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Add normalisation checkbox to CoR finder app #111

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Merged
yousefmoazzam merged 1 commit into from
Apr 29, 2026
Merged

Add normalisation checkbox to CoR finder app #111

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55 changes: 44 additions & 11 deletions frontend/tomography/src/components/workflows/sweepPipeline/SubmissionFormCOR.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,9 @@ import {
Snackbar,
Stack,
Typography,
FormGroup,
FormControlLabel,
Checkbox,
useTheme,
} from "@mui/material";
import { JSONObject } from "../../../types";
Expand Down Expand Up @@ -62,6 +65,9 @@ const SubmissionFormCOR = (props: {
return (props.prepopulatedParameters as JSONObject) ?? ({} as JSONObject);
});

const [isNormalisationChecked, setIsNormalisationChecked] =
useState<boolean>(true);

// Derived child slices
const sweepValues = useMemo<SweepValues>(() => {
// keep empty-string while typing; numbers are coerced by AJV at submit
Expand Down Expand Up @@ -154,22 +160,12 @@ const SubmissionFormCOR = (props: {
}
}

return [
let pipeline = [
{
method: method,
module_path: module_path,
parameters: updatedLoaderParams,
},
{
method: "normalize",
module_path: "tomopy.prep.normalize",
parameters: { cutoff: null, averaging: "mean" },
},
{
method: "minus_log",
module_path: "tomopy.prep.normalize",
parameters: {},
},
{
method: "recon",
module_path: "tomopy.recon.algorithm",
Expand All @@ -185,6 +181,25 @@ const SubmissionFormCOR = (props: {
},
},
];

const normalisationMethods = [
{
method: "normalize",
module_path: "tomopy.prep.normalize",
parameters: { cutoff: null, averaging: "mean" },
},
{
method: "minus_log",
module_path: "tomopy.prep.normalize",
parameters: {},
},
];

if (isNormalisationChecked) {
pipeline = [pipeline[0], ...normalisationMethods, pipeline[1]];
}

return pipeline;
};

// ---- Submit handler (validate just before submit) ----
Expand Down Expand Up @@ -291,6 +306,24 @@ const SubmissionFormCOR = (props: {

<Divider />

<Typography variant="h6">Pipeline Configuration</Typography>
<FormGroup>
<FormControlLabel
control={
<Checkbox
checked={isNormalisationChecked}
onChange={(e: React.ChangeEvent<HTMLInputElement>) => {
setIsNormalisationChecked(e.target.checked);
}}
slotProps={{
input: { "aria-label": "controlled" },
}}
/>
}
label="Apply normalisation to raw data"
/>
</FormGroup>

<Typography variant="h6">Parameter Sweep Configuration</Typography>
<ParameterSweepForm values={sweepValues} onChange={setSweepValues} />

Expand Down
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