feat: add Bruker NanoScope AFM support

Cargo.toml

@@ -43,7 +43,7 @@ repository = "https://github.com/nmrtist/plotx"
 colorous = "1"
 num-complex = "0.4"
 rustfft = "6.4"
-serde = { version = "1.0", features = ["derive"] }
+serde = { version = "1.0", features = ["derive", "rc"] }
 serde_json = "1.0"
 semver = "1"
 sha2 = "0.10"

crates/app/src/ui/file_dialogs.rs

@@ -320,9 +320,10 @@ pub(crate) fn load_and_note(app: &mut PlotxApp, path: &std::path::Path) {
 pub(crate) fn open_file(app: &mut PlotxApp) {
     if let Some(paths) = rfd::FileDialog::new()
         .add_filter(
-            "All supported data (*.abf, *.jdf, fid, ser, *.zip)",
-            &["abf", "jdf", "fid", "ser", "zip"],
+            "All supported data (*.spm, *.pfc, *.abf, *.jdf, fid, ser, *.zip)",
+            &["spm", "pfc", "abf", "jdf", "fid", "ser", "zip"],
         )
+        .add_filter("Bruker NanoScope AFM (*.spm, *.pfc)", &["spm", "pfc"])
         .add_filter("Axon Binary Format 2 (*.abf)", &["abf"])
         .add_filter("JEOL Delta (*.jdf)", &["jdf"])
         .add_filter("Bruker TopSpin (fid, ser)", &["fid", "ser"])
@@ -362,7 +363,7 @@ pub(crate) fn save_project_as(app: &mut PlotxApp, include_view_snapshots: bool)
 
 pub(crate) fn open_folder(app: &mut PlotxApp) {
     if let Some(path) = rfd::FileDialog::new()
-        .set_title("Open a data folder (Bruker acquisition or recursive ABF2 import)")
+        .set_title("Open a data folder (Bruker acquisition or recursive AFM/ABF2 import)")
         .pick_folder()
     {
         open_folder_path(app, &path);
@@ -375,13 +376,23 @@ pub(crate) fn open_folder(app: &mut PlotxApp) {
 /// any file of the batch loaded, not just the last one.
 fn open_folder_path(app: &mut PlotxApp, path: &std::path::Path) {
     let before = app.doc.datasets.len();
-    let mut abf_files = Vec::new();
-    discovery::collect_abf_files(path, &mut abf_files);
-    if abf_files.is_empty() {
+    let mut data_files = Vec::new();
+    discovery::collect_data_files(path, &mut data_files);
+    if data_files.is_empty() {
         app.load_from(path);
     } else {
-        abf_files.sort();
-        for file in abf_files {
+        data_files.sort();
+        let companion_paths: std::collections::HashSet<std::path::PathBuf> = data_files
+            .iter()
+            .filter(|file| {
+                file.extension()
+                    .is_some_and(|ext| ext.eq_ignore_ascii_case("pfc"))
+            })
+            .filter_map(|file| plotx_io::load_path(file).ok())
+            .flat_map(|loaded| loaded.provenance.companion_paths)
+            .collect();
+        data_files.retain(|file| !companion_paths.contains(file));
+        for file in data_files {
             app.load_from(&file);
         }
     }

crates/app/src/ui/file_dialogs/discovery.rs

@@ -1,6 +1,6 @@
 use std::path::{Path, PathBuf};
 
-pub(super) fn collect_abf_files(folder: &Path, output: &mut Vec<PathBuf>) {
+pub(super) fn collect_data_files(folder: &Path, output: &mut Vec<PathBuf>) {
     let Ok(entries) = std::fs::read_dir(folder) else {
         return;
     };
@@ -10,13 +10,18 @@ pub(super) fn collect_abf_files(folder: &Path, output: &mut Vec<PathBuf>) {
             continue;
         };
         if kind.is_dir() && !kind.is_symlink() {
-            collect_abf_files(&path, output);
-        } else if kind.is_file()
-            && path
+            collect_data_files(&path, output);
+        } else if kind.is_file() {
+            let extension = path
                 .extension()
-                .is_some_and(|extension| extension.eq_ignore_ascii_case("abf"))
-        {
-            output.push(path);
+                .and_then(|value| value.to_str())
+                .unwrap_or("");
+            if ["abf", "spm", "pfc"]
+                .iter()
+                .any(|supported| extension.eq_ignore_ascii_case(supported))
+            {
+                output.push(path);
+            }
         }
     }
 }

crates/app/src/ui/tools/processing/editors.rs

@@ -492,6 +492,7 @@ fn raw_point_count(dataset: &Dataset) -> usize {
             .and_then(|s| s.channels.first())
             .map(Vec::len)
             .unwrap_or(0),
+        Dataset::Afm(_) => 0,
     }
 }
 

crates/app/src/ui/tools/processing/mod.rs

@@ -56,6 +56,7 @@ fn badge(dataset: &Dataset) -> (String, bool) {
         Dataset::Nmr2D(n) => n.preset.label().to_owned(),
         Dataset::Table(_) => String::new(),
         Dataset::Electrophysiology(_) => "Patch clamp".to_owned(),
+        Dataset::Afm(_) => "AFM".to_owned(),
     };
     (name, default)
 }
@@ -496,6 +497,7 @@ fn set_group_delay(app: &mut PlotxApp, di: usize, on: bool) {
         }
         Dataset::Table(_) => {}
         Dataset::Electrophysiology(_) => {}
+        Dataset::Afm(_) => {}
     }
 }
 
@@ -505,6 +507,7 @@ fn group_delay(dataset: &Dataset) -> bool {
         Dataset::Nmr2D(n) => n.group_delay_correct,
         Dataset::Table(_) => true,
         Dataset::Electrophysiology(_) => true,
+        Dataset::Afm(_) => true,
     }
 }
 

crates/core/src/actions/app_impl/mod.rs

@@ -414,18 +414,19 @@ impl PlotxApp {
                     if *canvas_index != self.doc.canvases.len() {
                         return;
                     }
-                    let mut canvas = CanvasDocument::new(canvas_name.clone(), *size_mm);
-                    canvas.resource_id.clone_from(canvas_resource_id);
-                    canvas.board_pos = crate::state::next_page_board_pos(self);
-                    let page = canvas.size_pt();
-                    let id = canvas.allocate_object_id();
-                    let object = self.build_plot_object(
+                    let mut canvas = crate::workflow::build_default_canvas_for_dataset(
+                        &self.doc.datasets[*dataset_index],
                         *dataset_index,
-                        ObjectFrame::new(0.0, 0.0, page[0], page[1]),
-                        id,
-                        "Plot 1".to_owned(),
+                        canvas_name.clone(),
+                        *size_mm,
                     );
-                    canvas.objects.push(object);
+                    canvas.resource_id.clone_from(canvas_resource_id);
+                    canvas.board_pos = crate::state::next_page_board_pos(self);
+                    for object in &mut canvas.objects {
+                        if let Some(plot) = object.plot_mut() {
+                            plot.figure.typography = self.doc.style_library.figure_typography;
+                        }
+                    }
                     self.doc.canvases.push(canvas);
                     self.session.active_canvas = Some(*canvas_index);
                 }

crates/core/src/actions/mod.rs

@@ -36,6 +36,7 @@ pub enum DatasetProcessingState {
     /// through their own actions.
     Table,
     Electrophysiology(crate::state::ElectrophysiologyProcessing),
+    Afm,
 }
 
 #[derive(Clone)]

crates/core/src/actions/processing_state.rs

@@ -13,6 +13,7 @@ impl DatasetProcessingState {
             },
             Dataset::Table(_) => Self::Table,
             Dataset::Electrophysiology(d) => Self::Electrophysiology(d.processing),
+            Dataset::Afm(_) => Self::Afm,
         }
     }
 
@@ -66,6 +67,7 @@ impl DatasetProcessingState {
                 data.processing = *processing;
                 Ok(ProcessingRebuild::Rebuilt)
             }
+            (Dataset::Afm(_), Self::Afm) => Ok(ProcessingRebuild::Unchanged),
             (dataset, state) => Err(ProcessingStateError {
                 dataset_kind: dataset.kind_label(),
                 state_kind: state.kind_label(),
@@ -79,6 +81,7 @@ impl DatasetProcessingState {
             Self::Nmr2D { .. } => "NMR 2D",
             Self::Table => "Data Table",
             Self::Electrophysiology(_) => "Electrophysiology",
+            Self::Afm => "AFM",
         }
     }
 }

crates/core/src/automation/resources.rs

@@ -109,6 +109,30 @@ impl<'a> ProjectResourceProvider<'a> {
                 vec!["s".to_owned()],
                 Vec::new(),
             ),
+            Dataset::Afm(afm) => {
+                let dimensions = afm.data.forces.as_ref().map_or_else(
+                    || {
+                        afm.data
+                            .images
+                            .first()
+                            .map_or_else(Vec::new, |image| vec![image.height, image.width])
+                    },
+                    |forces| {
+                        vec![
+                            forces.grid_height,
+                            forces.grid_width,
+                            forces.samples_per_curve,
+                        ]
+                    },
+                );
+                let units = afm
+                    .data
+                    .images
+                    .iter()
+                    .map(|image| image.scale.unit.clone())
+                    .collect();
+                (dimensions, units, Vec::new())
+            }
         };
         ResourceDescriptor {
             resource: top_ref(&id, KIND_DATASET),
@@ -538,6 +562,29 @@ fn preview_dataset(
             serde_json::json!({"summary": dataset.summary()}),
             recording.data.sweeps.len(),
         ),
+        Dataset::Afm(afm) => {
+            let shape = afm.data.forces.as_ref().map_or_else(
+                || {
+                    afm.data
+                        .images
+                        .first()
+                        .map_or_else(Vec::new, |image| vec![image.height, image.width])
+                },
+                |forces| {
+                    vec![
+                        forces.grid_height,
+                        forces.grid_width,
+                        forces.samples_per_curve,
+                    ]
+                },
+            );
+            let total = shape.iter().copied().fold(1usize, usize::saturating_mul);
+            (
+                shape,
+                serde_json::json!({"summary": dataset.summary()}),
+                total,
+            )
+        }
     };
     let returned = total.min(limit);
     Ok(DataPreview {

crates/core/src/data_export.rs

@@ -198,6 +198,7 @@ fn processed_data_available(dataset: &Dataset) -> bool {
                     })
         }
         Dataset::Table(_) => false,
+        Dataset::Afm(_) => false,
     }
 }
 
@@ -450,6 +451,7 @@ fn capture_processed(dataset: &Dataset) -> Result<SnapshotData, DataExportError>
             })
         }
         Dataset::Table(_) => Err(DataExportError::ContentUnavailable),
+        Dataset::Afm(_) => Err(DataExportError::ContentUnavailable),
     }
 }