From 1037479d6b7a4c299412400d5783c8dde40f76ae Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Tue, 24 Sep 2024 14:13:15 +0200 Subject: [PATCH 01/25] Update FrequencyRange component --- gui_dev/bun.lockb | Bin 239053 -> 246999 bytes gui_dev/src/App.jsx | 16 +- gui_dev/src/components/TitledBox.jsx | 8 +- gui_dev/src/pages/Settings/FrequencyRange.jsx | 156 +++++++++-------- gui_dev/src/pages/Settings/Settings.jsx | 165 +++++++++++------- py_neuromodulation/gui/backend/app_backend.py | 2 +- py_neuromodulation/utils/types.py | 6 +- pyproject.toml | 2 +- 8 files changed, 203 insertions(+), 152 deletions(-) diff --git a/gui_dev/bun.lockb b/gui_dev/bun.lockb index ae7d827b00f431779b90f1d41f170aebf07b6c4f..cafed1a34c58bcd17f9621a80286e99fce910eea 100755 GIT binary patch delta 53049 zcmeFad3;UR|22N^kxMROjtnFukqD8<=!PUWf*@jwDTE**Bt$|I#F&_es_9^pqGBr5 z8j7N7s;Z$i&p{2XN^7dAMO%Jroq>G&Z9h-H&+mDjzj|KQUHiTE^xnhSd*73sIR15o zi!&uUmat%D}7fy!cvq 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state.connectSocket); const disconnectSocket = useSocketStore((state) => state.disconnectSocket); - useEffect(() => { - console.log("Connecting socket from App component..."); - connectSocket(); - return () => { - console.log("Disconnecting socket from App component..."); - disconnectSocket(); - }; - }, [connectSocket, disconnectSocket]); + // useEffect(() => { + // console.log("Connecting socket from App component..."); + // connectSocket(); + // return () => { + // console.log("Disconnecting socket from App component..."); + // disconnectSocket(); + // }; + // }, [connectSocket, disconnectSocket]); return ( diff --git a/gui_dev/src/components/TitledBox.jsx b/gui_dev/src/components/TitledBox.jsx index 56f0266b..a86b6009 100644 --- a/gui_dev/src/components/TitledBox.jsx +++ b/gui_dev/src/components/TitledBox.jsx @@ -1,4 +1,4 @@ -import { Container } from "@mui/material"; +import { Box, Container } from "@mui/material"; /** * Component that uses the Box component to render an HTML fieldset element @@ -13,14 +13,14 @@ export const TitledBox = ({ children, ...props }) => ( - {title} {children} - + ); diff --git a/gui_dev/src/pages/Settings/FrequencyRange.jsx b/gui_dev/src/pages/Settings/FrequencyRange.jsx index 5def783b..cdf27f24 100644 --- a/gui_dev/src/pages/Settings/FrequencyRange.jsx +++ b/gui_dev/src/pages/Settings/FrequencyRange.jsx @@ -1,88 +1,94 @@ -import { useState } from "react"; +import { TextField, Button, Box, Typography, IconButton } from "@mui/material"; +import { Add, Close } from "@mui/icons-material"; -// const onChange = (key, newValue) => { -// settings.frequencyRanges[key] = newValue; -// }; - -// Object.entries(settings.frequencyRanges).map(([key, value]) => ( -// -// )); +export const FrequencyRange = ({ name, range, onChange, onRemove }) => { + const handleChange = (field, value) => { + onChange(name, { ...range, [field]: value }); + }; -/** */ + return ( + + onChange(e.target.value, range, name)} + sx={{ mr: 1, width: "30%" }} + /> + handleChange("frequency_low_hz", e.target.value)} + label="Low Hz" + sx={{ mr: 1, width: "30%" }} + /> + handleChange("frequency_high_hz", e.target.value)} + label="High Hz" + sx={{ mr: 1, width: "30%" }} + /> + onRemove(name)} color="error"> + + + + ); +}; -/** - * - * @param {String} key - * @param {Array} freqRange - * @param {Function} onChange - * @returns - */ -export const FrequencyRange = ({ settings }) => { - const [frequencyRanges, setFrequencyRanges] = useState(settings || {}); - // Handle changes in the text fields - const handleInputChange = (label, key, newValue) => { - setFrequencyRanges((prevState) => ({ - ...prevState, - [label]: { - ...prevState[label], - [key]: newValue, - }, - })); +export const FrequencyRangeList = ({ ranges, onChange }) => { + const handleChange = (newName, newRange, oldName = newName) => { + const updatedRanges = { ...ranges }; + if (newName !== oldName) { + delete updatedRanges[oldName]; + } + updatedRanges[newName] = newRange; + onChange(["frequency_ranges_hz"], updatedRanges); }; - // Add a new band - const addBand = () => { - const newLabel = `Band ${Object.keys(frequencyRanges).length + 1}`; - setFrequencyRanges((prevState) => ({ - ...prevState, - [newLabel]: { frequency_high_hz: "", frequency_low_hz: "" }, - })); + const handleRemove = (name) => { + const updatedRanges = { ...ranges }; + delete updatedRanges[name]; + onChange(["frequency_ranges_hz"], updatedRanges); }; - // Remove a band - const removeBand = (label) => { - const updatedRanges = { ...frequencyRanges }; - delete updatedRanges[label]; - setFrequencyRanges(updatedRanges); + const addRange = () => { + let newName = "NewRange"; + let counter = 0; + while (ranges.hasOwnProperty(newName)) { + counter++; + newName = `NewRange${counter}`; + } + const updatedRanges = { + ...ranges, + [newName]: { frequency_low_hz: "", frequency_high_hz: "" }, + }; + onChange(["frequency_ranges_hz"], updatedRanges); }; return ( -

-
Frequency Bands
- {Object.keys(frequencyRanges).map((label) => ( -
- { - const newLabel = e.target.value; - const updatedRanges = { ...frequencyRanges }; - updatedRanges[newLabel] = updatedRanges[label]; - delete updatedRanges[label]; - setFrequencyRanges(updatedRanges); - }} - placeholder="Band Name" - /> - - handleInputChange(label, "frequency_high_hz", e.target.value) - } - placeholder="High Hz" - /> - - handleInputChange(label, "frequency_low_hz", e.target.value) - } - placeholder="Low Hz" - /> - -
+ + + Frequency Ranges + + {Object.entries(ranges).map(([name, range]) => ( + ))} - -
+ + ); }; diff --git a/gui_dev/src/pages/Settings/Settings.jsx b/gui_dev/src/pages/Settings/Settings.jsx index c2f1dff9..01706d38 100644 --- a/gui_dev/src/pages/Settings/Settings.jsx +++ b/gui_dev/src/pages/Settings/Settings.jsx @@ -1,4 +1,6 @@ +import { useState } from "react"; import { + Box, Button, InputAdornment, Stack, @@ -8,7 +10,7 @@ import { } from "@mui/material"; import { Link } from "react-router-dom"; import { CollapsibleBox, TitledBox } from "@/components"; -import { FrequencyRange } from "./FrequencyRange"; +import { FrequencyRangeList } from "./FrequencyRange"; import { useSettingsStore } from "@/stores"; import { filterObjectByKeys } from "@/utils/functions"; @@ -44,13 +46,13 @@ const NumberField = ({ value, onChange, label }) => { value={value} onChange={handleChange} label={label} - InputProps={{ - endAdornment: ( - - Hz - - ), - }} + // InputProps={{ + // endAdornment: ( + // + // Hz + // + // ), + // }} inputProps={{ pattern: "[0-9]*", }} @@ -58,16 +60,11 @@ const NumberField = ({ value, onChange, label }) => { ); }; -const FrequencyRangeField = ({ value, onChange, label }) => ( - -); - // Map component types to their respective wrappers const componentRegistry = { boolean: BooleanField, string: StringField, number: NumberField, - FrequencyRange: FrequencyRangeField, }; const SettingsField = ({ path, Component, label, value, onChange, depth }) => { @@ -96,11 +93,25 @@ const SettingsSection = ({ onChange, depth = 0, }) => { - if (Object.keys(settings).length === 0) { - return null; - } const boxTitle = title ? title : formatKey(path[path.length - 1]); + // If we receive a primitive value, we need to render a component + + if (typeof settings !== "object") { + const Component = componentRegistry[typeof settings]; + if (!Component) { + console.error(`Invalid component type: ${typeof settings}`); + return null; + } + return ( + + {boxTitle} + + + ); + } + + // If we receive a nested object, we iterate over it and render recursively return ( {Object.entries(settings).map(([key, value]) => { @@ -144,6 +155,7 @@ const SettingsSection = ({ }; const SettingsContent = () => { + const [selectedFeature, setSelectedFeature] = useState(""); const settings = useSettingsStore((state) => state.settings); const updateSettings = useSettingsStore((state) => state.updateSettings); @@ -151,6 +163,8 @@ const SettingsContent = () => { return
Loading settings...
; } + console.log(settings); + const handleChange = (path, value) => { updateSettings((settings) => { let current = settings; @@ -181,32 +195,23 @@ const SettingsContent = () => { "project_subcortex_settings", ]; + const generalSettingsKeys = [ + "sampling_rate_features_hz", + "segment_length_features_ms", + ]; + return ( - - - - - - - {preprocessingSettingsKeys.map((key) => ( + + + {generalSettingsKeys.map((key) => ( { depth={0} /> ))} - + - - {postprocessingSettingsKeys.map((key) => ( - - ))} - + + + - - {Object.entries(enabledFeatures).map(([feature, featureSettings]) => ( - + + {preprocessingSettingsKeys.map((key) => ( + + ))} + + + + {postprocessingSettingsKeys.map((key) => ( + + ))} + + + + + - - ))} - + + + {Object.entries(enabledFeatures).map( + ([feature, featureSettings]) => ( + + + + ) + )} + + + ); }; diff --git a/py_neuromodulation/gui/backend/app_backend.py b/py_neuromodulation/gui/backend/app_backend.py index b173ced7..10a8c158 100644 --- a/py_neuromodulation/gui/backend/app_backend.py +++ b/py_neuromodulation/gui/backend/app_backend.py @@ -100,7 +100,7 @@ async def get_settings(): async def update_settings(data: dict): try: self.pynm_state.settings = NMSettings.model_validate(data) - self.logger.info(self.pynm_state.settings.features) + self.logger.debug(self.pynm_state.settings.features) return self.pynm_state.settings.model_dump() except ValueError as e: raise HTTPException( diff --git a/py_neuromodulation/utils/types.py b/py_neuromodulation/utils/types.py index 7886685d..06a6cf7b 100644 --- a/py_neuromodulation/utils/types.py +++ b/py_neuromodulation/utils/types.py @@ -124,12 +124,10 @@ def process_for_frontend(self) -> dict[str, Any]: """ Process the model for frontend use, adding __field_type__ information. """ - result = {} + result: dict[str, Any] = {"__field_type__": self.__class__.__name__} for field_name, field_value in self.__dict__.items(): if isinstance(field_value, NMBaseModel): - processed_value = field_value.process_for_frontend() - processed_value["__field_type__"] = field_value.__class__.__name__ - result[field_name] = processed_value + result[field_name] = field_value.process_for_frontend() elif isinstance(field_value, list): result[field_name] = [ item.process_for_frontend() diff --git a/pyproject.toml b/pyproject.toml index c20736da..095dcf80 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -72,7 +72,7 @@ dev = [ "pytest-cov", "pytest-sugar", "notebook", - "watchdog", + "uvicorn[standard]", ] docs = [ "py-neuromodulation[dev]", From 447fc201897c58eeb83b54e6548e0e6260c60708 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Tue, 24 Sep 2024 14:47:09 +0200 Subject: [PATCH 02/25] Fix Number input fields --- gui_dev/src/pages/Settings/FrequencyRange.jsx | 49 ++++++++++++++----- 1 file changed, 38 insertions(+), 11 deletions(-) diff --git a/gui_dev/src/pages/Settings/FrequencyRange.jsx b/gui_dev/src/pages/Settings/FrequencyRange.jsx index cdf27f24..34c9aaf7 100644 --- a/gui_dev/src/pages/Settings/FrequencyRange.jsx +++ b/gui_dev/src/pages/Settings/FrequencyRange.jsx @@ -1,39 +1,66 @@ -import { TextField, Button, Box, Typography, IconButton } from "@mui/material"; +import { + TextField, + Button, + Box, + Typography, + IconButton, + Stack, +} from "@mui/material"; import { Add, Close } from "@mui/icons-material"; +const NumberField = ({ ...props }) => ( + +); + export const FrequencyRange = ({ name, range, onChange, onRemove }) => { const handleChange = (field, value) => { onChange(name, { ...range, [field]: value }); }; return ( - + onChange(e.target.value, range, name)} - sx={{ mr: 1, width: "30%" }} /> - handleChange("frequency_low_hz", e.target.value)} label="Low Hz" - sx={{ mr: 1, width: "30%" }} /> - handleChange("frequency_high_hz", e.target.value)} label="High Hz" - sx={{ mr: 1, width: "30%" }} /> - onRemove(name)} color="error"> + onRemove(name)} + color="primary" + disableRipple + sx={{ m: 0, p: 0 }} + > - + ); }; @@ -68,7 +95,7 @@ export const FrequencyRangeList = ({ ranges, onChange }) => { }; return ( - + Frequency Ranges @@ -89,6 +116,6 @@ export const FrequencyRangeList = ({ ranges, onChange }) => { > Add Range - + ); }; From 1b066deacae9b4c8efe9a787f159ec5ec07dd9ec Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Wed, 25 Sep 2024 14:51:38 +0200 Subject: [PATCH 03/25] Disable autocomplete from TextFields --- gui_dev/src/theme.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gui_dev/src/theme.js b/gui_dev/src/theme.js index 5e2b5f11..cc99909c 100644 --- a/gui_dev/src/theme.js +++ b/gui_dev/src/theme.js @@ -22,6 +22,11 @@ export const theme = createTheme({ disableRipple: true, }, }, + MuiTextField: { + defaultProps: { + autoComplete: "off", + }, + }, MuiStack: { defaultProps: { alignItems: "center", From 3cc373c49abd693ce3bc6512746b3526a50896e8 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Wed, 25 Sep 2024 14:51:49 +0200 Subject: [PATCH 04/25] Fix FrequencyRangeList --- gui_dev/src/pages/Settings/FrequencyRange.jsx | 109 +++++++++++++----- gui_dev/src/pages/Settings/Settings.jsx | 56 ++++++--- gui_dev/src/stores/settingsStore.js | 21 +++- gui_dev/src/utils/functions.js | 1 + py_neuromodulation/gui/backend/app_backend.py | 10 +- 5 files changed, 147 insertions(+), 50 deletions(-) diff --git a/gui_dev/src/pages/Settings/FrequencyRange.jsx b/gui_dev/src/pages/Settings/FrequencyRange.jsx index 34c9aaf7..e881b459 100644 --- a/gui_dev/src/pages/Settings/FrequencyRange.jsx +++ b/gui_dev/src/pages/Settings/FrequencyRange.jsx @@ -1,12 +1,7 @@ -import { - TextField, - Button, - Box, - Typography, - IconButton, - Stack, -} from "@mui/material"; +import { useState } from "react"; +import { TextField, Button, IconButton, Stack } from "@mui/material"; import { Add, Close } from "@mui/icons-material"; +import { debounce } from "@/utils"; const NumberField = ({ ...props }) => ( ( /> ); -export const FrequencyRange = ({ name, range, onChange, onRemove }) => { - const handleChange = (field, value) => { - onChange(name, { ...range, [field]: value }); +export const FrequencyRange = ({ + id, + name, + range, + onChangeName, + onChangeRange, + onRemove, +}) => { + const [localName, setLocalName] = useState(name); + + const debouncedChangeName = debounce((newName) => { + onChangeName(newName, name); + }, 1000); + + const handleNameChange = (e) => { + const newName = e.target.value; + setLocalName(newName); + debouncedChangeName(newName); + }; + + const handleNameBlur = () => { + onChangeName(localName, name); + }; + + const handleKeyPress = (e) => { + if (e.key === "Enter") { + console.log(e.target.value, name); + onChangeName(localName, name); + } + }; + + const handleRangeChange = (field, value) => { + onChangeRange(id, { ...range, [field]: value }); }; return ( onChange(e.target.value, range, name)} + onChange={handleNameChange} + onBlur={handleNameBlur} + onKeyPress={handleKeyPress} /> handleChange("frequency_low_hz", e.target.value)} + onChange={(e) => handleRangeChange("frequency_low_hz", e.target.value)} label="Low Hz" /> handleChange("frequency_high_hz", e.target.value)} + onChange={(e) => handleRangeChange("frequency_high_hz", e.target.value)} label="High Hz" /> { ); }; -export const FrequencyRangeList = ({ ranges, onChange }) => { - const handleChange = (newName, newRange, oldName = newName) => { +export const FrequencyRangeList = ({ + ranges, + rangeOrder, + onChange, + onOrderChange, +}) => { + const handleChangeRange = (name, newRange) => { const updatedRanges = { ...ranges }; - if (newName !== oldName) { - delete updatedRanges[oldName]; + updatedRanges[name] = newRange; + onChange(["frequency_ranges_hz"], updatedRanges); + }; + + const handleChangeName = (newName, oldName) => { + if (oldName === newName) { + return; } - updatedRanges[newName] = newRange; + + const updatedRanges = { ...ranges, [newName]: ranges[oldName] }; + delete updatedRanges[oldName]; onChange(["frequency_ranges_hz"], updatedRanges); + + const updatedOrder = rangeOrder.map((name) => + name === oldName ? newName : name + ); + onOrderChange(updatedOrder); }; const handleRemove = (name) => { const updatedRanges = { ...ranges }; delete updatedRanges[name]; onChange(["frequency_ranges_hz"], updatedRanges); + + const updatedOrder = rangeOrder.filter((item) => item !== name); + onOrderChange(updatedOrder); }; const addRange = () => { let newName = "NewRange"; let counter = 0; - while (ranges.hasOwnProperty(newName)) { + // Find first available name + while (Object.hasOwn(ranges, newName)) { counter++; newName = `NewRange${counter}`; } + const updatedRanges = { ...ranges, - [newName]: { frequency_low_hz: "", frequency_high_hz: "" }, + [newName]: { frequency_low_hz: 1, frequency_high_hz: 500 }, }; onChange(["frequency_ranges_hz"], updatedRanges); + + const updatedOrder = [...rangeOrder, newName]; + onOrderChange(updatedOrder); }; return ( - - Frequency Ranges - - {Object.entries(ranges).map(([name, range]) => ( + {rangeOrder.map((name, index) => ( ))} diff --git a/gui_dev/src/pages/Settings/Settings.jsx b/gui_dev/src/pages/Settings/Settings.jsx index 01706d38..188b996c 100644 --- a/gui_dev/src/pages/Settings/Settings.jsx +++ b/gui_dev/src/pages/Settings/Settings.jsx @@ -2,6 +2,7 @@ import { useState } from "react"; import { Box, Button, + ButtonGroup, InputAdornment, Stack, Switch, @@ -96,7 +97,6 @@ const SettingsSection = ({ const boxTitle = title ? title : formatKey(path[path.length - 1]); // If we receive a primitive value, we need to render a component - if (typeof settings !== "object") { const Component = componentRegistry[typeof settings]; if (!Component) { @@ -104,10 +104,17 @@ const SettingsSection = ({ return null; } return ( - - {boxTitle} - - + + // + // {boxTitle} + // + // ); } @@ -158,6 +165,12 @@ const SettingsContent = () => { const [selectedFeature, setSelectedFeature] = useState(""); const settings = useSettingsStore((state) => state.settings); const updateSettings = useSettingsStore((state) => state.updateSettings); + const frequencyRangeOrder = useSettingsStore( + (state) => state.frequencyRangeOrder + ); + const updateFrequencyRangeOrder = useSettingsStore( + (state) => state.updateFrequencyRangeOrder + ); if (!settings) { return
Loading settings...
; @@ -209,7 +222,7 @@ const SettingsContent = () => { gap={2} p={2} > - + {generalSettingsKeys.map((key) => ( { @@ -302,15 +317,28 @@ export const Settings = () => { return ( - + + + ); }; diff --git a/gui_dev/src/stores/settingsStore.js b/gui_dev/src/stores/settingsStore.js index f9930d06..7064ec98 100644 --- a/gui_dev/src/stores/settingsStore.js +++ b/gui_dev/src/stores/settingsStore.js @@ -25,11 +25,13 @@ const uploadSettingsToServer = async (settings) => { export const useSettingsStore = createStore("settings", (set, get) => ({ settings: null, + frequencyRangeOrder: [], isLoading: false, error: null, retryCount: 0, setSettings: (settings) => set({ settings }), + setFrequencyRangeOrder: (order) => set({ frequencyRangeOrder: order }), fetchSettingsWithDelay: () => { set({ isLoading: true, error: null }); @@ -46,7 +48,11 @@ export const useSettingsStore = createStore("settings", (set, get) => ({ throw new Error("Failed to fetch settings"); } const data = await response.json(); - set({ settings: data, retryCount: 0 }); + set({ + settings: data, + frequencyRangeOrder: Object.keys(data.frequency_ranges_hz || {}), + retryCount: 0, + }); } catch (error) { console.log("Error fetching settings:", error); set((state) => ({ @@ -65,8 +71,13 @@ export const useSettingsStore = createStore("settings", (set, get) => ({ resetRetryCount: () => set({ retryCount: 0 }), + updateFrequencyRangeOrder: (newOrder) => { + set({ frequencyRangeOrder: newOrder }); + }, + updateSettings: async (updater) => { const currentSettings = get().settings; + const currentOrder = get().frequencyRangeOrder; // Apply the update optimistically set((state) => { @@ -75,18 +86,22 @@ export const useSettingsStore = createStore("settings", (set, get) => ({ const newSettings = get().settings; + // Update the frequency range order + const newOrder = Object.keys(newSettings.frequency_ranges_hz || {}); + set({ frequencyRangeOrder: newOrder }); + try { const result = await uploadSettingsToServer(newSettings); if (!result.success) { // Revert the local state if the server update failed - set({ settings: currentSettings }); + set({ settings: currentSettings, frequencyRangeOrder: currentOrder }); } return result; } catch (error) { // Revert the local state if there was an error - set({ settings: currentSettings }); + set({ settings: currentSettings, frequencyRangeOrder: currentOrder }); throw error; } }, diff --git a/gui_dev/src/utils/functions.js b/gui_dev/src/utils/functions.js index 04289d5c..1f8ae90a 100644 --- a/gui_dev/src/utils/functions.js +++ b/gui_dev/src/utils/functions.js @@ -17,6 +17,7 @@ export function debounce(func, wait) { timeout = setTimeout(later, wait); }; } + export const flattenDictionary = (dict, parentKey = "", result = {}) => { for (let key in dict) { const newKey = parentKey ? `${parentKey}.${key}` : key; diff --git a/py_neuromodulation/gui/backend/app_backend.py b/py_neuromodulation/gui/backend/app_backend.py index 10a8c158..114b9f04 100644 --- a/py_neuromodulation/gui/backend/app_backend.py +++ b/py_neuromodulation/gui/backend/app_backend.py @@ -72,7 +72,9 @@ def __init__( def push_features_to_frontend(self, feature_queue: Queue) -> None: while True: - time.sleep(0.002) # NOTE: should be adapted depending on feature sampling rate + time.sleep( + 0.002 + ) # NOTE: should be adapted depending on feature sampling rate if feature_queue.empty() is False: self.logger.info("data in feature queue") features = feature_queue.get() @@ -98,11 +100,13 @@ async def get_settings(): @self.post("/api/settings") async def update_settings(data: dict): + print(data) try: self.pynm_state.settings = NMSettings.model_validate(data) self.logger.debug(self.pynm_state.settings.features) return self.pynm_state.settings.model_dump() except ValueError as e: + self.logger.error(f"Error updating settings: {e}") raise HTTPException( status_code=422, detail={"error": "Validation failed", "details": str(e)}, @@ -122,7 +126,7 @@ async def handle_stream_control(data: dict): experiment_name=data["experiment_name"], websocket_manager_features=self.websocket_manager_features, ) - + # this also fails due to pickling error # self.push_features_process = Process( # target=self.push_features_to_frontend, @@ -388,5 +392,3 @@ async def websocket_endpoint(websocket: WebSocket): # # Serve the index.html for any path that doesn't match an API route # print(Path.cwd()) # return FileResponse("frontend/index.html") - - From 2518990bf84d4e8fad0d9385284376bdebba09b9 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Mon, 7 Oct 2024 01:09:54 +0200 Subject: [PATCH 05/25] Add subclass of Pydantic Field that carries additional metadata for frontend --- .../processing/normalization.py | 2 +- py_neuromodulation/processing/resample.py | 3 +- .../utils/pydantic_extensions.py | 129 ++++++++++++++++++ py_neuromodulation/utils/types.py | 87 +++--------- 4 files changed, 150 insertions(+), 71 deletions(-) create mode 100644 py_neuromodulation/utils/pydantic_extensions.py diff --git a/py_neuromodulation/processing/normalization.py b/py_neuromodulation/processing/normalization.py index 3345b122..66419cec 100644 --- a/py_neuromodulation/processing/normalization.py +++ b/py_neuromodulation/processing/normalization.py @@ -2,10 +2,10 @@ import numpy as np from typing import TYPE_CHECKING, Callable, Literal, get_args +from pydantic import Field from py_neuromodulation.utils.types import ( NMBaseModel, - Field, NormMethod, NMPreprocessor, ) diff --git a/py_neuromodulation/processing/resample.py b/py_neuromodulation/processing/resample.py index e793a824..73014d3a 100644 --- a/py_neuromodulation/processing/resample.py +++ b/py_neuromodulation/processing/resample.py @@ -1,7 +1,8 @@ """Module for resampling.""" import numpy as np -from py_neuromodulation.utils.types import NMBaseModel, Field, NMPreprocessor +from pydantic import Field +from py_neuromodulation.utils.types import NMBaseModel, NMPreprocessor class ResamplerSettings(NMBaseModel): diff --git a/py_neuromodulation/utils/pydantic_extensions.py b/py_neuromodulation/utils/pydantic_extensions.py new file mode 100644 index 00000000..65d6cb4e --- /dev/null +++ b/py_neuromodulation/utils/pydantic_extensions.py @@ -0,0 +1,129 @@ +from typing import Any, get_type_hints +from pydantic.fields import FieldInfo, _FieldInfoInputs, _FromFieldInfoInputs +from pydantic import BaseModel, ConfigDict, model_serializer +from pydantic_core import PydanticUndefined +from typing_extensions import Unpack, TypedDict +from pprint import pformat + + +class _NMExtraFieldInputs(TypedDict, total=False): + """Additional fields to add on top of the pydantic FieldInfo""" + + meta: dict[str, Any] + + +class _NMFieldInfoInputs(_FieldInfoInputs, _NMExtraFieldInputs, total=False): + """Combine pydantic FieldInfo inputs with PyNM additional inputs""" + + pass + + +class _NMFromFieldInfoInputs(_FromFieldInfoInputs, _NMExtraFieldInputs, total=False): + """Combine pydantic FieldInfo.from_field inputs with PyNM additional inputs""" + + pass + + +class NMFieldInfo(FieldInfo): + # Add default values for any other custom fields here + _default_values = {} + + def __init__(self, **kwargs: Unpack[_NMFieldInfoInputs]) -> None: + extra_fields = get_type_hints(_NMExtraFieldInputs) + for field, field_type in extra_fields.items(): + # If no default value, try to instantiate the field type with no arguments, if it fails, set to None + try: + value = ( + kwargs.pop(field, self._default_values.get(field, field_type())), # type: ignore + ) + except Exception: + value = None + + setattr(self, field, value) + super().__init__(**kwargs) + + @staticmethod + def from_field( + default: Any = PydanticUndefined, + **kwargs: Unpack[_NMFromFieldInfoInputs], + ) -> "NMFieldInfo": + if "annotation" in kwargs: + raise TypeError('"annotation" is not permitted as a Field keyword argument') + return NMFieldInfo(default=default, **kwargs) + + def __repr_args__(self): + yield from super().__repr_args__() + extra_fields = get_type_hints(_NMExtraFieldInputs) + for field in extra_fields: + value = getattr(self, field) + yield field, value + + +def NMField( + default: Any = PydanticUndefined, + **kwargs: Unpack[_NMFromFieldInfoInputs], +) -> Any: + return NMFieldInfo.from_field(default=default, **kwargs) + + +class NMBaseModel(BaseModel): + model_config = ConfigDict(validate_assignment=False, extra="allow") + + def __init__(self, *args, **kwargs) -> None: + if kwargs: + super().__init__(**kwargs) + else: + field_names = list(self.model_fields.keys()) + kwargs = {} + for i in range(len(args)): + kwargs[field_names[i]] = args[i] + super().__init__(**kwargs) + + def __str__(self): + return pformat(self.model_dump()) + + def __repr__(self): + return pformat(self.model_dump()) + + def validate(self) -> Any: # type: ignore + return self.model_validate(self.model_dump()) + + def __getitem__(self, key): + return getattr(self, key) + + def __setitem__(self, key, value) -> None: + setattr(self, key, value) + + @classmethod + def get_fields(cls) -> dict[str, NMFieldInfo]: + return cls.model_fields # type: ignore + + @model_serializer + def serialize_model(self) -> dict[str, Any]: + result = {"__field_type__": self.__class__.__name__} + for field_name, field_info in self.model_fields.items(): + value = getattr(self, field_name) + if isinstance(value, NMBaseModel): + result[field_name] = value.serialize_model() + elif isinstance(value, list): + result[field_name] = [ + item.serialize_model() if isinstance(item, NMBaseModel) else item + for item in value + ] + elif isinstance(value, dict): + result[field_name] = { + k: v.serialize_model() if isinstance(v, NMBaseModel) else v + for k, v in value.items() + } + else: + result[field_name] = value + + # Extract unit information from Annotated type + if get_origin(field_info.annotation) is Annotated: + metadata = get_args(field_info.annotation)[1:] + for item in metadata: + if isinstance(item, dict) and "unit" in item: + result[f"{field_name}_metadata"] = {"unit": item["unit"]} + break + + return result diff --git a/py_neuromodulation/utils/types.py b/py_neuromodulation/utils/types.py index 06a6cf7b..1aad1b08 100644 --- a/py_neuromodulation/utils/types.py +++ b/py_neuromodulation/utils/types.py @@ -1,9 +1,18 @@ from os import PathLike from math import isnan -from typing import Any, Literal, Protocol, TYPE_CHECKING, runtime_checkable -from pydantic import ConfigDict, Field, model_validator, BaseModel +from typing import ( + Literal, + Protocol, + TYPE_CHECKING, + runtime_checkable, +) +from pydantic import ( + BaseModel, + model_validator, +) from pydantic_core import ValidationError, InitErrorDetails -from pprint import pformat +from .pydantic_extensions import NMBaseModel, NMField + from collections.abc import Sequence from datetime import datetime @@ -54,6 +63,7 @@ "minmax", ] + ################################### ######## PROTOCOL CLASSES ######## ################################### @@ -87,68 +97,11 @@ def __init__(self, sfreq: float, settings: "NMSettings") -> None: ... def process(self, data: "np.ndarray") -> "np.ndarray": ... -################################### -######## PYDANTIC CLASSES ######## -################################### - - -class NMBaseModel(BaseModel): - model_config = ConfigDict(validate_assignment=False, extra="allow") - - def __init__(self, *args, **kwargs) -> None: - if kwargs: - super().__init__(**kwargs) - else: - field_names = list(self.model_fields.keys()) - kwargs = {} - for i in range(len(args)): - kwargs[field_names[i]] = args[i] - super().__init__(**kwargs) - - def __str__(self): - return pformat(self.model_dump()) - - def __repr__(self): - return pformat(self.model_dump()) - - def validate(self) -> Any: # type: ignore - return self.model_validate(self.model_dump()) - - def __getitem__(self, key): - return getattr(self, key) - - def __setitem__(self, key, value) -> None: - setattr(self, key, value) - - def process_for_frontend(self) -> dict[str, Any]: - """ - Process the model for frontend use, adding __field_type__ information. - """ - result: dict[str, Any] = {"__field_type__": self.__class__.__name__} - for field_name, field_value in self.__dict__.items(): - if isinstance(field_value, NMBaseModel): - result[field_name] = field_value.process_for_frontend() - elif isinstance(field_value, list): - result[field_name] = [ - item.process_for_frontend() - if isinstance(item, NMBaseModel) - else item - for item in field_value - ] - elif isinstance(field_value, dict): - result[field_name] = { - k: v.process_for_frontend() if isinstance(v, NMBaseModel) else v - for k, v in field_value.items() - } - else: - result[field_name] = field_value - - return result - - class FrequencyRange(NMBaseModel): - frequency_low_hz: float = Field(gt=0) - frequency_high_hz: float = Field(gt=0) + # frequency_low_hz: Annotated[list[float], {"unit": "Hz"}] = Field(gt=0) + # frequency_high_hz: FrequencyHz = Field(gt=0) + frequency_low_hz: float = NMField(gt=0, meta={"unit": "Hz"}) + frequency_high_hz: float = NMField(gt=0, meta={"unit": "Hz"}) def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) @@ -236,14 +189,10 @@ def print_all(cls): for f in cls.list_all(): print(f) - @classmethod - def get_fields(cls): - return cls.model_fields - def create_validation_error( error_message: str, - loc: list[str | int] = None, + loc: list[str | int] | None = None, title: str = "Validation Error", input_type: Literal["python", "json"] = "python", hide_input: bool = False, From 166ad98832a28e109c9d8208bed6aad460c2f2cf Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Thu, 10 Oct 2024 15:34:57 +0200 Subject: [PATCH 06/25] display Pydantic errors in Settings page --- gui_dev/bun.lockb | Bin 246999 -> 254737 bytes gui_dev/package.json | 21 +- .../src/components/StatusBar/StatusBar.jsx | 56 ++- gui_dev/src/pages/Settings/Dropdown.jsx | 18 +- gui_dev/src/pages/Settings/FrequencyRange.jsx | 8 +- gui_dev/src/pages/Settings/Settings.jsx | 348 +++++++++++------- gui_dev/src/pages/Settings/index.js | 1 - gui_dev/src/stores/createStore.js | 19 +- gui_dev/src/stores/settingsStore.js | 106 +++--- py_neuromodulation/__init__.py | 5 +- py_neuromodulation/gui/backend/app_backend.py | 62 +++- .../utils/pydantic_extensions.py | 48 +-- py_neuromodulation/utils/types.py | 25 +- pyproject.toml | 5 +- 14 files changed, 441 insertions(+), 281 deletions(-) delete mode 100644 gui_dev/src/pages/Settings/index.js diff --git a/gui_dev/bun.lockb b/gui_dev/bun.lockb index cafed1a34c58bcd17f9621a80286e99fce910eea..929e237a89336bd38e10ff03594c899074767620 100755 GIT binary patch delta 67914 zcmeFad0b8F|2Dq&)}~ES5fxFCN>U+}YBwmNP?QEjn$w_3Whzq2oQ0(lGG?CVkU3-K zA%)Ddk|Fc&dhfOJ**MSV`@Ejt>v{e<>t*ljzOH+E-|zc<4|^TwoSQi z+O=hA7kdwIZQjgjQ1bj^W11alWIfSv#7Nr%?k(ICBc?uRB%r5%u1|-wHBKTK`Onvc zq=dx4m|($bp+KM_5Tq9XCBXQQz@S7F`;H34!+@&5;XtMTQZ57aHIN?>9UT&n`Z3_@ z;Qbm41g+AL2!x;vjBg?kGzEt9DC^K9BBA3Se3v3uz8FXy&w({$P*7At3Jv2q%9CNw z(Lr-y1{!S%41nGY*d1SLz@UVL#I)3LA%cw%s9+wSQGiy7&jeCK6M*E2XdoFni!Yy$ zm>Lz4AQ0SvNF!>f*B<$;z@5-xTVPjUYv76&oB<7niJJ(t1lq`W3lE^}^ajg6k>yO4 zux(lh3~hs)8rabl*kEFVX$_{FL_V3Y6aA78Hvq{ei-BaybbQg6hFysPQ3! zX|SsUcnXl}MFMH);eiRU$uWX7K?!=NF>50O!%9yLjE*8FkHeHw2cbZ!I7pN8l{t`x z6cQgF8*dVl(npJ{r^Dx0fRit~!Z96zm%yohP<8=&ZVRN5>H;Z$MJKLd0XV9p*PtO9X=Fl3 zLXbcp*sLcIzzOML`doPrAWiLJ=!D^Dl%}u(*23B8=0XhMS6DL23T@M34LK8H0%Kw$ zf(3$*gfU4GQNe-_UAQLh0jcU49(VFs$YVB;x<~|4RE*})okuGk^>|d_@tcvXd|LW5 zE|Gp6NMUr0$E`dr<#8sE!YzfzP#(Q_bmB2SHYzGuI z7ax+C7!eZR8qOy@Bq1syCQ%^hZHs85XfUG$u!P6XJPx**83EH3@g<*3b>2CHM-wLF9ML?Q-5%MVmwp8CN@4qAlT3I(1@5|6Zm+k6PKUM<2aM3*r32fSQ8Zy9g!%=?Zf4-M?DJL zj?P@WV?$EM(}0#Z!~fI)7Gq*!NU$Iu1!)8!2}y|&SV$oWaY-TZse&^uT*Z(CI1`4< zK)IGE=iHYYX<$%nJh^BhbQ;;%ew;oIoZ3$gj|d7!endh@3aSfUA)op=;tK!E<|r^R z+yrJdY#H2E@jverfswL-2xG*uAX-<=zY#X!#TsX($!A4nD4QIQ(#2BctX2UG*90clP}Kq?nJn0e8p zecGGeT=AnG+^W0|PQktxNYxu+uc2H+GYt;?4%?`FHL#sr`35r@%H?@+W;B??$9kXi z*~lP=S`Xu}VMfxS)66t<*f5iSZk768jK5;%w1%^#VdrevVH-BYG##$_h7IwjFBif0 zfgRAz$Kl*sI|8l?E(zcQA~i4y$7`bC`v}gQ@6c&?!*&`N6&M^+0}k`k(kqc5zh459 z-S<#|9C!gp{@;LxY1{J!(!_TIb^*d~vWWZBpaw%4>YoY}2(WLYZvc{`eSuwp(}A67 zSL%%fb*Ku*ks%Xeu{q;W04E2J4&|`H6AhkfI0PGx7^*`{;7!?3;4U|6sou=+Kbn<8*IL*BUmM~4> zBN)&E_-#D=Pjfpbnd{&p-{E9%73fhwvNVX#uSEkif-7i%I=G4Q&4CBO+W=SdxPZ@3 z0aAz8VE}b_6&_Fpen&lOXLKC=PZqnOAQ@r{q=ML=<3qwiQjEc=LPSDfe0*T4KpmV$ za(ptUx1Yj|P!T$L>@9E5V<2rB`+!uw7^nhV3Zx*P2BdzH(vYBv>(jXmdvK~~1f+^$ zAdT!JKLXup+=w56lLyuS$?*9+rUO;L`vThny8&r{`WQKFHw{00*Wu0C zoJU&Bp2hZ0MdYG0ja&v_3%Hr)((OZP!p&J{94SN2@QuwIe1s- z>w)CTEFj%jSM1{q4*;k7#=!2tH$?)0DX`(NYB+qjL+3w-kU||EkN?XJRkxvJp@P%zgf@v4}=Rr58^M5rOpbFs-$d!&f{uzV~LDuk-Fz^}| z%?-h(je2^hzXb!*0cHa+!t^mbp5gmR0FozL0_|LoxW0@Vc{Xq$_+X$lunmx0)l9&x z`-Uswfjitt8*Y4OTo@;{zRY|zLk*Ly8+1Kwv+V~h@f*GNiN@FP)H8>_?5?}Yc(l}D zYSawFhu$6jaClXEvqQ7r_igny^;GL09bJxWy*gKE!=+2T6_$oSI~U||^X+`QYmaox za}Jq}v;LT<)GU?BbejJ{#lvB{L#Lw!~+*_wBx zq4NVFt*+>{sQIC#uCF?^)6nw`#%YEt^eRdDYRD9~wA%Ts
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"@babel/eslint-parser": "^7.25.1", - "@babel/preset-env": "^7.25.4", - "@babel/preset-react": "^7.24.7", - "@eslint/compat": "^1.1.1", - "@vitejs/plugin-react": "^4.3.1", + "@babel/core": "^7.25.7", + "@babel/eslint-parser": "^7.25.7", + "@babel/preset-env": "^7.25.7", + "@babel/preset-react": "^7.25.7", + "@eslint/compat": "^1.2.0", + "@vitejs/plugin-react": "^4.3.2", "@welldone-software/why-did-you-render": "^8.0.3", "babel-plugin-react-compiler": "latest", - "eslint": "^9.10.0", + "eslint": "^9.12.0", "eslint-config-prettier": "^9.1.0", - "eslint-plugin-jsdoc": "^50.2.3", - "eslint-plugin-react": "^7.36.1", + "eslint-plugin-jsdoc": "^50.3.1", + "eslint-plugin-react": "^7.37.1", "eslint-plugin-react-compiler": "latest", "eslint-plugin-react-hooks": "^4.6.2", "eslint-plugin-react-refresh": "^0.4.12", "prettier": "^3.3.3", - "vite": "^5.4.6" + "vite": "^5.4.8" } } diff --git a/gui_dev/src/components/StatusBar/StatusBar.jsx b/gui_dev/src/components/StatusBar/StatusBar.jsx index 36aaf1dc..6bffbe15 100644 --- a/gui_dev/src/components/StatusBar/StatusBar.jsx +++ b/gui_dev/src/components/StatusBar/StatusBar.jsx @@ -1,13 +1,28 @@ +import { useState } from "react"; + import { ResizeHandle } from "./ResizeHandle"; import { SocketStatus } from "./SocketStatus"; import { WebviewStatus } from "./WebviewStatus"; +import { useSettingsStore } from "@/stores"; import { useWebviewStore } from "@/stores"; -import { Stack } from "@mui/material"; +import { Popover, Stack, Typography } from "@mui/material"; export const StatusBar = () => { - const { isWebView } = useWebviewStore((state) => state.isWebView); + const isWebView = useWebviewStore((state) => state.isWebView); + const validationErrors = useSettingsStore((state) => state.validationErrors); + + const [anchorEl, setAnchorEl] = useState(null); + const open = Boolean(anchorEl); + + const handleOpenErrorsPopover = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleCloseErrorsPopover = () => { + setAnchorEl(null); + }; return ( { bgcolor="background.level1" borderTop="2px solid" borderColor="background.level3" + height="2rem" > - + {validationErrors?.length > 0 && ( + <> + + {validationErrors?.length} errors found in Settings + + + + + {validationErrors.map((error, index) => ( + + {index} - [{error.type}] {error.msg} + + ))} + + + + )} + {/* */} {/* Current experiment */} {/* Current stream */} {/* Current activity */} diff --git a/gui_dev/src/pages/Settings/Dropdown.jsx b/gui_dev/src/pages/Settings/Dropdown.jsx index ad662eef..9dbc9833 100644 --- a/gui_dev/src/pages/Settings/Dropdown.jsx +++ b/gui_dev/src/pages/Settings/Dropdown.jsx @@ -1,34 +1,30 @@ import { useState } from "react"; -import "../App.css"; var stringJson = '{"sampling_rate_features_hz":10.0,"segment_length_features_ms":1000.0,"frequency_ranges_hz":{"theta":{"frequency_low_hz":4.0,"frequency_high_hz":8.0},"alpha":{"frequency_low_hz":8.0,"frequency_high_hz":12.0},"low beta":{"frequency_low_hz":13.0,"frequency_high_hz":20.0},"high beta":{"frequency_low_hz":20.0,"frequency_high_hz":35.0},"low gamma":{"frequency_low_hz":60.0,"frequency_high_hz":80.0},"high gamma":{"frequency_low_hz":90.0,"frequency_high_hz":200.0},"HFA":{"frequency_low_hz":200.0,"frequency_high_hz":400.0}},"preprocessing":["raw_resampling","notch_filter","re_referencing"],"raw_resampling_settings":{"resample_freq_hz":1000.0},"preprocessing_filter":{"bandstop_filter":true,"bandpass_filter":true,"lowpass_filter":true,"highpass_filter":true,"bandstop_filter_settings":{"frequency_low_hz":100.0,"frequency_high_hz":160.0},"bandpass_filter_settings":{"frequency_low_hz":2.0,"frequency_high_hz":200.0},"lowpass_filter_cutoff_hz":200.0,"highpass_filter_cutoff_hz":3.0},"raw_normalization_settings":{"normalization_time_s":30.0,"normalization_method":"zscore","clip":3.0},"postprocessing":{"feature_normalization":true,"project_cortex":false,"project_subcortex":false},"feature_normalization_settings":{"normalization_time_s":30.0,"normalization_method":"zscore","clip":3.0},"project_cortex_settings":{"max_dist_mm":20.0},"project_subcortex_settings":{"max_dist_mm":5.0},"features":{"raw_hjorth":true,"return_raw":true,"bandpass_filter":false,"stft":false,"fft":true,"welch":true,"sharpwave_analysis":true,"fooof":false,"nolds":false,"coherence":false,"bursts":true,"linelength":true,"mne_connectivity":false,"bispectrum":false},"fft_settings":{"windowlength_ms":1000,"log_transform":true,"features":{"mean":true,"median":false,"std":false,"max":false},"return_spectrum":false},"welch_settings":{"windowlength_ms":1000,"log_transform":true,"features":{"mean":true,"median":false,"std":false,"max":false},"return_spectrum":false},"stft_settings":{"windowlength_ms":1000,"log_transform":true,"features":{"mean":true,"median":false,"std":false,"max":false},"return_spectrum":false},"bandpass_filter_settings":{"segment_lengths_ms":{"theta":1000,"alpha":500,"low beta":333,"high beta":333,"low gamma":100,"high gamma":100,"HFA":100},"bandpower_features":{"activity":true,"mobility":false,"complexity":false},"log_transform":true,"kalman_filter":false},"kalman_filter_settings":{"Tp":0.1,"sigma_w":0.7,"sigma_v":1.0,"frequency_bands":["theta","alpha","low_beta","high_beta","low_gamma","high_gamma","HFA"]},"burst_settings":{"threshold":75.0,"time_duration_s":30.0,"frequency_bands":["low beta","high beta","low gamma"],"burst_features":{"duration":true,"amplitude":true,"burst_rate_per_s":true,"in_burst":true}},"sharpwave_analysis_settings":{"sharpwave_features":{"peak_left":false,"peak_right":false,"trough":false,"width":false,"prominence":true,"interval":true,"decay_time":false,"rise_time":false,"sharpness":true,"rise_steepness":false,"decay_steepness":false,"slope_ratio":false},"filter_ranges_hz":[{"frequency_low_hz":5.0,"frequency_high_hz":80.0},{"frequency_low_hz":5.0,"frequency_high_hz":30.0}],"detect_troughs":{"estimate":true,"distance_troughs_ms":10.0,"distance_peaks_ms":5.0},"detect_peaks":{"estimate":true,"distance_troughs_ms":10.0,"distance_peaks_ms":5.0},"estimator":{"mean":["interval"],"median":[],"max":["prominence","sharpness"],"min":[],"var":[]},"apply_estimator_between_peaks_and_troughs":true},"mne_connectivity":{"method":"plv","mode":"multitaper"},"coherence":{"features":{"mean_fband":true,"max_fband":true,"max_allfbands":true},"method":{"coh":true,"icoh":true},"channels":[],"frequency_bands":["high beta"]},"fooof":{"aperiodic":{"exponent":true,"offset":true,"knee":true},"periodic":{"center_frequency":false,"band_width":false,"height_over_ap":false},"windowlength_ms":800.0,"peak_width_limits":{"frequency_low_hz":0.5,"frequency_high_hz":12.0},"max_n_peaks":3,"min_peak_height":0.0,"peak_threshold":2.0,"freq_range_hz":{"frequency_low_hz":2.0,"frequency_high_hz":40.0},"knee":true},"nolds_features":{"raw":true,"frequency_bands":["low beta"],"features":{"sample_entropy":false,"correlation_dimension":false,"lyapunov_exponent":true,"hurst_exponent":false,"detrended_fluctuation_analysis":false}},"bispectrum":{"f1s":{"frequency_low_hz":5.0,"frequency_high_hz":35.0},"f2s":{"frequency_low_hz":5.0,"frequency_high_hz":35.0},"compute_features_for_whole_fband_range":true,"frequency_bands":["theta","alpha","low_beta","high_beta"],"components":{"absolute":true,"real":true,"imag":true,"phase":true},"bispectrum_features":{"mean":true,"sum":true,"var":true}}}'; const nm_settings = JSON.parse(stringJson); -const filterByKeys = (dict, keys) => { +const filterByKeys = (obj, keys) => { const filteredDict = {}; keys.forEach((key) => { if (typeof key === "string") { // Top-level key - if (dict.hasOwnProperty(key)) { - filteredDict[key] = dict[key]; + if (obj.hasOwn(key)) { + filteredDict[key] = obj[key]; } } else if (typeof key === "object") { // Nested key const topLevelKey = Object.keys(key)[0]; const nestedKeys = key[topLevelKey]; - if ( - dict.hasOwnProperty(topLevelKey) && - typeof dict[topLevelKey] === "object" - ) { - filteredDict[topLevelKey] = filterByKeys(dict[topLevelKey], nestedKeys); + if (obj.hasOwn(topLevelKey) && typeof obj[topLevelKey] === "object") { + filteredDict[topLevelKey] = filterByKeys(obj[topLevelKey], nestedKeys); } } }); return filteredDict; }; -const Dropdown = ({ onChange, keysToInclude }) => { +export const Dropdown = ({ onChange, keysToInclude }) => { const filteredSettings = filterByKeys(nm_settings, keysToInclude); const [selectedOption, setSelectedOption] = useState(""); @@ -62,5 +58,3 @@ const Dropdown = ({ onChange, keysToInclude }) => { ); }; - -export default Dropdown; diff --git a/gui_dev/src/pages/Settings/FrequencyRange.jsx b/gui_dev/src/pages/Settings/FrequencyRange.jsx index e881b459..83ee09d5 100644 --- a/gui_dev/src/pages/Settings/FrequencyRange.jsx +++ b/gui_dev/src/pages/Settings/FrequencyRange.jsx @@ -138,7 +138,11 @@ export const FrequencyRangeList = ({ const updatedRanges = { ...ranges, - [newName]: { frequency_low_hz: 1, frequency_high_hz: 500 }, + [newName]: { + __field_type__: "FrequencyRange", + frequency_low_hz: 1, + frequency_high_hz: 500, + }, }; onChange(["frequency_ranges_hz"], updatedRanges); @@ -147,7 +151,7 @@ export const FrequencyRangeList = ({ }; return ( - + {rangeOrder.map((name, index) => ( { - // console.log(key); return key .split("_") .map((word) => word.charAt(0).toUpperCase() + word.slice(1)) @@ -24,15 +25,32 @@ const formatKey = (key) => { }; // Wrapper components for each type -const BooleanField = ({ value, onChange }) => ( +const BooleanField = ({ value, onChange, error }) => ( onChange(e.target.checked)} /> ); -const StringField = ({ value, onChange, label }) => ( - +const StringField = ({ value, onChange, label, error }) => ( + onChange(e.target.value)} + label={label} + sx={{ + "& .MuiOutlinedInput-root": { + "& fieldset": { + borderColor: error ? "error.main" : "inherit", + }, + "&:hover fieldset": { + borderColor: error ? "error.main" : "primary.main", + }, + "&.Mui-focused fieldset": { + borderColor: error ? "error.main" : "primary.main", + }, + }, + }} + /> ); -const NumberField = ({ value, onChange, label }) => { +const NumberField = ({ value, onChange, label, error }) => { const handleChange = (event) => { const newValue = event.target.value; // Only allow numbers and decimal point @@ -47,6 +65,19 @@ const NumberField = ({ value, onChange, label }) => { value={value} onChange={handleChange} label={label} + sx={{ + "& .MuiOutlinedInput-root": { + "& fieldset": { + borderColor: error ? "error.main" : "inherit", + }, + "&:hover fieldset": { + borderColor: error ? "error.main" : "primary.main", + }, + "&.Mui-focused fieldset": { + borderColor: error ? "error.main" : "primary.main", + }, + }, + }} // InputProps={{ // endAdornment: ( // @@ -66,24 +97,22 @@ const componentRegistry = { boolean: BooleanField, string: StringField, number: NumberField, + Array: Dropdown, }; -const SettingsField = ({ path, Component, label, value, onChange, depth }) => { +const SettingsField = ({ path, Component, label, value, onChange, error }) => { return ( - - {label} - onChange(path, newValue)} - label={label} - /> - + + + {label} + onChange(path, newValue)} + label={label} + error={error} + /> + + ); }; @@ -92,10 +121,23 @@ const SettingsSection = ({ title = null, path = [], onChange, - depth = 0, + errors, }) => { const boxTitle = title ? title : formatKey(path[path.length - 1]); + // Function to get the error corresponding to this field or its children + const getFieldError = (fieldPath) => { + if (!errors) return null; + + return errors.find((error) => { + const errorPath = error.loc.join("."); + const currentPath = fieldPath.join("."); + return ( + errorPath === currentPath || errorPath.startsWith(currentPath + ".") + ); + }); + }; + // If we receive a primitive value, we need to render a component if (typeof settings !== "object") { const Component = componentRegistry[typeof settings]; @@ -103,32 +145,35 @@ const SettingsSection = ({ console.error(`Invalid component type: ${typeof settings}`); return null; } + + const error = getFieldError(path); + return ( - // - // {boxTitle} - // - // ); } // If we receive a nested object, we iterate over it and render recursively return ( - + <> {Object.entries(settings).map(([key, value]) => { if (key === "__field_type__") return null; + if (value === null) return null; const newPath = [...path, key]; const label = key; const isPydanticModel = typeof value === "object" && "__field_type__" in value; + const error = getFieldError(newPath); + const fieldType = isPydanticModel ? value.__field_type__ : typeof value; const Component = componentRegistry[fieldType]; @@ -142,29 +187,34 @@ const SettingsSection = ({ label={formatKey(label)} value={value} onChange={onChange} - depth={depth + 1} + error={error} /> ); } else { return ( - + + + ); } })} - + ); }; -const SettingsContent = () => { - const [selectedFeature, setSelectedFeature] = useState(""); +export const Settings = () => { + // Get all necessary state from the settings store const settings = useSettingsStore((state) => state.settings); - const updateSettings = useSettingsStore((state) => state.updateSettings); + const uploadSettings = useSettingsStore((state) => state.uploadSettings); + const resetSettings = useSettingsStore((state) => state.resetSettings); + const validationErrors = useSettingsStore((state) => state.validationErrors); + + // This is needed so that the frequency ranges stay in order between updates const frequencyRangeOrder = useSettingsStore( (state) => state.frequencyRangeOrder ); @@ -172,20 +222,35 @@ const SettingsContent = () => { (state) => state.updateFrequencyRangeOrder ); + // Here I handle the selected feature in the feature settings component + const [selectedFeature, setSelectedFeature] = useState(""); + + useEffect(() => { + uploadSettings(null, true); // validateOnly = true + }, [settings]); + + // This has to be after all the hooks, otherwise React will complain if (!settings) { return

    Loading settings...
    ; } - console.log(settings); - - const handleChange = (path, value) => { - updateSettings((settings) => { + // This are the callbacks for the different buttons + const handleChangeSettings = async (path, value) => { + uploadSettings((settings) => { let current = settings; for (let i = 0; i < path.length - 1; i++) { current = current[path[i]]; } current[path[path.length - 1]] = value; - }); + }, true); // validateOnly = true + }; + + const handleSaveSettings = () => { + uploadSettings(() => settings); + }; + + const handleResetSettings = async () => { + await resetSettings(); }; const featureSettingsKeys = Object.keys(settings.features) @@ -214,109 +279,102 @@ const SettingsContent = () => { ]; return ( - - - - {generalSettingsKeys.map((key) => ( + + {/* SETTINGS LAYOUT */} + + {/* GENERAL SETTINGS + FREQUENCY RANGES */} + + + {generalSettingsKeys.map((key) => ( + + ))} + + + + + + + + {/* POSTPROCESSING + PREPROCESSING SETTINGS */} + + {preprocessingSettingsKeys.map((key) => ( ))} - - - - - - - {preprocessingSettingsKeys.map((key) => ( - - ))} - - - - {postprocessingSettingsKeys.map((key) => ( - - ))} - - - - - + + {postprocessingSettingsKeys.map((key) => ( - - - {Object.entries(enabledFeatures).map( - ([feature, featureSettings]) => ( - - - - ) - )} + ))} + + + {/* FEATURE SETTINGS */} + + + + + + + {Object.entries(enabledFeatures).map( + ([feature, featureSettings]) => ( + + + + ) + )} + - - - - ); -}; + + {/* END SETTINGS LAYOUT */} + -export const Settings = () => { - return ( - - + {/* BUTTONS */} { borderColor={"divider"} p={1} > - + {/* */} + diff --git a/gui_dev/src/pages/Settings/index.js b/gui_dev/src/pages/Settings/index.js deleted file mode 100644 index 16355023..00000000 --- a/gui_dev/src/pages/Settings/index.js +++ /dev/null @@ -1 +0,0 @@ -export { TextField } from './TextField'; diff --git a/gui_dev/src/stores/createStore.js b/gui_dev/src/stores/createStore.js index 762d9340..e683a35c 100644 --- a/gui_dev/src/stores/createStore.js +++ b/gui_dev/src/stores/createStore.js @@ -2,16 +2,23 @@ import { create } from "zustand"; import { immer } from "zustand/middleware/immer"; import { devtools, persist as persistMiddleware } from "zustand/middleware"; -export const createStore = (name, initializer, persist = false) => { +export const createStore = ( + name, + initializer, + persist = false, + dev = false +) => { const fn = persist ? persistMiddleware(immer(initializer), name) : immer(initializer); - return create( - devtools(fn, { - name: name, - }) - ); + const dev_fn = dev + ? devtools(fn, { + name: name, + }) + : fn; + + return create(dev_fn); }; export const createPersistStore = (name, initializer) => { diff --git a/gui_dev/src/stores/settingsStore.js b/gui_dev/src/stores/settingsStore.js index 7064ec98..634c445f 100644 --- a/gui_dev/src/stores/settingsStore.js +++ b/gui_dev/src/stores/settingsStore.js @@ -4,34 +4,18 @@ const INITIAL_DELAY = 3000; // wait for Flask const RETRY_DELAY = 1000; // ms const MAX_RETRIES = 100; -const uploadSettingsToServer = async (settings) => { - try { - const response = await fetch("/api/settings", { - method: "POST", - headers: { - "Content-Type": "application/json", - }, - body: JSON.stringify(settings), - }); - if (!response.ok) { - throw new Error("Failed to update settings"); - } - return { success: true }; - } catch (error) { - console.error("Error updating settings:", error); - return { success: false, error }; - } -}; - export const useSettingsStore = createStore("settings", (set, get) => ({ settings: null, + lastValidSettings: null, frequencyRangeOrder: [], isLoading: false, error: null, + validationErrors: null, retryCount: 0, - setSettings: (settings) => set({ settings }), - setFrequencyRangeOrder: (order) => set({ frequencyRangeOrder: order }), + updateLocalSettings: (updater) => { + set((state) => updater(state.settings)); + }, fetchSettingsWithDelay: () => { set({ isLoading: true, error: null }); @@ -40,16 +24,22 @@ export const useSettingsStore = createStore("settings", (set, get) => ({ }, INITIAL_DELAY); }, - fetchSettings: async () => { + fetchSettings: async (reset = false) => { + console.log("Fetching settings..."); try { - console.log("Fetching settings..."); - const response = await fetch("/api/settings"); + const response = await fetch( + `/api/settings${reset ? "?reset=true" : ""}` + ); + if (!response.ok) { throw new Error("Failed to fetch settings"); } + const data = await response.json(); + set({ settings: data, + lastValidSettings: data, frequencyRangeOrder: Object.keys(data.frequency_ranges_hz || {}), retryCount: 0, }); @@ -60,6 +50,8 @@ export const useSettingsStore = createStore("settings", (set, get) => ({ retryCount: state.retryCount + 1, })); + console.log(get().retryCount); + if (get().retryCount < MAX_RETRIES) { await new Promise((resolve) => setTimeout(resolve, RETRY_DELAY)); return get().fetchSettings(); @@ -71,38 +63,62 @@ export const useSettingsStore = createStore("settings", (set, get) => ({ resetRetryCount: () => set({ retryCount: 0 }), + resetSettings: async () => { + await get().fetchSettings(true); + }, + updateFrequencyRangeOrder: (newOrder) => { set({ frequencyRangeOrder: newOrder }); }, - updateSettings: async (updater) => { - const currentSettings = get().settings; - const currentOrder = get().frequencyRangeOrder; - - // Apply the update optimistically - set((state) => { - updater(state.settings); - }); - - const newSettings = get().settings; + uploadSettings: async (updater, validateOnly = false) => { + if (updater) { + set((state) => { + updater(state.settings); + }); + } - // Update the frequency range order - const newOrder = Object.keys(newSettings.frequency_ranges_hz || {}); - set({ frequencyRangeOrder: newOrder }); + const currentSettings = get().settings; try { - const result = await uploadSettingsToServer(newSettings); + const response = await fetch( + `/api/settings${validateOnly ? "?validate_only=true" : ""}`, + { + method: "POST", + headers: { + "Content-Type": "application/json", + }, + body: JSON.stringify(currentSettings), + } + ); - if (!result.success) { - // Revert the local state if the server update failed - set({ settings: currentSettings, frequencyRangeOrder: currentOrder }); + const data = await response.json(); + + if (!response.ok) { + throw new Error("Failed to upload settings to backend"); } - return result; + if (data.valid) { + // Settings are valid + set({ + lastValidSettings: currentSettings, + validationErrors: null, + }); + return true; + } else { + // Settings are invalid + set({ + validationErrors: data.errors, + }); + // Note: We don't revert the settings here, keeping the potentially invalid state + return false; + } } catch (error) { - // Revert the local state if there was an error - set({ settings: currentSettings, frequencyRangeOrder: currentOrder }); - throw error; + console.error( + `Error ${validateOnly ? "validating" : "updating"} settings:`, + error + ); + return false; } }, })); diff --git a/py_neuromodulation/__init__.py b/py_neuromodulation/__init__.py index 688393fd..864df345 100644 --- a/py_neuromodulation/__init__.py +++ b/py_neuromodulation/__init__.py @@ -4,11 +4,12 @@ from importlib.metadata import version from py_neuromodulation.utils.logging import NMLogger + ##################################### # Globals and environment variables # ##################################### -__version__ = version("py_neuromodulation") # get version from pyproject.toml +__version__ = version("py_neuromodulation") # Check if the module is running headless (no display) for tests and doc builds PYNM_HEADLESS: bool = not os.environ.get("DISPLAY") @@ -18,6 +19,7 @@ os.environ["LSLAPICFG"] = str(PYNM_DIR / "lsl_api.cfg") # LSL config file + # Set environment variable MNE_LSL_LIB (required to import Stream below) LSL_DICT = { "windows_32bit": "windows/x86/liblsl.1.16.2.dll", @@ -36,6 +38,7 @@ PLATFORM = platform.system().lower().strip() ARCH = platform.architecture()[0] + match PLATFORM: case "windows": KEY = PLATFORM + "_" + ARCH diff --git a/py_neuromodulation/gui/backend/app_backend.py b/py_neuromodulation/gui/backend/app_backend.py index 114b9f04..9c7b0a88 100644 --- a/py_neuromodulation/gui/backend/app_backend.py +++ b/py_neuromodulation/gui/backend/app_backend.py @@ -15,6 +15,7 @@ from fastapi.responses import FileResponse from fastapi.staticfiles import StaticFiles from fastapi.middleware.cors import CORSMiddleware +from pydantic import ValidationError from . import app_pynm from .app_socket import WebSocketManager @@ -93,23 +94,62 @@ async def healthcheck(): #################### ##### SETTINGS ##### #################### - @self.get("/api/settings") - async def get_settings(): - return self.pynm_state.settings.process_for_frontend() + async def get_settings( + reset: bool = Query(False, description="Reset settings to default"), + ): + if reset: + settings = NMSettings.get_default() + else: + settings = self.pynm_state.settings + + return settings.serialize_with_metadata() @self.post("/api/settings") - async def update_settings(data: dict): - print(data) + async def update_settings(data: dict, validate_only: bool = Query(False)): try: - self.pynm_state.settings = NMSettings.model_validate(data) - self.logger.debug(self.pynm_state.settings.features) - return self.pynm_state.settings.model_dump() - except ValueError as e: - self.logger.error(f"Error updating settings: {e}") + # First, validate with Pydantic + try: + validated_settings = NMSettings.model_validate(data) + except ValidationError as e: + if not validate_only: + # If validation failed but we wanted to upload, return error + self.logger.error(f"Error validating settings: {e}") + raise HTTPException( + status_code=422, + detail={ + "error": "Error validating settings", + "details": str(e), + }, + ) + # Else return list of errors + return { + "valid": False, + "errors": [err for err in e.errors()], + "details": str(e), + } + + # If validation succesful, return or update settings + if validate_only: + return { + "valid": True, + "settings": validated_settings.serialize_with_metadata(), + } + + self.pynm_state.settings = validated_settings + self.logger.info("Settings successfully updated") + + return { + "valid": True, + "settings": self.pynm_state.settings.serialize_with_metadata(), + } + + # If something else than validation went wrong, return error + except Exception as e: + self.logger.error(f"Error validating/updating settings: {e}") raise HTTPException( status_code=422, - detail={"error": "Validation failed", "details": str(e)}, + detail={"error": "Error uploading settings", "details": str(e)}, ) ######################## diff --git a/py_neuromodulation/utils/pydantic_extensions.py b/py_neuromodulation/utils/pydantic_extensions.py index 65d6cb4e..556f751c 100644 --- a/py_neuromodulation/utils/pydantic_extensions.py +++ b/py_neuromodulation/utils/pydantic_extensions.py @@ -1,6 +1,6 @@ from typing import Any, get_type_hints from pydantic.fields import FieldInfo, _FieldInfoInputs, _FromFieldInfoInputs -from pydantic import BaseModel, ConfigDict, model_serializer +from pydantic import BaseModel, ConfigDict, SerializationInfo, model_serializer from pydantic_core import PydanticUndefined from typing_extensions import Unpack, TypedDict from pprint import pformat @@ -9,7 +9,7 @@ class _NMExtraFieldInputs(TypedDict, total=False): """Additional fields to add on top of the pydantic FieldInfo""" - meta: dict[str, Any] + custom_metadata: dict[str, Any] class _NMFieldInfoInputs(_FieldInfoInputs, _NMExtraFieldInputs, total=False): @@ -29,17 +29,7 @@ class NMFieldInfo(FieldInfo): _default_values = {} def __init__(self, **kwargs: Unpack[_NMFieldInfoInputs]) -> None: - extra_fields = get_type_hints(_NMExtraFieldInputs) - for field, field_type in extra_fields.items(): - # If no default value, try to instantiate the field type with no arguments, if it fails, set to None - try: - value = ( - kwargs.pop(field, self._default_values.get(field, field_type())), # type: ignore - ) - except Exception: - value = None - - setattr(self, field, value) + self.custom_metadata = kwargs.pop("custom_metadata", {}) super().__init__(**kwargs) @staticmethod @@ -94,36 +84,34 @@ def __getitem__(self, key): def __setitem__(self, key, value) -> None: setattr(self, key, value) - @classmethod - def get_fields(cls) -> dict[str, NMFieldInfo]: - return cls.model_fields # type: ignore + @property + def fields(self) -> dict[str, FieldInfo | NMFieldInfo]: + return self.model_fields # type: ignore + + def serialize_with_metadata(self): + result: dict[str, Any] = {"__field_type__": self.__class__.__name__} - @model_serializer - def serialize_model(self) -> dict[str, Any]: - result = {"__field_type__": self.__class__.__name__} - for field_name, field_info in self.model_fields.items(): + for field_name, field_info in self.fields.items(): value = getattr(self, field_name) if isinstance(value, NMBaseModel): - result[field_name] = value.serialize_model() + result[field_name] = value.serialize_with_metadata() elif isinstance(value, list): result[field_name] = [ - item.serialize_model() if isinstance(item, NMBaseModel) else item + item.serialize_with_metadata() + if isinstance(item, NMBaseModel) + else item for item in value ] elif isinstance(value, dict): result[field_name] = { - k: v.serialize_model() if isinstance(v, NMBaseModel) else v + k: v.serialize_with_metadata() if isinstance(v, NMBaseModel) else v for k, v in value.items() } else: result[field_name] = value # Extract unit information from Annotated type - if get_origin(field_info.annotation) is Annotated: - metadata = get_args(field_info.annotation)[1:] - for item in metadata: - if isinstance(item, dict) and "unit" in item: - result[f"{field_name}_metadata"] = {"unit": item["unit"]} - break - + if isinstance(field_info, NMFieldInfo): + for tag, value in field_info.custom_metadata.items(): + result[f"__{tag}__"] = value return result diff --git a/py_neuromodulation/utils/types.py b/py_neuromodulation/utils/types.py index 1aad1b08..f5921281 100644 --- a/py_neuromodulation/utils/types.py +++ b/py_neuromodulation/utils/types.py @@ -1,21 +1,14 @@ from os import PathLike from math import isnan -from typing import ( - Literal, - Protocol, - TYPE_CHECKING, - runtime_checkable, -) -from pydantic import ( - BaseModel, - model_validator, -) +from typing import Literal, TYPE_CHECKING +from pydantic import BaseModel, model_validator from pydantic_core import ValidationError, InitErrorDetails from .pydantic_extensions import NMBaseModel, NMField from collections.abc import Sequence from datetime import datetime + if TYPE_CHECKING: import numpy as np from py_neuromodulation import NMSettings @@ -26,7 +19,6 @@ _PathLike = str | PathLike - FeatureName = Literal[ "raw_hjorth", "return_raw", @@ -69,8 +61,7 @@ ################################### -@runtime_checkable -class NMFeature(Protocol): +class NMFeature: def __init__( self, settings: "NMSettings", ch_names: Sequence[str], sfreq: int | float ) -> None: ... @@ -91,17 +82,15 @@ def calc_feature(self, data: "np.ndarray") -> dict: ... -class NMPreprocessor(Protocol): - def __init__(self, sfreq: float, settings: "NMSettings") -> None: ... - +class NMPreprocessor: def process(self, data: "np.ndarray") -> "np.ndarray": ... class FrequencyRange(NMBaseModel): # frequency_low_hz: Annotated[list[float], {"unit": "Hz"}] = Field(gt=0) # frequency_high_hz: FrequencyHz = Field(gt=0) - frequency_low_hz: float = NMField(gt=0, meta={"unit": "Hz"}) - frequency_high_hz: float = NMField(gt=0, meta={"unit": "Hz"}) + frequency_low_hz: float = NMField(gt=0, custom_metadata={"unit": "Hz"}) + frequency_high_hz: float = NMField(gt=0, custom_metadata={"unit": "Hz"}) def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) diff --git a/pyproject.toml b/pyproject.toml index 095dcf80..395b003b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,6 @@ dependencies = [ "nolds", "numpy >= 1.21.2", "pandas >= 2.0.0", - "scikit-image", "scikit-learn >= 0.24.2", "scikit-optimize", "scipy >= 1.7.1", @@ -55,12 +54,10 @@ dependencies = [ "statsmodels", "mne-lsl>=1.2.0", "pynput", - "pyqt5", "pydantic>=2.7.3", "pywebview", "fastapi", - "uvicorn>=0.30.6", - "websockets>=13.0", + "uvicorn[standard]>=0.30.6", "seaborn >= 0.11", ] From 446b194e11c4385aef8ff3b80c4b183d4e26e4a1 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Mon, 14 Oct 2024 14:00:24 +0200 Subject: [PATCH 07/25] Refactor SettingsSection recursive rendering component --- .../src/components/StatusBar/StatusBar.jsx | 55 +----- gui_dev/src/pages/Settings/Settings.jsx | 175 ++++++++++++------ gui_dev/src/stores/uiStore.js | 21 +++ 3 files changed, 147 insertions(+), 104 deletions(-) diff --git a/gui_dev/src/components/StatusBar/StatusBar.jsx b/gui_dev/src/components/StatusBar/StatusBar.jsx index 6bffbe15..f011e2b9 100644 --- a/gui_dev/src/components/StatusBar/StatusBar.jsx +++ b/gui_dev/src/components/StatusBar/StatusBar.jsx @@ -1,28 +1,15 @@ -import { useState } from "react"; - import { ResizeHandle } from "./ResizeHandle"; import { SocketStatus } from "./SocketStatus"; import { WebviewStatus } from "./WebviewStatus"; -import { useSettingsStore } from "@/stores"; - -import { useWebviewStore } from "@/stores"; -import { Popover, Stack, Typography } from "@mui/material"; +import { useUiStore, useWebviewStore } from "@/stores"; +import { Stack } from "@mui/material"; export const StatusBar = () => { const isWebView = useWebviewStore((state) => state.isWebView); - const validationErrors = useSettingsStore((state) => state.validationErrors); - - const [anchorEl, setAnchorEl] = useState(null); - const open = Boolean(anchorEl); - - const handleOpenErrorsPopover = (event) => { - setAnchorEl(event.currentTarget); - }; + const createStatusBarContent = useUiStore((state) => state.statusBarContent); - const handleCloseErrorsPopover = () => { - setAnchorEl(null); - }; + const StatusBarContent = createStatusBarContent(); return ( { borderColor="background.level3" height="2rem" > - {validationErrors?.length > 0 && ( - <> - - {validationErrors?.length} errors found in Settings - + {StatusBarContent && } - - - {validationErrors.map((error, index) => ( - - {index} - [{error.type}] {error.msg} - - ))} - - - - )} {/* */} {/* Current experiment */} {/* Current stream */} diff --git a/gui_dev/src/pages/Settings/Settings.jsx b/gui_dev/src/pages/Settings/Settings.jsx index 839a89ad..60b238d6 100644 --- a/gui_dev/src/pages/Settings/Settings.jsx +++ b/gui_dev/src/pages/Settings/Settings.jsx @@ -4,6 +4,7 @@ import { Button, ButtonGroup, InputAdornment, + Popover, Stack, Switch, TextField, @@ -14,7 +15,7 @@ import { Link } from "react-router-dom"; import { CollapsibleBox, TitledBox } from "@/components"; import { FrequencyRangeList } from "./FrequencyRange"; import { Dropdown } from "./Dropdown"; -import { useSettingsStore } from "@/stores"; +import { useSettingsStore, useStatusBarContent } from "@/stores"; import { filterObjectByKeys } from "@/utils/functions"; const formatKey = (key) => { @@ -116,6 +117,17 @@ const SettingsField = ({ path, Component, label, value, onChange, error }) => { ); }; +// Function to get the error corresponding to this field or its children +const getFieldError = (fieldPath, errors) => { + if (!errors) return null; + + return errors.find((error) => { + const errorPath = error.loc.join("."); + const currentPath = fieldPath.join("."); + return errorPath === currentPath || errorPath.startsWith(currentPath + "."); + }); +}; + const SettingsSection = ({ settings, title = null, @@ -124,29 +136,32 @@ const SettingsSection = ({ errors, }) => { const boxTitle = title ? title : formatKey(path[path.length - 1]); + /* + 3 possible cases: + 1. Primitive type || 2. Object with component -> Don't iterate, render directly + 3. Object without component or 4. Array -> Iterate and render recursively + */ + + const type = typeof settings; + const isObject = type === "object" && !Array.isArray(settings); + const isArray = Array.isArray(settings); + + // __field_type__ should be always present + if (isObject && !settings.__field_type__) { + console.log(settings); + throw new Error("Invalid settings object"); + } + const fieldType = isObject ? settings.__field_type__ : type; + const Component = componentRegistry[fieldType]; - // Function to get the error corresponding to this field or its children - const getFieldError = (fieldPath) => { - if (!errors) return null; - - return errors.find((error) => { - const errorPath = error.loc.join("."); - const currentPath = fieldPath.join("."); - return ( - errorPath === currentPath || errorPath.startsWith(currentPath + ".") - ); - }); - }; - - // If we receive a primitive value, we need to render a component - if (typeof settings !== "object") { - const Component = componentRegistry[typeof settings]; + // Case 1: Primitive type -> Don't iterate, render directly + if (!isObject && !isArray) { if (!Component) { - console.error(`Invalid component type: ${typeof settings}`); + console.error(`Invalid component type: ${type}`); return null; } - const error = getFieldError(path); + const error = getFieldError(path, errors); return ( - {Object.entries(settings).map(([key, value]) => { - if (key === "__field_type__") return null; - if (value === null) return null; - - const newPath = [...path, key]; - const label = key; - const isPydanticModel = - typeof value === "object" && "__field_type__" in value; - - const error = getFieldError(newPath); + // Case 2: Object with component -> Don't iterate, render directly + if (isObject && Component) { + return ( + + ); + } - const fieldType = isPydanticModel ? value.__field_type__ : typeof value; + // Case 3: Object without component or 4. Array -> Iterate and render recursively + if ((isObject && !Component) || isArray) { + return ( + + {/* Handle recursing through both objects and arrays */} + {(isArray ? settings : Object.entries(settings)).map((item, index) => { + const [key, value] = isArray ? [index.toString(), item] : item; + if (key.startsWith("__")) return null; // Skip metadata fields - const Component = componentRegistry[fieldType]; + const newPath = [...path, key]; - if (Component) { return ( - ); - } else { - return ( - - - - ); - } - })} + })} + + ); + } + + // Default case: return null and log an error + console.error(`Invalid settings object, returning null`); + return null; +}; + +const StatusBarSettingsInfo = () => { + const validationErrors = useSettingsStore((state) => state.validationErrors); + const [anchorEl, setAnchorEl] = useState(null); + const open = Boolean(anchorEl); + + const handleOpenErrorsPopover = (event) => { + setAnchorEl(event.currentTarget); + }; + + const handleCloseErrorsPopover = () => { + setAnchorEl(null); + }; + + return ( + <> + {validationErrors?.length > 0 && ( + <> + + {validationErrors?.length} errors found in Settings + + + + {validationErrors.map((error, index) => ( + + {index} - [{error.type}] {error.msg} + + ))} + + + + )} ); }; @@ -213,6 +277,7 @@ export const Settings = () => { const uploadSettings = useSettingsStore((state) => state.uploadSettings); const resetSettings = useSettingsStore((state) => state.resetSettings); const validationErrors = useSettingsStore((state) => state.validationErrors); + useStatusBarContent(StatusBarSettingsInfo); // This is needed so that the frequency ranges stay in order between updates const frequencyRangeOrder = useSettingsStore( @@ -229,6 +294,8 @@ export const Settings = () => { uploadSettings(null, true); // validateOnly = true }, [settings]); + // Inject validation error info into status bar + // This has to be after all the hooks, otherwise React will complain if (!settings) { return
    Loading settings...
    ; diff --git a/gui_dev/src/stores/uiStore.js b/gui_dev/src/stores/uiStore.js index a229ec06..25b44382 100644 --- a/gui_dev/src/stores/uiStore.js +++ b/gui_dev/src/stores/uiStore.js @@ -1,4 +1,5 @@ import { createPersistStore } from "./createStore"; +import { useEffect } from "react"; export const useUiStore = createPersistStore("ui", (set, get) => ({ activeDrawer: null, @@ -28,4 +29,24 @@ export const useUiStore = createPersistStore("ui", (set, get) => ({ state.accordionStates[id] = defaultState; } }), + + // Hook to inject UI elements into the status bar + statusBarContent: () => {}, + setStatusBarContent: (content) => set({ statusBarContent: content }), + clearStatusBarContent: () => set({ statusBarContent: null }), })); + +// Use this hook from Page components to inject page-specific UI elements into the status bar +export const useStatusBarContent = (content) => { + const createStatusBarContent = () => content; + + const setStatusBarContent = useUiStore((state) => state.setStatusBarContent); + const clearStatusBarContent = useUiStore( + (state) => state.clearStatusBarContent + ); + + useEffect(() => { + setStatusBarContent(createStatusBarContent); + return () => clearStatusBarContent(); + }, [content, setStatusBarContent, clearStatusBarContent]); +}; From 820e80bc517524ca70e74704e8dd3a73700627a8 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Fri, 8 Nov 2024 12:28:40 +0100 Subject: [PATCH 08/25] delete unused components --- .../src/pages/Settings/DragAndDropList.jsx | 65 ------- .../pages/Settings/DragAndDropList.module.css | 72 ------- gui_dev/src/pages/Settings/Dropdown.jsx | 60 ------ gui_dev/src/pages/Settings/FrequencyRange.jsx | 176 ------------------ .../Settings/FrequencySettings.module.css | 67 ------- gui_dev/src/pages/Settings/TextField.jsx | 77 -------- .../src/pages/Settings/TextField.module.css | 67 ------- 7 files changed, 584 deletions(-) delete mode 100644 gui_dev/src/pages/Settings/DragAndDropList.jsx delete mode 100644 gui_dev/src/pages/Settings/DragAndDropList.module.css delete mode 100644 gui_dev/src/pages/Settings/Dropdown.jsx delete mode 100644 gui_dev/src/pages/Settings/FrequencyRange.jsx delete mode 100644 gui_dev/src/pages/Settings/FrequencySettings.module.css delete mode 100644 gui_dev/src/pages/Settings/TextField.jsx delete mode 100644 gui_dev/src/pages/Settings/TextField.module.css diff --git a/gui_dev/src/pages/Settings/DragAndDropList.jsx b/gui_dev/src/pages/Settings/DragAndDropList.jsx deleted file mode 100644 index afa74b02..00000000 --- a/gui_dev/src/pages/Settings/DragAndDropList.jsx +++ /dev/null @@ -1,65 +0,0 @@ -import { useRef } from "react"; -import styles from "./DragAndDropList.module.css"; -import { useOptionsStore } from "@/stores"; - -export const DragAndDropList = () => { - const { options, setOptions, addOption, removeOption } = useOptionsStore(); - - const predefinedOptions = [ - { id: 1, name: "raw_resampling" }, - { id: 2, name: "notch_filter" }, - { id: 3, name: "re_referencing" }, - { id: 4, name: "preprocessing_filter" }, - { id: 5, name: "raw_normalization" }, - ]; - - const dragOption = useRef(0); - const draggedOverOption = useRef(0); - - function handleSort() { - const optionsClone = [...options]; - const temp = optionsClone[dragOption.current]; - optionsClone[dragOption.current] = optionsClone[draggedOverOption.current]; - optionsClone[draggedOverOption.current] = temp; - setOptions(optionsClone); - } - - return ( -
    -

    List

    - {options.map((option, index) => ( -
    (dragOption.current = index)} - onDragEnter={() => (draggedOverOption.current = index)} - onDragEnd={handleSort} - onDragOver={(e) => e.preventDefault()} - > -

    - {[option.id, ". ", option.name.replace("_", " ")]} -

    - -
    - ))} -
    -

    Add Elements

    - {predefinedOptions.map((option) => ( - - ))} -
    -
    - ); -}; diff --git a/gui_dev/src/pages/Settings/DragAndDropList.module.css b/gui_dev/src/pages/Settings/DragAndDropList.module.css deleted file mode 100644 index 76bd7861..00000000 --- a/gui_dev/src/pages/Settings/DragAndDropList.module.css +++ /dev/null @@ -1,72 +0,0 @@ -.dragDropList { - max-width: 400px; - margin: 0 auto; - padding: 20px; -} - -.title { - text-align: center; - color: #333; - margin-bottom: 20px; -} - -.item { - background-color: #f0f0f0; - border-radius: 8px; - padding: 15px; - margin-bottom: 10px; - cursor: move; - transition: background-color 0.3s ease; - display: flex; - justify-content: space-between; - align-items: center; -} - -.item:hover { - background-color: #e0e0e0; -} - -.itemText { - margin: 0; - color: #333; - font-size: 16px; -} - -.removeButton { - background-color: #ff4d4d; - border: none; - border-radius: 4px; - color: white; - padding: 5px 10px; - cursor: pointer; - transition: background-color 0.3s ease; -} - -.removeButton:hover { - background-color: #ff1a1a; -} - -.addSection { - margin-top: 20px; - text-align: center; -} - -.subtitle { - color: #333; - margin-bottom: 10px; -} - -.addButton { - background-color: #4CAF50; - border: none; - border-radius: 4px; - color: white; - padding: 10px 15px; - margin: 5px; - cursor: pointer; - transition: background-color 0.3s ease; -} - -.addButton:hover { - background-color: #45a049; -} \ No newline at end of file diff --git a/gui_dev/src/pages/Settings/Dropdown.jsx b/gui_dev/src/pages/Settings/Dropdown.jsx deleted file mode 100644 index 9dbc9833..00000000 --- a/gui_dev/src/pages/Settings/Dropdown.jsx +++ /dev/null @@ -1,60 +0,0 @@ -import { useState } from "react"; - -var stringJson = - '{"sampling_rate_features_hz":10.0,"segment_length_features_ms":1000.0,"frequency_ranges_hz":{"theta":{"frequency_low_hz":4.0,"frequency_high_hz":8.0},"alpha":{"frequency_low_hz":8.0,"frequency_high_hz":12.0},"low beta":{"frequency_low_hz":13.0,"frequency_high_hz":20.0},"high beta":{"frequency_low_hz":20.0,"frequency_high_hz":35.0},"low gamma":{"frequency_low_hz":60.0,"frequency_high_hz":80.0},"high gamma":{"frequency_low_hz":90.0,"frequency_high_hz":200.0},"HFA":{"frequency_low_hz":200.0,"frequency_high_hz":400.0}},"preprocessing":["raw_resampling","notch_filter","re_referencing"],"raw_resampling_settings":{"resample_freq_hz":1000.0},"preprocessing_filter":{"bandstop_filter":true,"bandpass_filter":true,"lowpass_filter":true,"highpass_filter":true,"bandstop_filter_settings":{"frequency_low_hz":100.0,"frequency_high_hz":160.0},"bandpass_filter_settings":{"frequency_low_hz":2.0,"frequency_high_hz":200.0},"lowpass_filter_cutoff_hz":200.0,"highpass_filter_cutoff_hz":3.0},"raw_normalization_settings":{"normalization_time_s":30.0,"normalization_method":"zscore","clip":3.0},"postprocessing":{"feature_normalization":true,"project_cortex":false,"project_subcortex":false},"feature_normalization_settings":{"normalization_time_s":30.0,"normalization_method":"zscore","clip":3.0},"project_cortex_settings":{"max_dist_mm":20.0},"project_subcortex_settings":{"max_dist_mm":5.0},"features":{"raw_hjorth":true,"return_raw":true,"bandpass_filter":false,"stft":false,"fft":true,"welch":true,"sharpwave_analysis":true,"fooof":false,"nolds":false,"coherence":false,"bursts":true,"linelength":true,"mne_connectivity":false,"bispectrum":false},"fft_settings":{"windowlength_ms":1000,"log_transform":true,"features":{"mean":true,"median":false,"std":false,"max":false},"return_spectrum":false},"welch_settings":{"windowlength_ms":1000,"log_transform":true,"features":{"mean":true,"median":false,"std":false,"max":false},"return_spectrum":false},"stft_settings":{"windowlength_ms":1000,"log_transform":true,"features":{"mean":true,"median":false,"std":false,"max":false},"return_spectrum":false},"bandpass_filter_settings":{"segment_lengths_ms":{"theta":1000,"alpha":500,"low beta":333,"high beta":333,"low gamma":100,"high gamma":100,"HFA":100},"bandpower_features":{"activity":true,"mobility":false,"complexity":false},"log_transform":true,"kalman_filter":false},"kalman_filter_settings":{"Tp":0.1,"sigma_w":0.7,"sigma_v":1.0,"frequency_bands":["theta","alpha","low_beta","high_beta","low_gamma","high_gamma","HFA"]},"burst_settings":{"threshold":75.0,"time_duration_s":30.0,"frequency_bands":["low beta","high beta","low gamma"],"burst_features":{"duration":true,"amplitude":true,"burst_rate_per_s":true,"in_burst":true}},"sharpwave_analysis_settings":{"sharpwave_features":{"peak_left":false,"peak_right":false,"trough":false,"width":false,"prominence":true,"interval":true,"decay_time":false,"rise_time":false,"sharpness":true,"rise_steepness":false,"decay_steepness":false,"slope_ratio":false},"filter_ranges_hz":[{"frequency_low_hz":5.0,"frequency_high_hz":80.0},{"frequency_low_hz":5.0,"frequency_high_hz":30.0}],"detect_troughs":{"estimate":true,"distance_troughs_ms":10.0,"distance_peaks_ms":5.0},"detect_peaks":{"estimate":true,"distance_troughs_ms":10.0,"distance_peaks_ms":5.0},"estimator":{"mean":["interval"],"median":[],"max":["prominence","sharpness"],"min":[],"var":[]},"apply_estimator_between_peaks_and_troughs":true},"mne_connectivity":{"method":"plv","mode":"multitaper"},"coherence":{"features":{"mean_fband":true,"max_fband":true,"max_allfbands":true},"method":{"coh":true,"icoh":true},"channels":[],"frequency_bands":["high beta"]},"fooof":{"aperiodic":{"exponent":true,"offset":true,"knee":true},"periodic":{"center_frequency":false,"band_width":false,"height_over_ap":false},"windowlength_ms":800.0,"peak_width_limits":{"frequency_low_hz":0.5,"frequency_high_hz":12.0},"max_n_peaks":3,"min_peak_height":0.0,"peak_threshold":2.0,"freq_range_hz":{"frequency_low_hz":2.0,"frequency_high_hz":40.0},"knee":true},"nolds_features":{"raw":true,"frequency_bands":["low beta"],"features":{"sample_entropy":false,"correlation_dimension":false,"lyapunov_exponent":true,"hurst_exponent":false,"detrended_fluctuation_analysis":false}},"bispectrum":{"f1s":{"frequency_low_hz":5.0,"frequency_high_hz":35.0},"f2s":{"frequency_low_hz":5.0,"frequency_high_hz":35.0},"compute_features_for_whole_fband_range":true,"frequency_bands":["theta","alpha","low_beta","high_beta"],"components":{"absolute":true,"real":true,"imag":true,"phase":true},"bispectrum_features":{"mean":true,"sum":true,"var":true}}}'; -const nm_settings = JSON.parse(stringJson); - -const filterByKeys = (obj, keys) => { - const filteredDict = {}; - keys.forEach((key) => { - if (typeof key === "string") { - // Top-level key - if (obj.hasOwn(key)) { - filteredDict[key] = obj[key]; - } - } else if (typeof key === "object") { - // Nested key - const topLevelKey = Object.keys(key)[0]; - const nestedKeys = key[topLevelKey]; - if (obj.hasOwn(topLevelKey) && typeof obj[topLevelKey] === "object") { - filteredDict[topLevelKey] = filterByKeys(obj[topLevelKey], nestedKeys); - } - } - }); - return filteredDict; -}; - -export const Dropdown = ({ onChange, keysToInclude }) => { - const filteredSettings = filterByKeys(nm_settings, keysToInclude); - const [selectedOption, setSelectedOption] = useState(""); - - const handleChange = (event) => { - const newValue = event.target.value; - setSelectedOption(newValue); - onChange(keysToInclude, newValue); - }; - - return ( -
    - -
    - ); -}; diff --git a/gui_dev/src/pages/Settings/FrequencyRange.jsx b/gui_dev/src/pages/Settings/FrequencyRange.jsx deleted file mode 100644 index 83ee09d5..00000000 --- a/gui_dev/src/pages/Settings/FrequencyRange.jsx +++ /dev/null @@ -1,176 +0,0 @@ -import { useState } from "react"; -import { TextField, Button, IconButton, Stack } from "@mui/material"; -import { Add, Close } from "@mui/icons-material"; -import { debounce } from "@/utils"; - -const NumberField = ({ ...props }) => ( - -); - -export const FrequencyRange = ({ - id, - name, - range, - onChangeName, - onChangeRange, - onRemove, -}) => { - const [localName, setLocalName] = useState(name); - - const debouncedChangeName = debounce((newName) => { - onChangeName(newName, name); - }, 1000); - - const handleNameChange = (e) => { - const newName = e.target.value; - setLocalName(newName); - debouncedChangeName(newName); - }; - - const handleNameBlur = () => { - onChangeName(localName, name); - }; - - const handleKeyPress = (e) => { - if (e.key === "Enter") { - console.log(e.target.value, name); - onChangeName(localName, name); - } - }; - - const handleRangeChange = (field, value) => { - onChangeRange(id, { ...range, [field]: value }); - }; - - return ( - - - handleRangeChange("frequency_low_hz", e.target.value)} - label="Low Hz" - /> - handleRangeChange("frequency_high_hz", e.target.value)} - label="High Hz" - /> - onRemove(name)} - color="primary" - disableRipple - sx={{ m: 0, p: 0 }} - > - - - - ); -}; - -export const FrequencyRangeList = ({ - ranges, - rangeOrder, - onChange, - onOrderChange, -}) => { - const handleChangeRange = (name, newRange) => { - const updatedRanges = { ...ranges }; - updatedRanges[name] = newRange; - onChange(["frequency_ranges_hz"], updatedRanges); - }; - - const handleChangeName = (newName, oldName) => { - if (oldName === newName) { - return; - } - - const updatedRanges = { ...ranges, [newName]: ranges[oldName] }; - delete updatedRanges[oldName]; - onChange(["frequency_ranges_hz"], updatedRanges); - - const updatedOrder = rangeOrder.map((name) => - name === oldName ? newName : name - ); - onOrderChange(updatedOrder); - }; - - const handleRemove = (name) => { - const updatedRanges = { ...ranges }; - delete updatedRanges[name]; - onChange(["frequency_ranges_hz"], updatedRanges); - - const updatedOrder = rangeOrder.filter((item) => item !== name); - onOrderChange(updatedOrder); - }; - - const addRange = () => { - let newName = "NewRange"; - let counter = 0; - // Find first available name - while (Object.hasOwn(ranges, newName)) { - counter++; - newName = `NewRange${counter}`; - } - - const updatedRanges = { - ...ranges, - [newName]: { - __field_type__: "FrequencyRange", - frequency_low_hz: 1, - frequency_high_hz: 500, - }, - }; - onChange(["frequency_ranges_hz"], updatedRanges); - - const updatedOrder = [...rangeOrder, newName]; - onOrderChange(updatedOrder); - }; - - return ( - - {rangeOrder.map((name, index) => ( - - ))} - - - ); -}; diff --git a/gui_dev/src/pages/Settings/FrequencySettings.module.css b/gui_dev/src/pages/Settings/FrequencySettings.module.css deleted file mode 100644 index a638ad93..00000000 --- a/gui_dev/src/pages/Settings/FrequencySettings.module.css +++ /dev/null @@ -1,67 +0,0 @@ -.container { - background-color: #f9f9f9; /* Light gray background for the container */ - padding: 20px; - border-radius: 10px; /* Rounded corners */ - box-shadow: 0 2px 10px rgba(0, 0, 0, 0.1); /* Subtle shadow */ - max-width: 600px; - margin: auto; - } - - .header { - font-size: 1.5rem; - color: #333; /* Darker text color */ - margin-bottom: 20px; - text-align: center; - } - - .bandContainer { - display: flex; - align-items: center; - margin-bottom: 15px; - padding: 10px; - border: 1px solid #ddd; /* Light border for each band */ - border-radius: 8px; /* Rounded corners for individual bands */ - background-color: #fff; /* White background for bands */ - box-shadow: 0 1px 5px rgba(0, 0, 0, 0.1); /* Light shadow for depth */ - } - - .bandNameInput, .frequencyInput { - border: 1px solid #ccc; /* Light gray border */ - border-radius: 5px; /* Slightly rounded corners */ - padding: 8px; - margin-right: 10px; - font-size: 0.875rem; - } - - .bandNameInput::placeholder, .frequencyInput::placeholder { - color: #aaa; /* Light gray placeholder text */ - } - - .removeButton, .addButton { - border: none; - border-radius: 5px; /* Rounded corners */ - padding: 8px 12px; - font-size: 0.875rem; - cursor: pointer; - transition: background-color 0.3s, color 0.3s; - } - - .removeButton { - background-color: #e57373; /* Light red color */ - color: white; - } - - .removeButton:hover { - background-color: #d32f2f; /* Darker red on hover */ - } - - .addButton { - background-color: #4caf50; /* Green color */ - color: white; - margin-top: 10px; - } - - .addButton:hover { - background-color: #388e3c; /* Darker green on hover */ - } - \ No newline at end of file diff --git a/gui_dev/src/pages/Settings/TextField.jsx b/gui_dev/src/pages/Settings/TextField.jsx deleted file mode 100644 index 86ab07b8..00000000 --- a/gui_dev/src/pages/Settings/TextField.jsx +++ /dev/null @@ -1,77 +0,0 @@ -import { useState, useEffect } from "react"; -import { - Box, - Grid, - TextField as MUITextField, - Typography, -} from "@mui/material"; -import { useSettingsStore } from "@/stores"; -import styles from "./TextField.module.css"; - -const flattenDictionary = (dict, parentKey = "", result = {}) => { - for (let key in dict) { - const newKey = parentKey ? `${parentKey}.${key}` : key; - if (typeof dict[key] === "object" && dict[key] !== null) { - flattenDictionary(dict[key], newKey, result); - } else { - result[newKey] = dict[key]; - } - } - return result; -}; - -const filterByKeys = (flatDict, keys) => { - const filteredDict = {}; - keys.forEach((key) => { - if (flatDict.hasOwnProperty(key)) { - filteredDict[key] = flatDict[key]; - } - }); - return filteredDict; -}; - -export const TextField = ({ keysToInclude }) => { - const settings = useSettingsStore((state) => state.settings); - const flatSettings = flattenDictionary(settings); - const filteredSettings = filterByKeys(flatSettings, keysToInclude); - const [textLabels, setTextLabels] = useState({}); - - useEffect(() => { - setTextLabels(filteredSettings); - }, [settings]); - - const handleTextFieldChange = (label, value) => { - setTextLabels((prevLabels) => ({ - ...prevLabels, - [label]: value, - })); - }; - - // Function to format the label - const formatLabel = (label) => { - const labelAfterDot = label.split(".").pop(); // Get everything after the last dot - return labelAfterDot.replace(/_/g, " "); // Replace underscores with spaces - }; - - return ( -
    - {Object.keys(textLabels).map((label, index) => ( -
    - - handleTextFieldChange(label, e.target.value)} - className={styles.textFieldInput} - /> -
    - ))} -
    - ); -}; diff --git a/gui_dev/src/pages/Settings/TextField.module.css b/gui_dev/src/pages/Settings/TextField.module.css deleted file mode 100644 index 37791c40..00000000 --- a/gui_dev/src/pages/Settings/TextField.module.css +++ /dev/null @@ -1,67 +0,0 @@ -/* TextField.module.css */ - -/* Container for the text fields */ -.textFieldContainer { - display: flex; - flex-direction: column; - margin: 1.5rem 0; /* Increased margin for better spacing */ - } - - /* Row for each text field */ - .textFieldRow { - display: flex; - flex-direction: column; /* Stack label and input vertically */ - margin-bottom: 1rem; /* Increased margin for better separation */ - } - - /* Label for each text field */ - .textFieldLabel { - margin-bottom: 0.5rem; /* Space between label and input */ - font-weight: 600; /* Increased weight for better visibility */ - color: #333; /* Dark gray for the label */ - font-size: 1.1rem; /* Increased font size for the label */ - transition: all 0.2s ease; /* Smooth transition for label */ - } - - /* Input field styles */ - .textFieldInput { - padding: 12px 14px; /* Padding for a filled look */ - border: 1px solid #ccc; /* Light gray border */ - border-radius: 4px; /* Rounded corners */ - width: 100%; /* Full width */ - font-size: 1rem; /* Font size */ - background-color: #f5f5f5; /* Light background color for filled effect */ - transition: border-color 0.2s ease, background-color 0.2s ease; /* Smooth transitions */ - box-shadow: none; /* Remove default shadow */ - height: 48px; /* Fixed height for a more square appearance */ - } - - /* Focus styles for the input */ - .textFieldInput:focus { - border-color: #1976d2; /* Blue border color on focus */ - background-color: #fff; /* Change background to white on focus */ - outline: none; /* Remove default outline */ - } - - /* Hover effect for the input */ - .textFieldInput:hover { - border-color: #1976d2; /* Change border color on hover */ - } - - /* Placeholder styles */ - .textFieldInput::placeholder { - color: #aaa; /* Light gray placeholder text */ - opacity: 1; /* Ensure placeholder is fully opaque */ - } - - /* Hide the number input spinners in webkit browsers */ - .textFieldInput::-webkit-inner-spin-button, - .textFieldInput::-webkit-outer-spin-button { - -webkit-appearance: none; /* Remove default styling */ - margin: 0; /* Remove margin */ - } - - /* Hide the number input spinners in Firefox */ - .textFieldInput[type='number'] { - -moz-appearance: textfield; /* Use textfield appearance */ - } \ No newline at end of file From 9e3f2b26d8a96d505b66fe089a9acfea59de6811 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Fri, 8 Nov 2024 12:29:23 +0100 Subject: [PATCH 09/25] Change NMSettings.get_default() from reading settings from file to reading them from the default class members --- py_neuromodulation/stream/settings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py_neuromodulation/stream/settings.py b/py_neuromodulation/stream/settings.py index 7e25ec24..c8ac742c 100644 --- a/py_neuromodulation/stream/settings.py +++ b/py_neuromodulation/stream/settings.py @@ -250,7 +250,7 @@ def from_file(PATH: _PathLike) -> "NMSettings": @staticmethod def get_default() -> "NMSettings": - return NMSettings.from_file(PYNM_DIR / "default_settings.yaml") + return NMSettings() @staticmethod def list_normalization_methods() -> list[NormMethod]: From dd535908a8d8d0bd301eb4419176966319667bbf Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Fri, 8 Nov 2024 12:29:51 +0100 Subject: [PATCH 10/25] fix zustand version --- gui_dev/package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gui_dev/package.json b/gui_dev/package.json index 9329eca5..2850e8bf 100644 --- a/gui_dev/package.json +++ b/gui_dev/package.json @@ -18,7 +18,7 @@ "react": "next", "react-dom": "next", "react-router-dom": "^6.26.2", - "zustand": "next" + "zustand": "latest" }, "devDependencies": { "@babel/core": "^7.25.7", From 56d7806b6a1e2ee8c27bd425f0f27b6002600f4a Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Fri, 8 Nov 2024 14:48:26 +0100 Subject: [PATCH 11/25] Add classes NMSequenceModel and NMValueModel --- py_neuromodulation/default_settings.yaml | 28 +- py_neuromodulation/features/bursts.py | 2 +- py_neuromodulation/stream/settings.py | 38 +-- .../utils/pydantic_extensions.py | 252 +++++++++++++++++- py_neuromodulation/utils/types.py | 117 ++------ 5 files changed, 309 insertions(+), 128 deletions(-) diff --git a/py_neuromodulation/default_settings.yaml b/py_neuromodulation/default_settings.yaml index c98b2c0e..0019a78d 100644 --- a/py_neuromodulation/default_settings.yaml +++ b/py_neuromodulation/default_settings.yaml @@ -1,4 +1,15 @@ ---- +# We +# should +# have +# a +# brief +# explanation +# of +# the +# settings +# format +# here + ######################## ### General settings ### ######################## @@ -51,12 +62,8 @@ preprocessing_filter: lowpass_filter: true highpass_filter: true bandpass_filter: true - bandstop_filter_settings: - frequency_low_hz: 100 - frequency_high_hz: 160 - bandpass_filter_settings: - frequency_low_hz: 3 - frequency_high_hz: 200 + bandstop_filter_settings: [100, 160] # [low_hz, high_hz] + bandpass_filter_settings: [3, 200] # [hz, _hz] lowpass_filter_cutoff_hz: 200 highpass_filter_cutoff_hz: 3 @@ -162,10 +169,8 @@ sharpwave_analysis_settings: decay_steepness: false slope_ratio: false filter_ranges_hz: - - frequency_low_hz: 5 - frequency_high_hz: 80 - - frequency_low_hz: 5 - frequency_high_hz: 30 + - [5, 80] + - [5, 30] detect_troughs: estimate: true distance_troughs_ms: 10 @@ -174,6 +179,7 @@ sharpwave_analysis_settings: estimate: true distance_troughs_ms: 5 distance_peaks_ms: 10 + # TONI: Reverse this setting? e.g. interval: [mean, var] estimator: mean: [interval] median: [] diff --git a/py_neuromodulation/features/bursts.py b/py_neuromodulation/features/bursts.py index 83d63bf8..2ff8ceac 100644 --- a/py_neuromodulation/features/bursts.py +++ b/py_neuromodulation/features/bursts.py @@ -11,7 +11,7 @@ from py_neuromodulation.utils.types import BoolSelector, NMBaseModel, NMFeature from typing import TYPE_CHECKING, Callable -from py_neuromodulation.utils.types import create_validation_error +from py_neuromodulation.utils.pydantic_extensions import create_validation_error if TYPE_CHECKING: from py_neuromodulation import NMSettings diff --git a/py_neuromodulation/stream/settings.py b/py_neuromodulation/stream/settings.py index c8ac742c..39a9b6fd 100644 --- a/py_neuromodulation/stream/settings.py +++ b/py_neuromodulation/stream/settings.py @@ -4,15 +4,15 @@ from typing import ClassVar from pydantic import Field, model_validator -from py_neuromodulation import PYNM_DIR, logger, user_features +from py_neuromodulation import logger, user_features from py_neuromodulation.utils.types import ( BoolSelector, FrequencyRange, - PreprocessorName, _PathLike, NMBaseModel, NormMethod, + PreprocessorList, ) from py_neuromodulation.processing.filter_preprocessing import FilterSettings @@ -72,11 +72,14 @@ class NMSettings(NMBaseModel): } # Preproceessing settings - preprocessing: list[PreprocessorName] = [ - "raw_resampling", - "notch_filter", - "re_referencing", - ] + preprocessing: PreprocessorList = PreprocessorList( + [ + "raw_resampling", + "notch_filter", + "re_referencing", + ] + ) + raw_resampling_settings: ResamplerSettings = ResamplerSettings() preprocessing_filter: FilterSettings = FilterSettings() raw_normalization_settings: NormalizationSettings = NormalizationSettings() @@ -144,26 +147,29 @@ def validate_settings(self): if self.bandpass_filter_settings.kalman_filter: self.kalman_filter_settings.validate_fbands(self) - for k, v in self.frequency_ranges_hz.items(): - if not isinstance(v, FrequencyRange): - self.frequency_ranges_hz[k] = FrequencyRange.create_from(v) + # TONI: not needed after NMSequenceModel, remove in the future + # for k, v in self.frequency_ranges_hz.items(): + # if not isinstance(v, FrequencyRange): + # self.frequency_ranges_hz[k] = FrequencyRange.create_from(v) return self def reset(self) -> "NMSettings": self.features.disable_all() - self.preprocessing = [] + self.preprocessing = PreprocessorList() self.postprocessing.disable_all() return self def set_fast_compute(self) -> "NMSettings": self.reset() self.features.fft = True - self.preprocessing = [ - "raw_resampling", - "notch_filter", - "re_referencing", - ] + self.preprocessing = PreprocessorList( + [ + "raw_resampling", + "notch_filter", + "re_referencing", + ] + ) self.postprocessing.feature_normalization = True self.postprocessing.project_cortex = False self.postprocessing.project_subcortex = False diff --git a/py_neuromodulation/utils/pydantic_extensions.py b/py_neuromodulation/utils/pydantic_extensions.py index 556f751c..be677243 100644 --- a/py_neuromodulation/utils/pydantic_extensions.py +++ b/py_neuromodulation/utils/pydantic_extensions.py @@ -1,11 +1,48 @@ -from typing import Any, get_type_hints -from pydantic.fields import FieldInfo, _FieldInfoInputs, _FromFieldInfoInputs -from pydantic import BaseModel, ConfigDict, SerializationInfo, model_serializer -from pydantic_core import PydanticUndefined +from typing import Any, get_type_hints, TypeVar, Generic, Literal, overload from typing_extensions import Unpack, TypedDict +from pydantic import BaseModel, ConfigDict, model_validator +from pydantic_core import PydanticUndefined, ValidationError, InitErrorDetails +from pydantic.fields import FieldInfo, _FieldInfoInputs, _FromFieldInfoInputs from pprint import pformat +def create_validation_error( + error_message: str, + loc: list[str | int] | None = None, + title: str = "Validation Error", + input_type: Literal["python", "json"] = "python", + hide_input: bool = False, +) -> ValidationError: + """ + Factory function to create a Pydantic v2 ValidationError instance from a single error message. + + Args: + error_message (str): The error message for the ValidationError. + loc (List[str | int], optional): The location of the error. Defaults to None. + title (str, optional): The title of the error. Defaults to "Validation Error". + input_type (Literal["python", "json"], optional): Whether the error is for a Python object or JSON. Defaults to "python". + hide_input (bool, optional): Whether to hide the input value in the error message. Defaults to False. + + Returns: + ValidationError: A Pydantic ValidationError instance. + """ + if loc is None: + loc = [] + + line_errors = [ + InitErrorDetails( + type="value_error", loc=tuple(loc), input=None, ctx={"error": error_message} + ) + ] + + return ValidationError.from_exception_data( + title=title, + line_errors=line_errors, + input_type=input_type, + hide_input=hide_input, + ) + + class _NMExtraFieldInputs(TypedDict, total=False): """Additional fields to add on top of the pydantic FieldInfo""" @@ -60,14 +97,36 @@ class NMBaseModel(BaseModel): model_config = ConfigDict(validate_assignment=False, extra="allow") def __init__(self, *args, **kwargs) -> None: - if kwargs: - super().__init__(**kwargs) - else: - field_names = list(self.model_fields.keys()) - kwargs = {} - for i in range(len(args)): - kwargs[field_names[i]] = args[i] + """Pydantic does not support positional arguments by default. + This is a workaround to support positional arguments for models like FrequencyRange. + It converts positional arguments to kwargs and then calls the base class __init__. + """ + if not args: + # Simple case - just use kwargs super().__init__(**kwargs) + return + + field_names = list(self.model_fields.keys()) + # If we have more positional args than fields, that's an error + if len(args) > len(field_names): + raise ValueError( + f"Too many positional arguments. Expected at most {len(field_names)}, got {len(args)}" + ) + + # Convert positional args to kwargs, checking for duplicates if args: + complete_kwargs = {} + for i, arg in enumerate(args): + field_name = field_names[i] + if field_name in kwargs: + raise ValueError( + f"Got multiple values for field '{field_name}': " + f"positional argument and keyword argument" + ) + complete_kwargs[field_name] = arg + + # Add remaining kwargs + complete_kwargs.update(kwargs) + super().__init__(**complete_kwargs) def __str__(self): return pformat(self.model_dump()) @@ -115,3 +174,174 @@ def serialize_with_metadata(self): for tag, value in field_info.custom_metadata.items(): result[f"__{tag}__"] = value return result + + +################################# +#### Generic Pydantic models #### +################################# + + +def create_alias_property(index: int, alias: str, classname: str): + """Creates a property that accesses the root sequence at the given index""" + + def getter(self): + return self.root[index] + + def setter(self, value): + if isinstance(self.root, tuple): + new_values = list(self.root) + new_values[index] = value + self.root = tuple(new_values) + else: + self.root[index] = value + + return property( + fget=getter, + fset=setter, + doc=f"Alias '{alias}' for position [{index}] of class '{classname}'.", + ) + + +T = TypeVar("T") +C = TypeVar("C", list, tuple) + + +class NMSequenceModel(NMBaseModel, Generic[C]): + """Base class for sequence models with a single root value""" + + root: C = NMField(default_factory=list) + + # Class variable for aliases - override in subclasses + __aliases__: dict[int, list[str]] = {} + + def __init__(self, *args, **kwargs) -> None: + # Generate properties programatically (not used currently) + # for index, aliases in self.__aliases__.items(): + # for alias in aliases: + # if not hasattr(self.__class__, alias): + # setattr( + # self.__class__, + # alias, + # create_alias_property(index, alias, self.__class__.__name__), + # ) + + if len(args) == 1 and isinstance(args[0], (list, tuple)): + kwargs["root"] = args[0] + elif len(args) == 1: + kwargs["root"] = [args[0]] + elif len(args) > 1: # Add this case + kwargs["root"] = tuple(args) + super().__init__(**kwargs) + + def __iter__(self): # type: ignore[reportIncompatibleMethodOverride] + return iter(self.root) + + def __getitem__(self, idx): + return self.root[idx] + + def __len__(self): + return len(self.root) + + def model_dump(self): # type: ignore[reportIncompatibleMethodOverride] + return self.root + + def model_dump_json(self, **kwargs): + import json + + return json.dumps(self.root, **kwargs) + + def serialize_with_metadata(self) -> dict[str, Any]: + result = {"__field_type__": self.__class__.__name__, "value": self.root} + + # Add any field metadata from the root field + field_info = self.model_fields.get("root") + if isinstance(field_info, NMFieldInfo): + for tag, value in field_info.custom_metadata.items(): + result[f"__{tag}__"] = value + + return result + + @model_validator(mode="before") + @classmethod + def validate_input(cls, value: Any) -> dict[str, Any]: + # If it's a dict, just return it + if isinstance(value, dict): + if "root" in value: + return value + + # Check for aliased fields if class has aliases defined + if hasattr(cls, "__aliases__"): + # Collect all possible alias names for each position + alias_values = [] + max_index = max(cls.__aliases__.keys()) if cls.__aliases__ else -1 + + # Try to find a value for each position using its aliases + for i in range(max_index + 1): + aliases = cls.__aliases__.get(i, []) + value_found = None + + # Try each alias for this position + for alias in aliases: + if alias in value: + value_found = value[alias] + break + + if value_found is not None: + alias_values.append(value_found) + else: + # If we're missing any position's value, don't use aliases + break + + # If we found all values through aliases, use them + if len(alias_values) == max_index + 1: + return {"root": alias_values} + + # if it's a sequence, return the value as the root + if isinstance(value, (list, tuple)): + return {"root": value} + + # Else, make it a list + return {"root": [value]} + + +class NMValueModel(NMBaseModel, Generic[T]): + """Base class for single-value models that behave like their contained type""" + + root: T + + @model_validator(mode="before") + @classmethod + def validate_input(cls, value: Any) -> dict[str, Any]: + if isinstance(value, dict): + if "root" in value: + return value + # If it's a dict without root, assume the first value is our value + if len(value) > 0: + return {"root": next(iter(value.values()))} + return {"root": None} + return {"root": value} + + def __str__(self) -> str: + return str(self.root) + + def __repr__(self) -> str: + return f"{self.__class__.__name__}({repr(self.root)})" + + def model_dump(self): # type: ignore[reportIncompatibleMethodOverride] + return self.root + + def model_dump_json(self, **kwargs): + import json + + return json.dumps(self.root, **kwargs) + + def serialize_with_metadata(self) -> dict[str, Any]: + result = {"__field_type__": self.__class__.__name__, "value": self.root} + + # Add any field metadata from the root field + field_info = self.model_fields.get("root") + if isinstance(field_info, NMFieldInfo): + for tag, value in field_info.custom_metadata.items(): + result[f"__{tag}__"] = value + + return result diff --git a/py_neuromodulation/utils/types.py b/py_neuromodulation/utils/types.py index f5921281..a2c22db9 100644 --- a/py_neuromodulation/utils/types.py +++ b/py_neuromodulation/utils/types.py @@ -1,9 +1,8 @@ from os import PathLike from math import isnan from typing import Literal, TYPE_CHECKING -from pydantic import BaseModel, model_validator -from pydantic_core import ValidationError, InitErrorDetails -from .pydantic_extensions import NMBaseModel, NMField +from pydantic import BaseModel, ConfigDict, model_validator +from .pydantic_extensions import NMBaseModel, NMSequenceModel from collections.abc import Sequence from datetime import datetime @@ -86,66 +85,43 @@ class NMPreprocessor: def process(self, data: "np.ndarray") -> "np.ndarray": ... -class FrequencyRange(NMBaseModel): - # frequency_low_hz: Annotated[list[float], {"unit": "Hz"}] = Field(gt=0) - # frequency_high_hz: FrequencyHz = Field(gt=0) - frequency_low_hz: float = NMField(gt=0, custom_metadata={"unit": "Hz"}) - frequency_high_hz: float = NMField(gt=0, custom_metadata={"unit": "Hz"}) +class PreprocessorList(NMSequenceModel[list[PreprocessorName]]): + model_config = ConfigDict(arbitrary_types_allowed=True) + # Useless contructor to prevent linter from complaining def __init__(self, *args, **kwargs) -> None: super().__init__(*args, **kwargs) - def __getitem__(self, item: int): - match item: - case 0: - return self.frequency_low_hz - case 1: - return self.frequency_high_hz - case _: - raise IndexError(f"Index {item} out of range") - def as_tuple(self) -> tuple[float, float]: - return (self.frequency_low_hz, self.frequency_high_hz) +class FrequencyRange(NMSequenceModel[tuple[float, float]]): + """Frequency range as (low, high) tuple""" - def __iter__(self): # type: ignore - return iter(self.as_tuple()) + __aliases__ = { + 0: ["frequency_low_hz", "low_frequency_hz"], + 1: ["frequency_high_hz", "high_frequency_hz"], + } + + # Useless contructor to prevent linter from complaining + def __init__(self, *args, **kwargs) -> None: + super().__init__(*args, **kwargs) @model_validator(mode="after") def validate_range(self): - if not (isnan(self.frequency_high_hz) or isnan(self.frequency_low_hz)): - assert ( - self.frequency_high_hz > self.frequency_low_hz - ), "Frequency high must be greater than frequency low" + low, high = self.root + if not (isnan(low) or isnan(high)): + assert high > low, "High frequency must be greater than low frequency" return self - @classmethod - def create_from(cls, input) -> "FrequencyRange": - match input: - case FrequencyRange(): - return input - case dict() if "frequency_low_hz" in input and "frequency_high_hz" in input: - return FrequencyRange( - input["frequency_low_hz"], input["frequency_high_hz"] - ) - case Sequence() if len(input) == 2: - return FrequencyRange(input[0], input[1]) - case _: - raise ValueError("Invalid input for FrequencyRange creation.") - - @model_validator(mode="before") - @classmethod - def check_input(cls, input): - match input: - case dict() if "frequency_low_hz" in input and "frequency_high_hz" in input: - return input - case Sequence() if len(input) == 2: - return {"frequency_low_hz": input[0], "frequency_high_hz": input[1]} - case _: - raise ValueError( - "Value for FrequencyRange must be a dictionary, " - "or a sequence of 2 numeric values, " - f"but got {input} instead." - ) + # Alias properties + @property + def frequency_low_hz(self) -> float: + """Lower frequency bound in Hz""" + return self.root[0] + + @property + def frequency_high_hz(self) -> float: + """Upper frequency bound in Hz""" + return self.root[1] class BoolSelector(NMBaseModel): @@ -179,43 +155,6 @@ def print_all(cls): print(f) -def create_validation_error( - error_message: str, - loc: list[str | int] | None = None, - title: str = "Validation Error", - input_type: Literal["python", "json"] = "python", - hide_input: bool = False, -) -> ValidationError: - """ - Factory function to create a Pydantic v2 ValidationError instance from a single error message. - - Args: - error_message (str): The error message for the ValidationError. - loc (List[str | int], optional): The location of the error. Defaults to None. - title (str, optional): The title of the error. Defaults to "Validation Error". - input_type (Literal["python", "json"], optional): Whether the error is for a Python object or JSON. Defaults to "python". - hide_input (bool, optional): Whether to hide the input value in the error message. Defaults to False. - - Returns: - ValidationError: A Pydantic ValidationError instance. - """ - if loc is None: - loc = [] - - line_errors = [ - InitErrorDetails( - type="value_error", loc=tuple(loc), input=None, ctx={"error": error_message} - ) - ] - - return ValidationError.from_exception_data( - title=title, - line_errors=line_errors, - input_type=input_type, - hide_input=hide_input, - ) - - ################# ### GUI TYPES ### ################# From 34a44127e116acdebf1965600e4bdc28c3c2e7cd Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Fri, 8 Nov 2024 17:07:23 +0100 Subject: [PATCH 12/25] bugfix: in NMBaseModel.validate() method, change model_validate() for model_validate_string() which correctly interprets the string keys produced by model_dump() as member variables --- py_neuromodulation/utils/pydantic_extensions.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py_neuromodulation/utils/pydantic_extensions.py b/py_neuromodulation/utils/pydantic_extensions.py index be677243..e679eec4 100644 --- a/py_neuromodulation/utils/pydantic_extensions.py +++ b/py_neuromodulation/utils/pydantic_extensions.py @@ -135,7 +135,7 @@ def __repr__(self): return pformat(self.model_dump()) def validate(self) -> Any: # type: ignore - return self.model_validate(self.model_dump()) + return self.model_validate_strings(self.model_dump()) def __getitem__(self, key): return getattr(self, key) From f56262110795fb75be69e0d3511817401630ab3c Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Mon, 25 Nov 2024 11:49:58 +0100 Subject: [PATCH 13/25] Improve error collection for the Settings page --- gui_dev/src/pages/Settings/Settings.jsx | 66 ++--- .../Settings/components/FrequencyRange.jsx | 182 ++++++++++++ py_neuromodulation/default_settings.yaml | 6 +- py_neuromodulation/features/bandpower.py | 88 ++++-- py_neuromodulation/features/bursts.py | 7 +- py_neuromodulation/features/coherence.py | 9 +- .../features/feature_processor.py | 8 +- py_neuromodulation/features/fooof.py | 9 +- .../features/mne_connectivity.py | 28 +- py_neuromodulation/features/oscillatory.py | 3 +- py_neuromodulation/filter/kalman_filter.py | 23 +- py_neuromodulation/gui/backend/app_backend.py | 1 + py_neuromodulation/gui/backend/app_pynm.py | 2 - .../processing/data_preprocessor.py | 4 +- .../processing/filter_preprocessing.py | 32 +- .../processing/normalization.py | 16 +- py_neuromodulation/processing/projection.py | 4 +- py_neuromodulation/processing/resample.py | 6 +- py_neuromodulation/stream/settings.py | 54 ++-- py_neuromodulation/stream/stream.py | 6 +- .../utils/pydantic_extensions.py | 273 +++++++++++------- py_neuromodulation/utils/types.py | 148 +++++++++- tests/test_osc_features.py | 4 +- 23 files changed, 723 insertions(+), 256 deletions(-) create mode 100644 gui_dev/src/pages/Settings/components/FrequencyRange.jsx diff --git a/gui_dev/src/pages/Settings/Settings.jsx b/gui_dev/src/pages/Settings/Settings.jsx index 60b238d6..045603be 100644 --- a/gui_dev/src/pages/Settings/Settings.jsx +++ b/gui_dev/src/pages/Settings/Settings.jsx @@ -2,8 +2,6 @@ import { useEffect, useState } from "react"; import { Box, Button, - ButtonGroup, - InputAdornment, Popover, Stack, Switch, @@ -13,8 +11,7 @@ import { } from "@mui/material"; import { Link } from "react-router-dom"; import { CollapsibleBox, TitledBox } from "@/components"; -import { FrequencyRangeList } from "./FrequencyRange"; -import { Dropdown } from "./Dropdown"; +import { FrequencyRangeList } from "./components/FrequencyRange"; import { useSettingsStore, useStatusBarContent } from "@/stores"; import { filterObjectByKeys } from "@/utils/functions"; @@ -30,28 +27,33 @@ const BooleanField = ({ value, onChange, error }) => ( onChange(e.target.checked)} /> ); -const StringField = ({ value, onChange, label, error }) => ( - onChange(e.target.value)} - label={label} - sx={{ - "& .MuiOutlinedInput-root": { - "& fieldset": { - borderColor: error ? "error.main" : "inherit", - }, - "&:hover fieldset": { - borderColor: error ? "error.main" : "primary.main", - }, - "&.Mui-focused fieldset": { - borderColor: error ? "error.main" : "primary.main", - }, - }, - }} - /> -); +const errorStyle = { + "& .MuiOutlinedInput-root": { + "& fieldset": { borderColor: "error.main" }, + "&:hover fieldset": { + borderColor: "error.main", + }, + "&.Mui-focused fieldset": { + borderColor: "error.main", + }, + }, +}; + +const StringField = ({ value, onChange, label, error }) => { + const errorSx = error ? errorStyle : {}; + return ( + onChange(e.target.value)} + label={label} + sx={{ ...errorSx }} + /> + ); +}; const NumberField = ({ value, onChange, label, error }) => { + const errorSx = error ? errorStyle : {}; + const handleChange = (event) => { const newValue = event.target.value; // Only allow numbers and decimal point @@ -66,19 +68,7 @@ const NumberField = ({ value, onChange, label, error }) => { value={value} onChange={handleChange} label={label} - sx={{ - "& .MuiOutlinedInput-root": { - "& fieldset": { - borderColor: error ? "error.main" : "inherit", - }, - "&:hover fieldset": { - borderColor: error ? "error.main" : "primary.main", - }, - "&.Mui-focused fieldset": { - borderColor: error ? "error.main" : "primary.main", - }, - }, - }} + sx={{ ...errorSx }} // InputProps={{ // endAdornment: ( // @@ -98,7 +88,6 @@ const componentRegistry = { boolean: BooleanField, string: StringField, number: NumberField, - Array: Dropdown, }; const SettingsField = ({ path, Component, label, value, onChange, error }) => { @@ -376,6 +365,7 @@ export const Settings = () => { rangeOrder={frequencyRangeOrder} onOrderChange={updateFrequencyRangeOrder} onChange={handleChangeSettings} + errors={validationErrors} />     diff --git a/gui_dev/src/pages/Settings/components/FrequencyRange.jsx b/gui_dev/src/pages/Settings/components/FrequencyRange.jsx new file mode 100644 index 00000000..16333166 --- /dev/null +++ b/gui_dev/src/pages/Settings/components/FrequencyRange.jsx @@ -0,0 +1,182 @@ +import { useState } from "react"; +import { TextField, Button, IconButton, Stack } from "@mui/material"; +import { Add, Close } from "@mui/icons-material"; +import { debounce } from "@/utils"; + +const NumberField = ({ ...props }) => ( + +); + +export const FrequencyRange = ({ + name, + range, + onChangeName, + onChangeRange, + onRemove, + error, +}) => { + const [localName, setLocalName] = useState(name); + + const debouncedChangeName = debounce((newName) => { + onChangeName(newName, name); + }, 1000); + + const handleNameChange = (e) => { + const newName = e.target.value; + setLocalName(newName); + debouncedChangeName(newName); + }; + + const handleNameBlur = () => { + onChangeName(localName, name); + }; + + const handleKeyPress = (e) => { + if (e.key === "Enter") { + console.log(e.target.value, name); + onChangeName(localName, name); + } + }; + + const handleRangeChange = (name, field, value) => { + // onChangeRange takes the name of the range as the first argument + onChangeRange(name, { ...range, [field]: value }); + }; + + return ( + + + + handleRangeChange(name, "frequency_low_hz", e.target.value) + } + label="Low Hz" + /> + + handleRangeChange(name, "frequency_high_hz", e.target.value) + } + label="High Hz" + /> + onRemove(name)} + color="primary" + disableRipple + sx={{ m: 0, p: 0 }} + > + + + + ); +}; + +export const FrequencyRangeList = ({ + ranges, + rangeOrder, + onChange, + onOrderChange, + errors, +}) => { + const handleChangeRange = (name, newRange) => { + const updatedRanges = { ...ranges }; + updatedRanges[name] = newRange; + onChange(["frequency_ranges_hz"], updatedRanges); + }; + + const handleChangeName = (newName, oldName) => { + if (oldName === newName) { + return; + } + + const updatedRanges = { ...ranges, [newName]: ranges[oldName] }; + delete updatedRanges[oldName]; + onChange(["frequency_ranges_hz"], updatedRanges); + + const updatedOrder = rangeOrder.map((name) => + name === oldName ? newName : name + ); + onOrderChange(updatedOrder); + }; + + const handleRemove = (name) => { + const updatedRanges = { ...ranges }; + delete updatedRanges[name]; + onChange(["frequency_ranges_hz"], updatedRanges); + + const updatedOrder = rangeOrder.filter((item) => item !== name); + onOrderChange(updatedOrder); + }; + + const addRange = () => { + let newName = "NewRange"; + let counter = 0; + // Find first available name + while (Object.hasOwn(ranges, newName)) { + counter++; + newName = `NewRange${counter}`; + } + + const updatedRanges = { + ...ranges, + [newName]: { + __field_type__: "FrequencyRange", + frequency_low_hz: 1, + frequency_high_hz: 500, + }, + }; + onChange(["frequency_ranges_hz"], updatedRanges); + + const updatedOrder = [...rangeOrder, newName]; + onOrderChange(updatedOrder); + }; + + return ( + + {rangeOrder.map((name, index) => ( + + ))} + + + ); +}; diff --git a/py_neuromodulation/default_settings.yaml b/py_neuromodulation/default_settings.yaml index 0019a78d..81c533e3 100644 --- a/py_neuromodulation/default_settings.yaml +++ b/py_neuromodulation/default_settings.yaml @@ -168,7 +168,7 @@ sharpwave_analysis_settings: rise_steepness: false decay_steepness: false slope_ratio: false - filter_ranges_hz: + filter_ranges_hz: # list of [low_hz, high_hz] - [5, 80] - [5, 30] detect_troughs: @@ -228,8 +228,8 @@ nolds_settings: frequency_bands: [low_beta] mne_connectiviy_settings: - method: plv - mode: multitaper + method: plv # One of ['coh', 'cohy', 'imcoh', 'cacoh', 'mic', 'mim', 'plv', 'ciplv', 'ppc', 'pli', 'dpli','wpli', 'wpli2_debiased', 'gc', 'gc_tr'] + mode: multitaper # One of ['multitaper', 'fourier', 'cwt_morlet'] bispectrum_settings: f1s: [5, 35] diff --git a/py_neuromodulation/features/bandpower.py b/py_neuromodulation/features/bandpower.py index dac13f4b..72dab126 100644 --- a/py_neuromodulation/features/bandpower.py +++ b/py_neuromodulation/features/bandpower.py @@ -2,8 +2,13 @@ from collections.abc import Sequence from typing import TYPE_CHECKING from pydantic import field_validator - from py_neuromodulation.utils.types import NMBaseModel, BoolSelector, NMFeature +from py_neuromodulation.utils.pydantic_extensions import ( + NMField, + NMErrorList, + create_validation_error, +) +from py_neuromodulation import logger if TYPE_CHECKING: from py_neuromodulation.stream.settings import NMSettings @@ -17,15 +22,18 @@ class BandpowerFeatures(BoolSelector): class BandPowerSettings(NMBaseModel): - segment_lengths_ms: dict[str, int] = { - "theta": 1000, - "alpha": 500, - "low beta": 333, - "high beta": 333, - "low gamma": 100, - "high gamma": 100, - "HFA": 100, - } + segment_lengths_ms: dict[str, int] = NMField( + default={ + "theta": 1000, + "alpha": 500, + "low beta": 333, + "high beta": 333, + "low gamma": 100, + "high gamma": 100, + "HFA": 100, + }, + custom_metadata={"field_type": "FrequencySegmentLength"}, + ) bandpower_features: BandpowerFeatures = BandpowerFeatures() log_transform: bool = True kalman_filter: bool = False @@ -33,24 +41,58 @@ class BandPowerSettings(NMBaseModel): @field_validator("bandpower_features") @classmethod def bandpower_features_validator(cls, bandpower_features: BandpowerFeatures): - assert ( - len(bandpower_features.get_enabled()) > 0 - ), "Set at least one bandpower_feature to True." - + if not len(bandpower_features.get_enabled()) > 0: + raise create_validation_error( + error_message="Set at least one bandpower_feature to True.", + location=["bandpass_filter_settings", "bandpower_features"], + ) return bandpower_features - def validate_fbands(self, settings: "NMSettings") -> None: + def validate_fbands(self, settings: "NMSettings") -> NMErrorList: + """_summary_ + + :param settings: _description_ + :type settings: NMSettings + :raises create_validation_error: _description_ + :raises create_validation_error: _description_ + :raises ValueError: _description_ + """ + errors: NMErrorList = NMErrorList() + for fband_name, seg_length_fband in self.segment_lengths_ms.items(): - assert seg_length_fband <= settings.segment_length_features_ms, ( - f"segment length {seg_length_fband} needs to be smaller than " - f" settings['segment_length_features_ms'] = {settings.segment_length_features_ms}" - ) + # Check that all frequency bands are defined in settings.frequency_ranges_hz + if fband_name not in settings.frequency_ranges_hz: + logger.warning( + f"Frequency band {fband_name} in bandpass_filter_settings.segment_lengths_ms" + " is not defined in settings.frequency_ranges_hz" + ) + + # Check that all segment lengths are smaller than settings.segment_length_features_ms + if not seg_length_fband <= settings.segment_length_features_ms: + errors.add_error( + f"segment length {seg_length_fband} needs to be smaller than " + f" settings['segment_length_features_ms'] = {settings.segment_length_features_ms}", + location=[ + "bandpass_filter_settings", + "segment_lengths_ms", + fband_name, + ], + ) + # Check that all frequency bands defined in settings.frequency_ranges_hz for fband_name in settings.frequency_ranges_hz.keys(): - assert fband_name in self.segment_lengths_ms, ( - f"frequency range {fband_name} " - "needs to be defined in settings.bandpass_filter_settings.segment_lengths_ms]" - ) + if fband_name not in self.segment_lengths_ms: + errors.add_error( + f"frequency range {fband_name} " + "needs to be defined in settings.bandpass_filter_settings.segment_lengths_ms", + location=[ + "bandpass_filter_settings", + "segment_lengths_ms", + fband_name, + ], + ) + + return errors class BandPower(NMFeature): diff --git a/py_neuromodulation/features/bursts.py b/py_neuromodulation/features/bursts.py index 2ff8ceac..e9f5b632 100644 --- a/py_neuromodulation/features/bursts.py +++ b/py_neuromodulation/features/bursts.py @@ -7,8 +7,9 @@ from collections.abc import Sequence from itertools import product -from pydantic import Field, field_validator +from pydantic import field_validator from py_neuromodulation.utils.types import BoolSelector, NMBaseModel, NMFeature +from py_neuromodulation.utils.pydantic_extensions import NMField from typing import TYPE_CHECKING, Callable from py_neuromodulation.utils.pydantic_extensions import create_validation_error @@ -46,8 +47,8 @@ class BurstFeatures(BoolSelector): class BurstsSettings(NMBaseModel): - threshold: float = Field(default=75, ge=0, le=100) - time_duration_s: float = Field(default=30, ge=0) + threshold: float = NMField(default=75, ge=0) + time_duration_s: float = NMField(default=30, ge=0, custom_metadata={"unit": "s"}) frequency_bands: list[str] = ["low_beta", "high_beta", "low_gamma"] burst_features: BurstFeatures = BurstFeatures() diff --git a/py_neuromodulation/features/coherence.py b/py_neuromodulation/features/coherence.py index 21ca471b..6a100710 100644 --- a/py_neuromodulation/features/coherence.py +++ b/py_neuromodulation/features/coherence.py @@ -3,7 +3,7 @@ from typing import TYPE_CHECKING, Annotated -from pydantic import Field, field_validator +from pydantic import field_validator from py_neuromodulation.utils.types import ( NMFeature, @@ -11,6 +11,7 @@ FrequencyRange, NMBaseModel, ) +from py_neuromodulation.utils.pydantic_extensions import NMField from py_neuromodulation import logger if TYPE_CHECKING: @@ -28,14 +29,16 @@ class CoherenceFeatures(BoolSelector): max_allfbands: bool = True -ListOfTwoStr = Annotated[list[str], Field(min_length=2, max_length=2)] +# TODO: make this into a pydantic model that only accepts names from +# the channels objects and does not accept the same string twice +ListOfTwoStr = Annotated[list[str], NMField(min_length=2, max_length=2)] class CoherenceSettings(NMBaseModel): features: CoherenceFeatures = CoherenceFeatures() method: CoherenceMethods = CoherenceMethods() channels: list[ListOfTwoStr] = [] - frequency_bands: list[str] = Field(default=["high_beta"], min_length=1) + frequency_bands: list[str] = NMField(default=["high_beta"], min_length=1) @field_validator("frequency_bands") def fbands_spaces_to_underscores(cls, frequency_bands): diff --git a/py_neuromodulation/features/feature_processor.py b/py_neuromodulation/features/feature_processor.py index 9e970e8f..dbb7e5c9 100644 --- a/py_neuromodulation/features/feature_processor.py +++ b/py_neuromodulation/features/feature_processor.py @@ -1,13 +1,13 @@ from typing import Type, TYPE_CHECKING -from py_neuromodulation.utils.types import NMFeature, FeatureName +from py_neuromodulation.utils.types import NMFeature, FEATURE_NAME if TYPE_CHECKING: import numpy as np from py_neuromodulation import NMSettings -FEATURE_DICT: dict[FeatureName | str, str] = { +FEATURE_DICT: dict[FEATURE_NAME | str, str] = { "raw_hjorth": "Hjorth", "return_raw": "Raw", "bandpass_filter": "BandPower", @@ -42,7 +42,7 @@ def __init__( from importlib import import_module # Accept 'str' for custom features - self.features: dict[FeatureName | str, NMFeature] = { + self.features: dict[FEATURE_NAME | str, NMFeature] = { feature_name: getattr( import_module("py_neuromodulation.features"), FEATURE_DICT[feature_name] )(settings, ch_names, sfreq) @@ -83,7 +83,7 @@ def estimate_features(self, data: "np.ndarray") -> dict: return feature_results - def get_feature(self, fname: FeatureName) -> NMFeature: + def get_feature(self, fname: FEATURE_NAME) -> NMFeature: return self.features[fname] diff --git a/py_neuromodulation/features/fooof.py b/py_neuromodulation/features/fooof.py index 683c5304..9f4b9544 100644 --- a/py_neuromodulation/features/fooof.py +++ b/py_neuromodulation/features/fooof.py @@ -9,6 +9,7 @@ BoolSelector, FrequencyRange, ) +from py_neuromodulation.utils.pydantic_extensions import NMField if TYPE_CHECKING: from py_neuromodulation import NMSettings @@ -29,11 +30,11 @@ class FooofPeriodicSettings(BoolSelector): class FooofSettings(NMBaseModel): aperiodic: FooofAperiodicSettings = FooofAperiodicSettings() periodic: FooofPeriodicSettings = FooofPeriodicSettings() - windowlength_ms: float = 800 + windowlength_ms: float = NMField(800, gt=0, custom_metadata={"unit": "ms"}) peak_width_limits: FrequencyRange = FrequencyRange(0.5, 12) - max_n_peaks: int = 3 - min_peak_height: float = 0 - peak_threshold: float = 2 + max_n_peaks: int = NMField(3, ge=0) + min_peak_height: float = NMField(0, ge=0) + peak_threshold: float = NMField(2, ge=0) freq_range_hz: FrequencyRange = FrequencyRange(2, 40) knee: bool = True diff --git a/py_neuromodulation/features/mne_connectivity.py b/py_neuromodulation/features/mne_connectivity.py index 88883771..f7a186e7 100644 --- a/py_neuromodulation/features/mne_connectivity.py +++ b/py_neuromodulation/features/mne_connectivity.py @@ -1,8 +1,9 @@ from collections.abc import Iterable import numpy as np -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Literal from py_neuromodulation.utils.types import NMFeature, NMBaseModel +from py_neuromodulation.utils.pydantic_extensions import NMField if TYPE_CHECKING: from py_neuromodulation import NMSettings @@ -10,9 +11,30 @@ from mne import Epochs +MNE_CONNECTIVITY_METHOD = Literal[ + "coh", + "cohy", + "imcoh", + "cacoh", + "mic", + "mim", + "plv", + "ciplv", + "ppc", + "pli", + "dpli", + "wpli", + "wpli2_debiased", + "gc", + "gc_tr", +] + +MNE_CONNECTIVITY_MODE = Literal["multitaper", "fourier", "cwt_morlet"] + + class MNEConnectivitySettings(NMBaseModel): - method: str = "plv" - mode: str = "multitaper" + method: MNE_CONNECTIVITY_METHOD = NMField(default="plv") + mode: MNE_CONNECTIVITY_MODE = NMField(default="multitaper") class MNEConnectivity(NMFeature): diff --git a/py_neuromodulation/features/oscillatory.py b/py_neuromodulation/features/oscillatory.py index b8b54005..7ee8a20a 100644 --- a/py_neuromodulation/features/oscillatory.py +++ b/py_neuromodulation/features/oscillatory.py @@ -3,6 +3,7 @@ from itertools import product from py_neuromodulation.utils.types import NMBaseModel, BoolSelector, NMFeature +from py_neuromodulation.utils.pydantic_extensions import NMField from typing import TYPE_CHECKING if TYPE_CHECKING: @@ -17,7 +18,7 @@ class OscillatoryFeatures(BoolSelector): class OscillatorySettings(NMBaseModel): - windowlength_ms: int = 1000 + windowlength_ms: int = NMField(1000, gt=0, custom_metadata={"unit": "ms"}) log_transform: bool = True features: OscillatoryFeatures = OscillatoryFeatures( mean=True, median=False, std=False, max=False diff --git a/py_neuromodulation/filter/kalman_filter.py b/py_neuromodulation/filter/kalman_filter.py index b7ae1075..0ebfe195 100644 --- a/py_neuromodulation/filter/kalman_filter.py +++ b/py_neuromodulation/filter/kalman_filter.py @@ -1,7 +1,9 @@ import numpy as np from typing import TYPE_CHECKING + from py_neuromodulation.utils.types import NMBaseModel +from py_neuromodulation.utils.pydantic_extensions import NMErrorList if TYPE_CHECKING: @@ -22,13 +24,22 @@ class KalmanSettings(NMBaseModel): "HFA", ] - def validate_fbands(self, settings: "NMSettings") -> None: - assert all( + def validate_fbands(self, settings: "NMSettings") -> NMErrorList: + errors: NMErrorList = NMErrorList() + + if not all( (item in settings.frequency_ranges_hz for item in self.frequency_bands) - ), ( - "Frequency bands for Kalman filter must also be specified in " - "bandpass_filter_settings." - ) + ): + errors.add_error( + "Frequency bands for Kalman filter must also be specified in " + "frequency_ranges_hz.", + location=[ + "kalman_filter_settings", + "frequency_bands", + ], + ) + + return errors def define_KF(Tp, sigma_w, sigma_v): diff --git a/py_neuromodulation/gui/backend/app_backend.py b/py_neuromodulation/gui/backend/app_backend.py index 9c7b0a88..abbccfee 100644 --- a/py_neuromodulation/gui/backend/app_backend.py +++ b/py_neuromodulation/gui/backend/app_backend.py @@ -110,6 +110,7 @@ async def update_settings(data: dict, validate_only: bool = Query(False)): try: # First, validate with Pydantic try: + # TODO: check if this works properly or needs model_validate_strings validated_settings = NMSettings.model_validate(data) except ValidationError as e: if not validate_only: diff --git a/py_neuromodulation/gui/backend/app_pynm.py b/py_neuromodulation/gui/backend/app_pynm.py index 282f3252..f4853e75 100644 --- a/py_neuromodulation/gui/backend/app_pynm.py +++ b/py_neuromodulation/gui/backend/app_pynm.py @@ -69,7 +69,6 @@ async def start_run_function( # time.sleep(2) # self.logger.info(f"Stream running: {self.stream.is_running}") - def setup_lsl_stream( self, lsl_stream_name: str | None = None, @@ -154,4 +153,3 @@ def setup_offline_stream( line_noise=line_noise, sampling_rate_features_hz=sampling_rate_features, ) - diff --git a/py_neuromodulation/processing/data_preprocessor.py b/py_neuromodulation/processing/data_preprocessor.py index 2946ba6c..d1677db0 100644 --- a/py_neuromodulation/processing/data_preprocessor.py +++ b/py_neuromodulation/processing/data_preprocessor.py @@ -1,12 +1,12 @@ from typing import TYPE_CHECKING, Type -from py_neuromodulation.utils.types import PreprocessorName, NMPreprocessor +from py_neuromodulation.utils.types import PREPROCESSOR_NAME, NMPreprocessor if TYPE_CHECKING: import numpy as np import pandas as pd from py_neuromodulation.stream.settings import NMSettings -PREPROCESSOR_DICT: dict[PreprocessorName, str] = { +PREPROCESSOR_DICT: dict[PREPROCESSOR_NAME, str] = { "preprocessing_filter": "PreprocessingFilter", "notch_filter": "NotchFilter", "raw_resampling": "Resampler", diff --git a/py_neuromodulation/processing/filter_preprocessing.py b/py_neuromodulation/processing/filter_preprocessing.py index e6515ae0..2c5addbc 100644 --- a/py_neuromodulation/processing/filter_preprocessing.py +++ b/py_neuromodulation/processing/filter_preprocessing.py @@ -1,22 +1,14 @@ import numpy as np -from pydantic import Field from typing import TYPE_CHECKING from py_neuromodulation.utils.types import BoolSelector, FrequencyRange, NMPreprocessor +from py_neuromodulation.utils.pydantic_extensions import NMField if TYPE_CHECKING: from py_neuromodulation import NMSettings -FILTER_SETTINGS_MAP = { - "bandstop_filter": "bandstop_filter_settings", - "bandpass_filter": "bandpass_filter_settings", - "lowpass_filter": "lowpass_filter_cutoff_hz", - "highpass_filter": "highpass_filter_cutoff_hz", -} - - class FilterSettings(BoolSelector): bandstop_filter: bool = True bandpass_filter: bool = True @@ -25,21 +17,23 @@ class FilterSettings(BoolSelector): bandstop_filter_settings: FrequencyRange = FrequencyRange(100, 160) bandpass_filter_settings: FrequencyRange = FrequencyRange(2, 200) - lowpass_filter_cutoff_hz: float = Field(default=200) - highpass_filter_cutoff_hz: float = Field(default=3) - - def get_filter_tuple(self, filter_name) -> tuple[float | None, float | None]: - filter_value = self[FILTER_SETTINGS_MAP[filter_name]] - + lowpass_filter_cutoff_hz: float = NMField( + default=200, gt=0, custom_metadata={"unit": "Hz"} + ) + highpass_filter_cutoff_hz: float = NMField( + default=3, gt=0, custom_metadata={"unit": "Hz"} + ) + + def get_filter_tuple(self, filter_name) -> FrequencyRange: match filter_name: case "bandstop_filter": - return (filter_value.frequency_high_hz, filter_value.frequency_low_hz) + return self.bandstop_filter_settings case "bandpass_filter": - return (filter_value.frequency_low_hz, filter_value.frequency_high_hz) + return self.bandpass_filter_settings case "lowpass_filter": - return (None, filter_value) + return FrequencyRange(None, self.lowpass_filter_cutoff_hz) case "highpass_filter": - return (filter_value, None) + return FrequencyRange(self.highpass_filter_cutoff_hz, None) case _: raise ValueError( "Filter name must be one of 'bandstop_filter', 'lowpass_filter', " diff --git a/py_neuromodulation/processing/normalization.py b/py_neuromodulation/processing/normalization.py index 66419cec..08008614 100644 --- a/py_neuromodulation/processing/normalization.py +++ b/py_neuromodulation/processing/normalization.py @@ -2,11 +2,11 @@ import numpy as np from typing import TYPE_CHECKING, Callable, Literal, get_args -from pydantic import Field +from py_neuromodulation.utils.pydantic_extensions import NMField from py_neuromodulation.utils.types import ( NMBaseModel, - NormMethod, + NORM_METHOD, NMPreprocessor, ) @@ -17,13 +17,13 @@ class NormalizationSettings(NMBaseModel): - normalization_time_s: float = 30 - normalization_method: NormMethod = "zscore" - clip: float = Field(default=3, ge=0) + normalization_time_s: float = NMField(30, gt=0, custom_metadata={"unit": "s"}) + normalization_method: NORM_METHOD = NMField(default="zscore") + clip: float = NMField(default=3, ge=0, custom_metadata={"unit": "a.u."}) @staticmethod - def list_normalization_methods() -> list[NormMethod]: - return list(get_args(NormMethod)) + def list_normalization_methods() -> list[NORM_METHOD]: + return list(get_args(NORM_METHOD)) class Normalizer(NMPreprocessor): @@ -55,7 +55,7 @@ def __init__( if self.using_sklearn: import sklearn.preprocessing as skpp - NORM_METHODS_SKLEARN: dict[NormMethod, Callable] = { + NORM_METHODS_SKLEARN: dict[NORM_METHOD, Callable] = { "quantile": lambda: skpp.QuantileTransformer(n_quantiles=300), "robust": skpp.RobustScaler, "minmax": skpp.MinMaxScaler, diff --git a/py_neuromodulation/processing/projection.py b/py_neuromodulation/processing/projection.py index 4cdc3610..3a83a29f 100644 --- a/py_neuromodulation/processing/projection.py +++ b/py_neuromodulation/processing/projection.py @@ -1,6 +1,6 @@ import numpy as np -from pydantic import Field from py_neuromodulation.utils.types import NMBaseModel +from py_neuromodulation.utils.pydantic_extensions import NMField from typing import TYPE_CHECKING if TYPE_CHECKING: @@ -9,7 +9,7 @@ class ProjectionSettings(NMBaseModel): - max_dist_mm: float = Field(default=20.0, gt=0.0) + max_dist_mm: float = NMField(default=20.0, gt=0.0, custom_metadata={"unit": "mm"}) class Projection: diff --git a/py_neuromodulation/processing/resample.py b/py_neuromodulation/processing/resample.py index 73014d3a..949e9e57 100644 --- a/py_neuromodulation/processing/resample.py +++ b/py_neuromodulation/processing/resample.py @@ -1,12 +1,14 @@ """Module for resampling.""" import numpy as np -from pydantic import Field from py_neuromodulation.utils.types import NMBaseModel, NMPreprocessor +from py_neuromodulation.utils.pydantic_extensions import NMField class ResamplerSettings(NMBaseModel): - resample_freq_hz: float = Field(default=1000, gt=0) + resample_freq_hz: float = NMField( + default=1000, gt=0, custom_metadata={"unit": "Hz"} + ) class Resampler(NMPreprocessor): diff --git a/py_neuromodulation/stream/settings.py b/py_neuromodulation/stream/settings.py index 39a9b6fd..14bc29d8 100644 --- a/py_neuromodulation/stream/settings.py +++ b/py_neuromodulation/stream/settings.py @@ -1,19 +1,22 @@ """Module for handling settings.""" from pathlib import Path -from typing import ClassVar -from pydantic import Field, model_validator +from typing import Any, ClassVar +from pydantic import model_validator, ValidationError +from pydantic.functional_validators import ModelWrapValidatorHandler from py_neuromodulation import logger, user_features +from types import SimpleNamespace from py_neuromodulation.utils.types import ( BoolSelector, FrequencyRange, _PathLike, NMBaseModel, - NormMethod, + NORM_METHOD, PreprocessorList, ) +from py_neuromodulation.utils.pydantic_extensions import NMErrorList, NMField from py_neuromodulation.processing.filter_preprocessing import FilterSettings from py_neuromodulation.processing.normalization import NormalizationSettings @@ -31,7 +34,9 @@ from py_neuromodulation.features import BurstsSettings -class FeatureSelection(BoolSelector): +# TONI: this class has the proble that if a feature is absent, +# it won't default to False but to whatever is defined here as default +class FeatureSelector(BoolSelector): raw_hjorth: bool = True return_raw: bool = True bandpass_filter: bool = False @@ -59,8 +64,12 @@ class NMSettings(NMBaseModel): _instances: ClassVar[list["NMSettings"]] = [] # General settings - sampling_rate_features_hz: float = Field(default=10, gt=0) - segment_length_features_ms: float = Field(default=1000, gt=0) + sampling_rate_features_hz: float = NMField( + default=10, gt=0, custom_metadata={"unit": "Hz"} + ) + segment_length_features_ms: float = NMField( + default=1000, gt=0, custom_metadata={"unit": "ms"} + ) frequency_ranges_hz: dict[str, FrequencyRange] = { "theta": FrequencyRange(4, 8), "alpha": FrequencyRange(8, 12), @@ -91,7 +100,7 @@ class NMSettings(NMBaseModel): project_subcortex_settings: ProjectionSettings = ProjectionSettings(max_dist_mm=5) # Feature settings - features: FeatureSelection = FeatureSelection() + features: FeatureSelector = FeatureSelector() fft_settings: OscillatorySettings = OscillatorySettings() welch_settings: OscillatorySettings = OscillatorySettings() @@ -129,10 +138,23 @@ def _remove_feature(cls, feature: str) -> None: for instance in cls._instances: delattr(instance.features, feature) - @model_validator(mode="after") - def validate_settings(self): + @model_validator(mode="wrap") # type: ignore[reportIncompatibleMethodOverride] + def validate_settings(self, handler: ModelWrapValidatorHandler) -> Any: + # Perform all necessary custom validations in the settings class and also + # all validations in the feature classes that need additional information from + # the settings class + errors: NMErrorList = NMErrorList() + + try: + # validate the model + handler(self) + except ValidationError as e: + self = NMSettings.unvalidated(**self) + NMSettings.model_fields_set + errors.extend(NMErrorList(e.errors())) + if len(self.features.get_enabled()) == 0: - raise ValueError("At least one feature must be selected.") + errors.add_error("At least one feature must be selected.") # Replace spaces with underscores in frequency band names self.frequency_ranges_hz = { @@ -141,16 +163,14 @@ def validate_settings(self): if self.features.bandpass_filter: # Check BandPass settings frequency bands - self.bandpass_filter_settings.validate_fbands(self) + errors.extend(self.bandpass_filter_settings.validate_fbands(self)) # Check Kalman filter frequency bands if self.bandpass_filter_settings.kalman_filter: - self.kalman_filter_settings.validate_fbands(self) + errors.extend(self.kalman_filter_settings.validate_fbands(self)) - # TONI: not needed after NMSequenceModel, remove in the future - # for k, v in self.frequency_ranges_hz.items(): - # if not isinstance(v, FrequencyRange): - # self.frequency_ranges_hz[k] = FrequencyRange.create_from(v) + if len(errors) > 0: + raise errors.create_error() return self @@ -259,7 +279,7 @@ def get_default() -> "NMSettings": return NMSettings() @staticmethod - def list_normalization_methods() -> list[NormMethod]: + def list_normalization_methods() -> list[NORM_METHOD]: return NormalizationSettings.list_normalization_methods() def save( diff --git a/py_neuromodulation/stream/stream.py b/py_neuromodulation/stream/stream.py index 2f22aac4..240efae8 100644 --- a/py_neuromodulation/stream/stream.py +++ b/py_neuromodulation/stream/stream.py @@ -9,7 +9,7 @@ from contextlib import suppress from py_neuromodulation.stream.data_processor import DataProcessor -from py_neuromodulation.utils.types import _PathLike, FeatureName +from py_neuromodulation.utils.types import _PathLike, FEATURE_NAME from py_neuromodulation.stream.settings import NMSettings if TYPE_CHECKING: @@ -84,7 +84,7 @@ def __init__( raise ValueError("Either `channels` or `data` must be passed to `Stream`.") # If features that use frequency ranges are on, test them against nyquist frequency - use_freq_ranges: list[FeatureName] = [ + use_freq_ranges: list[FEATURE_NAME] = [ "bandpass_filter", "stft", "fft", @@ -328,7 +328,7 @@ async def run( # if self.feature_queue is not None: # self.feature_queue.put(feature_dict) - + if websocket_featues is not None: await websocket_featues.send_message(feature_dict) self.batch_count += 1 diff --git a/py_neuromodulation/utils/pydantic_extensions.py b/py_neuromodulation/utils/pydantic_extensions.py index e679eec4..ee89ccea 100644 --- a/py_neuromodulation/utils/pydantic_extensions.py +++ b/py_neuromodulation/utils/pydantic_extensions.py @@ -1,48 +1,114 @@ -from typing import Any, get_type_hints, TypeVar, Generic, Literal, overload +import copy +from typing import ( + Any, + get_origin, + get_args, + get_type_hints, + TypeVar, + Generic, + Literal, + cast, + Sequence, +) from typing_extensions import Unpack, TypedDict -from pydantic import BaseModel, ConfigDict, model_validator -from pydantic_core import PydanticUndefined, ValidationError, InitErrorDetails +from pydantic import BaseModel, ConfigDict, model_validator, model_serializer + +from pydantic_core import ( + ErrorDetails, + PydanticUndefined, + InitErrorDetails, + ValidationError, +) from pydantic.fields import FieldInfo, _FieldInfoInputs, _FromFieldInfoInputs from pprint import pformat def create_validation_error( error_message: str, - loc: list[str | int] | None = None, + location: list[str | int] = [], title: str = "Validation Error", - input_type: Literal["python", "json"] = "python", - hide_input: bool = False, + error_type="value_error", ) -> ValidationError: """ - Factory function to create a Pydantic v2 ValidationError instance from a single error message. + Factory function to create a Pydantic v2 ValidationError. Args: error_message (str): The error message for the ValidationError. loc (List[str | int], optional): The location of the error. Defaults to None. title (str, optional): The title of the error. Defaults to "Validation Error". - input_type (Literal["python", "json"], optional): Whether the error is for a Python object or JSON. Defaults to "python". - hide_input (bool, optional): Whether to hide the input value in the error message. Defaults to False. Returns: ValidationError: A Pydantic ValidationError instance. """ - if loc is None: - loc = [] - - line_errors = [ - InitErrorDetails( - type="value_error", loc=tuple(loc), input=None, ctx={"error": error_message} - ) - ] return ValidationError.from_exception_data( title=title, - line_errors=line_errors, - input_type=input_type, - hide_input=hide_input, + line_errors=[ + InitErrorDetails( + type=error_type, + loc=tuple(location), + input=None, + ctx={"error": error_message}, + ) + ], + input_type="python", + hide_input=False, ) +class NMErrorList: + """Class to handle data about Pydantic errors. + Stores data in a list of InitErrorDetails. Errors can be accessed but not modified. + + :return: _description_ + :rtype: _type_ + """ + + def __init__( + self, errors: Sequence[InitErrorDetails | ErrorDetails] | None = None + ) -> None: + self.__errors: list[InitErrorDetails | ErrorDetails] = [e for e in errors or []] + + def add_error( + self, + error_message: str, + location: list[str | int] = [], + error_type="value_error", + ) -> None: + self.__errors.append( + InitErrorDetails( + type=error_type, + loc=tuple(location), + input=None, + ctx={"error": error_message}, + ) + ) + + def create_error(self, title: str = "Validation Error") -> ValidationError: + return ValidationError.from_exception_data( + title=title, line_errors=cast(list[InitErrorDetails], self.__errors) + ) + + def extend(self, errors: "NMErrorList"): + self.__errors.extend(errors.__errors) + + def __iter__(self): + return iter(self.__errors) + + def __len__(self): + return len(self.__errors) + + def __getitem__(self, idx): + # Return a copy of the error to prevent modification + return copy.deepcopy(self.__errors[idx]) + + def __repr__(self): + return repr(self.__errors) + + def __str__(self): + return str(self.__errors) + + class _NMExtraFieldInputs(TypedDict, total=False): """Additional fields to add on top of the pydantic FieldInfo""" @@ -66,7 +132,7 @@ class NMFieldInfo(FieldInfo): _default_values = {} def __init__(self, **kwargs: Unpack[_NMFieldInfoInputs]) -> None: - self.custom_metadata = kwargs.pop("custom_metadata", {}) + self.custom_metadata: dict[str, Any] = kwargs.pop("custom_metadata", {}) super().__init__(**kwargs) @staticmethod @@ -94,16 +160,17 @@ def NMField( class NMBaseModel(BaseModel): - model_config = ConfigDict(validate_assignment=False, extra="allow") + # model_config = ConfigDict(validate_assignment=False, extra="allow") def __init__(self, *args, **kwargs) -> None: """Pydantic does not support positional arguments by default. This is a workaround to support positional arguments for models like FrequencyRange. It converts positional arguments to kwargs and then calls the base class __init__. """ + if not args: # Simple case - just use kwargs - super().__init__(**kwargs) + super().__init__(*args, **kwargs) return field_names = list(self.model_fields.keys()) @@ -128,14 +195,16 @@ def __init__(self, *args, **kwargs) -> None: complete_kwargs.update(kwargs) super().__init__(**complete_kwargs) + __init__.__pydantic_base_init__ = True # type: ignore + def __str__(self): return pformat(self.model_dump()) - def __repr__(self): - return pformat(self.model_dump()) + # def __repr__(self): + # return pformat(self.model_dump()) - def validate(self) -> Any: # type: ignore - return self.model_validate_strings(self.model_dump()) + def validate(self, context: Any | None = None) -> Any: # type: ignore + return self.model_validate(self.model_dump(), context=context) def __getitem__(self, key): return getattr(self, key) @@ -171,37 +240,69 @@ def serialize_with_metadata(self): # Extract unit information from Annotated type if isinstance(field_info, NMFieldInfo): - for tag, value in field_info.custom_metadata.items(): - result[f"__{tag}__"] = value + # Convert scalar value to dict with metadata + field_dict = { + "value": value, + # __field_type__ will be overwritte if set in custom_metadata + "__field_type__": type(value).__name__, + **{ + f"__{tag}__": value + for tag, value in field_info.custom_metadata.items() + }, + } + # Add possible values for Literal types + if get_origin(field_info.annotation) is Literal: + field_dict["__valid_values__"] = list( + get_args(field_info.annotation) + ) + + result[field_name] = field_dict return result + @classmethod + def unvalidated(cls, **data: Any) -> Any: + def process_value(value: Any, field_type: Any) -> Any: + if isinstance(value, dict) and hasattr( + field_type, "__pydantic_core_schema__" + ): + # Recursively handle nested Pydantic models + return field_type.unvalidated(**value) + elif isinstance(value, list): + # Handle lists of Pydantic models + if hasattr(field_type, "__args__") and hasattr( + field_type.__args__[0], "__pydantic_core_schema__" + ): + return [ + field_type.__args__[0].unvalidated(**item) + if isinstance(item, dict) + else item + for item in value + ] + return value + + processed_data = {} + for name, field in cls.model_fields.items(): + try: + value = data[name] + processed_data[name] = process_value(value, field.annotation) + except KeyError: + if not field.is_required(): + processed_data[name] = copy.deepcopy(field.default) + else: + raise TypeError(f"Missing required keyword argument {name!r}") + + self = cls.__new__(cls) + object.__setattr__(self, "__dict__", processed_data) + object.__setattr__(self, "__pydantic_private__", {"extra": None}) + object.__setattr__(self, "__pydantic_fields_set__", set(processed_data.keys())) + return self + ################################# #### Generic Pydantic models #### ################################# -def create_alias_property(index: int, alias: str, classname: str): - """Creates a property that accesses the root sequence at the given index""" - - def getter(self): - return self.root[index] - - def setter(self, value): - if isinstance(self.root, tuple): - new_values = list(self.root) - new_values[index] = value - self.root = tuple(new_values) - else: - self.root[index] = value - - return property( - fget=getter, - fset=setter, - doc=f"Alias '{alias}' for position [{index}] of class '{classname}'.", - ) - - T = TypeVar("T") C = TypeVar("C", list, tuple) @@ -215,16 +316,6 @@ class NMSequenceModel(NMBaseModel, Generic[C]): __aliases__: dict[int, list[str]] = {} def __init__(self, *args, **kwargs) -> None: - # Generate properties programatically (not used currently) - # for index, aliases in self.__aliases__.items(): - # for alias in aliases: - # if not hasattr(self.__class__, alias): - # setattr( - # self.__class__, - # alias, - # create_alias_property(index, alias, self.__class__.__name__), - # ) - if len(args) == 1 and isinstance(args[0], (list, tuple)): kwargs["root"] = args[0] elif len(args) == 1: @@ -303,45 +394,27 @@ def validate_input(cls, value: Any) -> dict[str, Any]: # Else, make it a list return {"root": [value]} - -class NMValueModel(NMBaseModel, Generic[T]): - """Base class for single-value models that behave like their contained type""" - - root: T - - @model_validator(mode="before") - @classmethod - def validate_input(cls, value: Any) -> dict[str, Any]: - if isinstance(value, dict): - if "root" in value: - return value - # If it's a dict without root, assume the first value is our value - if len(value) > 0: - return {"root": next(iter(value.values()))} - return {"root": None} - return {"root": value} - - def __str__(self) -> str: - return str(self.root) - - def __repr__(self) -> str: - return f"{self.__class__.__name__}({repr(self.root)})" - - def model_dump(self): # type: ignore[reportIncompatibleMethodOverride] + @model_serializer + def ser_model(self): return self.root - def model_dump_json(self, **kwargs): - import json - - return json.dumps(self.root, **kwargs) - - def serialize_with_metadata(self) -> dict[str, Any]: - result = {"__field_type__": self.__class__.__name__, "value": self.root} - - # Add any field metadata from the root field - field_info = self.model_fields.get("root") - if isinstance(field_info, NMFieldInfo): - for tag, value in field_info.custom_metadata.items(): - result[f"__{tag}__"] = value - - return result + # Custom validator to skip the 'root' field in validation errors + @model_validator(mode="wrap") # type: ignore[reportIncompatibleMethodOverride] + def rewrite_error_locations(self, handler): + try: + return handler(self) + except ValidationError as e: + errors = [] + for err in e.errors(): + loc = list(err["loc"]) + # Find and remove 'root' from the location path + if "root" in loc: + root_idx = loc.index("root") + if root_idx < len(loc) - 1: + loc = loc[:root_idx] + loc[root_idx + 1 :] + err["loc"] = tuple(loc) + errors.append(err) + print(errors) + raise ValidationError.from_exception_data( + title="ValidationError", line_errors=errors + ) diff --git a/py_neuromodulation/utils/types.py b/py_neuromodulation/utils/types.py index a2c22db9..13b2923e 100644 --- a/py_neuromodulation/utils/types.py +++ b/py_neuromodulation/utils/types.py @@ -1,8 +1,9 @@ from os import PathLike from math import isnan -from typing import Literal, TYPE_CHECKING +from typing import Literal, TYPE_CHECKING, Any, TypeVar from pydantic import BaseModel, ConfigDict, model_validator -from .pydantic_extensions import NMBaseModel, NMSequenceModel +from .pydantic_extensions import NMBaseModel, NMSequenceModel, NMField +from abc import abstractmethod from collections.abc import Sequence from datetime import datetime @@ -18,7 +19,7 @@ _PathLike = str | PathLike -FeatureName = Literal[ +FEATURE_NAME = Literal[ "raw_hjorth", "return_raw", "bandpass_filter", @@ -35,7 +36,7 @@ "bispectrum", ] -PreprocessorName = Literal[ +PREPROCESSOR_NAME = Literal[ "preprocessing_filter", "notch_filter", "raw_resampling", @@ -43,7 +44,7 @@ "raw_normalization", ] -NormMethod = Literal[ +NORM_METHOD = Literal[ "mean", "median", "zscore", @@ -55,11 +56,6 @@ ] -################################### -######## PROTOCOL CLASSES ######## -################################### - - class NMFeature: def __init__( self, settings: "NMSettings", ch_names: Sequence[str], sfreq: int | float @@ -85,7 +81,7 @@ class NMPreprocessor: def process(self, data: "np.ndarray") -> "np.ndarray": ... -class PreprocessorList(NMSequenceModel[list[PreprocessorName]]): +class PreprocessorList(NMSequenceModel[list[PREPROCESSOR_NAME]]): model_config = ConfigDict(arbitrary_types_allowed=True) # Useless contructor to prevent linter from complaining @@ -155,6 +151,136 @@ def print_all(cls): print(f) +################################################ +### Generic Pydantic models for the frontend ### +################################################ + + +class UniqueStringSequence(NMSequenceModel[list[str]]): + """ + A sequence of strings where: + - Values must come from a predefined set + - Each value can only appear once + - Order is preserved + """ + + @property + @abstractmethod + def valid_values(self) -> list[str]: + """Each subclass must implement this to provide its valid values""" + raise NotImplementedError + + def __init__(self, **data): + valid_values = data.pop("valid_values", []) + super().__init__(**data) + object.__setattr__(self, "valid_values", valid_values) + + @model_validator(mode="after") + def validate_sequence(self): + seen = set() + validated = [] + for item in self.root: + if item not in seen and item in self.valid_values: + seen.add(item) + validated.append(item) + self.root = validated + return self + + def serialize_with_metadata(self) -> dict[str, Any]: + result = super().serialize_with_metadata() + result["__valid_values__"] = self.valid_values + return result + + +class DependentKeysList(NMSequenceModel[list[str]]): + """ + A list of strings where valid values are keys from another settings field + """ + + root: list[str] = NMField(default_factory=list) + source_dict: dict[str, Any] = NMField(default_factory=dict, exclude=True) + + def __init__(self, **data): + source_dict = data.pop("source_dict", {}) + super().__init__(**data) + object.__setattr__(self, "source_dict", source_dict) + + @model_validator(mode="after") + def validate_keys(self): + valid_keys = set(self.source_dict.keys()) + seen = set() + validated = [] + for item in self.root: + if item not in seen and item in valid_keys: + seen.add(item) + validated.append(item) + self.root = validated + return self + + def serialize_with_metadata(self) -> dict[str, Any]: + result = super().serialize_with_metadata() + result["__valid_values__"] = list(self.source_dict.keys()) + result["__dependent__"] = True # Indicates this needs dynamic updating + return result + + +class StringPairsList(NMSequenceModel[list[tuple[str, str]]]): + """ + A list of string pairs where values must come from predetermined lists + """ + + root: list[tuple[str, str]] = NMField(default_factory=list) + valid_first: list[str] = NMField(default_factory=list, exclude=True) + valid_second: list[str] = NMField(default_factory=list, exclude=True) + + def __init__(self, **data): + valid_first = data.pop("valid_first", []) + valid_second = data.pop("valid_second", []) + super().__init__(**data) + object.__setattr__(self, "valid_first", valid_first) + object.__setattr__(self, "valid_second", valid_second) + + @model_validator(mode="after") + def validate_pairs(self): + validated = [ + (first, second) + for first, second in self.root + if first in self.valid_first and second in self.valid_second + ] + self.root = validated + return self + + def serialize_with_metadata(self) -> dict[str, Any]: + result = super().serialize_with_metadata() + result["__valid_first__"] = self.valid_first + result["__valid_second__"] = self.valid_second + return result + + +# class LiteralValue(NMValueModel[str]): +# """ +# A string field that must be one of a predefined set of literals +# """ + +# valid_values: list[str] = NMField(default_factory=list, exclude=True) + +# def __init__(self, **data): +# valid_values = data.pop("valid_values", []) +# super().__init__(**data) +# object.__setattr__(self, "valid_values", valid_values) + +# @model_validator(mode="after") +# def validate_value(self): +# if self.root not in self.valid_values: +# raise ValueError(f"Value must be one of: {self.valid_values}") +# return self + +# def serialize_with_metadata(self) -> dict[str, Any]: +# result = super().serialize_with_metadata() +# result["__valid_values__"] = self.valid_values +# return result + + ################# ### GUI TYPES ### ################# diff --git a/tests/test_osc_features.py b/tests/test_osc_features.py index 8cf84111..fd2428d1 100644 --- a/tests/test_osc_features.py +++ b/tests/test_osc_features.py @@ -3,11 +3,11 @@ import numpy as np from py_neuromodulation import NMSettings, Stream, features -from py_neuromodulation.utils.types import FeatureName +from py_neuromodulation.utils.types import FEATURE_NAME def setup_osc_settings( - osc_feature_name: FeatureName, + osc_feature_name: FEATURE_NAME, osc_feature_setting: str, windowlength_ms: int, log_transform: bool, From 550bd497bc822ba6a1b0865707cfce728c8001bd Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Mon, 25 Nov 2024 11:59:55 +0100 Subject: [PATCH 14/25] bugfix in settings wrap validator --- py_neuromodulation/stream/settings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py_neuromodulation/stream/settings.py b/py_neuromodulation/stream/settings.py index 14bc29d8..764ee547 100644 --- a/py_neuromodulation/stream/settings.py +++ b/py_neuromodulation/stream/settings.py @@ -147,7 +147,7 @@ def validate_settings(self, handler: ModelWrapValidatorHandler) -> Any: try: # validate the model - handler(self) + self = handler(self) except ValidationError as e: self = NMSettings.unvalidated(**self) NMSettings.model_fields_set From d8581c1ad1952a0d59afbb1f6869c9b06b745073 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Mon, 25 Nov 2024 13:24:27 +0100 Subject: [PATCH 15/25] Add Folder selection to FileBrowser component --- gui_dev/package.json | 36 +++++++-------- .../components/FileBrowser/FileBrowser.jsx | 45 +++++++++++++------ .../components/FileBrowser/QuickAccess.jsx | 1 - .../pages/SourceSelection/FileSelector.jsx | 35 ++++++++++++--- py_neuromodulation/gui/backend/app_backend.py | 1 - 5 files changed, 78 insertions(+), 40 deletions(-) diff --git a/gui_dev/package.json b/gui_dev/package.json index 2850e8bf..0e31e9cc 100644 --- a/gui_dev/package.json +++ b/gui_dev/package.json @@ -9,34 +9,34 @@ "preview": "vite preview" }, "dependencies": { - "@emotion/react": "^11.13.3", - "@emotion/styled": "^11.13.0", - "@mui/icons-material": "latest", - "@mui/material": "latest", + "@emotion/react": "^11.13.5", + "@emotion/styled": "^11.13.5", + "@mui/icons-material": "^6.1.8", + "@mui/material": "^6.1.8", "immer": "^10.1.1", "plotly.js-basic-dist-min": "^2.35.2", "react": "next", "react-dom": "next", - "react-router-dom": "^6.26.2", - "zustand": "latest" + "react-router-dom": "^7.0.1", + "zustand": "^5.0.1" }, "devDependencies": { - "@babel/core": "^7.25.7", - "@babel/eslint-parser": "^7.25.7", - "@babel/preset-env": "^7.25.7", - "@babel/preset-react": "^7.25.7", - "@eslint/compat": "^1.2.0", - "@vitejs/plugin-react": "^4.3.2", + "@babel/core": "^7.26.0", + "@babel/eslint-parser": "^7.25.9", + "@babel/preset-env": "^7.26.0", + "@babel/preset-react": "^7.25.9", + "@eslint/compat": "^1.2.3", + "@vitejs/plugin-react": "^4.3.3", "@welldone-software/why-did-you-render": "^8.0.3", "babel-plugin-react-compiler": "latest", - "eslint": "^9.12.0", + "eslint": "^9.15.0", "eslint-config-prettier": "^9.1.0", - "eslint-plugin-jsdoc": "^50.3.1", - "eslint-plugin-react": "^7.37.1", + "eslint-plugin-jsdoc": "^50.5.0", + "eslint-plugin-react": "^7.37.2", "eslint-plugin-react-compiler": "latest", - "eslint-plugin-react-hooks": "^4.6.2", - "eslint-plugin-react-refresh": "^0.4.12", + "eslint-plugin-react-hooks": "^5.0.0", + "eslint-plugin-react-refresh": "^0.4.14", "prettier": "^3.3.3", - "vite": "^5.4.8" + "vite": "^5.4.11" } } diff --git a/gui_dev/src/components/FileBrowser/FileBrowser.jsx b/gui_dev/src/components/FileBrowser/FileBrowser.jsx index 3c50c6b0..a902a931 100644 --- a/gui_dev/src/components/FileBrowser/FileBrowser.jsx +++ b/gui_dev/src/components/FileBrowser/FileBrowser.jsx @@ -1,6 +1,7 @@ import { useReducer, useEffect } from "react"; import { Box, + Button, Paper, Typography, TextField, @@ -14,6 +15,7 @@ import { TableSortLabel, Modal, Select, + Stack, FormControl, InputLabel, Snackbar, @@ -89,8 +91,10 @@ const columns = [ export const FileBrowser = ({ isModal = false, directory = null, + onlyDirectories = false, + allowedExtensions = ALLOWED_EXTENSIONS, onClose, - onFileSelect, + onSelect, }) => { const [state, dispatch] = useReducer(reducer, initialState); @@ -141,11 +145,16 @@ export const FileBrowser = ({ const fetchFiles = async (path) => { try { - const files = await fileManager.getFiles({ + let files = await fileManager.getFiles({ path, - allowedExtensions: ALLOWED_EXTENSIONS.join(","), + allowedExtensions: allowedExtensions.join(","), showHidden: state.showHiddenFiles, }); + + if (onlyDirectories) { + files = files.filter((file) => file.is_directory); + } + dispatch({ type: "SET_FILES", payload: files.map((file) => ({ @@ -164,13 +173,13 @@ export const FileBrowser = ({ } }; - const handleFileClick = (file) => { + const handleRowClick = (file) => { if (file.is_directory) { dispatch({ type: "SET_CURRENT_PATH", payload: file.path }); } else if ( ALLOWED_EXTENSIONS.some((ext) => file.name.toLowerCase().endsWith(ext)) ) { - onFileSelect(file); + onSelect(file); } }; @@ -272,9 +281,9 @@ export const FileBrowser = ({ }; const FileBrowserContent = ( - - - + + + {state.drives.length > 1 && ( Drive @@ -333,7 +342,7 @@ export const FileBrowser = ({ {" "} - +     handleFileClick(file)} + onClick={() => handleRowClick(file)} sx={{ cursor: "pointer" }} > {columns.map((column) => ( @@ -399,13 +406,25 @@ export const FileBrowser = ({ + + + {onlyDirectories && ( + + )} + + dispatch({ type: "SET_ERROR", payload: "" })} message={state.error} /> - +     ); return isModal ? ( diff --git a/gui_dev/src/components/FileBrowser/QuickAccess.jsx b/gui_dev/src/components/FileBrowser/QuickAccess.jsx index 47dfaa34..f5778060 100644 --- a/gui_dev/src/components/FileBrowser/QuickAccess.jsx +++ b/gui_dev/src/components/FileBrowser/QuickAccess.jsx @@ -57,7 +57,6 @@ export const QuickAccessSidebar = ({ onItemClick }) => { flexGrow: 1, display: "flex", flexDirection: "column", - maxHeight: 400, overflowX: "hidden", overflowY: "auto", scrollbarWidth: "thin", diff --git a/gui_dev/src/pages/SourceSelection/FileSelector.jsx b/gui_dev/src/pages/SourceSelection/FileSelector.jsx index c5f149d8..39eaa592 100644 --- a/gui_dev/src/pages/SourceSelection/FileSelector.jsx +++ b/gui_dev/src/pages/SourceSelection/FileSelector.jsx @@ -23,15 +23,12 @@ export const FileSelector = () => { const [isSelecting, setIsSelecting] = useState(false); const [showFileBrowser, setShowFileBrowser] = useState(false); + const [showFolderBrowser, setShowFolderBrowser] = useState(false); useEffect(() => { setSourceType("lsl"); }, []); - const handleSelectFile = () => { - setShowFileBrowser(true); - }; - const handleFileSelect = (file) => { setIsSelecting(true); @@ -50,11 +47,17 @@ export const FileSelector = () => { } }; + const handleFolderSelect = (folder) => { + setShowFolderBrowser(false); + }; + return ( + {streamSetupMessage && ( { isModal={true} directory={fileBrowserDirRef.current} onClose={() => setShowFileBrowser(false)} - onFileSelect={handleFileSelect} + onSelect={handleFileSelect} + /> + )} + {showFolderBrowser && ( + setShowFolderBrowser(false)} + onSelect={handleFolderSelect} + onlyDirectories={true} /> )} diff --git a/py_neuromodulation/gui/backend/app_backend.py b/py_neuromodulation/gui/backend/app_backend.py index abbccfee..9847baf4 100644 --- a/py_neuromodulation/gui/backend/app_backend.py +++ b/py_neuromodulation/gui/backend/app_backend.py @@ -12,7 +12,6 @@ Query, WebSocket, ) -from fastapi.responses import FileResponse from fastapi.staticfiles import StaticFiles from fastapi.middleware.cors import CORSMiddleware from pydantic import ValidationError From f8375c55125c4ace1245d47da81a80f0e3248121 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Wed, 27 Nov 2024 12:54:07 +0100 Subject: [PATCH 16/25] Add scan JSON and port selection to App --- gui_dev/package.json | 1 + gui_dev/src/main.jsx | 11 +++++++ gui_dev/vite.config.js | 1 - py_neuromodulation/gui/backend/app_manager.py | 33 ++++++++++++++++--- py_neuromodulation/stream/settings.py | 1 - .../utils/pydantic_extensions.py | 3 +- py_neuromodulation/utils/types.py | 2 +- 7 files changed, 43 insertions(+), 9 deletions(-) diff --git a/gui_dev/package.json b/gui_dev/package.json index 0e31e9cc..6c65000b 100644 --- a/gui_dev/package.json +++ b/gui_dev/package.json @@ -37,6 +37,7 @@ "eslint-plugin-react-hooks": "^5.0.0", "eslint-plugin-react-refresh": "^0.4.14", "prettier": "^3.3.3", + "react-scan": "^0.0.31", "vite": "^5.4.11" } } diff --git a/gui_dev/src/main.jsx b/gui_dev/src/main.jsx index f4524069..fde760f2 100644 --- a/gui_dev/src/main.jsx +++ b/gui_dev/src/main.jsx @@ -1,7 +1,18 @@ +if (JSON.parse(import.meta.env.VITE_REACT_SCAN) === true) { + import("react-scan").then(({ scan }) => { + scan({ + enabled: true, + log: true, // logs render info to console + }); + }); +} + import { StrictMode } from "react"; import ReactDOM from "react-dom/client"; import { App } from "./App.jsx"; +// Set up react-scan + // Ignore React 19 warning about accessing element.ref const originalConsoleError = console.error; console.error = (message, ...messageArgs) => { diff --git a/gui_dev/vite.config.js b/gui_dev/vite.config.js index f38a5299..1d6fd6b3 100644 --- a/gui_dev/vite.config.js +++ b/gui_dev/vite.config.js @@ -50,7 +50,6 @@ export default defineConfig(() => { }, }, server: { - port: 54321, proxy: { "/api": { target: `http://localhost:${BACKEND_PORT}`, diff --git a/py_neuromodulation/gui/backend/app_manager.py b/py_neuromodulation/gui/backend/app_manager.py index a9829ccd..7f46163f 100644 --- a/py_neuromodulation/gui/backend/app_manager.py +++ b/py_neuromodulation/gui/backend/app_manager.py @@ -18,6 +18,9 @@ # Shared memory configuration ARRAY_SIZE = 1000 # Adjust based on your needs +SERVER_PORT = 50001 +DEV_SERVER_PORT = 54321 + def create_backend() -> "PyNMBackend": from .app_pynm import PyNMState @@ -26,7 +29,12 @@ def create_backend() -> "PyNMBackend": return PyNMBackend(pynm_state=PyNMState()) -def run_vite(shutdown_event: "Event", debug: bool = False) -> None: +def run_vite( + shutdown_event: "Event", + debug: bool = False, + scan: bool = False, + dev_port: int = DEV_SERVER_PORT, +) -> None: """Run Vite in a separate shell""" import subprocess @@ -38,6 +46,8 @@ def run_vite(shutdown_event: "Event", debug: bool = False) -> None: logging.DEBUG if debug else logging.INFO, ) + os.environ["VITE_REACT_SCAN"] = "true" if scan else "false" + def output_reader(shutdown_event: "Event", process: subprocess.Popen): logger.debug("Initialized output stream") color = ansi_color(color="magenta", bright=True, styles=["BOLD"]) @@ -70,7 +80,7 @@ def read_stream(stream, stream_name): subprocess_flags = subprocess.CREATE_NEW_PROCESS_GROUP if os.name == "nt" else 0 process = subprocess.Popen( - "bun run dev", + "bun run dev --port " + str(dev_port), cwd="gui_dev", stdout=subprocess.PIPE, stderr=subprocess.PIPE, @@ -175,7 +185,13 @@ class AppManager: LAUNCH_FLAG = "PYNM_RUNNING" def __init__( - self, debug: bool = False, dev: bool = True, run_in_webview=False + self, + debug: bool = False, + dev: bool = True, + run_in_webview=False, + scan=False, + server_port=SERVER_PORT, + dev_port=DEV_SERVER_PORT, ) -> None: """_summary_ @@ -190,6 +206,10 @@ def __init__( self.debug = debug self.dev = dev self.run_in_webview = run_in_webview + self.scan = scan + self.server_port = server_port + self.dev_port = dev_port + self._reset() # Prevent launching multiple instances of the app due to multiprocessing # This allows the absence of a main guard in the main script @@ -269,7 +289,12 @@ def launch(self) -> None: self.logger.info("Starting Vite server...") self.tasks["vite"] = mp.Process( target=run_vite, - kwargs={"shutdown_event": self.shutdown_event, "debug": self.debug}, + kwargs={ + "shutdown_event": self.shutdown_event, + "debug": self.debug, + "scan": self.scan, + "dev_port": self.dev_port, + }, name="Vite", ) diff --git a/py_neuromodulation/stream/settings.py b/py_neuromodulation/stream/settings.py index 764ee547..79f9985b 100644 --- a/py_neuromodulation/stream/settings.py +++ b/py_neuromodulation/stream/settings.py @@ -6,7 +6,6 @@ from pydantic.functional_validators import ModelWrapValidatorHandler from py_neuromodulation import logger, user_features -from types import SimpleNamespace from py_neuromodulation.utils.types import ( BoolSelector, diff --git a/py_neuromodulation/utils/pydantic_extensions.py b/py_neuromodulation/utils/pydantic_extensions.py index ee89ccea..461291fd 100644 --- a/py_neuromodulation/utils/pydantic_extensions.py +++ b/py_neuromodulation/utils/pydantic_extensions.py @@ -11,7 +11,7 @@ Sequence, ) from typing_extensions import Unpack, TypedDict -from pydantic import BaseModel, ConfigDict, model_validator, model_serializer +from pydantic import BaseModel, model_validator, model_serializer from pydantic_core import ( ErrorDetails, @@ -414,7 +414,6 @@ def rewrite_error_locations(self, handler): loc = loc[:root_idx] + loc[root_idx + 1 :] err["loc"] = tuple(loc) errors.append(err) - print(errors) raise ValidationError.from_exception_data( title="ValidationError", line_errors=errors ) diff --git a/py_neuromodulation/utils/types.py b/py_neuromodulation/utils/types.py index 13b2923e..59ed7201 100644 --- a/py_neuromodulation/utils/types.py +++ b/py_neuromodulation/utils/types.py @@ -1,6 +1,6 @@ from os import PathLike from math import isnan -from typing import Literal, TYPE_CHECKING, Any, TypeVar +from typing import Literal, TYPE_CHECKING, Any from pydantic import BaseModel, ConfigDict, model_validator from .pydantic_extensions import NMBaseModel, NMSequenceModel, NMField from abc import abstractmethod From 9a323a8777774b3ad38409afcfa34847caafb725 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Wed, 27 Nov 2024 22:50:19 +0100 Subject: [PATCH 17/25] Fix merge errors --- gui_dev/src/main.jsx | 16 +++++----- gui_dev/src/pages/Settings/Settings.jsx | 7 ++++- gui_dev/src/stores/settingsStore.js | 23 ++------------ py_neuromodulation/gui/backend/app_backend.py | 3 +- py_neuromodulation/stream/settings.py | 30 +++++++++++++++---- py_neuromodulation/stream/stream.py | 2 +- .../utils/pydantic_extensions.py | 11 +++---- pyproject.toml | 9 +----- 8 files changed, 52 insertions(+), 49 deletions(-) diff --git a/gui_dev/src/main.jsx b/gui_dev/src/main.jsx index fde760f2..bcd9d537 100644 --- a/gui_dev/src/main.jsx +++ b/gui_dev/src/main.jsx @@ -1,11 +1,11 @@ -if (JSON.parse(import.meta.env.VITE_REACT_SCAN) === true) { - import("react-scan").then(({ scan }) => { - scan({ - enabled: true, - log: true, // logs render info to console - }); - }); -} +// if (JSON.parse(import.meta.env.VITE_REACT_SCAN) === true) { +// import("react-scan").then(({ scan }) => { +// scan({ +// enabled: true, +// log: true, // logs render info to console +// }); +// }); +// } import { StrictMode } from "react"; import ReactDOM from "react-dom/client"; diff --git a/gui_dev/src/pages/Settings/Settings.jsx b/gui_dev/src/pages/Settings/Settings.jsx index 045603be..abf1ec1a 100644 --- a/gui_dev/src/pages/Settings/Settings.jsx +++ b/gui_dev/src/pages/Settings/Settings.jsx @@ -87,6 +87,8 @@ const NumberField = ({ value, onChange, label, error }) => { const componentRegistry = { boolean: BooleanField, string: StringField, + int: NumberField, + float: NumberField, number: NumberField, }; @@ -166,11 +168,13 @@ const SettingsSection = ({ // Case 2: Object with component -> Don't iterate, render directly if (isObject && Component) { + const value = "__value__" in settings ? settings.__value__ : settings; + return ( { const validationErrors = useSettingsStore((state) => state.validationErrors); + console.log("validationErrors:", validationErrors); const [anchorEl, setAnchorEl] = useState(null); const open = Boolean(anchorEl); diff --git a/gui_dev/src/stores/settingsStore.js b/gui_dev/src/stores/settingsStore.js index 68929f1e..2cf8b2b3 100644 --- a/gui_dev/src/stores/settingsStore.js +++ b/gui_dev/src/stores/settingsStore.js @@ -5,25 +5,6 @@ const INITIAL_DELAY = 3000; // wait for Flask const RETRY_DELAY = 1000; // ms const MAX_RETRIES = 100; -const uploadSettingsToServer = async (settings) => { - try { - const response = await fetch(getBackendURL("/api/settings"), { - method: "POST", - headers: { - "Content-Type": "application/json", - }, - body: JSON.stringify(settings), - }); - if (!response.ok) { - throw new Error("Failed to update settings"); - } - return { success: true }; - } catch (error) { - console.error("Error updating settings:", error); - return { success: false, error }; - } -}; - export const useSettingsStore = createStore("settings", (set, get) => ({ settings: null, lastValidSettings: null, @@ -99,7 +80,9 @@ export const useSettingsStore = createStore("settings", (set, get) => ({ try { const response = await fetch( - `/api/settings${validateOnly ? "?validate_only=true" : ""}`, + getBackendURL( + `/api/settings${validateOnly ? "?validate_only=true" : ""}` + ), { method: "POST", headers: { diff --git a/py_neuromodulation/gui/backend/app_backend.py b/py_neuromodulation/gui/backend/app_backend.py index 01858fe6..2dbbf490 100644 --- a/py_neuromodulation/gui/backend/app_backend.py +++ b/py_neuromodulation/gui/backend/app_backend.py @@ -1,3 +1,4 @@ +from email import errors import logging import asyncio import importlib.metadata @@ -94,9 +95,9 @@ async def update_settings(data: dict, validate_only: bool = Query(False)): # TODO: check if this works properly or needs model_validate_strings validated_settings = NMSettings.model_validate(data) except ValidationError as e: + self.logger.error(f"Error validating settings: {e}") if not validate_only: # If validation failed but we wanted to upload, return error - self.logger.error(f"Error validating settings: {e}") raise HTTPException( status_code=422, detail={ diff --git a/py_neuromodulation/stream/settings.py b/py_neuromodulation/stream/settings.py index a7e86542..89b68664 100644 --- a/py_neuromodulation/stream/settings.py +++ b/py_neuromodulation/stream/settings.py @@ -18,7 +18,10 @@ from py_neuromodulation.utils.pydantic_extensions import NMErrorList, NMField from py_neuromodulation.processing.filter_preprocessing import FilterSettings -from py_neuromodulation.processing.normalization import FeatureNormalizationSettings, NormalizationSettings +from py_neuromodulation.processing.normalization import ( + FeatureNormalizationSettings, + NormalizationSettings, +) from py_neuromodulation.processing.resample import ResamplerSettings from py_neuromodulation.processing.projection import ProjectionSettings @@ -94,7 +97,9 @@ class NMSettings(NMBaseModel): # Postprocessing settings postprocessing: PostprocessingSettings = PostprocessingSettings() - feature_normalization_settings: FeatureNormalizationSettings = FeatureNormalizationSettings() + feature_normalization_settings: FeatureNormalizationSettings = ( + FeatureNormalizationSettings() + ) project_cortex_settings: ProjectionSettings = ProjectionSettings(max_dist_mm=20) project_subcortex_settings: ProjectionSettings = ProjectionSettings(max_dist_mm=5) @@ -144,12 +149,27 @@ def validate_settings(self, handler: ModelWrapValidatorHandler) -> Any: # the settings class errors: NMErrorList = NMErrorList() + def remove_private_keys(data): + if isinstance(data, dict): + if "__value__" in data: + return data["__value__"] + else: + return { + key: remove_private_keys(value) + for key, value in data.items() + if not key.startswith("__") + } + elif isinstance(data, (list, tuple, set)): + return type(data)(remove_private_keys(item) for item in data) + else: + return data + + self = remove_private_keys(self) + try: - # validate the model - self = handler(self) + self = handler(self) # validate the model except ValidationError as e: self = NMSettings.unvalidated(**self) - NMSettings.model_fields_set errors.extend(NMErrorList(e.errors())) if len(self.features.get_enabled()) == 0: diff --git a/py_neuromodulation/stream/stream.py b/py_neuromodulation/stream/stream.py index df8338aa..97446085 100644 --- a/py_neuromodulation/stream/stream.py +++ b/py_neuromodulation/stream/stream.py @@ -10,7 +10,7 @@ from contextlib import suppress from py_neuromodulation.stream.data_processor import DataProcessor -from py_neuromodulation.utils.types import _PathLike, FeatureName +from py_neuromodulation.utils.types import _PathLike, FEATURE_NAME from py_neuromodulation.utils.file_writer import MsgPackFileWriter from py_neuromodulation.stream.settings import NMSettings from py_neuromodulation.analysis.decode import RealTimeDecoder diff --git a/py_neuromodulation/utils/pydantic_extensions.py b/py_neuromodulation/utils/pydantic_extensions.py index 461291fd..b82f1bcf 100644 --- a/py_neuromodulation/utils/pydantic_extensions.py +++ b/py_neuromodulation/utils/pydantic_extensions.py @@ -67,7 +67,10 @@ class NMErrorList: def __init__( self, errors: Sequence[InitErrorDetails | ErrorDetails] | None = None ) -> None: - self.__errors: list[InitErrorDetails | ErrorDetails] = [e for e in errors or []] + if errors is None: + self.__errors: list[InitErrorDetails | ErrorDetails] = [] + else: + self.__errors: list[InitErrorDetails | ErrorDetails] = [e for e in errors] def add_error( self, @@ -160,8 +163,6 @@ def NMField( class NMBaseModel(BaseModel): - # model_config = ConfigDict(validate_assignment=False, extra="allow") - def __init__(self, *args, **kwargs) -> None: """Pydantic does not support positional arguments by default. This is a workaround to support positional arguments for models like FrequencyRange. @@ -242,7 +243,7 @@ def serialize_with_metadata(self): if isinstance(field_info, NMFieldInfo): # Convert scalar value to dict with metadata field_dict = { - "value": value, + "__value__": value, # __field_type__ will be overwritte if set in custom_metadata "__field_type__": type(value).__name__, **{ @@ -342,7 +343,7 @@ def model_dump_json(self, **kwargs): return json.dumps(self.root, **kwargs) def serialize_with_metadata(self) -> dict[str, Any]: - result = {"__field_type__": self.__class__.__name__, "value": self.root} + result = {"__field_type__": self.__class__.__name__, "__value__": self.root} # Add any field metadata from the root field field_info = self.model_fields.get("root") diff --git a/pyproject.toml b/pyproject.toml index 29c85832..7ad64fae 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,14 +70,7 @@ dependencies = [ [project.optional-dependencies] test = ["pytest>=8.0.2", "pytest-xdist"] -dev = [ - "ruff", - "pytest>=8.0.2", - "pytest-cov", - "pytest-sugar", - "notebook", - "uvicorn[standard]", -] +dev = ["ruff", "pytest>=8.0.2", "pytest-cov", "pytest-sugar", "notebook"] docs = [ "py-neuromodulation[dev]", "sphinx", From f5f810dcbfdef67fd40cf1c0376ff82335eb3c97 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Thu, 28 Nov 2024 10:38:52 +0100 Subject: [PATCH 18/25] Fix StatusBar bug --- gui_dev/src/components/StatusBar/StatusBar.jsx | 4 +--- gui_dev/src/main.jsx | 13 +++++-------- 2 files changed, 6 insertions(+), 11 deletions(-) diff --git a/gui_dev/src/components/StatusBar/StatusBar.jsx b/gui_dev/src/components/StatusBar/StatusBar.jsx index f011e2b9..825b73c6 100644 --- a/gui_dev/src/components/StatusBar/StatusBar.jsx +++ b/gui_dev/src/components/StatusBar/StatusBar.jsx @@ -7,9 +7,7 @@ import { Stack } from "@mui/material"; export const StatusBar = () => { const isWebView = useWebviewStore((state) => state.isWebView); - const createStatusBarContent = useUiStore((state) => state.statusBarContent); - - const StatusBarContent = createStatusBarContent(); + const StatusBarContent = useUiStore((state) => state.statusBarContent); return ( { -// scan({ -// enabled: true, -// log: true, // logs render info to console -// }); -// }); -// } +// import { scan } from "react-scan"; +// scan({ +// enabled: true, +// log: true, // logs render info to console +// }); import { StrictMode } from "react"; import ReactDOM from "react-dom/client"; From f571c50c7e71d58575c2b3b7a4224ccf6f019d82 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Thu, 28 Nov 2024 10:39:37 +0100 Subject: [PATCH 19/25] Allow passing app server and Vite server ports as params for nm.App --- gui_dev/src/utils/getBackendURL.js | 4 +- py_neuromodulation/gui/backend/app_backend.py | 9 ++-- py_neuromodulation/gui/backend/app_manager.py | 42 +++++++++++++------ 3 files changed, 38 insertions(+), 17 deletions(-) diff --git a/gui_dev/src/utils/getBackendURL.js b/gui_dev/src/utils/getBackendURL.js index b35c21de..efaaa485 100644 --- a/gui_dev/src/utils/getBackendURL.js +++ b/gui_dev/src/utils/getBackendURL.js @@ -1,3 +1,3 @@ export const getBackendURL = (route) => { - return "http://localhost:50001" + route; -} + return "http://localhost:" + import.meta.env.VITE_BACKEND_PORT + route; +}; diff --git a/py_neuromodulation/gui/backend/app_backend.py b/py_neuromodulation/gui/backend/app_backend.py index 2dbbf490..efdaa226 100644 --- a/py_neuromodulation/gui/backend/app_backend.py +++ b/py_neuromodulation/gui/backend/app_backend.py @@ -1,6 +1,4 @@ -from email import errors import logging -import asyncio import importlib.metadata from datetime import datetime from pathlib import Path @@ -34,6 +32,7 @@ def __init__( pynm_state: app_pynm.PyNMState, debug=False, dev=True, + dev_port: int | None = None, fastapi_kwargs: dict = {}, ) -> None: super().__init__(debug=debug, **fastapi_kwargs) @@ -45,10 +44,14 @@ def __init__( self.logger = logging.getLogger("uvicorn.error") self.logger.warning(PYNM_DIR) + cors_origins = ( + ["http://localhost:" + str(dev_port)] if dev_port is not None else [] + ) + # Configure CORS self.add_middleware( CORSMiddleware, - allow_origins=["http://localhost:54321"], + allow_origins=cors_origins, allow_credentials=True, allow_methods=["*"], allow_headers=["*"], diff --git a/py_neuromodulation/gui/backend/app_manager.py b/py_neuromodulation/gui/backend/app_manager.py index 3fb7764a..ec1587da 100644 --- a/py_neuromodulation/gui/backend/app_manager.py +++ b/py_neuromodulation/gui/backend/app_manager.py @@ -12,7 +12,6 @@ if TYPE_CHECKING: from multiprocessing.synchronize import Event - from .app_backend import PyNMBackend # Shared memory configuration @@ -22,21 +21,32 @@ DEV_SERVER_PORT = 54321 -def create_backend() -> "PyNMBackend": +def create_backend(): + """Factory function passed to Uvicorn to create the web application instance. + + :return: The web application instance. + :rtype: PyNMBackend + """ from .app_pynm import PyNMState from .app_backend import PyNMBackend debug = os.environ.get("PYNM_DEBUG", "False").lower() == "true" dev = os.environ.get("PYNM_DEV", "True").lower() == "true" + dev_port = os.environ.get("PYNM_DEV_PORT", str(DEV_SERVER_PORT)) - return PyNMBackend(pynm_state=PyNMState(), debug=debug, dev=dev) + return PyNMBackend( + pynm_state=PyNMState(), + debug=debug, + dev=dev, + dev_port=int(dev_port), + ) def run_vite( shutdown_event: "Event", debug: bool = False, - scan: bool = False, dev_port: int = DEV_SERVER_PORT, + backend_port: int = SERVER_PORT, ) -> None: """Run Vite in a separate shell""" import subprocess @@ -49,7 +59,7 @@ def run_vite( logging.DEBUG if debug else logging.INFO, ) - os.environ["VITE_REACT_SCAN"] = "true" if scan else "false" + os.environ["VITE_BACKEND_PORT"] = str(backend_port) def output_reader(shutdown_event: "Event", process: subprocess.Popen): logger.debug("Initialized output stream") @@ -116,7 +126,9 @@ def read_stream(stream, stream_name): logger.info("Development server stopped") -def run_uvicorn(debug: bool = False, reload=False) -> None: +def run_uvicorn( + debug: bool = False, reload=False, server_port: int = SERVER_PORT +) -> None: from uvicorn.server import Server from uvicorn.config import LOGGING_CONFIG, Config @@ -141,7 +153,7 @@ def run_uvicorn(debug: bool = False, reload=False) -> None: host="localhost", reload=reload, factory=True, - port=50001, + port=server_port, log_level="debug" if debug else "info", log_config=log_config, ) @@ -170,17 +182,23 @@ def restart(self) -> None: def run_backend( - shutdown_event: "Event", debug: bool = False, reload: bool = True, dev: bool = True + shutdown_event: "Event", + dev: bool = True, + debug: bool = False, + reload: bool = True, + server_port: int = SERVER_PORT, + dev_port: int = DEV_SERVER_PORT, ) -> None: signal.signal(signal.SIGINT, signal.SIG_IGN) # Pass create_backend parameters through environment variables os.environ["PYNM_DEBUG"] = str(debug) os.environ["PYNM_DEV"] = str(dev) + os.environ["PYNM_DEV_PORT"] = str(dev_port) server_process = mp.Process( target=run_uvicorn, - kwargs={"debug": debug, "reload": reload}, + kwargs={"debug": debug, "reload": reload, "server_port": server_port}, name="Server", ) server_process.start() @@ -196,7 +214,6 @@ def __init__( debug: bool = False, dev: bool = True, run_in_webview=False, - scan=False, server_port=SERVER_PORT, dev_port=DEV_SERVER_PORT, ) -> None: @@ -213,7 +230,6 @@ def __init__( self.debug = debug self.dev = dev self.run_in_webview = run_in_webview - self.scan = scan self.server_port = server_port self.dev_port = dev_port @@ -293,8 +309,8 @@ def launch(self) -> None: kwargs={ "shutdown_event": self.shutdown_event, "debug": self.debug, - "scan": self.scan, "dev_port": self.dev_port, + "backend_port": self.server_port, }, name="Vite", ) @@ -307,6 +323,8 @@ def launch(self) -> None: "debug": self.debug, "reload": self.dev, "dev": self.dev, + "server_port": self.server_port, + "dev_port": self.dev_port, }, name="Backend", ) From 9cf3ff08e19119ced33f28b3c235ba54c05cfc3e Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Thu, 28 Nov 2024 10:40:13 +0100 Subject: [PATCH 20/25] remove react-scan from dev deps --- gui_dev/package.json | 1 - 1 file changed, 1 deletion(-) diff --git a/gui_dev/package.json b/gui_dev/package.json index dafcefc7..5fa2d606 100644 --- a/gui_dev/package.json +++ b/gui_dev/package.json @@ -41,7 +41,6 @@ "eslint-plugin-react-hooks": "^5.0.0", "eslint-plugin-react-refresh": "^0.4.14", "prettier": "^3.3.3", - "react-scan": "^0.0.31", "vite": "^5.4.11" } } From 511bdbc990837d16bc06ea5004550baa0f411035 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Thu, 28 Nov 2024 11:30:37 +0100 Subject: [PATCH 21/25] Refactor useStatusBar hook --- gui_dev/src/components/StatusBar/StatusBar.jsx | 4 +++- gui_dev/src/pages/Settings/Settings.jsx | 6 +++++- gui_dev/src/stores/uiStore.js | 13 +++++++------ 3 files changed, 15 insertions(+), 8 deletions(-) diff --git a/gui_dev/src/components/StatusBar/StatusBar.jsx b/gui_dev/src/components/StatusBar/StatusBar.jsx index 825b73c6..81f1b32b 100644 --- a/gui_dev/src/components/StatusBar/StatusBar.jsx +++ b/gui_dev/src/components/StatusBar/StatusBar.jsx @@ -7,7 +7,9 @@ import { Stack } from "@mui/material"; export const StatusBar = () => { const isWebView = useWebviewStore((state) => state.isWebView); - const StatusBarContent = useUiStore((state) => state.statusBarContent); + const getStatusBarContent = useUiStore((state) => state.getStatusBarContent); + + const StatusBarContent = getStatusBarContent(); return ( { diff --git a/gui_dev/src/stores/uiStore.js b/gui_dev/src/stores/uiStore.js index 25b44382..0462871f 100644 --- a/gui_dev/src/stores/uiStore.js +++ b/gui_dev/src/stores/uiStore.js @@ -1,7 +1,7 @@ -import { createPersistStore } from "./createStore"; +import { createStore } from "./createStore"; import { useEffect } from "react"; -export const useUiStore = createPersistStore("ui", (set, get) => ({ +export const useUiStore = createStore("ui", (set, get) => ({ activeDrawer: null, toggleDrawer: (drawerName) => set((state) => { @@ -31,13 +31,14 @@ export const useUiStore = createPersistStore("ui", (set, get) => ({ }), // Hook to inject UI elements into the status bar - statusBarContent: () => {}, - setStatusBarContent: (content) => set({ statusBarContent: content }), - clearStatusBarContent: () => set({ statusBarContent: null }), + getStatusBarContent: () => null, + setStatusBarContent: (contentGetter) => + set({ getStatusBarContent: contentGetter }), + clearStatusBarContent: () => set({ getStatusBarContent: () => null }), })); // Use this hook from Page components to inject page-specific UI elements into the status bar -export const useStatusBarContent = (content) => { +export const useStatusBar = (content) => { const createStatusBarContent = () => content; const setStatusBarContent = useUiStore((state) => state.setStatusBarContent); From 59b372b5298994374a95acd6354c1a67e121981e Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Thu, 28 Nov 2024 11:46:35 +0100 Subject: [PATCH 22/25] f --- gui_dev/src/pages/Settings/Settings.jsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gui_dev/src/pages/Settings/Settings.jsx b/gui_dev/src/pages/Settings/Settings.jsx index 373e37de..6d9921e6 100644 --- a/gui_dev/src/pages/Settings/Settings.jsx +++ b/gui_dev/src/pages/Settings/Settings.jsx @@ -15,7 +15,7 @@ import { FrequencyRangeList, FrequencyRange, } from "./components/FrequencyRange"; -import { useSettingsStore, useStatusBarContent } from "@/stores"; +import { useSettingsStore, useStatusBar } from "@/stores"; import { filterObjectByKeys } from "@/utils/functions"; const formatKey = (key) => { @@ -275,7 +275,7 @@ export const Settings = () => { const uploadSettings = useSettingsStore((state) => state.uploadSettings); const resetSettings = useSettingsStore((state) => state.resetSettings); const validationErrors = useSettingsStore((state) => state.validationErrors); - useStatusBarContent(StatusBarSettingsInfo); + useStatusBar(StatusBarSettingsInfo); // This is needed so that the frequency ranges stay in order between updates const frequencyRangeOrder = useSettingsStore( From 35f3a89bec18841f5df1cca212ed1bdda637a875 Mon Sep 17 00:00:00 2001 From: "Toni M. Brotons" <10654467+toni-neurosc@users.noreply.github.com> Date: Thu, 28 Nov 2024 14:21:12 +0100 Subject: [PATCH 23/25] More improvements to settings --- gui_dev/src/pages/Settings/Settings.jsx | 141 +++++++------- .../Settings/components/FrequencyRange.jsx | 70 ++++--- py_neuromodulation/gui/backend/app_backend.py | 25 +-- py_neuromodulation/stream/settings.py | 35 ++-- .../utils/pydantic_extensions.py | 148 +++----------- py_neuromodulation/utils/types.py | 180 ++---------------- 6 files changed, 183 insertions(+), 416 deletions(-) diff --git a/gui_dev/src/pages/Settings/Settings.jsx b/gui_dev/src/pages/Settings/Settings.jsx index 6d9921e6..69458cbc 100644 --- a/gui_dev/src/pages/Settings/Settings.jsx +++ b/gui_dev/src/pages/Settings/Settings.jsx @@ -2,6 +2,7 @@ import { useEffect, useState } from "react"; import { Box, Button, + InputAdornment, Popover, Stack, Switch, @@ -26,10 +27,12 @@ const formatKey = (key) => { }; // Wrapper components for each type -const BooleanField = ({ value, onChange, error }) => ( - onChange(e.target.checked)} /> +const BooleanField = ({ label, value, onChange, error }) => ( + + {label} + onChange(e.target.checked)} /> + ); - const errorStyle = { "& .MuiOutlinedInput-root": { "& fieldset": { borderColor: "error.main" }, @@ -42,19 +45,22 @@ const errorStyle = { }, }; -const StringField = ({ value, onChange, label, error }) => { +const StringField = ({ label, value, onChange, error }) => { const errorSx = error ? errorStyle : {}; return ( - onChange(e.target.value)} - label={label} - sx={{ ...errorSx }} - /> + + {label} + onChange(e.target.value)} + label={label} + sx={{ ...errorSx }} + /> + ); }; -const NumberField = ({ value, onChange, label, error }) => { +const NumberField = ({ label, value, onChange, error, unit }) => { const errorSx = error ? errorStyle : {}; const handleChange = (event) => { @@ -66,26 +72,31 @@ const NumberField = ({ value, onChange, label, error }) => { }; return ( - - // Hz - // - // ), - // }} - inputProps={{ - pattern: "[0-9]*", - }} - /> + + {label} + + {unit}, + }} + inputProps={{ + pattern: "[0-9]*", + }} + /> + ); }; +const FrequencyRangeField = ({ label, value, onChange, error }) => { + console.log(label, value); + return ; +}; + // Map component types to their respective wrappers const componentRegistry = { boolean: BooleanField, @@ -93,21 +104,27 @@ const componentRegistry = { int: NumberField, float: NumberField, number: NumberField, - // FrequencyRange: FrequencyRange, + FrequencyRange: FrequencyRangeField, }; -const SettingsField = ({ path, Component, label, value, onChange, error }) => { +const SettingsField = ({ + path, + Component, + label, + value, + onChange, + error, + unit, +}) => { return ( - - {label} - onChange(path, newValue)} - label={label} - error={error} - /> - + onChange(path, newValue)} + label={label} + error={error} + unit={unit} + /> ); }; @@ -131,48 +148,22 @@ const SettingsSection = ({ errors, }) => { const boxTitle = title ? title : formatKey(path[path.length - 1]); - /* - 3 possible cases: - 1. Primitive type || 2. Object with component -> Don't iterate, render directly - 3. Object without component or 4. Array -> Iterate and render recursively - */ - const type = typeof settings; const isObject = type === "object" && !Array.isArray(settings); const isArray = Array.isArray(settings); // __field_type__ should be always present if (isObject && !settings.__field_type__) { - console.log(settings); throw new Error("Invalid settings object"); } const fieldType = isObject ? settings.__field_type__ : type; const Component = componentRegistry[fieldType]; - // Case 1: Primitive type -> Don't iterate, render directly - if (!isObject && !isArray) { - if (!Component) { - console.error(`Invalid component type: ${type}`); - return null; - } - - const error = getFieldError(path, errors); - - return ( - - ); - } - - // Case 2: Object with component -> Don't iterate, render directly - if (isObject && Component) { - const value = "__value__" in settings ? settings.__value__ : settings; + // Case 1: Object or primitive with component -> Don't iterate, render directly + if (Component) { + const value = + isObject && "__value__" in settings ? settings.__value__ : settings; + const unit = isObject && "__unit__" in settings ? settings.__unit__ : null; return ( ); } - // Case 3: Object without component or 4. Array -> Iterate and render recursively - if ((isObject && !Component) || isArray) { + // Case 2: Object without component or Array -> Iterate and render recursively + else { return ( {/* Handle recursing through both objects and arrays */} @@ -210,15 +202,10 @@ const SettingsSection = ({ ); } - - // Default case: return null and log an error - console.error(`Invalid settings object, returning null`); - return null; }; const StatusBarSettingsInfo = () => { const validationErrors = useSettingsStore((state) => state.validationErrors); - console.log("validationErrors:", validationErrors); const [anchorEl, setAnchorEl] = useState(null); const open = Boolean(anchorEl); diff --git a/gui_dev/src/pages/Settings/components/FrequencyRange.jsx b/gui_dev/src/pages/Settings/components/FrequencyRange.jsx index 16333166..7fb50a23 100644 --- a/gui_dev/src/pages/Settings/components/FrequencyRange.jsx +++ b/gui_dev/src/pages/Settings/components/FrequencyRange.jsx @@ -1,5 +1,11 @@ import { useState } from "react"; -import { TextField, Button, IconButton, Stack } from "@mui/material"; +import { + TextField, + Button, + IconButton, + Stack, + Typography, +} from "@mui/material"; import { Add, Close } from "@mui/icons-material"; import { debounce } from "@/utils"; @@ -25,9 +31,10 @@ export const FrequencyRange = ({ range, onChangeName, onChangeRange, - onRemove, error, + nameEditable = false, }) => { + console.log(range); const [localName, setLocalName] = useState(name); const debouncedChangeName = debounce((newName) => { @@ -35,16 +42,19 @@ export const FrequencyRange = ({ }, 1000); const handleNameChange = (e) => { + if (!nameEditable) return; const newName = e.target.value; setLocalName(newName); debouncedChangeName(newName); }; const handleNameBlur = () => { + if (!nameEditable) return; onChangeName(localName, name); }; const handleKeyPress = (e) => { + if (!nameEditable) return; if (e.key === "Enter") { console.log(e.target.value, name); onChangeName(localName, name); @@ -58,14 +68,18 @@ export const FrequencyRange = ({ return ( - + {nameEditable ? ( + + ) : ( + {name} + )} - onRemove(name)} - color="primary" - disableRipple - sx={{ m: 0, p: 0 }} - > - - ); }; @@ -159,15 +165,25 @@ export const FrequencyRangeList = ({ return ( {rangeOrder.map((name, index) => ( - + + + handleRemove(name)} + color="primary" + disableRipple + sx={{ m: 0, p: 0 }} + > + + + ))}