Open AmiraMesh 3.0 in ChimeraX
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" shows no result. Can anyone kindly help here? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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@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://www.rbvi.ucsf.edu/pipermail/chimerax-users>" shows no result. Can anyone kindly help here?
Many thanks, Roden
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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-f02d2fe070b... https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.... Thanks, Roden On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <goddard@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@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-use...>" shows no result. Can anyone kindly help here?
Many thanks, Roden
------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...>
-- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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@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-f02d2fe070b... <https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b...> https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.... <https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond....>
Thanks, Roden
On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <goddard@sonic.net <mailto:goddard@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@cgl.ucsf.edu <mailto:chimerax-users@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-use...>" shows no result. Can anyone kindly help here?
Many thanks, Roden
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...>
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
Hi Andrea, I am encountering the below error in ChimeraX. Would it be okay that I share the 64MB .am file you sent to me earlier with Tom, the developer of ChimeraX? They do have a line "any information or data you wish to keep confidential should be sent separately" in the bug report guide. Many thanks, Roden On Mon, Oct 25, 2021 at 9:36 PM Tom Goddard <goddard@sonic.net> 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@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-f02d2fe070b... <https://urldefense.com/v3/__https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/3...>
https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.... <https://urldefense.com/v3/__https://edmond.mpdl.mpg.de/imeji/exportServlet?f...>
Thanks, Roden
On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <goddard@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@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-use...>" shows no result. Can anyone kindly help here?
Many thanks, Roden
------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...>
------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
-- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
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@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@kaust.edu.sa <mailto:deng.luo@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-f02d2fe070b... <https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b...> https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.... <https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond....>
Thanks, Roden
On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <goddard@sonic.net <mailto:goddard@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@cgl.ucsf.edu <mailto:chimerax-users@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-use...>" shows no result. Can anyone kindly help here?
Many thanks, Roden
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...>
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Roden Deng Luo -
Tom Goddard