From 500360ba54fa7250c4104951452cce37039c79d3 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Wed, 5 Oct 2022 00:42:15 +0200
Subject: [PATCH] rename plugin
---
src/napari_segment/__init__.py | 4 ++--
src/napari_segment/_sample_data.py | 2 +-
src/napari_segment/_widget.py | 6 ++++--
src/napari_segment/napari.yaml | 28 ++++++++++++++--------------
4 files changed, 21 insertions(+), 19 deletions(-)
diff --git a/src/napari_segment/__init__.py b/src/napari_segment/__init__.py
index 7146cba..f1c0b60 100644
--- a/src/napari_segment/__init__.py
+++ b/src/napari_segment/__init__.py
@@ -6,7 +6,7 @@ except ImportError:
from ._reader import napari_get_reader
from ._sample_data import make_sample_data
-from ._widget import ExampleQWidget, example_magic_widget
+from ._widget import SegmentStack, example_magic_widget
from ._writer import write_multiple, write_single_image
__ALL__ = [
@@ -14,6 +14,6 @@ __ALL__ = [
write_multiple,
write_single_image,
make_sample_data,
- ExampleQWidget,
+ SegmentStack,
example_magic_widget,
]
diff --git a/src/napari_segment/_sample_data.py b/src/napari_segment/_sample_data.py
index b2b7663..4a12af5 100644
--- a/src/napari_segment/_sample_data.py
+++ b/src/napari_segment/_sample_data.py
@@ -12,4 +12,4 @@ import numpy
def make_sample_data():
"""Generates an image"""
- return numpy.random.rand(512, 512)
+ return [(numpy.random.rand(512, 512),)]
diff --git a/src/napari_segment/_widget.py b/src/napari_segment/_widget.py
index 155a253..d701950 100644
--- a/src/napari_segment/_widget.py
+++ b/src/napari_segment/_widget.py
@@ -57,7 +57,7 @@ ff.setFormatter(formatter)
logger.addHandler(ff)
-class ExampleQWidget(q.QWidget):
+class SegmentStack(q.QWidget):
# your QWidget.__init__ can optionally request the napari viewer instance
# in one of two ways:
# 1. use a parameter called `napari_viewer`, as done here
@@ -327,13 +327,15 @@ class ExampleQWidget(q.QWidget):
opacity=0.3,
**{"name": name, "scale": self.scale},
)
- self.viewer.layers[name].contour = 8 // self.binning
else:
logger.debug(f'Updating Detections layer with {self.labels}')
self.viewer.layers[name].data = self.labels
self.viewer.layers[name].scale = self.scale
+ self.viewer.layers[name].contour = 8 // self.binning
+
+
logger.debug(f'Thresholding succesful. \
Sending labels {self.labels} to filtering')
self.update_out()
diff --git a/src/napari_segment/napari.yaml b/src/napari_segment/napari.yaml
index e98f5bf..99d3917 100644
--- a/src/napari_segment/napari.yaml
+++ b/src/napari_segment/napari.yaml
@@ -15,14 +15,14 @@ contributions:
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.segment_organoid
- python_name: napari_segment._widget:segment_organoid
- title: Segment organoid
+ python_name: napari_segment._widget:SegmentStack
+ title: Segment nd2 stack with multiple positions
+ # - 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: True
@@ -40,9 +40,9 @@ contributions:
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.segment_organoid
- # autogenerate: true
- display_name: Segment organoid
+ display_name: Segment multipos
+ # - command: napari-segment.make_magic_widget
+ # display_name: Example Magic Widget
+ # - command: napari-segment.segment_organoid
+ # # autogenerate: true
+ # display_name: Segment organoid
--
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