Add clamp option

Optionally ensure that min and max are withon floor and limit.

pytools/ng/build_histogram.py

@@ -167,6 +167,11 @@ def histogram_stats(hist, bin_edges):
     mutually_exclusive=["sigma", "mad"],
     help="Use INPUT_IMAGE's middle percentile (option's value) of data for minimum and maximum range.",
 )
+@click.option(
+    "--clamp/--no-clamp",
+    default=False,
+    help="Clamps minimum and maximum range to existing intensity values (floor and limit).",
+)
 @click.option(
     "--output-json",
     type=click.Path(exists=False, dir_okay=False, resolve_path=True),
@@ -175,7 +180,7 @@ def histogram_stats(hist, bin_edges):
     "elements of a double numeric value.",
 )
 @click.version_option(__version__)
-def main(input_image, mad, sigma, percentile, output_json):
+def main(input_image, mad, sigma, percentile, clamp, output_json):
     """
     Reads the INPUT_IMAGE to compute an estimated minimum and maximum range to be used for visualization of the
     data set. The image is required to have an integer pixel type.
@@ -247,6 +252,9 @@ def main(input_image, mad, sigma, percentile, output_json):
 
     floor_limit = weighted_quantile(mids, quantiles=[0.0, 1.0], sample_weight=h, values_sorted=True)
 
+    if clamp:
+        min_max = (max(min_max[0], floor_limit[0]), min(min_max[1], floor_limit[1]))
+
     output = {
         "neuroglancerPrecomputedMin": str(floor(min_max[0])),
         "neuroglancerPrecomputedMax": str(ceil(min_max[1])),

test/fixtures.py

@@ -18,7 +18,7 @@
 
 @pytest.fixture(
     scope="session",
-    params=[sitk.sitkUInt8, sitk.sitkInt16, sitk.sitkUInt16, sitk.sitkFloat32, "uint16_uniform"],
+    params=[sitk.sitkUInt8, sitk.sitkInt16, sitk.sitkUInt16, sitk.sitkFloat32, "uint16_uniform", "uint8_bimodal"],
 )
 def image_mrc(request, tmp_path_factory):
     if isinstance(request.param, str) and request.param == "uint16_uniform":
@@ -29,6 +29,16 @@ def image_mrc(request, tmp_path_factory):
         a = np.linspace(0, 2**16 - 1, num=2**16, dtype="uint16").reshape(16, 64, 64)
         img = sitk.GetImageFromArray(a)
         img.SetSpacing([1.23, 1.23, 4.96])
+
+    elif isinstance(request.param, str) and request.param == "uint8_bimodal":
+
+        print(f"Calling image_mrc with {request.param}")
+        fn = f"image_mrc_{request.param.replace(' ', '_')}.mrc"
+
+        a = np.zeros([16, 16, 16], np.uint8)
+        a[len(a) // 2 :] = 255
+        img = sitk.GetImageFromArray(a)
+        img.SetSpacing([12.3, 12.3, 56.7])
     else:
         pixel_type = request.param
         print(f"Calling image_mrc with {sitk.GetPixelIDValueAsString(pixel_type)}")

test/test_histogram.py

@@ -108,22 +108,27 @@ def test_histogram_mai_help(cli_args):
 
 
 @pytest.mark.parametrize(
-    "image_mrc,expected_min, expected_max, expected_floor, expected_limit",
+    "image_mrc,expected_min, expected_max, expected_floor, expected_limit, clamp",
     [
-        (sitk.sitkUInt8, 0, 0, 0, 0),
-        (sitk.sitkInt16, 0, 0, 0, 0),
-        (sitk.sitkUInt16, 0, 0, 0, 0),
-        ("uint16_uniform", 8191, 57344, 0, 65535),
+        (sitk.sitkUInt8, 0, 0, 0, 0, False),
+        (sitk.sitkInt16, 0, 0, 0, 0, True),
+        (sitk.sitkUInt16, 0, 0, 0, 0, False),
+        ("uint16_uniform", 8191, 57344, 0, 65535, True),
+        ("uint16_uniform", 8191, 57344, 0, 65535, False),
+        ("uint8_bimodal", 0, 255, 0, 255, True),
+        ("uint8_bimodal", -64, 319, 0, 255, False),
     ],
     indirect=["image_mrc"],
 )
-def test_build_histogram_main(image_mrc, expected_min, expected_max, expected_floor, expected_limit):
+def test_build_histogram_main(image_mrc, expected_min, expected_max, expected_floor, clamp, expected_limit):
     runner = CliRunner()
     output_filename = "out.json"
+    args = [image_mrc, "--mad", "1.5", "--output-json", output_filename]
+    if clamp:
+        args.append("--clamp")
+    print(args)
     with runner.isolated_filesystem():
-        result = runner.invoke(
-            pytools.ng.build_histogram.main, [image_mrc, "--mad", "1.5", "--output-json", output_filename]
-        )
+        result = runner.invoke(pytools.ng.build_histogram.main, args=args)
         assert not result.exception
         with open(output_filename) as fp:
             res = json.load(fp)