<div dir="ltr">Hi Jonathan,<div><br></div><div>I just tried this using WDMerger_hdf5_chk_1000 (see <a href="http://yt-project.org/data">yt-project.org/data</a>), which is a FLASH dataset from a simulation done in cylindrical coordinates, but it seems to work for me ok using that dataset:</div><div><br></div><div><div> $ yt load WDMerger_hdf5_chk_1000/WDMerger_hdf5_chk_1000.hdf5</div><div><br></div><div> In [1]: slc = ds.slice(2, 0.)</div><div><br></div><div> In [2]: slc['dr'].min()</div><div> Out[2]: 25600000.0 code_length</div></div><div><br></div><div>Somehow something is getting set to a NaN, my guess is <span style="font-size:12.8px">gobj.LeftEdge[i]. In this context gobj is a grid object, so for some reason grid.LeftEdge is NaN along one of your axes for at least one of your grids. You can navigate the grid hierarchy by looking at the grid array: ds.index.grids[0] should be a reference to the root grid. You can also just iterate over ds.index.grids to look at all the grids in your dataset.</span></div><div><br></div><div>Is there any chance you can share the dataset that's causing this issue? We have the yt curldrop (<a href="https://docs.hub.yt/services.html#curldrop">https://docs.hub.yt/services.html#curldrop</a>) available for sharing data publicly. If it's not ok to share the dataset publicly we can try sharing it off-list.</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 24, 2017 at 11:43 AM, Slavin, Jonathan <span dir="ltr"><<a href="mailto:jslavin@cfa.harvard.edu" target="_blank">jslavin@cfa.harvard.edu</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 class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Hi all,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">After upgrading yt to 3.3.3 I'm having trouble with slices. Specifically I'm doing:</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">ds = yt.load(file)</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">slc = ds.slice(2,0.)</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">dx = slc['dr'].min()</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">This is for FLASH data from a run in cylindrical (r,z) symmetry. What I get is:</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div><div>ValueError Traceback (most recent call last)</div><div>/export/slavin/FLASH/mmsnr/<wbr>plot_image.py in <module>()</div><div> 101 slc = ds.slice(2,0.)</div><div> 102 if first:</div><div>--> 103 dx = slc['dr'].min()</div><div> 104 xgl = ds.index.grids[0].LeftEdge[0]</div><div> 105 xgr = ds.index.grids[-1].RightEdge[<wbr>0]</div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/data_objects/data_<wbr>containers.pyc in __getitem__(self, key)</div><div> 270 return self.field_data[f]</div><div> 271 else:</div><div>--> 272 self.get_data(f)</div><div> 273 # fi.units is the unit expression string. We depend on the registry</div><div> 274 # hanging off the dataset to define this unit object.</div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/data_objects/data_<wbr>containers.pyc in get_data(self, fields)</div><div> 1119 def get_data(self, fields=None):</div><div> 1120 if self._current_chunk is None:</div><div>-> 1121 self.index._identify_base_<wbr>chunk(self)</div><div> 1122 if fields is None: return</div><div> 1123 nfields = []</div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/geometry/grid_<wbr>geometry_handler.pyc in _identify_base_chunk(self, dobj)</div><div> 302 # fast_index = self._get_grid_tree()</div><div> 303 if getattr(dobj, "size", None) is None:</div><div>--> 304 dobj.size = self._count_selection(dobj, fast_index = fast_index)</div><div> 305 if getattr(dobj, "shape", None) is None:</div><div> 306 dobj.shape = (dobj.size,)</div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/geometry/grid_<wbr>geometry_handler.pyc in _count_selection(self, dobj, grids, fast_index)</div><div> 312 return fast_index.count(dobj.<wbr>selector)</div><div> 313 if grids is None: grids = dobj._chunk_info</div><div>--> 314 count = sum((g.count(dobj.selector) for g in grids))</div><div> 315 return count</div><div> 316 </div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/geometry/grid_<wbr>geometry_handler.pyc in <genexpr>((g,))</div><div> 312 return fast_index.count(dobj.<wbr>selector)</div><div> 313 if grids is None: grids = dobj._chunk_info</div><div>--> 314 count = sum((g.count(dobj.selector) for g in grids))</div><div> 315 return count</div><div> 316 </div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/data_objects/grid_<wbr>patch.pyc in count(self, selector)</div><div> 381 </div><div> 382 def count(self, selector):</div><div>--> 383 mask = self._get_selector_mask(<wbr>selector)</div><div> 384 if mask is None: return 0</div><div> 385 return self._last_count</div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/data_objects/grid_<wbr>patch.pyc in _get_selector_mask(self, selector)</div><div> 363 mask = self._last_mask</div><div> 364 else:</div><div>--> 365 mask = selector.fill_mask(self)</div><div> 366 if self._cache_mask:</div><div> 367 self._last_mask = mask</div><div><br></div><div>/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/geometry/<wbr>selection_routines.pyx in yt.geometry.selection_<wbr>routines.SliceSelector.fill_<wbr>mask (yt/geometry/selection_<wbr>routines.c:21029)()</div><div> 1235 if i == self.axis:</div><div> 1236 ind[i][0] = \</div><div>-> 1237 <int> ((self.coord - (gobj.LeftEdge[i]).to_ndarray(<wbr>)) /</div><div> 1238 gobj.dds[i])</div><div> 1239 ind[i][1] = ind[i][0] + 1</div><div><br></div><div>ValueError: cannot convert float NaN to integer</div></div><div><br></div><div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Anyone have any ideas on why this is happening?</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Jon</div><span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888">-- <br><div class="m_-2288720728299154188gmail_signature"><div dir="ltr"><div><div dir="ltr">______________________________<wbr>__________________________<br>Jonathan D. Slavin Harvard-Smithsonian CfA<br><a href="mailto:jslavin@cfa.harvard.edu" target="_blank">jslavin@cfa.harvard.edu</a> 60 Garden Street, MS 83<br>phone: <a href="tel:(617)%20496-7981" value="+16174967981" target="_blank">(617) 496-7981</a> Cambridge, MA 02138-1516<br>cell: <a href="tel:(781)%20363-0035" value="+17813630035" target="_blank">(781) 363-0035</a> USA<br>______________________________<wbr>__________________________<br><br></div></div></div></div>
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