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nvladimus / npy2bdv

Fast writing of numpy 3d-arrays into HDF5 Fiji/BigDataViewer files.
GNU General Public License v3.0
34 stars 11 forks source link

Relative HDF5 filepath #9

Closed miketaormina closed 3 years ago

miketaormina commented 3 years ago

Examine the XML for a path to the image data instead of assuming file name.

I'd like to keep different XML files that point to the same data, so that additional transformations can be applied for different needs. I think this will be useful for data acquired with e.g. tilted light sheets and stage scanning, where the optical resolution may be in a different viewing angle than what is convenient to view for the overall sample geometry. In this case, one can keep the native view for computer vision purposes and a rotated view for visual inspection by having an XML file with additional transformations that points to the original data.

This branch looks at the xml file and finds the "ImageLoader" tag, which has the relative filepath to the hdf5 file. Prior to merging, it may benefit from additional book keeping, cleaner exception handling, or more appropriate parsing of the xml file.

nvladimus commented 3 years ago

Merged with minor edits and tests. Thanks!