MotionCorr drift plot now shows individual frame shifts

src/relion/zocalo/motioncorr.py

@@ -96,7 +96,6 @@ class MotionCorr(CommonService):
     # Values to extract for ISPyB
     x_shift_list = []
     y_shift_list = []
-    each_total_motion = []
 
     def initializing(self):
         """Subscribe to a queue. Received messages must be acknowledged."""
@@ -122,9 +121,6 @@ def parse_mc_output(self, mc_stdout: str):
                 line_split = line.split()
                 self.x_shift_list.append(float(line_split[-2]))
                 self.y_shift_list.append(float(line_split[-1]))
-                self.each_total_motion.append(
-                    hypot(float(line_split[-2]), float(line_split[-1]))
-                )
 
             # Alternative frame reading for MotionCorr 1.6.3
             if not line:
@@ -133,9 +129,6 @@ def parse_mc_output(self, mc_stdout: str):
                 line_split = line.split()
                 self.x_shift_list.append(float(line_split[1]))
                 self.y_shift_list.append(float(line_split[2]))
-                self.each_total_motion.append(
-                    hypot(float(line_split[1]), float(line_split[2]))
-                )
             if "x Shift" in line:
                 frames_line = True
 
@@ -306,9 +299,7 @@ def dummy(self, *args, **kwargs):
         average_motion_per_frame = total_motion / len(self.x_shift_list)
 
         # Extract results for ispyb
-        drift_plot_x = [range(0, len(self.x_shift_list))]
-        drift_plot_y = self.each_total_motion
-        fig = px.scatter(x=drift_plot_x, y=drift_plot_y)
+        fig = px.scatter(x=self.x_shift_list, y=self.y_shift_list)
         drift_plot_name = str(Path(mc_params.movie).stem) + "_drift_plot.json"
         plot_path = Path(mc_params.mrc_out).parent / drift_plot_name
         snapshot_path = Path(mc_params.mrc_out).with_suffix(".jpeg")
@@ -541,4 +532,3 @@ def dummy(self, *args, **kwargs):
         rw.transport.ack(header)
         self.x_shift_list = []
         self.y_shift_list = []
-        self.each_total_motion = []

src/relion/zocalo/motioncorr_wilson.py

@@ -6,7 +6,6 @@
 import subprocess
 import time
 from collections import ChainMap
-from math import hypot
 from pathlib import Path
 
 import yaml
@@ -83,9 +82,6 @@ def parse_mc_output(self, mc_output_file):
                     line_split = line.split()
                     self.x_shift_list.append(float(line_split[-2]))
                     self.y_shift_list.append(float(line_split[-1]))
-                    self.each_total_motion.append(
-                        hypot(float(line_split[-2]), float(line_split[-1]))
-                    )
 
                 # Alternative frame reading for MotionCorr 1.6.3
                 if not line:
@@ -94,9 +90,6 @@ def parse_mc_output(self, mc_output_file):
                     line_split = line.split()
                     self.x_shift_list.append(float(line_split[1]))
                     self.y_shift_list.append(float(line_split[2]))
-                    self.each_total_motion.append(
-                        hypot(float(line_split[1]), float(line_split[2]))
-                    )
                 if "x Shift" in line:
                     frames_line = True
 
@@ -238,7 +231,7 @@ def motioncor2(self, command: list, mrc_out: Path):
             stderr = f"Reading MotionCor output file {mc_output_file} failed"
             slurm_job_state = "FAILED"
 
-        if self.x_shift_list and self.y_shift_list and self.each_total_motion:
+        if self.x_shift_list and self.y_shift_list:
             Path(mc_output_file).unlink()
             Path(mc_error_file).unlink()
             Path(submission_file).unlink()

tests/zocalo/test_motioncorr_service.py

@@ -485,4 +485,3 @@ def test_parse_motioncorr_output(mock_environment, offline_transport):
     )
     assert service.x_shift_list == [-3.0, 3.0]
     assert service.y_shift_list == [4.0, -4.0]
-    assert service.each_total_motion == [5.0, 5.0]