Merge pull request #157 from flatironinstitute/bmw/analysis.R

Consolidate script editors, add analysis.R

gui/src/app/Project/FileMapping.ts

@@ -25,6 +25,7 @@ export enum FileNames {
   STANFILE = "main.stan",
   DATAFILE = "data.json",
   ANALYSISPYFILE = "analysis.py",
+  ANALYSISRFILE = "analysis.R",
   DATAPYFILE = "data.py",
   DATARFILE = "data.R",
 }
@@ -46,6 +47,7 @@ export const ProjectFileMap: FileMapType = {
   stanFileContent: FileNames.STANFILE,
   dataFileContent: FileNames.DATAFILE,
   analysisPyFileContent: FileNames.ANALYSISPYFILE,
+  analysisRFileContent: FileNames.ANALYSISRFILE,
   dataPyFileContent: FileNames.DATAPYFILE,
   dataRFileContent: FileNames.DATARFILE,
 };

gui/src/app/Project/ProjectDataModel.ts

@@ -4,6 +4,7 @@ export enum ProjectKnownFiles {
   STANFILE = "stanFileContent",
   DATAFILE = "dataFileContent",
   ANALYSISPYFILE = "analysisPyFileContent",
+  ANALYSISRFILE = "analysisRFileContent",
   DATAPYFILE = "dataPyFileContent",
   DATARFILE = "dataRFileContent",
 }
@@ -130,12 +131,14 @@ export const initialDataModel: ProjectDataModel = {
     stanFileContent: "",
     dataFileContent: "",
     analysisPyFileContent: "",
+    analysisRFileContent: "",
     dataPyFileContent: "",
     dataRFileContent: "",
   },
   stanFileContent: "",
   dataFileContent: "",
   analysisPyFileContent: "",
+  analysisRFileContent: "",
   dataPyFileContent: "",
   dataRFileContent: "",
   samplingOpts: defaultSamplingOpts,

gui/src/app/Scripting/Analysis/AnalysisPyWindow.tsx

@@ -0,0 +1,97 @@
+import { FunctionComponent, RefObject, useCallback, useMemo } from "react";
+import { StanRun } from "@SpStanSampler/useStanSampler";
+import { FileNames } from "@SpCore/FileMapping";
+import { ProjectKnownFiles } from "@SpCore/ProjectDataModel";
+import useTemplatedFillerText from "@SpScripting/useTemplatedFillerText";
+import {
+  clearOutputDivs,
+  writeConsoleOutToDiv,
+} from "@SpScripting/OutputDivUtils";
+import usePyodideWorker from "@SpScripting/pyodide/usePyodideWorker";
+import PlottingScriptEditor from "@SpScripting/PlottingScriptEditor";
+import useAnalysisState from "./useAnalysisState";
+
+import analysisPyTemplate from "./analysis_template.py?raw";
+
+export type GlobalDataForAnalysis = {
+  draws: number[][];
+  paramNames: string[];
+  numChains: number;
+};
+
+type AnalysisWindowProps = {
+  latestRun: StanRun;
+};
+
+const AnalysisPyWindow: FunctionComponent<AnalysisWindowProps> = ({
+  latestRun,
+}) => {
+  const {
+    consoleRef,
+    imagesRef,
+    spData,
+    status,
+    onStatus,
+    runnable,
+    notRunnableReason,
+  } = useAnalysisState(latestRun);
+
+  const callbacks = useMemo(
+    () => ({
+      onStdout: (x: string) => writeConsoleOutToDiv(consoleRef, x, "stdout"),
+      onStderr: (x: string) => writeConsoleOutToDiv(consoleRef, x, "stderr"),
+      onImage: (b64: string) => addImageToDiv(imagesRef, b64),
+      onStatus,
+    }),
+    [consoleRef, imagesRef, onStatus],
+  );
+
+  const { run } = usePyodideWorker(callbacks);
+
+  const handleRun = useCallback(
+    (code: string) => {
+      clearOutputDivs(consoleRef, imagesRef);
+      run(code, spData, {
+        loadsDraws: true,
+        showsPlots: true,
+        producesData: false,
+      });
+    },
+    [consoleRef, imagesRef, run, spData],
+  );
+
+  const contentOnEmpty = useTemplatedFillerText(
+    "Use the draws object to access the samples. ",
+    analysisPyTemplate,
+    ProjectKnownFiles.ANALYSISPYFILE,
+  );
+
+  return (
+    <PlottingScriptEditor
+      filename={FileNames.ANALYSISPYFILE}
+      dataKey={ProjectKnownFiles.ANALYSISPYFILE}
+      language="python"
+      status={status}
+      onRun={handleRun}
+      runnable={runnable}
+      notRunnableReason={notRunnableReason}
+      imagesRef={imagesRef}
+      consoleRef={consoleRef}
+      contentOnEmpty={contentOnEmpty}
+    />
+  );
+};
+
+const addImageToDiv = (imagesRef: RefObject<HTMLDivElement>, b64: string) => {
+  const imageUrl = `data:image/png;base64,${b64}`;
+
+  const img = document.createElement("img");
+  img.style.width = "100%";
+  img.src = imageUrl;
+
+  const divElement = document.createElement("div");
+  divElement.appendChild(img);
+  imagesRef.current?.appendChild(divElement);
+};
+
+export default AnalysisPyWindow;

gui/src/app/Scripting/Analysis/AnalysisRWindow.tsx

@@ -0,0 +1,68 @@
+import { FunctionComponent, useCallback } from "react";
+import { StanRun } from "@SpStanSampler/useStanSampler";
+import { FileNames } from "@SpCore/FileMapping";
+import { ProjectKnownFiles } from "@SpCore/ProjectDataModel";
+import PlottingScriptEditor from "@SpScripting/PlottingScriptEditor";
+import runR from "@SpScripting/webR/runR";
+import useTemplatedFillerText from "@SpScripting/useTemplatedFillerText";
+import { clearOutputDivs } from "@SpScripting/OutputDivUtils";
+import loadDrawsCode from "@SpScripting/webR/sp_load_draws.R?raw";
+import useAnalysisState from "./useAnalysisState";
+
+import analysisRTemplate from "./analysis_template.R?raw";
+
+type AnalysisWindowProps = {
+  latestRun: StanRun;
+};
+
+const AnalysisRWindow: FunctionComponent<AnalysisWindowProps> = ({
+  latestRun,
+}) => {
+  const {
+    consoleRef,
+    imagesRef,
+    spData,
+    status,
+    onStatus,
+    runnable,
+    notRunnableReason,
+  } = useAnalysisState(latestRun);
+
+  const handleRun = useCallback(
+    async (userCode: string) => {
+      clearOutputDivs(consoleRef, imagesRef);
+      const code = loadDrawsCode + userCode;
+      await runR({
+        code,
+        imagesRef,
+        consoleRef,
+        onStatus,
+        spData,
+      });
+    },
+    [consoleRef, imagesRef, onStatus, spData],
+  );
+
+  const contentOnEmpty = useTemplatedFillerText(
+    "Use the draws object (a posterior::draws_array) to access the samples. ",
+    analysisRTemplate,
+    ProjectKnownFiles.ANALYSISRFILE,
+  );
+
+  return (
+    <PlottingScriptEditor
+      filename={FileNames.ANALYSISRFILE}
+      dataKey={ProjectKnownFiles.ANALYSISRFILE}
+      language="r"
+      status={status}
+      onRun={handleRun}
+      runnable={runnable}
+      notRunnableReason={notRunnableReason}
+      imagesRef={imagesRef}
+      consoleRef={consoleRef}
+      contentOnEmpty={contentOnEmpty}
+    />
+  );
+};
+
+export default AnalysisRWindow;

gui/src/app/Scripting/Analysis/analysis_template.R

@@ -0,0 +1,7 @@
+library(posterior)
+print(summary(draws))
+
+install.packages("bayesplot")
+library(bayesplot)
+
+mcmc_hist(draws, pars=c("lp__"))

gui/src/app/Scripting/Analysis/analysis_template.py

@@ -0,0 +1,14 @@
+import matplotlib.pyplot as plt
+
+# Print the draws object
+print(draws)
+
+# Print parameter names
+print(draws.parameter_names)
+
+# plot the lp parameter
+samples = draws.get("lp__")
+print(samples.shape)
+plt.hist(samples.ravel(), bins=30)
+plt.title("lp__")
+plt.show()

gui/src/app/Scripting/Analysis/useAnalysisState.ts

@@ -0,0 +1,71 @@
+import {
+  InterpreterStatus,
+  isInterpreterBusy,
+} from "@SpScripting/InterpreterTypes";
+import { clearOutputDivs } from "@SpScripting/OutputDivUtils";
+import { StanRun } from "@SpStanSampler/useStanSampler";
+import { useEffect, useMemo, useRef, useState } from "react";
+
+export type GlobalDataForAnalysis = {
+  draws: number[][];
+  paramNames: string[];
+  numChains: number;
+};
+
+// A custom hook to share logic between the Python and R analysis windows
+// This contains the output div refs, the interpreter state, and the data from
+// the latest run.
+const useAnalysisState = (latestRun: StanRun) => {
+  const consoleRef = useRef<HTMLDivElement | null>(null);
+  const imagesRef = useRef<HTMLDivElement | null>(null);
+
+  useEffect(() => {
+    clearOutputDivs(consoleRef, imagesRef);
+  }, [latestRun.draws]);
+
+  const { draws, paramNames, samplingOpts, status: samplerStatus } = latestRun;
+  const numChains = samplingOpts?.num_chains;
+  const spData = useMemo(() => {
+    if (samplerStatus === "completed" && draws && numChains && paramNames) {
+      return {
+        draws,
+        paramNames,
+        numChains,
+      };
+    } else {
+      return undefined;
+    }
+  }, [samplerStatus, draws, numChains, paramNames]);
+
+  const [status, setStatus] = useState<InterpreterStatus>("idle");
+
+  const [runnable, setRunnable] = useState<boolean>(true);
+  const [notRunnableReason, setNotRunnableReason] = useState<string>("");
+
+  const isDataDefined = useMemo(() => spData !== undefined, [spData]);
+
+  useEffect(() => {
+    if (!isDataDefined) {
+      setRunnable(false);
+      setNotRunnableReason("Run sampler first.");
+    } else if (isInterpreterBusy(status)) {
+      setRunnable(false);
+      setNotRunnableReason("");
+    } else {
+      setRunnable(true);
+      setNotRunnableReason("");
+    }
+  }, [isDataDefined, status]);
+
+  return {
+    consoleRef,
+    imagesRef,
+    spData,
+    status,
+    onStatus: setStatus,
+    runnable,
+    notRunnableReason,
+  };
+};
+
+export default useAnalysisState;