diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7d452ebae8ad0d1ae9b3d7009569042a3e8c4ed7..dcc9a2b78e06b63b2a4a0c995aaf41bab730caf2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.0.1
+ rev: v4.1.0
hooks:
- id: check-docstring-first
- id: end-of-file-fixer
@@ -24,11 +24,11 @@ repos:
hooks:
- id: isort
- repo: https://github.com/psf/black
- rev: 21.11b1
+ rev: 22.1.0
hooks:
- id: black
- repo: https://github.com/asottile/pyupgrade
- rev: v2.29.1
+ rev: v2.31.1
hooks:
- id: pyupgrade
args: [--py38-plus, --keep-runtime-typing]
diff --git a/src/napari_segment/_reader.py b/src/napari_segment/_reader.py
index 8c324fc583bceae3fc721491f5debc0ea059df72..80560e03a6cbe1d78a2691df8e208b294537307c 100644
--- a/src/napari_segment/_reader.py
+++ b/src/napari_segment/_reader.py
@@ -5,6 +5,7 @@ It implements the Reader specification, but your plugin may choose to
implement multiple readers or even other plugin contributions. see:
https://napari.org/plugins/stable/guides.html#readers
"""
+import nd2
import numpy as np
@@ -29,13 +30,30 @@ def napari_get_reader(path):
path = path[0]
# if we know we cannot read the file, we immediately return None.
- if not path.endswith(".npy"):
- return None
+ if path.endswith(".nd2"):
+ return read_nd2
# otherwise we return the *function* that can read ``path``.
return reader_function
+def read_nd2(path):
+ data = nd2.ND2File(path)
+ ddata = data.to_dask()
+ return [
+ (
+ ddata,
+ dict(
+ channel_axis=1,
+ name=["BF", "fluo"],
+ colormap=["gray", "green"],
+ contrast_limits=[(8500, 35000), (150, 20000)],
+ ),
+ "image",
+ )
+ ]
+
+
def reader_function(path):
"""Take a path or list of paths and return a list of LayerData tuples.
@@ -54,7 +72,8 @@ def reader_function(path):
A list of LayerData tuples where each tuple in the list contains
(data, metadata, layer_type), where data is a numpy array, metadata is
a dict of keyword arguments for the corresponding viewer.add_* method
- in napari, and layer_type is a lower-case string naming the type of layer.
+ in napari, and layer_type is a lower-case string naming the type of
+ layer.
Both "meta", and "layer_type" are optional. napari will default to
layer_type=="image" if not provided
"""
diff --git a/src/napari_segment/_widget.py b/src/napari_segment/_widget.py
index 7f2fc5d116fb41de6ace8fb15e7a359906cca142..a7c0317830f4a87d4a7acac4a22ad8502ed17aaa 100644
--- a/src/napari_segment/_widget.py
+++ b/src/napari_segment/_widget.py
@@ -6,8 +6,16 @@ see: https://napari.org/plugins/stable/guides.html#widgets
Replace code below according to your needs.
"""
-from qtpy.QtWidgets import QWidget, QHBoxLayout, QPushButton
+from functools import partial
+from multiprocessing import Pool
+
+import napari
+import numpy as np
from magicgui import magic_factory
+from qtpy.QtWidgets import QHBoxLayout, QPushButton, QWidget
+from scipy.ndimage import binary_dilation
+from segment.seg import segment_bf
+from skimage.measure import regionprops_table
class ExampleQWidget(QWidget):
@@ -37,5 +45,53 @@ def example_magic_widget(img_layer: "napari.layers.Image"):
# Uses the `autogenerate: true` flag in the plugin manifest
# to indicate it should be wrapped as a magicgui to autogenerate
# a widget.
-def example_function_widget(img_layer: "napari.layers.Image"):
- print(f"you have selected {img_layer}")
+@magic_factory()
+def segment_organoid(
+ BF_layer: "napari.layers.Image",
+ fluo_layer: "napari.layers.Image",
+ donut=10,
+ thr: float = 0.4,
+) -> napari.types.LabelsData:
+ # frame = napari.current_viewer().cursor.position[0]
+ try:
+ p = Pool()
+ stack = list(
+ p.map(
+ partial(seg_frame, thr=thr, donut=donut),
+ zip(BF_layer.data.compute(), fluo_layer.data.compute()),
+ )
+ )
+ except Exception as e:
+ print(e.args)
+ finally:
+ p.close()
+
+ return np.array(stack)
+ # (bg_mask.astype('uint8'), {"name": "donut", **kwargs}, 'image')
+
+
+def seg_frame(data, thr, donut):
+ bf, fluo = data
+ label = segment_bf(bf, thr=thr, plot=False)
+ print(bf.dtype, bf.shape)
+ props = regionprops_table(
+ label,
+ intensity_image=fluo,
+ properties=(
+ "label",
+ "centroid",
+ "bbox",
+ "mean_intensity",
+ "area",
+ "major_axis_length",
+ ),
+ )
+ # print(props)
+ biggest_prop_index = np.argmax(props["area"])
+ label_of_biggest_object = props["label"][biggest_prop_index]
+ spheroid_mask = label == label_of_biggest_object
+ bg_mask = np.bitwise_xor(
+ binary_dilation(spheroid_mask, structure=np.ones((donut, donut))),
+ spheroid_mask,
+ )
+ return spheroid_mask.astype("uint16") + 2 * bg_mask.astype("uint8")
diff --git a/src/napari_segment/napari.yaml b/src/napari_segment/napari.yaml
index 45fe55a77c234b219e3c9e59dfa8031c7124df16..14dfbbb0fcd2f2613d67de57761b8998efdd758b 100644
--- a/src/napari_segment/napari.yaml
+++ b/src/napari_segment/napari.yaml
@@ -13,36 +13,36 @@ contributions:
title: Save image data with Segment organoid
- id: napari-segment.make_sample_data
python_name: napari_segment._sample_data:make_sample_data
- title: Load sample data from Segment organoid
- - id: napari-segment.make_qwidget
- python_name: napari_segment._widget:ExampleQWidget
- title: Make example QWidget
- - id: napari-segment.make_magic_widget
- python_name: napari_segment._widget:example_magic_widget
- title: Make example magic widget
- - id: napari-segment.make_func_widget
- python_name: napari_segment._widget:example_function_widget
- title: Make example function widget
+ title: Load sample data from Segment organoid
+ # - id: napari-segment.make_qwidget
+ # python_name: napari_segment._widget:ExampleQWidget
+ # title: Make example QWidget
+ # - id: napari-segment.make_magic_widget
+ # python_name: napari_segment._widget:example_magic_widget
+ # title: Make example magic widget
+ - id: napari-segment.segment_organoid
+ python_name: napari_segment._widget:segment_organoid
+ title: Segment organoid
readers:
- command: napari-segment.get_reader
accepts_directories: false
- filename_patterns: ['*.npy']
+ filename_patterns: ['*.npy', '*.nd2']
writers:
- command: napari-segment.write_multiple
layer_types: ['image*','labels*']
filename_extensions: []
- command: napari-segment.write_single_image
layer_types: ['image']
- filename_extensions: ['.npy']
+ filename_extensions: ['.npy']
sample_data:
- command: napari-segment.make_sample_data
display_name: Segment organoid
- key: unique_id.1
+ key: unique_id.1
widgets:
- - command: napari-segment.make_qwidget
- display_name: Example QWidget
- - command: napari-segment.make_magic_widget
- display_name: Example Magic Widget
- - command: napari-segment.make_func_widget
- autogenerate: true
- display_name: Example Function Widget
\ No newline at end of file
+ # - command: napari-segment.make_qwidget
+ # display_name: Example QWidget
+ # - command: napari-segment.make_magic_widget
+ # display_name: Example Magic Widget
+ - command: napari-segment.segment_organoid
+ # autogenerate: true
+ display_name: Segment organoid