afm-analysis / pyjibe Goto Github PK

AFM-analysis/nanite#21

• bump nanite version
• add user interface extension
  • method button: that shows fit method + number of kwargs
  • UI that lets the user select the parameters

tests: export and check whether parameters are preserved for rating

• test that expression parameters are exported and are computed from the fit parameters, not from the initial parameters
• test that ancillary parameters are exported in autosave
• test that hidden parameters are only exported in developer mode

The Combobox just shows the previous value.

This is the difference between maximal indentation depth and fitted contact point.

Hi Paul,
I find your calculation of the E vs delta curves very interesting. Nonetheless, if I got it right, you use as point of contact your first guess, rather then the one that is determined by the fit. In the case of my curves, because of the reflectivity of the sample surface, I often have a detectable laser interference, that affects the most the first guess of the point of contact while is less problematic when it is determined by the fit. The question then is: would it be possible to update the POC position before the calculation of the E vs delta curves? By the way, when you calculate this curve, the POC is fixed for each indentation depth, right?
Thanking you in advance
best
Simone

• This will set nanite.read.DEFAULT_MODALITY to None (loading data slower)
• Add entry in the docs

Not sure what is causing this. Help appreciated.

If the indented object is spherical, there is a correction factor that can be applied to the radius.

• collect literature
• find a user-friendly way (that is not confusing) to implement a helper function
• make sure this works with data export

Hello Paul! Today I tried to open the dataset zef18.h5 that I downloaded from:

• https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/13481393/zef18.h5

• https://zenodo.org/record/1551200/files/zef18.h5

I got this error:

Unhandled exception in PyJibe version 0.8.2:
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pyjibe/head/main.py", line 165, in on_open_single
self.load_data(files=n, retry_open=self.on_open_single)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pyjibe/head/main.py", line 224, in load_data
self.add_subwindow(aclass, flist)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pyjibe/head/main.py", line 84, in add_subwindow
inst.add_files(flist)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pyjibe/fd/main.py", line 147, in add_files
grp = nanite.IndentationGroup(f, callback=callback)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/nanite/group.py", line 48, in init
self += load_group(path, callback=callback)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/nanite/group.py", line 23, in load_group
data = load_data(path, callback=callback)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/nanite/read.py", line 55, in load_data
measurements = afmformats.load_data(pp, callback=callback)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/afmformats/formats.py", line 162, in load_data
meta_override=meta_override):
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/afmformats/fmt_hdf5.py", line 103, in load_hdf5
metadata["enum"] = int(enum_key)
ValueError: invalid literal for int() with base 10: 'analysis'

When I try to download from https://b2share.eudat.eu/api/files/bf481c9b-14ff-47b1-baf5-e569d0199be6/zef18.h5 the download fails.

I am using MacOS Mojave version 10.14.6.

Associate PyJibe with all supported AFM file types via Info_plist (https://developer.apple.com/library/archive/documentation/General/Reference/InfoPlistKeyReference/Articles/CoreFoundationKeys.html#//apple_ref/doc/uid/20001431-101685)

• Link to the main preprocessing page on top of the page.
• Link to the POC docs for each method.

Some signals are defined in fd/main and some in fd/tab_fit. It should be clarified why this is so or changed.

EDIT: It would probably be better to work with signals than calling parent class functions....

Hi,
I am working with Asulym Research AFM and PyJibe. The data I acquire are maps of force-distance curves, that are generated into a *.ARDF format. From the Asylum Research program I can extract each force-distance curve individually into *.ibw files, in order to analyze them with PyJibe afterwards. However, and opposite to what happens to 'standard' *.ibw files, which I successfully open, I cannot import the extracted force-distance curves of this force map into PyJibe. The error bellow appears. Thanks in advance!

Unhandled exception in PyJibe version 2022.01.08.post21:
Traceback (most recent call last):
File "/Users/maria/Downloads/PyJibe-master/pyjibe/head/main.py", line 286, in on_open_single
self.load_data(files=n, retry_open=self.on_open_single)
File "/Users/maria/Downloads/PyJibe-master/pyjibe/head/main.py", line 149, in load_data
self.add_subwindow(aclass, flist)
File "/Users/maria/Downloads/PyJibe-master/pyjibe/head/main.py", line 156, in add_subwindow
inst.add_files(flist)
File "/Users/maria/Downloads/PyJibe-master/pyjibe/fd/main.py", line 223, in add_files
user_metadata=user_metadata)
File "/Users/maria/Downloads/PyJibe-master/pyjibe/fd/main.py", line 122, in load_file
grp = nanite.IndentationGroup(path, callback=callback)
File "/Users/maria/opt/anaconda3/envs/pyjibe/lib/python3.7/site-packages/nanite/group.py", line 61, in init
**get_load_data_modality_kwargs()
File "/Users/maria/opt/anaconda3/envs/pyjibe/lib/python3.7/site-packages/afmformats/afm_group.py", line 43, in init
data_classes_by_modality=data_classes_by_modality
File "/Users/maria/opt/anaconda3/envs/pyjibe/lib/python3.7/site-packages/afmformats/formats/init.py", line 257, in load_data
meta_override=meta_override):
File "/Users/maria/opt/anaconda3/envs/pyjibe/lib/python3.7/site-packages/afmformats/formats/fmt_igor.py", line 72, in load_igor
metadata["date"] = notes["Date"]
KeyError: 'Date'

Preprocessing should be a little smarter, i.e.

• allow to set parameters for certain preprocessors in nanite
• CP estimation agorithm selection combobox AFM-analysis/nanite#12 (with help page?)

This could be made available via the menu (see metadata export) and should create files as generated with the "DAT" export button.

• test that expression parameters are exported and are computed from the fit parameters, not from the initial parameters
• test that ancillary parameters are exported in autosave
• test that hidden parameters are only exported in developer mode

This appears to be random.

Hey Paul,
Is it possible to have the curve baseline calculation more interactive where the use can choose a region (maybe by typing two indentation limits) to calculate the baseline from? I think now it's calculated from the last few points of the curve and I often have tilts of some noise at the end.
Thank you
Shada

• register supported file types (file formats) in InnoSetup

When an analysis contains bad curves, "Apply Model and Fit All" does not run through. There should be a dialog at the end that notifies the user which curves where affected instead.

They take up too much vertical space and are not modified anyway.

• about
• software libraries used
• documentation link

Some file formats do not store sufficient metadata (e.g. spring constant and sensitivity). Upon loading new data, the user should be asked about these values in a dialog. This will be possible with afmformats 0.10.0.

• implement missing metadata property keywords in afmformats.erros
• catch those errors, extract the missing metadata, and open a dialog for user interaction
• call the open function again with the given meta_override set

There should be an advanced mode and a developer mode

• expert mode will only show fitting method
• hidden parameters should only be visible in developer mode

Wanted is a feature that serves to convert JPK force files into HDF5 files and simultaneously provides the option to remove any date and time stamps (in name and/or header for instance). This feature is implemented, but

• It is currently not possible to apply this to multiple files at once that are located in different folders.
• The file structure needs to be maintained (converted files must not mix with files from other folders). However, the location of converted files is not the same as the original location, but one level up in the hierarchy.
• The newly assigned file name currently contains a seemingly random index (Could that be removed? Why not?)

If a model in nanite contains helper parameters (e.g. lmfit constraints), the developer should be able to hide it. The best way of defining such a parameter is by prefixing it with an underscore.

• update the nanite docs with this information (dec3025b4884fe8c29cc9d7802df1ba24bfdb72f)
• write a test function
• add logic to hide parameters prefixed with "_" from the parameter view ( 55ad5b2 )

Hi,
I am working with Asylum Research AFM and PyJibe. The data I acquire are maps of force-distance curves, which are generated as *.ARDF files. I translate these files into *.h5 files to be able to read them in PyJibe, but it does not work. This is the error message:
"No AFM data files could be found in the location specified"
Thanks in advance!