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Vmxm spotfinding #343

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a067e3d
custom spotfinding parameters for VMXm
amyjaynethompson Feb 19, 2026
d808c41
tidy
amyjaynethompson Feb 19, 2026
b4be34d
addressing comments
amyjaynethompson Feb 23, 2026
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15 changes: 15 additions & 0 deletions src/dlstbx/mimas/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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, ...] = ()
Expand Down
20 changes: 17 additions & 3 deletions src/dlstbx/wrapper/xia2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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":
Expand Down Expand Up @@ -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:
Comment on lines 60 to 62
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@pblowey pblowey Feb 20, 2026

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A bit nit-picky but I think this would be more readable as an if and statement rather than nested if statements

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@pblowey pblowey Feb 20, 2026

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On second thoughts, if you keep the nested if statement, you could create a list of the spotfinder commands and use that later on to create the phil file, rhater than looping through all of the parameters again.

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@amyjaynethompson amyjaynethompson Feb 23, 2026

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Have kept nested if statement here and saved parameters to list.

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,
Expand Down Expand Up @@ -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))
Expand Down Expand Up @@ -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}")

Comment on lines 209 to 216
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@pblowey pblowey Feb 20, 2026 •
edited
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If you moved the block that creates the find_spots phil file before the xia2_script you wouldn't need to distinguish run_command and command and I think the code would be more readable as a result

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@pblowey pblowey Feb 20, 2026

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To add to the comment I made on the earlier code block, if you created a list of spotfinder params, you could just do if spotfinder_params: and write the list to file, rather than looping over all of the parameters again. This would also still save you having to distinguish command and run command.

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@amyjaynethompson amyjaynethompson Feb 23, 2026

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Run commands back to how they were before and now use spot finding parameters from earlier.

if "dials.integrate.phil_file" in params["xia2"]:
dials_integrate_phil_file = subprocess_directory / params["xia2"].get(
"dials.integrate.phil_file"
Expand Down