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Service to run imod batchruntomo #258
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e01e08e
Move tomo align to be named as aretomo
stephen-riggs c1efed6
Add imod tomo service
stephen-riggs a3990bd
Alter pyproject names
stephen-riggs 5bb7166
Merge branch 'main' into imod-tomo-service
stephen-riggs 9de305a
Bugfixes
stephen-riggs 76367ca
Update imod script
stephen-riggs f65e84b
Merge branch 'main' into imod-tomo-service
stephen-riggs af3a430
A few parameter changes
stephen-riggs cc019ff
stem not name
stephen-riggs 1fa45be
Merge branch 'main' into imod-tomo-service
stephen-riggs ce0f9ff
Add imod recipes
stephen-riggs cfbb317
Renaming
stephen-riggs cfb2018
Merge branch 'main' into imod-tomo-service
stephen-riggs 9d28536
Update tests
stephen-riggs c44e53d
Test some of the imod service
stephen-riggs c538ff2
Don't need relion options for sxt
stephen-riggs 8c5999d
Reversion to imod 4.9
stephen-riggs 0f53457
remove tilt series alignment calls
stephen-riggs File filter
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| { | ||
| "1": { | ||
| "output": 2, | ||
| "parameters": { | ||
| "dcid": "{dcid}", | ||
| "ispyb_command": "insert_tomogram", | ||
| "program_id": "{appid}", | ||
| "store_result": "ispyb_tomogram_id" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "2": { | ||
| "output": { | ||
| "denoise": 5, | ||
| "failure": 3, | ||
| "images": 6, | ||
| "ispyb_connector": 4, | ||
| "movie": 6, | ||
| "projxy": 6, | ||
| "projxz": 6, | ||
| "success": 7 | ||
| }, | ||
| "parameters": { | ||
| "manual_tilt_offset": "{manual_tilt_offset}", | ||
| "out_bin": 1, | ||
| "patch": 0, | ||
| "pixel_size": "{pixel_size}", | ||
| "sirt": 0, | ||
| "stack_file": "{stack_file}", | ||
| "tilt_axis": 0, | ||
| "txrm_file": "{txrm_file}", | ||
| "wbp": 1 | ||
| }, | ||
| "queue": "tomo_align_imod", | ||
| "service": "ImodTomoAlign" | ||
| }, | ||
| "3": { | ||
| "parameters": { | ||
| "ispyb_command": "update_processing_status", | ||
| "status_message": "processing failure", | ||
| "program_id": "{appid}", | ||
| "status": "failure" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "4": { | ||
| "parameters": { | ||
| "dcid": "{dcid}", | ||
| "ispyb_command": "multipart_message", | ||
| "program_id": "{appid}", | ||
| "tomogram_id": "$ispyb_tomogram_id" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "5": { | ||
| "output": { | ||
| "images": 6, | ||
| "ispyb_connector": 9, | ||
| "movie": 6, | ||
| "segmentation": 8 | ||
| }, | ||
| "queue": "denoise", | ||
| "service": "Denoise" | ||
| }, | ||
| "6": { | ||
| "queue": "images", | ||
| "service": "Images" | ||
| }, | ||
| "7": { | ||
| "parameters": { | ||
| "ispyb_command": "update_processing_status", | ||
| "status_message": "processing successful", | ||
| "program_id": "{appid}", | ||
| "status": "success" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "8": { | ||
| "output": { | ||
| "images": 6, | ||
| "ispyb_connector": 9, | ||
| "movie": 6 | ||
| }, | ||
| "queue": "segmentation", | ||
| "service": "MembrainSeg" | ||
| }, | ||
| "9": { | ||
| "parameters": { | ||
| "ispyb_command": "insert_processed_tomogram", | ||
| "tomogram_id": "$ispyb_tomogram_id" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "start": [[1, []]] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| { | ||
| "1": { | ||
| "output": 2, | ||
| "parameters": { | ||
| "dcid": "{dcid}", | ||
| "ispyb_command": "insert_tomogram", | ||
| "program_id": "{appid}", | ||
| "store_result": "ispyb_tomogram_id" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "2": { | ||
| "output": { | ||
| "denoise": 5, | ||
| "failure": 3, | ||
| "images": 6, | ||
| "ispyb_connector": 4, | ||
| "movie": 6, | ||
| "projxy": 6, | ||
| "projxz": 6, | ||
| "success": 7 | ||
| }, | ||
| "parameters": { | ||
| "manual_tilt_offset": "{manual_tilt_offset}", | ||
| "out_bin": 1, | ||
| "patch": 1, | ||
| "pixel_size": "{pixel_size}", | ||
| "sirt": 0, | ||
| "stack_file": "{stack_file}", | ||
| "tilt_axis": 0, | ||
| "txrm_file": "{txrm_file}", | ||
| "wbp": 1 | ||
| }, | ||
| "queue": "tomo_align_imod", | ||
| "service": "ImodTomoAlign" | ||
| }, | ||
| "3": { | ||
| "parameters": { | ||
| "ispyb_command": "update_processing_status", | ||
| "status_message": "processing failure", | ||
| "program_id": "{appid}", | ||
| "status": "failure" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "4": { | ||
| "parameters": { | ||
| "dcid": "{dcid}", | ||
| "ispyb_command": "multipart_message", | ||
| "program_id": "{appid}", | ||
| "tomogram_id": "$ispyb_tomogram_id" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "5": { | ||
| "output": { | ||
| "images": 6, | ||
| "ispyb_connector": 9, | ||
| "movie": 6, | ||
| "segmentation": 8 | ||
| }, | ||
| "queue": "denoise", | ||
| "service": "Denoise" | ||
| }, | ||
| "6": { | ||
| "queue": "images", | ||
| "service": "Images" | ||
| }, | ||
| "7": { | ||
| "parameters": { | ||
| "ispyb_command": "update_processing_status", | ||
| "status_message": "processing successful", | ||
| "program_id": "{appid}", | ||
| "status": "success" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "8": { | ||
| "output": { | ||
| "images": 6, | ||
| "ispyb_connector": 9, | ||
| "movie": 6 | ||
| }, | ||
| "queue": "segmentation", | ||
| "service": "MembrainSeg" | ||
| }, | ||
| "9": { | ||
| "parameters": { | ||
| "ispyb_command": "insert_processed_tomogram", | ||
| "tomogram_id": "$ispyb_tomogram_id" | ||
| }, | ||
| "queue": "ispyb_connector", | ||
| "service": "EMISPyB" | ||
| }, | ||
| "start": [[1, []]] | ||
| } |
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You're capturing the output, but it doesn't look there are any logs in place to note the output.