allowing timing measurement

src/sc3D/sc3D.py

@@ -21,6 +21,7 @@
 from seaborn import scatterplot
 import json
 from pathlib import Path
+from time import time
 
 import anndata
 from sc3D.transformations import transformations as tr
@@ -537,7 +538,7 @@ def build_pairing(self, cs1, cs2, rebuild=False, refine=False, th_d=None):
         return pos_ref, pos_flo
 
     def register_cs(
-        self, cs1, cs2, refine=False, rigid=False, final=False, th_d=None
+        self, cs1, cs2, refine=False, rigid=False, final=False, th_d=None, timing=False
     ):
         """
         Registers the puck `cs2` onto the puck `cs1`.
@@ -560,8 +561,16 @@ def register_cs(
                 Usually used as a float.
 
         """
+        if timing:
+            start = time()
+            if not hasattr(self, "timing"):
+                self.timing = {}
+            current_cs_timing = self.timing.setdefault((cs1, cs2), {})
         if self.registered_pos is None:
             self.register_with_tissues()
+            if timing:
+                current_cs_timing["register_with_tissues"] = time() - start
+                start = time()
         if (self.final is None) and final:
             self.final = {
                 c: self.centered_pos[c]
@@ -570,9 +579,15 @@ def register_cs(
         pos_ref, pos_flo = self.build_pairing(
             cs1, cs2, rebuild=False, refine=refine, th_d=th_d
         )
+        if timing:
+            current_cs_timing["build_pairing"] = time(time() - start)
+            start = time()
         M = self.register(
             np.array(pos_ref), np.array(pos_flo), apply=False, rigid=rigid
         )
+        if timing:
+            current_cs_timing["register"] = time(time() - start)
+            start = time()
         cells_cs2 = self.cells_from_cover_slip[cs2]
         if refine:
             positions_cs2 = np.array([self.pos_reg_aff[c] for c in cells_cs2])
@@ -588,6 +603,9 @@ def register_cs(
         self.pos_reg_aff.update(zip(cells_cs2, new_pos))
         if final:
             self.final.update(zip(cells_cs2, new_pos))
+        if timing:
+            current_cs_timing["apply"] = time(time() - start)
+            start = time()
         return M
 
     @staticmethod
@@ -1052,8 +1070,6 @@ def registration_3d(
         if self.z_pos is None or set(self.z_pos) != set(self.all_cells):
             self.set_zpos()
         if timing:
-            from time import time
-
             start = current_time = time()
             times = []
         self.trsfs = {}