Calibration Unit - Githubissues

fiji / HDF5_Vibez

HDF5 plugin for ImageJ and Fiji.

https://imagej.net/HDF5_Vibez

GNU General Public License v2.0

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Calibration Unit #10

Open ThorstenFalk opened 5 years ago

ThorstenFalk commented 5 years ago

Respect Calibration Unit for element_size_um computation
For 2D datasets element_size_um might be stored as 2-element-vector leading to "Array out of bounds" exceptions. This case is now detected and a one prepended.

ThorstenFalk commented 5 years ago

I currently maintain my own version of the HDF5_Vibez plugin on the U-Net Segmentation site which includes the proposed patch. Currently the plugin simply assumes that Calibration is in micrometers, the patch should catch at least all metric units and scale the values accordingly. Feel free to also add inch or other unit names respected by Fiji.

ThorstenFalk commented 5 years ago

My tree is based on the original version from Olaf, so I think we used the same code base. Besides some newline and whitespace changes my tree is just behind your version and with the merge mine becomes obsolete.

ThorstenFalk commented 5 years ago

Ah, I just realized, the getElementSizeUm(imp) method will return the element size as 2-element vector if the hyperstack has only on spatial slice. With the proposed changes in the load methods, this should be no issue, but for backward-compatibility you may want to change this to a three-element vector.

rejsmont commented 5 years ago

Hi,

I am terribly sorry for the delay, it has been crazy setting up my lab. Could you please re-merge your branch with master and I will take a look at the code again.

Thanks,