tweaks

slice-register.py

@@ -132,6 +132,9 @@ from tirl.transformations.linear.scale import TxScale, TxIsoScale
 from tirl.transformations.linear.translation import TxTranslation
 from tirl.transformations.nonlinear.displacement import TxDisplacementField
 
+import matplotlib.pyplot as plt
+import os.path as op
+
 # TIRL IMPORTS
 # DEFINITIONS
 
@@ -180,6 +183,8 @@ def run(cnf=None, **options):
         p.moving.export = \
             os.path.join(p.general.outputdir, f"moving.{ext}")
     moving = tirl.scripts.mnd.inout.load_image(scope=globals(), **p.moving)
+
+
     if p.fixed.export is True:
         ext = ts.EXTENSIONS["TImage"]
         p.fixed.export = os.path.join(p.general.outputdir, f"fixed.{ext}")
@@ -208,6 +213,15 @@ def run(cnf=None, **options):
             fixed, *p.preprocessing.fixed, scope=globals(), other=moving, cnf=p)
         fixed.centralise(weighted=True)
 
+
+    # if p.moving.snapshot is True:
+    #     print(moving.mask.shape)
+    #     plt.imsave(op.join(p.general.outputdir, 'moving_mask.png'), moving.mask)
+    #
+    # if p.fixed.snapshot is True:
+    #     print(fixed.mask.shape)
+    #     plt.imsave(op.join(p.general.outputdir, 'fixed_mask.png'), fixed.mask)
+
     # Run the registration routine
     try:
         register(fixed, moving, p)
@@ -681,7 +695,7 @@ def rgb2hsv(x):
 
 def match_fixed_resolution(img, **kwargs):
     """
-    Resamples histology image to match the resolution of another 2D image.
+    Resamples histology image to match the resolution of the fixed image.
 
     """
     p = AttrMap(kwargs.get("cnf"))
@@ -892,13 +906,13 @@ def create_cli(parser):
     """
     parser.add_argument("--moving", metavar="image",
                         help="Moving slide", default=None, type=str,
-                        required=False)
+                        required=True)
     parser.add_argument("--fixed", metavar="image",
                         help="Fixed slide", default=None, type=str,
-                        required=False)
+                        required=True)
     parser.add_argument("--out", metavar="dir",
                         help="Output directory", default=None, type=str,
-                        required=False)
+                        required=True)
     parser.add_argument("--config", metavar="cnf_file.json",
                         help="configuration file", default='default.json', type=str,
                         required=False)
@@ -913,7 +927,7 @@ def main(*args):
     """ Main program code. """
 
     parser = argparse.ArgumentParser(
-        prog="slide_to_slide",
+        prog="slice-register.py",
         description="Registers a histology slide to "
                     "another histology slide.")
     parser = create_cli(parser)