Merge pull request #777 from AFM-SPM/ns-rse/776-config-jigging

Restore cmap to config; simplify config of  cmap/dpi/image format

tests/test_plotting.py

@@ -1,4 +1,5 @@
 """Tests for the plotting module."""
+
 import importlib.resources as pkg_resources
 from pathlib import Path
 
@@ -58,7 +59,7 @@ def test_toposum_class(toposum_object_multiple_directories: TopoSum) -> None:
     assert isinstance(toposum_object_multiple_directories.image_id, str)
     assert isinstance(toposum_object_multiple_directories.hist, bool)
     assert isinstance(toposum_object_multiple_directories.kde, bool)
-    assert isinstance(toposum_object_multiple_directories.file_ext, str)
+    assert isinstance(toposum_object_multiple_directories.savefig_format, str)
     assert isinstance(toposum_object_multiple_directories.output_dir, Path)
     assert isinstance(toposum_object_multiple_directories.var_to_label, dict)
 

tests/test_plottingfuncs.py

@@ -1,4 +1,5 @@
 """Tests of plotting functions."""
+
 from pathlib import Path
 
 import matplotlib as mpl
@@ -282,7 +283,7 @@ def test_mask_cmap(plotting_config: dict, tmp_path: Path) -> None:
 @pytest.mark.mpl_image_compare(baseline_dir="resources/img/", savefig_kwargs={"dpi": DPI})
 def test_high_dpi(minicircle_grain_gaussian_filter: Grains, plotting_config: dict, tmp_path: Path) -> None:
     """Test plotting with high DPI."""
-    plotting_config["dpi"] = DPI
+    plotting_config["savefig_dpi"] = DPI
     fig, _ = Images(
         data=minicircle_grain_gaussian_filter.images["gaussian_filtered"],
         output_dir=tmp_path,

tests/test_processing.py

@@ -1,4 +1,5 @@
 """Test end-to-end running of topostats."""
+
 from pathlib import Path
 
 import filetype
@@ -108,7 +109,7 @@ def test_save_cropped_grains(
     """Tests if cropped grains are saved only when image set is 'all' rather than 'core'."""
     process_scan_config["plotting"]["image_set"] = image_set
     process_scan_config["plotting"] = update_plotting_config(process_scan_config["plotting"])
-    process_scan_config["plotting"]["dpi"] = 50
+    process_scan_config["plotting"]["savefig_dpi"] = 50
 
     img_dic = load_scan_data.img_dict
     _, _, _ = process_scan(
@@ -152,7 +153,7 @@ def test_save_cropped_grains(
 def test_save_format(process_scan_config: dict, load_scan_data: LoadScans, tmp_path: Path, extension: str):
     """Tests if save format applied to cropped images."""
     process_scan_config["plotting"]["image_set"] = "all"
-    process_scan_config["plotting"]["save_format"] = extension
+    process_scan_config["plotting"]["savefig_format"] = extension
     process_scan_config["plotting"] = update_plotting_config(process_scan_config["plotting"])
 
     img_dic = load_scan_data.img_dict

topostats/default_config.yaml

@@ -61,13 +61,15 @@ dnatracing:
 plotting:
   run: true # Options : true, false
   style: topostats.mplstyle # Options : topostats.mplstyle or path to a matplotlibrc params file
-  save_format: png # Options : see https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html
+  savefig_format: null # Options : null (defaults to png) or 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
   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
   colorbar: true # Options : true, false
   axes: true # Options : true, false (due to off being a bool when parsed)
   num_ticks: [null, null] # Number of ticks to have along the x and y axes. Options : null (auto) or integer > 1
+  cmap: null # Colormap/colourmap to use (default is 'nanoscope' which is used if null, other options are 'afmhot', 'viridis' etc.)
   mask_cmap: blu # Options : blu, jet_r and any in matplotlib
   histogram_log_axis: false # Options : true, false
 summary_stats:

topostats/entry_point.py

@@ -2,6 +2,7 @@
 
 Parses command-line arguments and passes input on to the relevant functions / modules.
 """
+
 import argparse as arg
 import sys
 
@@ -10,6 +11,8 @@
 from topostats.plotting import run_toposum
 from topostats.run_topostats import run_topostats
 
+# pylint: disable=too-many-statements
+
 
 def create_parser() -> arg.ArgumentParser:
     """Create a parser for reading options."""
@@ -29,8 +32,8 @@ def create_parser() -> arg.ArgumentParser:
     # Create a sub-parsers for different stages of processing and tasks
     process_parser = subparsers.add_parser(
         "process",
-        description="Process AFM images. Additional arguments over-ride those in the configuration file.",
-        help="Process AFM images. Additional arguments over-ride those in the configuration file.",
+        description="Process AFM images. Additional arguments over-ride defaults or those in the configuration file.",
+        help="Process AFM images. Additional arguments over-ride defaults or those in the configuration file.",
     )
     process_parser.add_argument(
         "-c",
@@ -106,6 +109,27 @@ def create_parser() -> arg.ArgumentParser:
         required=False,
         help="Whether to save plots.",
     )
+    process_parser.add_argument(
+        "--savefig-format",
+        dest="savefig_format",
+        type=str,
+        required=False,
+        help="Format for saving figures to, options are 'png', 'svg', or other valid Matplotlib supported formats.",
+    )
+    process_parser.add_argument(
+        "--savefig-dpi",
+        dest="savefig_dpi",
+        type=int,
+        required=False,
+        help="Dots Per Inch for plots, should be integer for dots per inch.",
+    )
+    process_parser.add_argument(
+        "--cmap",
+        dest="cmap",
+        type=str,
+        required=False,
+        help="Colormap to use, options include 'nanoscope', 'afmhot' and any valid Matplotlib colormap.",
+    )
     process_parser.add_argument("-m", "--mask", dest="mask", type=bool, required=False, help="Mask the image.")
     process_parser.add_argument(
         "-w",
@@ -151,6 +175,13 @@ def create_parser() -> arg.ArgumentParser:
         required=False,
         help="Filename to write a sample YAML label file to (should end in '.yaml').",
     )
+    toposum_parser.add_argument(
+        "--savefig-format",
+        dest="savefig_format",
+        type=str,
+        required=False,
+        help="Format for saving figures to, options are 'png', 'svg', or other valid Matplotlib supported formats.",
+    )
     toposum_parser.set_defaults(func=run_toposum)
 
     load_parser = subparsers.add_parser(

topostats/plotting.py

@@ -1,4 +1,5 @@
 """Plotting and summary of TopoStats output statistics."""
+
 from collections import defaultdict
 
 import importlib.resources as pkg_resources
@@ -43,7 +44,7 @@ def __init__(
         figsize: tuple = (16, 9),
         alpha: float = 0.5,
         palette: str = "deep",
-        file_ext: str = "png",
+        savefig_format: str = "png",
         output_dir: Union[str, Path] = ".",
         var_to_label: dict = None,
         hue: str = "basename",
@@ -105,7 +106,7 @@ def __init__(
         self.figsize = figsize
         self.alpha = alpha
         self.palette = palette
-        self.file_ext = file_ext
+        self.savefig_format = savefig_format
         self.output_dir = Path(output_dir)
         self.output_dir.mkdir(parents=True, exist_ok=True)
         self.var_to_label = var_to_label
@@ -264,9 +265,10 @@ def save_plot(self, outfile: Path) -> None:
         outfile: str
             Output file name to save figure to.
         """
-        plt.savefig(self.output_dir / f"{outfile}.{self.file_ext}")
+        plt.savefig(self.output_dir / f"{outfile}.{self.savefig_format}")
         LOGGER.info(
-            f"[plotting] Plotted {self.stat_to_sum} to : " f"{str(self.output_dir / f'{outfile}.{self.file_ext}')}"
+            f"[plotting] Plotted {self.stat_to_sum} to : "
+            f"{str(self.output_dir / f'{outfile}.{self.savefig_format}')}"
         )
 
     def _set_label(self, var: str):