feat(nmr): support 3D spectra in the workspace

Cargo.toml

@@ -40,7 +40,7 @@ publish = false
 repository = "https://github.com/nmrtist/plotium"
 
 [workspace.dependencies]
-nmr = "=0.1.2"
+nmr = "=0.1.3"
 colorous = "1"
 num-complex = "0.4"
 rustfft = "6"
@@ -65,7 +65,7 @@ substrait = { version = "0.63", default-features = false, features = ["serde"] }
 prost = "0.14"
 pbjson-types = "0.8"
 chrono-tz = "0.10"
-calamine = { version = "0.37", default-features = false, features = ["dates"] }
+calamine = { version = "0.38", default-features = false, features = ["dates"] }
 rust_xlsxwriter = { version = "0.100", default-features = false, features = ["constant_memory"] }
 tokio = { version = "1", features = ["rt"] }
 egui = "0.34"

crates/agent/src/capabilities.rs

@@ -4,12 +4,13 @@ use plotium_core::automation::{
 };
 use serde_json::{Value, json};
 
-pub(crate) const EDIT_OPERATIONS: [&str; 26] = [
+pub(crate) const EDIT_OPERATIONS: [&str; 27] = [
     "analysis.diffusion.plot",
     "plot.field.create",
     "analysis.dosy.build",
     "analysis.regions.extract",
     "analysis.diffusion.fit",
+    "nmr.volume.edit",
     "processing.edit",
     "processing.apply_scheme",
     "diffusion.set_input",
@@ -35,7 +36,11 @@ pub(crate) const EDIT_OPERATIONS: [&str; 26] = [
 
 /// One line per editable operation, so a caller can map a task to an operation
 /// before fetching its schema.
-const PURPOSES: [(&str, &str); 29] = [
+const PURPOSES: [(&str, &str); 30] = [
+    (
+        "nmr.volume.edit",
+        "Select a 3D spectrum plane and optionally adjust per-axis phase",
+    ),
     (
         "analysis.diffusion.plot",
         "Plot a diffusion fit with residuals on a new canvas",

crates/agent/src/native_import_tests.rs

@@ -332,3 +332,26 @@ fn native_reservations_are_shared_and_released_on_every_plan_consumption() {
     );
     assert_eq!(s.remaining_import_bytes(), NATIVE_IMPORT_BYTES);
 }
+
+#[test]
+fn mcp_can_import_and_select_a_three_dimensional_plane() {
+    let mut app = PlotiumApp::new_with_settings(Default::default());
+    let mut s = session();
+    let p = plan(&mut s, &mut app, &[fixture("bruker-3d-qf")]);
+    execute(&mut s, &mut app, &p).unwrap();
+    let deadline = Instant::now() + Duration::from_secs(10);
+    while app.compute_busy() && Instant::now() < deadline {
+        app.poll_compute();
+        std::thread::sleep(Duration::from_millis(2));
+    }
+    app.poll_compute();
+    assert!(!app.compute_busy());
+    let id = app.doc.datasets[0].resource_id().to_string();
+    let args = json!({"tool_id":"nmr.volume.edit","parameters":{"fixed_axis":2,"index":1},"ids":[id],"expected_revision":app.doc.automation_revision,"expected_project_context":app.session.project_context});
+    let p = s.call(&mut app, "plotium_plan", args).unwrap();
+    let result = execute(&mut s, &mut app, &p).unwrap();
+    assert_eq!(result["value"]["fixed_axis"], 2);
+    assert_eq!(result["value"]["index"], 1);
+    let n = app.doc.datasets[0].as_nmr2d().unwrap();
+    assert_eq!(n.volume.as_ref().unwrap().processed.shape(), [5, 3, 4]);
+}

crates/agent/src/session.rs

@@ -420,6 +420,7 @@ impl Session {
             if matches!(
                 args.tool_id.as_str(),
                 PROCESSING_EDIT
+                    | "nmr.volume.edit"
                     | DIFFUSION_SET_INPUT
                     | DOSY_BUILD
                     | REGIONS_EXTRACT

crates/app/src/ui/canvas/cursors.rs

@@ -383,6 +383,36 @@ fn inspect_text(app: &PlotiumApp, dataset: usize, point: CursorPoint) -> String
             )
         }
         Dataset::Nmr2D(n) => {
+            if let Some(volume) = &n.volume {
+                let remaining: Vec<_> = (0..3).filter(|axis| *axis != volume.fixed_axis).collect();
+                let mut indices = volume.anchor;
+                for (axis, coordinate) in [
+                    (remaining[0], point.y.unwrap_or_default()),
+                    (remaining[1], point.x),
+                ] {
+                    match volume.processed.nearest(axis, coordinate) {
+                        Ok(index) => indices[axis] = index,
+                        Err(error) => return format!("Coordinate unavailable: {error}"),
+                    }
+                }
+                let mut values = Vec::new();
+                for (axis, index) in indices.into_iter().enumerate() {
+                    let value = match volume.processed.axis_coordinate(axis, index) {
+                        Ok(value) => value,
+                        Err(error) => return format!("Coordinate unavailable: {error}"),
+                    };
+                    let nucleus = volume.source.axes()[axis]
+                        .nucleus
+                        .as_deref()
+                        .unwrap_or("unknown");
+                    values.push(format!("{nucleus}(F{}) {value:.4} ppm", axis + 1));
+                }
+                return format!(
+                    "{} · sampled I {}",
+                    values.join(" · "),
+                    fmt_number(point.intensity)
+                );
+            }
             let Processed2D::Ft(s) = &n.processed else {
                 return String::new();
             };

crates/app/src/ui/canvas/mod.rs

@@ -135,6 +135,7 @@ pub(crate) enum CanvasInteractionClearScope {
 }
 
 pub fn render_central(app: &mut PlotiumApp, ui: &mut Ui) {
+    super::nmr_volume::poll_phase(app, ui.ctx());
     let Some(ci) = app.session.active_canvas else {
         if app.doc.canvases.is_empty() && !board_frames(app).is_empty() {
             board::render_sheets_only(app, ui);
@@ -144,6 +145,7 @@ pub fn render_central(app: &mut PlotiumApp, ui: &mut Ui) {
         return;
     };
     canvas_breadcrumb(app, ci, ui);
+    super::nmr_volume::navigation(app, ui);
     let avail = ui.available_rect_before_wrap();
     let (resp, painter) = ui.allocate_painter(avail.size(), Sense::click_and_drag());
     let geometry = super::workspace_geometry(app, resp.rect, ui.ctx());

crates/app/src/ui/command_exec.rs

@@ -60,6 +60,11 @@ fn execute_inner(
         }
         CommandId::OpenFile => super::file_dialogs::open_file(app),
         CommandId::OpenFolder => super::file_dialogs::open_folder(app),
+        CommandId::CancelNmrVolumePhase => super::nmr_volume::cancel_phase(ctx),
+        CommandId::ApplyNmrVolumePhase => super::nmr_volume::apply_phase(app, ctx),
+        CommandId::PreviousNmrPlane | CommandId::NextNmrPlane => {
+            super::nmr_volume::step(app, id == CommandId::NextNmrPlane);
+        }
         CommandId::ImportNmrSampling => super::file_dialogs::nmr_sampling::open(app),
         CommandId::AgentConnections => {
             app.open_settings();
@@ -99,6 +104,7 @@ fn execute_inner(
         }
         CommandId::ImportTiffPages => super::file_dialogs::image_import::import_tiff_pages(app),
         CommandId::PasteImage => super::file_dialogs::image_import::paste_clipboard_image(app),
+        CommandId::CancelDataImport => app.cancel_data_imports(),
         CommandId::CancelImageImport => super::file_dialogs::image_import::cancel_all(app),
         CommandId::ReplaceImage => super::file_dialogs::image_import::replace_selected_image(app),
         CommandId::PasteTable => {

crates/app/src/ui/commands.rs

@@ -1,12 +1,11 @@
+pub use super::command_exec::{execute, execute_without_clipboard};
 use plotium_core::actions::ZOrder;
 use plotium_core::export::ExportFormat;
 use plotium_core::layout::{Align, Distribute, GutterPreset, SpacingMode};
 use plotium_core::properties::PropertyStep;
 #[cfg(test)]
 use plotium_core::state::WorkflowTab;
 use plotium_core::state::{Dataset, PlotiumApp, Tool, ToolGroup};
-
-pub use super::command_exec::{execute, execute_without_clipboard};
 mod craft;
 mod identity;
 use identity::command_identity;
@@ -23,7 +22,6 @@ pub(crate) use ribbon::stack_row;
 pub use ribbon::{Applicability, RibbonPlacement};
 use roster::command_ids;
 pub(crate) const MANUAL_URL: &str = "https://plotium.nmrtist.space/";
-/// The public source repository, linked from About.
 pub(crate) const REPOSITORY_URL: &str = "https://github.com/nmrtist/plotium";
 #[derive(Clone, Copy, Debug, PartialEq, Eq)]
 pub enum CommandId {
@@ -35,6 +33,10 @@ pub enum CommandId {
     OpenFile,
     OpenFolder,
     ImportNmrSampling,
+    ApplyNmrVolumePhase,
+    CancelNmrVolumePhase,
+    PreviousNmrPlane,
+    NextNmrPlane,
     RunBatchWorkflow,
     AgentConnections,
     RunScientificScript,
@@ -50,6 +52,7 @@ pub enum CommandId {
     ImportImageWithoutMetadata,
     ImportTiffPages,
     PasteImage,
+    CancelDataImport,
     CancelImageImport,
     ReplaceImage,
     PasteTable,
@@ -163,7 +166,6 @@ pub enum CommandId {
     CycleCursor,
     Tool(Tool),
 }
-
 /// Architectural ownership for commands that expose or consume results. New
 /// commands must choose a class instead of bypassing the automation registry
 /// with an arbitrary Action.
@@ -173,7 +175,6 @@ pub enum CommandExecutionClass {
     ToolEditor,
     ToolBacked,
 }
-
 pub struct CommandDescriptor {
     pub id: CommandId,
     pub execution_class: CommandExecutionClass,
@@ -188,7 +189,6 @@ pub struct CommandDescriptor {
     pub shortcut: Option<String>,
     pub ribbon: Option<RibbonPlacement>,
 }
-
 pub fn catalog(app: &PlotiumApp) -> Vec<CommandDescriptor> {
     command_ids(app.session.recent_files.len())
         .into_iter()
@@ -206,7 +206,6 @@ pub fn catalog(app: &PlotiumApp) -> Vec<CommandDescriptor> {
         })
         .collect()
 }
-
 pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
     let has_canvas = app.session.active_canvas.is_some();
     let selected = app.session.ui.selection.objects().len();
@@ -238,9 +237,7 @@ pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
     let has_selectable_analysis_trace = || has_trace() && !is_time_nmr();
     let has_generic_peak_fit_trace = || has_trace() && (is_frequency_nmr() || is_table());
     let range = || active_dataset.and_then(|di| app.analysis_range_for(di));
-
     let is_series = || dataset().is_some_and(Dataset::supports_region_analysis);
-
     let (label, icon, checked) = command_identity(app, id);
     // The gate decides the enabled state and the disabled tooltip together, so a
     // command can never be blocked by one requirement while explaining another.
@@ -296,6 +293,11 @@ pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
             app.session.ui.table_import_preview.is_none(),
             "Finish or cancel the current table import preview before importing another table.",
         ),
+        CommandId::CancelNmrVolumePhase => requires(app.session.ui.nmr_volume_phase_busy, "Start phase processing before cancelling it."),
+        CommandId::ApplyNmrVolumePhase => super::nmr_volume::phase_gate(app),
+        CommandId::PreviousNmrPlane | CommandId::NextNmrPlane => {
+            super::nmr_volume::step_gate(app, id == CommandId::NextNmrPlane)
+        }
         CommandId::ImportNmrSampling => requires(
             app.session.ui.nmr_import.is_none(),
             "Finish or cancel the current NMR import before importing another acquisition.",
@@ -305,6 +307,7 @@ pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
         | CommandId::ImportImageWithoutMetadata
         | CommandId::ImportTiffPages
         | CommandId::PasteImage => Ok(()),
+        CommandId::CancelDataImport => requires(app.session.data_imports.is_pending(), "Start a data import before cancelling it."),
         CommandId::CancelImageImport => requires(
             super::file_dialogs::image_import::has_active_jobs(),
             "Start an image import before cancelling it.",
@@ -330,7 +333,7 @@ pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
             dataset().is_some_and(|dataset| {
                 !plotium_core::data_export::DataExportAvailability::for_dataset(dataset).is_empty()
             }),
-            "Select a dataset with processed data or analysis results to export.",
+            "Select a supported dataset for numerical export; save 3D data as a project or export its figure.",
         ),
         CommandId::Export(_) => requires(has_canvas, "Open a canvas before exporting a figure."),
         CommandId::CopyFigure => requires(
@@ -709,9 +712,7 @@ pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
                 .is_some_and(|dataset| dataset.supports_symmetry_review()),
             "Select a homonuclear COSY, TOCSY, or NOESY / ROESY contour spectrum.",
         ),
-        // On-plot phasing needs a spectrum with a phase step to act on. The
-        // gate is the Phase settings tile's, so the tool and the settings it
-        // drives never disagree about when phasing is possible.
+        // Share the Phase settings gate so its tool stays consistent.
         CommandId::Tool(Tool::ManualPhase) => requires(
             super::properties::discovery::group_applies(
                 app,
@@ -726,6 +727,7 @@ pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
         CommandId::Tool(_) => requires(has_canvas, "Open a canvas before using this tool."),
         _ => Ok(()),
     };
+    let gate = super::nmr_volume::editing_gate(app, id).and(gate);
     // The palette cannot be opened over a modal or active gesture. Those states
     // hide every surface that could display its disabled tooltip, so this is the
     // one intentional disabled-without-reason path.
@@ -773,11 +775,9 @@ pub fn describe(app: &PlotiumApp, id: CommandId) -> CommandDescriptor {
         ribbon,
     }
 }
-
 #[cfg(test)]
 #[path = "commands_alignment_tests.rs"]
 mod alignment_tests;
-
 #[cfg(test)]
 #[path = "commands_craft_tests.rs"]
 mod craft_tests;

crates/app/src/ui/commands/identity.rs

@@ -55,6 +55,10 @@ pub(super) fn command_identity(
         CommandId::CloseWindow => plain("Close Window", Some(icon::X)),
         CommandId::OpenFile => plain("Open File…", Some(icon::FILE)),
         CommandId::OpenFolder => plain("Open Folder…", Some(icon::FOLDER)),
+        CommandId::CancelNmrVolumePhase => plain("Cancel 3D NMR Phase", Some(icon::X)),
+        CommandId::ApplyNmrVolumePhase => plain("Apply 3D NMR Phase", Some(icon::PLAY)),
+        CommandId::PreviousNmrPlane => plain("Previous NMR Plane", Some(icon::CARET_LEFT)),
+        CommandId::NextNmrPlane => plain("Next NMR Plane", Some(icon::CARET_RIGHT)),
         CommandId::ImportNmrSampling => plain("Import NMR with Sampling Table…", Some(icon::FILE)),
         CommandId::AgentConnections => plain("AI connections (MCP)…", None),
         CommandId::RunBatchWorkflow => plain("Automation…", Some(icon::PLAY)),
@@ -88,6 +92,7 @@ pub(super) fn command_identity(
         }
         CommandId::ImportTiffPages => plain("Add All TIFF Pages…", Some(icon::IMAGES_SQUARE)),
         CommandId::PasteImage => plain("Paste Image", Some(icon::CLIPBOARD_TEXT)),
+        CommandId::CancelDataImport => plain("Cancel Data Import", Some(icon::X)),
         CommandId::CancelImageImport => plain("Cancel Image Import", Some(icon::X)),
         CommandId::ReplaceImage => plain("Replace Image…", Some(icon::ARROWS_CLOCKWISE)),
         CommandId::PasteTable => plain("Paste Table from Clipboard", Some(icon::CLIPBOARD_TEXT)),
@@ -455,6 +460,10 @@ fn simple_stable_id(id: CommandId) -> &'static str {
         CommandId::OpenFile => "file.open_file",
         CommandId::OpenFolder => "file.open_folder",
         CommandId::ImportNmrSampling => "file.import_nmr_sampling",
+        CommandId::CancelNmrVolumePhase => "nmr.phase.cancel",
+        CommandId::ApplyNmrVolumePhase => "nmr.phase.apply",
+        CommandId::PreviousNmrPlane => "nmr.plane.previous",
+        CommandId::NextNmrPlane => "nmr.plane.next",
         CommandId::RunBatchWorkflow => "tools.automation",
         CommandId::AgentConnections => "file.agent_connections",
         CommandId::RunScientificScript => "tools.run_scientific_script",
@@ -465,6 +474,7 @@ fn simple_stable_id(id: CommandId) -> &'static str {
         CommandId::ImportImageWithoutMetadata => "figure.import_image_without_metadata",
         CommandId::ImportTiffPages => "figure.import_tiff_pages",
         CommandId::PasteImage => "figure.paste_image",
+        CommandId::CancelDataImport => "file.cancel_data_import",
         CommandId::CancelImageImport => "figure.cancel_image_import",
         CommandId::ReplaceImage => "figure.replace_image",
         CommandId::PasteTable => "file.paste_table",

crates/app/src/ui/commands/roster.rs

@@ -20,6 +20,10 @@ pub(super) fn command_ids(recent_files: usize) -> Vec<CommandId> {
         CommandId::OpenFile,
         CommandId::OpenFolder,
         CommandId::ImportNmrSampling,
+        CommandId::ApplyNmrVolumePhase,
+        CommandId::CancelNmrVolumePhase,
+        CommandId::PreviousNmrPlane,
+        CommandId::NextNmrPlane,
         CommandId::RunBatchWorkflow,
         CommandId::AgentConnections,
         CommandId::RunScientificScript,
@@ -32,6 +36,7 @@ pub(super) fn command_ids(recent_files: usize) -> Vec<CommandId> {
         CommandId::ImportImageWithoutMetadata,
         CommandId::ImportTiffPages,
         CommandId::PasteImage,
+        CommandId::CancelDataImport,
         CommandId::CancelImageImport,
         CommandId::ReplaceImage,
         CommandId::PasteTable,

crates/app/src/ui/commands_tests.rs

@@ -469,7 +469,9 @@ fn data_export_requires_exportable_current_data() {
     assert!(!command.enabled);
     assert_eq!(
         command.disabled_reason,
-        Some("Select a dataset with processed data or analysis results to export.")
+        Some(
+            "Select a supported dataset for numerical export; save 3D data as a project or export its figure."
+        )
     );
 
     let table = app_with_table(1);