changed affine to rigid

slider/chart_reg.py

@@ -32,16 +32,20 @@ import numpy as np
 import matplotlib.pyplot as plt
 
 
-def register_chart_to_slide(chart, slide, slide_res, out, config=None):
+def register_chart_to_slide(chart, slide, slide_res, out, boundary_key=None, config=None):
 
     if config is None:
         config = util.get_resource("chart.yaml")
 
     with open(config, "r") as f:
-        config = yaml.load(f)
+        config = yaml.load(f, Loader=yaml.FullLoader)
 
     rlevel = config["slide"]["resolution_level"]
-    boundary_key = config["chart"]["boundary_key"]
+
+    if boundary_key is None:
+        boundary_key = config["chart"]["boundary_key"]
+
+    print(boundary_key)
 
     # set global variables required for summary plots
     plots = config["general"]["plots"]
@@ -74,9 +78,9 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
     edge_crds = contour[boundary_idx[0]][1][:, :2] * [1, -1]
     init = _init_scale(img, slide_res, edge_crds, verbose=True)
     print(init)
-    print(
-        f"Rotation: {init.rotation}, Translation: {init.translation}, Scale: {init.scale}, Shear: {init.shear}"
-    )
+    # print(
+    #     f"Rotation: {init.rotation}, Translation: {init.translation}, Scale: {init.scale}, Shear: {init.shear}"
+    # )
 
     # calculate normal line to boundary points
     xfm_edge_coords = _apply_xfm(init, edge_crds)
@@ -88,12 +92,12 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
     )
 
     # estimate opimised affine transform
-    opt = transform.AffineTransform()
+    opt = transform.SimilarityTransform()
     opt.estimate(edge_crds, refined_edge_coords)
     print(opt)
-    print(
-        f"Rotation:\t{opt.rotation}\nTranslation:\t{opt.translation}\nScale:\t\t{list(opt.scale)}\nShear:\t\t{opt.shear}"
-    )
+    # print(
+    #     f"Rotation:\t{opt.rotation}\nTranslation:\t{opt.translation}\nScale:\t\t{list(opt.scale)}\nShear:\t\t{opt.shear}"
+    # )
 
     # save opt transform
     np.savetxt(f"{out}/chart-to-image.xfm", opt.params)
@@ -140,9 +144,9 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
         json.dump(contour_xfm, fp, indent=4)
 
     if cells.size > 0:
-        cells_xfm = _apply_xfm(cells[:, :2] * [1, -1])
+        cells_xfm = _apply_xfm(opt, cells[:, :2] * [1, -1])
         with open(f"{out}/cells.json", "w") as fp:
-            json.dump(cells_xfm, fp, indent=4)
+            json.dump(cells_xfm.tolist(), fp, indent=4)
 
 
 def _refine_edge_coord(img, img_res, edge_coords, normals):
@@ -360,7 +364,7 @@ def _init_scale(img, img_resolution, crd, verbose=False):
     src = np.array(crd_p["bbox"])[idx]
     dest = np.array(img_p["bbox"])[idx]
 
-    a = transform.AffineTransform()
+    a = transform.SimilarityTransform()
     a.estimate(src, dest)
 
     return a