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Feat 279 fiberprobe #293

Merged
merged 12 commits into from
Nov 11, 2024
Merged

Feat 279 fiberprobe #293

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82d381f
adds standard probe mappings
mekhlakapoor Oct 31, 2024
9a1d172
adds fiber names based on coords (WIP)
mekhlakapoor Oct 31, 2024
2daed98
fixed probe name assignment
mekhlakapoor Oct 31, 2024
0bcdb29
updating tests (WIP)
mekhlakapoor Nov 1, 2024
3b6f0df
updating examples (WIP)
mekhlakapoor Nov 4, 2024
c7c5591
completes coverage
mekhlakapoor Nov 5, 2024
7796da2
numerical aperature fix
mekhlakapoor Nov 5, 2024
70c6493
adds manufacturer, reformats examples
mekhlakapoor Nov 6, 2024
2f5f8ab
linters
mekhlakapoor Nov 6, 2024
2a37189
merging dev into branch
mekhlakapoor Nov 6, 2024
8080d5a
revert gitignore
mekhlakapoor Nov 6, 2024
f7eaa86
adds underscores to fiber name
mekhlakapoor Nov 11, 2024
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267 changes: 119 additions & 148 deletions src/aind_metadata_service/sharepoint/nsb2023/mapping.py
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212 changes: 152 additions & 60 deletions tests/resources/sharepoint/nsb2023/mapped/mapped_list_item14.json
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Original file line number Diff line number Diff line change
@@ -1,221 +1,313 @@
[
{
"procedure_type": "Surgery",
"start_date": "2022-01-03",
"experimenter_full_name": "NSB-187",
"iacuc_protocol": "2103",
"animal_weight_prior": "25.2",
"animal_weight_post": "28.2",
"weight_unit": "gram",
"anaesthesia": {
"type": "isoflurane",
"duration": "90.0",
"level": "2.0",
"duration_unit": "minute"
"duration_unit": "minute",
"level": "2.0"
},
"workstation_id": "SWS 4",
"procedures": [
{
"procedure_type": "Headframe",
"headframe_type": "Frontal Ctx",
"headframe_part_number": "0160-100-46",
"headframe_material": null,
"well_part_number": "0160-055-08",
"well_type": "WHC NP",
"procedure_type": "Headframe",
"headframe_material": null
"well_type": "WHC NP"
},
{
"injection_materials": [],
"recovery_time": "25.0",
"recovery_time_unit": "minute",
"injection_duration": null,
"injection_duration_unit": "minute",
"instrument_id": null,
"injection_coordinate_ml": "-5.2",
"injection_coordinate_ap": "-0.85",
"injection_coordinate_depth": [
"-3.1"
],
"injection_coordinate_unit": "millimeter",
"injection_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"bregma_to_lambda_unit": "millimeter",
"injection_angle": "0.0",
"injection_angle_unit": "degrees",
"targeted_structure": null,
"injection_hemisphere": "Left",
"procedure_type": "Nanoject injection",
"injection_volume": [
"600.0"
],
"recovery_time_unit": "minute",
"injection_duration_unit": "minute",
"injection_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"injection_angle_unit": "degrees",
"targeted_structure": null,
"procedure_type": "Nanoject injection",
"injection_volume_unit": "nanoliter"
},
{
"procedure_type": "Fiber implant",
"probes": [
{
"ophys_probe": {
"device_type": "Fiber optic probe",
"serial_number": null,
"manufacturer": {
"name": "Neurophotometrics",
"abbreviation": null,
"registry": null,
"registry_identifier": null
},
"model": null,
"path_to_cad": null,
"port_index": null,
"additional_settings": {},
"notes": null,
"core_diameter": 200,
"core_diameter_unit": "micrometer",
"ferrule_material": "Ceramic",
"numerical_aperture": 0.37,
"active_length": null,
"total_length": null,
"length_unit": "millimeter",
"name": "Fiber_1"
},
"targeted_structure": null,
"stereotactic_coordinate_ap": "-0.85",
"stereotactic_coordinate_ml": "-5.2",
"stereotactic_coordinate_dv": "-2.95",
"stereotactic_coordinate_unit": "millimeter",
"stereotactic_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"angle": "0.0",
"stereotactic_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"angle": "0.0",
"angle_unit": "degrees",
"notes": null
}
],
"procedure_type": "Fiber implant"
]
},
{
"injection_materials": [],
"recovery_time": "25.0",
"recovery_time_unit": "minute",
"injection_duration": null,
"injection_duration_unit": "minute",
"instrument_id": null,
"injection_coordinate_ml": "-0.5",
"injection_coordinate_ap": "2.0",
"injection_coordinate_depth": [
"5.0"
],
"injection_coordinate_unit": "millimeter",
"injection_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"injection_angle": "0.0",
"injection_hemisphere": "Left",
"injection_current": null,
"alternating_current": "7/7",
"recovery_time_unit": "minute",
"injection_duration_unit": "minute",
"injection_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"injection_angle": "0.0",
"injection_angle_unit": "degrees",
"targeted_structure": null,
"injection_hemisphere": "Left",
"procedure_type": "Iontophoresis injection",
"injection_current_unit": "microamps"
"injection_current": null,
"injection_current_unit": "microamps",
"alternating_current": "7/7"
},
{
"procedure_type": "Fiber implant",
"probes": [
{
"ophys_probe": {
"device_type": "Fiber optic probe",
"serial_number": null,
"manufacturer": {
"name": "Neurophotometrics",
"abbreviation": null,
"registry": null,
"registry_identifier": null
},
"model": null,
"path_to_cad": null,
"port_index": null,
"additional_settings": {},
"notes": null,
"core_diameter": 200,
"numerical_aperture": 0.37,
"core_diameter_unit": "micrometer",
"ferrule_material": "Ceramic",
"active_length": null,
"total_length": "2.5",
"length_unit": "millimeter",
"name": "Fiber_0"
},
"targeted_structure": null,
"stereotactic_coordinate_ap": "2.0",
"stereotactic_coordinate_ml": "-0.5",
"stereotactic_coordinate_dv": "-1.05",
"stereotactic_coordinate_unit": "millimeter",
"stereotactic_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"angle": "0.0",
"stereotactic_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"angle": "0.0",
"angle_unit": "degrees",
"notes": null
}
],
"procedure_type": "Fiber implant"
]
}
],
"notes": null,
"procedure_type": "Surgery",
"weight_unit": "gram"
"notes": null
},
{
"procedure_type": "Surgery",
"start_date": "2022-01-03",
"experimenter_full_name": "NSB-187",
"iacuc_protocol": "2103",
"animal_weight_prior": "25.2",
"animal_weight_post": "28.2",
"weight_unit": "gram",
"anaesthesia": {
"type": "isoflurane",
"duration": "90.0",
"level": "2.0",
"duration_unit": "minute"
"duration_unit": "minute",
"level": "2.0"
},
"workstation_id": "SWS 4",
"procedures": [
{
"injection_materials": [],
"recovery_time": "25.0",
"recovery_time_unit": "minute",
"injection_duration": null,
"injection_duration_unit": "minute",
"instrument_id": null,
"injection_coordinate_ml": "-2.2",
"injection_coordinate_ap": "-6.1",
"injection_coordinate_depth": [
"3.1"
],
"injection_coordinate_unit": "millimeter",
"injection_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"injection_angle": "0.0",
"injection_hemisphere": "Left",
"injection_current": "5",
"alternating_current": "7/7",
"recovery_time_unit": "minute",
"injection_duration_unit": "minute",
"injection_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"injection_angle": "0.0",
"injection_angle_unit": "degrees",
"targeted_structure": null,
"injection_hemisphere": "Left",
"procedure_type": "Iontophoresis injection",
"injection_current_unit": "microamps"
"injection_current": "5",
"injection_current_unit": "microamps",
"alternating_current": "7/7"
},
{
"procedure_type": "Fiber implant",
"probes": [
{
"ophys_probe": {
"device_type": "Fiber optic probe",
"serial_number": null,
"manufacturer": {
"name": "Neurophotometrics",
"abbreviation": null,
"registry": null,
"registry_identifier": null
},
"model": null,
"path_to_cad": null,
"port_index": null,
"additional_settings": {},
"notes": null,
"core_diameter": 200,
"numerical_aperture": 0.37,
"core_diameter_unit": "micrometer",
"ferrule_material": "Ceramic",
"active_length": null,
"total_length": null,
"length_unit": "millimeter",
"name": "Fiber_1"
},
"targeted_structure": null,
"stereotactic_coordinate_ap": "-6.1",
"stereotactic_coordinate_ml": "-2.2",
"stereotactic_coordinate_dv": "-1.85",
"stereotactic_coordinate_unit": "millimeter",
"stereotactic_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"angle": "0.0",
"stereotactic_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"angle": "0.0",
"angle_unit": "degrees",
"notes": null
}
],
"procedure_type": "Fiber implant"
]
},
{
"injection_materials": [],
"recovery_time": "25.0",
"recovery_time_unit": "minute",
"injection_duration": null,
"injection_duration_unit": "minute",
"instrument_id": null,
"injection_coordinate_ml": "-2.5",
"injection_coordinate_ap": "1.0",
"injection_coordinate_depth": [
"3.0"
],
"injection_coordinate_unit": "millimeter",
"injection_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"injection_angle": "0.0",
"injection_hemisphere": "Right",
"injection_current": "5",
"alternating_current": "7/7",
"recovery_time_unit": "minute",
"injection_duration_unit": "minute",
"injection_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"injection_angle": "0.0",
"injection_angle_unit": "degrees",
"targeted_structure": null,
"injection_hemisphere": "Right",
"procedure_type": "Iontophoresis injection",
"injection_current_unit": "microamps"
"injection_current": "5",
"injection_current_unit": "microamps",
"alternating_current": "7/7"
},
{
"procedure_type": "Fiber implant",
"probes": [
{
"ophys_probe": {
"device_type": "Fiber optic probe",
"serial_number": null,
"manufacturer": {
"name": "Neurophotometrics",
"abbreviation": null,
"registry": null,
"registry_identifier": null
},
"model": null,
"path_to_cad": null,
"port_index": null,
"additional_settings": {},
"notes": null,
"core_diameter": 200,
"numerical_aperture": 0.37,
"core_diameter_unit": "micrometer",
"ferrule_material": "Ceramic",
"active_length": null,
"total_length": null,
"length_unit": "millimeter",
"name": "Fiber_0"
},
"targeted_structure": null,
"stereotactic_coordinate_ap": "1.0",
"stereotactic_coordinate_ml": "-2.5",
"stereotactic_coordinate_dv": "-1.8",
"stereotactic_coordinate_unit": "millimeter",
"stereotactic_coordinate_reference": "Bregma",
"bregma_to_lambda_distance": null,
"angle": "0.0",
"stereotactic_coordinate_unit": "millimeter",
"bregma_to_lambda_unit": "millimeter",
"angle": "0.0",
"angle_unit": "degrees",
"notes": null
}
],
"procedure_type": "Fiber implant"
]
}
],
"notes": null,
"procedure_type": "Surgery",
"weight_unit": "gram"
"notes": null
}
]
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