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Mpes elab metadata #551

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Merged
merged 6 commits into from
Apr 4, 2025
Merged

Mpes elab metadata #551

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935dfeb
fix beam status
rettigl Feb 10, 2025
9bc2f8b
allow disabling copy tool
rettigl Feb 10, 2025
2289c9c
add pump2, and fix polarization and pump status conversion
rettigl Feb 11, 2025
4bec385
Merge branch 'mpes_elab_metadata' into fix_mpes_metadata_and_copy_tool
rettigl Mar 25, 2025
027c684
Merge pull request #569 from OpenCOMPES/fix_mpes_metadata_and_copy_tool
rettigl Mar 26, 2025
bb5f7f9
add compatibility to old pre-2020 datasets
rettigl Apr 3, 2025
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1 change: 1 addition & 0 deletions src/sed/core/config_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ class CopyToolModel(BaseModel):

source: DirectoryPath
dest: DirectoryPath
use: Optional[bool] = None
safety_margin: Optional[float] = None
gid: Optional[int] = None
scheduler: Optional[str] = None
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4 changes: 3 additions & 1 deletion src/sed/core/processor.py
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Expand Up @@ -162,7 +162,9 @@ def __init__(
verbose=self._verbose,
)

self.use_copy_tool = "copy_tool" in self._config["core"]
self.use_copy_tool = "copy_tool" in self._config["core"] and self._config["core"][
"copy_tool"
].pop("use", True)
if self.use_copy_tool:
try:
self.ct = CopyTool(
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8 changes: 8 additions & 0 deletions src/sed/loader/mpes/loader.py
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Expand Up @@ -792,6 +792,14 @@ def get_files_from_run_id(
recursive=True,
),
)
# Compatibility for old scan format
if not run_files:
run_files = natsorted(
glob.glob(
folder + "/**/Scan" + str(run_id).zfill(3) + "_*." + extension,
recursive=True,
),
)
files.extend(run_files)

# Check if any files are found
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53 changes: 52 additions & 1 deletion src/sed/loader/mpes/metadata.py
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Expand Up @@ -340,6 +340,13 @@ def fetch_elab_metadata(self, runs: list[str], metadata: dict) -> dict:
metadata["elabFTW"]["scan"]["pump_polarization"] = 90
elif metadata["elabFTW"]["scan"]["pump_polarization"] == "p":
metadata["elabFTW"]["scan"]["pump_polarization"] = 0
else:
try:
metadata["elabFTW"]["scan"]["pump_polarization"] = float(
metadata["elabFTW"]["scan"]["pump_polarization"],
)
except ValueError:
pass

if (
"scan" in metadata["elabFTW"]
Expand All @@ -350,14 +357,58 @@ def fetch_elab_metadata(self, runs: list[str], metadata: dict) -> dict:
metadata["elabFTW"]["scan"]["probe_polarization"] = 90
elif metadata["elabFTW"]["scan"]["probe_polarization"] == "p":
metadata["elabFTW"]["scan"]["probe_polarization"] = 0
else:
try:
metadata["elabFTW"]["scan"]["probe_polarization"] = float(
metadata["elabFTW"]["scan"]["probe_polarization"],
)
except ValueError:
pass

if (
"scan" in metadata["elabFTW"]
and "pump2_polarization" in metadata["elabFTW"]["scan"]
and isinstance(metadata["elabFTW"]["scan"]["pump2_polarization"], str)
):
if metadata["elabFTW"]["scan"]["pump2_polarization"] == "s":
metadata["elabFTW"]["scan"]["pump2_polarization"] = 90
elif metadata["elabFTW"]["scan"]["pump2_polarization"] == "p":
metadata["elabFTW"]["scan"]["pump2_polarization"] = 0
else:
try:
metadata["elabFTW"]["scan"]["pump2_polarization"] = float(
metadata["elabFTW"]["scan"]["pump2_polarization"],
)
except ValueError:
pass

# fix pump status
if "scan" in metadata["elabFTW"] and "pump_status" in metadata["elabFTW"]["scan"]:
try:
metadata["elabFTW"]["scan"]["pump_status"] = (
"open" if int(metadata["elabFTW"]["scan"]["pump_status"]) else "closed"
)
except ValueError:
pass
if "scan" in metadata["elabFTW"] and "pump2_status" in metadata["elabFTW"]["scan"]:
try:
metadata["elabFTW"]["scan"]["pump2_status"] = (
"open" if int(metadata["elabFTW"]["scan"]["pump2_status"]) else "closed"
)
except ValueError:
pass

# remove pump information if pump not applied:
if not metadata["elabFTW"]["scan"].get("pump_status", 0):
if metadata["elabFTW"]["scan"].get("pump_status", "closed") == "closed":
if "pump_photon_energy" in metadata["elabFTW"].get("laser_status", {}):
del metadata["elabFTW"]["laser_status"]["pump_photon_energy"]
if "pump_repetition_rate" in metadata["elabFTW"].get("laser_status", {}):
del metadata["elabFTW"]["laser_status"]["pump_repetition_rate"]

if metadata["elabFTW"]["scan"].get("pump2_status", "closed") == "closed":
if "pump2_photon_energy" in metadata["elabFTW"].get("laser_status", {}):
del metadata["elabFTW"]["laser_status"]["pump2_photon_energy"]

return metadata


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