[feature] : Support for old-style Bruker file format e.g. .000

[tcatley]

Is your feature request related to a problem?

No response

Describe the solution you would like.

The old style of Bruker file format (ending in e.g. .001, .002 etc.) cannot currently be loaded using AFMReader as far as I'm aware. It would be good to have this functionality to allow the files to be processed with TopoStats. I have added link to example of the file type I am referring to. https://drive.google.com/drive/folders/1CvNDgcTpzYNCEAVT0u9aNWNBsPgpL3jH?usp=sharing

Describe the alternatives you have considered.

No response

Sample Image

No response

Additional context

No response

[alicepyne]

This was possible with the original TopoStats so should be possible to add back in!

…

On Thu, 19 Jun 2025 at 06:58, tcatley ***@***.***> wrote: *tcatley* created an issue (AFM-SPM/AFMReader#157) <#157> Is your feature request related to a problem? *No response* Describe the solution you would like. The old style of Bruker file format (ending in e.g. .001, .002 etc.) cannot currently be loaded using AFMReader as far as I'm aware. It would be good to have this functionality to allow the files to be processed with TopoStats. I have added link to example of the file type I am referring to. https://drive.google.com/drive/folders/1CvNDgcTpzYNCEAVT0u9aNWNBsPgpL3jH?usp=sharing Describe the alternatives you have considered. *No response* Sample Image *No response* Additional context *No response* — Reply to this email directly, view it on GitHub <#157>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJSFML2KBKLEILU5F45G433EJGRJAVCNFSM6AAAAAB7U62SVKVHI2DSMVQWIX3LMV43ASLTON2WKOZTGE2TSMBWGA4DAMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[ns-rse]

Hi @tcatley

Is the desire to load .spm.### files with AFMReader or is it functionality that you would like in TopoStats?

I ask because AFMReader is indifferent to the file extension itself, if its told to load a SPM "format" file it doesn't matter what the extension is.

Get a .spm.001 file

We clone the repository, copy and rename a file to use

git clone git@github.com:AFM-SPM/AFMReader.git
cd AFMREader
mkdir tmp
cp tests/resources/sample_0.spm tmp/sample_0.spm.001

Load with AFMReader

Fire up Python and load the file...

In [1]: from AFMReader.spm import load_spm

In [2]: load_spm("tmp/sample_0.spm.001")
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[2], line 1
----> 1 load_spm("tmp/sample_0.spm.001")

TypeError: load_spm() missing 1 required positional argument: 'channel'

In [3]: load_spm("tmp/sample_0.spm.001", channel="Height")
13:50:39 | INFO |spm.py:spm:load_spm:80 | Loading image from : tmp/sample_0.spm.001
13:50:39 | INFO |spm.py:spm:load_spm:85 | [sample_0.spm] : Loaded image from : tmp/sample_0.spm.001
13:50:39 | INFO |spm.py:spm:load_spm:87 | [sample_0.spm] : Extracted channel Height
13:50:39 | INFO |spm.py:spm:spm_pixel_to_nm_scaling:44 | [sample_0.spm] : Pixel to nm scaling : 0.4940029296875
Out[3]: 
(array([[30.77585799, 30.65906157, 30.70077458, ..., 33.5956574 ,
         33.55394439, 33.19521251],
        [30.3337001 , 30.07507944, 30.3503853 , ..., 33.24526812,
         32.661286  , 32.81145283],
        [29.69131976, 29.91657001, 30.00833863, ..., 32.71134161,
         33.22024032, 33.41212016],
        ...,
        [22.14960775, 21.71579245, 21.9410427 , ..., 25.1946574 ,
         25.00277756, 25.15294439],
        [21.79087587, 21.4905422 , 21.78253327, ..., 25.27808342,
         25.31145382, 24.86929593],
        [21.9410427 , 22.21634856, 22.20800596, ..., 25.52836147,
         25.38653724, 25.47830586]]),
 0.4940029296875)

Its returning a tuple with the first item being the image as a Numpy array and the second a float of the pixel to nanometer scaling.

NB That I opted to rename as .spm.001 doesn't matter, I could have just used .001 and the file still loads because load_spm() doesn't do anything with the file extension, it expects to find a SPM formatted file.

Providing the internal format doesn't differ considerably between .spm.### and newer .spm then we should be able to add the functionality to TopoStats to get a list of files that are .### but it will be something I will have to defer until next week (and if there are any other devices that ever output files with a period and three numbers that will cause problems but lets deal with that further down the line!).

[ns-rse]

And to make doubly sure what I wrote above is correct I've just tried loading your two files and they load fine...

from AFMReader.spm import load_spm

In [7]: load_spm("tmp/tc_ls6_3007.002", channel="Height")
14:05:59 | INFO |spm.py:spm:load_spm:80 | Loading image from : tmp/tc_ls6_3007.002
14:05:59 | INFO |spm.py:spm:load_spm:85 | [tc_ls6_3007] : Loaded image from : tmp/tc_ls6_3007.002
14:05:59 | INFO |spm.py:spm:load_spm:87 | [tc_ls6_3007] : Extracted channel Height
14:05:59 | INFO |spm.py:spm:spm_pixel_to_nm_scaling:44 | [tc_ls6_3007] : Pixel to nm scaling : 58.59375
Out[7]: 
(array([[178.85347871, 171.56985288, 139.70398988, ..., 521.99318448,
         488.30641502, 512.88865219],
        [273.13596862, 255.83735728, 222.45407222, ..., 406.4667859 ,
         426.49675693, 519.96995508],
        [311.67848864, 304.79950869, 276.06965125, ..., 394.7320554 ,
         418.40383934, 508.33638605],
        ...,
        [233.58183391, 282.34166238, 312.28545746, ..., 449.05576471,
         425.5863037 , 427.10372575],
        [238.23526152, 298.02169021, 319.16443741, ..., 423.76539725,
         426.09211105, 427.00256428],
        [230.54698981, 282.64514679, 311.67848864, ..., 422.55145961,
         425.48514223, 426.5979184 ]]),
 58.59375)

In [8]: load_spm("tmp/tc_ls6_3007.004", channel="Height")
14:06:04 | INFO |spm.py:spm:load_spm:80 | Loading image from : tmp/tc_ls6_3007.004
14:06:04 | INFO |spm.py:spm:load_spm:85 | [tc_ls6_3007] : Loaded image from : tmp/tc_ls6_3007.004
14:06:04 | INFO |spm.py:spm:load_spm:87 | [tc_ls6_3007] : Extracted channel Height
14:06:04 | INFO |spm.py:spm:spm_pixel_to_nm_scaling:44 | [tc_ls6_3007] : Pixel to nm scaling : 58.59375
Out[8]: 
(array([[-362.86205946, -397.56426101, -431.74540848, ..., -139.22564947,
         -109.1087238 , -102.85607487],
        [-316.07140331, -351.50308057, -386.41370376, ..., -116.29927006,
          -82.74338748,  -81.70127933],
        [-312.00718151, -347.54306959, -382.45369277, ..., -110.4634644 ,
          -89.51709049,  -89.30866886],
        ...,
        [-909.13515414, -943.2120908 , -976.8721842 , ..., -696.44087977,
         -649.96285607, -626.82805504],
        [-919.24360324, -953.21632909, -956.23844274, ..., -681.95557642,
         -641.83441247, -627.8701632 ],
        [-943.62893406, -977.18481664, -964.7837296 , ..., -668.09553797,
         -633.81017968, -629.43332543]]),
 58.59375)

[tcatley]

Hi @ns-rse,

Perhaps the issue is with TopoStats then (I'd assumed because the error came as the file was being loaded that it was an AFMReader error)? When I set the file format in the config file to .spm, it can't find the .002 file in the folder.

(topo_new_main) work@Mac TopoStats % topostats --config /Users/work/Documents/config.yaml process
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] The YAML configuration file is valid.
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] The YAML plotting configuration file is valid.
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] Configuration run options are consistent, processing can proceed.
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] Configuration file loaded from      : /Users/work/Documents/config.yaml
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] Scanning for images in              : /Users/work/Documents/Format test
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] Output directory                    : /Users/work/Documents/Format test
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] Looking for images with extension   : .spm
[Thu, 19 Jun 2025 07:12:07] [INFO    ] [topostats] Images with extension .spm in /Users/work/Documents/Format test : 0
[Thu, 19 Jun 2025 07:12:07] [ERROR   ] [topostats] No images with extension .spm in /Users/work/Documents/Format test
[Thu, 19 Jun 2025 07:12:07] [ERROR   ] [topostats] [run_modules.py] [146] No images with extension .spm in /Users/work/Documents/Format test
[Thu, 19 Jun 2025 07:12:07] [ERROR   ] [topostats] Please check your configuration and directories.
[Thu, 19 Jun 2025 07:12:07] [ERROR   ] [topostats] [run_modules.py] [147] Please check your configuration and directories. 

If needed I can open this issue in the TopoStats page.

[ns-rse]

Its to do with how TopoStats decides which loader to use from AFMReader and TopoStats does that based on the file_ext: .spm configuration option, so if files have only got the numeric extension then setting it to .spm would never work because its looking for files that end with .spm which .002 etc. don't

No need to open an issue on TopoStats repository, I can gather all the information here and write it up as a task for me to do next week.

Some more questions though....

• Are there instances where they might be .spm.002 or is .spm always missing?
• Do you know if any other machines other than Bruker produce output with only numeric extensions?

[tcatley]

Thanks @ns-rse!
There won't be any instances of .spm.002 - the file format is a fully numeric extension. I believe that it is only older Bruker systems that produce this output, but it is actually quite common. Correct me if wrong on this @alicepyne

[ns-rse]

Closed by #1182 in TopoStats.

[rgurrola003-boop]

Hi all, so what was the fix for this? I also am using old Bruker type files and am confused if spm is the file type to use?

[tcatley]

Yes, if you use .spm as the file_ext in the config it should now recognise the old file types

[ns-rse]

Hi @rgurrola003-boop

@tcatley is correct use file_ext: spm in the configuration file or your command line call so you can use topostats --file-ext spm too (the linked pull-request #1182 which closed this issue covered this).