<div dir="ltr"><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div class="gmail_extra"><div class="gmail_quote">On Mon, Jun 6, 2016 at 2:47 PM, Nathan Goldbaum <span dir="ltr"><<a>nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Stephanie,<div><br></div><div>So I think I know what's happening here. Here's a reduced, simplified version of your script that illustrates the issue:</div><div><br></div><div><a href="http://paste.yt-project.org/show/6589/" target="_blank">http://paste.yt-project.org/show/6589/</a></div></div></blockquote></div></div></blockquote><div><br></div><div>Oops, it looks like I pasted the wrong thing. Here's what I originally meant to paste:</div><div><br></div><div><a href="http://paste.yt-project.org/show/6592/" target="_blank">http://paste.yt-project.org/show/6592/</a></div></div><br>On Monday, June 6, 2016, Stephanie Tonnesen <<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi Nathan,<br><br></div><div>How do I put in that request? I am trying to do direct comparisons with observations, and unfortunately chose my line of sight axis to be the y axis. In future simulations I can change that, but I agree that this would be a nice feature. <br></div></div></blockquote><div><br></div><div>You can create issues here:</div><div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/issues/new" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/new</a> </div><div><br></div><div>Mark it as an enhancement for 3.4, and include a link to this e-mail thread:</div><div><br></div><div><a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2016-June/007893.html" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2016-June/007893.html</a></div><div><br></div><div>as well as the test script we came up with:</div><div><br></div><div><a href="http://paste.yt-project.org/show/6592/" target="_blank">http://paste.yt-project.org/show/6592/</a><br></div><div><br></div><div>Unfortunately we have a code freeze coming up starting this Wednesday, so we may not be able to get to this until after yt 3.3 comes out.</div><div><br></div><div>One very hacky, no-good, awful, but perhaps practical way to force the plots to look how you want them to look would be to make the following small adjustment to the yt source code:</div><div><br></div><div><div>diff -r 068d09108046 yt/visualization/fixed_resolution.py</div><div>--- a/yt/visualization/fixed_resolution.py Thu Jun 02 11:49:11 2016 -0500</div><div>+++ b/yt/visualization/fixed_resolution.py Mon Jun 06 17:48:27 2016 -0500</div><div>@@ -576,7 +576,7 @@ class OffAxisProjectionFixedResolutionBu</div><div> interpolated=dd.interpolated,</div><div> north_vector=dd.north_vector,</div><div> method=dd.method)</div><div>- ia = ImageArray(buff.swapaxes(0,1), info=self._get_info(item))</div><div>+ ia = ImageArray(np.fliplr(buff.swapaxes(0,1)), info=self._get_info(item))</div><div> self[item] = ia</div><div> return ia</div></div><div><br></div><div>That said, having a generic interface for declaring the orientation of individual plots would definitely be nice...</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Thanks!<br></div><div>Stephanie<br></div></div><div class="gmail_extra"><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a>stonnes@gmail.com</a><br></font></div></div></div>
<div class="gmail_quote"><br></div></div></blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><br></div><div><br></div><div>In this example I've tried to construct the SlicePlot and OffAxisProjectionPlot to be as similar as possible to ease comparison.</div><div><br></div><div>In your slices, when we you do:</div><span><div><br></div><div><div>ds.coordinates.x_axis[1] = 0</div><div>ds.coordinates.x_axis['y'] = 0</div><div>ds.coordinates.y_axis[1] = 2</div><div>ds.coordinates.y_axis['y'] = 2</div></div><div><br></div></span><div>You're explicitly asking for a non-right handed representation of the simulation's coordinate system. Note that the SlicePlot and OffAxisProjecitonPlot coordinate system *would* line up, if you didn't adjust ds.coordinates.x_axis and ds.coordinates.y_axis, so long as you set north_vector = [1, 0, 0].</div><div><br></div><div>The trouble for your use comes comes when you try to generate a plot with an inverted coordinate system using OffAxisProjectionPlot. That doesn't work because OffAxisProjectionPlot doesn't have a way to declare the orientation of the plot coordinate system. As you said, if it were possible to specify an east_vector (or a coordinate system orientation) you would be able to work around this. Unfortunately, that's not supported right now.</div><div><br></div><div>Assuming there isn't anything special about the 'y' axis as opposed to the 'x' axis, I think a simpler way to handle this would be to make plots along the 'x' axis instead of the 'y' axis. Here's an example script that illustrates how the issues you're running into go away when you do that:</div><div><br></div><div><div><a href="http://paste.yt-project.org/show/6590/" target="_blank">http://paste.yt-project.org/show/6590/</a></div></div><div><br></div><div>If you *need* to slice along 'y', *and* for the coordinate systems in the two plots to have identical orientations, then we would need to modify OffAxisProjectionPlot to add an API hook that causes the plot orientation to be flipped. I think this is a totally reasonable thing to request as a feature - it's pretty common that people want to do this for SlicePlot and ProjectionPlot along the 'y' axis. Having a general interface for this for all plots would be very useful.</div><span><font color="#888888"><div><br></div><div>-Nathan</div><div><br></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 6, 2016 at 4:12 PM, Stephanie Tonnesen <span dir="ltr"><<a>stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div>Hi Nathan (and anyone reading this string!),<br><br></div>Sorry it took a little while, but I wrote a short version of the code that shows the same problem/difference between the y slice and OffAxisProjection. The difference is most easily seen comparing the velocity_x panels it writes out. You will probably have to change the exact file path to wherever you keep your IsolatedGalaxy data, but otherwise it should happily run! Also, just a note that the zoom is a bit extreme in the OffAxisProjection, but you still see the problem. <br><br></div>Thanks,<br></div>Stephanie<br><br></div><div class="gmail_extra"><span><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a>stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Fri, Jun 3, 2016 at 3:44 PM, Nathan Goldbaum <span dir="ltr"><<a>nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Is there any chance you can make a self-contained example using one of the test datasets on <a href="http://yt-project.org/data" target="_blank">yt-project.org/data</a>? That will make it easier for one of us to take a shot at figuring out what's going wrong. I usually use "IsolatedGalaxy" - it has a disk in the center of the simulation box with an angular momentum vector aligned with the z axis.</div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 3, 2016 at 5:10 PM, Stephanie Tonnesen <span dir="ltr"><<a>stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Right, I have my north vector, which I *think* is why my z-axis (Image y) looks correct. Unfortunately I can't specify an east_vector. I will keep playing and if I come up with something clever I will let ppl know. <br><br></div><div>Thanks for thinking about this with me!<span><font color="#888888"><br><br></font></span></div><span><font color="#888888"><div>Stephanie<br></div><div><br><br></div><div><br><br></div></font></span></div><div class="gmail_extra"><span><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a>stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Fri, Jun 3, 2016 at 2:10 PM, Nathan Goldbaum <span dir="ltr"><<a>nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span>On Fri, Jun 3, 2016 at 4:08 PM, Stephanie Tonnesen <span dir="ltr"><<a>stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi Nathan,<br><br><br></div><div>So I tried two of your ideas, and don't get the last one. <br><span><br><span><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div>ds.coordinates.x_axis[1] = 0<br> ds.coordinates.x_axis['y'] = 0<br> ds.coordinates.y_axis[1] = 2<br> ds.coordinates.y_axis['y'] = 2<br></div></div></div></div></div></blockquote><div><br></div></span><div>Is the orientation correct (albeit with z along the horizontal axis and x along the vertical axis) if you don't do this ^ ?<br><br></div></span><div>If I don't do that but still have the same L and north_vector, I get the same results. <br><br></div><div>If I change L = [0,1,0] and north_vector=[0,0,1], I get the same results as well.<br><br></div><div>Ugh! <br><br></div><div>I am not sure what "x" and "z" fields you think I should be making OffAxisProjection s for? Do you mean have L = [1,0,0] and [0,0,1], or have it project an "x" and "z" field onto my off-axis projection?<br></div></div></div></blockquote><div><br></div></span><div>'x' and 'z' don't really have a meaning for OffAxisProjectionPlot, that's why they're dispalyed as "image x" and "image y". However, if you specify a north_vector, that should disambiguate things.</div><div><br></div><div>It's entirely possible there's a bug here.</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><br></div><div>Thanks,<br><br></div><div>Stephanie<br></div><div><br><br></div><br></div></div><div class="gmail_extra"><span><br clear="all"><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a>stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Thu, Jun 2, 2016 at 5:14 PM, Nathan Goldbaum <span dir="ltr"><<a>nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span>On Thu, Jun 2, 2016 at 6:45 PM, Stephanie Tonnesen <span dir="ltr"><<a>stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Hi all, <br><br></div>The quick summary of what I want to do is switch the coordinates of the x-axis on a OffAxisProjection plot. Basically, what I am trying to do is get a LOS look at a galaxy , so I need a 20 degree tilt in the y-z plane. For some reason this is swapping the x-axis direction from my plain old y slice. The relevant parts of my code look like this:<br><br>ds.coordinates.x_axis[1] = 0<br> ds.coordinates.x_axis['y'] = 0<br> ds.coordinates.y_axis[1] = 2<br> ds.coordinates.y_axis['y'] = 2<br></div></div></div></div></div></blockquote><div><br></div></span><div>Is the orientation correct (albeit with z along the horizontal axis and x along the vertical axis) if you don't do this ^ ?</div><div><br></div><div>What happens if you make an off-axis projection aligned with the y axis, i.e. L = [0, 1, 0], north_vector = [0, 0, 1]?</div><div><br></div><div>Can you try making an off-axis projection of the 'x' and 'z' fields?</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div><div><div dir="ltr"><div><div><div><div> <br> plot6=yt.SlicePlot(ds,"y","density")<br> plot6.save()<br><br> plot8=yt.SlicePlot(ds,"y","velocity_z")<br> plot8.save()<br><br> plot9 = yt.SlicePlot(ds,"y","velocity_y")<br> plot9.save()<br><br> plot10 = yt.SlicePlot(ds,"y","velocity_x")<br> plot10.save()<br><br> ds.periodicity=(True,True,True)<br><br> L = [0.0,0.93969,-0.342]<br> #W = [0.5,0.5,0.5]<br> #c = [0.5,0.5,0.5] <br> #N = 1028<br> north_vector = [0,0.342,0.93969]<br> plot12 = yt.OffAxisProjectionPlot(ds,L,'density',width=(100,'kpc'),north_vector=north_vector)<br> plot12.save()<br><br> plot13 = yt.OffAxisProjectionPlot(ds,L,'velocity_x',width=(100,'kpc'),north_vector=north_vector)<br> plot13.save()<br> plot14 = yt.OffAxisProjectionPlot(ds,L,'velocity_y',width=(100,'kpc'),north_vector=north_vector)<br> plot14.save()<br> plot15 = yt.OffAxisProjectionPlot(ds,L,'velocity_z',width=(100,'kpc'),north_vector=north_vector)<br> plot15.save()<br><br></div>I have attached four files: the slices of velocity_y and velocity_x and the OffAxisProjections of the same. You can see that the x-axis seems to be flipped. You will also notice that the OffAxisProjection is more zoomed than the Slice, but don't let this distract you :) <br><br></div>I have no idea what has gone wrong here. Any help, as always, is really appreciated.<br><br></div>Thanks,<br></div>Stephanie<br clear="all"><div><div><div><div><div><div><div><div data-smartmail="gmail_signature"><div dir="ltr"><div><div><div><font face="garamond,serif">--<br>Dr. Stephanie Tonnesen<br></font></div><font face="garamond,serif">Alvin E. Nashman Postdoctoral Fellow<br></font></div><font face="garamond,serif">Carnegie Observatories, Pasadena, CA<br></font></div><font face="garamond,serif"><a>stonnes@gmail.com</a><br></font></div></div></div>
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