<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Hello,</div><div><br></div><div><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">I heard a lot of good in the past about the legendary support for ome. I’m glad to experience it for real :)</div></blockquote><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><br></div><div>I’m happy I gave you a good week end start ;)</div></div></div></div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><blockquote type="cite">It looks like the performance of this reader is unlikely to be improved<br><span style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">further. (…)</span><br style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">You said that it was taking a very long time to initialise. Could you</span><br style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">possibly let us know any quantitative measurements of that time? And do</span><br style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">you know how many files/directories are in the dataset in question?</span><br style="font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"></blockquote></div><div><br></div><div>I’ll try next week to disable file grouping, and also to benchmark import with different options next week.</div></div></blockquote><br></div><div>Here you go:</div>I did the tests with a directory that contains the following files (time lapse at 5 positions acquired with micro-manager)<div><br><div><div> 595 20150304_exp_settings.txt</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos0_1.ome.tif</div><div>2.7G 20150304_glu_multiexp_1_MMStack_Pos0_2.ome.tif</div><div> 20M 20150304_glu_multiexp_1_MMStack_Pos0_metadata.txt</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos0.ome.tif</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos1_1.ome.tif</div><div>2.7G 20150304_glu_multiexp_1_MMStack_Pos1_2.ome.tif</div><div> 20M 20150304_glu_multiexp_1_MMStack_Pos1_metadata.txt</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos1.ome.tif</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos2_1.ome.tif</div><div>2.7G 20150304_glu_multiexp_1_MMStack_Pos2_2.ome.tif</div><div> 20M 20150304_glu_multiexp_1_MMStack_Pos2_metadata.txt</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos2.ome.tif</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos3_1.ome.tif</div><div>2.7G 20150304_glu_multiexp_1_MMStack_Pos3_2.ome.tif</div><div> 20M 20150304_glu_multiexp_1_MMStack_Pos3_metadata.txt</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos3.ome.tif</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos4_1.ome.tif</div><div>2.7G 20150304_glu_multiexp_1_MMStack_Pos4_2.ome.tif</div><div> 20M 20150304_glu_multiexp_1_MMStack_Pos4_metadata.txt</div><div>4.0G 20150304_glu_multiexp_1_MMStack_Pos4.ome.tif</div></div></div><div><br></div><div>I tried to read the first 10 frames of the first stack (≈11gb; split into 3 files by micro-manager) using ImageReader() as described early in this thread (see attached file).</div><div>with default options: « 494.016s to create a reader. »</div><div>with no grouping: « 489.204s to create a reader. » </div><div>with no grouping, minimum metadata: « 474.095s to create a reader. » </div><div><br></div><div>I guess the little speed up is due to repeated file access: if I use default options once again at the end I get « 460.052s to create a reader. »</div><div><br></div><div>Whether I disable grouping or not, I always get 5 messages « Reading IFDs; Populating metadata »; so I guess that grouping is actually not disabled. correct?</div><div>I suspect a function disabling grouping of « series » might be what I’m after here, though I don’t know which one exactly…</div><div><br></div><div>This is maybe not so slow if you consider that it’s parsing all metadata; but in my case, what I would like would be to simply access the data of the first frames, don’t care about what happens later.</div><div><br></div><div>Any hint to help us handle these datasets in a faster way will be very appreciated.</div><div>Best,</div><div><br></div><div>Thomas</div><div><div><br></div><div>--</div><div>Thomas Julou | Computational & Systems Biology | Biozentrum – University of Basel | Klingelbergstrasse 50/70 CH-4056 Basel | +41 (0)61 267 16 21</div></div><div><br></div><div><br></div><div></div></body></html>