FIX: now works with multi-channel psoct data

linc_convert/modalities/psoct/_utils.py

@@ -156,6 +156,7 @@ def generate_pyramid(
         "dtype": omz["0"]._dtype,
         "fill_value": omz["0"]._fill_value,
         "compressor": omz["0"]._compressor,
+        "chunks": omz["0"].chunks,
     }
 
     # Select windowing function
@@ -190,7 +191,7 @@ def generate_pyramid(
         print("Compute level", level, "with shape", shape)
 
         allshapes.append(shape)
-        omz.create_dataset(str(level), shape=shape, **opt)
+        omz.create_dataset(str(level), shape=batch + shape, **opt)
 
         # Iterate across `max_load` chunks
         # (note that these are unrelared to underlying zarr chunks)

linc_convert/modalities/psoct/multi_slice.py

@@ -262,7 +262,7 @@ def convert(
     ni = len(inp)
 
     nblevels = min(
-        [int(math.ceil(math.log2(x))) for i, x in enumerate(inp_shape) if i != no_pool]
+        [int(math.ceil(math.log2(x))) for i, x in enumerate(inp_shape[-3:]) if i != no_pool]
     )
     nblevels = min(nblevels, int(math.ceil(math.log2(max_load))))
     nblevels = min(nblevels, max_levels)
@@ -291,8 +291,8 @@ def convert(
             # save current chunk
             omz["0"][
                 ...,
-                k * inp_chunk[0] : k * inp_chunk[0] + loaded_chunk.shape[0],
-                j * inp_chunk[1] : j * inp_chunk[1] + loaded_chunk.shape[1],
+                k * inp_chunk[-3] : k * inp_chunk[-3] + loaded_chunk.shape[-2],
+                j * inp_chunk[-2] : j * inp_chunk[-2] + loaded_chunk.shape[-1],
                 i,
             ] = loaded_chunk
 
@@ -308,7 +308,7 @@ def convert(
     ome_unit = to_ome_unit(unit)
     write_ome_metadata(
         omz,
-        axes=["z", "y", "x"],
+        axes=(["c"] if len(inp_shape) == 4 else []) + ["z", "y", "x"],
         no_pool=no_pool,
         space_unit=ome_unit,
         space_scale=vx,