Sylvia whittle/596 zscale grains

tests/test_utils.py

@@ -43,7 +43,13 @@ def test_update_config(caplog) -> None:
 
 @pytest.mark.parametrize(
     "image_name, core_set, title, zrange",
-    [("extracted_channel", False, "Raw Height", KeyError()), ("z_threshed", True, "Height Thresholded", [0, 3])],
+    [
+        ("extracted_channel", False, "Raw Height", [0, 3]),
+        ("z_threshed", True, "Height Thresholded", [0, 3]),
+        ("grain_image", False, "", [0, 3]),  # non-binary image
+        ("grain_mask", False, "", [None, None]),  # binary image
+        ("grain_mask_image", False, "", [0, 3]),  # non-binary image
+    ],
 )
 def test_update_plotting_config(
     process_scan_config: dict, image_name: str, core_set: bool, title: str, zrange: tuple
@@ -52,12 +58,13 @@ def test_update_plotting_config(
     for each image in the plotting dictionary plot_dict."""
     process_scan_config["plotting"] = update_plotting_config(process_scan_config["plotting"])
     assert process_scan_config["plotting"]["plot_dict"][image_name]["core_set"] == core_set
-    assert process_scan_config["plotting"]["plot_dict"][image_name]["title"] == title
-    if image_name == "extracted_channel":
-        with pytest.raises(KeyError):
-            _ = process_scan_config["plotting"]["plot_dict"][image_name]["zrange"]
-    else:
-        assert process_scan_config["plotting"]["plot_dict"][image_name]["zrange"] == zrange
+    # Only check titles for images that have titles. grain_image, grain_mask, grain_mask_image don't
+    # have titles since they're created dynamically.
+    if title in ["extracted_channel", "z_threshed"]:
+        assert process_scan_config["plotting"]["plot_dict"][image_name]["title"] == title
+    # Ensure that both types (binary, non-binary) of image have the correct z-ranges
+    # ([None, None] for binary, user defined for non-binary)
+    assert process_scan_config["plotting"]["plot_dict"][image_name]["zrange"] == zrange
 
 
 def test_get_thresholds_otsu(image_random: np.ndarray) -> None:

topostats/plotting_dictionary.yaml

@@ -137,7 +137,7 @@ grain_image:
   image_type: "non-binary"
   core_set: false
 grain_mask:
-  image_type: "non-binary"
+  image_type: "binary"
   core_set: false
 grain_mask_image:
   image_type: "non-binary"

topostats/utils.py

@@ -102,8 +102,10 @@ def update_plotting_config(plotting_config: dict) -> dict:
         main_config.pop(opt)
     for image, options in plotting_config["plot_dict"].items():
         plotting_config["plot_dict"][image] = {**options, **main_config}
-        if image not in ["z_threshed", "mask_overlay"]:
-            plotting_config["plot_dict"][image].pop("zrange")
+        # Make it so that binary images do not have the user-defined z-scale
+        # applied, but non-binary images do.
+        if plotting_config["plot_dict"][image]["image_type"] == "binary":
+            plotting_config["plot_dict"][image]["zrange"] = [None, None]
 
     return plotting_config