<div dir="ltr">Right, typically if I don't know the cell, I'll index a bunch of images with no target, then use cluster.unit_cell on the results to get a consensus cell, then re-index with that cell.<div><br></div><div>For dials.stills_process, the default of fft1d works pretty well generally, but to get the best results, indexing.method_list=fft1d,fft3d might be better. There, if the first method fails the second is tried. real_space_grid_search can also be used.</div><div><br></div><div>Getting a specific image in a composite file (such as hdf5) isn't a use case I've hit often, so I don't have an easy solution there. It's possible an image range parameter to dials.import would be useful?</div><div><br></div><div>-Aaron</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Feb 3, 2018 at 1:02 AM, Graeme Winter <span dir="ltr"><<a href="mailto:graeme.winter@gmail.com" target="_blank">graeme.winter@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 style="word-wrap:break-word;line-break:after-white-space">Hi Aaron<div><br></div><div>(and DIALS)</div><div><br></div><div>For stills / single images - should dials.index switch by magic to default fft1d? </div><div><br></div><div>Of is that the responsibility of e.g. xia2 / cctbx.xfel to worry about?</div><div><br></div><div>It has to be said, more often than not, particularly for screening, we do not know cell / symmetry a priori (at diamond anyways) </div><div><br></div><div>A related question</div><div><br></div><div>If I have a data block / strong pickle from 1000 stills, how can I index e.g. image 672? Do I have to split this into 1000 separate things?</div><div><br></div><div>@JH - thanks for this - I think some rigorous testing will be useful here. </div><div><br></div><div>Cheers Graeme<br><div><br><blockquote type="cite"><div><div class="h5"><div>On 3 Feb 2018, at 08:37, Aaron Brewster <<a href="mailto:asbrewster@lbl.gov" target="_blank">asbrewster@lbl.gov</a>> wrote:</div><br class="m_2250465256792134629Apple-interchange-newline"></div></div><div><div><div class="h5"><div dir="ltr">Hi James, thanks. I looked at random image 15 and after trying a bunch of stuff it indexes fine if I use indexing.method=fft3d. The default for stills processing is fft1d, so I find this super interesting.<div><br></div><div>For what it's worth, I pretty much never process stills without a target cell. I generated ~30 random images using your script and indexed them, then I got the unit cells with "dials.show *refined*.json | grep cell". They were all about the same. So I re-indexed random image 15 using fft1d but I also specified known_symmetry.cell=50,60,70,9<wbr>0,90,90 and it indexed fine.</div><div><br></div><div>So, either <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">indexing.method=fft3d or <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">known_symmetry.cell=50,60,7<wbr>0,90,90,90 is sufficient to index random image 15. Certainly for experimental data I would recommend using known_symmetry as the results are always better. However, I'd like to look deeper at fft1d vs fft3d at some point.</span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Cc'ing dials-support.</span></span></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></span></div><div>Thanks!</div><div>-Aaron</div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Feb 2, 2018 at 1:35 PM, James Holton <span dir="ltr"><<a href="mailto:jmholton@lbl.gov" target="_blank">jmholton@lbl.gov</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><div><div><div><div><div><div><div>While testing the new simTBX diffraction image simulator Aaron and I found that some rather beautiful-looking images still won't index. Subsequently, I followed up with mosflm, which does succeed in these cases, even without prior knowledge of the cell or space group.<br><br></div>I have now run this 1000 times, varying only the crystal orientation, and found 171 cases of dials.stills_process failing to index the simulated image whereas mosflm had no trouble, and 5 cases where mosflm failed and dials.stills_process succeeded. There were no overlapping cases where both programs failed. <br><br></div>I have tarballed up the relevant files here:<br><a href="http://bl831.als.lbl.gov/~jamesh/bugreports/dials_index_020218.tgz" target="_blank">http://bl831.als.lbl.gov/~jame<wbr>sh/bugreports/dials_index_0202<wbr>18.tgz</a><br><br></div>The tarball contains a "<a href="http://runme.com/" target="_blank">runme.com</a>" shell script for reproducing these results, and also the tst_nanoBragg_forindex.py jiffy for making a test image given a provided random-number seed. For example:<br><br></div>libtbx.python ./tst_nanoBragg_forindex.py random 15<br><br></div>will create a file called noiseimage_001.cbf that dials.stills_process cannot index (at least in my hands). For those of you who don't have mosflm installed, the tarball incluses a copy, and the "<a href="http://autoindex.com/" target="_blank">autoindex.com</a>" script should run on any linux system.<br><br></div>Any ideas as to why there is this discrepancy? Feels like an opportunity for a non-trivial improvement.<br><br></div>Something to ponder over the weekend, I suppose. Note that I recently checked in a few bug fixes to simTBX, but this
analysis is unaffected by them, so you shouldn't have to update your
build to reproduce this.<br><br></div>Cheers,<br><div><br>-James Holton<br></div><div>MAD Scientist<br><br></div><div><br></div></div>
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