diff --git a/src/napari_segment/__init__.py b/src/napari_segment/__init__.py index 7146cbaef5e9f35c0712ceea617e424cee1238fe..f1c0b601f071591147cb63cb7db9f013053f07bd 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 b2b76636417243ecf1b0db1d82707e7cada2876e..4a12af50bfc0fb00af8b85e8fe20f98acff45d78 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 155a2532f84d94f4646a2024821d57356c2b6e12..d70195064e324fabe81d4f8e84b5d771be67a0a9 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 e98f5bf1bc839adb59b0f0524e271909df6bdf2e..99d3917476afd0d9b08289e8da722b60ba531d14 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