Merge pull request #238 from imagej/dim-order-kwargs-tests

Enable `dim_order` kwargs for direct image conversions

Author: hinerm

doc/06-Working-with-Images.ipynb

@@ -419,7 +419,7 @@ def sync_image(self, imp: "jc.ImagePlus" = None):
         pixels = imp.getProcessor().getPixels()
         stack.setPixels(pixels, imp.getCurrentSlice())
 
-    def to_dataset(self, data):
+    def to_dataset(self, data, dim_order=None):
         """Convert the data into an ImageJ2 Dataset.
 
         Converts a Python image (e.g. xarray or numpy array) or Java image (e.g.
@@ -428,7 +428,6 @@ def to_dataset(self, data):
         :param data: Image object to be converted to Dataset.
         :return: A net.imagej.Dataset.
         """
-        dim_order = None
         if sj.isjava(data):
             if dim_order:
                 _logger.warning(
@@ -447,7 +446,7 @@ def to_dataset(self, data):
 
         raise TypeError(f"Type not supported: {type(data)}")
 
-    def to_img(self, data):
+    def to_img(self, data, dim_order=None):
         """Convert the data into an ImgLib2 Img.
 
         Converts a Python image (e.g. xarray or numpy array) or Java image (e.g.
@@ -456,7 +455,6 @@ def to_img(self, data):
         :param data: Image object to be converted to Img.
         :return: A net.imglib2.img.Img.
         """
-        dim_order = None
         if sj.isjava(data):
             if dim_order:
                 _logger.warning(
@@ -500,7 +498,7 @@ def to_java(self, data, **hints):
 
         return sj.to_java(data, **hints)
 
-    def to_xarray(self, data):
+    def to_xarray(self, data, dim_order=None):
         """Convert the data into an ImgLib2 Img.
 
         Converts a Python image (e.g. xarray or numpy array) or Java image (e.g.
@@ -509,21 +507,24 @@ def to_xarray(self, data):
         :param data: Image object to be converted to xarray.DataArray.
         :return: An xarray.DataArray.
         """
-        dim_order = None
         if sj.isjava(data):
+            if dim_order:
+                _logger.warning(f"Conversion hints are not supported for {type(data)}.")
+            if isinstance(data, jc.ImagePlus):
+                data = convert.imageplus_to_imgplus(self._ij, data)
             if convert.supports_java_to_xarray(self._ij, data):
-                if dim_order:
-                    _logger.warning(
-                        f"Conversion hints are not supported for {type(data)}."
-                    )
                 return convert.java_to_xarray(self._ij, data)
+            if convert.supports_java_to_ndarray(self._ij, data):
+                return convert.ndarray_to_xarray(
+                    convert.java_to_ndarray(self._ij, data)
+                )
 
         if images.is_xarraylike(data):
             return convert._rename_xarray_dims(data, dim_order)
         if images.is_arraylike(data):
             return convert.ndarray_to_xarray(data, dim_order)
 
-        return TypeError(f"Type not supported: {type(data)}.")
+        raise TypeError(f"Type not supported: {type(data)}.")
 
     # -- Deprecated methods --
 

src/imagej/__init__.py

@@ -143,10 +143,7 @@ def ndarray_to_xarray(narr: np.ndarray, dim_order=None) -> xr.DataArray:
     assert images.is_arraylike(narr)
     if dim_order:
         # check dim length
-        if narr.ndim != len(dim_order):
-            raise ValueError(
-                f"Expected {narr.ndim} dimensions but got {len(dim_order)}."
-            )
+        dim_order = dims._validate_dim_order(dim_order, narr.shape)
         return xr.DataArray(narr, dims=dim_order)
     return xr.DataArray(narr)
 
@@ -557,8 +554,7 @@ def _rename_xarray_dims(xarr, new_dims: Sequence[str]):
     if not new_dims:
         return xarr
     # check dim length
-    if xarr.ndim != len(new_dims):
-        raise ValueError(f"Expected {xarr.ndim} dimensions but got {len(new_dims)}.")
+    new_dims = dims._validate_dim_order(new_dims, xarr.shape)
     dim_map = {}
     for i in range(xarr.ndim):
         dim_map[curr_dims[i]] = new_dims[i]

src/imagej/convert.py

@@ -284,7 +284,13 @@ def _get_scale(axis):
     :return: The scale for this axis or None if it is a non-numeric scale.
     """
     try:
-        return axis.values[1] - axis.values[0]
+        # HACK: This axis length check is a work around for singleton dimensions.
+        # You can't calculate the slope of a singleton dimension.
+        # This section will be removed when axis-scale-logic is merged.
+        if len(axis) <= 1:
+            return 1
+        else:
+            return axis.values[1] - axis.values[0]
     except TypeError:
         return None
 
@@ -397,6 +403,27 @@ def _convert_dims(dimensions: List[str], direction: str) -> List[str]:
         return dimensions
 
 
+def _validate_dim_order(dim_order: List[str], shape: tuple) -> List[str]:
+    """
+    Validate a List of dimensions. If the dimension list is smaller
+    fill the rest of the list with "dim_n" (following xarrray convention).
+
+    :param dim_order: List of dimensions (e.g. X, Y, Channel, Z, Time)
+    :param shape: Shape image for the dimension order.
+    :return: List with "dim_n" dimensions added to match shape length.
+    """
+    dim_len = len(dim_order)
+    shape_len = len(shape)
+    if dim_len < shape_len:
+        d = shape_len - dim_len
+        for i in range(d):
+            dim_order.append(f"dim_{i}")
+        return dim_order
+    if dim_len > shape_len:
+        raise ValueError(f"Expected {shape_len} dimensions but got {dim_len}.")
+    return dim_order
+
+
 def _has_axis(rai: "jc.RandomAccessibleInterval"):
     """Check if a RandomAccessibleInterval has axes."""
     if sj.isjava(rai):

src/imagej/dims.py

@@ -25,7 +25,6 @@ def rai_slice(rai, imin: Tuple, imax: Tuple, istep: Tuple):
     dim_itr = range(len(shape))
 
     for py_dim, j_dim in zip(dim_itr, dim_itr):
-
         # Set minimum
         if imin[py_dim] is None:
             index = 0