Import header from brainglobe-utils (#399)

* import header from brainglobe-utils

* bump brainglobe-utils version and ensure new header is created every time

cellfinder/napari/detect/detect.py

@@ -11,9 +11,8 @@
 from cellfinder.core.classify.cube_generator import get_cube_depth_min_max
 from cellfinder.napari.utils import (
     add_layers,
-    header_label_widget,
+    cellfinder_header,
     html_label_widget,
-    widget_header,
 )
 
 from .detect_containers import (
@@ -40,7 +39,6 @@ def detect_widget() -> FunctionGui:
     progress_bar = ProgressBar()
 
     @magicgui(
-        header=header_label_widget,
         detection_label=html_label_widget("Cell detection", tag="h3"),
         **DataInputs.widget_representation(),
         **DetectionInputs.widget_representation(),
@@ -52,7 +50,6 @@ def detect_widget() -> FunctionGui:
         scrollable=True,
     )
     def widget(
-        header,
         detection_label,
         data_options,
         viewer: napari.Viewer,
@@ -205,8 +202,7 @@ def update_progress_bar(label: str, max: int, value: int):
         worker.update_progress_bar.connect(update_progress_bar)
         worker.start()
 
-    widget.header.value = widget_header
-    widget.header.native.setOpenExternalLinks(True)
+    widget.native.layout().insertWidget(0, cellfinder_header())
 
     @widget.reset_button.changed.connect
     def restore_defaults():

cellfinder/napari/train/train.py

@@ -8,11 +8,7 @@
 from qtpy.QtWidgets import QScrollArea
 
 from cellfinder.core.train.train_yml import run as train_yml
-from cellfinder.napari.utils import (
-    header_label_widget,
-    html_label_widget,
-    widget_header,
-)
+from cellfinder.napari.utils import cellfinder_header, html_label_widget
 
 from .train_containers import (
     MiscTrainingInputs,
@@ -41,7 +37,6 @@ def run_training(
 
 def training_widget() -> FunctionGui:
     @magicgui(
-        header=header_label_widget,
         training_label=html_label_widget("Network training", tag="h3"),
         **TrainingDataInputs.widget_representation(),
         **OptionalNetworkInputs.widget_representation(),
@@ -52,7 +47,6 @@ def training_widget() -> FunctionGui:
         scrollable=True,
     )
     def widget(
-        header: dict,
         training_label: dict,
         data_options: dict,
         yaml_files: Path,
@@ -161,8 +155,7 @@ def widget(
             )
             worker.start()
 
-    widget.header.value = widget_header
-    widget.header.native.setOpenExternalLinks(True)
+    widget.native.layout().insertWidget(0, cellfinder_header())
 
     @widget.reset_button.changed.connect
     def restore_defaults():

cellfinder/napari/utils.py

@@ -4,21 +4,7 @@
 import numpy as np
 import pandas as pd
 from brainglobe_utils.cells.cells import Cell
-from pkg_resources import resource_filename
-
-brainglobe_logo = resource_filename(
-    "cellfinder", "napari/images/brainglobe.png"
-)
-
-
-widget_header = """
-<p>Efficient cell detection in large images.</p>
-<p><a href="https://brainglobe.info" style="color:gray;">Website</a></p>
-<p><a href="https://brainglobe.info/documentation/cellfinder/user-guide/napari-plugin/index.html" style="color:gray;">Documentation</a></p>
-<p><a href="https://github.com/brainglobe/cellfinder" style="color:gray;">Source</a></p>
-<p><a href="https://doi.org/10.1371/journal.pcbi.1009074" style="color:gray;">Citation</a></p>
-<p><small>For help, hover the cursor over each parameter.</small>
-"""  # noqa: E501
+from brainglobe_utils.qtpy.logo import header_widget
 
 
 def html_label_widget(label: str, *, tag: str = "b") -> dict:
@@ -31,13 +17,18 @@ def html_label_widget(label: str, *, tag: str = "b") -> dict:
     )
 
 
-header_label_widget = html_label_widget(
-    f"""
-<img src="{brainglobe_logo}"width="100">
-<p>cellfinder</p>
-""",
-    tag="h1",
-)
+def cellfinder_header():
+    """
+    Create the header containing the brainglobe logo and documentation links
+    for all cellfinder widgets.
+    """
+    return header_widget(
+        "cellfinder",
+        "Efficient cell detection in large images.",
+        documentation_path="cellfinder/user-guide/napari-plugin/index.html",
+        citation_doi="https://doi.org/10.1371/journal.pcbi.1009074",
+        help_text="For help, hover the cursor over each parameter.",
+    )
 
 
 def add_layers(points: List[Cell], viewer: napari.Viewer) -> None:

pyproject.toml

@@ -20,7 +20,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "brainglobe-utils>=0.4.2",
+    "brainglobe-utils>=0.4.3",
     "brainglobe-napari-io>=0.3.4",
     "dask[array]",
     "fancylog>=0.0.7",