Rename wells functionality, fixed style errors

iohub/cli/cli.py

@@ -1,9 +1,11 @@
+import csv
 import pathlib
 
 import click
 
 from iohub._version import __version__
 from iohub.convert import TIFFConverter
+from iohub.ngff import open_ome_zarr, rename_well
 from iohub.reader import print_info
 
 VERSION = __version__
@@ -87,3 +89,60 @@ def convert(input, output, grid_layout, chunks):
         chunks=chunks,
     )
     converter()
+
+
+@click.command()
+@click.help_option("-h", "--help")
+@click.argument(
+    "csvfile",
+    type=click.File("r"),
+)
+@click.argument(
+    "zarrfile",
+    type=click.Path(
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        resolve_path=True,
+        path_type=pathlib.Path,
+    ),
+)
+def rename_wells_cli(csvfile, zarrfile):
+    """Rename wells based on CSV file
+
+    The CSV file should have two columns: old_well_path and new_well_path.
+    """
+    names = []
+
+    csvreader = csv.reader(csvfile)
+    for row in csvreader:
+        if len(row) != 2:
+            raise ValueError(
+                f"Invalid row format: {row}."
+                f"Each row must have two columns."
+            )
+        names.append([row[0], row[1]])
+
+    plate = open_ome_zarr(zarrfile, mode="a")
+
+    modified = {}
+    modified["wells"] = []
+    modified["rows"] = []
+    modified["columns"] = []
+
+    well_paths = [
+        plate.metadata.wells[i].path for i in range(len(plate.metadata.wells))
+    ]
+
+    for old_well_path, new_well_path in names:
+        if old_well_path not in well_paths:
+            raise ValueError(
+                f"Old well path '{old_well_path}' not found "
+                f"in the plate metadata."
+            )
+        for well in plate.metadata.wells:
+            if well.path == old_well_path and well not in modified["wells"]:
+                rename_well(
+                    plate, well, old_well_path, new_well_path, modified, False
+                )
+                modified["wells"].append(well)

iohub/ngff.py

@@ -1565,6 +1565,50 @@ def positions(self) -> Generator[tuple[str, Position], None, None]:
             for _, position in well.positions():
                 yield position.zgroup.path, position
 
+    def rename_well(
+        self,
+        well,
+        old_well_path: str,
+        new_well_path: str,
+        modified={},
+        single_well=True,
+    ):
+        """Rename a well.
+
+        Parameters
+        ----------
+        old_well_path : str
+            Old name of well
+        new_well_path : str
+            New name of well
+        modified : dict, optional
+            Tracks modified wells
+        single well: bool, optional
+            True: renaming one well, False: renaming multiple wells
+        """
+        old_row, old_column = old_well_path.split("/")
+        new_row, new_column = new_well_path.split("/")
+
+        if well.path == old_well_path:
+            well.path = new_well_path  # update well metadata
+            zarr.storage.rename(
+                self.zgroup._store, old_well_path, new_well_path
+            )  # update well paths
+
+        for column in self.metadata.columns:
+            if column.name == old_column and column not in modified["columns"]:
+                column.name = new_column  # update column metadata
+                if not single_well:
+                    modified["columns"].append(column)
+
+        for row in self.metadata.rows:
+            if row.name == old_row and row not in modified["rows"]:
+                row.name = new_row  # update row metadata
+                if not single_well:
+                    modified["rows"].append(row)
+
+        self.dump_meta()
+
 
 def open_ome_zarr(
     store_path: StrOrBytesPath,