<div dir="ltr">pdb is the Python debugger, see:<div><br></div><div><a href="https://docs.python.org/2/library/pdb.html">https://docs.python.org/2/library/pdb.html</a><br></div><div><br></div><div>But I really wouldn't recommend using a debugger to solve your problem with labels -- just to find out what the problem is (which I think we already have). It would be better to make it so the label is valid in the first place. Or if it is valid to have a label with non-increasing / non-unique vertices, then we should support it properly in mne-python.</div><div><br></div><div>You could also write a script to deduplicate the vertices in your label file. Label files are human-readable ASCII files, so you could even do it manually if you want. This gives you a clue as to the approximate line numbers you'd need to remove:</div><div><br></div><div><div>(Pdb) p np.where(np.diff(vertices) == 0)[0]</div><div>array([840, 860, 862, 864, 866, 868])</div></div><div><br></div><div>HTH,</div><div>Eric</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 26, 2015 at 11:37 AM, David I Leitman <span dir="ltr"><<a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a>></span> wrote:<br><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 Eric,<div> let me clarify: How can I use pdb like you did below (...<span style="font-family:monospace,monospace">p np.unique(vertices).shape) to automatically remove a duplicate vertice?</span><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">//thanks dave<br></font><div><div><div class="h5"><div>On May 26, 2015, at 2:33 PM, David I Leitman <<a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a>> wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5"><div style="word-wrap:break-word">Hi Eric, <div>it is complicated but essentially, I have structural labels derived from the aprac 2009 atlas I then pass an fmri activation label derived my fsl volumetric pipeline and warped into subject freesurfer space, and then within the intersection of these labels find the source center of gravity and generate a sphere with an 8mm diameter.<div><br></div><div>here is the script, attached...</div><div>given that it is a hack (perhaps idiosyncratic to my barouque processing stream) is this pdb function you use a good way to check for duplicates?</div><div><br></div><div>thanks// dave</div><div><br></div><div><br></div><div><br><div><div>On May 26, 2015, at 12:18 PM, Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr"><div>Hey David,</div><div><br></div>There appear to be duplicate vertices in your label (which I renamed to "rh.label"):<div><br></div><div><div><font face="monospace, monospace">>>> import mne</font></div><div><font face="monospace, monospace">>>> import numpy as np</font></div><div><font face="monospace, monospace">>>> label = mne.read_label('rh.label')</font></div><div><font face="monospace, monospace">Traceback (most recent call last):</font></div><div><font face="monospace, monospace">...</font></div><div><font face="monospace, monospace">ValueError: Vertices must be ordered in increasing order.<br></font></div><div><font face="monospace, monospace">>>> import pdb; <a href="http://pdb.pm/" target="_blank">pdb.pm</a>()</font></div><div><font face="monospace, monospace">> /home/larsoner/custombuilds/mne-python/mne/label.py(206)__init__()</font></div><div><font face="monospace, monospace">-> raise ValueError('Vertices must be ordered in increasing order.')</font></div><div><font face="monospace, monospace">(Pdb) p np.unique(vertices).shape<br></font></div><div><font face="monospace, monospace">(1081,)</font></div><div><font face="monospace, monospace">(Pdb) p vertices.shape</font></div><div><font face="monospace, monospace">(1087,)</font></div></div><div><br></div><div>How did you create this label? It might be possible for us to de-duplicate vertices or even reorder them when loading a label in mne-python, I'd have to think about if that would create issues elsewhere. Please open an issue for it on GitHub and we can discuss more there.</div><div><br></div><div>Eric</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 26, 2015 at 7:13 AM, David Leitman <span dir="ltr"><<a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
<br>
<br>
When I run the following: roi=mne.read_label('/mnt/thothdisk2/K_AWARD/K_DATA/MEG_DATA/L13420/label/rh.K_IFG_pars_tri_operc_FMRI_ZCUE.label')<br>
<br>
<br>
i get:<br>
/home/leitman/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/mne/label.pyc in __init__(self, vertices, pos, values, hemi, comment, name, filename, subject, color, verbose)<br>
201 vertices = np.asarray(vertices)<br>
202 if np.any(np.diff(vertices.astype(int)) <= 0):<br>
--> 203 raise ValueError('Vertices must be ordered in increasing order.')<br>
204<br>
205 if color is not None:<br>
<br>
ValueError: Vertices must be ordered in increasing order.<br>
<br>
yet the vertices are in the correct order?<br>
<br>
I have attached the label file, any suggestions ?<br>
<br>
thanks// dave<br>
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</div>
</div></div></div></div></div><span><K_plot_label_from_stc_v12.py></span><div style="word-wrap:break-word"><div></div></div></blockquote></div><span class=""><br><div>
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Leitman PhD</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px"><br></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="'Lucida Grande'" size="2"><span style="font-size:10px">Research Assistant Professor</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Department of Psychiatry-</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Neuropsychiatry program</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Perelman School of Medicine</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">University of Pennsylvania</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Gates Pavilion 10th floor room 1042</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">3400 Spruce St</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">Philadelphia, PA 19104-4283</span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">P: <a href="tel:%28215%29%20662-7389" value="+12156627389" target="_blank">(215) 662-7389</a></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">F: <a href="tel:%28215%29%20662-7903" value="+12156627903" target="_blank">(215) 662-7903</a></span></font></div><div style="font-weight:normal;font-style:normal;font-family:Helvetica;font-size:16px"><font face="Lucida Grande" size="2"><span style="font-size:10px">E: <a href="mailto:leitman@mail.med.upenn.edu" target="_blank">leitman@mail.med.upenn.edu</a></span></font></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span><span style="font-family:'Lucida Grande';font-size:x-small">Faculty page:<span style="white-space:pre-wrap"> </span></span><a href="http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343" style="font-size:11px" target="_blank">http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343</a><div><span style="font-family:'Lucida Grande';font-size:x-small">Lab website:</span></div><div><span style="font-family:'Lucida Grande';font-size:x-small"> </span><span style="font-family:'Lucida Grande';font-size:x-small"><a href="http://davidileitman.com" target="_blank">http://davidileitman.com</a></span></div><div><br></div><div>The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. 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