Merge pull request #487 from NeurodataWithoutBorders/bruker-single-co…

…nverter Add BrukerTiffSinglePlaneConverter
NeurodataWithoutBorders · Oct 31, 2023 · 11b6fc8 · 11b6fc8
2 parents 4815403 + 5e1b58e
commit 11b6fc8
Show file tree

Hide file tree

Showing 8 changed files with 207 additions and 3 deletions.
diff --git a/generateInterfaceSchema.py b/generateInterfaceSchema.py
@@ -1,6 +1,6 @@
 from pathlib import Path
 import json
-from neuroconv import datainterfaces, NWBConverter
+from neuroconv import converters, datainterfaces, NWBConverter
 
 filepath = Path("guideGlobalMetadata.json")
 generatedJSONSchemaPath = Path("schemas", "json", "generated")
@@ -16,7 +16,7 @@
 
     class CustomNWBConverter(NWBConverter):
         data_interface_classes = {
-            custom_name: getattr(datainterfaces, interface_name)
+            custom_name: getattr(datainterfaces, interface_name, getattr(converters, interface_name, None))
             for custom_name, interface_name in interface_class_dict.items()
         }
 

diff --git a/guideGlobalMetadata.json b/guideGlobalMetadata.json
@@ -37,6 +37,9 @@
         "AudioInterface",
         "MiniscopeBehaviorInterface",
         "EDFRecordingInterface",
-        "SpikeGLXConverterPipe"
+        "SpikeGLXConverterPipe",
+        "BrukerTiffSinglePlaneConverter",
+        "BrukerTiffMultiPlaneConverter",
+        "MiniscopeConverter"
     ]
 }
diff --git a/schemas/json/generated/BrukerTiffMultiPlaneConverter.json b/schemas/json/generated/BrukerTiffMultiPlaneConverter.json
@@ -0,0 +1,35 @@
+{
+    "required": [],
+    "properties": {
+        "BrukerTiffMultiPlaneConverter": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "plane_separation_type": {
+                    "enum": [
+                        "disjoint",
+                        "contiguous"
+                    ]
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": false
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
diff --git a/schemas/json/generated/BrukerTiffSinglePlaneConverter.json b/schemas/json/generated/BrukerTiffSinglePlaneConverter.json
@@ -0,0 +1,29 @@
+{
+    "required": [],
+    "properties": {
+        "BrukerTiffSinglePlaneConverter": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": false
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
diff --git a/schemas/json/generated/EDFRecordingInterface.json b/schemas/json/generated/EDFRecordingInterface.json
@@ -0,0 +1,33 @@
+{
+    "required": [],
+    "properties": {
+        "EDFRecordingInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeries"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
diff --git a/schemas/json/generated/MiniscopeConverter.json b/schemas/json/generated/MiniscopeConverter.json
@@ -0,0 +1,29 @@
+{
+    "required": [],
+    "properties": {
+        "MiniscopeConverter": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
diff --git a/schemas/json/generated/SpikeGLXConverterPipe.json b/schemas/json/generated/SpikeGLXConverterPipe.json
@@ -0,0 +1,30 @@
+{
+    "required": [],
+    "properties": {
+        "SpikeGLXConverterPipe": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string",
+                    "description": "Path to the folder containing SpikeGLX streams."
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": false
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
diff --git a/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js b/src/renderer/src/stories/pages/guided-mode/SourceData.stories.js
@@ -35,6 +35,11 @@ import SLEAPInterfaceSchema from "../../../../../../schemas/json/generated/SLEAP
 import FicTracDataInterfaceSchema from "../../../../../../schemas/json/generated/FicTracDataInterface.json";
 import AudioInterfaceSchema from "../../../../../../schemas/json/generated/AudioInterface.json";
 import MiniscopeBehaviorInterfaceSchema from "../../../../../../schemas/json/generated/MiniscopeBehaviorInterface.json";
+import EDFRecordingInterfaceSchema from "../../../../../../schemas/json/generated/EDFRecordingInterface.json";
+import SpikeGLXConverterPipeSchema from "../../../../../../schemas/json/generated/SpikeGLXConverterPipe.json";
+import BrukerTiffSinglePlaneConverterSchema from "../../../../../../schemas/json/generated/BrukerTiffSinglePlaneConverter.json";
+import BrukerTiffMultiPlaneConverterSchema from "../../../../../../schemas/json/generated/BrukerTiffMultiPlaneConverter.json";
+import MiniscopeConverterSchema from "../../../../../../schemas/json/generated/MiniscopeConverter.json";
 
 export default {
     title: "Pages/Guided Mode/Source Data",
@@ -116,6 +121,16 @@ globalStateCopy.schema.source_data.properties.FicTracDataInterface =
 globalStateCopy.schema.source_data.properties.AudioInterface = AudioInterfaceSchema.properties.AudioInterface;
 globalStateCopy.schema.source_data.properties.MiniscopeBehaviorInterface =
     MiniscopeBehaviorInterfaceSchema.properties.MiniscopeBehaviorInterface;
+globalStateCopy.schema.source_data.properties.EDFRecordingInterface =
+    EDFRecordingInterfaceSchema.properties.EDFRecordingInterface;
+globalStateCopy.schema.source_data.properties.SpikeGLXConverterPipe =
+    SpikeGLXConverterPipeSchema.properties.SpikeGLXConverterPipe;
+globalStateCopy.schema.source_data.properties.BrukerTiffSinglePlaneConverter =
+    BrukerTiffSinglePlaneConverterSchema.properties.BrukerTiffSinglePlaneConverter;
+globalStateCopy.schema.source_data.properties.BrukerTiffMultiPlaneConverter =
+    BrukerTiffMultiPlaneConverterSchema.properties.BrukerTiffMultiPlaneConverter;
+globalStateCopy.schema.source_data.properties.MiniscopeConverter =
+    MiniscopeConverterSchema.properties.MiniscopeConverter;
 
 const results = globalStateCopy.results;
 for (let sub in results) {
@@ -344,3 +359,33 @@ const MiniscopeBehaviorInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalSta
 MiniscopeBehaviorInterfaceGlobalCopy.interfaces.interface = MiniscopeBehaviorInterface;
 MiniscopeBehaviorInterfaceGlobalCopy.schema.source_data = MiniscopeBehaviorInterfaceSchema;
 MiniscopeBehaviorInterface.args = { activePage, globalState: MiniscopeBehaviorInterfaceGlobalCopy };
+
+export const EDFRecordingInterface = PageTemplate.bind({});
+const EDFRecordingInterfaceGlobalCopy = JSON.parse(JSON.stringify(globalState));
+EDFRecordingInterfaceGlobalCopy.interfaces.interface = EDFRecordingInterface;
+EDFRecordingInterfaceGlobalCopy.schema.source_data = EDFRecordingInterfaceSchema;
+EDFRecordingInterface.args = { activePage, globalState: EDFRecordingInterfaceGlobalCopy };
+
+export const SpikeGLXConverterPipe = PageTemplate.bind({});
+const SpikeGLXConverterPipeGlobalCopy = JSON.parse(JSON.stringify(globalState));
+SpikeGLXConverterPipeGlobalCopy.interfaces.interface = SpikeGLXConverterPipe;
+SpikeGLXConverterPipeGlobalCopy.schema.source_data = SpikeGLXConverterPipeSchema;
+SpikeGLXConverterPipe.args = { activePage, globalState: SpikeGLXConverterPipeGlobalCopy };
+
+export const BrukerTiffSinglePlaneConverter = PageTemplate.bind({});
+const BrukerTiffSinglePlaneConverterGlobalCopy = JSON.parse(JSON.stringify(globalState));
+BrukerTiffSinglePlaneConverterGlobalCopy.interfaces.interface = BrukerTiffSinglePlaneConverter;
+BrukerTiffSinglePlaneConverterGlobalCopy.schema.source_data = BrukerTiffSinglePlaneConverterSchema;
+BrukerTiffSinglePlaneConverter.args = { activePage, globalState: BrukerTiffSinglePlaneConverterGlobalCopy };
+
+export const BrukerTiffMultiPlaneConverter = PageTemplate.bind({});
+const BrukerTiffMultiPlaneConverterGlobalCopy = JSON.parse(JSON.stringify(globalState));
+BrukerTiffMultiPlaneConverterGlobalCopy.interfaces.interface = BrukerTiffMultiPlaneConverter;
+BrukerTiffMultiPlaneConverterGlobalCopy.schema.source_data = BrukerTiffMultiPlaneConverterSchema;
+BrukerTiffMultiPlaneConverter.args = { activePage, globalState: BrukerTiffMultiPlaneConverterGlobalCopy };
+
+export const MiniscopeConverter = PageTemplate.bind({});
+const MiniscopeConverterGlobalCopy = JSON.parse(JSON.stringify(globalState));
+MiniscopeConverterGlobalCopy.interfaces.interface = MiniscopeConverter;
+MiniscopeConverterGlobalCopy.schema.source_data = MiniscopeConverterSchema;
+MiniscopeConverter.args = { activePage, globalState: MiniscopeConverterGlobalCopy };