diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 1ae8ae98..2bf9e976 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -65,11 +65,13 @@ jobs:
- uses: neuroinformatics-unit/actions/test@v2
with:
python-version: ${{ matrix.python-version }}
+ secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
use-xvfb: true
test_numba_disabled:
needs: [linting, manifest]
name: Run tests with numba disabled
+ timeout-minutes: 60
runs-on: ubuntu-latest
env:
NUMBA_DISABLE_JIT: "1"
@@ -89,6 +91,7 @@ jobs:
- uses: neuroinformatics-unit/actions/test@v2
with:
python-version: "3.10"
+ secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
codecov-flags: "numba"
# Run brainglobe-workflows brainmapper-CLI tests to check for
@@ -96,6 +99,7 @@ jobs:
test_brainmapper_cli:
needs: [linting, manifest]
name: Run brainmapper tests to check for breakages
+ timeout-minutes: 60
runs-on: ubuntu-latest
steps:
- name: Cache tensorflow model
diff --git a/cellfinder/core/download/download.py b/cellfinder/core/download/download.py
index 00d6dee3..cd96616f 100644
--- a/cellfinder/core/download/download.py
+++ b/cellfinder/core/download/download.py
@@ -2,6 +2,7 @@
import shutil
import tarfile
import urllib.request
+from pathlib import Path
from brainglobe_utils.general.config import get_config_obj
from brainglobe_utils.general.system import disk_free_gb
@@ -124,5 +125,8 @@ def write_model_to_config(new_model_path, orig_config, custom_config):
data[i] = line.replace(
f"model_path = '{orig_path}", f"model_path = '{new_model_path}"
)
+
+ custom_config_path = Path(custom_config)
+ custom_config_path.parent.mkdir(parents=True, exist_ok=True)
with open(custom_config, "w") as out_conf:
out_conf.writelines(data)
diff --git a/cellfinder/napari/detect/detect.py b/cellfinder/napari/detect/detect.py
index 396f90b6..eaaab20f 100644
--- a/cellfinder/napari/detect/detect.py
+++ b/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 (
@@ -39,8 +38,60 @@ def detect_widget() -> FunctionGui:
"""
progress_bar = ProgressBar()
+ # options that is filled in from the gui
+ options = {"signal_image": None, "background_image": None, "viewer": None}
+
+ # signal and background images are separated out from the main magicgui
+ # parameter selections and are inserted as widget children in their own
+ # sub-containers of the root. Because if these image parameters are
+ # included in the root widget, every time *any* parameter updates, the gui
+ # freezes for a bit likely because magicgui is processing something for
+ # all the parameters when any parameter changes. And this processing takes
+ # particularly long for image parameters. Placing them as sub-containers
+ # alleviates this
+ @magicgui(
+ call_button=False,
+ persist=False,
+ scrollable=False,
+ labels=False,
+ auto_call=True,
+ )
+ def signal_image_opt(
+ viewer: napari.Viewer,
+ signal_image: napari.layers.Image,
+ ):
+ """
+ magicgui widget for setting the signal_image parameter.
+
+ Parameters
+ ----------
+ signal_image : napari.layers.Image
+ Image layer containing the labelled cells
+ """
+ options["signal_image"] = signal_image
+ options["viewer"] = viewer
+
+ @magicgui(
+ call_button=False,
+ persist=False,
+ scrollable=False,
+ labels=False,
+ auto_call=True,
+ )
+ def background_image_opt(
+ background_image: napari.layers.Image,
+ ):
+ """
+ magicgui widget for setting the background image parameter.
+
+ Parameters
+ ----------
+ background_image : napari.layers.Image
+ Image layer without labelled cells
+ """
+ options["background_image"] = background_image
+
@magicgui(
- header=header_label_widget,
detection_label=html_label_widget("Cell detection", tag="h3"),
**DataInputs.widget_representation(),
**DetectionInputs.widget_representation(),
@@ -52,12 +103,8 @@ def detect_widget() -> FunctionGui:
scrollable=True,
)
def widget(
- header,
detection_label,
data_options,
- viewer: napari.Viewer,
- signal_image: napari.layers.Image,
- background_image: napari.layers.Image,
voxel_size_z: float,
voxel_size_y: float,
voxel_size_x: float,
@@ -86,10 +133,6 @@ def widget(
Parameters
----------
- signal_image : napari.layers.Image
- Image layer containing the labelled cells
- background_image : napari.layers.Image
- Image layer without labelled cells
voxel_size_z : float
Size of your voxels in the axial dimension
voxel_size_y : float
@@ -132,9 +175,24 @@ def widget(
reset_button :
Reset parameters to default
"""
+ # we must manually call so that the parameters of these functions are
+ # initialized and updated. Because, if the images are open in napari
+ # before we open cellfinder, then these functions may never be called,
+ # even though the image filenames are shown properly in the parameters
+ # in the gui. Likely auto_call doesn't make magicgui call the functions
+ # in this circumstance, only if the parameters are updated once
+ # cellfinder plugin is fully open and initialized
+ signal_image_opt()
+ background_image_opt()
+
+ signal_image = options["signal_image"]
+ background_image = options["background_image"]
+ viewer = options["viewer"]
+
if signal_image is None or background_image is None:
show_info("Both signal and background images must be specified.")
return
+
data_inputs = DataInputs(
signal_image.data,
background_image.data,
@@ -205,8 +263,7 @@ 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():
@@ -226,6 +283,20 @@ def restore_defaults():
# Insert progress bar before the run and reset buttons
widget.insert(-3, progress_bar)
+ # add the signal and background image parameters
+ # make it look as if it's directly in the root container
+ signal_image_opt.margins = 0, 0, 0, 0
+ # the parameters are updated using `auto_call` only. If False, magicgui
+ # passes these as args to widget(), which doesn't list them as args
+ signal_image_opt.gui_only = True
+ widget.insert(3, signal_image_opt)
+ widget.signal_image_opt.label = "Signal image"
+
+ background_image_opt.margins = 0, 0, 0, 0
+ background_image_opt.gui_only = True
+ widget.insert(4, background_image_opt)
+ widget.background_image_opt.label = "Background image"
+
scroll = QScrollArea()
scroll.setWidget(widget._widget._qwidget)
widget._widget._qwidget = scroll
diff --git a/cellfinder/napari/images/brainglobe.png b/cellfinder/napari/images/brainglobe.png
deleted file mode 100644
index 427bdaba..00000000
Binary files a/cellfinder/napari/images/brainglobe.png and /dev/null differ
diff --git a/cellfinder/napari/train/train.py b/cellfinder/napari/train/train.py
index 4d5e005b..d604bf4b 100644
--- a/cellfinder/napari/train/train.py
+++ b/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():
diff --git a/cellfinder/napari/utils.py b/cellfinder/napari/utils.py
index 689b2842..d48b81fb 100644
--- a/cellfinder/napari/utils.py
+++ b/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 = """
-Efficient cell detection in large images.
-Website
-Documentation
-Source
-Citation
-For help, hover the cursor over each parameter.
-""" # 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"""
-
-
cellfinder
-""",
- 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:
diff --git a/pyproject.toml b/pyproject.toml
index efdb36f0..2eeeb61e 100644
--- a/pyproject.toml
+++ b/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",
@@ -120,7 +120,7 @@ python =
3.10: py310
[testenv]
-commands = python -m pytest -v --color=yes
+commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml
deps =
pytest
pytest-cov