Merge pull request #808 from AFM-SPM/ns-rse/807-dpi

tests/test_utils.py

@@ -1,4 +1,4 @@
-"""Test utils."""
+"""Test the utils module."""
 
 from pathlib import Path
 
@@ -46,11 +46,14 @@ def test_update_config(caplog) -> None:
 @pytest.mark.parametrize(
     ("image_name", "core_set", "title", "zrange"),
     [
-        ("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
+        pytest.param("extracted_channel", False, "Raw Height", [0, 3], id="Non-binary image, not in core, with title"),
+        pytest.param("z_threshed", True, "Height Thresholded", [0, 3], id="Non-binary image, in core, with title"),
+        pytest.param(
+            "grain_mask", False, "", [None, None], id="Binary image, not in core, set no title"
+        ),  # binary image
+        pytest.param(
+            "grain_mask_image", False, "", [0, 3], id="Non-binary image, not in core, set no title"
+        ),  # non-binary image
     ],
 )
 def test_update_plotting_config(
@@ -68,6 +71,75 @@ def test_update_plotting_config(
     assert process_scan_config["plotting"]["plot_dict"][image_name]["zrange"] == zrange
 
 
+@pytest.mark.parametrize(
+    ("plotting_config", "target_config"),
+    [
+        pytest.param(
+            {
+                "run": True,
+                "savefig_dpi": None,
+                "pixel_interpolation": None,
+                "plot_dict": {
+                    "extracted_channel": {
+                        "filename": "00-raw_heightmap",
+                        "image_type": "non-binary",
+                        "savefig_dpi": 100,
+                    }
+                },
+            },
+            {
+                "run": True,
+                "savefig_dpi": None,
+                "pixel_interpolation": None,
+                "plot_dict": {
+                    "extracted_channel": {
+                        "filename": "00-raw_heightmap",
+                        "image_type": "non-binary",
+                        "savefig_dpi": 100,
+                        "pixel_interpolation": None,
+                    }
+                },
+            },
+            id="DPI None in main, extracted channel DPI should stay at 100",
+        ),
+        pytest.param(
+            {
+                "run": True,
+                "savefig_dpi": 600,
+                "pixel_interpolation": None,
+                "plot_dict": {
+                    "extracted_channel": {
+                        "filename": "00-raw_heightmap",
+                        "image_type": "non-binary",
+                        "savefig_dpi": 100,
+                    }
+                },
+            },
+            {
+                "run": True,
+                "savefig_dpi": 600,
+                "pixel_interpolation": None,
+                "plot_dict": {
+                    "extracted_channel": {
+                        "filename": "00-raw_heightmap",
+                        "image_type": "non-binary",
+                        "savefig_dpi": 600,
+                        "pixel_interpolation": None,
+                    }
+                },
+            },
+            id="DPI 600 in main, extracted channel DPI should update to 600",
+        ),
+    ],
+)
+def test_udpate_plotting_config_adding_required_options(plotting_config: dict, target_config: dict, caplog) -> None:
+    """Only updates plotting_dict parameters from parent plotting config if value is not None."""
+    update_plotting_config(plotting_config)
+    assert plotting_config == target_config
+    if plotting_config["savefig_dpi"] == 600:
+        assert "100 > 600" in caplog.text
+
+
 def test_get_thresholds_otsu(image_random: np.ndarray) -> None:
     """Test of get_thresholds() method otsu threshold."""
     thresholds = get_thresholds(image=image_random, threshold_method="otsu", **THRESHOLD_OPTIONS)

topostats/default_config.yaml

@@ -62,7 +62,7 @@ plotting:
   run: true # Options : true, false
   style: topostats.mplstyle # Options : topostats.mplstyle or path to a matplotlibrc params file
   savefig_format: null # Options : null, png, svg or pdf. tif is also available although no metadata will be saved. (defaults to png) See https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
-  savefig_dpi: null # Options : null (defaults to figure) see https://afm-spm.github.io/TopoStats/main/configuration.html#further-customisation and https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
+  savefig_dpi: null # Options : null (defaults to the value in topostats/plotting_dictionary.yaml), see https://afm-spm.github.io/TopoStats/main/configuration.html#further-customisation and https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
   pixel_interpolation: null # Options : https://matplotlib.org/stable/gallery/images_contours_and_fields/interpolation_methods.html
   image_set: core # Options : all, core
   zrange: [null, null] # low and high height range for core images (can take [null, null]). low <= high

topostats/io.py

@@ -1015,7 +1015,7 @@ def dict_to_hdf5(open_hdf5_file: h5py.File, group_path: str, dictionary: dict) -
     None
     """
     for key, item in dictionary.items():
-        LOGGER.info(f"Saving key: {key}")
+        LOGGER.debug(f"Saving key: {key}")
 
         if item is None:
             LOGGER.warning(f"Item '{key}' is None. Skipping.")

topostats/utils.py

@@ -6,6 +6,7 @@
 from argparse import Namespace
 from collections import defaultdict
 from pathlib import Path
+from pprint import pformat
 
 import numpy as np
 import numpy.typing as npt
@@ -105,8 +106,20 @@ def update_plotting_config(plotting_config: dict) -> dict:
     main_config = plotting_config.copy()
     for opt in ["plot_dict", "run"]:
         main_config.pop(opt)
+    LOGGER.debug(
+        f"Main plotting options that need updating/adding to plotting dict :\n{pformat(main_config, indent=4)}"
+    )
     for image, options in plotting_config["plot_dict"].items():
-        plotting_config["plot_dict"][image] = {**options, **main_config}
+        LOGGER.debug(f"Dictionary for image : {image}")
+        LOGGER.debug(f"{pformat(options, indent=4)}")
+        # First update options with values that exist in main_config
+        plotting_config["plot_dict"][image] = update_config(options, main_config)
+        LOGGER.debug(f"Updated values :\n{pformat(plotting_config['plot_dict'][image])}")
+        # Then combine the remaining key/values we need from main_config that don't already exist
+        for key_main, value_main in main_config.items():
+            if key_main not in plotting_config["plot_dict"][image]:
+                plotting_config["plot_dict"][image][key_main] = value_main
+        LOGGER.debug(f"After adding missing configuration options :\n{pformat(plotting_config['plot_dict'][image])}")
         # 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":