jeng87
commented
2 years ago This problem has been fixed.
Regarding to the specific cell of Rigid z-alignment to be ran in TubeMap. Check the inputting image files of expression_raw and expression_arteries which have to be adjacent to each other. In the other words, this cell is about to align 2 tiles in the same depth or same Z axis. Therefore, the expression_raw should contain files include vessel related tile_1 and tile_2, and its same to the inputting of expression_arteries with arteries of tile_1 and tile_2. Again, these two tiles need to be adjacent to each other.
runcell('Rigid z-alignment', '/home/ClearMap2/Documentation/Example/TubeMap/TubeMap_test.py') Traceback (most recent call last):
File "/home/ClearMap2/Documentation/Example/TubeMap/TubeMap_test.py", line 103, in
layout = stw.WobblyLayout(expression=ws.filename('raw'), tile_axes=['X','Y'], overlaps=(45, 155));
File "/home/ClearMap2/ClearMap/Alignment/Stitching/StitchingWobbly.py", line 725, in init strg.TiledLayout.init(self, sources = sources, expression = expression, tile_axes = tile_axes, tile_shape = tile_shape, tile_positions = tile_positions, positions = positions, overlaps = overlaps, alignments = alignments, position = position, shape = shape, dtype = dtype, order = order);
File "/home/ClearMap2/ClearMap/Alignment/Stitching/StitchingRigid.py", line 1923, in init self.update_sources_from_alignments();
File "/home/ClearMap2/ClearMap/Alignment/Stitching/StitchingRigid.py", line 1328, in update_sources_from_alignments positions = positions_from_tree(sources = self.sources, alignments = self.alignments, fixed_source=self.sources[0]);
File "/home/ClearMap2/ClearMap/Alignment/Stitching/StitchingRigid.py", line 3714, in positions_from_tree ndim = alignments[0].ndim
IndexError: list index out of range