From ebafe3cf15eed523726c2915f0b50ff069caf780 Mon Sep 17 00:00:00 2001
From: Jean <mdu12@sheffield.ac.uk>
Date: Mon, 14 Oct 2024 17:08:53 +0200
Subject: [PATCH] Minor changes for thesis writing needs

---
 topostats/default_config.yaml |  2 +-
 topostats/theme.py            | 14 ++++++++++++++
 topostats/validation.py       |  1 +
 3 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/topostats/default_config.yaml b/topostats/default_config.yaml
index d333098306..4adbe2d4cf 100644
--- a/topostats/default_config.yaml
+++ b/topostats/default_config.yaml
@@ -7,7 +7,7 @@ loading:
   channel: Height # Channel to pull data from in the data files.
 filter:
   run: true # Options : true, false
-  row_alignment_quantile: 0.5 # below values may improve flattening of larger features
+  row_alignment_quantile: 0.5 # Lower values may improve flattening of larger features
   threshold_method: std_dev # Options : otsu, std_dev, absolute
   otsu_threshold_multiplier: 1.0
   threshold_std_dev:
diff --git a/topostats/theme.py b/topostats/theme.py
index 0436c31004..ded4a393cc 100644
--- a/topostats/theme.py
+++ b/topostats/theme.py
@@ -34,6 +34,8 @@ def set(self, name: str):
             self.cmap = self.gwyddion()
         elif name.lower() == "blu":
             self.cmap = self.blu()
+        elif name.lower() == "white":
+            self.cmap = self.white()
         else:
             # Get one of the matplotlib colormaps
             self.cmap = mpl.colormaps[name]
@@ -120,3 +122,15 @@ def gwyddion():
     def blu():
         "RGBA colour map of just the colour blue."
         return ListedColormap([[32 / 256, 226 / 256, 205 / 256]], "blu", N=256)
+
+    @staticmethod
+    def white():
+        "RGBA colour map of just the colour white."
+        N = 256  # Number of values
+        vals = np.ones((N, 4))  # Initialise the array to be full of 1.0
+        vals[0] = [0.0, 0.0, 0.0, 1]
+        for i in range(1, 255):
+            vals[i] = [32 / 256, 226 / 256, 205 / 256, 1.0]
+
+        colormap = LinearSegmentedColormap.from_list("gwyddion", vals, N=256)
+        return colormap
diff --git a/topostats/validation.py b/topostats/validation.py
index 5ff98e3df9..86134c8d41 100644
--- a/topostats/validation.py
+++ b/topostats/validation.py
@@ -272,6 +272,7 @@ def validate_config(config: dict, schema: Schema, config_type: str) -> None:
                 "afmhot",
                 "nanoscope",
                 "gwyddion",
+                "white",
                 error="Invalid value in config for 'plotting.cmap', valid values are 'afmhot', 'nanoscope' or 'gwyddion'",
             ),
             "mask_cmap": str,