Add custom volumes defined in settings about simpa

[jgroehl]

Not sure what exactly you mean.
Do you mean that additional volumetric representations of tissue properties should be addable to the dictionary?
Or that the volumes that are included should be completely customisable?

[kdreher]

@leoyala meant that custom volumes can be defined for mua, mus and so on instead of using one of the volume creators. So for example just defining mua as an array full of ones.
This is actually already possible by defining the volumes, saving them in the standard simpa path and then using the run_optical_forward_model function.

[jgroehl]

Furthermore, we have the SegmentationMaskLoader that you can use to load segmentation masks and populate the segmentation classes with customised structures.
You could even go so far as to define mua, mus, and g maps and call the run_optical_forward_model without any HDF5 load/save interactions.

[leoyala]

Furthermore, we have the SegmentationMaskLoader that you can use to load segmentation masks and populate the segmentation classes with customised structures.
You could even go so far as to define mua, mus, and g maps and call the run_optical_forward_model without any HDF5 load/save interactions.

Currently run_optical_model loads the volume properties from the saved HDF5, so it would not work without saving it. Or is this being modified in develop?

[jgroehl]

Correct. There needs to be an HDF5 input file. The location of this file is defined via the Settings dictionary.
As long as the file exists, it will be loaded :)

[jgroehl]

The volume creator module already saves the HDF5 file.