramses at 6 different times and I want to make projections at each
> time
> and place than in a multi plot to show evolution of the system. However
> when
> the code that I have written gives the results below.
>
>
> <Screen Shot 2013-11-11 at 15.12.13.png>
>
>
> Can anyone offer any suggestions as to wear my code is going wrong?
>
> Thanks
>
> Kearn
>
> The code I’m using ( the for dax lines have been commented out because
> every time they are included I get the error at the bottom)
>
> from yt.mods import * # set up our namespace
> import matplotlib.colorbar as cb
> from matplotlib.colors import LogNorm
>
> p1 = load("output_00001/info_00001.txt")
> p2 = load("output_00002/info_00002.txt")
> p3 = load("output_00003/info_00003.txt")
> p4 = load("output_00004/info_00004.txt")
> p5 = load("output_00005/info_00005.txt")
> p6 = load("output_00006/info_00006.txt")
>
> cen = [0,0,0]
> orient = 'vertical'
>
> fig, axes, colorbars = get_multi_plot(3, 2, colorbar=orient, bw = 4)
> proj1 = p1.h.proj(2, "Density", center=cen)
> proj2 = p2.h.proj(2, "Density", center=cen)
> proj3 = p3.h.proj(2, "Density", center=cen)
> proj4 = p4.h.proj(2, "Density", center=cen)
> proj5 = p5.h.proj(2, "Density", center=cen)
> proj6 = p6.h.proj(2, "Density", center=cen)
>
> proj1_frb = proj1.to_frb((0.7,"cm"),512)
> proj2_frb = proj2.to_frb((0.7,"cm"),512)
> proj3_frb = proj3.to_frb((0.7,"cm"),512)
> proj4_frb = proj4.to_frb((0.7,"cm"),512)
> proj5_frb = proj5.to_frb((0.7,"cm"),512)
> proj6_frb = proj6.to_frb((0.7,"cm"),512)
>
> dens_axes = [axes[0][0], axes[1][0]]
>
> #for dax in zip(dens_axes) :
>
>
>
> I'm not sure what you're doing here -- this will yield:
>
> [(axes[0][0],), (axes[1][0],)]
>
> So you'll be getting back a tuple of length one inside the loop. You
> should
> be able to do dax[0]? But I'm not sure you need to zip in the first
> place,
> either.
>
> -Matt
>
>
>
> # dax.xaxis.set_visible(False)
> # dax.yaxis.set_visible(False)
>
> plots = [dens_axes[0].imshow(proj1_frb["Density"],origin ='lower'),
> dens_axes[0].imshow(proj2_frb["Density"],origin ='lower'),
> dens_axes[0].imshow(proj3_frb["Density"],origin ='lower'),
> dens_axes[0].imshow(proj4_frb["Density"],origin ='lower'),
> dens_axes[0].imshow(proj5_frb["Density"],origin ='lower'),
> dens_axes[0].imshow(proj6_frb["Density"],origin ='lower')]
>
> plots[0].set_clim((0.0,0.34))
> plots[0].set_cmap("YlOrRd")
> plots[1].set_clim((0.0,0.345))
> plots[1].set_cmap("YlOrRd")
> plots[2].set_clim((0.0,0.34))
> plots[2].set_cmap("YlOrRd")
> plots[3].set_clim((0.0,0.34))
> plots[3].set_cmap("YlOrRd")
> plots[4].set_clim((0.0,0.34))
> plots[4].set_cmap("YlOrRd")
> plots[5].set_clim((0.0,0.34))
> plots[5].set_cmap("YlOrRd")
>
> fig.savefig("test”)
>
>
> error:
>
> Traceback (most recent call last):
> File "plotterm2.py", line 34, in <module>
> dax.xaxis.set_visible(False)
> AttributeError: 'tuple' object has no attribute 'xaxis'
>
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