Added napari integration to docs

colabseg/napari_integration.py

@@ -1,3 +1,5 @@
+from typing import List, Dict
+
 import threading
 import numpy as np
 import napari
@@ -11,7 +13,28 @@
 
 
 class ColabSegNapariWidget(widgets.Container):
-    def __init__(self, viewer, colabsegdata_instance: type) -> "ColabSegNapariWidget":
+    """
+    A widget for napari viewer to manage and visualize data from ColabSegData instances.
+
+    Parameters
+    ----------
+    viewer : napari.Viewer
+        The napari viewer instance to which this widget will be added.
+    colabsegdata_instance : :py:class:`colabseg.new_gui_functions.ColabSegData`, optional
+        An instance of ColabSegData containing the data to be visualized.
+
+    Attributes
+    ----------
+    viewer : napari.Viewer
+        The napari viewer instance.
+    pixel_size : float
+        Pixel size of the data, obtained from colabsegdata_instance.
+    dropdown : magicgui.widgets.ComboBox
+        Dropdown menu for selecting clusters to highlight.
+    _previous_selection : str or None
+        The previously selected cluster name.
+    """
+    def __init__(self, viewer, colabsegdata_instance: "ColabSegData") -> "ColabSegNapariWidget":
         super().__init__(layout="vertical")
 
         self.viewer = viewer
@@ -31,12 +54,32 @@ def __init__(self, viewer, colabsegdata_instance: type) -> "ColabSegNapariWidget
 
         self.append(self.dropdown)
 
-    def _get_point_layers(self) -> None:
+    def _get_point_layers(self) -> List[str]:
+        """
+        Returns a sorted list of point layer names from the napari viewer.
+
+        Returns
+        -------
+        list
+            A sorted list of strings of point layers present in the viewer.
+        """
         return sorted(
             [layer.name for layer in self.viewer.layers if isinstance(layer, Points)]
         )
 
-    def load_data(self, data: type) -> None:
+    def load_data(self, data: "ColabSegData") -> None:
+        """
+        Loads and visualizes data from a given ColabSegData instance. Points are
+        divided by the pixel_size attribute of the ColabSegData instance. Currently,
+        the attributes cluster_list_tv, cluster_list_fits, protein_positions_list
+        from the ColabSegData instance are visualized as point clouds.
+
+        Parameters
+        ----------
+        data : type
+            An instance of ColabSegData containing the data to be visualized.
+        """
+
         for index, cluster in enumerate(data.cluster_list_tv):
             scaled_points = np.divide(cluster, self.pixel_size)
             self.viewer.add_points(
@@ -71,6 +114,14 @@ def load_data(self, data: type) -> None:
             )
 
     def _on_cluster_selected(self, event) -> None:
+        """
+        Callback function for dropdown selection changes. Highlights the selected cluster.
+
+        Parameters
+        ----------
+        event
+            The event triggered on changing the dropdown selection.
+        """
         if self.dropdown.value is None:
             for point_cloud in self._get_point_layers():
                 selected_layer = self.viewer.layers[point_cloud]
@@ -86,7 +137,18 @@ def _on_cluster_selected(self, event) -> None:
 
         self._previous_selection = self.dropdown.value
 
-    def export_data(self) -> {str : [np.ndarray]}:
+    def export_data(self) -> Dict[str, List[np.ndarray]]:
+        """
+        Exports the point cloud data currently visualized in the napari viewer.
+        The order of the output lists correspond to the input order. Deleted
+        point clouds will be represented as empty lists.
+
+        Returns
+        -------
+        dict of {str : list of numpy.ndarray}
+            A dictionary where keys are point cloud class names and values
+            are lists of numpy arrays representing point cloud coordinates.
+        """
         ret = {}
 
         point_clouds = self._get_point_layers()
@@ -105,7 +167,24 @@ def export_data(self) -> {str : [np.ndarray]}:
 
 
 class NapariManager:
-    def __init__(self, display_data=None, colabsegdata_instance=None, **kwargs):
+    """
+    Manages the napari viewer and associated widgets for data visualization and interaction.
+
+    Parameters
+    ----------
+    display_data : array-like, optional
+        Data to be displayed in the napari viewer, typically image data.
+    colabsegdata_instance : :py:class:`colabseg.new_gui_functions.ColabSegData`, optional
+        An instance of ColabSegData for data visualization.
+
+    Attributes
+    ----------
+    viewer : napari.Viewer
+        The napari viewer instance.
+    colabseg_widget : :py:class:`ColabSegNapariWidget`
+        The widget for managing and visualizing ColabSegData instances.
+    """
+    def __init__(self, display_data : np.ndarray=None, colabsegdata_instance : "ColabSegData" = None, **kwargs):
         self.viewer = napari.Viewer()
 
         if display_data is not None:
@@ -122,10 +201,28 @@ def __init__(self, display_data=None, colabsegdata_instance=None, **kwargs):
         )
 
     def run(self):
+        """
+        Launches the napari viewer.
+        """
         napari.run()
 
     def close(self):
+        """
+        Closes the napari viewer.
+        """
         self.viewer.close()
 
     def export_data(self):
+        """
+        Exports the point cloud data from the colabseg_widget.
+
+        Returns
+        -------
+        dict
+            The point cloud data exported from the colabseg_widget.
+
+        See Also
+        --------
+        :py:meth:`ColabSegNapariWidget.export_data`
+        """
         return self.colabseg_widget.export_data()

colabseg/segmentation_gui.py

@@ -287,6 +287,9 @@ def open_napari_wrapper(change):
         self.all_widgets["load_raw_image_button"].on_click(open_napari_wrapper)
 
         def sync_napari_wrapper(change):
+            if self.napari_manager is None:
+                return None
+
             data = self.napari_manager.export_data()
 
             mapping = {
@@ -303,6 +306,7 @@ def sync_napari_wrapper(change):
 
             if self.napari_manager is not None:
                 self.napari_manager.close()
+                self.napari_manager = None
             self.reload_gui()
 
         self.all_widgets["save_raw_image_button"] = widgets.Button(

doc/_templates/autosummary/README.txt

@@ -0,0 +1,33 @@
+class.rst is largely taken from the pandas python library (https://github.com/pandas-dev/pandas/blob/main/doc/source/_static/), which operates under the following license:
+
+BSD 3-Clause License
+
+Copyright (c) 2008-2011, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team
+All rights reserved.
+
+Copyright (c) 2011-2023, Open source contributors.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

doc/_templates/autosummary/class.rst

@@ -1,36 +1,34 @@
-{% extends "!autosummary/class.rst" %}
+{{ objname | escape | underline}}
 
-{{ objname | escape }}
-{{ underline }}
+.. currentmodule:: {{ module }}
 
-.. .. currentmodule:: {{ module }}
+.. autoclass:: {{ objname }}
 
-.. .. autoclass:: {{ objname }}
+   {% block methods %}
 
-{% block methods %}
-{% if methods %}
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
 
    .. autosummary::
       :toctree:
-      {% for item in all_methods %}
-      {%- if not item.startswith('_') or item in ['__call__'] %}
-      {{ name }}.{{ item }}
-      {%- endif -%}
+      {% for item in attributes %}
+         {% if item in members and not item.startswith('_') %}
+           {{ name }}.{{ item }}
+         {% endif %}
       {%- endfor %}
+   {% endif %}
+   {% endblock %}
 
-{% endif %}
-{% endblock %}
-
-{% block attributes %}
-{% if attributes %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
 
    .. autosummary::
       :toctree:
-      {% for item in all_attributes %}
-      {%- if not item.startswith('_') %}
-      {{ name }}.{{ item }}
-      {%- endif -%}
+      {% for item in methods %}
+         {% if item in members and (not item.startswith('_') or item in ['__call__']) %}
+           {{ name }}.{{ item }}
+         {% endif %}
       {%- endfor %}
-
-{% endif %}
-{% endblock %}
+   {% endif %}
+   {% endblock %}

doc/conf.py

@@ -23,11 +23,12 @@
 autosummary_imported_members = True
 add_module_names = False
 
-autodoc_typehints_format = "short"
+numpydoc_show_class_members = False
+numpydoc_show_inherited_class_members = False
 
+autodoc_typehints_format = "short"
 autodoc_typehints = "none"
 
-
 templates_path = ["_templates"]
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 

doc/reference/helpers.rst

@@ -4,4 +4,21 @@ Helpers
 .. automodule:: colabseg.utilities
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
+
+
+.. currentmodule:: colabseg.napari_integration
+
+ColabSegNapariWidget
+~~~~~~~~~~~~~~~~~~~~
+.. autosummary::
+   :toctree: api/
+
+   ColabSegNapariWidget
+
+NapariManager
+~~~~~~~~~~~~~
+.. autosummary::
+   :toctree: api/
+
+   NapariManager