Script to export patch stacks from non-PA TREC data

extensions/chaeo/batch_jobs/20231023_Porto_4ch.py

@@ -22,15 +22,18 @@ if __name__ == '__main__':
 
     # write single-position TIF color stacks
     where_proc = Path(where_output) / 'proc'
-    for pos in range(0, cf.shape[cf.axes.index('S')]):
-        fname = f'{czi_filepath.stem}_p{pos:02d}.tif'
-        write_accessor_data_to_file(
-            where_proc / fname,
-            get_accessor_from_multiposition_czi(cf, pos)
-        )
-        print(f'Wrote file {fname}')
+    # for pos in range(0, cf.shape[cf.axes.index('S')]):
+    # for pos in [0, 50, 100, 150, 200]:
+    #     fname = f'{czi_filepath.stem}_p{pos:02d}.tif'
+    #     write_accessor_data_to_file(
+    #         where_proc / fname,
+    #         get_accessor_from_multiposition_czi(cf, pos)
+    #     )
+    #     print(f'Wrote file {fname}')
 
-    px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/pxAF405_dim8bit.ilp').__str__()
+    px_ilp = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/ilastik/px_4ch_02.ilp').__str__()
+
+    where_proc = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/output/batch-output-20240126-0003/proc')
 
     params = {
         'pxmap_threshold': 0.25,