added left or right justification

slider/chart_reg.py

@@ -64,7 +64,7 @@ def estimate_field(img):
 
 
 
-def register_chart_to_slide(chart, slide, slide_res, outdir, boundary_key=None, config=None, do_plots=None):
+def register_chart_to_slide(chart, slide, slide_res, outdir, boundary_key=None, config=None, do_plots=None, justify=None):
 
     if config is None:
         config = util.get_resource("chart.yaml")
@@ -113,7 +113,7 @@ def register_chart_to_slide(chart, slide, slide_res, outdir, boundary_key=None,
 
     # initial alignment based on boundng boxes
 
-    init_xfm, img_props, coord_props = init_scale(img, slide_res, edge_crds_cat)
+    init_xfm, img_props, coord_props = init_scale(img, slide_res, edge_crds_cat, justify=justify)
 
     # print(init_xfm)
     tr_x, tr_y = init_xfm.translation
@@ -325,8 +325,8 @@ def refine_edge_coord(img, img_res, edge_coords, xfm_init):
     line_x = np.round(line_x / img_res).astype(int)
     line_y = np.round(line_y / img_res).astype(int)
 
-    
-    line_int = brainmask[line_y, line_x]
+    y, x = brainmask.shape
+    line_int = brainmask[np.clip(line_y, 0, y-1), np.clip(line_x, 0, x-1)]
 
     # exlude constant rows
     constant_idx = np.all(line_int == line_int[:, 0][:, np.newaxis], axis=1)
@@ -395,7 +395,7 @@ def point_props(pnts):
 
 
 
-def init_scale(img, img_resolution, crd, tol=0.05):
+def init_scale(img, img_resolution, crd, tol=0.05, justify=None):
 
     img_p = image_props(img, img_resolution)
     crd_p = point_props(crd)
@@ -403,29 +403,29 @@ def init_scale(img, img_resolution, crd, tol=0.05):
     # print(img_p)
     # print(crd_p)
 
-    # justify='right'
-
-    # if justify=='right':
+    if justify=='right':
 
-    #     bbox = img_p['bbox']
-    #     h, w = img_p['shape']
+        print(f'justify chart bbox to {justify} in image bbox')
 
-    #     scale_factor = crd_p['aspect_ratio'] / img_p['aspect_ratio']
+        bbox = img_p['bbox']
+        h, w = img_p['shape']
 
-    #     new_w = w * scale_factor
-    #     bbox[1] += (w - new_w)
-    #     centroid = (
-    #         (bbox[0] + bbox[2]) / 2,
-    #         (bbox[1] + bbox[3]) / 2,
-    #     )
+        scale_factor = crd_p['aspect_ratio'] / img_p['aspect_ratio']
 
-    #     img_p = {
-    #         "bbox": bbox,
-    #         "bbox_centroid": centroid,
-    #         "shape": (bbox[2] - bbox[0], bbox[3] - bbox[1]),
-    #         "aspect_ratio": (bbox[3] - bbox[1]) / (bbox[2] - bbox[0]),
+        new_w = w * scale_factor
+        bbox[1] += (w - new_w)
+        centroid = (
+            (bbox[0] + bbox[2]) / 2,
+            (bbox[1] + bbox[3]) / 2,
+        )
 
-    #     }
+        img_p = {
+            "bbox": bbox,
+            "bbox_centroid": centroid,
+            "shape": (bbox[2] - bbox[0], bbox[3] - bbox[1]),
+            "aspect_ratio": (bbox[3] - bbox[1]) / (bbox[2] - bbox[0]),
+            "mask": img_p['mask'],
+        }
 
     # print(img_p)
     # print(crd_p)