From 3579261ffb4e27f4d65b223fb8aa399848c20d12 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Fri, 10 Oct 2025 14:42:52 +0100
Subject: [PATCH 01/19] Add starting page and route for JF rotations

---
 src/App.tsx                     |  4 ++++
 src/routes/JungfrauRotation.tsx | 19 +++++++++++++++++++
 2 files changed, 23 insertions(+)
 create mode 100644 src/routes/JungfrauRotation.tsx

diff --git a/src/App.tsx b/src/App.tsx
index bb65e9f..6aa3f6b 100644
--- a/src/App.tsx
+++ b/src/App.tsx
@@ -6,6 +6,7 @@ import { BeamlineI24 } from "./routes/BeamlineI24";
 import { FixedTarget } from "./routes/FixedTarget";
 import { SerialNavBar } from "./components/SerialNavBar";
 import { Extruder } from "./routes/Extruder";
+import { JfRotation } from "./routes/JungfrauRotation";
 
 function App() {
   const theme = useTheme();
@@ -31,6 +32,9 @@ function App() {
         <Route path="/extruder">
           <Extruder />
         </Route>
+        <Route path="/jungfrau">
+          <JfRotation />
+        </Route>
       </Switch>
       <Footer
         logo={theme.logos?.short}
diff --git a/src/routes/JungfrauRotation.tsx b/src/routes/JungfrauRotation.tsx
new file mode 100644
index 0000000..a43d49a
--- /dev/null
+++ b/src/routes/JungfrauRotation.tsx
@@ -0,0 +1,19 @@
+import { Box, Typography, useTheme } from "@mui/material";
+
+export function JfRotation() {
+  const theme = useTheme();
+  return (
+    <Box marginTop={2}>
+      <Typography
+        variant="h1"
+        sx={{
+          color: theme.palette.info.main,
+          fontSize: 24,
+          fontWeight: "fontWeightBold",
+        }}
+      >
+        Jungfrau Rotation Scans Setup
+      </Typography>
+    </Box>
+  );
+}

From 7ce2b13b6ff5f910bd5f84b7dd9284c1f9c02eee Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Fri, 10 Oct 2025 14:49:53 +0100
Subject: [PATCH 02/19] Add link to navbar

---
 src/components/SerialNavBar.tsx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/components/SerialNavBar.tsx b/src/components/SerialNavBar.tsx
index 160cea1..6ee2d20 100644
--- a/src/components/SerialNavBar.tsx
+++ b/src/components/SerialNavBar.tsx
@@ -27,6 +27,9 @@ export function SerialNavBar() {
         <NavLink linkComponent={Link} to="/extruder">
           Extruder
         </NavLink>
+        <NavLink linkComponent={Link} to="/jungfrau">
+          JF Rotation
+        </NavLink>
       </NavLinks>
     </Navbar>
   );

From 59346f0ca5650c607666c096e94b99323c5eb52c Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Mon, 13 Oct 2025 17:18:55 +0100
Subject: [PATCH 03/19] Add jungfrau do darks

---
 src/components/Extruder/CollectionSetupEx.tsx |  3 +-
 src/components/JungFrau/CollectDarksPanel.tsx | 69 +++++++++++++++++++
 src/routes/JungfrauRotation.tsx               | 10 ++-
 src/screens/CollectionPanel.tsx               |  3 +-
 4 files changed, 81 insertions(+), 4 deletions(-)
 create mode 100644 src/components/JungFrau/CollectDarksPanel.tsx

diff --git a/src/components/Extruder/CollectionSetupEx.tsx b/src/components/Extruder/CollectionSetupEx.tsx
index 1063824..b8c3096 100644
--- a/src/components/Extruder/CollectionSetupEx.tsx
+++ b/src/components/Extruder/CollectionSetupEx.tsx
@@ -1,4 +1,4 @@
-import { Box, Button, Grid2, Stack } from "@mui/material";
+import { Box, Grid2, Stack } from "@mui/material";
 import React from "react";
 import { ParameterInput } from "../ParameterInputs";
 import {
@@ -7,7 +7,6 @@ import {
   PumpProbeSetup,
 } from "./PumpProbeSelection";
 import { AbortButton, RunPlanButton } from "../../blueapi/BlueapiComponents";
-import { DetailsRounded } from "@mui/icons-material";
 
 /**Main collection input window for the extruderpanel. */
 export function CollectionSetupEx() {
diff --git a/src/components/JungFrau/CollectDarksPanel.tsx b/src/components/JungFrau/CollectDarksPanel.tsx
new file mode 100644
index 0000000..3f8cabb
--- /dev/null
+++ b/src/components/JungFrau/CollectDarksPanel.tsx
@@ -0,0 +1,69 @@
+import {
+  Box,
+  Button,
+  Card,
+  CardContent,
+  Stack,
+  Typography,
+  useTheme,
+} from "@mui/material";
+import React from "react";
+import { ParameterInput } from "../ParameterInputs";
+import { RunPlanButton } from "../../blueapi/BlueapiComponents";
+
+export function CollectDarksPanel() {
+  const theme = useTheme();
+  const [expTime, setExpTime] = React.useState<number>(0.001);
+  const [pedestalFrames, setPedestalFrames] = React.useState<number>(20);
+  const [pedestalLoops, setPedestalLoops] = React.useState<number>(200);
+  //   const [filePath, setFilePath] = React.useState<string>("");
+  return (
+    <Box sx={{ flexGrow: 1, marginLeft: 15, marginRight: 5 }}>
+      <Card variant="outlined" sx={{ minWidth: 300, minHeight: 600 }}>
+        <CardContent>
+          <Typography
+            variant="h2"
+            sx={{
+              color: theme.palette.primary.contrastText,
+              fontSize: 24,
+              fontWeight: "fontWeightBold",
+            }}
+          >
+            Collect darks
+          </Typography>
+          <Stack spacing={1} margin={2} alignContent={"center"}>
+            <ParameterInput
+              value={expTime}
+              onSet={setExpTime}
+              label="Exposure time (s)"
+              tooltip="Set exposure time for darks collection."
+            />
+            <ParameterInput
+              value={pedestalFrames}
+              onSet={setPedestalFrames}
+              label="Pedestal frames"
+              tooltip="Number of pedestal frames to collect."
+            />
+            <ParameterInput
+              value={pedestalLoops}
+              onSet={setPedestalLoops}
+              label="Pedestal loops"
+              tooltip="Number of pedestal loops."
+            />
+          </Stack>
+          <RunPlanButton
+            btnLabel="Pedestal darks"
+            planName="do_pedestal_darks"
+            planParams={{
+              exp_time_s: expTime,
+              pedestal_frame: pedestalFrames,
+              pedestal_loops: pedestalLoops,
+            }}
+            title="Collect pedestal darks"
+            btnSize="large"
+          />
+        </CardContent>
+      </Card>
+    </Box>
+  );
+}
diff --git a/src/routes/JungfrauRotation.tsx b/src/routes/JungfrauRotation.tsx
index a43d49a..65dd79f 100644
--- a/src/routes/JungfrauRotation.tsx
+++ b/src/routes/JungfrauRotation.tsx
@@ -1,4 +1,6 @@
-import { Box, Typography, useTheme } from "@mui/material";
+import { Box, Grid2, Typography, useTheme } from "@mui/material";
+import { ParamsPanel } from "../screens/CollectionPanel";
+import { CollectDarksPanel } from "../components/JungFrau/CollectDarksPanel";
 
 export function JfRotation() {
   const theme = useTheme();
@@ -14,6 +16,12 @@ export function JfRotation() {
       >
         Jungfrau Rotation Scans Setup
       </Typography>
+      <Grid2 container marginTop={2} spacing={2}>
+        <Grid2 size={5}>
+          <CollectDarksPanel />
+        </Grid2>
+        <ParamsPanel expt="jf" />
+      </Grid2>
     </Box>
   );
 }
diff --git a/src/screens/CollectionPanel.tsx b/src/screens/CollectionPanel.tsx
index 9629d9d..a5e186e 100644
--- a/src/screens/CollectionPanel.tsx
+++ b/src/screens/CollectionPanel.tsx
@@ -3,7 +3,7 @@ import { CollectionSetupFt } from "../components/FixedTarget/CollectionSetupFt";
 import { CollectionSetupEx } from "../components/Extruder/CollectionSetupEx";
 
 type ExptType = {
-  expt: "extruder" | "fixed-target";
+  expt: "extruder" | "fixed-target" | "jf";
 };
 
 function FallbackScreen() {
@@ -22,6 +22,7 @@ export function ParamsPanel(expt: ExptType) {
       return <CollectionSetupFt />;
     case "extruder":
       return <CollectionSetupEx />;
+    case "jf":
     default:
       return <FallbackScreen />;
   }

From 208ba8ea58590894fc84694a86986e3d6e1e6562 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Mon, 13 Oct 2025 17:46:25 +0100
Subject: [PATCH 04/19] Without file path it works... sigh

---
 src/components/JungFrau/CollectDarksPanel.tsx | 3 +--
 src/components/JungFrau/CollectionSetupJf.tsx | 0
 2 files changed, 1 insertion(+), 2 deletions(-)
 create mode 100644 src/components/JungFrau/CollectionSetupJf.tsx

diff --git a/src/components/JungFrau/CollectDarksPanel.tsx b/src/components/JungFrau/CollectDarksPanel.tsx
index 3f8cabb..ceea22f 100644
--- a/src/components/JungFrau/CollectDarksPanel.tsx
+++ b/src/components/JungFrau/CollectDarksPanel.tsx
@@ -1,6 +1,5 @@
 import {
   Box,
-  Button,
   Card,
   CardContent,
   Stack,
@@ -16,7 +15,7 @@ export function CollectDarksPanel() {
   const [expTime, setExpTime] = React.useState<number>(0.001);
   const [pedestalFrames, setPedestalFrames] = React.useState<number>(20);
   const [pedestalLoops, setPedestalLoops] = React.useState<number>(200);
-  //   const [filePath, setFilePath] = React.useState<string>("");
+
   return (
     <Box sx={{ flexGrow: 1, marginLeft: 15, marginRight: 5 }}>
       <Card variant="outlined" sx={{ minWidth: 300, minHeight: 600 }}>
diff --git a/src/components/JungFrau/CollectionSetupJf.tsx b/src/components/JungFrau/CollectionSetupJf.tsx
new file mode 100644
index 0000000..e69de29

From a1d1cc2a01d8bd05df051eec99d64ac7b97b2dfd Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Mon, 27 Oct 2025 11:34:05 +0000
Subject: [PATCH 05/19] New changes

---
 src/components/JungFrau/CollectionSetupJf.tsx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/JungFrau/CollectionSetupJf.tsx b/src/components/JungFrau/CollectionSetupJf.tsx
index e69de29..1016708 100644
--- a/src/components/JungFrau/CollectionSetupJf.tsx
+++ b/src/components/JungFrau/CollectionSetupJf.tsx
@@ -0,0 +1 @@
+export function CollectionSetJf() {}

From 7e1afc46dd3a5aafa127a6e1b71f0e1d85a1c77a Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Mon, 27 Oct 2025 17:03:49 +0000
Subject: [PATCH 06/19] Update

---
 package-lock.json | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 3989513..89e9671 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -9677,20 +9677,6 @@
         }
       }
     },
-    "node_modules/vitest/node_modules/yaml": {
-      "version": "2.8.1",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.1.tgz",
-      "integrity": "sha512-lcYcMxX2PO9XMGvAJkJ3OsNMw+/7FKes7/hgerGUYWIoWu5j/+YQqcZr5JnPZWzOsEBgMbSbiSTn/dv/69Mkpw==",
-      "dev": true,
-      "optional": true,
-      "peer": true,
-      "bin": {
-        "yaml": "bin.mjs"
-      },
-      "engines": {
-        "node": ">= 14.6"
-      }
-    },
     "node_modules/vt-pbf": {
       "version": "3.1.3",
       "resolved": "https://registry.npmjs.org/vt-pbf/-/vt-pbf-3.1.3.tgz",

From 7dfa14a7753e535ed4e780fc7d9676f117e7da26 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 12 Nov 2025 10:26:23 +0000
Subject: [PATCH 07/19] Hopefully fix lint

---
 package-lock.json | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/package-lock.json b/package-lock.json
index 91e7872..ea23530 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10306,6 +10306,20 @@
         }
       }
     },
+    "node_modules/vitest/node_modules/yaml": {
+      "version": "2.8.1",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.1.tgz",
+      "integrity": "sha512-lcYcMxX2PO9XMGvAJkJ3OsNMw+/7FKes7/hgerGUYWIoWu5j/+YQqcZr5JnPZWzOsEBgMbSbiSTn/dv/69Mkpw==",
+      "dev": true,
+      "optional": true,
+      "peer": true,
+      "bin": {
+        "yaml": "bin.mjs"
+      },
+      "engines": {
+        "node": ">= 14.6"
+      }
+    },
     "node_modules/vt-pbf": {
       "version": "3.1.3",
       "license": "MIT",

From c4a7a6bbe1b8d08b043b36ce68e56c5e31c09a9e Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 19 Nov 2025 14:34:38 +0000
Subject: [PATCH 08/19] Wrap everything in the fallback just in case

---
 src/routes/Extruder.tsx         | 38 ++++++++++++++++++---------------
 src/screens/CollectionPanel.tsx |  5 +++--
 2 files changed, 24 insertions(+), 19 deletions(-)

diff --git a/src/routes/Extruder.tsx b/src/routes/Extruder.tsx
index 922ce92..5cb9806 100644
--- a/src/routes/Extruder.tsx
+++ b/src/routes/Extruder.tsx
@@ -1,26 +1,30 @@
 import { Box, Typography, useTheme } from "@mui/material";
 import { ReadOnlyInputs } from "components/ReadOnlyInputs";
 import { ParamsPanel } from "screens/CollectionPanel";
+import { ErrorBoundary } from "react-error-boundary";
+import { FallbackScreen } from "screens/FallbackScreen";
 
 export function Extruder() {
   const theme = useTheme();
   return (
-    <Box marginTop={2}>
-      <Typography
-        variant="h1"
-        sx={{
-          color: theme.palette.info.main,
-          fontSize: 24,
-          fontWeight: "fontWeightBold",
-        }}
-      >
-        Extruder Data Collection Setup
-      </Typography>
-      <ReadOnlyInputs
-        visit="ca://BL24I-MO-IOC-13:GP1"
-        detector="ca://BL24I-MO-IOC-13:GP15"
-      />
-      <ParamsPanel expt="extruder" />
-    </Box>
+    <ErrorBoundary fallback={<FallbackScreen />}>
+      <Box marginTop={2}>
+        <Typography
+          variant="h1"
+          sx={{
+            color: theme.palette.info.main,
+            fontSize: 24,
+            fontWeight: "fontWeightBold",
+          }}
+        >
+          Extruder Data Collection Setup
+        </Typography>
+        <ReadOnlyInputs
+          visit="ca://BL24I-MO-IOC-13:GP1"
+          detector="ca://BL24I-MO-IOC-13:GP15"
+        />
+        <ParamsPanel expt="extruder" />
+      </Box>
+    </ErrorBoundary>
   );
 }
diff --git a/src/screens/CollectionPanel.tsx b/src/screens/CollectionPanel.tsx
index fb548c9..6b94e7f 100644
--- a/src/screens/CollectionPanel.tsx
+++ b/src/screens/CollectionPanel.tsx
@@ -1,14 +1,15 @@
 import { Box, Typography } from "@mui/material";
 import { CollectionSetupFt } from "components/FixedTarget/CollectionSetupFt";
 import { CollectionSetupEx } from "components/Extruder/CollectionSetupEx";
-
+import ErrorOutlineIcon from "@mui/icons-material/ErrorOutline";
 type ExptType = {
   expt: "extruder" | "fixed-target" | "jf";
 };
 
 function FallbackScreen() {
   return (
-    <Box>
+    <Box alignContent={"center"}>
+      <ErrorOutlineIcon color="error" fontSize="large" />
       <Typography component="h1" variant="h4">
         Page currently unavailable
       </Typography>

From e7bf064c67b85794ace4f59e25b239454405fc1e Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 19 Nov 2025 14:36:23 +0000
Subject: [PATCH 09/19] And maybe save everything

---
 src/routes/BeamlineI24.tsx      | 62 ++++++++++++++++++---------------
 src/routes/FixedTarget.tsx      | 38 +++++++++++---------
 src/routes/JungfrauRotation.tsx | 38 +++++++++++---------
 src/screens/FallbackScreen.tsx  | 14 ++++++++
 4 files changed, 89 insertions(+), 63 deletions(-)
 create mode 100644 src/screens/FallbackScreen.tsx

diff --git a/src/routes/BeamlineI24.tsx b/src/routes/BeamlineI24.tsx
index 4d0e37c..5d49c3c 100644
--- a/src/routes/BeamlineI24.tsx
+++ b/src/routes/BeamlineI24.tsx
@@ -3,6 +3,8 @@ import { BeamlineStatsTabPanel } from "screens/BeamlineStats";
 import { DetectorMotionTabPanel } from "screens/DetectorMotion";
 import { OavMover } from "screens/OavMover/OavMover";
 import React from "react";
+import { ErrorBoundary } from "react-error-boundary";
+import { FallbackScreen } from "screens/FallbackScreen";
 
 interface TabPanelProps {
   children?: React.ReactNode;
@@ -41,36 +43,38 @@ export function BeamlineI24() {
     setTab(newTab);
   };
   return (
-    <Box>
-      <Box
-        component="section"
-        sx={{
-          borderBottom: 1,
-          borderColor: "divider",
-          color: theme.palette.text.secondary,
-        }}
-      >
-        <Tabs
-          value={tab}
-          onChange={handleChange}
-          aria-label="basic tabs example"
-          textColor="secondary"
-          centered
+    <ErrorBoundary fallback={<FallbackScreen />}>
+      <Box>
+        <Box
+          component="section"
+          sx={{
+            borderBottom: 1,
+            borderColor: "divider",
+            color: theme.palette.text.secondary,
+          }}
         >
-          <Tab label="Beamline info" {...a11yProps(0)} />
-          <Tab label="Detector position" {...a11yProps(1)} />
-          <Tab label="OAV view" {...a11yProps(2)} />
-        </Tabs>
+          <Tabs
+            value={tab}
+            onChange={handleChange}
+            aria-label="basic tabs example"
+            textColor="secondary"
+            centered
+          >
+            <Tab label="Beamline info" {...a11yProps(0)} />
+            <Tab label="Detector position" {...a11yProps(1)} />
+            <Tab label="OAV view" {...a11yProps(2)} />
+          </Tabs>
+        </Box>
+        <CustomTabPanel value={tab} index={0}>
+          <BeamlineStatsTabPanel />
+        </CustomTabPanel>
+        <CustomTabPanel value={tab} index={1}>
+          <DetectorMotionTabPanel />
+        </CustomTabPanel>
+        <CustomTabPanel value={tab} index={2}>
+          <OavMover />
+        </CustomTabPanel>
       </Box>
-      <CustomTabPanel value={tab} index={0}>
-        <BeamlineStatsTabPanel />
-      </CustomTabPanel>
-      <CustomTabPanel value={tab} index={1}>
-        <DetectorMotionTabPanel />
-      </CustomTabPanel>
-      <CustomTabPanel value={tab} index={2}>
-        <OavMover />
-      </CustomTabPanel>
-    </Box>
+    </ErrorBoundary>
   );
 }
diff --git a/src/routes/FixedTarget.tsx b/src/routes/FixedTarget.tsx
index 6226125..1258508 100644
--- a/src/routes/FixedTarget.tsx
+++ b/src/routes/FixedTarget.tsx
@@ -1,26 +1,30 @@
 import { Box, Typography, useTheme } from "@mui/material";
 import { ParamsPanel } from "screens/CollectionPanel";
 import { ReadOnlyInputs } from "components/ReadOnlyInputs";
+import { ErrorBoundary } from "react-error-boundary";
+import { FallbackScreen } from "screens/FallbackScreen";
 
 export function FixedTarget() {
   const theme = useTheme();
   return (
-    <Box marginTop={2}>
-      <Typography
-        variant="h1"
-        sx={{
-          color: theme.palette.info.main,
-          fontSize: 24,
-          fontWeight: "fontWeightBold",
-        }}
-      >
-        Fixed Target Data Collection Setup
-      </Typography>
-      <ReadOnlyInputs
-        visit="ca://BL24I-MO-IOC-13:GP100"
-        detector="ca://BL24I-MO-IOC-13:GP101"
-      />
-      <ParamsPanel expt="fixed-target" />
-    </Box>
+    <ErrorBoundary fallback={<FallbackScreen />}>
+      <Box marginTop={2}>
+        <Typography
+          variant="h1"
+          sx={{
+            color: theme.palette.info.main,
+            fontSize: 24,
+            fontWeight: "fontWeightBold",
+          }}
+        >
+          Fixed Target Data Collection Setup
+        </Typography>
+        <ReadOnlyInputs
+          visit="ca://BL24I-MO-IOC-13:GP100"
+          detector="ca://BL24I-MO-IOC-13:GP101"
+        />
+        <ParamsPanel expt="fixed-target" />
+      </Box>
+    </ErrorBoundary>
   );
 }
diff --git a/src/routes/JungfrauRotation.tsx b/src/routes/JungfrauRotation.tsx
index 65dd79f..5e37c7a 100644
--- a/src/routes/JungfrauRotation.tsx
+++ b/src/routes/JungfrauRotation.tsx
@@ -1,27 +1,31 @@
 import { Box, Grid2, Typography, useTheme } from "@mui/material";
 import { ParamsPanel } from "../screens/CollectionPanel";
 import { CollectDarksPanel } from "../components/JungFrau/CollectDarksPanel";
+import { ErrorBoundary } from "react-error-boundary";
+import { FallbackScreen } from "screens/FallbackScreen";
 
 export function JfRotation() {
   const theme = useTheme();
   return (
-    <Box marginTop={2}>
-      <Typography
-        variant="h1"
-        sx={{
-          color: theme.palette.info.main,
-          fontSize: 24,
-          fontWeight: "fontWeightBold",
-        }}
-      >
-        Jungfrau Rotation Scans Setup
-      </Typography>
-      <Grid2 container marginTop={2} spacing={2}>
-        <Grid2 size={5}>
-          <CollectDarksPanel />
+    <ErrorBoundary fallback={<FallbackScreen />}>
+      <Box marginTop={2}>
+        <Typography
+          variant="h1"
+          sx={{
+            color: theme.palette.info.main,
+            fontSize: 24,
+            fontWeight: "fontWeightBold",
+          }}
+        >
+          Jungfrau Rotation Scans Setup
+        </Typography>
+        <Grid2 container marginTop={2} spacing={2}>
+          <Grid2 size={5}>
+            <CollectDarksPanel />
+          </Grid2>
+          <ParamsPanel expt="jf" />
         </Grid2>
-        <ParamsPanel expt="jf" />
-      </Grid2>
-    </Box>
+      </Box>
+    </ErrorBoundary>
   );
 }
diff --git a/src/screens/FallbackScreen.tsx b/src/screens/FallbackScreen.tsx
new file mode 100644
index 0000000..27725b8
--- /dev/null
+++ b/src/screens/FallbackScreen.tsx
@@ -0,0 +1,14 @@
+import { Box, Typography } from "@mui/material";
+
+import ErrorOutlineIcon from "@mui/icons-material/ErrorOutline";
+
+export function FallbackScreen() {
+  return (
+    <Box alignContent={"center"}>
+      <ErrorOutlineIcon color="error" fontSize="large" />
+      <Typography component="h1" variant="h4">
+        Page currently unavailable
+      </Typography>
+    </Box>
+  );
+}

From cfaa9dc3bb93fcfc216aa60ce325106a7e26ec18 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 19 Nov 2025 16:17:44 +0000
Subject: [PATCH 10/19] Start using context and filling in params

---
 src/components/JungFrau/CollectionSetupJf.tsx | 110 +++++++++++++++++-
 .../jungfrau/JungfrauRotationContext.ts       |  30 +++++
 .../jungfrau/JungfrauRotationProvider.tsx     |  45 +++++++
 src/screens/CollectionPanel.tsx               |   7 ++
 vite.config.ts                                |   1 +
 5 files changed, 192 insertions(+), 1 deletion(-)
 create mode 100644 src/context/jungfrau/JungfrauRotationContext.ts
 create mode 100644 src/context/jungfrau/JungfrauRotationProvider.tsx

diff --git a/src/components/JungFrau/CollectionSetupJf.tsx b/src/components/JungFrau/CollectionSetupJf.tsx
index 1016708..b9b8712 100644
--- a/src/components/JungFrau/CollectionSetupJf.tsx
+++ b/src/components/JungFrau/CollectionSetupJf.tsx
@@ -1 +1,109 @@
-export function CollectionSetJf() {}
+import {
+  Box,
+  Grid2 as Grid,
+  Stack,
+  TextField,
+  Typography,
+  useTheme,
+} from "@mui/material";
+import { ParameterInput } from "components/ParameterInputs";
+import { JungfrauRotationContext } from "context/jungfrau/JungfrauRotationContext";
+import { useContext, useState } from "react";
+
+function fullStorageDirectory(visit: string, subDir: string): string {
+  const date = new Date();
+  const year = date.getFullYear();
+  return `/dls/i24/data/${year}/${visit}/jungfrau/${subDir}`;
+}
+
+export function CollectionSetupJf() {
+  const theme = useTheme();
+  const context = useContext(JungfrauRotationContext);
+  const [visit, setVisit] = useState<string>("cm40647-5");
+  const storageDirectory = fullStorageDirectory(visit, context.directory);
+  return (
+    <Box sx={{ flexGrow: 1 }}>
+      <Stack direction={"column"} alignItems={"center"} spacing={2}>
+        <Typography
+          variant="h2"
+          sx={{
+            color: theme.palette.primary.contrastText,
+            fontSize: 24,
+            fontWeight: "fontWeightBold",
+          }}
+        >
+          Parameters
+        </Typography>
+        <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
+          <ParameterInput
+            value={visit}
+            onSet={setVisit}
+            label="Visit"
+            tooltip="Current visit directory"
+          />
+          <ParameterInput
+            value={context.directory}
+            onSet={context.setDirectory}
+            label="Sub-directory"
+            tooltip="Location inside visit directory to save data"
+          />
+          <ParameterInput
+            value={context.fileName}
+            onSet={context.setFileName}
+            label="File Name"
+            tooltip="Name to use to save the data"
+          />
+        </Grid>
+        <TextField
+          size="small"
+          label="Storage Directory"
+          value={storageDirectory}
+          style={{ width: 570 }}
+          slotProps={{
+            input: { readOnly: true },
+          }}
+        />
+        <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
+          <ParameterInput
+            value={context.expTime}
+            onSet={context.setExpTime}
+            label="Exposure Time (s)"
+            tooltip="Exposure time for each window, in seconds"
+          />
+          <ParameterInput
+            value={context.detDist}
+            onSet={context.setDetDist}
+            label="Detector Distance (mm)"
+            tooltip="Sample detector distance, in millimeters"
+          />
+          <ParameterInput
+            value={context.shutterOpenT}
+            onSet={context.setShutterOpenT}
+            label="Shutter opening time (s)"
+            tooltip="Fast shutter opening time, in seconds"
+          />
+        </Grid>
+        <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
+          <ParameterInput
+            value={context.omegaStart}
+            onSet={context.setOmegaStart}
+            label="Omega start (deg)"
+            tooltip="Rotation start value, in deg"
+          />
+          <ParameterInput
+            value={context.omegaIncrement}
+            onSet={context.setOmegaIncrement}
+            label="Omega increment (deg)"
+            tooltip="Rotation increment step, in deg"
+          />
+          <ParameterInput
+            value={context.scanWidth}
+            onSet={context.setScanWidth}
+            label="Scan Width (deg)"
+            tooltip="Total scan width, in deg"
+          />
+        </Grid>
+      </Stack>
+    </Box>
+  );
+}
diff --git a/src/context/jungfrau/JungfrauRotationContext.ts b/src/context/jungfrau/JungfrauRotationContext.ts
new file mode 100644
index 0000000..1c42adb
--- /dev/null
+++ b/src/context/jungfrau/JungfrauRotationContext.ts
@@ -0,0 +1,30 @@
+// Note not adding visit to it as I want to get that into an overall context
+
+import { createContext } from "react";
+
+// changeble only by staff. For now just a text field
+export type JungfrauRotationContextType = {
+  directory: string;
+  fileName: string;
+  expTime: number;
+  detDist: number;
+  shutterOpenT: number;
+  transFract: number[];
+  omegaStart: number;
+  omegaIncrement: number;
+  scanWidth: number;
+  setDirectory: React.Dispatch<React.SetStateAction<string>>;
+  setFileName: React.Dispatch<React.SetStateAction<string>>;
+  setExpTime: React.Dispatch<React.SetStateAction<number>>;
+  setDetDist: React.Dispatch<React.SetStateAction<number>>;
+  setShutterOpenT: React.Dispatch<React.SetStateAction<number>>;
+  setTransFract: React.Dispatch<React.SetStateAction<number[]>>;
+  setOmegaStart: React.Dispatch<React.SetStateAction<number>>;
+  setOmegaIncrement: React.Dispatch<React.SetStateAction<number>>;
+  setScanWidth: React.Dispatch<React.SetStateAction<number>>;
+};
+
+export const JungfrauRotationContext =
+  createContext<JungfrauRotationContextType>(
+    null as unknown as JungfrauRotationContextType
+  );
diff --git a/src/context/jungfrau/JungfrauRotationProvider.tsx b/src/context/jungfrau/JungfrauRotationProvider.tsx
new file mode 100644
index 0000000..3f74edd
--- /dev/null
+++ b/src/context/jungfrau/JungfrauRotationProvider.tsx
@@ -0,0 +1,45 @@
+import { ReactNode, useState } from "react";
+import { JungfrauRotationContext } from "./JungfrauRotationContext";
+
+export const JungfrauRotationProvider = ({
+  children,
+}: {
+  children: ReactNode;
+}) => {
+  const [directory, setDirectory] = useState<string>("test");
+  const [fileName, setFileName] = useState<string>("thau");
+  const [expTime, setExpTime] = useState<number>(0.001);
+  const [detDist, setDetDist] = useState<number>(200);
+  const [shutterOpenT, setShutterOpenT] = useState<number>(0.25);
+  const [transFract, setTransFract] = useState<number[]>([0.5]);
+  const [omegaStart, setOmegaStart] = useState<number>(0);
+  const [omegaIncrement, setOmegaIncrement] = useState<number>(0.1);
+  const [scanWidth, setScanWidth] = useState<number>(360);
+
+  return (
+    <JungfrauRotationContext.Provider
+      value={{
+        directory,
+        fileName,
+        expTime,
+        detDist,
+        shutterOpenT,
+        transFract,
+        omegaStart,
+        omegaIncrement,
+        scanWidth,
+        setDirectory,
+        setFileName,
+        setExpTime,
+        setDetDist,
+        setShutterOpenT,
+        setTransFract,
+        setOmegaStart,
+        setOmegaIncrement,
+        setScanWidth,
+      }}
+    >
+      {children}
+    </JungfrauRotationContext.Provider>
+  );
+};
diff --git a/src/screens/CollectionPanel.tsx b/src/screens/CollectionPanel.tsx
index 6b94e7f..b64de7a 100644
--- a/src/screens/CollectionPanel.tsx
+++ b/src/screens/CollectionPanel.tsx
@@ -2,6 +2,8 @@ import { Box, Typography } from "@mui/material";
 import { CollectionSetupFt } from "components/FixedTarget/CollectionSetupFt";
 import { CollectionSetupEx } from "components/Extruder/CollectionSetupEx";
 import ErrorOutlineIcon from "@mui/icons-material/ErrorOutline";
+import { CollectionSetupJf } from "components/JungFrau/CollectionSetupJf";
+import { JungfrauRotationProvider } from "context/jungfrau/JungfrauRotationProvider";
 type ExptType = {
   expt: "extruder" | "fixed-target" | "jf";
 };
@@ -24,6 +26,11 @@ export function ParamsPanel(expt: ExptType) {
     case "extruder":
       return <CollectionSetupEx />;
     case "jf":
+      return (
+        <JungfrauRotationProvider>
+          <CollectionSetupJf />
+        </JungfrauRotationProvider>
+      );
     default:
       return <FallbackScreen />;
   }
diff --git a/vite.config.ts b/vite.config.ts
index d817bea..3ddbe57 100644
--- a/vite.config.ts
+++ b/vite.config.ts
@@ -16,6 +16,7 @@ export default defineConfig({
       assets: path.resolve(__dirname, "./src/assets"),
       blueapi: path.resolve(__dirname, "./src/blueapi"),
       components: path.resolve(__dirname, "./src/components"),
+      context: path.resolve(__dirname, "./src/context"),
       pv: path.resolve(__dirname, "./src/pv"),
       routes: path.resolve(__dirname, "./src/routes"),
       screens: path.resolve(__dirname, "./src/screens"),

From 236143232e70908d6407031fa04bc47958f70faf Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 19 Nov 2025 16:32:27 +0000
Subject: [PATCH 11/19] Finish filling everything in

---
 src/components/JungFrau/CollectionSetupJf.tsx | 75 ++++++++++++++++++-
 1 file changed, 74 insertions(+), 1 deletion(-)

diff --git a/src/components/JungFrau/CollectionSetupJf.tsx b/src/components/JungFrau/CollectionSetupJf.tsx
index b9b8712..02f6363 100644
--- a/src/components/JungFrau/CollectionSetupJf.tsx
+++ b/src/components/JungFrau/CollectionSetupJf.tsx
@@ -6,8 +6,10 @@ import {
   Typography,
   useTheme,
 } from "@mui/material";
+import { AbortButton, RunPlanButton } from "blueapi/BlueapiComponents";
 import { ParameterInput } from "components/ParameterInputs";
 import { JungfrauRotationContext } from "context/jungfrau/JungfrauRotationContext";
+import React from "react";
 import { useContext, useState } from "react";
 
 function fullStorageDirectory(visit: string, subDir: string): string {
@@ -16,6 +18,68 @@ function fullStorageDirectory(visit: string, subDir: string): string {
   return `/dls/i24/data/${year}/${visit}/jungfrau/${subDir}`;
 }
 
+function RunButtons({
+  visit,
+  storageDirectory,
+}: {
+  visit: string;
+  storageDirectory: string;
+}): JSX.Element {
+  const {
+    expTime,
+    detDist,
+    fileName,
+    shutterOpenT,
+    omegaStart,
+    omegaIncrement,
+    scanWidth,
+    transFract,
+  } = useContext(JungfrauRotationContext);
+  return (
+    <React.Fragment>
+      <Stack direction={"row"} spacing={4} justifyContent={"center"}>
+        <RunPlanButton
+          btnLabel="Run single rotation"
+          planName="run_single_rotation_plan"
+          planParams={{
+            exposure_time_s: expTime,
+            omega_start_deg: omegaStart,
+            omega_increment_deg: omegaIncrement,
+            total_scan_width_deg: scanWidth,
+            detector_distance_mm: detDist,
+            visit: visit,
+            file_name: fileName,
+            storage_directory: storageDirectory,
+            shutter_opening_time_s: shutterOpenT,
+            transmission: transFract[0],
+          }}
+          title="Run single rotation scan"
+          btnSize="large"
+        />
+        <RunPlanButton
+          btnLabel="Run multiple rotations"
+          planName="run_multi_rotation_plan"
+          planParams={{
+            exposure_time_s: expTime,
+            omega_start_deg: omegaStart,
+            omega_increment_deg: omegaIncrement,
+            total_scan_width_deg: scanWidth,
+            detector_distance_mm: detDist,
+            visit: visit,
+            file_name: fileName,
+            storage_directory: storageDirectory,
+            shutter_opening_time_s: shutterOpenT,
+            transmission_fractions: transFract,
+          }}
+          title="Run multiple rotation scans ar different transmissions"
+          btnSize="large"
+        />
+        <AbortButton />
+      </Stack>
+    </React.Fragment>
+  );
+}
+
 export function CollectionSetupJf() {
   const theme = useTheme();
   const context = useContext(JungfrauRotationContext);
@@ -23,7 +87,7 @@ export function CollectionSetupJf() {
   const storageDirectory = fullStorageDirectory(visit, context.directory);
   return (
     <Box sx={{ flexGrow: 1 }}>
-      <Stack direction={"column"} alignItems={"center"} spacing={2}>
+      <Stack direction={"column"} alignItems={"center"} spacing={3}>
         <Typography
           variant="h2"
           sx={{
@@ -103,6 +167,15 @@ export function CollectionSetupJf() {
             tooltip="Total scan width, in deg"
           />
         </Grid>
+        <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
+          <ParameterInput
+            value={context.transFract}
+            onSet={context.setTransFract}
+            label="Transmission (fraction)"
+            tooltip="Request transmission value(s) for collection, expressed as a fraction. If running a single rotation, just input one value, if running multiples please pass a list."
+          />
+        </Grid>
+        <RunButtons visit={visit} storageDirectory={storageDirectory} />
       </Stack>
     </Box>
   );

From 601fe681f2ab9b292c48718fce031d484a30e662 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Thu, 20 Nov 2025 09:57:30 +0000
Subject: [PATCH 12/19] Run prettier on changes

---
 src/context/jungfrau/JungfrauRotationContext.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/context/jungfrau/JungfrauRotationContext.ts b/src/context/jungfrau/JungfrauRotationContext.ts
index 1c42adb..fc8988f 100644
--- a/src/context/jungfrau/JungfrauRotationContext.ts
+++ b/src/context/jungfrau/JungfrauRotationContext.ts
@@ -26,5 +26,5 @@ export type JungfrauRotationContextType = {
 
 export const JungfrauRotationContext =
   createContext<JungfrauRotationContextType>(
-    null as unknown as JungfrauRotationContextType
+    null as unknown as JungfrauRotationContextType,
   );

From fda3f1301289049644349848cc1a6a63cb203f3b Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Thu, 20 Nov 2025 10:05:55 +0000
Subject: [PATCH 13/19] Fix the contrast text in light mode

---
 src/CustomTheme.tsx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/CustomTheme.tsx b/src/CustomTheme.tsx
index 075e73f..93a206b 100644
--- a/src/CustomTheme.tsx
+++ b/src/CustomTheme.tsx
@@ -27,11 +27,14 @@ const I24DiamondThemeOptions = mergeThemeOptions(
     colorSchemes: {
       light: {
         palette: {
+          primary: {
+            contrastText: "#000000",
+          },
           custom: {
             main: "#1976d2",
             light: "#68a0e2",
             dark: "#10569b",
-            contrastText: "#ffffff", // white
+            contrastText: "#ffffff",
           },
         },
       },

From c7af19390ec582310769af9d5b5332c626b24731 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 21 Jan 2026 16:15:13 +0000
Subject: [PATCH 14/19] Update darks collection

---
 src/components/JungFrau/CollectDarksPanel.tsx | 137 ++++++++++++++----
 src/components/JungFrau/constants.ts          |  16 ++
 2 files changed, 125 insertions(+), 28 deletions(-)
 create mode 100644 src/components/JungFrau/constants.ts

diff --git a/src/components/JungFrau/CollectDarksPanel.tsx b/src/components/JungFrau/CollectDarksPanel.tsx
index ceea22f..61b7626 100644
--- a/src/components/JungFrau/CollectDarksPanel.tsx
+++ b/src/components/JungFrau/CollectDarksPanel.tsx
@@ -2,19 +2,28 @@ import {
   Box,
   Card,
   CardContent,
+  FormControl,
+  InputLabel,
+  MenuItem,
+  Select,
   Stack,
+  Tooltip,
   Typography,
   useTheme,
 } from "@mui/material";
 import React from "react";
 import { ParameterInput } from "../ParameterInputs";
 import { RunPlanButton } from "../../blueapi/BlueapiComponents";
+import { GainModes } from "./constants";
 
 export function CollectDarksPanel() {
   const theme = useTheme();
+  const [filename, setFilename] = React.useState<string>("darks");
   const [expTime, setExpTime] = React.useState<number>(0.001);
   const [pedestalFrames, setPedestalFrames] = React.useState<number>(20);
   const [pedestalLoops, setPedestalLoops] = React.useState<number>(200);
+  const [totTriggers, setTotTriggers] = React.useState<number>(1000);
+  const [gainMode, setGainMode] = React.useState<string>(GainModes[0]);
 
   return (
     <Box sx={{ flexGrow: 1, marginLeft: 15, marginRight: 5 }}>
@@ -30,37 +39,109 @@ export function CollectDarksPanel() {
           >
             Collect darks
           </Typography>
-          <Stack spacing={1} margin={2} alignContent={"center"}>
-            <ParameterInput
-              value={expTime}
-              onSet={setExpTime}
-              label="Exposure time (s)"
-              tooltip="Set exposure time for darks collection."
+          <Stack spacing={4} margin={4} alignItems={"center"}>
+            <Stack direction={"row"} spacing={2}>
+              <ParameterInput
+                value={filename}
+                onSet={setFilename}
+                label="Filename"
+                tooltip="Set filename for darks collection."
+              />
+              <ParameterInput
+                value={expTime}
+                onSet={setExpTime}
+                label="Exposure time (s)"
+                tooltip="Set exposure time for darks collection."
+              />
+            </Stack>
+            <Typography
+              variant="body1"
+              sx={{
+                color: theme.palette.primary.contrastText,
+                fontSize: 20,
+                fontWeight: "fontWeightBold",
+              }}
+            >
+              Pedestal
+            </Typography>
+            <Stack direction={"row"} spacing={2}>
+              <ParameterInput
+                value={pedestalFrames}
+                onSet={setPedestalFrames}
+                label="Pedestal frames"
+                tooltip="Number of pedestal frames to collect."
+              />
+              <ParameterInput
+                value={pedestalLoops}
+                onSet={setPedestalLoops}
+                label="Pedestal loops"
+                tooltip="Number of pedestal loops."
+              />
+            </Stack>
+            <RunPlanButton
+              btnLabel="Pedestal darks"
+              planName="do_pedestal_darks"
+              planParams={{
+                exp_time_s: expTime,
+                pedestal_frame: pedestalFrames,
+                pedestal_loops: pedestalLoops,
+                filename: filename,
+              }}
+              title="Collect pedestal darks"
+              btnSize="large"
             />
-            <ParameterInput
-              value={pedestalFrames}
-              onSet={setPedestalFrames}
-              label="Pedestal frames"
-              tooltip="Number of pedestal frames to collect."
-            />
-            <ParameterInput
-              value={pedestalLoops}
-              onSet={setPedestalLoops}
-              label="Pedestal loops"
-              tooltip="Number of pedestal loops."
+            <Typography
+              variant="body1"
+              sx={{
+                color: theme.palette.primary.contrastText,
+                fontSize: 20,
+                fontWeight: "fontWeightBold",
+              }}
+            >
+              Standard
+            </Typography>
+            <Stack direction={"row"} spacing={2}>
+              <ParameterInput
+                value={totTriggers}
+                onSet={setTotTriggers}
+                label="Total Triggers"
+                tooltip="Total triggers for the dark scan."
+              />
+              <Tooltip
+                title="Select gain mode before starting the darks acquisition."
+                placement="right"
+              >
+                <FormControl size="small" style={{ width: 180 }}>
+                  <InputLabel id="gain-label">Gain Mode</InputLabel>
+                  <Select
+                    labelId="gain-label"
+                    id="gain"
+                    value={gainMode}
+                    label="Gain Mode"
+                    onChange={(e) => setGainMode(e.target.value)}
+                  >
+                    {GainModes.map((choice) => (
+                      <MenuItem key={choice} value={choice}>
+                        {choice}
+                      </MenuItem>
+                    ))}
+                  </Select>
+                </FormControl>
+              </Tooltip>
+            </Stack>
+            <RunPlanButton
+              btnLabel="Standard darks"
+              planName="do_non_pedestal_darks"
+              planParams={{
+                gain_mode: gainMode,
+                exp_time_s: expTime,
+                total_triggers: totTriggers,
+                filename: filename,
+              }}
+              title="Collect non pedestal darks"
+              btnSize="large"
             />
           </Stack>
-          <RunPlanButton
-            btnLabel="Pedestal darks"
-            planName="do_pedestal_darks"
-            planParams={{
-              exp_time_s: expTime,
-              pedestal_frame: pedestalFrames,
-              pedestal_loops: pedestalLoops,
-            }}
-            title="Collect pedestal darks"
-            btnSize="large"
-          />
         </CardContent>
       </Card>
     </Box>
diff --git a/src/components/JungFrau/constants.ts b/src/components/JungFrau/constants.ts
new file mode 100644
index 0000000..6a5ba9a
--- /dev/null
+++ b/src/components/JungFrau/constants.ts
@@ -0,0 +1,16 @@
+export type GainModeType =
+  | "Dynamic"
+  | "ForceSwitchG1"
+  | "ForceSwitchG2"
+  | "FixG1"
+  | "FixG2"
+  | "FixG0";
+
+export const GainModes = [
+  "Dynamic",
+  "ForceSwitchG1",
+  "ForceSwitchG2",
+  "FixG1",
+  "FixG2",
+  "FixG0",
+];

From dbff12c3f463035b78e68aa9d30f71d025e32ded Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 21 Jan 2026 16:30:31 +0000
Subject: [PATCH 15/19] Update JF context

---
 src/context/jungfrau/JungfrauRotationContext.ts   |  8 ++------
 src/context/jungfrau/JungfrauRotationProvider.tsx | 14 ++++----------
 2 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/src/context/jungfrau/JungfrauRotationContext.ts b/src/context/jungfrau/JungfrauRotationContext.ts
index fc8988f..e014211 100644
--- a/src/context/jungfrau/JungfrauRotationContext.ts
+++ b/src/context/jungfrau/JungfrauRotationContext.ts
@@ -4,24 +4,20 @@ import { createContext } from "react";
 
 // changeble only by staff. For now just a text field
 export type JungfrauRotationContextType = {
-  directory: string;
   fileName: string;
   expTime: number;
   detDist: number;
-  shutterOpenT: number;
   transFract: number[];
   omegaStart: number;
   omegaIncrement: number;
-  scanWidth: number;
-  setDirectory: React.Dispatch<React.SetStateAction<string>>;
+  sampleId: number;
   setFileName: React.Dispatch<React.SetStateAction<string>>;
   setExpTime: React.Dispatch<React.SetStateAction<number>>;
   setDetDist: React.Dispatch<React.SetStateAction<number>>;
-  setShutterOpenT: React.Dispatch<React.SetStateAction<number>>;
   setTransFract: React.Dispatch<React.SetStateAction<number[]>>;
   setOmegaStart: React.Dispatch<React.SetStateAction<number>>;
   setOmegaIncrement: React.Dispatch<React.SetStateAction<number>>;
-  setScanWidth: React.Dispatch<React.SetStateAction<number>>;
+  setSampleId: React.Dispatch<React.SetStateAction<number>>;
 };
 
 export const JungfrauRotationContext =
diff --git a/src/context/jungfrau/JungfrauRotationProvider.tsx b/src/context/jungfrau/JungfrauRotationProvider.tsx
index 3f74edd..f825624 100644
--- a/src/context/jungfrau/JungfrauRotationProvider.tsx
+++ b/src/context/jungfrau/JungfrauRotationProvider.tsx
@@ -6,37 +6,31 @@ export const JungfrauRotationProvider = ({
 }: {
   children: ReactNode;
 }) => {
-  const [directory, setDirectory] = useState<string>("test");
-  const [fileName, setFileName] = useState<string>("thau");
+  const [fileName, setFileName] = useState<string>("jf_rotation");
   const [expTime, setExpTime] = useState<number>(0.001);
   const [detDist, setDetDist] = useState<number>(200);
-  const [shutterOpenT, setShutterOpenT] = useState<number>(0.25);
   const [transFract, setTransFract] = useState<number[]>([0.5]);
   const [omegaStart, setOmegaStart] = useState<number>(0);
   const [omegaIncrement, setOmegaIncrement] = useState<number>(0.1);
-  const [scanWidth, setScanWidth] = useState<number>(360);
+  const [sampleId, setSampleId] = useState<number>(0);
 
   return (
     <JungfrauRotationContext.Provider
       value={{
-        directory,
         fileName,
         expTime,
         detDist,
-        shutterOpenT,
         transFract,
         omegaStart,
         omegaIncrement,
-        scanWidth,
-        setDirectory,
+        sampleId,
         setFileName,
         setExpTime,
         setDetDist,
-        setShutterOpenT,
         setTransFract,
         setOmegaStart,
         setOmegaIncrement,
-        setScanWidth,
+        setSampleId,
       }}
     >
       {children}

From 565310c1b79e8085e52571623ce0fac47f07e429 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 21 Jan 2026 16:50:56 +0000
Subject: [PATCH 16/19] Add a visit provider and update the JF rotation
 parameters

---
 src/components/JungFrau/CollectionSetupJf.tsx | 98 +++++--------------
 src/context/VisitContext.ts                   | 10 ++
 src/context/VisitProvider.tsx                 | 14 +++
 .../jungfrau/JungfrauRotationContext.ts       |  3 -
 src/screens/CollectionPanel.tsx               |  9 +-
 5 files changed, 56 insertions(+), 78 deletions(-)
 create mode 100644 src/context/VisitContext.ts
 create mode 100644 src/context/VisitProvider.tsx

diff --git a/src/components/JungFrau/CollectionSetupJf.tsx b/src/components/JungFrau/CollectionSetupJf.tsx
index 02f6363..7c9b4f5 100644
--- a/src/components/JungFrau/CollectionSetupJf.tsx
+++ b/src/components/JungFrau/CollectionSetupJf.tsx
@@ -9,69 +9,43 @@ import {
 import { AbortButton, RunPlanButton } from "blueapi/BlueapiComponents";
 import { ParameterInput } from "components/ParameterInputs";
 import { JungfrauRotationContext } from "context/jungfrau/JungfrauRotationContext";
+import { VisitContext } from "context/VisitContext";
 import React from "react";
-import { useContext, useState } from "react";
+import { useContext } from "react";
 
-function fullStorageDirectory(visit: string, subDir: string): string {
+function fullStorageDirectory(visit: string): string {
   const date = new Date();
   const year = date.getFullYear();
-  return `/dls/i24/data/${year}/${visit}/jungfrau/${subDir}`;
+  return `/dls/i24/data/${year}/${visit}/jungfrau/`;
 }
 
-function RunButtons({
-  visit,
-  storageDirectory,
-}: {
-  visit: string;
-  storageDirectory: string;
-}): JSX.Element {
+function RunButtons(): JSX.Element {
   const {
     expTime,
     detDist,
     fileName,
-    shutterOpenT,
     omegaStart,
     omegaIncrement,
-    scanWidth,
     transFract,
+    sampleId,
   } = useContext(JungfrauRotationContext);
+  console.log(transFract);
   return (
     <React.Fragment>
       <Stack direction={"row"} spacing={4} justifyContent={"center"}>
         <RunPlanButton
-          btnLabel="Run single rotation"
-          planName="run_single_rotation_plan"
+          btnLabel="Run rotation scan"
+          planName="gui_run_jf_rotation_scan"
           planParams={{
             exposure_time_s: expTime,
             omega_start_deg: omegaStart,
             omega_increment_deg: omegaIncrement,
-            total_scan_width_deg: scanWidth,
             detector_distance_mm: detDist,
-            visit: visit,
-            file_name: fileName,
-            storage_directory: storageDirectory,
-            shutter_opening_time_s: shutterOpenT,
-            transmission: transFract[0],
+            filename: fileName,
+            transmissions: transFract,
+            sample_id: sampleId,
           }}
-          title="Run single rotation scan"
-          btnSize="large"
-        />
-        <RunPlanButton
-          btnLabel="Run multiple rotations"
-          planName="run_multi_rotation_plan"
-          planParams={{
-            exposure_time_s: expTime,
-            omega_start_deg: omegaStart,
-            omega_increment_deg: omegaIncrement,
-            total_scan_width_deg: scanWidth,
-            detector_distance_mm: detDist,
-            visit: visit,
-            file_name: fileName,
-            storage_directory: storageDirectory,
-            shutter_opening_time_s: shutterOpenT,
-            transmission_fractions: transFract,
-          }}
-          title="Run multiple rotation scans ar different transmissions"
+          title="Run the jungfrau rotation scan plan"
           btnSize="large"
         />
         <AbortButton />
@@ -83,8 +57,8 @@ function RunButtons({
 export function CollectionSetupJf() {
   const theme = useTheme();
   const context = useContext(JungfrauRotationContext);
-  const [visit, setVisit] = useState<string>("cm40647-5");
-  const storageDirectory = fullStorageDirectory(visit, context.directory);
+  const { visit } = useContext(VisitContext);
+  const storageDirectory = fullStorageDirectory(visit);
   return (
     <Box sx={{ flexGrow: 1 }}>
       <Stack direction={"column"} alignItems={"center"} spacing={3}>
@@ -98,26 +72,6 @@ export function CollectionSetupJf() {
         >
           Parameters
         </Typography>
-        <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
-          <ParameterInput
-            value={visit}
-            onSet={setVisit}
-            label="Visit"
-            tooltip="Current visit directory"
-          />
-          <ParameterInput
-            value={context.directory}
-            onSet={context.setDirectory}
-            label="Sub-directory"
-            tooltip="Location inside visit directory to save data"
-          />
-          <ParameterInput
-            value={context.fileName}
-            onSet={context.setFileName}
-            label="File Name"
-            tooltip="Name to use to save the data"
-          />
-        </Grid>
         <TextField
           size="small"
           label="Storage Directory"
@@ -128,6 +82,12 @@ export function CollectionSetupJf() {
           }}
         />
         <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
+          <ParameterInput
+            value={context.fileName}
+            onSet={context.setFileName}
+            label="File Name"
+            tooltip="Name to use to save the data"
+          />
           <ParameterInput
             value={context.expTime}
             onSet={context.setExpTime}
@@ -140,12 +100,6 @@ export function CollectionSetupJf() {
             label="Detector Distance (mm)"
             tooltip="Sample detector distance, in millimeters"
           />
-          <ParameterInput
-            value={context.shutterOpenT}
-            onSet={context.setShutterOpenT}
-            label="Shutter opening time (s)"
-            tooltip="Fast shutter opening time, in seconds"
-          />
         </Grid>
         <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
           <ParameterInput
@@ -161,10 +115,10 @@ export function CollectionSetupJf() {
             tooltip="Rotation increment step, in deg"
           />
           <ParameterInput
-            value={context.scanWidth}
-            onSet={context.setScanWidth}
-            label="Scan Width (deg)"
-            tooltip="Total scan width, in deg"
+            value={context.sampleId}
+            onSet={context.setSampleId}
+            label="Sample ID"
+            tooltip="Sample id"
           />
         </Grid>
         <Grid container spacing={2} marginTop={3} justifyContent={"center"}>
@@ -175,7 +129,7 @@ export function CollectionSetupJf() {
             tooltip="Request transmission value(s) for collection, expressed as a fraction. If running a single rotation, just input one value, if running multiples please pass a list."
           />
         </Grid>
-        <RunButtons visit={visit} storageDirectory={storageDirectory} />
+        <RunButtons />
       </Stack>
     </Box>
   );
diff --git a/src/context/VisitContext.ts b/src/context/VisitContext.ts
new file mode 100644
index 0000000..dde7f83
--- /dev/null
+++ b/src/context/VisitContext.ts
@@ -0,0 +1,10 @@
+import React, { createContext } from "react";
+
+export type VisitContextType = {
+  visit: string;
+  setVisit: React.Dispatch<React.SetStateAction<string>>;
+};
+
+export const VisitContext = createContext<VisitContextType>(
+  null as unknown as VisitContextType,
+);
diff --git a/src/context/VisitProvider.tsx b/src/context/VisitProvider.tsx
new file mode 100644
index 0000000..ee1fbe5
--- /dev/null
+++ b/src/context/VisitProvider.tsx
@@ -0,0 +1,14 @@
+import { ReactNode, useState } from "react";
+import { VisitContext } from "./VisitContext";
+
+const defaultVisit = "cm44177-1"; // Until we can grab it after authentication
+
+export const VisitProvider = ({ children }: { children: ReactNode }) => {
+  const [visit, setVisit] = useState<string>(defaultVisit);
+
+  return (
+    <VisitContext.Provider value={{ visit, setVisit }}>
+      {children}
+    </VisitContext.Provider>
+  );
+};
diff --git a/src/context/jungfrau/JungfrauRotationContext.ts b/src/context/jungfrau/JungfrauRotationContext.ts
index e014211..857642e 100644
--- a/src/context/jungfrau/JungfrauRotationContext.ts
+++ b/src/context/jungfrau/JungfrauRotationContext.ts
@@ -1,8 +1,5 @@
-// Note not adding visit to it as I want to get that into an overall context
-
 import { createContext } from "react";
 
-// changeble only by staff. For now just a text field
 export type JungfrauRotationContextType = {
   fileName: string;
   expTime: number;
diff --git a/src/screens/CollectionPanel.tsx b/src/screens/CollectionPanel.tsx
index b64de7a..91b2227 100644
--- a/src/screens/CollectionPanel.tsx
+++ b/src/screens/CollectionPanel.tsx
@@ -4,6 +4,7 @@ import { CollectionSetupEx } from "components/Extruder/CollectionSetupEx";
 import ErrorOutlineIcon from "@mui/icons-material/ErrorOutline";
 import { CollectionSetupJf } from "components/JungFrau/CollectionSetupJf";
 import { JungfrauRotationProvider } from "context/jungfrau/JungfrauRotationProvider";
+import { VisitProvider } from "context/VisitProvider";
 type ExptType = {
   expt: "extruder" | "fixed-target" | "jf";
 };
@@ -27,9 +28,11 @@ export function ParamsPanel(expt: ExptType) {
       return <CollectionSetupEx />;
     case "jf":
       return (
-        <JungfrauRotationProvider>
-          <CollectionSetupJf />
-        </JungfrauRotationProvider>
+        <VisitProvider>
+          <JungfrauRotationProvider>
+            <CollectionSetupJf />
+          </JungfrauRotationProvider>
+        </VisitProvider>
       );
     default:
       return <FallbackScreen />;

From ac18c1fc2f31e597933d89e588ee70838d95b5f6 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 21 Jan 2026 16:51:38 +0000
Subject: [PATCH 17/19] Save everything

---
 src/components/JungFrau/CollectDarksPanel.tsx | 2 +-
 src/components/JungFrau/CollectionSetupJf.tsx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/components/JungFrau/CollectDarksPanel.tsx b/src/components/JungFrau/CollectDarksPanel.tsx
index 61b7626..ed3f1f3 100644
--- a/src/components/JungFrau/CollectDarksPanel.tsx
+++ b/src/components/JungFrau/CollectDarksPanel.tsx
@@ -37,7 +37,7 @@ export function CollectDarksPanel() {
               fontWeight: "fontWeightBold",
             }}
           >
-            Collect darks
+            Collect Darks
           </Typography>
           <Stack spacing={4} margin={4} alignItems={"center"}>
             <Stack direction={"row"} spacing={2}>
diff --git a/src/components/JungFrau/CollectionSetupJf.tsx b/src/components/JungFrau/CollectionSetupJf.tsx
index 7c9b4f5..dbdaeed 100644
--- a/src/components/JungFrau/CollectionSetupJf.tsx
+++ b/src/components/JungFrau/CollectionSetupJf.tsx
@@ -70,7 +70,7 @@ export function CollectionSetupJf() {
             fontWeight: "fontWeightBold",
           }}
         >
-          Parameters
+          Collection Parameters
         </Typography>
         <TextField
           size="small"

From 4cb6289ed9901b5461a6855c67e8c6c1a8574dec Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Wed, 21 Jan 2026 16:52:16 +0000
Subject: [PATCH 18/19] Increase spacing a bit

---
 src/components/JungFrau/CollectionSetupJf.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/JungFrau/CollectionSetupJf.tsx b/src/components/JungFrau/CollectionSetupJf.tsx
index dbdaeed..2d7c3f0 100644
--- a/src/components/JungFrau/CollectionSetupJf.tsx
+++ b/src/components/JungFrau/CollectionSetupJf.tsx
@@ -61,7 +61,7 @@ export function CollectionSetupJf() {
   const storageDirectory = fullStorageDirectory(visit);
   return (
     <Box sx={{ flexGrow: 1 }}>
-      <Stack direction={"column"} alignItems={"center"} spacing={3}>
+      <Stack direction={"column"} alignItems={"center"} spacing={5}>
         <Typography
           variant="h2"
           sx={{

From 94784b8b622e37f9bc781cc3888456cd9a74d619 Mon Sep 17 00:00:00 2001
From: Noemi Frisina <noemi.frisina@diamond.ac.uk>
Date: Fri, 30 Jan 2026 11:09:02 +0000
Subject: [PATCH 19/19] Add warning to tooltip

---
 src/components/JungFrau/CollectDarksPanel.tsx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/components/JungFrau/CollectDarksPanel.tsx b/src/components/JungFrau/CollectDarksPanel.tsx
index ed3f1f3..724da16 100644
--- a/src/components/JungFrau/CollectDarksPanel.tsx
+++ b/src/components/JungFrau/CollectDarksPanel.tsx
@@ -108,7 +108,8 @@ export function CollectDarksPanel() {
                 tooltip="Total triggers for the dark scan."
               />
               <Tooltip
-                title="Select gain mode before starting the darks acquisition."
+                title="Select gain mode before starting the darks acquisition.
+                WARNING. FixGO may damage the detector - use with caution."
                 placement="right"
               >
                 <FormControl size="small" style={{ width: 180 }}>