<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Roden,<div class=""><br class=""></div><div class=""> I looked at the ChimeraX bug report you submitted</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5467" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5467</a></div><div class=""><br class=""></div><div class="">and as I describe there the Amira 3.0 file looks the same as 2.1 but the example files you gave are segmentations which are encoded as bytes and run-length encoded compression. The ChimeraX Amira reader only handles float and unsigned 16-bit volumes with no compression. While reading bytes would be easy to add, the run-length encoding would be more work, requiring some C++ code to decompress without taking forever.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 25, 2021, at 11:36 AM, Tom Goddard via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Roden,</div><div class=""><br class=""></div>I think you can attach a 64 Mbyte file to a ChimeraX bug report (menu Help / Report a Bug...). I would be interested in looking at the file to see how different it is from the 2.1 version files.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Oct 25, 2021, at 11:29 AM, Roden Deng Luo <<a href="mailto:deng.luo@kaust.edu.sa" class="">deng.luo@kaust.edu.sa</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Tom,<div class=""><br class=""></div><div class="">Thanks very much! After changing the first line to 2.1, it tells me "Did not find "define Lattice" mesh size line". So I guess there are some "fundamental" changes. </div><div class=""><br class=""></div><div class="">The only .am file I have now is quite large in terms of debugging (64MB). I found two examples by googling "AmiraMesh BINARY-LITTLE-ENDIAN "3.0"". They give me "Did not find "Lattice { float ... }" line" after fooling ChimeraX. In case I get a smaller one or I got to know the way to crop only a small section and export a smaller one. I will let you know. I will also go through "Report a Bug".</div><div class=""><br class=""></div><div class=""><a href="https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am" class="">https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am</a></div><div class=""><a href="https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX" class="">https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX</a><br class=""></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Roden</div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Hi Roden,<div class=""><br class=""></div><div class="">The ChimeraX reader is for AmiraMesh format 2.1 and you are trying to read a version 3.0 file. I don't know if those are compatible. You can test by making ChimeraX not check the Amira file version by editing the following file (location for Mac, ChimeraX 1.3 daily build shown)<div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/map_data/amira/amira_format.py<br class=""><div class=""><br class=""></div><div class="">changing these lines</div><div class=""><br class=""></div><div class=""><div class=""> if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or</div><div class=""> line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):</div><div class=""> raise SyntaxError('First line of AmiraMesh file must start with '</div><div class=""> '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '</div><div class=""> 'instead got "%s"' % line[:256])</div></div><div class=""><br class=""></div><div class="">to</div><div class=""><br class=""></div><div class=""><div class=""># if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or</div><div class=""># line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):</div><div class=""># raise SyntaxError('First line of AmiraMesh file must start with '</div><div class=""># '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '</div><div class=""># 'instead got "%s"' % line[:256])</div><div class=""><br class=""></div><div class="">so the version test will not be done.</div><div class=""><br class=""></div><div class=""> Or you could use ChimeraX menu Help / Report a Bug... and attach a modest size Amira 3.0 file and I can try it.</div><div class=""><br class=""></div><div class=""> Or you could make a copy of your Amira file and edit the first line so instead of saying it is version 3.0 it says it is version 2.1.</div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Oct 23, 2021, at 8:12 AM, Roden Deng Luo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Dear ChimeraX Users,<div class=""><br class=""></div><div class="">I have an AmiraMesh .am file exported from Amira 3D 2021.1 (Build date: 2021-06-21 13:21:22, SHA id: 213bd1......13c73e). When I load it into ChimeraX 1.2.5 or ChimeraX 1.3.dev202110231141, ChimeraX tells me the following error.</div><div class=""><br class=""></div><div class=""><div style="margin:0px;white-space:pre-wrap" class="">First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'"</div></div><div class=""><br class=""></div><div class="">Googling "AmiraMesh site:<a href="https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-users__;!!Nmw4Hv0!gswyBcLggCUszrrkzuG1NAh0dA6mXVnN-mOrDaZJKGhoRMCix2NZTs_HZ5w3Eiak_ks$" target="_blank" class="">https://www.rbvi.ucsf.edu/pipermail/chimerax-users</a>" shows no result. Can anyone kindly help here? <br class=""></div><div class=""><br class=""></div><div class="">Many thanks,</div><div class="">Roden</div><div class=""><br class=""></div><div class=""><br class=""></div></div>
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