[chimerax-users] Open AmiraMesh 3.0 in ChimeraX

Mon Oct 25 12:22:51 PDT 2021

Hi Roden,

  I looked at the ChimeraX bug report you submitted

	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5467 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5467>

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.

	Tom

> On Oct 25, 2021, at 11:36 AM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Roden,
> 
> 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.
> 
> 	Tom
> 
> 
>> On Oct 25, 2021, at 11:29 AM, Roden Deng Luo <deng.luo at kaust.edu.sa <mailto:deng.luo at kaust.edu.sa>> wrote:
>> 
>> Hi Tom,
>> 
>> 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. 
>> 
>> 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".
>> 
>> https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am <https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am>
>> https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX <https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX>
>> 
>> Thanks,
>> Roden
>> 
>> 
>> On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> Hi Roden,
>> 
>> 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)
>> 
>> 	ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/map_data/amira/amira_format.py
>> 
>> changing these lines
>> 
>>     if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or
>>             line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):
>>       raise SyntaxError('First line of AmiraMesh file must start with '
>>                         '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '
>>                         'instead got "%s"' % line[:256])
>> 
>> to
>> 
>> #    if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or
>> #            line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):
>> #      raise SyntaxError('First line of AmiraMesh file must start with '
>> #                        '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '
>> #                        'instead got "%s"' % line[:256])
>> 
>> so the version test will not be done.
>> 
>>   Or you could use ChimeraX menu Help / Report a Bug... and attach a modest size Amira 3.0 file and I can try it.
>> 
>>   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.
>> 
>> 	Tom
>> 
>> 
>>> On Oct 23, 2021, at 8:12 AM, Roden Deng Luo via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>>> 
>>> Dear ChimeraX Users,
>>> 
>>> 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.
>>> 
>>> First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'"
>>> 
>>> Googling "AmiraMesh site:https://www.rbvi.ucsf.edu/pipermail/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-users__;!!Nmw4Hv0!gswyBcLggCUszrrkzuG1NAh0dA6mXVnN-mOrDaZJKGhoRMCix2NZTs_HZ5w3Eiak_ks$>" shows no result. Can anyone kindly help here? 
>>> 
>>> Many thanks,
>>> Roden
>>> 
>>> 
>>> 
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>> 
>> 
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