add loading of an example dataset with image and seed layers

.copier-answers.yml

@@ -4,7 +4,7 @@ _src_path: https://github.com/napari/napari-plugin-template
 display_name: Cotcotcot
 email: romain.guiet@epfl.ch
 full_name: Romain Guiet
-github_repository_url: provide later
+github_repository_url: https://github.com/BIOP/napari-cotcotcot
 github_username_or_organization: romainGuiet
 include_reader_plugin: true
 include_sample_data_plugin: true

pyproject.toml

@@ -35,8 +35,8 @@ dependencies = [
     "pandas",
     "tqdm",
     "tifffile",
-    "napari",  # Add this since your plugin is for napari
-    "torch",  # See note below about PyTorch
+    "napari",  
+    "torch", 
 ]
 
 [project.optional-dependencies]
@@ -56,7 +56,7 @@ dev = [
 [project.entry-points."napari.manifest"]
 napari-cotcotcot = "napari_cotcotcot:napari.yaml"
 
-# to enable command line interface
+# to enable command line interface, starting rom terminal with naparicot
 [project.scripts]
 naparicot = "napari_cotcotcot:main"
 
@@ -72,6 +72,8 @@ where = ["src"]
 
 [tool.setuptools.package-data]
 "*" = ["*.yaml"]
+# to enable package data inclusion
+"napari_cotcotcot" = ["/data/Gallus_gallus_domesticus/chicken-run.gif" , "/data/Gallus_gallus_domesticus/seed_Chicken1.csv" ]
 
 [tool.setuptools_scm]
 write_to = "src/napari_cotcotcot/_version.py"

src/napari_cotcotcot/_sample_data.py

@@ -1,22 +1,85 @@
-"""
-This module is an example of a barebones sample data provider for napari.
 
-It implements the "sample data" specification.
-see: https://napari.org/stable/plugins/building_a_plugin/guides.html#sample-data
+from pathlib import Path
+from typing import List
 
-Replace code below according to your needs.
-"""
+import numpy as np
+import pandas as pd
+from skimage.io import imread
+from napari.types import LayerData
 
-from __future__ import annotations
+def _load_seed_from_csv_standalone(csv_path: str) -> np.ndarray:
+    """
+    Load seed points from a CSV file.
 
-import numpy
+    Parameters
+    ----------
+    csv_path : str
+        Path to the CSV file containing seed point coordinates.
 
+    Returns
+    -------
+    np.ndarray
+        Array of shape (n_points, 3) containing seed point coordinates.
 
-def make_sample_data():
-    """Generates an image"""
-    # Return list of tuples
-    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
-    # Check the documentation for more information about the
-    # add_image_kwargs
-    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
-    return [(numpy.random.rand(512, 512), {})]
+    Raises
+    ------
+    ValueError
+        If the CSV format is invalid (missing required columns).
+    """
+    df = pd.read_csv(csv_path)
+
+    required_cols = ["axis-0", "axis-1", "axis-2"]
+    if not all(col in df.columns for col in required_cols):
+        if all(col in df.columns for col in ["t", "y", "x"]):
+            df = df.rename(columns={"t": "axis-0", "y": "axis-1", "x": "axis-2"})
+        else:
+            raise ValueError("CSV must contain columns: axis-0, axis-1, axis-2 (or t, y, x)")
+
+    return df[["axis-0", "axis-1", "axis-2"]].values
+
+def load_sample_data() -> List[LayerData]:
+    """
+    Loads sample data for demonstration in napari.
+
+    This function loads:
+        - A GIF image ("chicken-run.gif") from a remote URL:
+          https://raw.githubusercontent.com/BIOP/napari-cotcotcot/refs/heads/main/src/napari_cotcotcot/data/Gallus_gallus_domesticus/chicken-run.gif
+        - Seed points from a local CSV file ("seed_Chicken1.csv") if available at:
+          <package_dir>/data/Gallus_gallus_domesticus/seed_Chicken1.csv
+
+    Returns
+    -------
+    List[LayerData]
+        A list of tuples (data, metadata, layer_type) suitable for napari, where:
+            - The first tuple contains the image data, metadata with name "cotcotcot", and layer_type "image".
+            - The second tuple (if CSV is found and loaded) contains the seed points, metadata with name "seed_Chicken1", and layer_type "points".
+
+    Data Sources
+    -----------
+    - GIF image: downloaded from the above URL.
+    - Seed points: loaded from a local CSV file.
+
+    Exceptions
+    ----------
+    - If the CSV file is missing, empty, or malformed, an error is printed and only the image is returned.
+    - If the GIF image cannot be downloaded or read, an exception may be raised by skimage.io.imread.
+    """
+    URL = "https://raw.githubusercontent.com/BIOP/napari-cotcotcot/refs/heads/main/src/napari_cotcotcot/data/Gallus_gallus_domesticus/chicken-run.gif"
+    print(f"Downloading sample data from {URL}...")
+    try:
+        gif_data = imread(URL)
+        print("Downloading completed!")
+        sample_datasets = [(gif_data, {"name": "cotcotcot"}, "image")]
+    except (IOError, ValueError, Exception) as e:
+        print(f"Error downloading or reading image from {URL}: {e}")
+        sample_datasets = []
+    # Load CSV
+    csv_data_path = Path(__file__).parent / "data" / "Gallus_gallus_domesticus" / "seed_Chicken1.csv"
+    if csv_data_path.exists():
+        try:
+            csv_data = _load_seed_from_csv_standalone(str(csv_data_path))
+            sample_datasets.append((csv_data, {"name": "seed_Chicken1"}, "points"))
+        except (FileNotFoundError, ValueError, pd.errors.EmptyDataError, pd.errors.ParserError) as e:
+            print(f"Error loading CSV data: {e}")
+
+    return sample_datasets

src/napari_cotcotcot/_widget.py

@@ -9,7 +9,7 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-
+import napari
 import numpy as np
 import pandas as pd
 from magicgui.widgets import (
@@ -292,6 +292,24 @@ def __init__(
         # Auto-initialize if we have an image
         if self._get_image_layers():
             self.image_selector.value = self._get_image_layers()[0]
+
+        # Auto-initialize seed manager if seed layers are already present
+        self._check_and_auto_initialize()
+
+    def _check_and_auto_initialize(self):
+        """Check for existing seed layers and auto-initialize if found."""
+        if self.seed_manager is None:
+            seed_like_layers = [
+                layer.name for layer in self.viewer.layers 
+                if isinstance(layer, napari.layers.Points) and 
+                (layer.name.startswith("seed_") or "seed" in layer.name.lower())
+            ]
+
+            if seed_like_layers:
+                print(f"Auto-initializing seed manager on startup due to detected seed layers: {seed_like_layers}")
+                self._ensure_seed_manager_initialized()
+                self._refresh_seed_list()
+                self._check_enable_tracking()
 
     def _pick_custom_color(self):
         """Open color picker dialog for custom color selection."""
@@ -389,6 +407,20 @@ def _disconnect_seed_layer_events(self, layer_name):
     def _on_layer_change(self, event):
         """Handle layer changes in viewer."""
         self.image_selector.choices = self._get_image_layers()
+
+        # Auto-initialize seed manager if we detect seed layers but manager is None
+        if self.seed_manager is None:
+            # Check if there are any layers that look like seed layers
+            seed_like_layers = [
+                layer.name for layer in self.viewer.layers 
+                if isinstance(layer, napari.layers.Points) and 
+                (layer.name.startswith("seed_") or "seed" in layer.name.lower())
+            ]
+
+            if seed_like_layers:
+                print(f"Auto-initializing seed manager due to detected seed layers: {seed_like_layers}")
+                self._ensure_seed_manager_initialized()
+
         if self.seed_manager:
             self._refresh_seed_list()
             # Check if tracking buttons should be enabled

src/napari_cotcotcot/data/Gallus_gallus_domesticus/seed_Chicken1.csv

@@ -0,0 +1,5 @@
+index,axis-0,axis-1,axis-2
+0.0,0.0,92.83061471930142,59.76071319110557
+1.0,23.0,163.09295583101897,78.5809831317442
+2.0,10.0,93.00985538540276,73.9207258131099
+3.0,18.0,128.6787479395655,85.57136910969572

src/napari_cotcotcot/napari.yaml

@@ -6,31 +6,15 @@ visibility: public
 # categories: []
 contributions:
   commands:
-    - id: napari-cotcotcot.get_reader
-      python_name: napari_cotcotcot._reader:napari_get_reader
-      title: Open data with CoTracker
-    - id: napari-cotcotcot.write_image
-      python_name: napari_cotcotcot._writer:napari_write_image
-      title: Save image data with CoTracker
-    - id: napari-cotcotcot.make_sample_data
-      python_name: napari_cotcotcot._sample_data:make_sample_data
+    - id: napari-cotcotcot.load_sample_data
+      python_name: napari_cotcotcot._sample_data:load_sample_data
       title: Load sample data from CoTracker
     - id: napari-cotcotcot.cotracker_widget
       python_name: napari_cotcotcot._widget:cotracker_widget
       title: CoTracker Control Panel
 
-  readers:
-    - command: napari-cotcotcot.get_reader
-      accepts_directories: false
-      filename_patterns: ['*.tif', '*.tiff']
-
-  writers:
-    - command: napari-cotcotcot.write_image
-      layer_types: ['image']
-      filename_extensions: ['.tif', '.tiff']
-
   sample_data:
-    - command: napari-cotcotcot.make_sample_data
+    - command: napari-cotcotcot.load_sample_data
       display_name: CoTracker sample
       key: unique_id.1