As already discussed the binaries are provided in the release zip. Currently the plugin is just intended to provide methods (accessible by DM scripting) to query HDF5 files, and read datasets and attributes. Also a DM script is provided to read my own internal custom datasets. What's missing here is a DM script, which interprets the data/metadata stored in hyperspy files in a way DM will understand.
I'm not (yet) using hyperspy, and also try to avoid DM scripting, so I have no intention to write such a script myself in the next future. However, I'm happy to help anyone, who is willing to write such a script. I've had a bit of a play, and I can confirm that the plugin works great with hyperspy. My previous errors were due to the order of the data dimensions and the fact that my data was in float64.There are two requirements for the file to import correctly:.
The data type must not be float64, but float32 ( s.changedtype('float32')). The data must be transposed before saving ( s.T.save(filename) works great)The first point is only necessary if one wants to use the spectrum picker tool, for EELS and EDS, as far as I can tell.Finally, I have modified a single string in the import script, to default to importing '.hspy' files, rather than '.hdf5'. In case we want to put it on the website. I'm trying to work out how to look for the attribute 'units' located under axis-0 using your script, on the following file.I'm using HDFView to understand the layout of the file.
Here's what it looks like in this case:I suspect it's got something to do with the following lines, although simply replacing 'unit' for 'units' did nothing. Do you have any advice?
I'm afraid I'm not entirely sure how to debug scripts in DM. // Look for intensity scaleNumber datascale = 1.0if (TagGroupGetTagAsNumber(attr, 'scale', datascale))ImageSetIntensityScale(array, datascale)Number dataoffset = 0.0if (TagGroupGetTagAsNumber(attr, 'offset', dataoffset))ImageSetIntensityOrigin(array, dataoffset / datascale)String dataunitif (TagGroupGetTagAsString(attr, 'unit', dataunit))ImageSetIntensityUnitString(array, dataunit). I'm not really sure were the problem is. I would need to see more of the script you are using. Make sure you read the attributes of the right datasets/group. In the example file 'axis-0' is a group. Just seen this thread!
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I'm trying to get data from the FEI velox software into DM (technically HDF5 format but with the extension.emd). Currently I have tested the script on my GMS 3 and it does run without errors. Unfortunately, it slices up my data in wrong directions and I think the actual data cube I'm interested in is stored in the shape of 1xmany when I'm hoping it has 4 dimensions. I think I'm having the same ordering problem. Is there anyway to transpose in DM scripting easily/ import a different way around? I have just noticed that DM (only tested for GMS 2.3) has a function, which can transpose data: slice2/slice3., this might also be useful for a hspy import script, which does not rely on transposing the data before saving it.The syntax is a bit cumbersome, see the DM documentation for that (the doc in my installation is located in C:ProgramDataGatanDocumentationScriptingDigitalMicrograph.pdf). If you want to transpose an image 'img' with dimensions dimx=1024 dimy=20 dimz=10, corresponding to a numpy shape of (10, 20, 1024), into dimx=20 dimy=10 dimz=1024, it can be done with:ShowImage(slice3(img, 0, 0, 0, 1, 20, 1, 2, 10, 1, 0, 1024, 1))Note, that this creates a different 'view' (speaking in numpy terms) on the array and does not copy it (so still might work on larger arrays, which otherwise tend to crash DM).
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Sadly this works only for up to 3 dimensions (there is no slice4, at least in GMS 2.3).