Update image feature matching plotting

palom/cli/align_he.py

@@ -57,6 +57,15 @@ def align_he(
         test_intensity_invert=True,
         auto_mask=auto_mask
     )
+    fig, ax = plt.gcf(), plt.gca()
+    fig.suptitle(f"{p2.name} (coarse alignment)", fontsize=8)
+    ax.set_title(f"{p1.name} - {p2.name}", fontsize=6)
+    im_h, im_w = ax.images[0].get_array().shape
+    set_subplot_size(im_w/288, im_h/288, ax=ax)
+    ax.set_anchor('N')
+    # use 0.5 inch on the top for figure title
+    fig.subplots_adjust(top=1 - .5 / fig.get_size_inches()[1])
+    save_all_figs(out_dir=out_dir / 'qc', format='jpg', dpi=144)
 
     if viz_coarse_napari:
         _ = viz_coarse(r1, r2, LEVEL, LEVEL, channel1, channel2, aligner.affine_matrix)
@@ -195,6 +204,18 @@ def save_all_figs(dpi=300, format='pdf', out_dir=None, prefix=None):
         plt.close(f)
 
 
+def set_subplot_size(w, h, ax=None):
+    """ w, h: width, height in inches """
+    if not ax: ax=plt.gca()
+    l = ax.figure.subplotpars.left
+    r = ax.figure.subplotpars.right
+    t = ax.figure.subplotpars.top
+    b = ax.figure.subplotpars.bottom
+    figw = float(w)/(r-l)
+    figh = float(h)/(t-b)
+    ax.figure.set_size_inches(figw, figh)
+
+
 if __name__ == '__main__':
     import fire
     import sys

palom/register.py

@@ -10,6 +10,7 @@
 import scipy.fft
 import skimage.feature
 import skimage.registration
+import skimage.exposure
 
 from . import img_util, register_util
 
@@ -229,14 +230,21 @@ def ensambled_match(
         maxIters=5000
     )
     if plot_match_result == True:
-        plt.figure()
-        plt.gray()
+        _, ax = plt.subplots()
         skimage.feature.plot_matches(
-            plt.gca(), img_left, img_right,
+            ax,
+            np.log(skimage.exposure.rescale_intensity(img_left, out_range=(1, 4095))),
+            np.log(skimage.exposure.rescale_intensity(img_right, out_range=(1, 4095))),
             np.fliplr(all_src), np.fliplr(all_dst),
             np.arange(len(all_src)).repeat(2).reshape(-1, 2)[mask.flatten()>0],
+            keypoints_color=np.divide([255, 215, 0, 50], 255),
+            matches_color='deepskyblue',
             only_matches=False
         )
+        for line in ax.get_lines():
+            line.set_alpha(0.5)
+            line.set_linewidth(.5)
+
     return (t_matrix, mask) if return_match_mask else t_matrix
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "palom"
-version = "2023.8.2"
+version = "2023.9.1"
 description = "Piecewise alignment for layers of mosaics"
 authors = ["Yu-An Chen <[email protected]>"]
 readme = "README.md"