Merge pull request #13 from fmicompbio/fix-plate-sort

Sort layout and img_paths jointly

src/ez_zarr/ome_zarr.py

@@ -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)]

tests/test_ome_zarr.py

@@ -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 ..............................................