Add documentation on how to run retrievals.

docs/retrieval.md

@@ -1,5 +1,14 @@
 # Running retrievals
 
-Finally, retrieval models produced by in the training step can be retrieve precipitation
-and hydrometeor profiles from GPM observations.
+Finally, retrieval models produced by in the training step can be retrieve
+precipitation and hydrometeor profiles from GPM observations.
 
+## Command-line interface
+
+GPROF-NN retrieval on one or multiple input files can be run using the ``gprof_nn retrieve`` command. 
+
+```
+gprof_nn retrieve /path/to/retrieval_model.pt /path/to/input_data --output_path /path/to_output_data
+```
+
+The command can be used to run the trained retrieval model on L1C, preprocessor or training data files. 

gprof_nn/retrieval.py

@@ -263,11 +263,11 @@ def load_input_data_training_3d(
                 )
 
         aux = {
-            "longitude": targets.pop("longitude"),
-            "latitude": targets.pop("latitude"),
+            "longitude": targets.pop("longitude").numpy(),
+            "latitude": targets.pop("latitude").numpy(),
         }
         for name, target_data in targets.items():
-            aux[name + "_ref"] = target_data
+            aux[name + "_ref"] = target_data.numpy()
         return input_data, aux
 
     raise RuntimeError(
@@ -420,7 +420,7 @@ def finalize_results(
         output = xr.Dataset()
         for name, data in aux.items():
             data = data.squeeze()
-            if data.ndim > 2:
+            if data.ndim > 2 and data.shape[-1] != 28:
                 data = data.transpose((1, 2, 0))
             dims_v = dims[:data.ndim]
             output[name] = (dims_v, data)