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Sort layout and img_paths jointly #13

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Aug 5, 2024
Merged

Sort layout and img_paths jointly #13

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e113d26
Make sure layout and img_paths are sorted jointly
csoneson Jul 30, 2024
316d84e
Add unit tests for import_Fractal_plate with multiple wells
csoneson Jul 31, 2024
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5 changes: 4 additions & 1 deletion src/ez_zarr/ome_zarr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,8 +123,11 @@ def import_Fractal_plate(path: str, image_name: str = '0') -> "ImageList":

# build layout
layout = pd.DataFrame({'row_index': row_index,
'column_index': column_index})
'column_index': column_index,
'img_paths': img_paths})
layout = layout.sort_values(by=['row_index', 'column_index']).reset_index(drop=True)
img_paths = layout.img_paths.tolist()
layout = layout.drop('img_paths', axis='columns')

# set nrow, ncol
known_plate_dims = [(2, 3), (4, 6), (8, 12), (16, 24)]
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17 changes: 17 additions & 0 deletions tests/test_ome_zarr.py
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Expand Up @@ -92,6 +92,23 @@ def test_import_Fractal_plate(tmpdir: str):
assert imgL2.nrow == 8
assert imgL2.ncol == 12

shutil.copytree('tests/example_data/plate_ones_mip.zarr',
str(tmpdir) + '/example_img_multi')
assert tmpdir.join('/example_img_multi/.zattrs').check()
shutil.copytree(str(tmpdir) + '/example_img_multi/B/03',
str(tmpdir) + '/example_img_multi/C/02')
shutil.copytree(str(tmpdir) + '/example_img_multi/B/03',
str(tmpdir) + '/example_img_multi/G/06')
imgL3 = ome_zarr.import_Fractal_plate(str(tmpdir) + '/example_img_multi')
assert imgL3.nrow == 8
assert imgL3.ncol == 12
assert imgL3.layout.row_index.tolist() == [2, 3, 7]
assert imgL3.layout.column_index.tolist() == [3, 2, 6]
assert imgL3['B03'].get_path() == str(tmpdir) + '/example_img_multi/B/03/0'
assert imgL3['C02'].get_path() == str(tmpdir) + '/example_img_multi/C/02/0'
assert imgL3['G06'].get_path() == str(tmpdir) + '/example_img_multi/G/06/0'
assert imgL3.paths == [str(tmpdir) + '/example_img_multi/B/03/0', str(tmpdir) + '/example_img_multi/C/02/0', str(tmpdir) + '/example_img_multi/G/06/0']
assert imgL3.names == ['B03', 'C02', 'G06']

# ome_zarr.Image ----------------------------------------------------
# ... helper functions ..............................................
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