TubeMap Create a test data

[jeng87]

Hi,

Question about creating debug datasets by using my own data in the section of "Create a test data" in TubeMap script.

But displaying an value error like below, I am not sure if it's related to tag expression to the metadata.
ValueError: Cannot find name for type 'DN832-002 - Stitched_C1_XY01.npy'!

I skipped the section of Stitching(The whole input image has already been stitched from the microscope) and Resampling and atlas alignment(Don't need to know the exact location against atlas reference, and I use brown adipose tissue instead of brain).

And in my case, the Autofluorescence channel is unnecessary to be used because the project I am working on is to reconstruct the whole vascular and nerves in the tissue and their diameters, which are the two channels stained as the input datasets.

I modified the "Create a test data" section in the script like this:

#%% Crop test data

#select sublice for testing the pipeline
ws.debug = True;
#ws.debug = 'name_for_the_test_subset'
ws.debug = 'DN832-002 - Stitched_C1_XY01.npy'
ws.debug = 'DN832-002 - Stitched_C2_XY01.npy'
slicing = (slice(None),slice(None),slice(None));
#slicing = (slice(None),slice(0,1000),slice(900,1500)); #use for the wobly stitched data
ws.create_debug('DN832-002 - Stitched_C1_XY01.npy', slicing=slicing)
ws.create_debug('DN832-002 - Stitched_C2_XY01.npy', slicing=slicing);
#ws.create_debug('stitched', slicing=slicing); #use for the wobly stitched data
#ws.create_debug('stitched', postfix='arteries', slicing=slicing); #use for the wobly stitched data
#ws.debug = True;

Thank you.