Vmxm spotfinding (#343)

Include custom spot finding parameters for VMXm's dials autoprocessing, which will generate spots.phil in the xia2-dials working directory.

Author: amyjaynethompson

src/dlstbx/mimas/core.py

@@ -44,6 +44,19 @@
     mimas.MimasISPyBParameter(key="ice_rings.filter", value="true"),
 )
 
+XIA2_DIALS_VMXM_SPOTFINDING_PARAMS: Tuple[mimas.MimasISPyBParameter, ...] = (
+    mimas.MimasISPyBParameter(key="spotfinder.filter.max_separation", value="8"),
+    mimas.MimasISPyBParameter(
+        key="spotfinder.threshold.dispersion.kernel_size", value="6,6"
+    ),
+    mimas.MimasISPyBParameter(
+        key="spotfinder.threshold.dispersion.sigma_background", value="3"
+    ),
+    mimas.MimasISPyBParameter(
+        key="spotfinder.threshold.dispersion.sigma_strong", value="1"
+    ),
+)
+
 
 def xia2_dials_absorption_params(
     scenario: mimas.MimasScenario,
@@ -298,6 +311,8 @@ def handle_rotation_end(
         xia2_dials_beamline_extra_params = (
             *XIA2_DIALS_COPPER_RINGS_PARAMS,
             mimas.MimasISPyBParameter(key="failover", value="true"),
+            mimas.MimasISPyBParameter(key="remove_blanks", value="true"),
+            *XIA2_DIALS_VMXM_SPOTFINDING_PARAMS,
         )
 
     triggervars_pref: Tuple[mimas.MimasISPyBTriggerVariable, ...] = ()

src/dlstbx/wrapper/xia2.py

@@ -29,6 +29,7 @@ def construct_commandline(
         Takes job parameter dictionary, returns array."""
 
         command = ["xia2"]
+        spotfinding_params = []
 
         for param, values in params["xia2"].items():
             if param == "images":
@@ -56,9 +57,14 @@ def construct_commandline(
                 "unit_cell": "xia2.settings.unit_cell",
             }
             for param, value in params["ispyb_parameters"].items():
-                command.append(translation.get(param, param) + "=" + value)
+                if param.startswith("spotfinder"):
+                    spotfinding_params.append(f"{param}={value}\n")
+                    if "find_spots.phil_file=spots.phil" not in command:
+                        command.append("find_spots.phil_file=spots.phil")
+                else:
+                    command.append(translation.get(param, param) + "=" + value)
 
-        return command
+        return command, spotfinding_params
 
     def send_results_to_ispyb(
         self,
@@ -170,7 +176,7 @@ def run_xia2(self, working_directory: Path, params: dict):
                 )
                 return False
 
-        command = self.construct_commandline(
+        command, spotfinding_params = self.construct_commandline(
             working_directory, params, "s3_urls" in self.recwrap.environment
         )
         self.log.info("command: %s", " ".join(command))
@@ -200,6 +206,14 @@ def run_xia2(self, working_directory: Path, params: dict):
         subprocess_directory = working_directory / params["program_name"]
         subprocess_directory.mkdir(parents=True, exist_ok=True)
 
+        # Write out spot finding parameters that are not directly accessible in xia2 to phil file
+
+        if spotfinding_params:
+            with open(subprocess_directory / "spots.phil", "w") as phil:
+                for phil_param in spotfinding_params:
+                    phil.write(phil_param)
+            self.log.info(f"Created spots.phil in {subprocess_directory}")
+
         if "dials.integrate.phil_file" in params["xia2"]:
             dials_integrate_phil_file = subprocess_directory / params["xia2"].get(
                 "dials.integrate.phil_file"