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Added values used by Murfey's email notification workflow to the message sent back from cryolo #136

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Merged
stephen-riggs merged 4 commits into from
Mar 13, 2025
Merged

Added values used by Murfey's email notification workflow to the message sent back from cryolo #136

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6d962de
Added values used by Murfey's email notification workflow to the mess…
tieneupin Mar 12, 2025
a3c3524
Fixed astigmatism and defocus calculations
tieneupin Mar 12, 2025
b1c71be
Updated test for Cryolo service
tieneupin Mar 12, 2025
56dfc10
Use variables directly instead of re-defining
tieneupin Mar 12, 2025
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11 changes: 10 additions & 1 deletion src/cryoemservices/services/cryolo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -439,7 +439,7 @@ def cryolo(self, rw, header: dict, message: dict):
rw.send_to("images", images_parameters)

# Gather results needed for particle extraction
extraction_params = {
extraction_params: dict[str, Any] = {
"ctf_values": cryolo_params.ctf_values,
"micrographs_file": cryolo_params.input_path,
"coord_list_file": cryolo_params.output_path,
Expand All @@ -464,6 +464,15 @@ def cryolo(self, rw, header: dict, message: dict):
"motion_correction_id": cryolo_params.mc_uuid,
"micrograph": cryolo_params.input_path,
"particle_diameters": list(cryolo_particle_sizes),
"particle_count": len(cryolo_particle_sizes),
"resolution": cryolo_params.ctf_values["CtfMaxResolution"],
"astigmatism": cryolo_params.ctf_values["DefocusV"]
- cryolo_params.ctf_values["DefocusU"],
"defocus": (
cryolo_params.ctf_values["DefocusU"]
+ cryolo_params.ctf_values["DefocusV"]
)
/ 2,
"extraction_parameters": extraction_params,
},
)
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11 changes: 10 additions & 1 deletion tests/services/test_cryolo_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,11 @@ def test_cryolo_service_spa(mock_subprocess, offline_transport, tmp_path):

output_path = tmp_path / "AutoPick/job007/STAR/sample.star"
cbox_path = tmp_path / "AutoPick/job007/CBOX/sample.cbox"
ctf_test_values = {
"CtfMaxResolution": 0.00001,
"DefocusU": 0.05,
"DefocusV": 0.08,
}
cryolo_test_message = {
"pixel_size": 0.1,
"input_path": "MotionCorr/job002/sample.mrc",
Expand All @@ -52,7 +57,7 @@ def test_cryolo_service_spa(mock_subprocess, offline_transport, tmp_path):
"mc_uuid": 0,
"picker_uuid": 0,
"particle_diameter": 1.1,
"ctf_values": {"dummy": "dummy"},
"ctf_values": ctf_test_values,
"cryolo_command": "cryolo_predict.py",
"relion_options": {"batch_size": 20000, "downscale": True},
}
Expand Down Expand Up @@ -161,6 +166,10 @@ def test_cryolo_service_spa(mock_subprocess, offline_transport, tmp_path):
"motion_correction_id": cryolo_test_message["mc_uuid"],
"micrograph": cryolo_test_message["input_path"],
"particle_diameters": [10.0, 20.0],
"particle_count": 2,
"resolution": ctf_test_values["CtfMaxResolution"],
"astigmatism": ctf_test_values["DefocusV"] - ctf_test_values["DefocusU"],
"defocus": (ctf_test_values["DefocusU"] + ctf_test_values["DefocusV"]) / 2,
"extraction_parameters": extraction_params,
},
)
Expand Down