Add an option to turn off 3D classification

src/components/forms.tsx

@@ -22,6 +22,7 @@ const formDataSPA: { [key: string]: any } = {
   particle_diameter: null,
   extract_downscale: true,
   eer_fractionation: 20,
+  run_class3d: true,
 }
 
 const formDataTomo: { [key: string]: any } = {
@@ -36,12 +37,18 @@ const SpaForm = (submissionCallback: (arg0: any) => void) => {
   }
   const [symmetryType, setSymmetryType] = React.useState('C')
   const [particleDetection, setParticleDetection] = React.useState(true)
+  const [runClass3D, setRunClass3D] = React.useState(true)
   const handleChange = (event: React.ChangeEvent<HTMLSelectElement>) => {
     setSymmetryType(event.target.value)
   }
   const handleSwitchChange = (event: React.ChangeEvent<HTMLInputElement>) => {
     setParticleDetection(!particleDetection)
   }
+  const handleClass3DSwitchChange = (
+    event: React.ChangeEvent<HTMLInputElement>
+  ) => {
+    setRunClass3D(!runClass3D)
+  }
   const setFormElement = (
     event: React.FormEvent<HTMLFormElement>,
     callback: (arg0: any) => void
@@ -55,10 +62,11 @@ const SpaForm = (submissionCallback: (arg0: any) => void) => {
       ? (formData.get('symmetry1') as string)
       : (((formData.get('symmetry1') as string) +
           formData.get('symmetry2')) as string)
-    formDataSPA.particle_diameter = formData.get('detect-particle-size')
+    formDataSPA.particle_diameter = particleDetection
       ? null
       : formData.get('particle-diameter')
     formDataSPA.eer_fractionation = formData.get('eer-grouping')
+    formDataSPA.run_class3d = runClass3D
     callback(formDataSPA)
   }
 
@@ -127,8 +135,13 @@ const SpaForm = (submissionCallback: (arg0: any) => void) => {
             )}
             <VStack align="start" width="100%" display="flex">
               <HStack>
-                <FormLabel>Downscale in extraction</FormLabel>
-                <Switch defaultChecked colorScheme="murfey" name="downscale" />
+                <FormLabel>Run 3D classification</FormLabel>
+                <Switch
+                  defaultChecked
+                  colorScheme="murfey"
+                  onChange={handleClass3DSwitchChange}
+                  name="run-class3d"
+                />
               </HStack>
             </VStack>
           </VStack>

src/loaders/processingParameters.tsx

@@ -39,6 +39,7 @@ export const updateSessionProcessingParameters = async (
       dose_per_frame: params['dosePerFrame'] ?? null,
       eer_fractionation_file: params['eerFractionationFile'] ?? '',
       symmetry: params['symmetry'] ?? '',
+      run_class3d: params['run_class3d'] ?? null,
     }
   )
   if (response.status !== 200) {

src/routes/SessionParameters.tsx

@@ -42,6 +42,7 @@ const nameLabelMap: Map<string, string> = new Map([
   ['gain_ref', 'Gain Reference'],
   ['symmetry', 'Symmetry'],
   ['eer_fractionation_file', 'EER fractionation file (for motion correction)'],
+  ['run_class3d', 'Run 3D classification?'],
 ])
 
 export const SessionParameters = () => {
@@ -70,14 +71,15 @@ export const SessionParameters = () => {
     | 'dose_per_frame'
     | 'eer_fractionation_file'
     | 'symmetry'
+    | 'run_class3d'
     | ''
   const [paramName, setParamName] = React.useState('')
   const [paramValue, setParamValue] = React.useState('')
   const [paramKey, setParamKey] = React.useState<EditableParameter>('')
   Object.entries(sessionParams ? sessionParams : {}).forEach(([key, value]) =>
     tableRows.push({
       parameterName: nameLabelMap.get(key) ?? key,
-      parameterValue: value,
+      parameterValue: value.toString(),
       parameterKey: key,
     } as ProcessingRow)
   )
@@ -91,6 +93,7 @@ export const SessionParameters = () => {
       eerFractionationFile:
         paramKey === 'eer_fractionation_file' ? paramValue : '',
       symmetry: paramKey === 'symmetry' ? paramValue : '',
+      run_class3d: paramKey === 'run_class3d' ? paramValue : null,
     }
     await updateSessionProcessingParameters(sessid ?? '0', data)
     queryClient.refetchQueries({ queryKey: ['processingParameters', sessid] })
@@ -166,7 +169,6 @@ export const SessionParameters = () => {
           data={table.processingRows}
           headers={[
             { key: 'parameterName', label: 'Parameter' },
-            { key: 'parameterKey', label: 'Parameter internal name' },
             { key: 'parameterValue', label: 'Value' },
           ]}
           label={'sessionParameterData'}

src/schema/main.ts

@@ -888,6 +888,11 @@ export interface components {
        * @default
        */
       symmetry?: string
+      /**
+       * Run 3D classification?
+       * @default
+       */
+      run_class3d?: boolean
     }
     /** File */
     File: {
@@ -1557,6 +1562,11 @@ export interface components {
        * @default 20
        */
       eer_fractionation?: number
+      /**
+       * Run 3D classification?
+       * @default true
+       */
+      run_class3d?: boolean
     }
     /** RSyncerInfo */
     RSyncerInfo: {