Merge pull request #830 from NeurodataWithoutBorders/update-stories-w…

…ith-new-format-descriptions Generate all stories again given new descriptions
NeurodataWithoutBorders · Jun 5, 2024 · db12c65 · db12c65
2 parents 1057450 + 14ba221
commit db12c65
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Showing 34 changed files with 77 additions and 50 deletions.
diff --git a/generateInterfaceSchema.py b/generateInterfaceSchema.py
@@ -31,9 +31,7 @@ class CustomNWBConverter(NWBConverter):
 
 sourceDataStoryPath = Path("stories/pages/SourceData.stories.js")
 
-importCode = "\n".join(
-    map(lambda arr: f"import {arr[0]}Schema from '../inputs/interface_schemas/{arr[1]}'", paths.items())
-)
+importCode = "\n".join(map(lambda arr: f"import {arr[0]}Schema from '../{Path(*arr[1].parts[1:])}'", paths.items()))
 storyCode = "\n".join(
     map(
         lambda arr: f"""export const {arr[0]} = PageTemplate.bind({{}});

diff --git a/stories/inputs/interface_schemas/AlphaOmegaRecordingInterface.json b/stories/inputs/interface_schemas/AlphaOmegaRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the folder of .mpx files."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/AxonaRecordingInterface.json b/stories/inputs/interface_schemas/AxonaRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to .bin file."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/BiocamRecordingInterface.json b/stories/inputs/interface_schemas/BiocamRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the .bwr file."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/BlackrockRecordingInterface.json b/stories/inputs/interface_schemas/BlackrockRecordingInterface.json
@@ -8,7 +8,7 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "description": "Path to Blackrock file.",
+                    "description": "Path to the Blackrock file with suffix being .ns1, .ns2, .ns3, .ns4m .ns4, or .ns6.",
                     "type": "string"
                 },
                 "nsx_override": {

diff --git a/stories/inputs/interface_schemas/BlackrockSortingInterface.json b/stories/inputs/interface_schemas/BlackrockSortingInterface.json
@@ -8,7 +8,7 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "description": "Path to Blackrock file.",
+                    "description": "Path to Blackrock .nev file.",
                     "type": "string"
                 },
                 "sampling_frequency": {

diff --git a/stories/inputs/interface_schemas/BrukerTiffMultiPlaneConverter.json b/stories/inputs/interface_schemas/BrukerTiffMultiPlaneConverter.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "The folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env)."
                 },
                 "plane_separation_type": {
                     "enum": [

diff --git a/stories/inputs/interface_schemas/BrukerTiffMultiPlaneImagingInterface.json b/stories/inputs/interface_schemas/BrukerTiffMultiPlaneImagingInterface.json
@@ -9,7 +9,7 @@
                 "folder_path": {
                     "format": "directory",
                     "type": "string",
-                    "description": "The path that points to the folder containing the Bruker volumetric TIF image files and configuration files."
+                    "description": "The folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env)."
                 },
                 "stream_name": {
                     "type": "string"

diff --git a/stories/inputs/interface_schemas/BrukerTiffSinglePlaneImagingInterface.json b/stories/inputs/interface_schemas/BrukerTiffSinglePlaneImagingInterface.json
@@ -9,7 +9,7 @@
                 "folder_path": {
                     "format": "directory",
                     "type": "string",
-                    "description": "The path that points to the folder containing the Bruker TIF image files and configuration files."
+                    "description": "The folder containing the Bruker TIF image files and configuration files."
                 },
                 "stream_name": {
                     "type": "string"

diff --git a/stories/inputs/interface_schemas/CaimanSegmentationInterface.json b/stories/inputs/interface_schemas/CaimanSegmentationInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to .hdf5 file."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/CellExplorerRecordingInterface.json b/stories/inputs/interface_schemas/CellExplorerRecordingInterface.json
@@ -8,7 +8,7 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "description": "The folder where the session data is located. It should contain a\n`{folder.name}.session.mat` file and the binary files `{folder.name}.dat`\nor `{folder.name}.lfp` for the LFP interface.",
+                    "description": "Folder containing the .session.mat file",
                     "type": "string"
                 },
                 "verbose": {

diff --git a/stories/inputs/interface_schemas/DeepLabCutInterface.json b/stories/inputs/interface_schemas/DeepLabCutInterface.json
@@ -9,11 +9,13 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the .h5 file output by dlc."
                 },
                 "config_file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to .yml config file"
                 },
                 "subject_name": {
                     "type": "string",

diff --git a/stories/inputs/interface_schemas/EDFRecordingInterface.json b/stories/inputs/interface_schemas/EDFRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the .edf file."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/FicTracDataInterface.json b/stories/inputs/interface_schemas/FicTracDataInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the .dat file (the output of fictrac)"
                 },
                 "radius": {
                     "type": "number"

diff --git a/stories/inputs/interface_schemas/IntanRecordingInterface.json b/stories/inputs/interface_schemas/IntanRecordingInterface.json
@@ -8,11 +8,11 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to either a .rhd or a .rhs file"
                 },
                 "stream_id": {
-                    "type": "string",
-                    "default": "0"
+                    "type": "string"
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/KiloSortSortingInterface.json b/stories/inputs/interface_schemas/KiloSortSortingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the output Phy folder (containing the params.py)"
                 },
                 "keep_good_only": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/MCSRawRecordingInterface.json b/stories/inputs/interface_schemas/MCSRawRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the .raw file."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/MEArecRecordingInterface.json b/stories/inputs/interface_schemas/MEArecRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the MEArec .h5 file."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/MicroManagerTiffImagingInterface.json b/stories/inputs/interface_schemas/MicroManagerTiffImagingInterface.json
@@ -9,7 +9,7 @@
                 "folder_path": {
                     "format": "directory",
                     "type": "string",
-                    "description": "The path that points to the folder containing the OME-TIF image files."
+                    "description": "The folder containing the OME-TIF image files."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/MiniscopeBehaviorInterface.json b/stories/inputs/interface_schemas/MiniscopeBehaviorInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "The main Miniscope folder. The movie files are expected to be in sub folders within the main folder."
                 }
             },
             "type": "object",

diff --git a/stories/inputs/interface_schemas/MiniscopeConverter.json b/stories/inputs/interface_schemas/MiniscopeConverter.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "The path to the main Miniscope folder."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/MiniscopeImagingInterface.json b/stories/inputs/interface_schemas/MiniscopeImagingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "The main Miniscope folder. The microscope movie files are expected to be in sub folders within the main folder."
                 }
             },
             "type": "object",

diff --git a/stories/inputs/interface_schemas/NeuralynxRecordingInterface.json b/stories/inputs/interface_schemas/NeuralynxRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to Neuralynx directory containing \".nse\", \".ntt\", \".nse\", or \".nev\" files."
                 },
                 "stream_name": {
                     "type": "string"

diff --git a/stories/inputs/interface_schemas/NeuroScopeLFPInterface.json b/stories/inputs/interface_schemas/NeuroScopeLFPInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to .lfp or .eeg file."
                 },
                 "gain": {
                     "type": "number"

diff --git a/stories/inputs/interface_schemas/NeuroScopeRecordingInterface.json b/stories/inputs/interface_schemas/NeuroScopeRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to .dat file."
                 },
                 "gain": {
                     "type": "number"

diff --git a/stories/inputs/interface_schemas/NeuroScopeSortingInterface.json b/stories/inputs/interface_schemas/NeuroScopeSortingInterface.json
@@ -8,18 +8,22 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to folder containing .res and .clu files."
                 },
                 "keep_mua_units": {
                     "type": "boolean",
-                    "default": true
+                    "default": true,
+                    "description": "Whether to return sorted spikes from multi-unit activity."
                 },
                 "exclude_shanks": {
-                    "type": "array"
+                    "type": "array",
+                    "description": "List of indices to ignore."
                 },
                 "xml_file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to .xml file containing device and electrode configuration."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/OpenEphysRecordingInterface.json b/stories/inputs/interface_schemas/OpenEphysRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to OpenEphys directory (.continuous or .dat files)."
                 },
                 "stream_name": {
                     "type": "string"

diff --git a/stories/inputs/interface_schemas/PhySortingInterface.json b/stories/inputs/interface_schemas/PhySortingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the output Phy folder (containing the params.py)."
                 },
                 "exclude_cluster_groups": {
                     "type": "array",

diff --git a/stories/inputs/interface_schemas/PlexonRecordingInterface.json b/stories/inputs/interface_schemas/PlexonRecordingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the .plx file."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/PlexonSortingInterface.json b/stories/inputs/interface_schemas/PlexonSortingInterface.json
@@ -8,7 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the plexon spiking data (.plx file)."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/SLEAPInterface.json b/stories/inputs/interface_schemas/SLEAPInterface.json
@@ -8,11 +8,13 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the .slp file (the output of sleap)"
                 },
                 "video_file_path": {
                     "format": "file",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path of the video for extracting timestamps (optional)."
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/stories/inputs/interface_schemas/ScanImageImagingInterface.json b/stories/inputs/interface_schemas/ScanImageImagingInterface.json
@@ -11,6 +11,12 @@
                     "type": "string",
                     "description": "Path to Tiff file."
                 },
+                "channel_name": {
+                    "type": "string"
+                },
+                "plane_name": {
+                    "type": "string"
+                },
                 "fallback_sampling_frequency": {
                     "type": "number"
                 },

diff --git a/stories/inputs/interface_schemas/Spike2RecordingInterface.json b/stories/inputs/interface_schemas/Spike2RecordingInterface.json
@@ -8,7 +8,7 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "description": "Path to CED data file.",
+                    "description": "Path to .smr or .smrx file.",
                     "type": "string"
                 },
                 "verbose": {

diff --git a/stories/inputs/interface_schemas/Suite2pSegmentationInterface.json b/stories/inputs/interface_schemas/Suite2pSegmentationInterface.json
@@ -8,27 +8,22 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string"
+                    "type": "string",
+                    "description": "Path to the folder containing Suite2p segmentation data. Should contain 'plane#' subfolder(s)."
                 },
                 "channel_name": {
                     "type": "string"
                 },
                 "plane_name": {
-                    "type": "string"
+                    "type": "string",
+                    "description": "The name of the plane to load. This interface only loads one plane at a time. Use the full name, e.g. 'plane0'. If this value is omitted, the first plane found will be loaded."
                 },
                 "plane_segmentation_name": {
                     "type": "string"
                 },
                 "verbose": {
                     "type": "boolean",
                     "default": true
-                },
-                "combined": {
-                    "type": "boolean",
-                    "default": false
-                },
-                "plane_no": {
-                    "type": "number"
                 }
             },
             "type": "object",