.jpk-force file format not recognized (message: "No AFM data files could be found in the location specified.")

[lmortati-inrim]

I am trying to evaluate the Elastic Fit of some .jpk-force force-distance curves files taken with a Nanowizard II JPK and it seems that the file format isn't recognized (it appears a window with this message: "No AFM data files could be found in the location specified.")

[paulmueller]

Hi, please attach a zipped example file to this issue. Maybe this is an easy fix.

[lmortati-inrim]

Hello, I attached a typical .jpk-force file Thank you very much

…

On Tue, Feb 4, 2025 at 4:53 PM Paul Müller ***@***.***> wrote: Hi, please attach a zipped example file to this issue. Maybe this is an easy fix. — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AT7OM4ULIEGORQVA5TVYXC32ODPALAVCNFSM6AAAAABWOYEMSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMZUGM4DIOBWGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Leonardo Mortati, Eng. Ph.D. I.N.Ri.M. - Istituto Nazionale di Ricerca Metrologica Division of Advanced Materials and Life Sciences AFM and NonLinear Optics Microscopy Strada delle Cacce 91 I-10135 Torino Italy Tel Office: +39 011 3919975 Tel Lab: +39 011 3919958

-- Engineering is the art of making what you want from things you can get

-- Confidentially notice. This e-mail transmission may contain legally privileged and/or confidential information. Please do not read it if you are not the intended recipient(s). Any use, distribution, reproduction or disclosure by any other person is strictly prohibited. If you have received this e-mail in error, please notify.

[paulmueller]

This did not work, I believe you have to upload it here via the web interface.

[lmortati-inrim]

Good morning Paul, If you are meaning through github, it doesn't allow me to upload this format, but maybe you was saying something else, in this case, could you please explain me better what to do? Thank you. Regards, Leonardo Il Mar 4 Feb 2025, 20:26 Paul Müller ***@***.***> ha scritto:

…

This did not work, I believe you have to upload it here via the web interface. — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AT7OM4VJL2DFTADD2VBEU3D2OEIABAVCNFSM6AAAAABWOYEMSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMZUHA3TKNRSHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[paulmueller]

I think it should work through GitHub if you put the file into a .zip archive.

Best

[lmortati-inrim]

MLCT10UMPoint3_-2025.01.30-15.41.37.385.jpk-force.zip

[lmortati-inrim]

any ideas?

[paulmueller]

FYI I currently do not have the time to look into this. This will have to wait unless somebody else picks this up earlier.

[PinkShnack]

Hey @lmortati-inrim please also send on a code snippet that you used to try to pen the data. I can look into it.

[lmortati-inrim]

Hello PinkShnack, the file was created during the measurement by the software JPK Nanowizard Control Software v.5.0.145

…

On Tue, Feb 25, 2025 at 1:12 PM PinkShnack ***@***.***> wrote: Hey @lmortati-inrim <https://github.com/lmortati-inrim> please also send on a code snippet that you used to try to pen the data. I can look into it. — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AT7OM4X6WQLSIBSGBMR3PML2RRM4JAVCNFSM6AAAAABWOYEMSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBRG42TQNBUGU> . You are receiving this because you were mentioned.Message ID: ***@***.***> [image: PinkShnack]*PinkShnack* left a comment (AFM-analysis/afmformats#36) <#36 (comment)> Hey @lmortati-inrim <https://github.com/lmortati-inrim> please also send on a code snippet that you used to try to pen the data. I can look into it. — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AT7OM4X6WQLSIBSGBMR3PML2RRM4JAVCNFSM6AAAAABWOYEMSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBRG42TQNBUGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Leonardo Mortati, Eng. Ph.D. I.N.Ri.M. - Istituto Nazionale di Ricerca Metrologica Division of Advanced Materials and Life Sciences AFM and NonLinear Optics Microscopy Strada delle Cacce 91 I-10135 Torino Italy Tel Office: +39 011 3919975 Tel Lab: +39 011 3919958

-- Engineering is the art of making what you want from things you can get

-- Confidentially notice. This e-mail transmission may contain legally privileged and/or confidential information. Please do not read it if you are not the intended recipient(s). Any use, distribution, reproduction or disclosure by any other person is strictly prohibited. If you have received this e-mail in error, please notify.

[PinkShnack]

I am getting the following error when trying to load the file like so:

Code:

import afmformats

path = r'mypath/MLCT10UMPoint3_-2025.01.30-15.41.37.385.jpk-force'

# data extraction
data = afmformats.load_data(path)

Traceback:

Traceback (most recent call last):
  File "C:\Program Files\JetBrains\PyCharm 2022.1.4\plugins\python\helpers\pydev\pydevd.py", line 1496, in _exec
    pydev_imports.execfile(file, globals, locals)  # execute the script
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Program Files\JetBrains\PyCharm 2022.1.4\plugins\python\helpers\pydev\_pydev_imps\_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "\afmformats\open_jpk.py", line 7, in <module>
    data = afmformats.load_data(path)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "\afmformats\afmformats\formats\__init__.py", line 246, in load_data
    cur_recipe = get_recipe(path, modality=modality)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "\afmformats\afmformats\formats\__init__.py", line 203, in get_recipe
    raise errors.FileFormatNotSupportedError(
afmformats.errors.FileFormatNotSupportedError: Could not determine file format recipe for 'mypath\MLCT10UMPoint3_-2025.01.30-15.41.37.385.jpk-force'!
python-BaseException

Process finished with exit code 1

I have tracked the issue to Line 465 in afmformats/formats/fmt_jpk/jpk_reader.py, which tries to ensure that the "curve type" is "pause". Instead, for your data it is "retract" with the error "Segment 2 must be of type 'pause'!". It happens here:

            # For stress-relaxation, we extract the info from segment 2.
            if md_im["curve type"] != "pause":
                raise ValueError("Segment 2 must be of type 'pause'!")

I am not an AFM person, so perhaps @lmortati-inrim and @paulmueller might have an idea:

• Must it be "pause" for Segment 2?
• If so, why doesn't the data reflect this (experimental error?)

[paulmueller]

It looks like afmformats thinks this is a stress-relaxation measurement, while it should be a force-distance measurement.

[jasht1]

Hi, I think I'm having a similar issue to OP I have a large number of .force-save files generated by the old JPK DP software, none of which can be interpreted by afmformats.load_data failing with a similar traceback as shown by PinkShnack:

afmformats.errors.FileFormatNotSupportedError: Could not determine file format recipe for <path>!

They represent a number of different force indentation experiments some including "Retracted Pause" segments and some omitting them being 3 or 2 segments respectively. When using afmformats.formats.fmt_jpk.load_jpk;

Those with 3 segments fail with:

Traceback (most recent call last):
  File "/Workspace/Scripts/test_nanite.py", line 18, in <module>
    indent = afmformats.formats.fmt_jpk.load_jpk(path)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/joe/miniconda3/envs/AFM/lib/python3.12/site-packages/afmformats/formats/fmt_jpk/__init__.py", line 69, in load_jpk
    metadata = jpkr.get_metadata(index=index)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/joe/miniconda3/envs/AFM/lib/python3.12/site-packages/afmformats/formats/fmt_jpk/jpk_reader.py", line 352, in get_metadata
    mdap = copy.deepcopy(self.get_metadata(index, seg))
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/joe/miniconda3/envs/AFM/lib/python3.12/site-packages/afmformats/formats/fmt_jpk/jpk_reader.py", line 394, in get_metadata
    md["imaging mode"] = self.get_imaging_mode()
                         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/joe/miniconda3/envs/AFM/lib/python3.12/site-packages/afmformats/formats/fmt_jpk/jpk_reader.py", line 456, in get_imaging_mode
    raise ValueError("Segment 1 must be of type 'pause'!")
ValueError: Segment 1 must be of type 'pause'!

Whereas those with 2 segments fail with:

Traceback (most recent call last):
  File "/Workspace/Scripts/test_nanite.py", line 18, in <module>
    indent = afmformats.formats.fmt_jpk.load_jpk(path)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/joe/miniconda3/envs/AFM/lib/python3.12/site-packages/afmformats/formats/fmt_jpk/__init__.py", line 69, in load_jpk
    metadata = jpkr.get_metadata(index=index)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/joe/miniconda3/envs/AFM/lib/python3.12/site-packages/afmformats/formats/fmt_jpk/jpk_reader.py", line 352, in get_metadata
    mdap = copy.deepcopy(self.get_metadata(index, seg))
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/joe/miniconda3/envs/AFM/lib/python3.12/site-packages/afmformats/formats/fmt_jpk/jpk_reader.py", line 397, in get_metadata
    md_im["position index"])
    ~~~~~^^^^^^^^^^^^^^^^^^
KeyError: 'position index'

Indicating that:

• 3-segment files fail because afmformats assumes that the second segment must be a 'pause' under the assumption that it must be a stress-relaxation experiment. This is a hardcoded assumption that is not valid with all JPK files.

• 2-segment files fail because afmformats expects metadata keys that aren't getting populated, like "position index" which is not present in any of my .jpk-force files.

For reference below are example 3 and 2 segment force-indention experiments from my dataset:

example_force-indentation_experiments.zip

[PinkShnack]

I have a temporary workaround, which allows me to open @lmortati-inrim's data without issue. Can you please upload an example script showing me how you expect to use the data, @lmortati-inrim and @jasht1?

However, for @jasht1's data, I get the following error due to a missing property. Should the property be in the file (is it required), or is this another hard-coded thing that can be changed?

afmformats.formats.fmt_jpk.jpk_data.ReadJPKError: Could not find property: 'vDeflection multiplier in <zipfile.ZipExtFile name='segments/0/channels/vDeflection.dat' mode='r' compress_type=deflate>'. Please make sure you are working with raw data and not with data exported from the JPK software.

[lmortati-inrim]

@PinkShnack basically I would like to extract the curves to get the Young's modulus using PyJibe or Matlab. I needed to change the segments from the basic method, because in this way I can modify the target force automatically during the measurements using the ExperimentPlanner of JPK NanoWizard Control software. A this moment I am converting all the curves in txt file and then reading them using matlab to fit the curves and extract the young's moduli.