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Hi Matt,
<div><br>
</div>
<div>In addition to my last message I have just found that yt will no longer except python scripts and produce projection plots. If I have a script what and type python script_name.py I get the “Running with the wrong number of fields error” displayed in the
email below. However if I just copy and paste the same commands directly into yt I get out all the plots perfectly. </div>
<div><br>
</div>
<div>Any idea why this might be.</div>
<div><br>
</div>
<div>Here is the script incase that helps:</div>
<div><br>
</div>
<div><font color="#0061ff"><br>
</font></div>
<div>
<div><font color="#0061ff">from yt.mods import *</font></div>
<div><font color="#0061ff">p1 = load("output_00001/info_00001.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"])</font></div>
<div><font color="#0061ff">p2 = load("output_00002/info_00002.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"])</font></div>
<div><font color="#0061ff">p3 = load("output_00003/info_00003.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"])</font></div>
<div><font color="#0061ff">p4 = load("output_00004/info_00004.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"])</font></div>
<div><font color="#0061ff">p5 = load("output_00005/info_00005.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"])</font></div>
<div><font color="#0061ff">p6 = load("output_00006/info_00006.txt", fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure"])</font></div>
<div><font color="#0061ff">cen = [0,0,0]</font></div>
<div><font color="#0061ff"><br>
</font></div>
<div><font color="#0061ff">pr1 = ProjectionPlot(p1,'z','Density',center=cen)</font></div>
<div><font color="#0061ff">pr1.set_cmap('Density','YlOrRd')</font></div>
<div><font color="#0061ff">pr1.set_log("Density", False)</font></div>
<div><font color="#0061ff">pr1.set_zlim('Density', 0.01,0.35)</font></div>
<div><font color="#0061ff">pr1.save("p1")</font></div>
<div><font color="#0061ff">pr2 = ProjectionPlot(p2,'z','Density',center=cen)</font></div>
<div><font color="#0061ff">pr2.set_cmap('Density','YlOrRd')</font></div>
<div><font color="#0061ff">pr2.set_log("Density", False)</font></div>
<div><font color="#0061ff">pr2.set_zlim('Density', 0.01,0.35)</font></div>
<div><font color="#0061ff">pr2.save("p2")</font></div>
<div><font color="#0061ff">pr3 = ProjectionPlot(p3,'z','Density',center=cen)</font></div>
<div><font color="#0061ff">pr3.set_cmap('Density','YlOrRd')</font></div>
<div><font color="#0061ff">pr3.set_log("Density", False)</font></div>
<div><font color="#0061ff">pr3.set_zlim('Density', 0.01,0.35)</font></div>
<div><font color="#0061ff">pr3.save("p3")</font></div>
<div><font color="#0061ff">pr4 = ProjectionPlot(p4,'z','Density',center=cen)</font></div>
<div><font color="#0061ff">pr4.set_cmap('Density','YlOrRd')</font></div>
<div><font color="#0061ff">pr4.set_log("Density", False)</font></div>
<div><font color="#0061ff">pr4.set_zlim('Density', 0.01,0.35)</font></div>
<div><font color="#0061ff">pr4.save("p4")</font></div>
<div><font color="#0061ff">pr5 = ProjectionPlot(p5,'z','Density',center=cen)</font></div>
<div><font color="#0061ff">pr5.set_cmap('Density','YlOrRd')</font></div>
<div><font color="#0061ff">pr5.set_log("Density", False)</font></div>
<div><font color="#0061ff">pr5.set_zlim('Density', 0.01,0.35)</font></div>
<div><font color="#0061ff">pr5.save("p5")</font></div>
<div><font color="#0061ff">pr6 = ProjectionPlot(p6,'z','Density',center=cen)</font></div>
<div><font color="#0061ff">pr6.set_cmap('Density','YlOrRd')</font></div>
<div><font color="#0061ff">pr6.set_log("Density", False)</font></div>
<div><font color="#0061ff">pr6.set_zlim('Density', 0.01,0.35)</font></div>
<div><font color="#0061ff">pr6.save("p6")</font></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Kearn</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On 13 Nov 2013, at 13:26, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div>
<p dir="ltr">Hi Kearn,</p>
<p dir="ltr">Huh, weird. So in 3 we switched the order of projection arguments. Try swapping 0 and "Density".</p>
<p dir="ltr">Sorry this has been such a pain!!</p>
<p dir="ltr">Matt</p>
<div class="gmail_quote">On Nov 13, 2013 8:23 AM, <<a href="mailto:k.grisdale@surrey.ac.uk">k.grisdale@surrey.ac.uk</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Matt,
<div><br>
</div>
<div>Thanks for that yt now loads in Ramses data but I get new errors.</div>
<div><br>
</div>
<div><br>
</div>
<div>If I use:</div>
<div>p1 = load("output_00001/info_00001.txt")</div>
<div>pr1 = ProjectionPlot(p1,'z','Density',center=cen)</div>
<div><br>
</div>
<div>I get:</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div><font color="#0056d6">You are running with the wrong number of fields.</font></div>
<div><font color="#0056d6">Please specify these in the load command.</font></div>
<div><font color="#0056d6">We are looking for 6 fields.</font></div>
<div><font color="#0056d6">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]</font></div>
<div><font color="#0056d6">Traceback (most recent call last):</font></div>
<div><font color="#0056d6"> File "<stdin>", line 1, in <module></font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1441, in __init__</font></div>
<div><font color="#0056d6"> field_parameters = field_parameters)</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 234, in __init__</font></div>
<div><font color="#0056d6"> self.get_data(field)</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 278, in get_data</font></div>
<div><font color="#0056d6"> chunk_fields, "io")):</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 434, in parallel_objects</font></div>
<div><font color="#0056d6"> for obj_id, obj in oiter:</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 453, in chunks</font></div>
<div><font color="#0056d6"> self.get_data(fields)</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 531, in get_data</font></div>
<div><font color="#0056d6"> fluids, self, self._current_chunk)</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py", line 520, in _read_fluid_fields</font></div>
<div><font color="#0056d6"> chunk_size)</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/io.py", line 41, in _read_fluid_selection</font></div>
<div><font color="#0056d6"> rv = subset.fill(content, fields, selector)</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py", line 304, in fill</font></div>
<div><font color="#0056d6"> for level, offset in enumerate(self.domain.hydro_offset):</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py", line 102, in hydro_offset</font></div>
<div><font color="#0056d6"> hvals = fpu.read_attrs(f, header, "=")</font></div>
<div><font color="#0056d6"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py", line 74, in read_attrs</font></div>
<div><font color="#0056d6"> assert(s1 == s2)</font></div>
<div><font color="#0056d6">AssertionError</font></div>
<div><font color="#0056d6"><br>
</font></div>
<div>If I use the multi plot script that we have been discussing I get this error:</div>
<div><font color="#0056d6"><br>
</font></div>
<div>
<div style="color:rgb(0,86,214)">Traceback (most recent call last):</div>
<div style="color:rgb(0,86,214)"> File "plotterm3.py", line 20, in <module></div>
<div style="color:rgb(0,86,214)"> proj1 = p1.h.proj(0, "Density", center=cen)</div>
<div style="color:rgb(0,86,214)"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 234, in __init__</div>
<div style="color:rgb(0,86,214)"> self.get_data(field)</div>
<div style="color:rgb(0,86,214)"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py", line 266, in get_data</div>
<div style="color:rgb(0,86,214)"> fields = self._determine_fields(ensure_list(fields))</div>
<div style="color:rgb(0,86,214)"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 396, in _determine_fields</div>
<div style="color:rgb(0,86,214)"> finfo = self.pf._get_field_info("unknown", fname)</div>
<div style="color:rgb(0,86,214)"> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 331, in _get_field_info</div>
<div style="color:rgb(0,86,214)"> raise YTFieldNotFound((ftype, fname), self)</div>
<div style="color:rgb(0,86,214)">yt.utilities.exceptions.YTFieldNotFound: Could not find field '('gas', 0)' in info_00001.</div>
<div style="color:rgb(0,86,214)"><br>
</div>
<div>Ideas what I’ve done?</div>
</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Kearn</div>
<div><br>
</div>
<div>PS: As far as I know I am running yt 3. is there a way to check which version I have?</div>
<div><font color="#0056d6"><br>
</font></div>
<div>
<div>
<div>On 13 Nov 2013, at 13:08, Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:</div>
<br>
<div>Hi Kearn,<br>
<br>
Looks like you got back onto the yt-2.X branch. I of course screwed<br>
up and should have realized that you were on 3.0! :) (You were,<br>
right?) My fault completely. Give a shot at this:<br>
<br>
hg pull <a href="http://bitbucket.org/yt_analysis/yt-3.0" target="_blank">http://bitbucket.org/yt_analysis/yt-3.0</a><br>
hg up -C tip<br>
python2.7 setup.py build_ext -i -f<br>
<br>
That should get you back running.<br>
<br>
-Matt<br>
<br>
On Wed, Nov 13, 2013 at 5:23 AM, <<a href="mailto:k.grisdale@surrey.ac.uk" target="_blank">k.grisdale@surrey.ac.uk</a>> wrote:<br>
<blockquote type="cite">Hi Matt,<br>
<br>
I have just applied the pull request using the command:<br>
<br>
cd $YT_DEST/src/yt-hg<br>
hg pull && hg update yt<br>
<br>
But now when i tried to load RAMSES data into the YT I get the following<br>
error:<br>
<br>
yt : [ERROR ] 2013-11-13 10:22:49,486 Couldn't figure out output type for<br>
output_00001/info_00001.txt<br>
Traceback (most recent call last):<br>
File "<stdin>", line 1, in <module><br>
File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line<br>
90, in load<br>
raise YTOutputNotIdentified(args, kwargs)<br>
yt.utilities.exceptions.YTOutputNotIdentified: Supplied<br>
('output_00001/info_00001.txt',) {}, but could not load!<br>
<br>
Any idea what has happened?<br>
<br>
Thanks<br>
<br>
Kearn<br>
<br>
<br>
Traceback (most recent call last):<br>
File "plotterm3.py", line 7, in <module><br>
p1 = load("output_00001/info_00001.txt")<br>
File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line<br>
90, in load<br>
raise YTOutputNotIdentified(args, kwargs)<br>
yt.utilities.exceptions.YTOutputNotIdentified: Supplied<br>
('output_00001/info_00001.txt',) {}, but could not load!<br>
<br>
<br>
On 12 Nov 2013, at 14:57, Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:<br>
<br>
Hi Kearn,<br>
<br>
<br>
On Tue, Nov 12, 2013 at 9:47 AM, <<a href="mailto:k.grisdale@surrey.ac.uk" target="_blank">k.grisdale@surrey.ac.uk</a>> wrote:<br>
<blockquote type="cite"><br>
Dear Matt,<br>
<br>
Thanks again. The normalize command was just what I needed.<br>
<br>
Does the projection plot used in the multi-plot work differently to the<br>
normal ProjectionPlot?<br>
<br>
<br>
I ask because with the code below I get the image below, while using the<br>
same centre and width with the multi plot I get the image I sent in my last<br>
email. I have tried playing around with different centres, and projection<br>
radii but this only moves the image around or makes the square that it does<br>
plot different sizes(this is still the case even after changing to a linear<br>
scale). Both plots are using the same data set so i am explicating the same<br>
plot.<br>
</blockquote>
<br>
<br>
They sort of work the same. What you're doing with the FRBs is much<br>
lower-level, though, even though it's what the ProjectionPlot uses. I think<br>
the issue you're running into is that the FixedResolutionBuffer is *not*<br>
periodic by default, and to_frb() doesn't turn it on. I've issued a pull<br>
request that adds this functionality to the to_frb() command, as I think it<br>
is a problem not to have it!<br>
<br>
<a href="https://bitbucket.org/yt_analysis/yt/pull-request/639/adding-periodic-default-false-to-to_frb" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-request/639/adding-periodic-default-false-to-to_frb</a><br>
<br>
-Matt<br>
<br>
<blockquote type="cite"><br>
<br>
Thanks Kearn<br>
<br>
<br>
from yt.mods import *<br>
p6 = load("output_00006/info_00006.txt")<br>
cen = [0,0,0]<br>
pr6 = ProjectionPlot(p6,'z','Density',center=cen)<br>
pr6.set_cmap('Density','YlOrRd')<br>
pr6.set_zlim('Density', 0.0,0.35)<br>
pr6.save("p6")<br>
<br>
<br>
<p6_Projection_z_Density.png><br>
<br>
On 12 Nov 2013, at 11:33, Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:<br>
<br>
Hi Kearn,<br>
<br>
<br>
On Tue, Nov 12, 2013 at 3:46 AM, <<a href="mailto:k.grisdale@surrey.ac.uk" target="_blank">k.grisdale@surrey.ac.uk</a>> wrote:<br>
<blockquote type="cite"><br>
Hi Matt.<br>
<br>
The Script you sent me has been of great help! I have now managed to get<br>
yt to plot projections for my data.<br>
<br>
However I am still having small trouble. Firstly script only plots the 1<br>
quarter of each projection(I can change which quarter), [Graph below] and<br>
secondly I would like to set the colorbar to be linear for my data. How can<br>
I go about that?<br>
</blockquote>
<br>
<br>
If you change LogNorm to Normalize (and change the import) it should<br>
change to linear. You can probably then just remove the LogLocator ticker.<br>
To change the FOV, the 0.25 "unitary" is what I set, and you should be able<br>
to change it to whatever you like. Just be sure to also change the center<br>
value to be the center of the domain! :)<br>
<br>
-Matt<br>
<br>
<blockquote type="cite"><br>
<br>
Thanks<br>
<br>
Kearn<br>
<br>
<Screen Shot 2013-11-12 at 08.46.03.png><br>
On 11 Nov 2013, at 22:39, Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:<br>
<br>
Hi Kearn,<br>
<br>
Oops, I guess my reply was less than helpful! Sorry about that --<br>
been one of those days.<br>
<br>
On Mon, Nov 11, 2013 at 3:30 PM, <<a href="mailto:k.grisdale@surrey.ac.uk" target="_blank">k.grisdale@surrey.ac.uk</a>> wrote:<br>
<br>
Hi Matt,<br>
<br>
Thanks for the reply. The code that I used below is my attempt at<br>
adapting<br>
the script on the yt pages explaining how to use Multi-Plot Slice and<br>
Projections. As I couldn’t figure out how make multi-plots of yt<br>
Projections<br>
I thought I’d try the adapting route. Which means there bits there I<br>
don’t<br>
get but have included as I thought they where needed for the multi plot.<br>
<br>
<br>
I've spent a bit of time looking at this and I've been able to make a<br>
multi plot that I think matches what you're looking for. I've put the<br>
script here, and I've also tried to note where there might be issues<br>
with it that could be important when you adapt it to your data.<br>
<br>
<a href="http://paste.yt-project.org/show/4047/" target="_blank">http://paste.yt-project.org/show/4047/</a><br>
<br>
Let me know if that helps out, or if I can help in any other way.<br>
<br>
-Matt<br>
<br>
Thanks again<br>
<br>
Kearn<br>
<br>
<br>
<br>
On 11 Nov 2013, at 20:13, Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:<br>
<br>
Hi Kearn,<br>
<br>
<br>
On Mon, Nov 11, 2013 at 10:18 AM, <<a href="mailto:k.grisdale@surrey.ac.uk" target="_blank">k.grisdale@surrey.ac.uk</a>> wrote:<br>
<br>
<br>
Hi everyone<br>
<br>
I am trying to make a multi plot using data from Ramses. I have outputs<br>
from Ramses at 6 different times and I want to make projections at each<br>
time<br>
and place than in a multi plot to show evolution of the system. However<br>
when<br>
the code that I have written gives the results below.<br>
<br>
<br>
<Screen Shot 2013-11-11 at 15.12.13.png><br>
<br>
<br>
Can anyone offer any suggestions as to wear my code is going wrong?<br>
<br>
Thanks<br>
<br>
Kearn<br>
<br>
The code I’m using ( the for dax lines have been commented out because<br>
every time they are included I get the error at the bottom)<br>
<br>
from yt.mods import * # set up our namespace<br>
import matplotlib.colorbar as cb<br>
from matplotlib.colors import LogNorm<br>
<br>
p1 = load("output_00001/info_00001.txt")<br>
p2 = load("output_00002/info_00002.txt")<br>
p3 = load("output_00003/info_00003.txt")<br>
p4 = load("output_00004/info_00004.txt")<br>
p5 = load("output_00005/info_00005.txt")<br>
p6 = load("output_00006/info_00006.txt")<br>
<br>
cen = [0,0,0]<br>
orient = 'vertical'<br>
<br>
fig, axes, colorbars = get_multi_plot(3, 2, colorbar=orient, bw = 4)<br>
proj1 = p1.h.proj(2, "Density", center=cen)<br>
proj2 = p2.h.proj(2, "Density", center=cen)<br>
proj3 = p3.h.proj(2, "Density", center=cen)<br>
proj4 = p4.h.proj(2, "Density", center=cen)<br>
proj5 = p5.h.proj(2, "Density", center=cen)<br>
proj6 = p6.h.proj(2, "Density", center=cen)<br>
<br>
proj1_frb = proj1.to_frb((0.7,"cm"),512)<br>
proj2_frb = proj2.to_frb((0.7,"cm"),512)<br>
proj3_frb = proj3.to_frb((0.7,"cm"),512)<br>
proj4_frb = proj4.to_frb((0.7,"cm"),512)<br>
proj5_frb = proj5.to_frb((0.7,"cm"),512)<br>
proj6_frb = proj6.to_frb((0.7,"cm"),512)<br>
<br>
dens_axes = [axes[0][0], axes[1][0]]<br>
<br>
#for dax in zip(dens_axes) :<br>
<br>
<br>
<br>
I'm not sure what you're doing here -- this will yield:<br>
<br>
[(axes[0][0],), (axes[1][0],)]<br>
<br>
So you'll be getting back a tuple of length one inside the loop. You<br>
should<br>
be able to do dax[0]? But I'm not sure you need to zip in the first<br>
place,<br>
either.<br>
<br>
-Matt<br>
<br>
<br>
<br>
# dax.xaxis.set_visible(False)<br>
# dax.yaxis.set_visible(False)<br>
<br>
plots = [dens_axes[0].imshow(proj1_frb["Density"],origin ='lower'),<br>
dens_axes[0].imshow(proj2_frb["Density"],origin ='lower'),<br>
dens_axes[0].imshow(proj3_frb["Density"],origin ='lower'),<br>
dens_axes[0].imshow(proj4_frb["Density"],origin ='lower'),<br>
dens_axes[0].imshow(proj5_frb["Density"],origin ='lower'),<br>
dens_axes[0].imshow(proj6_frb["Density"],origin ='lower')]<br>
<br>
plots[0].set_clim((0.0,0.34))<br>
plots[0].set_cmap("YlOrRd")<br>
plots[1].set_clim((0.0,0.345))<br>
plots[1].set_cmap("YlOrRd")<br>
plots[2].set_clim((0.0,0.34))<br>
plots[2].set_cmap("YlOrRd")<br>
plots[3].set_clim((0.0,0.34))<br>
plots[3].set_cmap("YlOrRd")<br>
plots[4].set_clim((0.0,0.34))<br>
plots[4].set_cmap("YlOrRd")<br>
plots[5].set_clim((0.0,0.34))<br>
plots[5].set_cmap("YlOrRd")<br>
<br>
fig.savefig("test”)<br>
<br>
<br>
error:<br>
<br>
Traceback (most recent call last):<br>
File "plotterm2.py", line 34, in <module><br>
dax.xaxis.set_visible(False)<br>
AttributeError: 'tuple' object has no attribute 'xaxis'<br>
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