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Read tilt axis from mdoc and send to tomographic alignment #505

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Merged
stephen-riggs merged 2 commits into from
Mar 11, 2025
Merged

Read tilt axis from mdoc and send to tomographic alignment #505

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70396e3
Read tilt axis from mdoc and send to tomographic alignment
stephen-riggs Mar 7, 2025
81285d6
'RotationAngle' information found in 'mdoc_data_block', not 'mdoc_dat'
tieneupin Mar 10, 2025
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5 changes: 5 additions & 0 deletions src/murfey/client/contexts/tomo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,7 @@
ProcessingParameter("pixel_size_on_image", "Pixel Size"),
ProcessingParameter("motion_corr_binning", "Motion Correction Binning"),
ProcessingParameter("frame_count", "Number of image frames"),
ProcessingParameter("tilt_axis", "Stage rotation angle"),
ProcessingParameter("num_eer_frames", "Number of EER Frames"),
]

Expand Down Expand Up @@ -339,6 +340,9 @@
"frame_count": environment.data_collection_parameters.get(
"frame_count", 0
),
"tilt_axis": environment.data_collection_parameters.get(
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@tieneupin tieneupin Mar 10, 2025

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What's the rationale behind defaulting to 85 degrees?

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@stephen-riggs stephen-riggs Mar 10, 2025

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Typically the tilt axis is around that, on our microscopes it seems to be between about 83 and 87 degrees. This value gets sent to AreTomo which takes is as an initial guess to refine from, so it doesn't need to be exact

"tilt_axis", 85
),
"mc_binning": environment.data_collection_parameters.get(
"motion_corr_binning", 1
),
Expand Down Expand Up @@ -570,6 +574,7 @@
mdoc_metadata["experiment_type"] = "tomography"
mdoc_metadata["voltage"] = float(mdoc_data["Voltage"])
mdoc_metadata["frame_count"] = int(mdoc_data_block["NumSubFrames"])
mdoc_metadata["tilt_axis"] = float(mdoc_data_block["RotationAngle"])

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mdoc_metadata["image_size_x"] = int(mdoc_data["ImageSize"][0])
mdoc_metadata["image_size_y"] = int(mdoc_data["ImageSize"][1])
mdoc_metadata["magnification"] = int(mdoc_data_block["Magnification"])
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2 changes: 2 additions & 0 deletions src/murfey/server/__init__.py
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Expand Up @@ -2471,6 +2471,7 @@ def feedback_callback(header: dict, message: dict) -> None:
"dose_per_frame": preproc_params.dose_per_frame,
"frame_count": preproc_params.frame_count,
"kv": preproc_params.voltage,
"tilt_axis": preproc_params.tilt_axis,
"pixel_size": preproc_params.pixel_size,
"manual_tilt_offset": -tilt_offset,
"node_creator_queue": machine_config.node_creator_queue,
Expand Down Expand Up @@ -2841,6 +2842,7 @@ def feedback_callback(header: dict, message: dict) -> None:
voltage=message["voltage"],
dose_per_frame=message["dose_per_frame"],
frame_count=message["frame_count"],
tilt_axis=message["tilt_axis"],
motion_corr_binning=message["motion_corr_binning"],
gain_ref=message["gain_ref"],
eer_fractionation_file=message["eer_fractionation_file"],
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1 change: 1 addition & 0 deletions src/murfey/server/api/__init__.py
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Expand Up @@ -735,6 +735,7 @@ def register_completed_tilt_series(
"dose_per_frame": preproc_params.dose_per_frame,
"frame_count": preproc_params.frame_count,
"kv": preproc_params.voltage,
"tilt_axis": preproc_params.tilt_axis,
"pixel_size": preproc_params.pixel_size,
"manual_tilt_offset": -tilt_offset,
"node_creator_queue": machine_config.node_creator_queue,
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1 change: 1 addition & 0 deletions src/murfey/util/db.py
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Expand Up @@ -459,6 +459,7 @@ class TomographyPreprocessingParameters(SQLModel, table=True): # type: ignore
pixel_size: float
dose_per_frame: float
frame_count: int
tilt_axis: float
voltage: int
eer_fractionation_file: Optional[str] = None
motion_corr_binning: int = 1
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2 changes: 2 additions & 0 deletions src/murfey/util/models.py
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Expand Up @@ -316,6 +316,7 @@ class ProcessFile(BaseModel): # Rename to TomoProcessFile
pixel_size: float
dose_per_frame: float
frame_count: int
tilt_axis: Optional[float]
mc_uuid: Optional[int] = None
voltage: float = 300
mc_binning: int = 1
Expand Down Expand Up @@ -351,6 +352,7 @@ class CompletedTiltSeries(BaseModel):
class PreprocessingParametersTomo(BaseModel):
dose_per_frame: float
frame_count: int
tilt_axis: float
gain_ref: Optional[str]
experiment_type: str
voltage: float
Expand Down