diff --git a/package-lock.json b/package-lock.json index ffd157f0d..dc43b04b0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -22,7 +22,7 @@ "@patternfly/react-table": "^5.3.3", "@react-hook/resize-observer": "^2.0.1", "@tanstack/react-query": "^5.49.2", - "antd": "^5.19.0", + "antd": "^5.20.6", "axios": "^1.6.5", "chris-utility": "^1.1.6", "d3-hierarchy": "^1.1.9", @@ -30,6 +30,7 @@ "d3-shape": "^2.1.0", "d3-zoom": "^1.8.3", "date-fns": "^3.6.0", + "dcmjs": "^0.34.5", "dicom-parser": "^1.8.21", "email-validator": "^2.0.4", "fp-ts": "^2.16.2", @@ -101,8 +102,6 @@ }, "node_modules/@ampproject/remapping": { "version": "2.3.0", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", - "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==", "license": "Apache-2.0", "dependencies": { "@jridgewell/gen-mapping": "^0.3.5", @@ -114,17 +113,13 @@ }, "node_modules/@ant-design/colors": { "version": 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"engines": { "node": ">= 6" @@ -11216,8 +9542,6 @@ }, "node_modules/yargs": { "version": "15.4.1", - "resolved": "https://registry.npmjs.org/yargs/-/yargs-15.4.1.tgz", - "integrity": "sha512-aePbxDmcYW++PaqBsJ+HYUFwCdv4LVvdnhBy78E57PIor8/OVvhMrADFFEDh8DHDFRv/O9i3lPhsENjO7QX0+A==", "dev": true, "license": "MIT", "dependencies": { @@ -11239,8 +9563,6 @@ }, "node_modules/yargs-parser": { "version": "18.1.3", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-18.1.3.tgz", - "integrity": "sha512-o50j0JeToy/4K6OZcaQmW6lyXXKhq7csREXcDwk2omFPJEwUNOVtJKvmDr9EI1fAJZUyZcRF7kxGBWmRXudrCQ==", "dev": true, "license": "ISC", "dependencies": { diff --git a/package.json b/package.json index 689df5b47..59a155371 100644 --- a/package.json +++ b/package.json @@ -8,6 +8,7 @@ "dev": "npm run dev:local", "dev:local": "npm run test:prepare && vite", "dev:public": "vite -c testing/publicCUBE/vite.config.ts", + "dev:metal": "vite", "build": "vite build", "test": "vitest", "__test:prepare:comment": "# test:prepare runs CUBE locally and loads sample DICOM data into the PACS.", @@ -51,8 +52,9 @@ "@patternfly/react-table": "^5.3.3", "@react-hook/resize-observer": "^2.0.1", "@tanstack/react-query": "^5.49.2", - "antd": "^5.19.0", "axios": "^1.6.5", + "antd": "^5.20.6", + "dcmjs": "^0.34.5", "chris-utility": "^1.1.6", "d3-hierarchy": "^1.1.9", "d3-selection": "^1.4.2", diff --git a/src/components/CreateFeed/CreateFeed.tsx b/src/components/CreateFeed/CreateFeed.tsx index f67f6bb97..99e7ce2e7 100644 --- a/src/components/CreateFeed/CreateFeed.tsx +++ b/src/components/CreateFeed/CreateFeed.tsx @@ -1,4 +1,4 @@ -import { Feed } from "@fnndsc/chrisapi"; +import type { Feed } from "@fnndsc/chrisapi"; import { Button, Modal, @@ -71,14 +71,13 @@ export default function CreateFeed() { router.actions.clearFeedData(); }; - const enableSave = + const enableSave = !!( data.chrisFiles.length > 0 || data.localFiles.length > 0 || Object.keys(requiredInput).length > 0 || Object.keys(dropdownInput).length > 0 || pluginMeta !== undefined - ? true - : false; + ); const handleSave = async () => { setFeedProcessing(true); diff --git a/src/components/CreateFeed/createFeedHelper.ts b/src/components/CreateFeed/createFeedHelper.ts index 24452e198..28dc773d9 100644 --- a/src/components/CreateFeed/createFeedHelper.ts +++ b/src/components/CreateFeed/createFeedHelper.ts @@ -1,4 +1,4 @@ -import { +import type { Feed, Plugin, PluginInstance, @@ -10,10 +10,10 @@ import { limitConcurrency, uploadWrapper, } from "../../api/common"; -import { InputType } from "../AddNode/types"; +import type { InputType } from "../AddNode/types"; import { unpackParametersIntoObject } from "../AddNode/utils"; -import { PipelineState } from "../PipelinesCopy/context"; -import { CreateFeedData } from "./types/feed"; +import type { PipelineState } from "../PipelinesCopy/context"; +import type { CreateFeedData } from "./types/feed"; export const createFeed = async ( data: CreateFeedData, diff --git a/src/components/Pacs/components/SeriesCard.tsx b/src/components/Pacs/components/SeriesCard.tsx index de288af65..b74e2b020 100644 --- a/src/components/Pacs/components/SeriesCard.tsx +++ b/src/components/Pacs/components/SeriesCard.tsx @@ -1,3 +1,4 @@ +import { MinusCircleOutlined } from "@ant-design/icons"; import type { PACSFile } from "@fnndsc/chrisapi"; import { Badge, @@ -18,25 +19,53 @@ import { pluralize, } from "@patternfly/react-core"; import { useMutation, useQuery } from "@tanstack/react-query"; -import { Alert } from "antd"; +import { + Alert, + Modal as AntModal, + Dropdown, + Form, + type FormListFieldData, + Input, + Select, + Button as AntButton, + Space, + message, +} from "antd"; import axios from "axios"; +import PQueue from "p-queue"; import { useContext, useEffect, useState } from "react"; import { useNavigate } from "react-router"; import ChrisAPIClient from "../../../api/chrisapiclient"; import { MainRouterContext } from "../../../routes"; import { DotsIndicator } from "../../Common"; +import { ThemeContext } from "../../DarkTheme/useTheme"; import { CodeBranchIcon, DownloadIcon, LibraryIcon, PreviewIcon, + SettingsIcon, } from "../../Icons"; import FileDetailView from "../../Preview/FileDetailView"; import { PacsQueryContext, Types } from "../context"; import PFDCMClient, { type DataFetchQuery } from "../pfdcmClient"; import useSettings from "../useSettings"; import { CardHeaderComponent } from "./SettingsComponents"; -import PQueue from "p-queue"; +import type { AnonymizeTags } from "./usePipelinesMutation"; +import { usePipelinesMutation } from "./usePipelinesMutation"; +import { getBackgroundRowColor, getSeriesPath } from "./utils"; + +interface TagItem { + tag: string; + value: string; +} + +const tagOptions = [ + { label: "PatientName", value: "PatientName" }, + { label: "PatientID", value: "PatientID" }, + { label: "AccessionNumber", value: "AccessionNumber" }, + { label: "PatientBirthDate", value: "PatientBirthDate" }, +]; async function getPacsFile(file: PACSFile["data"]) { const { id } = file; @@ -51,7 +80,7 @@ async function getPacsFile(file: PACSFile["data"]) { } } -async function getTestData( +async function fetchPACSFilesData( pacsIdentifier: string, pullQuery: DataFetchQuery, protocolName?: string, @@ -117,6 +146,8 @@ const queue = new PQueue({ concurrency: 10 }); // Set concurrency limit here const SeriesCardCopy = ({ series }: { series: any }) => { const navigate = useNavigate(); const { state, dispatch } = useContext(PacsQueryContext); + const selectedSeries = state.selectedSeries; // Accessed only once + // Load user Preference Data const { data: userPreferenceData, @@ -126,6 +157,10 @@ const SeriesCardCopy = ({ series }: { series: any }) => { const userPreferences = userPreferenceData?.series; const userPreferencesArray = userPreferences && Object.keys(userPreferences); + // Pipeline creation mutation + const { isDarkTheme } = useContext(ThemeContext); + const { mutate } = usePipelinesMutation(); + const createFeed = useContext(MainRouterContext).actions.createFeedWithData; const { selectedPacsService, pullStudy, preview } = state; const client = new PFDCMClient(); @@ -140,7 +175,7 @@ const SeriesCardCopy = ({ series }: { series: any }) => { const seriesInstanceUID = SeriesInstanceUID.value; const accessionNumber = AccessionNumber.value; - // disable the card completely in this case + // Disable the card completely in this case const isDisabled = seriesInstances === 0; // This flag controls the start/stop for polling cube for files and display progress indicators const [isFetching, setIsFetching] = useState(false); @@ -149,6 +184,13 @@ const SeriesCardCopy = ({ series }: { series: any }) => { const [filePreviewForViewer, setFilePreviewForViewer] = useState(null); const [pacsFileError, setPacsFileError] = useState(""); + const [isConfigureModalOpen, setIsConfigureModalOpen] = useState(false); + // Save form data for submission on "Anonymize and Push" + const [formData, setFormData] = useState(() => { + const savedFormData = localStorage.getItem("savedFormData"); + return savedFormData ? JSON.parse(savedFormData) : {}; + }); + const [form] = Form.useForm(); const pullQuery: DataFetchQuery = { StudyInstanceUID: studyInstanceUID, @@ -176,7 +218,6 @@ const SeriesCardCopy = ({ series }: { series: any }) => { } = handleRetrieveMutation; // Polling cube files after a successful retrieve request from pfdcm; - async function fetchCubeFiles() { try { if (isDisabled) { @@ -194,7 +235,7 @@ const SeriesCardCopy = ({ series }: { series: any }) => { const [response, seriesRelatedInstance, pushCountInstance] = await Promise.all([ queue.add(() => - getTestData( + fetchPACSFilesData( selectedPacsService, pullQuery, "", @@ -202,14 +243,14 @@ const SeriesCardCopy = ({ series }: { series: any }) => { ), ), queue.add(() => - getTestData( + fetchPACSFilesData( "org.fnndsc.oxidicom", pullQuery, "NumberOfSeriesRelatedInstances", ), ), queue.add(() => - getTestData( + fetchPACSFilesData( "org.fnndsc.oxidicom", pullQuery, "OxidicomAttemptedPushCount", @@ -290,10 +331,9 @@ const SeriesCardCopy = ({ series }: { series: any }) => { queryKey: [SeriesInstanceUID.value, StudyInstanceUID.value], queryFn: fetchCubeFiles, refetchInterval: () => { - // Only fetch after a successfull response from pfdcm + // Only fetch after a successful response from pfdcm // Decrease polling frequency to avoid overwhelming cube with network requests - if (isFetching) return 1500; - return false; + return 1500; }, refetchOnMount: true, }); @@ -319,7 +359,6 @@ const SeriesCardCopy = ({ series }: { series: any }) => { useEffect(() => { // This is the preview all mode clicked on the study card - async function fetchPacsFile() { try { const file = await getPacsFile(data?.fileToPreview); @@ -328,16 +367,34 @@ const SeriesCardCopy = ({ series }: { series: any }) => { setFilePreviewForViewer(file); } } catch (e) { - //handle error + // Handle error if (e instanceof Error) { setPacsFileError(e.message); } } } - preview && data?.fileToPreview && fetchPacsFile(); + if (preview && data?.fileToPreview) { + fetchPacsFile(); + } }, [preview]); + useEffect(() => { + if (isConfigureModalOpen) { + const savedFormData = localStorage.getItem("savedFormData"); + if (savedFormData) { + const parsedFormData = JSON.parse(savedFormData); + const tags = Object.entries(parsedFormData).map(([tag, value]) => ({ + tag, + value, + })); + form.setFieldsValue({ tags }); + } else { + form.setFieldsValue({ tags: [{}] }); + } + } + }, [isConfigureModalOpen, form]); + // Error and loading state indicators for retrieving from pfdcm and polling cube for files. const isResourceBeingFetched = filesLoading || retrieveLoading; const resourceErrorFound = filesError || retrieveFetchError; @@ -609,19 +666,270 @@ const SeriesCardCopy = ({ series }: { series: any }) => { ); - return ( - - {preview && data?.fileToPreview ? filePreviewLayout : rowLayout} - {data?.fileToPreview && largeFilePreview} + const items = [ + { + key: "anonymize and push", + label: "Anonymize and Push", + disabled: selectedSeries.length === 0, // Disabled when no series is selected + icon: , + }, + { + key: "configure and push", + label: "Configure anon and push", + disabled: selectedSeries.length === 0, // Disabled when no series is selected + icon: , + }, + ]; + + // Get the series path for the current card + //@ts-ignore + const fname = data?.fileToPreview?.fname; + const seriesPath = fname ? getSeriesPath(fname) : ""; + + // Check if the current series is selected + const isSelected = selectedSeries.includes(seriesPath); + const backgroundColor = getBackgroundRowColor(isSelected, isDarkTheme); + + const handleConfigureSubmit = () => { + form + .validateFields() + .then((values) => { + const newFormData: AnonymizeTags = {}; + values.tags.forEach((item: any) => { + //@ts-ignore + newFormData[item.tag] = item.value; + }); + // Update formData state + setFormData(newFormData); + // Save formData to localStorage + localStorage.setItem("savedFormData", JSON.stringify(newFormData)); + // Close the modal + setIsConfigureModalOpen(false); + if (Object.keys(newFormData).length > 0) { + // Run the pipeline with formData + mutate({ + type: "configure and push", + paths: selectedSeries, + accessionNumber, + formData: newFormData, + }); + } + }) + .catch(() => { + message.error( + "Form validation failed. Please check the highlighted fields.", + ); + }); + }; - {pacsFileError && } - + return ( + <> + { + if (info.key === "configure and push") { + setIsConfigureModalOpen(true); + } else if (info.key === "anonymize and push") { + mutate({ + type: "anonymize and push", + paths: selectedSeries, + accessionNumber, + // No formData for default run + }); + } + }, + }} + trigger={["contextMenu"]} + onOpenChange={(open) => { + if (open && selectedSeries.length === 0) { + message.warning( + "Please select a series before running a pipeline.", + ); + } + }} + > + { + e.preventDefault(); + e.stopPropagation(); + + if (seriesPath) { + if (!isSelected) { + dispatch({ + type: Types.SET_SELECTED_SERIES, + payload: { + path: seriesPath, + }, + }); + } else { + dispatch({ + type: Types.REMOVE_SELECTED_SERIES, + payload: { + path: seriesPath, + }, + }); + } + } + }} + style={{ + backgroundColor, + }} + > + {preview && data?.fileToPreview ? filePreviewLayout : rowLayout} + {data?.fileToPreview && largeFilePreview} + + {pacsFileError && } + + + {/* Configuration Modal */} + setIsConfigureModalOpen(false)} + destroyOnClose + width={600} + footer={[ + { + localStorage.removeItem("savedFormData"); + setFormData({}); + form.setFieldsValue({ tags: [{}] }); + }} + > + Clear Saved Values + , + setIsConfigureModalOpen(false)} + > + Cancel + , + + Ok + , + ]} + > +
+ + {(fields: FormListFieldData[], { add, remove }) => { + const selectedTags = (form.getFieldValue("tags") as TagItem[]) + ?.map((item) => item?.tag) + .filter(Boolean); + + const addFieldIfNeeded = () => { + const currentFields = + (form.getFieldValue("tags") as TagItem[]) || []; + if ( + currentFields.length < tagOptions.length && + currentFields.every((field) => field.tag && field.value) + ) { + add(); + } + }; + + return ( + <> + {fields.map((field, index) => { + const availableTags = tagOptions.filter( + (option) => + !selectedTags?.includes(option.value) || + option.value === + form.getFieldValue(["tags", index, "tag"]), + ); + + return ( + + + + { + e.preventDefault(); + addFieldIfNeeded(); + }} + /> + + {fields.length > 1 && ( + + { + remove(field.name); + }} + style={{ + fontSize: "16px", + cursor: "pointer", + verticalAlign: "center", + }} + /> + + )} + + + ); + })} + + ); + }} + +
+ + ); }; diff --git a/src/components/Pacs/components/usePipelinesMutation.tsx b/src/components/Pacs/components/usePipelinesMutation.tsx new file mode 100644 index 000000000..6d232ec47 --- /dev/null +++ b/src/components/Pacs/components/usePipelinesMutation.tsx @@ -0,0 +1,191 @@ +import { LoadingOutlined } from "@ant-design/icons"; +import type { Feed, Pipeline } from "@fnndsc/chrisapi"; +import { useMutation } from "@tanstack/react-query"; +import { notification } from "antd"; +import ChrisAPIClient from "../../../api/chrisapiclient"; +import { getPlugin } from "../../CreateFeed/createFeedHelper"; + +type MutationPayload = { + type: string; + paths: string[]; + accessionNumber: string; + formData?: AnonymizeTags; +}; + +export type AnonymizeTags = { [tagName: string]: string }; + +export const handlePipelineCreation = async (payload: MutationPayload) => { + const { type, paths, accessionNumber, formData } = payload; + if (type !== "anonymize and push" && type !== "configure and push") return; + + const client = ChrisAPIClient.getClient(); + const dircopy = await getPlugin("pl-dircopy"); + if (!dircopy) { + throw new Error("Failed to fetch the 'pl-dircopy' plugin."); + } + + try { + const pipelineList = await client.getPipelines({ + name: "DICOM anonymization simple v20230926", + }); + const pipelines = pipelineList.getItems() as Pipeline[]; + if (pipelines.length === 0) { + throw new Error( + "The pipeline 'DICOM anonymization, extract, image conversion v20231027' is not registered.", + ); + } + const selectedPipeline = pipelines[0]; + + // Get plugin pipings and find the target piping + const pluginPipings = await selectedPipeline.getPluginPipings({ + limit: 100, + }); + const piping = pluginPipings.data.find( + (p) => p.plugin_name === "pl-dicom_headeredit", + ); + if (!piping) { + throw new Error( + "The plugin 'pl-dicom_headeredit' is not found in the pipeline.", + ); + } + + // Get default parameters and find 'tagInfo' parameter + const defaultParametersList = await selectedPipeline.getDefaultParameters({ + limit: 10000, + }); + const allParams = defaultParametersList.data.filter( + (param) => param.plugin_piping_id === piping.id, + ); + const tagInfoParam = allParams.find( + (param) => param.param_name === "tagInfo", + ); + + // Compute workflow nodes info and update the target node + const nodes_info = client.computeWorkflowNodesInfo( + defaultParametersList.data, + ); + const targetNode = nodes_info.find((node) => node.piping_id === piping.id); + + if (targetNode) { + if (type === "configure and push" && formData && tagInfoParam) { + const updatedTagInfoParam = updateTagInfoParam(tagInfoParam, formData); + targetNode.plugin_parameter_defaults = [updatedTagInfoParam]; + } + // For "anonymize and push", keep default parameters + } + + const feeds: Feed[] = []; + + for (const path of paths) { + // Create a plugin instance for each path + const pluginInstance = await client.createPluginInstance( + dircopy.data.id, + { + //@ts-ignore + dir: path, + }, + ); + + if (!pluginInstance) { + throw new Error("Failed to create plugin instance."); + } + + // Prepare the workflow creation data + const workflowData: any = { + previous_plugin_inst_id: pluginInstance.data.id as number, + nodes_info: nodes_info ? JSON.stringify(nodes_info) : undefined, + }; + + // Create a workflow for each plugin instance + await client.createWorkflow(selectedPipeline.data.id, workflowData); + + // Get the feed associated with the plugin instance + const feed = await pluginInstance.getFeed(); + + // Extract the series name from the path (last segment) + const seriesName = path.split("/").pop() || "Unknown Series"; + + // Update the feed name with accession number and series name + await feed?.put({ + name: `Analysis for Acc#: ${accessionNumber} - Series: ${seriesName}`, + }); + + if (!feed) { + throw new Error("Failed to create a Feed"); + } + + feeds.push(feed); + } + + return feeds; + } catch (e) { + // biome-ignore lint/complexity/noUselessCatch: + throw e; + } +}; + +const notificationKey = "pipelineCreation"; + +export const usePipelinesMutation = () => { + const handleMutation = useMutation({ + mutationFn: handlePipelineCreation, + onMutate: () => { + notification.open({ + key: notificationKey, + message: "Processing", + description: "Your analyses are being processed.", + icon: , + duration: 0, // Keep the notification open + }); + }, + onSuccess: () => { + notification.success({ + key: notificationKey, + message: "Success", + description: "Analyses created successfully.", + }); + }, + onError: (error: any) => { + notification.error({ + key: notificationKey, + message: "Error", + description: + error.message || + "An error occurred while creating the analyses. Please try again.", + }); + }, + }); + + return { + mutate: handleMutation.mutate, + }; +}; + +function updateTagInfoParam(tagInfoParam: any, formData: AnonymizeTags): any { + const tagMap: { [key: string]: string } = {}; + + // Handle cases where tagInfoParam.value might be undefined or empty + const existingValue = tagInfoParam.value || ""; + + // Split the existing value into tag-value pairs and populate tagMap + existingValue.split(",").forEach((pair: string) => { + const [tagName, value] = pair.split("="); + if (tagName && value) { + tagMap[tagName.trim()] = value.trim(); + } + }); + + // Update tagMap with formData values + Object.entries(formData).forEach(([tagName, formValue]) => { + if (formValue) { + tagMap[tagName.trim()] = formValue.trim(); + } + }); + + // Reconstruct the updated 'value' string + const updatedValue = Object.entries(tagMap) + .map(([tagName, value]) => `${tagName}=${value}`) + .join(","); + + return { name: "tagInfo", default: updatedValue }; +} diff --git a/src/components/Pacs/components/utils.ts b/src/components/Pacs/components/utils.ts index 87c242bef..ca73cf192 100644 --- a/src/components/Pacs/components/utils.ts +++ b/src/components/Pacs/components/utils.ts @@ -1,4 +1,4 @@ -import { parse, format } from "date-fns"; +import { format, parse } from "date-fns"; export const formatStudyDate = (studyDateString: string) => { // Parse the input string to a Date object @@ -34,3 +34,21 @@ const getDayWithSuffix = (day: number) => { return `${day}th`; } }; + +export function getBackgroundRowColor( + isSelected: boolean, + isDarkTheme: boolean, +) { + const backgroundColor = isDarkTheme ? "#002952" : "#E7F1FA"; + + const backgroundRow = "inherit"; + const selectedBgRow = isSelected ? backgroundColor : backgroundRow; + + return selectedBgRow; +} + +export function getSeriesPath(path: string): string { + const pathSegments = path.split("/"); + const seriesPathSegments = pathSegments.slice(0, -1); // Remove last segments + return seriesPathSegments.join("/"); +} diff --git a/src/components/Pacs/context/index.tsx b/src/components/Pacs/context/index.tsx index 38ef5e963..bc58abeab 100644 --- a/src/components/Pacs/context/index.tsx +++ b/src/components/Pacs/context/index.tsx @@ -1,4 +1,5 @@ -import React, { createContext, useReducer, type Dispatch } from "react"; +import type React from "react"; +import { createContext, useReducer, type Dispatch, type Reducer } from "react"; type ActionMap = { [Key in keyof M]: M[Key] extends undefined @@ -23,6 +24,8 @@ export enum Types { SET_PULL_STUDY = "SET_PULL_STUDY", SET_STUDY_PULL_TRACKER = "SET_STUDY_PULL_TRACKER", RESET_SEARCH_RESULTS = "RESET_SEARCH_RESULTS", + SET_SELECTED_SERIES = "SET_SELECTED_SERIES", + REMOVE_SELECTED_SERIES = "REMOVE_SELECTED_SERIES", } interface PacsQueryState { @@ -41,9 +44,10 @@ interface PacsQueryState { [key: string]: boolean; }; }; + selectedSeries: any[]; } -const initialState = { +const initialState: PacsQueryState = { selectedPacsService: "", pacsServices: [], currentQueryType: "PatientID", @@ -53,6 +57,7 @@ const initialState = { preview: false, pullStudy: {}, studyPullTracker: {}, + selectedSeries: [], }; type PacsQueryPayload = { @@ -61,7 +66,7 @@ type PacsQueryPayload = { }; [Types.SET_LIST_PACS_SERVICES]: { - pacsServices: ReadonlyArray; + pacsServices: string[]; }; [Types.SET_CURRENT_QUERY_TYPE]: { @@ -101,6 +106,13 @@ type PacsQueryPayload = { currentProgress: boolean; }; + [Types.SET_SELECTED_SERIES]: { + path: string; + }; + [Types.REMOVE_SELECTED_SERIES]: { + path: string; + }; + [Types.RESET_SEARCH_RESULTS]: null; }; @@ -120,7 +132,7 @@ export const QueryStages: { export function getIndex(value: string) { for (const key in QueryStages) { if (QueryStages[key] === value) { - return parseInt(key); + return Number.parseInt(key); } } return -1; // Return -1 if the value is not found in the object. @@ -134,7 +146,10 @@ const PacsQueryContext = createContext<{ dispatch: () => null, }); -const pacsQueryReducer = (state: PacsQueryState, action: PacsQueryActions) => { +const pacsQueryReducer: Reducer = ( + state: PacsQueryState, + action: PacsQueryActions, +) => { switch (action.type) { case Types.SET_LIST_PACS_SERVICES: { return { @@ -164,6 +179,22 @@ const pacsQueryReducer = (state: PacsQueryState, action: PacsQueryActions) => { }; } + case Types.SET_SELECTED_SERIES: { + return { + ...state, + selectedSeries: [...state.selectedSeries, action.payload.path], + }; + } + + case Types.REMOVE_SELECTED_SERIES: { + return { + ...state, + selectedSeries: state.selectedSeries.filter( + (series) => series !== action.payload.path, + ), + }; + } + case Types.RESET_SEARCH_RESULTS: { return { ...state, diff --git a/src/components/Pacs/pacs-copy.css b/src/components/Pacs/pacs-copy.css index 5aa12075d..86456918f 100644 --- a/src/components/Pacs/pacs-copy.css +++ b/src/components/Pacs/pacs-copy.css @@ -4,7 +4,9 @@ margin-top: 1em; } - +.full-width-row > .ant-row { + min-width: 100%; +} .patient-studies, .patient-series { diff --git a/src/components/Preview/FileDetailView.tsx b/src/components/Preview/FileDetailView.tsx index 0b6757a7c..c13f86adb 100644 --- a/src/components/Preview/FileDetailView.tsx +++ b/src/components/Preview/FileDetailView.tsx @@ -10,10 +10,14 @@ import { import ResetIcon from "@patternfly/react-icons/dist/esm/icons/history-icon"; import { useQuery } from "@tanstack/react-query"; import { Alert } from "antd"; -import * as dicomParser from "dicom-parser"; -import React, { Fragment, ReactElement, useCallback } from "react"; +import * as dcmjs from "dcmjs"; +import React, { Fragment, type ReactElement, useCallback } from "react"; import { ErrorBoundary } from "react-error-boundary"; -import { IFileBlob, fileViewerMap, getFileExtension } from "../../api/model"; +import { + type IFileBlob, + fileViewerMap, + getFileExtension, +} from "../../api/model"; import { useTypedSelector } from "../../store/hooks"; import { SpinContainer } from "../Common"; import { @@ -26,7 +30,6 @@ import { ZoomIcon, } from "../Icons"; import { TagInfoModal } from "./HelperComponent"; -import { dumpDataSet } from "./displays/dicomUtils/dicomDict"; const ViewerDisplay = React.lazy(() => import("./displays/ViewerDisplay")); @@ -95,34 +98,29 @@ const FileDetailView = (props: AllProps) => { }; }); - const displayTagInfo = useCallback((result: any) => { - const reader = new FileReader(); - - reader.onloadend = async () => { - try { - if (reader.result) { - //@ts-ignore - const byteArray = new Uint8Array(reader.result); - //@ts-ignore - const testOutput: any[] = []; - const output: any[] = []; - const dataSet = dicomParser.parseDicom(byteArray); - dumpDataSet(dataSet, output, testOutput); - const merged = Object.assign({}, ...testOutput); - setTagInfo(merged); - } - } catch (error) { - setError("Failed to parse the file for dicom tags"); - return { - blob: undefined, - file: undefined, - fileType: "", - }; + const displayTagInfo = useCallback(async () => { + try { + const blob = await selectedFile?.getFileBlob(); + if (!blob) { + throw new Error("Failed to fetch the file"); } - }; - if (result) { - reader.readAsArrayBuffer(result); + const arrayBuffer = await blob.arrayBuffer(); + const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer); + const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset( + dicomData.dict, + ); + // Sort the dataset keys alphabetically + const sortedDataset = Object.keys(dataset) + .sort() + .reduce((sortedObj: any, key) => { + sortedObj[key] = dataset[key]; + return sortedObj; + }, {}); + + setTagInfo(sortedDataset); + } catch (error) { + throw new Error("Failed to parse the file for DICOM tags"); } }, []); @@ -177,7 +175,7 @@ const FileDetailView = (props: AllProps) => { const handleEvents = (action: string, previouslyActive: string) => { if (action === "TagInfo" && data) { - displayTagInfo(data.blob); + displayTagInfo(); } const currentAction = actionState[action]; setActionState({ diff --git a/src/components/Preview/displays/DcmDisplay.tsx b/src/components/Preview/displays/DcmDisplay.tsx index 5bd39cde4..5a230d5d3 100644 --- a/src/components/Preview/displays/DcmDisplay.tsx +++ b/src/components/Preview/displays/DcmDisplay.tsx @@ -1,27 +1,27 @@ -import { useEffect, useState, useRef } from "react"; +import type { RenderingEngine } from "@cornerstonejs/core"; +import { useQuery } from "@tanstack/react-query"; +import { useEffect, useRef, useState } from "react"; +import { v4 } from "uuid"; import { FileViewerModel, - IFileBlob, + type IFileBlob, getFileExtension, } from "../../../api/model"; +import { SpinContainer } from "../../Common"; +import useSize from "../../FeedTree/useSize"; +import type { ActionState } from "../FileDetailView"; import { - displayDicomImage, - loadDicomImage, - basicInit, - handleEvents, type IStackViewport, - setUpTooling, + basicInit, cleanupCornerstoneTooling, + displayDicomImage, + handleEvents, + loadDicomImage, registerToolingOnce, removeTools, + setUpTooling, } from "./dicomUtils/utils"; -import useSize from "../../FeedTree/useSize"; -import { type ActionState } from "../FileDetailView"; import { _loadImageIntoBuffer } from "./dicomUtils/webImageLoader"; -import { RenderingEngine } from "@cornerstonejs/core"; -import { v4 } from "uuid"; -import { useQuery } from "@tanstack/react-query"; -import { SpinContainer } from "../../Common"; export type DcmImageProps = { fileItem: IFileBlob; diff --git a/src/components/Preview/displays/dicomUtils/dicomDict.ts b/src/components/Preview/displays/dicomUtils/dicomDict.ts deleted file mode 100644 index fa222a666..000000000 --- a/src/components/Preview/displays/dicomUtils/dicomDict.ts +++ /dev/null @@ -1,479 +0,0 @@ -import { TAG_DICT, uids } from "./dataDictionary"; -import Rusha from "rusha"; -import dicomParser from "dicom-parser"; - -function imageFrameLink(frameIndex: any) { - let linkText = " Frame #${frameIndex}`; - return linkText; -} - -const rusha = new Rusha(); - -// helper function to see if a string only has ascii characters in it -function isASCII(str: any) { - //Ts-ignore - // biome-ignore lint/suspicious/noControlCharactersInRegex: - return /^[\x00-\x7F]*$/.test(str); -} - -function sha1(byteArray: any, position?: any, length?: any) { - const subArray = dicomParser.sharedCopy( - byteArray, - position || 0, - length || byteArray.length, - ); - return rusha.digest(subArray); -} - -function sha1Text(byteArray: any, position?: any, length?: any) { - const showSHA1 = false; - if (showSHA1 === false) { - return ""; - } - const text = `; SHA1 ${sha1(byteArray, position, length)}`; - return text; -} - -function escapeSpecialCharacters(str: any) { - return str - .replace(/&/g, "&") - .replace(//g, ">") - .replace(/"/g, """); -} - -function isStringVr(vr: string) { - if ( - vr === "AT" || - vr === "FL" || - vr === "FD" || - vr === "OB" || - vr === "OF" || - vr === "OW" || - vr === "SI" || - vr === "SQ" || - vr === "SS" || - vr === "UL" || - vr === "US" - ) { - return false; - } - return true; -} - -function mapUid(str: any) { - //@ts-ignore - const uid = uids[str]; - if (uid) { - return ` [ ${uid} ]`; - } - return ""; -} - -const showPrivateElements = true; -const showP10Header = true; -const showEmptyValues = true; -const showLength = false; -const showVR = false; -const showFragments = true; -const showFrames = true; -const maxLength = 128; - -function getTag(tag: any) { - const group = tag.substring(1, 5); - const element = tag.substring(5, 9); - const tagIndex = `(${group},${element})`.toUpperCase(); - - //@ts-ignore - const attr = TAG_DICT[tagIndex]; - return attr; -} - -export function dumpDataSet(dataSet: any, output: any, testOutput: any) { - try { - const keys = []; - for (const propertyName in dataSet.elements) { - keys.push(propertyName); - } - keys.sort(); - - // the dataSet.elements object contains properties for each element parsed. The name of the property - // is based on the elements tag and looks like 'xGGGGEEEE' where GGGG is the group number and EEEE is the - // element number both with lowercase hexadecimal letters. For example, the Series Description DICOM element 0008,103E would - // be named 'x0008103e'. Here we iterate over each property (element) so we can build a string describing its - // contents to add to the output array - for (let k = 0; k < keys.length; k++) { - const propertyName = keys[k]; - const element = dataSet.elements[propertyName]; - - //@ts-ignore - if (showP10Header === false && element.tag <= "x0002ffff") { - continue; - } - - if ( - //@ts-ignore - showPrivateElements === false && - dicomParser.isPrivateTag(element.tag) - ) { - continue; - } - //@ts-ignore - if (showEmptyValues === false && element.length <= 0) { - continue; - } - let text = ""; - let title = ""; - - let color = "black"; - - const tag = getTag(element.tag); - - // The output string begins with the element name (or tag if not in data dictionary), length and VR (if present). VR is undefined for - // implicit transfer syntaxes - if (tag === undefined) { - let lengthText = `length=${element.length}`; - if (element.hadUndefinedLength) { - lengthText += " (-1)"; - } - //@ts-ignore - if (showLength === true) { - text += `${lengthText}; `; - } - - title += lengthText; - - let vrText = ""; - if (element.vr) { - vrText += `VR=${element.vr}`; - } - - if (showVR) { - text += `${vrText}; `; - } - if (vrText) { - title += `; ${vrText}`; - } - - title += `dataOffset=${element.dataOffset}`; - // make text lighter since this is an unknown attribute - color = "#C8C8C8"; - } else { - let vrText = ""; - if (element.vr) { - vrText += `VR=${element.vr}`; - } - - if (showVR) { - text += `${vrText}; `; - } - if (vrText) { - title += `${vrText}`; - } - - title += `; dataOffset=${element.dataOffset}`; - } - - // Here we check for Sequence items and iterate over them if present. items will not be set in the - // element object for elements that don't have SQ VR type. Note that implicit little endian - // sequences will are currently not parsed. - if (element.items) { - output.push(`
  • ${text}
    • `); - output.push("
      "); - - // each item contains its own data set so we iterate over the items - // and recursively call this function - let itemNumber = 0; - element.items.forEach((item: any) => { - output.push(`
    • Item #${itemNumber++} ${item.tag}`); - let lengthText = ` length=${item.length}`; - if (item.hadUndefinedLength) { - lengthText += " (-1)"; - } - //@ts-ignore - if (showLength === true) { - text += `${lengthText}; `; - output.push(lengthText); - } - output.push("
      • "); - output.push("
        "); - dumpDataSet(item.dataSet, output, testOutput); - output.push("
      "); - }); - output.push("
    "); - } else if (element.fragments) { - text += `encapsulated pixel data with ${element.basicOffsetTable.length} offsets and ${element.fragments.length} fragments`; - text += sha1Text(dataSet.byteArray, element.dataOffset, element.length); - - output.push(`
  • ${text}
    • `); - - if (showFragments && element.encapsulatedPixelData) { - output.push("Fragments:
    "); - output.push("
      "); - let itemNumber = 0; - element.fragments.forEach((fragment: any) => { - let str = `
    • Fragment #${itemNumber++} dataOffset = ${ - fragment.position - }`; - str += `; offset = ${fragment.offset}`; - str += `; length = ${fragment.length}`; - str += sha1Text( - dataSet.byteArray, - fragment.position, - fragment.length, - ); - str += "
      • "; - - output.push(str); - }); - output.push("
    "); - } - if (showFrames && element.encapsulatedPixelData) { - output.push("Frames:
    "); - output.push("
      "); - let bot = element.basicOffsetTable; - // if empty bot and not RLE, calculate it - if (bot.length === 0) { - bot = dicomParser.createJPEGBasicOffsetTable(dataSet, element); - } - - for (let frameIndex = 0; frameIndex < bot.length; frameIndex++) { - let str = "
    • "; - str += imageFrameLink(frameIndex); - str += ` dataOffset = ${ - element.fragments[0].position + bot[frameIndex] - }`; - str += `; offset = ${bot[frameIndex]}`; - const imageFrame = dicomParser.readEncapsulatedImageFrame( - dataSet, - element, - frameIndex, - bot, - ); - str += `; length = ${imageFrame.length}`; - str += sha1Text(imageFrame); - str += "
      • "; - output.push(str); - } - output.push("
    "); - } - } else { - // use VR to display the right value - let vr; - if (element.vr !== undefined) { - vr = element.vr; - } else { - if (tag !== undefined) { - vr = tag.vr; - } - } - - // if the length of the element is less than 128 we try to show it. We put this check in - // to avoid displaying large strings which makes it harder to use. - if (element.length < maxLength) { - // Since the dataset might be encoded using implicit transfer syntax and we aren't using - // a data dictionary, we need some simple logic to figure out what data types these - // elements might be. Since the dataset might also be explicit we could be switch on the - // VR and do a better job on this, perhaps we can do that in another example - - // First we check to see if the element's length is appropriate for a UI or US VR. - // US is an important type because it is used for the - // image Rows and Columns so that is why those are assumed over other VR types. - if (element.vr === undefined && tag === undefined) { - if (element.length === 2) { - text += ` (${dataSet.uint16(propertyName)})`; - } else if (element.length === 4) { - text += ` (${dataSet.uint32(propertyName)})`; - } - - // Next we ask the dataset to give us the element's data in string form. Most elements are - // strings but some aren't so we do a quick check to make sure it actually has all ascii - // characters so we know it is reasonable to display it. - const str = dataSet.string(propertyName); - const stringIsAscii = isASCII(str); - - if (stringIsAscii) { - // the string will be undefined if the element is present but has no data - // (i.e. attribute is of type 2 or 3 ) so we only display the string if it has - // data. Note that the length of the element will be 0 to indicate "no data" - // so we don't put anything here for the value in that case. - if (str !== undefined) { - text += escapeSpecialCharacters(str) + mapUid(str); - } - } else { - if (element.length !== 2 && element.length !== 4) { - color = "#C8C8C8"; - // If it is some other length and we have no string - text += "binary data"; - } - } - } else { - if (isStringVr(vr)) { - // Next we ask the dataset to give us the element's data in string form. Most elements are - // strings but some aren't so we do a quick check to make sure it actually has all ascii - // characters so we know it is reasonable to display it. - const str = dataSet.string(propertyName); - const stringIsAscii = isASCII(str); - - if (stringIsAscii) { - // the string will be undefined if the element is present but has no data - // (i.e. attribute is of type 2 or 3 ) so we only display the string if it has - // data. Note that the length of the element will be 0 to indicate "no data" - // so we don't put anything here for the value in that case. - if (str !== undefined) { - text += escapeSpecialCharacters(str) + mapUid(str); - } - } else { - if (element.length !== 2 && element.length !== 4) { - color = "#C8C8C8"; - // If it is some other length and we have no string - text += "binary data"; - } - } - } else if (vr === "US") { - text += dataSet.uint16(propertyName); - for ( - let i = 1; - i < dataSet.elements[propertyName].length / 2; - i++ - ) { - text += `\\${dataSet.uint16(propertyName, i)}`; - } - } else if (vr === "SS") { - text += dataSet.int16(propertyName); - for ( - let i = 1; - i < dataSet.elements[propertyName].length / 2; - i++ - ) { - text += `\\${dataSet.int16(propertyName, i)}`; - } - } else if (vr === "UL") { - text += dataSet.uint32(propertyName); - for ( - let i = 1; - i < dataSet.elements[propertyName].length / 4; - i++ - ) { - text += `\\${dataSet.uint32(propertyName, i)}`; - } - } else if (vr === "SL") { - text += dataSet.int32(propertyName); - for ( - let i = 1; - i < dataSet.elements[propertyName].length / 4; - i++ - ) { - text += `\\${dataSet.int32(propertyName, i)}`; - } - } else if (vr == "FD") { - text += dataSet.double(propertyName); - for ( - let i = 1; - i < dataSet.elements[propertyName].length / 8; - i++ - ) { - text += `\\${dataSet.double(propertyName, i)}`; - } - } else if (vr === "FL") { - text += dataSet.float(propertyName); - for ( - let i = 1; - i < dataSet.elements[propertyName].length / 4; - i++ - ) { - text += `\\${dataSet.float(propertyName, i)}`; - } - } else if ( - vr === "OB" || - vr === "OW" || - vr === "UN" || - vr === "OF" || - vr === "UT" - ) { - color = "#C8C8C8"; - // If it is some other length and we have no string - /* - if (element.length === 2) { - text += - "" + - dataDownloadLink(element, "binary data") + - " of length " + - element.length + - " as uint16: " + - dataSet.uint16(propertyName) + - ""; - } else if (element.length === 4) { - text += - "" + - dataDownloadLink(element, "binary data") + - " of length " + - element.length + - " as uint32: " + - dataSet.uint32(propertyName) + - ""; - } else { - text += - "" + - dataDownloadLink(element, "binary data") + - " of length " + - element.length + - " and VR " + - vr + - ""; - } - */ - } else if (vr === "AT") { - const group = dataSet.uint16(propertyName, 0); - const groupHexStr = `0000${group.toString(16)}`.substring(-4); - const element = dataSet.uint16(propertyName, 1); - const elementHexStr = `0000${element.toString(16)}`.substring(-4); - text += `x${groupHexStr}${elementHexStr}`; - } else if (vr === "SQ") { - } else { - // If it is some other length and we have no string - text += `no display code for VR ${vr} yet, sorry!`; - } - } - - if (element.length === 0) { - color = "#C8C8C8"; - } - } else { - color = "#C8C8C8"; - /* - // Add text saying the data is too long to show... - text += "" + dataDownloadLink(element, "data"); - text += " of length " + element.length + " for VR " + vr + " too long to show"; - text += sha1Text(dataSet.byteArray, element.dataOffset, element.length); - */ - } - // finally we add the string to our output array surrounded by li elements so it shows up in the - // DOM as a list - - if (tag) { - testOutput.push({ - [tag.name]: text, - }); - } - - output.push( - `
  • ${text}
    • `, - ); - } - } - } catch (err) { - return testOutput; - } - - return testOutput.sort((a: any, b: any) => { - const keyA = Object.keys(a)[0]; - const keyB = Object.keys(b)[0]; - - if (keyA < keyB) return -1; - if (keyA > keyB) return 1; - return 0; - }); -} diff --git a/src/components/Preview/displays/dicomUtils/utils.ts b/src/components/Preview/displays/dicomUtils/utils.ts index 60bbb9117..e0d1be416 100644 --- a/src/components/Preview/displays/dicomUtils/utils.ts +++ b/src/components/Preview/displays/dicomUtils/utils.ts @@ -1,27 +1,27 @@ import { - RenderingEngine, - init, - Types, Enums, + RenderingEngine, + type Types, imageLoader, + init, metaData, volumeLoader, } from "@cornerstonejs/core"; -import registerWebImageLoader from "./webImageLoader"; -import { - init as csToolsInit, - Types as CornerstoneToolTypes, -} from "@cornerstonejs/tools"; -import dicomParser from "dicom-parser"; import * as cornerstone from "@cornerstonejs/core"; -import * as cornerstoneTools from "@cornerstonejs/tools"; +import cornerstonejsDICOMImageLoader from "@cornerstonejs/dicom-image-loader"; import { - cornerstoneStreamingImageVolumeLoader, cornerstoneStreamingDynamicImageVolumeLoader, + cornerstoneStreamingImageVolumeLoader, } from "@cornerstonejs/streaming-image-volume-loader"; +import { + type Types as CornerstoneToolTypes, + init as csToolsInit, +} from "@cornerstonejs/tools"; +import * as cornerstoneTools from "@cornerstonejs/tools"; +import dicomParser from "dicom-parser"; import hardcodedMetaDataProvider from "./hardcodedMetaDataProvider"; -import cornerstonejsDICOMImageLoader from "@cornerstonejs/dicom-image-loader"; import ptScalingMetaDataProvider from "./ptScalingMetaDataProvider"; +import registerWebImageLoader from "./webImageLoader"; //@ts-ignore window.cornerstone = cornerstone; diff --git a/src/components/Wrapper/index.tsx b/src/components/Wrapper/index.tsx index 1f69834a0..48ec7a3e1 100644 --- a/src/components/Wrapper/index.tsx +++ b/src/components/Wrapper/index.tsx @@ -1,9 +1,9 @@ -import * as React from "react"; +import type * as React from "react"; import { connect } from "react-redux"; -import { Dispatch } from "redux"; -import { ApplicationState } from "../../store/root/applicationState"; -import { IUiState } from "../../store/ui/types"; -import { IUserState } from "../../store/user/types"; +import type { Dispatch } from "redux"; +import type { ApplicationState } from "../../store/root/applicationState"; +import type { IUiState } from "../../store/ui/types"; +import type { IUserState } from "../../store/user/types"; import { onSidebarToggle, setIsNavOpen } from "../../store/ui/actions"; import { Page } from "@patternfly/react-core"; import Header from "./Header"; diff --git a/src/types/index.d.ts b/src/types/index.d.ts index c329a683b..3d0afbb35 100644 --- a/src/types/index.d.ts +++ b/src/types/index.d.ts @@ -10,3 +10,4 @@ declare module "rusha"; declare module "hammerjs"; declare module "preval.macro"; declare module "@cornerstonejs/dicom-image-loader"; +declare module "dcmjs";