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refactor: Refactor sync modifiers to use shared Data1D processing logic #193

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e3093ce
refactor: Refactor sync modifiers to use shared Data1D processing logic
cursoragent Nov 1, 2025
d13436e
refactor: Address PR review comments for processData1D function
cursoragent Nov 1, 2025
47e8f17
refactor: Improve readability of data processing loop in processData1D
cursoragent Nov 1, 2025
f9fc7ef
Merge branch 'main' into cursor/solve-issue-186-and-create-pr-df44
andeplane Nov 1, 2025
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86 changes: 86 additions & 0 deletions src/modifiers/modifier.ts
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Original file line number Diff line number Diff line change
@@ -1,10 +1,96 @@
import { ModifierInput, ModifierOutput } from "./types";
import { LMPModifier, Data1D } from "../types";

interface ModifierProps {
name: string;
active: boolean;
}

/**
* Shared function to process Data1D from LMPModifier.
* Handles Data1D extraction, processing, and WASM memory cleanup.
*/
export function processData1D(
lmpModifier: LMPModifier,
data1D: Data1D | undefined,
input: ModifierInput,
everything: boolean,
syncDataPoints: boolean,
clearPerSync: boolean,
): { data1D: Data1D | undefined; hasData1D: boolean } {
// Get data1DNamesWrapper and extract size, then delete immediately
const data1DNamesWrapper = lmpModifier.getData1DNames();
const data1DNamesSize = data1DNamesWrapper.size();
const hasData1D = data1DNamesSize > 0;
data1DNamesWrapper.delete(); // Delete WASM wrapper to prevent memory leak

if (data1DNamesSize === 0) {
return { data1D, hasData1D: false };
}

// Initialize data1D if needed
let currentData1D = data1D;
if (currentData1D == null) {
currentData1D = {
data: [],
labels: [],
};
}

if (everything || syncDataPoints) {
// Data points is only for plotting figures
if (clearPerSync) {
// For histograms (compute rdf etc) we don't have time as x axis, so we clear every time
currentData1D.data = [];
}

const lengthBeforeWeStart = currentData1D.data.length; // Used to avoid copying all data every time

if (currentData1D.labels.length === 0) {
// First label is never visible
currentData1D.labels.push("x");
}

// Get data1DVector once before the loop for better performance
const data1DVector = lmpModifier.getData1D();

for (let j = 0; j < data1DNamesSize; j++) {
const lmpData = data1DVector.get(j);

if (currentData1D.labels.length - 1 === j) {
// Add missing labels
currentData1D.labels.push(lmpData.getLabel());
}

const xValuesPointer = lmpData.getXValuesPointer() / Float32Array.BYTES_PER_ELEMENT;
const yValuesPointer = lmpData.getYValuesPointer() / Float32Array.BYTES_PER_ELEMENT;
const xValues = input.wasm.HEAPF32.subarray(
xValuesPointer,
xValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
const yValues = input.wasm.HEAPF32.subarray(
yValuesPointer,
yValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
for (let k = lengthBeforeWeStart; k < xValues.length; k++) {
if (j === 0) {
currentData1D.data.push([xValues[k], yValues[k]]);
} else {
currentData1D.data[k].push(yValues[k]);
}
}

// Delete the Data1D copy to prevent memory leak
lmpData.delete();
}

// Delete the vector wrapper after the loop to prevent memory leak
data1DVector.delete();
}

return { data1D: currentData1D, hasData1D };
}

class Modifier {
public name: string;
public key: string;
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80 changes: 13 additions & 67 deletions src/modifiers/synccomputesmodifier.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import Modifier from "./modifier";
import { processData1D } from "./modifier";
import { ModifierInput, ModifierOutput } from "./types";

interface SyncComputesModifierProps {
Expand Down Expand Up @@ -51,73 +52,18 @@ class SyncComputesModifier extends Modifier {
compute.xLabel = compute.lmpCompute.getXLabel();
compute.yLabel = compute.lmpCompute.getYLabel();
compute.scalarValue = compute.lmpCompute.getScalarValue();

// Get data1DNamesWrapper and extract size, then delete immediately
const data1DNamesWrapper = compute.lmpCompute.getData1DNames();
compute.hasData1D = data1DNamesWrapper.size() > 0;
const data1DNamesSize = data1DNamesWrapper.size();
data1DNamesWrapper.delete(); // Delete WASM wrapper to prevent memory leak

if (data1DNamesSize > 0) {
compute.clearPerSync = compute.lmpCompute.getClearPerSync();

if (compute.data1D == null) {
compute.data1D = {
data: [],
labels: [],
};
}

if ((everything || compute.syncDataPoints) && compute.data1D) {
// Data points is only for plotting figures
if (compute.clearPerSync) {
// For histograms (compute rdf etc) we don't have time as x axis, so we clear every time
compute.data1D.data = [];
}

const lengthBeforeWeStart = compute.data1D.data.length; // Used to avoid coping all data every time

if (compute.data1D.labels.length === 0) {
// First label is never visible
compute.data1D.labels.push("x");
}

// Get data1DVector once before the loop for better performance
const data1DVector = compute.lmpCompute.getData1D();

for (let j = 0; j < data1DNamesSize; j++) {
const lmpData = data1DVector.get(j);

if (compute.data1D.labels.length - 1 === j) {
// Add missing labels
compute.data1D.labels.push(lmpData.getLabel());
}

const xValuesPointer = lmpData.getXValuesPointer() / 4;
const yValuesPointer = lmpData.getYValuesPointer() / 4;
const xValues = input.wasm.HEAPF32.subarray(
xValuesPointer,
xValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
const yValues = input.wasm.HEAPF32.subarray(
yValuesPointer,
yValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
for (let k = lengthBeforeWeStart; k < xValues.length; k++) {
if (j === 0) {
compute.data1D.data.push([xValues[k]]);
}
compute.data1D.data[k].push(yValues[k]);
}

// Delete the Data1D copy to prevent memory leak
lmpData.delete();
}

// Delete the vector wrapper after the loop to prevent memory leak
data1DVector.delete();
}
}
compute.clearPerSync = compute.lmpCompute.getClearPerSync();

const { data1D, hasData1D } = processData1D(
compute.lmpCompute,
compute.data1D,
input,
everything,
compute.syncDataPoints,
compute.clearPerSync,
);
compute.data1D = data1D;
compute.hasData1D = hasData1D;
}
output.computes[name] = compute;
}
Expand Down
76 changes: 12 additions & 64 deletions src/modifiers/syncfixesmodifier.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import Modifier from "./modifier";
import { processData1D } from "./modifier";
import { ModifierInput, ModifierOutput } from "./types";

interface SyncFixesModifierProps {
Expand Down Expand Up @@ -48,72 +49,19 @@ class SyncFixesModifier extends Modifier {
fix.xLabel = fix.lmpFix.getXLabel();
fix.yLabel = fix.lmpFix.getYLabel();
fix.scalarValue = fix.lmpFix.getScalarValue();
fix.clearPerSync = fix.lmpFix.getClearPerSync();

// Get data1DNamesWrapper and extract size, then delete immediately
const data1DNamesWrapper = fix.lmpFix.getData1DNames();
fix.hasData1D = data1DNamesWrapper.size() > 0;
const data1DNamesSize = data1DNamesWrapper.size();
data1DNamesWrapper.delete(); // Delete WASM wrapper to prevent memory leak
const { data1D, hasData1D } = processData1D(
fix.lmpFix,
fix.data1D,
input,
everything,
fix.syncDataPoints,
fix.clearPerSync,
);
fix.data1D = data1D;
fix.hasData1D = hasData1D;

if (data1DNamesSize > 0) {
fix.clearPerSync = fix.lmpFix.getClearPerSync();
if (fix.data1D == null) {
fix.data1D = {
data: [],
labels: [],
};
}

if ((everything || fix.syncDataPoints) && fix.data1D) {
// Data points is only for plotting figures
if (fix.clearPerSync) {
// For histograms (compute rdf etc) we don't have time as x axis, so we clear every time
fix.data1D.data = [];
}

const lengthBeforeWeStart = fix.data1D.data.length; // Used to avoid coping all data every time

if (fix.data1D.labels.length === 0) {
// First label is never visible
fix.data1D.labels.push("x");
}

// Get data1DVector once before the loop for better performance
const data1DVector = fix.lmpFix.getData1D();

for (let j = 0; j < data1DNamesSize; j++) {
const lmpData = data1DVector.get(j);

if (fix.data1D.labels.length - 1 === j) {
// Add missing labels
fix.data1D.labels.push(lmpData.getLabel());
}

const xValuesPointer = lmpData.getXValuesPointer() / 4;
const yValuesPointer = lmpData.getYValuesPointer() / 4;
const xValues = input.wasm.HEAPF32.subarray(
xValuesPointer,
xValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
const yValues = input.wasm.HEAPF32.subarray(
yValuesPointer,
yValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
for (let k = lengthBeforeWeStart; k < xValues.length; k++) {
if (j === 0) {
fix.data1D.data.push([xValues[k]]);
}
fix.data1D.data[k].push(yValues[k]);
}

// Delete the Data1D copy to prevent memory leak
lmpData.delete();
}

// Delete the vector wrapper after the loop to prevent memory leak
data1DVector.delete();
}
}
output.fixes[name] = fix;
}
};
Expand Down
76 changes: 12 additions & 64 deletions src/modifiers/syncvariablesmodifier.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import Modifier from "./modifier";
import { processData1D } from "./modifier";
import { ModifierInput, ModifierOutput } from "./types";

interface SyncVariablesModifierProps {
Expand Down Expand Up @@ -50,72 +51,19 @@ class SyncVariablesModifier extends Modifier {
variable.yLabel = variable.lmpVariable.getYLabel();
variable.scalarValue = variable.lmpVariable.getScalarValue();
variable.hasScalarData = variable.lmpVariable.hasScalarData();
variable.clearPerSync = variable.lmpVariable.getClearPerSync();

// Get data1DNamesWrapper and extract size, then delete immediately
const data1DNamesWrapper = variable.lmpVariable.getData1DNames();
variable.hasData1D = data1DNamesWrapper.size() > 0;
const data1DNamesSize = data1DNamesWrapper.size();
data1DNamesWrapper.delete(); // Delete WASM wrapper to prevent memory leak

if (data1DNamesSize > 0) {
variable.clearPerSync = variable.lmpVariable.getClearPerSync();
if (variable.data1D == null) {
variable.data1D = {
data: [],
labels: [],
};
}
const { data1D, hasData1D } = processData1D(
variable.lmpVariable,
variable.data1D,
input,
everything,
variable.syncDataPoints,
variable.clearPerSync,
);
variable.data1D = data1D;
variable.hasData1D = hasData1D;

if ((everything || variable.syncDataPoints) && variable.data1D) {
// Data points is only for plotting figures
if (variable.clearPerSync) {
// For histograms (compute rdf etc) we don't have time as x axis, so we clear every time
variable.data1D.data = [];
}

const lengthBeforeWeStart = variable.data1D.data.length; // Used to avoid coping all data every time

if (variable.data1D.labels.length === 0) {
// First label is never visible
variable.data1D.labels.push("x");
}

// Get data1DVector once before the loop for better performance
const data1DVector = variable.lmpVariable.getData1D();

for (let j = 0; j < data1DNamesSize; j++) {
const lmpData = data1DVector.get(j);

if (variable.data1D.labels.length - 1 === j) {
// Add missing labels
variable.data1D.labels.push(lmpData.getLabel());
}

const xValuesPointer = lmpData.getXValuesPointer() / 4;
const yValuesPointer = lmpData.getYValuesPointer() / 4;
const xValues = input.wasm.HEAPF32.subarray(
xValuesPointer,
xValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
const yValues = input.wasm.HEAPF32.subarray(
yValuesPointer,
yValuesPointer + lmpData.getNumPoints(),
) as Float32Array;
for (let k = lengthBeforeWeStart; k < xValues.length; k++) {
if (j === 0) {
variable.data1D.data.push([xValues[k]]);
}
variable.data1D.data[k].push(yValues[k]);
}

// Delete the Data1D copy to prevent memory leak
lmpData.delete();
}

// Delete the vector wrapper after the loop to prevent memory leak
data1DVector.delete();
}
}
output.variables[name] = variable;
}
};
Expand Down