Merge pull request #322 from imagej/dataset-dim-renaming

Dataset dimension/axis label renaming

Author: elevans

doc/06-Working-with-Images.ipynb

@@ -437,11 +437,7 @@ def to_dataset(self, data, dim_order=None) -> "jc.Dataset":
         :return: A net.imagej.Dataset.
         """
         if sj.isjava(data):
-            if dim_order:
-                _logger.warning(
-                    f"Dimension reordering is not supported for {type(data)}."
-                )
-            return convert.java_to_dataset(self._ij, data)
+            return convert.java_to_dataset(self._ij, data, dim_order)
 
         if images.is_xarraylike(data):
             return convert.xarray_to_dataset(

src/imagej/__init__.py

@@ -27,33 +27,35 @@
 ###############
 
 
-def java_to_dataset(ij: "jc.ImageJ", jobj) -> "jc.Dataset":
+def java_to_dataset(ij: "jc.ImageJ", jobj, dim_order=None) -> "jc.Dataset":
     """
     Convert the given Java image data into an ImageJ2 Dataset.
 
     :param ij: The ImageJ2 gateway (see imagej.init)
     :param jobj: The Java image (e.g. RandomAccessibleInterval)
+    :param dim_order: Sequence of desired dimensions for the Dataset.
     :return: The converted ImageJ2 Dataset
     """
     assert sj.isjava(jobj)
     if isinstance(jobj, jc.Dataset):
-        return jobj
+        return _rename_dataset_dims(jobj, dim_order)
 
     # NB: This try checking is necessary because the set of ImageJ2 converters is
     # not complete. E.g., there is no way to directly go from Img to Dataset,
     # instead you need to chain the Img->ImgPlus->Dataset converters.
     try:
         if ij.convert().supports(jobj, jc.Dataset):
-            return ij.convert().convert(jobj, jc.Dataset)
+            ds = ij.convert().convert(jobj, jc.Dataset)
         if ij.convert().supports(jobj, jc.ImgPlus):
             imgplus = ij.convert().convert(jobj, jc.ImgPlus)
-            return ij.dataset().create(imgplus)
+            ds = ij.dataset().create(imgplus)
         if ij.convert().supports(jobj, jc.Img):
             img = ij.convert().convert(jobj, jc.Img)
-            return ij.dataset().create(jc.ImgPlus(img))
+            ds = ij.dataset().create(jc.ImgPlus(img))
         if ij.convert().supports(jobj, jc.RandomAccessibleInterval):
             rai = ij.convert().convert(jobj, jc.RandomAccessibleInterval)
-            return ij.dataset().create(rai)
+            ds = ij.dataset().create(rai)
+        return _rename_dataset_dims(ds, dim_order)
     except Exception as exc:
         _log_exception(_logger, exc)
         raise exc
@@ -642,7 +644,38 @@ def _permute_rai_to_python(rich_rai: "jc.RandomAccessibleInterval"):
     return permuted_rai
 
 
+def _rename_dataset_dims(ds, new_dims: Sequence[str]):
+    """
+    Rename, without reshaping, a Dataset's dimension labels.
+
+    :param ds: Input Dataset.
+    :param new_dims: Dimension labels to apply
+    :return: Dataset with dimension labels renamed.
+    """
+    # return the dataset if no new_dims
+    if not new_dims:
+        return ds
+
+    # validate dim sequence
+    new_dims = dims._validate_dim_order(new_dims, ds.shape)
+
+    # set axis type for each axis
+    for i in range(ds.ndim):
+        new_axis_str = dims._convert_dim(new_dims[i], "java")
+        new_axis_type = jc.Axes.get(new_axis_str)
+        ds.dim_axes[i].setType(new_axis_type)
+
+    return ds
+
+
 def _rename_xarray_dims(xarr, new_dims: Sequence[str]):
+    """
+    Rename, without reshaping, an xarray's dimension labels.
+
+    :param xarr: Input xarray.
+    :param new_dims: Dimension labels to apply.
+    :return: xarray with dimension labels renamed.
+    """
     curr_dims = xarr.dims
     if not new_dims:
         return xarr

src/imagej/convert.py

@@ -521,15 +521,15 @@ def test_index_image_converts_to_imglib_roi(ij):
     (
         get_img,
         "java",
-        ["a", "b", "c", "d", "e"],
-        ("X", "Y", "Unknown", "Unknown", "Unknown"),
+        ["X", "Y", "monday", "green", "Time"],
+        ("X", "Y", "monday", "green", "Time"),
         (1, 2, 3, 4, 5),
     ),
     (
         get_imgplus,
         "java",
-        ["a", "b", "c", "d", "e", "f", "g"],
-        ("X", "Y", "foo", "bar", "Channel", "Time", "Z"),
+        ["Y", "X", "Channel", "gray", "e", "foo", "gold"],
+        ("Y", "X", "Channel", "gray", "e", "foo", "gold"),
         (7, 8, 4, 2, 3, 5, 6),
     ),
     (