Compatibility with latest version of HyperSpy

[tjof2]

Current HyperSpy wrapper was written for an old version - needs updating to work with v1.1.

[hentr]

hey, I am trying to test PGURE-SVT and seem to have hit this bug. Tried installing hyperspy 1.0, but could not get that working either. Suggestions?

[tjof2]

Hi @hentr, you could perhaps try v0.8.5 https://github.com/hyperspy/hyperspy/releases/tag/v0.8.5

Failing that, I'll address this issue this week.

[hentr]

Got it working with 0.8.5. Thanks, testing how well it works now with my data now :)

[hentr]

Great algorithm, it works really well with my data! However I cannot seem to save the image series after denoising, a bit frustrating when I have open a couple of image series that each took about 5 hrs to process. denoised_movie.save("s17_denoised.tif") gives:

TypeError                                 Traceback (most recent call last)
<ipython-input-3-ae9abdf9823c> in <module>()
----> 1 denoised_movie.save("s17_denoised.tif")

C:\Users\hent\AppData\Local\Continuum\Anaconda3\envs\hs0.85\lib\site-packages\hyperspy\signal.py in save(self, filename, overwrite, extension, **kwds)
   1893             basename, ext = os.path.splitext(filename)
   1894             filename = basename + '.' + extension
-> 1895         io.save(filename, self, overwrite=overwrite, **kwds)
   1896 
   1897     def _replot(self):

C:\Users\hent\AppData\Local\Continuum\Anaconda3\envs\hs0.85\lib\site-packages\hyperspy\io.py in save(filename, signal, overwrite, **kwds)
    424             overwrite = hyperspy.misc.io.tools.overwrite(filename)
    425         if overwrite is True:
--> 426             writer.file_writer(filename, signal, **kwds)
    427             print('The %s file was created' % filename)
    428             folder, filename = os.path.split(os.path.abspath(filename))

C:\Users\hent\AppData\Local\Continuum\Anaconda3\envs\hs0.85\lib\site-packages\hyperspy\io_plugins\tiff.py in file_writer(filename, signal, **kwds)
     89            software="hyperspy",
     90            photometric=photometric,
---> 91            **kwds)
     92 
     93 

C:\Users\hent\AppData\Local\Continuum\Anaconda3\envs\hs0.85\lib\site-packages\hyperspy\external\tifffile.py in imsave(filename, data, **kwargs)
    206 
    207     with TiffWriter(filename, **tifargs) as tif:
--> 208         tif.save(data, **kwargs)
    209 
    210 

C:\Users\hent\AppData\Local\Continuum\Anaconda3\envs\hs0.85\lib\site-packages\hyperspy\external\tifffile.py in save(self, data, photometric, planarconfig, resolution, description, volume, writeshape, compress, extratags)
    511 
    512         if self._software:
--> 513             addtag('software', 's', 0, self._software, writeonce=True)
    514             self._software = None  # only save to first page
    515         if description:

C:\Users\hent\AppData\Local\Continuum\Anaconda3\envs\hs0.85\lib\site-packages\hyperspy\external\tifffile.py in addtag(code, dtype, count, value, writeonce)
    480             rawcount = count
    481             if dtype == 's':
--> 482                 value = bytestr(value) + b'\0'
    483                 count = rawcount = len(value)
    484                 value = (value, )

C:\Users\hent\AppData\Local\Continuum\Anaconda3\envs\hs0.85\lib\site-packages\hyperspy\external\tifffile.py in <lambda>(x)
    455 
    456         bytestr = bytes if sys.version[0] == '2' else (
--> 457             lambda x: bytes(x) if isinstance(x, str) else x)
    458         tags = []  # list of (code, ifdentry, ifdvalue, writeonce)
    459 

TypeError: string argument without an encoding

Would guess current tifffile.py does not match well with the old hyperspy?

[tjof2]

@hentr That might be it - you can always export to HDF5 from the old HyperSpy and reimport that into a newer version of HyperSpy (virtual envs should be your friend here!)? The file format should be compatible across HS versions.

I'm sorry about this as a workaround, I'll fix this as soon as I can.

[hentr]

That was exactly what I ended up doing

[hentr]

@tjof2 is it a quick fix to update to newer HyperSpy? I am currently trying to automate denoising and analysis of larger amounts of data, and working in two environments for this is a pain. Do you have time to have a look at it?

[tjof2]

Hi @hentr sorry I've not had time, it's been incredibly busy here.

The bit that is broken is all in this file https://github.com/tjof2/pgure-svt/blob/master/pguresvt/hspysvt.py; the change required are in the HyperSpy signal (which changed when HyperSpy moved to v1+). @bm424 might be able to help as he wrote it.

If you're able to work out a way of fixing it yourself, please do submit a PR and I'll merge it.

[tjof2]

i.e. the key change in HyperSpy:

Changed in version 1.0: The Signal1D, Signal2D and BaseSignal classes deprecated the old Spectrum Image and Signal classes.

[hentr]

I'm not very good with python yet, but having had a quick look at it hspysvt.py, I think I should be able to figure it out.