Merge pull request #154 from TimMonko/ndev

switch all neuralDev to nDev

docs/beginner_setup.md

@@ -20,13 +20,13 @@ Inside napari, navigate to `Plugins` --> `Install/Uninstall Plugins...`. In the
 
 ![Console-installation](resources/gifs/console-full-installation.gif)
 
-This method only installs python libraries that are BSD3 licensed. Some image formats (such as czi and lif) are not available unless installing the full neuralDev package. To install extra plugins go to the integrated `napari console` (lower left button in UI) and enter `!pip install napari-ndev[all]`. **Note**: napari will freeze when you enter this command; please be patient as it downloads and sets up the remaining packages. **Restart napari for changes to take affect.**
+This method only installs python libraries that are BSD3 licensed. Some image formats (such as czi and lif) are not available unless installing the full nDev package. To install extra plugins go to the integrated `napari console` (lower left button in UI) and enter `!pip install napari-ndev[all]`. **Note**: napari will freeze when you enter this command; please be patient as it downloads and sets up the remaining packages. **Restart napari for changes to take affect.**
 
 ### opening widgets
 
 ![Widget opening](resources/gifs/widget-opening.gif)
 
-Navigate to `Plugins` --> `neuralDev` --> Click any widget. **Note:** Something (I believe napari) appears to be currently bugged and requires that the first widget be opened twice; the first time it will give a warning, the second time it should open.
+Navigate to `Plugins` --> `nDev` --> Click any widget. **Note:** Something (I believe napari) appears to be currently bugged and requires that the first widget be opened twice; the first time it will give a warning, the second time it should open.
 
 ### bio-formats support
 

docs/examples/utilities/image_utilities.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Image Utilities\n",
     "\n",
-    "This example will describe how to manage metadata, crop, and annotate images with the Image Utilities widget. The widget can be opened from `Plugins --> neuralDev --> Image Utilities`. To crop layers in the viewer, open `Plugins --> crop region (napari_crop)`. Below, we load napari and open the Image Utilities Widget and load in a large image originally saved with the widget from a multi-scene CZI file. Note that currently no metadata populates the widget because the file was not selected with `Select Files`. Instead, the image was opened with the [`napari-bioio`](https://github.com/TimMonko/napari-bioio) plugin; however, the metadata is saved and could normally be accessed from `viewer.layers[n].metadata['bioimage']`.\n",
+    "This example will describe how to manage metadata, crop, and annotate images with the Image Utilities widget. The widget can be opened from `Plugins --> nDev --> Image Utilities`. To crop layers in the viewer, open `Plugins --> crop region (napari_crop)`. Below, we load napari and open the Image Utilities Widget and load in a large image originally saved with the widget from a multi-scene CZI file. Note that currently no metadata populates the widget because the file was not selected with `Select Files`. Instead, the image was opened with the [`napari-bioio`](https://github.com/TimMonko/napari-bioio) plugin; however, the metadata is saved and could normally be accessed from `viewer.layers[n].metadata['bioimage']`.\n",
     "\n",
     "To access metadata from any image in the viewer, press the `Selected Layer` button in the `Update Metadata from:` box. "
    ]

docs/index.md

@@ -1,6 +1,5 @@
-# napari-ndev (neuralDev)
+# napari-ndev (nDev)
 
-<!-- ![Logo](images/neuralDev-logo.svg) -->
 [![License BSD-3](https://img.shields.io/pypi/l/napari-ndev.svg?color=green)](https://github.com/TimMonko/napari-ndev/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/napari-ndev.svg?color=green)](https://pypi.org/project/napari-ndev)
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-ndev.svg?color=green)](https://python.org)

docs/widget_further_info.md

@@ -2,7 +2,7 @@
 
 ## 1. Image Utilities
 
-A quick and easy way to save annotations (a napari labels layer) and corresponding images to corresponding folders. Best if the images are opened with the `neuralDev` reader (using [bioio] under the hood) -- which can be as simple as drag and drop opening by setting the appropriate default reader for each file type in Preferences -> Plugins--in order to utilize the metadata present for saving the image-label pairs.
+A quick and easy way to save annotations (a napari labels layer) and corresponding images to corresponding folders. Best if the images are opened with the `nDev` reader (using [bioio] under the hood) -- which can be as simple as drag and drop opening by setting the appropriate default reader for each file type in Preferences -> Plugins--in order to utilize the metadata present for saving the image-label pairs.
 
 Quick uniform adjustments to a folder of images, saving the output. Currently supports selecting channels, slicing Z, cropping/downsampling in XY, and doing a max projection of the sliced/cropped image data. To be added: alternative projection types, slicing in T, and compatibility with non TCZYX images (but this is not a priority since [bioio] currently always extracts images as TCZYX even if a dim is only length 1.
 

mkdocs.yml

@@ -3,12 +3,12 @@ site_url: https://TimMonko.github.io/napari-ndev/
 site_description: Napari widgets to process microscopy images
 repo_name: timmonko/napari-ndev
 repo_url: https://github.com/timmonko/napari-ndev
-copyright: Copyright © 2023-2024 Tim Monko
+copyright: Copyright © 2023-2025 Tim Monko
 
 theme:
   name: material
-  favicon: resources/images/neuralDev-icon.svg
-  logo: resources/images/neuralDev-icon.svg
+  favicon: resources/images/nDev-icon.svg
+  logo: resources/images/nDev-icon.svg
   icon:
     repo: fontawesome/brands/github
   palette:

src/napari_ndev/_tests/widgets/test_utilities_container.py

@@ -167,7 +167,6 @@ def test_update_metadata_from_layer(make_napari_viewer, test_data):
 
     assert (
         'Tried to update metadata, but could only update scale'
-        # ' because layer not opened with neuralDev reader'
     ) in container._results.value
     assert container._scale_tuple.value == (1, 2, 3)
 

src/napari_ndev/napari.yaml

@@ -1,5 +1,5 @@
 name: napari-ndev
-display_name: neuralDev
+display_name: nDev
 visibility: public
 contributions:
   commands:
@@ -18,9 +18,6 @@ contributions:
     - id: napari-ndev.make_apoc_container
       python_name: napari_ndev.widgets._apoc_container:ApocContainer
       title: Make Batch APOC
-    # - id: napari-ndev.make_custom_apoc
-    #   python_name: napari_ndev.widgets._apoc_feature_stack:ApocFeatureStack
-    #   title: Make Custom APOC Feature Set
     - id: napari-ndev.make_measure_container
       python_name: napari_ndev.widgets._measure_container:MeasureContainer
       title: Make Measure Container
@@ -34,8 +31,6 @@ contributions:
       display_name: Workflow Widget
     - command: napari-ndev.make_apoc_container
       display_name: APOC Widget
-    # - command: napari-ndev.make_custom_apoc
-    #   display_name: Custom APOC Feature Set
     - command: napari-ndev.make_measure_container
       display_name: Measure Widget
 

src/napari_ndev/widgets/_ndev_container.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-from pathlib import Path
 from typing import TYPE_CHECKING
 
 from magicclass.widgets import (
@@ -39,11 +38,10 @@ def __init__(self, viewer: napari.viewer.Viewer = None):
         """
         super().__init__(labels=False)
 
-        self.min_width = 600 # TODO: remove this hardcoded value
+        self.min_width = 700 # TODO: remove this hardcoded value
         self._viewer = viewer if viewer is not None else None
 
-        _logo_path = Path(__file__).parent.parent / 'resources' / 'nDev-logo-small.png'
-        # _logo_path = r'src\napari_ndev\resources\nDev-logo-small.png'
+        _logo_path = r'resources\nDev-logo-small.png'
         self._logo_label = Label(
             value='<h1 style="text-align: center;">'
             f'<img src="{_logo_path}"/>'

src/napari_ndev/widgets/_utilities_container.py

@@ -487,7 +487,7 @@ def append_scene_to_name(self):
             except AttributeError:
                 self._results.value = (
                     'Tried to append scene to name, but layer not opened with'
-                    ' neuralDev reader.'
+                    ' nDev reader.'
                 )
         else:
             self._results.value = (
@@ -529,7 +529,7 @@ def update_metadata_from_layer(self):
             )
             self._results.value = (
                 'Tried to update metadata, but could only update scale'
-                ' because layer not opened with neuralDev reader.'
+                ' because layer not opened with nDev reader.'
                 f'\nAt {time.strftime("%H:%M:%S")}'
             )