<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Nov 4, 2014 at 1:29 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Okay, I think I must be missing something because right now I am still getting log-spaced bins:<br><br>alld = ds.all_data()<br>gal = alld.cut_region("obj['density'] > 1.01e-28")<br>logs = {('index', 'cylindrical_r'): False}<span class=""><br>logs = {('gas', 'cell_mass'): False}<br></span></div></div></blockquote><div><br></div><div>Do you want both of these to be linearly spaced? Right now you're overwriting the first one when you redeclare "logs".</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><span class="">profile = yt.create_profile(gal,<br> [('index', 'cylindrical_r')], # the bin field<br> [('gas', 'cell_mass')], # profile field<br></span> weight_field=None, n_bins=17)<br></div></div></blockquote><div><br></div><div>Did you forget to pass logs in here?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>coldens = profile["gas","cell_mass"]/1.6733e-24<br>coldens[0] = coldens[0]/(3.14159*profile.x[0]*profile.x[0])<br>i = 1<br>while i < len(coldens):<br> coldens[i] = coldens[i]/((3.14159*profile.x[i]*profile.x[i]) - (3.14159*profile.x[i-1]*profile.x[i-1]))<br> i = i+1<br>mp.plot(profile.x/3.086e21,coldens)<br>mp.show()<br></div>print profile.x<br><br><pre>[ 2.59949407e+20 3.49922639e+20 4.71037249e+20 6.34071835e+20
8.53535665e+20 1.14895993e+21 1.54663592e+21 2.08195484e+21
2.80255739e+21 3.77257363e+21 5.07833019e+21 6.83603292e+21
9.20210863e+21 1.23871263e+22 1.66745367e+22 2.24458981e+22
3.02148330e+22] cm</pre><br></div><div class="gmail_extra"><span class=""><br clear="all"><div><div><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 href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Tue, Nov 4, 2014 at 12:32 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span>On Tue, Nov 4, 2014 at 12:26 PM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div>Okay, I've got that, but does that mean that I can't set something in the parenthesis to force the bins to be in linear space? and I need to do the take_log setting earlier in the code?<br></div></div></div></blockquote><div><br></div></span><div>You can, you would need to have something like:</div><div><br></div><div>logs = {('gas', 'cell_mass'): False}</div><div><br></div><div><span><span style="color:rgb(80,0,80)">profile = yt.create_profile(gal,</span><br style="color:rgb(80,0,80)"><span style="color:rgb(80,0,80)"> [('index', 'cylindrical_r')], # the bin field</span><br style="color:rgb(80,0,80)"><span style="color:rgb(80,0,80)"> [('gas', 'cell_mass')], # profile field</span><br style="color:rgb(80,0,80)"></span><span style="color:rgb(80,0,80)"> weight_field=None, logs=logs)</span><br></div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><br></div>Thanks,<br></div>Stephanie<br></div><div class="gmail_extra"><span><br clear="all"><div><div><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 href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Tue, Nov 4, 2014 at 11:10 AM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span>On Tue, Nov 4, 2014 at 10:59 AM, Stephanie Tonnesen <span dir="ltr"><<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div>Thank you both! I ended up generally following Suoqing's method, but tried to use create_profile. I want my radial spacing to be linear, and when I look at the help page:<br><a href="http://yt-project.org/docs/dev/reference/api/generated/yt.data_objects.profiles.create_profile.html#yt.data_objects.profiles.create_profile" target="_blank">http://yt-project.org/docs/dev/reference/api/generated/yt.data_objects.profiles.create_profile.html#yt.data_objects.profiles.create_profile</a><br><br></div>I read that I should set logs=False<br><br>So I type in:<br><br>profile = yt.create_profile(gal,<br> [('index', 'cylindrical_r')], # the bin field<br> [('gas', 'cell_mass')], # profile field<br> weight_field=None, logs=False)<br><br></div>and yt does not like that. Nor does it like take_log or log_space. Can someone tell me what I should be setting there?<br><br></div></div></blockquote><div><br></div></span><div>In this case, logs is a dictionary that maps field names to logging selection. From the docstrings for create_profile:</div><div><br></div><div><div>logs : dict of boolean values </div><div> Whether or not to log the bin_fields for the profiles. </div><div> The keys correspond to the field names. Defaults to the take_log </div><div> attribute of the field.</div></div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div></div>Thanks again!<span><font color="#888888"><br><br>Stephanie<br></font></span></div><div class="gmail_extra"><span><br clear="all"><div><div><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 href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
<br></span><div><div><div class="gmail_quote">On Mon, Nov 3, 2014 at 9:45 PM, Suoqing JI <span dir="ltr"><<a href="mailto:suoqing@physics.ucsb.edu" target="_blank">suoqing@physics.ucsb.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Stephanie,<div><br></div><div><blockquote type="cite"><div dir="ltr"><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 style="word-wrap:break-word"><div>profile.add_fields(‘cell_mass’, weight=None)</div></div></blockquote></div></div></div></blockquote><br></div><div>Sorry I’ve missed the later part of my old script — after getting the profile[‘cell_mass’] it should be divided by the unit surface area. The following is the full code and it has been tested with AMR data:</div><div><br></div><div><font face="Menlo">profile = BinnedProfile1D(mydisk, Nbin, 'cylindrical_r', rmin, rmax, log_space=True, lazy_reader=True, end_collect=False)</font></div><div><font face="Menlo">profile.add_fields('cell_mass', weight=None)</font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">R = profile['cylindrical_r’]</font></div><div><div><font face="Menlo">Sigma = profile[‘cell_mass']</font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">R_edge = np.logspace(np.log10(rmin), np.log10(rmax), num=Nbin+1)</font></div><div><font face="Menlo">for i in range(0, Nbin): Sigma[i] = Sigma[i] / (np.pi*(R_edge[i+1]**2 - R_edge[i]**2.))</font></div></div><div><br></div><div>And Nathan’s approach which takes the advantage of image buffer should also work.</div><div><br></div><div>Best wishes,</div><div><span><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div>--</div><div>Suoqing JI</div><div>Ph.D Student</div><div>Department of Physics</div><div>University of California, Santa Barbara</div><div>CA 93106, USA</div></div></div></div></div>
</div>
<br></span><div><div><div><blockquote type="cite"><div>On Nov 3, 2014, at 8:40 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Nov 3, 2014 at 5:29 PM, Suoqing JI <span dir="ltr"><<a href="mailto:suoqing@physics.ucsb.edu" target="_blank">suoqing@physics.ucsb.edu</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 style="word-wrap:break-word">Hi Stephanie,<div><br></div><div>Maybe you could specify a disk, use BinnedProfile1D to create bins along cylindrical radial ('cylindrical_r'), and do</div><div><br></div><div>profile.add_fields(‘cell_mass’, weight=None)</div><div><br></div><div>then you could plot profile[‘cell_mass’] vs. profile['cylindrical_r’] and get the 1-D plot the surface density.<br></div></div></blockquote><div><br></div><div>This will be a profile of the gas mass as a function of radius, but it's not quite a surface density profile. That said, for an unweighted projection, I think it's the same up to a constant scaling factor.<br></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 style="word-wrap:break-word"><div><br></div><div>Best wishes,</div><div><div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div>--</div><div>Suoqing JI</div><div>Ph.D Student</div><div>Department of Physics</div><div>University of California, Santa Barbara</div><div>CA 93106, USA</div></div></div></div></div>
</div>
<br><div><blockquote type="cite"><div><div><div>On Nov 3, 2014, at 5:17 PM, Stephanie Tonnesen <<a href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a>> wrote:</div><br></div></div><div><div><div><div dir="ltr"><div><div>Hi yt-users,<br><br></div>I would like to make a 1D plot of column density vs radius for a disk (to compare with observations). I can make a projectionplot, but want something a bit more simple to look at. I am using yt3.0.1--is there a nice way to to this?<br></div></div></div></div></div></blockquote></div></div></div></blockquote><div><br></div>The key is to use the numpy.digitize and numpy.bincount functions to find the histogram of the surface density as a function of radius. Here's an example:<br><br><a href="http://nbviewer.ipython.org/gist/ngoldbaum/af8e7f317efe8f115e8b" target="_blank">http://nbviewer.ipython.org/gist/ngoldbaum/af8e7f317efe8f115e8b</a><br></div><div class="gmail_quote"><div> <br></div><div>This is a simplified version of what I've done for a project I'm working on right now, which involves making a ton of radial plots of projected quantities:<br><br><a href="https://bitbucket.org/ngoldbaum/galaxy_analysis/src/910f5a7e278247a36f25d62bdc478a7b5a7fe8ce/galanyl/galaxy_analyzer.py?at=default#cl-338" target="_blank">https://bitbucket.org/ngoldbaum/galaxy_analysis/src/910f5a7e278247a36f25d62bdc478a7b5a7fe8ce/galanyl/galaxy_analyzer.py?at=default#cl-338</a><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 style="word-wrap:break-word"><div><div><blockquote type="cite"><div><div><div><div dir="ltr"><div><br></div>Thanks!<br><br>Stephanie<br><br clear="all"><div><div><div><div><div><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 href="mailto:stonnes@gmail.com" target="_blank">stonnes@gmail.com</a><br></font></div></div></div>
</div></div></div></div></div></div>
_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></div></blockquote></div><br></div></div><br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div></div>
_______________________________________________<br>yt-users mailing list<br><a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br><a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br></div></blockquote></div><br></div></div></div></div><br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div></div></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div></div></div><br></div></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div></div></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div></div></div><br></div></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div></div></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div></div>