@@ -94,19 +94,21 @@ folderpath = 'examples/example_brain/GLTa/'
9494# try with and without ensemble to find the model which best works for you
9595# if you have section numbers included in the filename as _sXXX specify this :)
9696Model.predict(folderpath, ensemble = True , section_numbers = True )
97- # This is an optional stage if you have damaged sections, or hemibrains they may negatively effect the propagation for the entire dataset
98- # simply set the bad sections here using a string which is unique to those each section you would like to label as bad. DeepSlice will
99- # not include it in the propagation and instead it will infer its position based on neighbouring sections.
97+ # This is an optional stage if you have damaged sections, or hemibrains they may negatively effect the
98+ # propagation for the entire dataset simply set the bad sections here using a string which is unique to
99+ # those each section you would like to label as bad. DeepSlice will not include it in the propagation
100+ # and instead it will infer its position based on neighbouring sections.
100101Model.set_bad_sections(bad_sections = [" _s094" , " s199" ])
101102# If you would like to normalise the angles (you should)
102103Model.propagate_angles()
103104# To reorder your sections according to the section numbers
104105Model.enforce_index_order()
105- # alternatively if you know the precise spacing (ie; 1, 2, 4, indicates that section 3 has been left out of the series) Then you can use
106+ # alternatively if you know the precise spacing (ie; 1, 2, 4, indicates that section 3 has been left out.
106107# Furthermore if you know the exact section thickness in microns this can be included instead of None
107108# if your sections are numbered rostral to caudal you will need to specify a negative section_thickness
108109Model.enforce_index_spacing(section_thickness = None )
109- # now we save which will produce a json file which can be placed in the same directory as your images and then opened with QuickNII.
110+ # now we save which will produce a json file which can be placed in the same directory as your images and
111+ # then opened with QuickNII.
110112Model.save_predictions(folderpath + ' MyResults' )
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