Read tilt axis from mdoc and send to tomographic alignment#505
Read tilt axis from mdoc and send to tomographic alignment#505stephen-riggs merged 2 commits intomainfrom
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## main #505 +/- ##
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+ Coverage 28.62% 28.64% +0.01%
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Files 78 78
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Branches 1354 1354
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- Misses 7194 7195 +1
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| "frame_count": environment.data_collection_parameters.get( | ||
| "frame_count", 0 | ||
| ), | ||
| "tilt_axis": environment.data_collection_parameters.get( |
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What's the rationale behind defaulting to 85 degrees?
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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
tieneupin
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Other than a question about the choice of default value for the angle, looks good!
src/murfey/client/contexts/tomo.py
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| 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["RotationAngle"]) |
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"RotationAngle" is found in mdoc_data_block, not mdoc_data
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With that |
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The tilt axis is present in the mdoc files. While it isn't required for tomogram alignment, AreTomo seems less prone to predicting wrong axes when one is provided