adding example for MRISession (#828)

* adding example for MRISession

* linters

* Update mri_session.py

* dummy info

Author: Sun-flow

examples/mri_session.json

@@ -0,0 +1,35 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/mri_session.py",
+   "schema_version": "0.3.4",
+   "subject_id": "",
+   "session_start_time": "2024-03-12T16:27:55.584892",
+   "session_end_time": "2024-03-12T16:27:55.584892",
+   "experimenter_full_name": [
+      "Allen Brain"
+   ],
+   "protocol_id": "dx.doi.org/10.57824/protocols.io.bh7kl4n6",
+   "iacuc_protocol": "12345",
+   "animal_weight_prior": null,
+   "animal_weight_post": null,
+   "weight_unit": "gram",
+   "anaesthesia": null,
+   "mri_scanner": {
+      "device_type": "Scanner",
+      "name": "Scanner 72",
+      "serial_number": null,
+      "manufacturer": null,
+      "model": null,
+      "path_to_cad": null,
+      "port_index": null,
+      "additional_settings": {},
+      "notes": null,
+      "scanner_location": "Fred Hutch",
+      "magnetic_strength": 7,
+      "magnetic_strength_unit": "T"
+   },
+   "scans": [
+      null,
+      null
+   ],
+   "notes": "There was some information about this scan session"
+}

examples/mri_session.py

@@ -0,0 +1,59 @@
+"""example MRISession and MRIScan"""
+from decimal import Decimal
+
+from aind_data_schema.core.mri_session import MRIScan, MriScanSequence, MriSession, ScanType, SubjectPosition
+from aind_data_schema.models.coordinates import Rotation3dTransform, Scale3dTransform, Translation3dTransform
+from aind_data_schema.models.devices import Scanner
+
+scan1 = MRIScan(
+    scan_index="1",
+    scan_type=ScanType.SETUP,
+    primary_scan=False,
+    scan_sequence_type=MriScanSequence.RARE,
+    rare_factor=8,
+    echo_time=Decimal(3.42),
+    repetition_time=Decimal(100.0),
+    subject_position=SubjectPosition.SUPINE,
+    voxel_sizes=Scale3dTransform(scale=[0.5, 0.4375, 0.52]),
+    processing_steps=[],
+    additional_scan_parameters={},
+    notes="Set up scan for the 3D scan.",
+)
+
+scan2 = MRIScan(
+    scan_index="2",
+    scan_type=ScanType.SCAN_3D,
+    primary_scan=True,
+    scan_sequence_type=MriScanSequence.RARE,
+    rare_factor=4,
+    echo_time=Decimal(5.33333333333333),
+    effective_echo_time=Decimal(10.6666666666666998253276688046753406524658203125),
+    repetition_time=Decimal(500.0),
+    vc_orientation=Rotation3dTransform(rotation=[1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 1.0, 0.0]),
+    vc_position=Translation3dTransform(translation=[-6.1, -7.0, 7.9]),
+    subject_position=SubjectPosition.SUPINE,
+    voxel_sizes=Scale3dTransform(scale=[0.1, 0.1, 0.1]),
+    processing_steps=[],
+    additional_scan_parameters={},
+    notes=None,
+)
+
+scans = [scan1, scan2]
+
+sess = MriSession(
+    subject_id="",
+    session_start_time="2024-03-12T16:27:55.584892",
+    session_end_time="2024-03-12T16:27:55.584892",
+    experimenter_full_name=["Allen Brain"],
+    protocol_id="dx.doi.org/10.57824/protocols.io.bh7kl4n6",
+    iacuc_protocol="12345",
+    mri_scanner=Scanner(
+        name="Scanner 72",
+        scanner_location="Fred Hutch",
+        magnetic_strength="7",
+    ),
+    scans=scans,
+    notes="There was some information about this scan session"
+)
+
+sess.write_standard_file()

examples/multiplane_ophys_session.py

@@ -2,9 +2,9 @@
 
 import datetime
 
-from aind_data_schema.core.session import FieldOfView, Session, Stream, LaserConfig
+from aind_data_schema.core.session import FieldOfView, LaserConfig, Session, Stream
 from aind_data_schema.models.modalities import Modality
-from aind_data_schema.models.units import SizeUnit, PowerUnit
+from aind_data_schema.models.units import PowerUnit, SizeUnit
 
 t = datetime.datetime(2022, 7, 12, 7, 00, 00)