Merge pull request #10 from LaboratoryOpticsBiosciences/update

Multiple improvements

src/napari_swc_editor/__init__.py

@@ -2,8 +2,8 @@
     from ._version import version as __version__
 except ImportError:
     __version__ = "unknown"
-from ._reader import napari_get_reader
-from ._sample_data import make_sample_data
+from ._reader import napari_get_reader, read_swc
+from ._sample_data import make_empty_sample, make_sample_data
 from ._widget import (
     ExampleQWidget,
     ImageThreshold,
@@ -14,9 +14,11 @@
 
 __all__ = (
     "napari_get_reader",
+    "read_swc",
     "write_single_image",
     "write_multiple",
     "make_sample_data",
+    "make_empty_sample",
     "ExampleQWidget",
     "ImageThreshold",
     "threshold_autogenerate_widget",

src/napari_swc_editor/_reader.py

@@ -8,8 +8,7 @@
 
 import napari
 
-from .bindings import bind_layers_with_events
-from .swc_io import parse_data_from_swc_file, structure_id_to_symbol
+from .bindings import add_napari_layers_from_swc_content
 
 
 def napari_get_reader(path):
@@ -66,29 +65,8 @@ def reader_function(path):
         with open(_path) as f:
             file_content = f.read()
 
-        points, radius, lines, structure = parse_data_from_swc_file(
-            file_content
-        )
+        point_layer, shape_layer = add_napari_layers_from_swc_content(file_content, viewer)
+    return (point_layer, shape_layer)
 
-        structure_symbol = structure_id_to_symbol(structure)
-
-        shape_layer = viewer.add_shapes(
-            lines, shape_type="line", edge_width=radius
-        )
-
-        add_kwargs_points = {
-            "n_dimensional": True,
-            "size": radius,
-            "blending": "additive",
-            "symbol": structure_symbol,
-            "metadata": {
-                "raw_swc": file_content,
-                "shape_layer": shape_layer,
-            },
-        }
-
-        point_layer = viewer.add_points(points, **add_kwargs_points)
-
-        bind_layers_with_events(point_layer, shape_layer)
-
-    return [point_layer, shape_layer]
+def read_swc(path):
+    return reader_function(path)

src/napari_swc_editor/_sample_data.py

@@ -9,6 +9,7 @@
 
 from __future__ import annotations
 
+import tempfile
 from urllib.request import urlretrieve
 
 from ._reader import reader_function
@@ -20,3 +21,14 @@ def make_sample_data():
     urlretrieve(url, "204-2-6nj.CNG.swc")
     result = reader_function("204-2-6nj.CNG.swc")
     return result
+
+
+def make_empty_sample():
+    content = "# SWC created using napari-swc-editor\n"
+    # create temp file
+    with tempfile.NamedTemporaryFile(
+        mode="w", suffix=".swc", delete=False
+    ) as f:
+        f.write(content)
+        result = reader_function(f.name)
+        return result

src/napari_swc_editor/bindings.py

@@ -1,17 +1,74 @@
+import napari
+
 from .swc_io import (
     add_edge,
     add_points,
+    create_line_data_from_swc_data,
     get_treenode_id_from_index,
     move_points,
+    parse_data_from_swc_file,
     parse_swc_content,
     remove_edge,
     remove_points,
     sort_edge_indices,
+    structure_id_to_symbol,
     symbol_to_structure_id,
     update_point_properties,
 )
 
 
+def add_napari_layers_from_swc_content(
+    file_content: str, viewer: napari.Viewer
+):
+    """Create layers from a swc file
+
+    Parameters
+    ----------
+    file_content : swc_content
+        Content of the swc file
+        Must have the following columns:
+            - treenode_id
+            - structure_id
+            - x
+            - y
+            - z
+            - r
+            - parent_treenode_id
+    viewer : napari.Viewer
+
+    Returns
+    -------
+    layers : list of tuples
+        List of layers to be added to the napari viewer
+    """
+
+    points, radius, lines, structure = parse_data_from_swc_file(file_content)
+
+    structure_symbol = structure_id_to_symbol(structure)
+
+    shape_layer = viewer.add_shapes(
+        lines, shape_type="line", edge_width=radius
+    )
+
+    add_kwargs_points = {
+        "n_dimensional": True,
+        "size": radius,
+        "blending": "additive",
+        "symbol": structure_symbol,
+        "metadata": {
+            "raw_swc": file_content,
+            "shape_layer": shape_layer,
+            "Ctrl_activated": False,
+        },
+    }
+
+    point_layer = viewer.add_points(points, **add_kwargs_points)
+
+    bind_layers_with_events(point_layer, shape_layer)
+
+    return [point_layer, shape_layer]
+
+
 def bind_layers_with_events(point_layer, shape_layer):
     """Bind the events of the point layer with the swc content
 
@@ -52,12 +109,33 @@ def event_add_points(event):
         new_pos = event.source.data[list(event.data_indices)]
         new_radius = event.source.size[list(event.data_indices)]
         new_structure = event.source.symbol[list(event.data_indices)]
+        new_parents = -1
 
-        new_swc = add_points(raw_swc, new_pos, new_radius, new_structure, df)
+        # if shift is activated, the add the new edges from previous selected point
+        if (
+            event.source.metadata["Ctrl_activated"]
+            and len(event.source.selected_data) > 0
+        ):
+
+            previous_selected = list(event.source.selected_data)[-1]
+            new_parents = get_treenode_id_from_index([previous_selected], df)[
+                0
+            ]
+
+        new_swc, df = add_points(
+            raw_swc, new_pos, new_radius, new_structure, new_parents, df
+        )
 
         event.source.metadata["raw_swc"] = new_swc
         event.source.metadata["swc_data"] = df
 
+        if new_parents != -1:
+            new_lines, new_r = create_line_data_from_swc_data(df)
+            event.source.metadata["shape_layer"].data = []
+            event.source.metadata["shape_layer"].add_lines(
+                new_lines, edge_width=new_r
+            )
+
 
 def event_move_points(event):
 
@@ -147,7 +225,7 @@ def event_add_edge_wo_sort(layer):
     event_add_edge(layer, sort=False)
 
 
-def event_add_edge(layer, sort=True):
+def event_add_edge(layer, indices=None, sort=True):
     """Add an edge between two selected points
 
     Parameters
@@ -162,7 +240,8 @@ def event_add_edge(layer, sort=True):
     raw_swc = layer.metadata["raw_swc"]
     df = parse_swc_content(raw_swc)
 
-    indices = get_treenode_id_from_index(list(layer.selected_data), df)
+    if indices is None:
+        indices = get_treenode_id_from_index(list(layer.selected_data), df)
 
     if sort:
         indices = sort_edge_indices(raw_swc, indices, df)

src/napari_swc_editor/napari.yaml

@@ -15,6 +15,9 @@ contributions:
     - id: napari-swc-editor.make_sample_data
       python_name: napari_swc_editor._sample_data:make_sample_data
       title: Load sample data from napari-swc-editor
+    - id: napari-swc-editor.make_empty_sample
+      python_name: napari_swc_editor._sample_data:make_empty_sample
+      title: Create empty swc from napari-swc-editor
     - id: napari-swc-editor.make_container_widget
       python_name: napari_swc_editor:ImageThreshold
       title: Make threshold Container widget
@@ -43,8 +46,11 @@ contributions:
       filename_extensions: ['.swc']
   sample_data:
     - command: napari-swc-editor.make_sample_data
-      display_name: napari-swc-editor
+      display_name: sample-napari-swc-editor
       key: unique_id.1
+    - command: napari-swc-editor.make_empty_sample
+      display_name: empty-napari-swc-editor
+      key: unique_id.2
   widgets:
     - command: napari-swc-editor.make_container_widget
       display_name: Container Threshold

src/napari_swc_editor/swc_io.py

@@ -147,7 +147,7 @@ def create_point_data_from_swc_data(df):
     Returns
     -------
     points : np.ndarray
-        All positions of the points
+        All positions of the points. The coordinates are in the napari order (z, y, x)
     radius : np.ndarray
         Radius of the points
     structure : np.ndarray
@@ -159,7 +159,7 @@ def create_point_data_from_swc_data(df):
     structure = df["structure_id"].values
 
     # for each node create a point
-    points = df[["x", "y", "z"]].values
+    points = df[["z", "y", "x"]].values
 
     return points, radius, structure
 
@@ -186,7 +186,7 @@ def create_line_data_from_swc_data(df):
     """
 
     # for each nodes create a point
-    points = df[["x", "y", "z"]].values
+    points = df[["z", "y", "x"]].values
 
     # for each edge create a line
     edges = df["parent_treenode_id"].values
@@ -196,7 +196,7 @@ def create_line_data_from_swc_data(df):
     edges = edges[edges != -1]
 
     # for each id in edges, get the corresponding node according to its index
-    prev_point = df.loc[edges, ["x", "y", "z"]].values
+    prev_point = df.loc[edges, ["z", "y", "x"]].values
 
     lines = np.array([points, prev_point])
     lines = np.moveaxis(lines, 0, 1)
@@ -245,7 +245,12 @@ def write_swc_content(df, swc_content=None):
 
 
 def add_points(
-    swc_content, new_positions, new_radius, new_structure=0, swc_df=None
+    swc_content,
+    new_positions,
+    new_radius,
+    structure_id=0,
+    parent_treenode_id=-1,
+    swc_df=None,
 ):
     """Add a point to the swc content
 
@@ -254,12 +259,15 @@ def add_points(
     swc_content : swc_content
         Content of the swc file
     new_positions : np.ndarray
-        New positions to be added
+        New positions to be added in napari order (z, y, x)
     new_radius : np.ndarray
         Radius of the new positions
-    new_structure : np.ndarray
+    structure_id : np.ndarray
         Structure of the new positions, see SWC_SYMBOL
         Default is 0 (undefined)
+    parent_treenode_id : np.ndarray
+        Parent of the new positions
+        Default is -1 (no parent)
     swc_df : pd.DataFrame
         Dataframe extracted from the swc file. Should have the following columns:
         - x: x coordinate of the node
@@ -280,10 +288,16 @@ def add_points(
     if swc_df is None:
         swc_df = parse_swc_content(swc_content)
 
-    new_points = pd.DataFrame(new_positions, columns=["x", "y", "z"])
+    # change napari position order to swc order
+    new_points = pd.DataFrame(new_positions, columns=["z", "y", "x"])
     new_points["r"] = new_radius
-    new_points["structure_id"] = new_structure
-    new_points["parent_treenode_id"] = -1
+    new_points["structure_id"] = structure_id
+    new_points["parent_treenode_id"] = parent_treenode_id
+
+    # order columns to respect swc format
+    new_points = new_points[
+        ["structure_id", "x", "y", "z", "r", "parent_treenode_id"]
+    ]
 
     if swc_df.size > 0:
         previous_max = swc_df.index.max()
@@ -294,11 +308,11 @@ def add_points(
 
         new_df = pd.concat([swc_df, new_points])
     else:
-        new_df = new_points
+        new_df = new_points.copy()
 
     new_df.index.name = "treenode_id"
     new_swc_content = write_swc_content(new_df, swc_content)
-    return new_swc_content
+    return new_swc_content, new_df
 
 
 def move_points(swc_content, index, new_positions, swc_df=None):
@@ -311,7 +325,7 @@ def move_points(swc_content, index, new_positions, swc_df=None):
     index : int
         Index of the point to be moved
     new_positions : np.ndarray
-        New positions of the point
+        New positions of the point in napari order (z, y, x)
     swc_df : pd.DataFrame
         Dataframe extracted from the swc file. Should have the following columns:
         - x: x coordinate of the node
@@ -333,7 +347,7 @@ def move_points(swc_content, index, new_positions, swc_df=None):
     if swc_df is None:
         swc_df = parse_swc_content(swc_content)
 
-    swc_df.loc[index, ["x", "y", "z"]] = new_positions
+    swc_df.loc[index, ["z", "y", "x"]] = new_positions
 
     new_swc_content = write_swc_content(swc_df, swc_content)
     moved_lines, _ = create_line_data_from_swc_data(swc_df)
@@ -593,7 +607,6 @@ def update_point_properties(swc_content, indices, new_properties, swc_df=None):
         swc_df = parse_swc_content(swc_content)
 
     for key, value in new_properties.items():
-        print(key, value)
         swc_df.loc[indices, key] = value
 
     new_lines, new_r = create_line_data_from_swc_data(swc_df)