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knossos-project / knossos

KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
https://knossos.app
GNU General Public License v2.0
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Tif stack exporter (raw data and overlay data) #147

Open jmrk84 opened 9 years ago

jmrk84 commented 9 years ago

Use numpy and PIL for tif export

unidesigner commented 8 years ago

It would be nice to export a Tiff stack for a whole volume in Knossos? Such as this one: https://segem.rzg.mpg.de/webdav/datasets/ek0563/

orenshatz commented 8 years ago

Hi Stephan. Yes, it would be nice. The problem is, at the moment knossos users access data mostly remotely, whereas the data actually loaded in knossos is only a small cubic subset, called "supercube". So this feature can only directly access the supercube, in case data is stored remotely.

We have a standalone python package called datasetUtils (in the knossos_python_tools repo, not knossos repo), where you can directly access a local dataset and perform operations such as you suggested. I do not recall whether a TIF export is available there, but that's where it should reside.

One might consider this an artificial strategic decision, to dedicate knossos to only survey portions of a dataset rather than be able to perform set-wide operations. We already have issues of this sort in another plugin, where a set-wide analysis is required within knossos, and datasetUtils is employed in this context as a helper package within knossos - in order to access this data on a locally attached hard-drive.. But this is consider "external" to the knossos core code or capabilities, until the unspoken consensus design is otherwise revised.

unidesigner commented 8 years ago

Hi! Thank you for the explanation. So this means I could pull all the files from said URL to my local machine and then use the datasetUtils. I looked at the code briefly, should I then use initialize_from_knossos_path to point to the knossos.conf file and then use export_to_image_stack to export to PNG images? That might already do it, I'll try later.

orenshatz commented 8 years ago

I guess that's the way to go, yes, except acquiring remote data on per-file basis is usually extremely inefficient. At least for raw data, which would probably be left unchanged in the future, it would make better sense to compress it first on server side, then transfer the compressed file.