[Gwyddion-users] Cannot load height data measured using Sensofar machine (.plux file)

[Zhang, Wentao]

Dear All,

I am running Gwyddion 2.41 on my Mac OS X 10.11 (EI Capitan) and I am trying to use Gwyddion to process some heights data measured using a Sensofar machine.

The height data file I got has an extension of .plux. Gwyddion failed to open it and complains “No module can load this file type”. I tried modifying the extension from “.plux” to “.plu.” but still the same error occurred. The tutorial (http://gwyddion.net/documentation/user-guide-en/file-formats.html) says Gwyddion supports .plu files so I am wondering whether someone can help me with this.

Any suggestions are greatly appreciated.

Best regards,
Wentao

[Daniil Bratashov]

On Sat, 10 Oct 2015 05:46:51 +0000

Post by Zhang, Wentao
Dear All,
I am running Gwyddion 2.41 on my Mac OS X 10.11 (EI Capitan) and I am
trying to use Gwyddion to process some heights data measured using a
Sensofar machine.

As usual we need some example of problematic file, you can put it on ftp
or some file hosting and send a link to the list, as list-mailer
rejects large attachments.

WBR, Daniil Bratashov.

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[Zhang, Wentao]

Thanks for your quick response. The data file can be accessed following this link:

https://www.dropbox.com/sh/kh1x9c3i6hldptt/AADsWZZZ7T3G68pGdKfpdbQ2a?dl=0

I am sorry that I don’t have a smaller one. I want to open the .plux file that contains the heights data of a sandpaper sample. I also put a jpg figure to show how it looks like.

Thank you for you help.

Best regards,
Wentao

Post by Daniil Bratashov
On Sat, 10 Oct 2015 05:46:51 +0000

Post by Zhang, Wentao
Dear All,
I am running Gwyddion 2.41 on my Mac OS X 10.11 (EI Capitan) and I am
trying to use Gwyddion to process some heights data measured using a
Sensofar machine.

As usual we need some example of problematic file, you can put it on ftp
or some file hosting and send a link to the list, as list-mailer
rejects large attachments.
WBR, Daniil Bratashov.
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[David Nečas (Yeti)]

Post by Zhang, Wentao
https://www.dropbox.com/sh/kh1x9c3i6hldptt/AADsWZZZ7T3G68pGdKfpdbQ2a?dl=0

Well, it has a different extension because it is a completely different
file format than .plu. So the error message in Gwyddion was telling
the truth.

But as it is a ZIP file with the raw data and some XML info (apparently
designed by monkeys) packed inside, writing an import module should not
be that difficult.

Instead of a JPEG, can you please specify numerically the physical
dimensions of the area and the height scale (minimum to maximum, or at
least something like rms value)?

The physical dimensions seem to be 2.58 × 2.58 of some unknown units.
So the pixels are non-square, because pixel dimensions are 9825 × 4805,
right? The height scale is even less clear; despite using a
floating-point format the heights are not in base units (metres).
Micrometres seem possible for a relatively rough sand paper but hard to
tell just by looking at the raw data...

Yeti


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[David Nečas (Yeti)]

Post by David Nečas (Yeti)
But as it is a ZIP file with the raw data and some XML info (apparently
designed by monkeys) packed inside, writing an import module should not
be that difficult.

I already wrote an initial version of the PLUx import module. However,
the physical scales are unclear. Looking at the image, the pixels seem
to be square, so disregard my previous remark.

But how are the FOV values in index.xml then used to obtain the physical
dimensions of the area? Apparently they could be pixel sizes in µm;
that would give physical dimensions of the area corresponding to values
called GRID_WIDTH and GRID_HEIGHT in recipe.txt (you can get all the
files inside by changing the extension from .plux to .zip and unzipping
the file). And 25 × 12 millimetres would give reasonable grain sizes
for a rougher sandpaper.

Can you provide the scales for the sandpaper data? Do the parameters in
index.xml file correspond to any values that are faimiliar to you? Is
any documentation for the file format available?

Yeti

[Zhang, Wentao]

Hi Yeti,

Thanks for your help. The size of the sandpaper is 25.348mm * 12.397mm. I contacted the SENSOFAR people who helped us with the measurement. They did not have a documentation about the .plux file but they mentioned that the new machine will generate both .plux file and .plu file for compatibility. Now I have got the corresponding .plu file and I can open it using Gwyddion.

If I know more information about .plux format, I will post it here. Thank you for your time.

Best regards,
Wentao

Post by David Nečas (Yeti)

Post by David Nečas (Yeti)
But as it is a ZIP file with the raw data and some XML info (apparently
designed by monkeys) packed inside, writing an import module should not
be that difficult.

I already wrote an initial version of the PLUx import module. However,
the physical scales are unclear. Looking at the image, the pixels seem
to be square, so disregard my previous remark.
But how are the FOV values in index.xml then used to obtain the physical
dimensions of the area? Apparently they could be pixel sizes in µm;
that would give physical dimensions of the area corresponding to values
called GRID_WIDTH and GRID_HEIGHT in recipe.txt (you can get all the
files inside by changing the extension from .plux to .zip and unzipping
the file). And 25 × 12 millimetres would give reasonable grain sizes
for a rougher sandpaper.
Can you provide the scales for the sandpaper data? Do the parameters in
index.xml file correspond to any values that are faimiliar to you? Is
any documentation for the file format available?
Yeti
<index.xml>------------------------------------------------------------------------------
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[David Nečas (Yeti)]

Post by Zhang, Wentao
Thanks for your help. The size of the sandpaper is 25.348mm *
12.397mm.

OK, good, these are the dimensions I know how to get.

Post by Zhang, Wentao
They did not have a documentation about the .plux file
but they mentioned that the new machine will generate both .plux file
and .plu file for compatibility. Now I have got the corresponding .plu
file and I can open it using Gwyddion.

Since I have already mostly written a file import module for the .plux
file format, it would be nice to finish it so that people who have these
files will be able to open them.

The lateral dimensions are OK. So I only need to verify the height
scale. Could you please open your .plux file(s) in the latest
development snapshot of Gwyddion (2.42.20151011 or later) and tell me if
they are loaded correctly?

Regards,

Yeti


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[Zhang, Wentao]

Post by David Nečas (Yeti)

Post by Zhang, Wentao
Thanks for your help. The size of the sandpaper is 25.348mm *
12.397mm.

OK, good, these are the dimensions I know how to get.

Post by Zhang, Wentao
They did not have a documentation about the .plux file
but they mentioned that the new machine will generate both .plux file
and .plu file for compatibility. Now I have got the corresponding .plu
file and I can open it using Gwyddion.

Since I have already mostly written a file import module for the .plux
file format, it would be nice to finish it so that people who have these
files will be able to open them.
The lateral dimensions are OK. So I only need to verify the height
scale. Could you please open your .plux file(s) in the latest
development snapshot of Gwyddion (2.42.20151011 or later) and tell me if
they are loaded correctly?

Yes, of course. How can I get this latest development snapshot of Gwyddion? I am using Macports on my Mac OS X for installing Gwyddion.

Best,
Wentao

Post by David Nečas (Yeti)
Regards,
Yeti
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[David Nečas (Yeti)]

Post by Zhang, Wentao
Yes, of course. How can I get this latest development snapshot of
Gwyddion? I am using Macports on my Mac OS X for installing Gwyddion.

Unfortunately, I do not know much about Mac (compilation from source
code is typically the only option for Linux while for MS Windows
packages are automatically created as a part of the snapshot). There is
a build script linked from

http://gwyddion.net/download.php#head

I cannot tell if it still works fine though.

Maybe someone else knows more.

Regards,

Yeti


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[Nicola Ferralis]

I have made and used the attached script which, although crude, allows
for quick testing. It assumes you have the macports intfrastructure in
place.

Nicola

Post by David Nečas (Yeti)

Post by Zhang, Wentao
Yes, of course. How can I get this latest development snapshot of
Gwyddion? I am using Macports on my Mac OS X for installing Gwyddion.

Unfortunately, I do not know much about Mac (compilation from source
code is typically the only option for Linux while for MS Windows
packages are automatically created as a part of the snapshot). There is
a build script linked from
http://gwyddion.net/download.php#head
I cannot tell if it still works fine though.
Maybe someone else knows more.
Regards,
Yeti
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[Zhang, Wentao]

Thanks. I used the script and updated my Gwyddion to 2.42.20151018. But when I tried to load a .plux file it still complains “No module can load this file type”.

Best regards,
Wentao

I have made and used the attached script which, although crude, allows for quick testing. It assumes you have the macports intfrastructure in place.
Nicola

Post by David Nečas (Yeti)

Post by Zhang, Wentao
Yes, of course. How can I get this latest development snapshot of
Gwyddion? I am using Macports on my Mac OS X for installing Gwyddion.

Unfortunately, I do not know much about Mac (compilation from source
code is typically the only option for Linux while for MS Windows
packages are automatically created as a part of the snapshot). There is
a build script linked from
http://gwyddion.net/download.php#head
I cannot tell if it still works fine though.
Maybe someone else knows more.
Regards,
Yeti
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[David Nečas (Yeti)]

Post by Zhang, Wentao
Thanks. I used the script and updated my Gwyddion to 2.42.20151018.
But when I tried to load a .plux file it still complains “No module
can load this file type”.

Please check that you have no ‘sensofarx’ module in the module list (and
then there is no opengps, nanoobserver, nanoscantech or spmxfile
either).

Gwyddion uses the minizip library to work with zip-compressed files
such as .plux. Minizip is widely available because it comes with zlib,
a base compression library used just about everywhere in everything.
But for some reason Macports do not offer minizip (Rowue, Nicola – can
you confirm/comment?).

So a bunch of file formats are unavailable on OS X, which I did not
know. The idea that minizip may be unavailable somewhere did not even
cross my mind.

There is no immediate remedy. Either Macports start providing minizip
or I have to write a zip-file handling abstraction that can work with
both minizip and another library (probably libzip) that is present in
Macports.

Regards,

Yeti


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