adding paper figure files

Author: carsen-stringer

paper/cpsam/fig_utils.py

@@ -0,0 +1,53 @@
+"""
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
+"""
+import string
+import matplotlib
+import matplotlib.pyplot as plt
+import matplotlib.transforms as mtransforms
+import numpy as np
+from matplotlib import rcParams
+from matplotlib.colors import ListedColormap
+from cellpose import utils
+
+default_font = 12
+rcParams["font.family"] = "Arial"
+rcParams["savefig.dpi"] = 300
+rcParams["axes.spines.top"] = False
+rcParams["axes.spines.right"] = False
+rcParams["axes.titlelocation"] = "left"
+rcParams["axes.titleweight"] = "normal"
+rcParams["font.size"] = default_font
+
+ltr = string.ascii_lowercase
+fs_title = 16
+weight_title = "normal"
+
+def plot_label(ltr, il, ax, trans, fs_title=20):
+    ax.text(
+        0.0,
+        1.0,
+        ltr[il],
+        transform=ax.transAxes + trans,
+        va="bottom",
+        fontsize=fs_title,
+        fontweight="bold",
+    )
+    il += 1
+    return il
+
+
+def outlines_img(imgi, maski, color=[1, 0, 0], weight=2):
+    img = np.tile(np.clip(imgi.copy(), 0, 1)[:, :, np.newaxis], (1, 1, 3))
+    out = np.nonzero(utils.masks_to_outlines(maski[1:-1, 1:-1]))
+    img[out[0], out[1]] = np.array(color)
+    if weight > 1:
+        if weight == 2:
+            ix, iy = np.meshgrid(np.arange(0, 3), np.arange(0, 3))
+        else:
+            ix = np.array([-1, 1, 0, 0])
+            iy = np.array([0, 0, 1, 1])
+        ix, iy = ix.flatten(), iy.flatten()
+        for i in range(len(ix)):
+            img[out[0] + ix[i], out[1] + iy[i]] = np.array(color)
+    return img