Cross-checked and polished remainders of fig_invariance_thresh_lp_species.pdf.

Added misc_functions.py for anything not plot-related.

python/misc_functions.py

@@ -0,0 +1,32 @@
+import numpy as np
+
+def shorten_species(name):
+    genus, species = name.split('_')
+    return genus[0] + '. ' + species
+
+def get_saturation(sigmoid, low=0.05, high=0.95, first=True, last=True,
+                   condense=None):
+    if condense == 'norm' and sigmoid.ndim == 2:
+        sigmoid = np.linalg.norm(sigmoid, axis=1)
+
+    min_value = sigmoid[0] if first else sigmoid.min(axis=0)
+    max_value = sigmoid[-1] if last else sigmoid.max(axis=0)
+    
+    span = max_value - min_value
+    low_value = min_value + low * span
+    high_value = min_value + high * span
+
+    low_mask = sigmoid >= low_value
+    high_mask = sigmoid >= high_value
+    if sigmoid.ndim == 1:
+        low_ind = np.nonzero(low_mask)[0][0]
+        high_ind = np.nonzero(high_mask)[0][0]
+    elif condense == 'all':
+        low_ind = np.nonzero(low_mask.all(axis=1))[0][0]
+        high_ind = np.nonzero(high_mask.all(axis=1))[0][0]
+    else:
+        low_ind, high_ind = [], []
+        for i in range(sigmoid.shape[1]):
+            low_ind.append(np.nonzero(low_mask[:, i])[0][0])
+            high_ind.append(np.nonzero(high_mask[:, i])[0][0])
+    return low_ind, high_ind