openfovea hangs up while loading folder of folders of .ibw files. (doesn't work with asylum files?)

[Jack Staunton]

Hi Charles

I want to try out your program with my force indentation curves but I can't get it to run.

I am using Ubuntu 12.04 LTS in Oracle VM Virtual Box. I installed using the .deb and I open OpenFovea by navigating to usr\share\applications\openfovea and double clicking. Is this much right?

Then when it is open I go to File>New> and browse to a force map - that is, a folder containing say 8 subfolders, with each subfolder containing 8 force curve files. My force curve files are Igor Binary Waves, file extension ' .ibw'

At this point, it says 'Please wait...' and hangs there.

Let me know if you need any more information. Thanks.

[Charles Roduit (charles-roduit)]

Hi Jack,

thank you for your bug report.

What is the version of OpenFovea you use ? (Help>About)

Can you launch it from the terminal and get me the output ? (open the terminal -> write "openfovea" or "openfovea-gtk" depending the version you use, and click Enter)

One laste question :
Don't you have an icon in the science menu ? If not, you can copy the file in /usr/share/applications/ to the desktop, it's an icon shortcut for the executable.

Thanks.

[Andrew Wang (ayjwang)]

Hi Charles,

I encountered a similar problem. I was trying to create a new experiment and selecte the main fold of a force map (which for Asylum's format contains subfolders for each line and each subfolder contains the force curves in the same line). Below is what I got from the command window. It seemed like I have too many force curves?

>>> openfovea_gui.main()
Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\openfovea\openfovea_gui.py", line 869, in
on_new_experiment_activate
    self.force_volume = self.experiment.get_file(0)
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1775, in get_f
ile
    self.update_switch()
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 2150, in updat
e_switch
    mask = self.file['list'][self.file['current']].get_switch('mask')
IndexError: list index out of range
Exception in thread Thread-2:
Traceback (most recent call last):
  File "C:\Python27\lib\threading.py", line 552, in __bootstrap_inner
    self.run()
  File "C:\Python27\lib\threading.py", line 505, in run
    self.__target(*self.__args, **self.__kwargs)
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1872, in load_
folder
    self.load_file(os.path.join(fv_folder, files))
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1853, in load_
file
    self.file['list'].append(ForceVolume(fv_file))
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 162, in __init
__
    _data = afm_file.load(fv_file)
  File "C:\Python27\lib\site-packages\openfovea\fovea_toolbox\file_util\afm_file
.py", line 122, in load
    [trace, retrace, value['piezo'], header] = asylum.load(file_name)
ValueError: too many values to unpack

Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\openfovea\openfovea_gui.py", line 869, in
on_new_experiment_activate
    self.force_volume = self.experiment.get_file(0)
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1775, in get_f
ile
    self.update_switch()
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 2150, in updat
e_switch
    mask = self.file['list'][self.file['current']].get_switch('mask')
IndexError: list index out of range

[mjb (mjbutte)]

Even with a single .ibw file (force curve) in a directory, OpenFovea still crashes (trace below). I'm running on Win7-64 on Xeon 2.67GHz with 6 GB RAM (a generic Dell box). Has anyone gotten the software to work with Asylum force maps? Could it be that something has changed in the Asylum .ibw file in a recent build of their software?

Exception in thread Thread-1:
Traceback (most recent call last):
  File "C:\Python27\lib\threading.py", line 551, in __bootstrap_inner
    self.run()
  File "C:\Python27\lib\threading.py", line 504, in run
    self.__target(*self.__args, **self.__kwargs)
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1713, in load_
folder
    self.load_file(os.path.join(fv_folder, files))
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1694, in load_
file
    self.file['list'].append(ForceVolume(fv_file))
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 165, in __init
__
    self.__array['Piezo']] = afm_file.load(fv_file)
  File "C:\Python27\lib\site-packages\openfovea\fovea_toolbox\file_util\afm_file
.py", line 88, in load
    [trace, retrace, piezo, header] = asylum.load(file_name)
  File "C:\Python27\lib\site-packages\openfovea\fovea_toolbox\file_util\asylum.p
y", line 72, in load
    trace, retrace, header, piezo = get_file(file_name)
  File "C:\Python27\lib\site-packages\openfovea\fovea_toolbox\file_util\asylum.p
y", line 282, in get_file
    header = parse_note(note[0])
  File "C:\Python27\lib\site-packages\openfovea\fovea_toolbox\file_util\asylum.p
y", line 315, in parse_note
    _index = note.index(_text)
ValueError: substring not found

Traceback (most recent call last):
  File "C:\Python27\lib\site-packages\openfovea\openfovea_gui.py", line 820, in
on_new_experiment_activate
    self.force_volume = self.experiment.get_file(0)
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1618, in get_f
ile
    self.update_switch()
  File "C:\Python27\lib\site-packages\openfovea\classes.py", line 1969, in updat
e_switch
    mask = self.file['list'][self.file['current']].get_switch('mask')
IndexError: list index out of range

[Charles Roduit (charles-roduit)]

Thank you for your bug reports.

OpenFovea used to work with force-map files and quantitative image files from JPK. I saw sometimes the files header change with upgrade of jpk software. Can you send me a file or a link to a file in order to investigate ?

About ibw files, they are from Asylum, isn't it ? They are not currently supported.

Thank you,

Charles

[mjb (mjbutte)]

I'd like to help get the code working for Asylum files. Has your software ever successfully worked with Asylum force maps? Your Nature Methods paper says Asylum files are supported. Did something change in the code or in their file format between the time of the publication and now?

I've tried the latest build of OpenFovea on Ubuntu and get this error on Asylum files, even with small directories:

  File "/usr/lib/python2.7/threading.py", line 552, in __bootstrap_inner
    self.run()
  File "/usr/lib/python2.7/threading.py", line 505, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/usr/lib/python2.7/dist-packages/openfovea/classes.py", line 1872, in load_folder
    self.load_file(os.path.join(fv_folder, files))
  File "/usr/lib/python2.7/dist-packages/openfovea/classes.py", line 1853, in load_file
    self.file['list'].append(ForceVolume(fv_file))
  File "/usr/lib/python2.7/dist-packages/openfovea/classes.py", line 162, in __init__
    _data = afm_file.load(fv_file)
  File "/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/afm_file.py", line 122, in load
    [trace, retrace, value['piezo'], header] = asylum.load(file_name)
  File "/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py", line 80, in load
    trace, retrace, header, piezo = get_file(file_name)
  File "/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py", line 309, in get_file
    header = parse_note(note[0])
  File "/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py", line 342, in parse_note
    _index = note.index(_text)
ValueError: substring not found

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/openfovea/openfovea_gui.py", line 869, in on_new_experiment_activate
    self.force_volume = self.experiment.get_file(0)
  File "/usr/lib/python2.7/dist-packages/openfovea/classes.py", line 1775, in get_file
    self.update_switch()
  File "/usr/lib/python2.7/dist-packages/openfovea/classes.py", line 2150, in update_switch
    mask = self.file['list'][self.file['current']].get_switch('mask')
IndexError: list index out of range

[Charles Roduit (charles-roduit)]

Dear mjb,

I made a mistake, OpenFovea works with asylum files, but, we do not have an asylum microscope in our lab to follow the evolution/diversity of files. The support was done during a collaboration with an external lab.

Can you open a new bug, this one is about the support of jpk microscope. With the new bug. can you send me files in order to investigate your problem ?

I put the bug back to incomplete as I am waiting for jpk file to solve the problem.

If you can code yourself, the files that manage the microscope support are in the openfovea/fovea_toolbox/file_util/

jpk.py manages jpk files
asylum.py manages asylum files

Thank you,

Charles

[Charles Roduit (charles-roduit)]

Sorry, every one exept me is speaking about asylum. I don't know why I'm speaking about JPK... The end of year seems to be difficult.

Nevertheless, can you provide me a copy of microscope file to investigate ?

All the best for the new year,

Charles

[Li Xiao (xiaomizhou)]

Dear mjbutte and charles-roduit, have you solved the problem yet? I have the same problem now, I can't import .ibw file