Merge pull request #1 from leaBroe/main

Merging

pyproject.toml

@@ -10,7 +10,6 @@ write_to = "src/arcospx/_version.py"
 line-length = 79
 target-version = ['py38', 'py39', 'py310']
 
-
 [tool.ruff]
 line-length = 79
 select = [

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = arcosPx-napari
-
+version = 0.0.1
 description = A plugin to track spatio-temporal correlations in images
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -34,6 +34,7 @@ install_requires =
     numpy
     magicgui
     qtpy
+    arcos4py
 
 python_requires = >=3.8
 include_package_data = True

src/arcospx/__init__.py

@@ -3,10 +3,10 @@
 except ImportError:
     __version__ = "unknown"
 from ._sample_data import make_sample_data
-from ._widget import ExampleQWidget, example_magic_widget
+from ._widget import remove_background, track_events
 
 __all__ = (
     "make_sample_data",
-    "ExampleQWidget",
-    "example_magic_widget",
+    "remove_background",
+    "track_events"
 )

src/arcospx/_sample_data.py

@@ -6,6 +6,7 @@
 
 Replace code below according to your needs.
 """
+
 from __future__ import annotations
 
 import numpy
@@ -16,6 +17,16 @@ def make_sample_data():
     # Return list of tuples
     # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
     # Check the documentation for more information about the
-    # add_image_kwargs
+    # add_image_kwargs:
     # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
-    return [(numpy.random.rand(512, 512), {})]
+    image_kwargs = {
+        "rgb": False,
+        "colormap": "gray",
+        "contrast_limits": [0, 255],
+        "visible": True,
+        "gamma": 1,
+        "interpolation2d":"nearest",
+        "name": "sample_data",
+    }
+    return [(numpy.random.rand(512, 512), image_kwargs)]
+

src/arcospx/_tests/test_sample_data.py

@@ -1,7 +1,19 @@
-# from arcospx import make_sample_data
+import pytest
+from arcospx import make_sample_data
+import numpy as np
+from qtpy import QtCore
 
-# add your tests here...
 
+def test_make_sample_data():
+    """Test make_sample_data."""
+    data = make_sample_data()
+
+    # Check the shape of the numpy array
+    assert data[0][0].shape == (512, 512)
+
+    # Check if the first element of the tuple is a numpy array
+    assert isinstance(data[0][0], np.ndarray)
+
+    # Check if the second element of the tuple is a dictionary
+    assert isinstance(data[0][1], dict)
 
-def test_something():
-    pass

src/arcospx/_tests/test_widget.py

@@ -1,36 +1,53 @@
 import numpy as np
-
-from arcospx import ExampleQWidget, example_magic_widget
-
-
-# make_napari_viewer is a pytest fixture that returns a napari viewer object
-# capsys is a pytest fixture that captures stdout and stderr output streams
-def test_example_q_widget(make_napari_viewer, capsys):
-    # make viewer and add an image layer using our fixture
+import pytest
+from qtpy import QtCore
+from arcospx import make_sample_data, remove_background, track_events
+import napari
+from skimage.io import imread
+from numpy.testing import assert_array_equal
+from qtpy.QtCore import QTimer
+from napari.layers.image import Image
+from arcos4py.tools import remove_image_background, track_events_image
+from pytestqt import qtbot
+
+def test_remove_background(make_napari_viewer, qtbot):
+    """
+    Test background removal on a simple image.
+    """
     viewer = make_napari_viewer()
-    viewer.add_image(np.random.random((100, 100)))
-
-    # create our widget, passing in the viewer
-    my_widget = ExampleQWidget(viewer)
-
-    # call our widget method
-    my_widget._on_click()
-
-    # read captured output and check that it's as we expected
-    captured = capsys.readouterr()
-    assert captured.out == "napari has 1 layers\n"
-
-
-def test_example_magic_widget(make_napari_viewer, capsys):
+    test_img = imread('test_data/1_growing.tif')
+    viewer.add_image(test_img, name='test_img')
+    true_img = imread('test_data/1_growing_true.tif')
+    _,widget = viewer.window.add_plugin_dock_widget("arcosPx-napari", "Remove Background")
+    widget.image.value = viewer.layers['test_img']
+    widget.filter_type.value = "gaussian"
+    widget.size_0.value = 1
+    widget.size_1.value = 1
+    widget.size_2.value = 1
+    worker = widget()
+    with qtbot.waitSignal(worker.finished, timeout=10000):
+        pass
+    assert_array_equal(viewer.layers[1].data, true_img)
+
+
+def test_track_events(make_napari_viewer, qtbot):
+    """
+    Test tracking on a simple image.
+    """
     viewer = make_napari_viewer()
-    layer = viewer.add_image(np.random.random((100, 100)))
-
-    # this time, our widget will be a MagicFactory or FunctionGui instance
-    my_widget = example_magic_widget()
-
-    # if we "call" this object, it'll execute our function
-    my_widget(viewer.layers[0])
+    test_img = imread('test_data/test_data_track_events.tif')
+    viewer.add_image(test_img, name='test_img')
+    true_img = imread('test_data/test_track_events_true.tif')
+    _, widget = viewer.window.add_plugin_dock_widget("arcosPx-napari", "Track Events")
+    widget.image_selector.value = viewer.layers['test_img']
+    widget.threshold.value = 300
+    widget.eps.value = 10
+    widget.epsPrev.value = 50
+    widget.minClSz.value = 50
+    widget.minSamples.value = 2
+    widget.nPrev.value = 2
+    worker = widget()
+    with qtbot.waitSignal(worker.finished, timeout=10000):
+        pass
+    assert_array_equal(viewer.layers[1].data, true_img)
 
-    # read captured output and check that it's as we expected
-    captured = capsys.readouterr()
-    assert captured.out == f"you have selected {layer}\n"

src/arcospx/_widget.py

@@ -8,39 +8,131 @@
 """
 from typing import TYPE_CHECKING
 
-from magicgui import magic_factory
+from arcos4py.tools import remove_image_background, track_events_image
+from magicgui import magic_factory, widgets
+from napari import viewer
 from qtpy.QtWidgets import QHBoxLayout, QPushButton, QWidget
+from napari.types import LayerDataTuple
+from napari.layers import Image
+from napari.qt.threading import thread_worker, FunctionWorker
+from napari.utils import progress
+from qtpy.QtWidgets import QWidget, QVBoxLayout, QPushButton, QLabel
+
+from magicgui import magicgui
+
 
 if TYPE_CHECKING:
     import napari
 
+# A global flag for aborting the process
+abort_flag = False
+
+# Optional: Define a custom exception for aborting the process
+class AbortException(Exception):
+    pass
+
+@magic_factory()
+def remove_background(
+        image: Image,
+        filter_type: str = "gaussian",
+        size_0: int = 20,
+        size_1: int = 5,
+        size_2: int = 5,
+        dims: str = "TXY",
+        crop_time_axis: bool = False
+    ) -> FunctionWorker[LayerDataTuple]:
+    size = (size_0, size_1, size_2)
+    pbar = progress(total=0)
+    @thread_worker(connect={'returned': pbar.close})
+    def remove_image_background_2() -> LayerDataTuple:
+        global abort_flag
+
+        # Reset the abort flag at the start of each execution
+        abort_flag = False
+
+        removed_background = remove_image_background(image.data, filter_type, size, dims, crop_time_axis)
+
+        if abort_flag:
+            pbar.close()
+            raise AbortException("Operation aborted by user.")
+
+        layer_properties = {
+            "name": f"{image.name} background removed",
+            "metadata": {
+                "filter_type": filter_type,
+                "size_0": size_0,
+                "size_1": size_1,
+                "size_2": size_2,
+                "dims": dims,
+                "crop_time_axis": crop_time_axis,
+                "filename": image.name,}}
+
+
+        return (removed_background, layer_properties, "image")
+
+    return remove_image_background_2()
+
+
+@magic_factory()
+def track_events(
+    image_selector: Image,
+    threshold: int = 300,
+    eps: int = 10,
+    epsPrev: int = 50,
+    minClSz: int = 50,
+    minSamples: int = 2,
+    nPrev: int = 2,
+    dims: str = "TXY",
+) -> FunctionWorker[LayerDataTuple]:
+    t_filter_size = 20
+    pbar = progress(total=0)
+
+    @thread_worker(connect={'returned': pbar.close})
+    def track_events_2() -> LayerDataTuple:
+        global abort_flag
+
+        # Reset the abort flag at the start of each execution
+        abort_flag = False
+
+        if abort_flag:
+            # Return an error message
+            # return "Interrupt error: Operation aborted by user."
+            # Or raise a custom exception
+            pbar.close()
+            raise AbortException("Operation aborted by user.")
 
-class ExampleQWidget(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
-    # 2. use a type annotation of 'napari.viewer.Viewer' for any parameter
-    def __init__(self, napari_viewer):
-        super().__init__()
-        self.viewer = napari_viewer
+        selected_image = image_selector.data
+        img_tracked = track_events_image(selected_image >= threshold, eps = eps, epsPrev = epsPrev, minClSz = minClSz, minSamples = minSamples, nPrev = nPrev, dims = dims)
 
-        btn = QPushButton("Click me!")
-        btn.clicked.connect(self._on_click)
+        if abort_flag:
+            # Return an error message
+            # return "Interrupt error: Operation aborted by user."
+            # Or raise a custom exception
+            pbar.close()
+            raise AbortException("Operation aborted by user.")
 
-        self.setLayout(QHBoxLayout())
-        self.layout().addWidget(btn)
+        # Like this we create the layer as a layer-data-tuple object which will automatically be parsed by napari and added to the viewer
+        # This is more flexible and does not require the function to know about the viewer directly
+        # Additionally like this you can now set the metadata of the layer
+        layer_properties = {
+            "name": f"{image_selector.name} tracked",
+            "metadata": {
+                "threshold": threshold,
+                "eps": eps,
+                "epsPrev": epsPrev,
+                "minClSz": minClSz,
+                "nPrev": nPrev,
+                "filename": image_selector.name,  ## eg. setting medatada to the name of the image layer
+         },}
+        return (img_tracked, layer_properties, "labels")
 
-    def _on_click(self):
-        print("napari has", len(self.viewer.layers), "layers")
+    # return the layer data tuple
+    return track_events_2()
 
 
-@magic_factory
-def example_magic_widget(img_layer: "napari.layers.Image"):
-    print(f"you have selected {img_layer}")
+@magic_factory()
+def abort_process():
+    global abort_flag
+    abort_flag = True
 
 
-# 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}")

src/arcospx/napari.yaml

@@ -6,27 +6,23 @@ visibility: public
 categories: ["Annotation", "Segmentation", "Acquisition"]
 contributions:
   commands:
-    - id: arcosPx-napari.make_sample_data
-      python_name: arcospx._sample_data:make_sample_data
-      title: Load sample data from arcosPx
-    - id: arcosPx-napari.make_qwidget
-      python_name: arcospx._widget:ExampleQWidget
-      title: Make example QWidget
-    - id: arcosPx-napari.make_magic_widget
-      python_name: arcospx._widget:example_magic_widget
-      title: Make example magic widget
-    - id: arcosPx-napari.make_func_widget
-      python_name: arcospx._widget:example_function_widget
-      title: Make example function widget
+    - id: arcosPx-napari.remove_background
+      python_name: arcospx._widget:remove_background
+      title: Remove Background
+    - id: arcosPx-napari.track_events
+      python_name: arcospx._widget:track_events
+      title: Track Events
+    - id: arcosPx-napari.abort_process
+      python_name: arcospx._widget:abort_process
+      title: Abort Process
   sample_data:
     - command: arcosPx-napari.make_sample_data
       display_name: arcosPx
       key: unique_id.1
   widgets:
-    - command: arcosPx-napari.make_qwidget
-      display_name: Example QWidget
-    - command: arcosPx-napari.make_magic_widget
-      display_name: Example Magic Widget
-    - command: arcosPx-napari.make_func_widget
-      autogenerate: true
-      display_name: Example Function Widget
+    - command: arcosPx-napari.remove_background
+      display_name: Remove Background
+    - command: arcosPx-napari.track_events
+      display_name: Track Events
+    - command: arcosPx-napari.abort_process
+      display_name: Abort Current Process