Merge pull request #264 from imagej/boolean-type-img-conversion

Add conversion for BitType and BoolType imgs

Author: elevans

src/imagej/images.py

@@ -6,6 +6,7 @@
 
 import numpy as np
 import scyjava as sj
+from jpype import JException
 
 from imagej._java import jc
 
@@ -15,6 +16,8 @@
 # fmt: off
 _imglib2_types = {
     "net.imglib2.type.logic.NativeBoolType":                          "bool_",
+    "net.imglib2.type.logic.BitType":                                 "bool_",
+    "net.imglib2.type.logic.BoolType":                                "bool_",
     "net.imglib2.type.numeric.integer.ByteType":                      "int8",
     "net.imglib2.type.numeric.integer.ByteLongAccessType":            "int8",
     "net.imglib2.type.numeric.integer.ShortType":                     "int16",
@@ -137,28 +140,57 @@ def copy_rai_into_ndarray(
     if not is_arraylike(narr):
         raise TypeError("narr is not arraylike")
 
+    # Suppose all mechanisms fail. Any one of these might be the one that was
+    # "supposed" to work.
+    failure_exceptions = []
+
     # Check imglib2 version for fast copy availability.
     imglib2_version = sj.get_version(jc.RandomAccessibleInterval)
     if sj.is_version_at_least(imglib2_version, "5.9.0"):
-        # ImgLib2 is new enough to use net.imglib2.util.ImgUtil.copy.
-        ImgUtil = sj.jimport("net.imglib2.util.ImgUtil")
-        ImgUtil.copy(rai, sj.to_java(narr))
-        return narr
+        try:
+            # ImgLib2 is new enough to use net.imglib2.util.ImgUtil.copy.
+            ImgUtil = sj.jimport("net.imglib2.util.ImgUtil")
+            ImgUtil.copy(rai, sj.to_java(narr))
+            return narr
+        except JException as exc:
+            # Try another method
+            failure_exceptions.append(
+                _format_copy_exception(exc.toString(), "net.imglib2.util.ImgUtil.copy")
+            )
 
     # Check imagej-common version for fast copy availability.
     imagej_common_version = sj.get_version(jc.Dataset)
     if sj.is_version_at_least(imagej_common_version, "0.30.0"):
-        # ImageJ Common is new enough to use (deprecated)
-        # net.imagej.util.Images.copy.
-        Images = sj.jimport("net.imagej.util.Images")
-        Images.copy(rai, sj.to_java(narr))
-        return narr
+        try:
+            # ImageJ Common is new enough to use (deprecated)
+            # net.imagej.util.Images.copy.
+            Images = sj.jimport("net.imagej.util.Images")
+            Images.copy(rai, sj.to_java(narr))
+            return narr
+        except JException as exc:
+            # Try another method
+            failure_exceptions.append(
+                _format_copy_exception(exc.toString(), "net.imglib2.util.Images.copy")
+            )
 
     # Fall back to copying with ImageJ Ops's copy.rai op. In theory, Ops
     # should always be faster. But in practice, the copy.rai operation is
     # slower than the hardcoded ones above. If we were to fix Ops to be
     # fast always, we could eliminate the above special casing.
-    ij.op().run("copy.rai", sj.to_java(narr), rai)
+    try:
+        ij.op().run("copy.rai", sj.to_java(narr), rai)
+        return
+    except JException as exc:
+        # Try another method
+        failure_exceptions.append(
+            _format_copy_exception(
+                exc.toString(), "net.imagej.ops.copy.CopyNamespace.rai"
+            )
+        )
+
+    # Failed
+    failure_msg = "\n".join(failure_exceptions)
+    raise Exception("\n" + failure_msg)
 
 
 def dtype(image_or_type) -> np.dtype:
@@ -215,3 +247,30 @@ def dtype(image_or_type) -> np.dtype:
         raise TypeError(f"Unsupported original ImageJ type: {imagej_type}")
 
     raise TypeError("Unsupported Java type: " + str(sj.jclass(image_or_type).getName()))
+
+
+def _format_copy_exception(exc: str, fun_name: str) -> str:
+    """Format copy exceptions strings.
+
+    :param exc: Exception as a String.
+    :param fun_name: Name of the function producing the exception.
+    :return: The formatted exception.
+    """
+    # format cast exception
+    exc = str(exc)
+    if "cannot be cast to" in exc:
+        m = exc.split(" ")
+        from_class = m[m.index("cannot") - 1]
+        # special case if "class" is present or not
+        ci = m.index("cast")
+        if m[ci + 2] == "class":
+            to_class = m[ci + 3]
+        else:
+            to_class = m[ci + 2]
+        return (
+            f"Error: Unsupported type cast via {fun_name}\n"
+            f"    Source type: {from_class}\n"
+            f"    Target type: {to_class}"
+        )
+    else:
+        return exc

tests/test_image_conversion.py

@@ -376,6 +376,28 @@ def test_dataset_converts_to_xarray(ij):
     assert_inverted_xarr_equal_to_xarr(dataset, ij, xarr)
 
 
+def test_bittype_img_to_ndarray(ij):
+    ops_version = sj.get_version(sj.jimport("net.imagej.ops.OpService"))
+    if not sj.is_version_at_least(ops_version, "2.1.0"):
+        pytest.skip("Fails without ImageJ Ops >= 2.1.0")
+
+    ArrayImgs = sj.jimport("net.imglib2.img.array.ArrayImgs")
+    # NB ArrayImgs requires a long[] - construct long[] {10, 10, 10}
+    dims = sj.jarray("j", 3)
+    dims[:] = [10] * 3
+    j_img = ArrayImgs.bits(dims)
+
+    p_img = ij.py.from_java(j_img)
+    assert p_img.dtype == np.bool_
+
+
+def test_boolean_ndarray_to_img(ij):
+    narr = np.ones((10, 10), dtype=np.bool_)
+    j_img = ij.py.to_java(narr)
+    BooleanType = sj.jimport("net.imglib2.type.BooleanType")
+    assert isinstance(j_img.firstElement(), BooleanType)
+
+
 def test_image_metadata_conversion(ij):
     # Create a ImageMetadata
     DefaultImageMetadata = sj.jimport("io.scif.DefaultImageMetadata")