Fix tensorstore empty array handling (#326)

* Fix tensorstore empty array handling

- Add validation for empty arrays in _save_transformed before tensorstore write
- Skip write operations for empty arrays with warning messages
- Add comprehensive error handling with detailed diagnostics for tensorstore failures
- Improve error messages to include array shapes, sizes, and tensorstore details

This resolves the ValueError: Error aligning dimensions issue when empty arrays
are passed to tensorstore write operations.

* Add empty results check to prevent tensorstore alignment errors

Adds validation in apply_transform_to_tczyx_and_save() to check for empty
results dictionary before calling _save_transformed(). When no valid time
points are available, logs diagnostic message and skips write operation
instead of attempting to write empty arrays to tensorstore, which causes
alignment dimension mismatches.

* Revert "Fix tensorstore empty array handling"

This reverts commit 65c9ddb.

* better handling of output_time_indices

* style

Author: ieivanov

iohub/ngff/utils.py

@@ -407,9 +407,8 @@ def apply_transform_to_tczyx_and_save(
         Additional arguments to pass to the function.
     """
     input_time_indices = _slice_to_list(input_time_indices)
-    output_time_indices = _slice_to_list(output_time_indices)
     results = {}
-    for input_time_index in input_time_indices:
+    for i, input_time_index in enumerate(input_time_indices):
         result = _apply_transform_to_czyx(
             func,
             input_position_path=input_position_path,
@@ -418,19 +417,28 @@ def apply_transform_to_tczyx_and_save(
             **kwargs,
         )
         if result is not None:
-            results[input_time_index] = result
+            results[i] = result
         else:
             _echo_finished(
                 input_time=input_time_index,
                 output_channel=output_channel_indices,
                 skipped=True,
             )
-    _save_transformed(
-        transformed=list(results.values()),
-        output_position_path=output_position_path,
-        output_channel_indices=output_channel_indices,
-        output_time_indices=list(results.keys()),
-    )
+    if results:
+        output_time_indices = _slice_to_list(output_time_indices)
+        output_time_indices = [output_time_indices[i] for i in results.keys()]
+        _save_transformed(
+            transformed=list(results.values()),
+            output_position_path=output_position_path,
+            output_channel_indices=output_channel_indices,
+            output_time_indices=output_time_indices,
+        )
+    else:
+        click.echo(
+            f"No valid time points to write for channel indices "
+            f"{output_channel_indices}, output time indices "
+            f"{output_time_indices}"
+        )
     del results
     _echo_finished(input_time_indices, output_channel_indices, skipped=False)