Merge pull request #379 from AllenNeuralDynamics/feat-imaging-calibra…

…tion Feat imaging calibration
AllenNeuralDynamics · Aug 25, 2023 · 6b8e638 · 6b8e638
2 parents bb0256a + 4ffff01
commit 6b8e638
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Showing 41 changed files with 475 additions and 96 deletions.
diff --git a/examples/aibs_smartspim_instrument.json b/examples/aibs_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
-   "schema_version": "0.7.6",
+   "schema_version": "0.7.7",
    "instrument_id": "SmartSPIM2-2",
    "instrument_type": "SmartSPIM",
    "manufacturer": {
@@ -71,7 +71,7 @@
    ],
    "light_sources": [
       {
-         "name": null,
+         "name": "Ex_488",
          "serial_number": "VL01222A11",
          "manufacturer": {
             "name": "Vortran",
@@ -89,7 +89,7 @@
          "power_unit": "milliwatt"
       },
       {
-         "name": null,
+         "name": "Ex_561",
          "serial_number": "417927",
          "manufacturer": {
             "name": "Coherent Scientific",
@@ -110,7 +110,7 @@
          "power_unit": "milliwatt"
       },
       {
-         "name": null,
+         "name": "Ex_647",
          "serial_number": "VL01222A10",
          "manufacturer": {
             "name": "Vortran",
@@ -130,7 +130,7 @@
    ],
    "fluorescence_filters": [
       {
-         "name": null,
+         "name": "Em_525",
          "serial_number": "Unknown-1",
          "manufacturer": {
             "name": "Semrock",
@@ -155,7 +155,7 @@
          "description": null
       },
       {
-         "name": null,
+         "name": "Em_600",
          "serial_number": "Unknown-2",
          "manufacturer": {
             "name": "Semrock",
@@ -180,7 +180,7 @@
          "description": null
       },
       {
-         "name": null,
+         "name": "Em_690",
          "serial_number": "Unknown-3",
          "manufacturer": {
             "name": "Chroma",

diff --git a/examples/aibs_smartspim_instrument.py b/examples/aibs_smartspim_instrument.py
@@ -40,6 +40,7 @@
     ],
     light_sources=[
         Lightsource(
+            name="Ex_488",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=488,
@@ -50,6 +51,7 @@
             notes="All lasers controlled via Vortran VersaLase System",
         ),
         Lightsource(
+            name="Ex_561",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=561,
@@ -60,6 +62,7 @@
             notes="All lasers controlled via Vortran VersaLase System",
         ),
         Lightsource(
+            name="Ex_647",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=647,
@@ -161,6 +164,7 @@
     ],
     fluorescence_filters=[
         Filter(
+            name="Em_525",
             filter_type="Band pass",
             manufacturer=Manufacturer.SEMROCK,
             diameter=25,
@@ -170,6 +174,7 @@
             serial_number="Unknown-1",
         ),
         Filter(
+            name="Em_600",
             filter_type="Band pass",
             manufacturer=Manufacturer.SEMROCK,
             diameter=25,
@@ -179,6 +184,7 @@
             serial_number="Unknown-2",
         ),
         Filter(
+            name="Em_690",
             filter_type="Band pass",
             manufacturer=Manufacturer.CHROMA,
             diameter=25,

diff --git a/examples/aibs_smartspim_procedures.py b/examples/aibs_smartspim_procedures.py
@@ -21,7 +21,11 @@
 
 easy_index = procedures.Reagent(name="Easy Index", lot_number="1234", source="Vendor")
 
-water = procedures.Reagent(name="Deionized water", lot_number="DDI/Filtered in house", source="This is not a reagent")
+water = procedures.Reagent(
+    name="Deionized water",
+    lot_number="DDI/Filtered in house",
+    source="This is not a reagent",
+)
 
 agarose = procedures.Reagent(name="Agarose", lot_number="1234", source="Other vendor")
 

diff --git a/examples/aind_smartspim_instrument.json b/examples/aind_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py",
-   "schema_version": "0.7.6",
+   "schema_version": "0.7.7",
    "instrument_id": "SmartSPIM1-3",
    "instrument_type": "SmartSPIM",
    "manufacturer": {
@@ -128,7 +128,7 @@
    ],
    "light_sources": [
       {
-         "name": null,
+         "name": "Ex_445",
          "serial_number": "VL08223M03",
          "manufacturer": {
             "name": "Vortran",
@@ -146,7 +146,7 @@
          "power_unit": "milliwatt"
       },
       {
-         "name": null,
+         "name": "Ex_488",
          "serial_number": "VL08223M03",
          "manufacturer": {
             "name": "Vortran",
@@ -164,7 +164,7 @@
          "power_unit": "milliwatt"
       },
       {
-         "name": null,
+         "name": "Ex_561",
          "serial_number": "VL08223M03",
          "manufacturer": {
             "name": "Vortran",
@@ -182,7 +182,7 @@
          "power_unit": "milliwatt"
       },
       {
-         "name": null,
+         "name": "Ex_594",
          "serial_number": "VL08223M03",
          "manufacturer": {
             "name": "Vortran",
@@ -200,7 +200,7 @@
          "power_unit": "milliwatt"
       },
       {
-         "name": null,
+         "name": "Ex_639",
          "serial_number": "VL08223M03",
          "manufacturer": {
             "name": "Vortran",
@@ -218,7 +218,7 @@
          "power_unit": "milliwatt"
       },
       {
-         "name": null,
+         "name": "Ex_665",
          "serial_number": "VL08223M03",
          "manufacturer": {
             "name": "Vortran",
@@ -238,7 +238,7 @@
    ],
    "fluorescence_filters": [
       {
-         "name": null,
+         "name": "Em_469",
          "serial_number": "Unknown-0",
          "manufacturer": {
             "name": "Semrock",
@@ -263,7 +263,7 @@
          "description": null
       },
       {
-         "name": null,
+         "name": "Em_525",
          "serial_number": "Unknown-1",
          "manufacturer": {
             "name": "Semrock",
@@ -288,7 +288,7 @@
          "description": null
       },
       {
-         "name": null,
+         "name": "Em_593",
          "serial_number": "Unknown-2",
          "manufacturer": {
             "name": "Semrock",
@@ -313,7 +313,7 @@
          "description": null
       },
       {
-         "name": null,
+         "name": "Em_624",
          "serial_number": "Unknown-3",
          "manufacturer": {
             "name": "Semrock",
@@ -338,7 +338,7 @@
          "description": null
       },
       {
-         "name": null,
+         "name": "Em_667",
          "serial_number": "Unknown-4",
          "manufacturer": {
             "name": "Chroma",
@@ -363,7 +363,7 @@
          "description": null
       },
       {
-         "name": null,
+         "name": "Em_700",
          "serial_number": "Unknown-5",
          "manufacturer": {
             "name": "Thorlabs",

diff --git a/examples/aind_smartspim_instrument.py b/examples/aind_smartspim_instrument.py
@@ -68,6 +68,7 @@
     ],
     light_sources=[
         Lightsource(
+            name="Ex_445",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=445,
@@ -78,6 +79,7 @@
             notes="All lasers controlled via Vortran VersaLase System",
         ),
         Lightsource(
+            name="Ex_488",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=488,
@@ -88,6 +90,7 @@
             notes="All lasers controlled via Vortran VersaLase System",
         ),
         Lightsource(
+            name="Ex_561",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=561,
@@ -98,6 +101,7 @@
             notes="All lasers controlled via Vortran VersaLase System",
         ),
         Lightsource(
+            name="Ex_594",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=594,
@@ -108,6 +112,7 @@
             notes="All lasers controlled via Vortran VersaLase System",
         ),
         Lightsource(
+            name="Ex_639",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=639,
@@ -118,6 +123,7 @@
             notes="All lasers controlled via Vortran VersaLase System",
         ),
         Lightsource(
+            name="Ex_665",
             type="laser",
             coupling="Single-mode fiber",
             wavelength=665,
@@ -219,6 +225,7 @@
     ],
     fluorescence_filters=[
         Filter(
+            name="Em_469",
             filter_type="Band pass",
             manufacturer=Manufacturer.SEMROCK,
             diameter=25,
@@ -228,6 +235,7 @@
             serial_number="Unknown-0",
         ),
         Filter(
+            name="Em_525",
             filter_type="Band pass",
             manufacturer=Manufacturer.SEMROCK,
             diameter=25,
@@ -237,6 +245,7 @@
             serial_number="Unknown-1",
         ),
         Filter(
+            name="Em_593",
             filter_type="Band pass",
             manufacturer=Manufacturer.SEMROCK,
             diameter=25,
@@ -246,6 +255,7 @@
             serial_number="Unknown-2",
         ),
         Filter(
+            name="Em_624",
             filter_type="Band pass",
             manufacturer=Manufacturer.SEMROCK,
             diameter=25,
@@ -255,6 +265,7 @@
             serial_number="Unknown-3",
         ),
         Filter(
+            name="Em_667",
             filter_type="Band pass",
             manufacturer=Manufacturer.CHROMA,
             diameter=25,
@@ -264,6 +275,7 @@
             serial_number="Unknown-4",
         ),
         Filter(
+            name="Em_700",
             filter_type="Long pass",
             manufacturer=Manufacturer.THORLABS,
             diameter=25,

diff --git a/examples/ephys_rig.json b/examples/ephys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/ephys/ephys_rig.py",
-   "schema_version": "0.7.6",
+   "schema_version": "0.7.7",
    "rig_id": "323_EPHYS1",
    "ephys_assemblies": [
       {

diff --git a/examples/ephys_rig.py b/examples/ephys_rig.py
@@ -96,7 +96,11 @@
 )
 
 
-filt = Filter(filter_type="Long pass", manufacturer=Manufacturer.THORLABS, description="850 nm longpass filter")
+filt = Filter(
+    filter_type="Long pass",
+    manufacturer=Manufacturer.THORLABS,
+    description="850 nm longpass filter",
+)
 
 lens = Lens(focal_length=15, manufacturer=Manufacturer.EDMUND_OPTICS, max_aperture="f/2")
 
@@ -113,7 +117,11 @@
 )
 
 camassm1 = CameraAssembly(
-    camera_assembly_name="Face Camera Assembly", camera=face_camera, camera_target="Face side", filter=filt, lens=lens
+    camera_assembly_name="Face Camera Assembly",
+    camera=face_camera,
+    camera_target="Face side",
+    filter=filt,
+    lens=lens,
 )
 
 body_camera = Camera(
@@ -129,7 +137,11 @@
 )
 
 camassm2 = CameraAssembly(
-    camera_assembly_name="Body Camera Assembly", camera=body_camera, camera_target="Body", filter=filt, lens=lens
+    camera_assembly_name="Body Camera Assembly",
+    camera=body_camera,
+    camera_target="Body",
+    filter=filt,
+    lens=lens,
 )
 
 rig = EphysRig(

diff --git a/examples/ephys_session.json b/examples/ephys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/ephys/ephys_session.py",
-   "schema_version": "0.4.7",
+   "schema_version": "0.4.8",
    "experimenter_full_name": [
       "Jane Doe"
    ],