Running stitching with only 2 axes

[lauhei]

Hi,

We are trying to run rigid stitching on lightsheet data that is only 1 tile wide in the Y axis. Our workspace looks like

Workspace[CellMap]{.../S-L}
              raw: 240918_Brain-S_hemisphereL_10-07-06/10-07-06_Brain-S_hemisphereL_UltraII[00 x <X,2>]_C00_xyz-Table Z<Z,4>.ome.npy {8775 files, ('X', 'Z'): (0, 0) -> (2, 2924)}
                   240918_Brain-S_hemisphereL_10-07-06/10-07-06_Brain-S_hemisphereL_UltraII[00 x <X,2>]_C00_xyz-Table Z<Z,4>.ome.tif {8775 files, ('X', 'Z'): (0, 0) -> (2, 2924)}
 autofluorescence: 240918_Brain-S_hemisphereL_AF_19-11-36/19-11-36_Brain-S_hemisphereL_AF_UltraII[00 x <X,2>]_C00_xyz-Table Z<Z,4>.ome.tif {1952 files, ('X', 'Z'): (0, 0) -> (1, 975)}
         stitched: no file
           layout: no file
       background: no file
        resampled: no file
resampled_to_auto: no file
auto_to_reference: no file
            cells: no file
          density: no file
   tile_extension: no file
         arteries: 240918_Brain-S_hemisphereL_10-07-06/10-07-06_Brain-S_hemisphereL_UltraII[00 x <X,2>]_C02_xyz-Table Z<Z,4>.ome.npy {8775 files, ('X', 'Z'): (0, 0) -> (2, 2924)}
                   240918_Brain-S_hemisphereL_10-07-06/10-07-06_Brain-S_hemisphereL_UltraII[00 x <X,2>]_C02_xyz-Table Z<Z,4>.ome.tif {8775 files, ('X', 'Z'): (0, 0) -> (2, 2924)}

With the resulting traceback when we run rigid stitching preview or run stitching:

Traceback (most recent call last):
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/gui/tabs.py", line 436, in preview_stitching_smart
    self.wrap_step('Stitching', self.preprocessor.stitch_rigid, step_kw_args={'force': True},
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/gui/interfaces.py", line 297, in wrap_step
    self.main_window.wrap_in_thread(func, *step_args, **step_kw_args)
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/gui/run_gui.py", line 619, in wrap_in_thread
    return result.get()
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Utils/utilities.py", line 171, in wraps
    return func(*args, **kwargs)
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/processors/sample_preparation.py", line 381, in stitch_rigid
    layout = self.get_wobbly_layout(overlaps)
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Utils/utilities.py", line 171, in wraps
    return func(*args, **kwargs)
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/processors/sample_preparation.py", line 414, in get_wobbly_layout
    layout = stitching_wobbly.WobblyLayout(expression=raw_path, tile_axes=['X', 'Y'], overlaps=overlaps)
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Stitching/StitchingWobbly.py", line 729, 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 ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Stitching/StitchingRigid.py", line 1910, in __init__
    sources, alignments, tile_positions = _initialize_tiles_from_expression(expression, tile_axes=tile_axes, tile_shape=tile_shape, tile_positions=tile_positions, overlaps=overlaps, positions=positions, alignments=alignments);
  File ".../miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Stitching/StitchingRigid.py", line 2247, in _initialize_tiles_from_expression
    raise ValueError('The expression does not have the named pattern %s' % n);
ValueError: The expression does not have the named pattern Y

Is there a way to resolve this? Any advice would be greatly appreciated.

Thank you

[crousseau]

Hi,

this is indeed an oversight. I will include a proper fix in the future version. In the mean time, I suggest you try to edit that line:

./miniconda3/envs/ClearMapUi39clean/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/processors/sample_preparation.py", line 414, in get_wobbly_layout
layout = stitching_wobbly.WobblyLayout(expression=raw_path, tile_axes=['X', 'Y'], overlaps=overlaps)

and remove from tile_axes=['X', 'Y'] the axis that you do not use (e.g. tile_axes=['Y'] if you only use the y axis.

@lauhei Please report back to me about that fix. If it works well for you, I will offer a proper fix using the expression next week.

[lauhei]

Hi,

Thank you for the advice. This change solved the initial error, but leads to a different one when trying to preview stitching:

Traceback (most recent call last):
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/gui/tabs.py", line 436, in preview_stitching_smart
    self.wrap_step('Stitching', self.preprocessor.stitch_rigid, step_kw_args={'force': True},
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/gui/interfaces.py", line 297, in wrap_step
    self.main_window.wrap_in_thread(func, *step_args, **step_kw_args)
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/gui/run_gui.py", line 619, in wrap_in_thread
    return result.get()
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Utils/utilities.py", line 171, in wraps
    return func(*args, **kwargs)
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/processors/sample_preparation.py", line 381, in stitch_rigid
    layout = self.get_wobbly_layout(overlaps)
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Utils/utilities.py", line 171, in wraps
    return func(*args, **kwargs)
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/processors/sample_preparation.py", line 414, in get_wobbly_layout
    layout = stitching_wobbly.WobblyLayout(expression=raw_path, tile_axes=['X', 'Z'], overlaps=overlaps)
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Stitching/StitchingWobbly.py", line 735, in __init__
    self.sources = [WobblySource(source = s, axis = axis) for s in sources];
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Stitching/StitchingWobbly.py", line 735, in <listcomp>
    self.sources = [WobblySource(source = s, axis = axis) for s in sources];
  File "./miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Stitching/StitchingWobbly.py", line 78, in __init__
    self._wobble = np.zeros((shape[self._axis], len(shape) - 1), dtype = int);
IndexError: tuple index out of range

We tried to fix this by changing self_axis to 1. This bypassed the error during preview stitching but led to the software freezing without an error message when trying to run stitching.