Merge pull request #28 from niaid/JSONoutputstr

JSON output as string

pytools/ng/build_histogram.py

@@ -18,6 +18,7 @@
 import SimpleITK as sitk
 from pytools.utils import MutuallyExclusiveOption
 from pytools import __version__
+from math import floor, ceil
 
 
 def weighted_quantile(values, quantiles, sample_weight=None, values_sorted=False, old_style=False):
@@ -66,7 +67,7 @@ def stream_build_histogram(filename: str, histogram_bin_edges, extract_axis=1, d
     Read image slice by slice, and build a histogram. The image file must be readable by SimpleITK.
     The SimpleITK is expected to support streaming the file format.
 
-    The np.histogram function is run on each image slice with the provided hitogram_bin_edges, and
+    The np.histogram function is run on each image slice with the provided histogram_bin_edges, and
     accumulated for the results.
 
     :param  filename: The path to the image file to read. MRC file type is recommend.
@@ -166,6 +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),
@@ -174,12 +180,12 @@ 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 am estimated minimum and maximum range to be used for visualization of the
-    data set.
+    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.
 
-    The optional OUTPUT_JSON filename will be created with the following data elements with a double numeric value:
+    The optional OUTPUT_JSON filename will be created with the following data elements with integer values as strings:
         "neuroglancerPrecomputedMin"
         "neuroglancerPrecomputedMax"
         "neuroglancerPrecomputedFloor"
@@ -246,12 +252,16 @@ 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": float(min_max[0]),
-        "neuroglancerPrecomputedMax": float(min_max[1]),
-        "neuroglancerPrecomputedFloor": float(floor_limit[0]),
-        "neuroglancerPrecomputedLimit": float(floor_limit[1]),
+        "neuroglancerPrecomputedMin": str(floor(min_max[0])),
+        "neuroglancerPrecomputedMax": str(ceil(min_max[1])),
+        "neuroglancerPrecomputedFloor": str(floor(floor_limit[0])),
+        "neuroglancerPrecomputedLimit": str(ceil(floor_limit[1])),
     }
+
     logger.debug(f"output: {output}")
     if output_json:
         import json

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", 8191.5, 57343.5, 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)
@@ -132,7 +137,11 @@ def test_build_histogram_main(image_mrc, expected_min, expected_max, expected_fl
     assert "neuroglancerPrecomputedMax" in res
     assert "neuroglancerPrecomputedFloor" in res
     assert "neuroglancerPrecomputedLimit" in res
-    assert res["neuroglancerPrecomputedMin"] == expected_min
-    assert res["neuroglancerPrecomputedMax"] == expected_max
-    assert res["neuroglancerPrecomputedFloor"] == expected_floor
-    assert res["neuroglancerPrecomputedLimit"] == expected_limit
+    assert float(res["neuroglancerPrecomputedMin"]) == expected_min
+    assert float(res["neuroglancerPrecomputedMax"]) == expected_max
+    assert float(res["neuroglancerPrecomputedFloor"]) == expected_floor
+    assert float(res["neuroglancerPrecomputedLimit"]) == expected_limit
+    assert type(res["neuroglancerPrecomputedMin"]) == str
+    assert type(res["neuroglancerPrecomputedMax"]) == str
+    assert type(res["neuroglancerPrecomputedFloor"]) == str
+    assert type(res["neuroglancerPrecomputedLimit"]) == str

test/test_mrc2ngpc.py

@@ -51,3 +51,7 @@ def test_mrc2ngpc(image_mrc, expected_pixel_type):
             assert "neuroglancerPrecomputedMin" in mm
             assert "neuroglancerPrecomputedFloor" in mm
             assert "neuroglancerPrecomputedLimit" in mm
+            assert type(mm["neuroglancerPrecomputedMin"]) == str
+            assert type(mm["neuroglancerPrecomputedMax"]) == str
+            assert type(mm["neuroglancerPrecomputedFloor"]) == str
+            assert type(mm["neuroglancerPrecomputedLimit"]) == str