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Import header from brainglobe-utils #399

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Apr 15, 2024
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Import header from brainglobe-utils #399

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132201a
import header from brainglobe-utils
K-Meech Apr 11, 2024
0039b1d
bump brainglobe-utils version and ensure new header is created every …
K-Meech Apr 11, 2024
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8 changes: 2 additions & 6 deletions cellfinder/napari/detect/detect.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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 (
Expand All @@ -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(),
Expand All @@ -52,7 +50,6 @@ def detect_widget() -> FunctionGui:
scrollable=True,
)
def widget(
header,
detection_label,
data_options,
viewer: napari.Viewer,
Expand Down Expand Up @@ -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():
Expand Down
Binary file removed cellfinder/napari/images/brainglobe.png
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11 changes: 2 additions & 9 deletions cellfinder/napari/train/train.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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(),
Expand All @@ -52,7 +47,6 @@ def training_widget() -> FunctionGui:
scrollable=True,
)
def widget(
header: dict,
training_label: dict,
data_options: dict,
yaml_files: Path,
Expand Down Expand Up @@ -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():
Expand Down
35 changes: 13 additions & 22 deletions cellfinder/napari/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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:
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
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