fix: Fix bug when loading already created project causing hide of ROI layer

.github/workflows/tests.yml

@@ -67,7 +67,7 @@ jobs:
       python_version: >-
         ["3.9"]
       os: >-
-        ["windows-2019", "ubuntu-20.04", "macos-11"]
+        ["windows-2019", "ubuntu-20.04", "macos-12"]
 
   test_coverage:
     needs: download_data

changelog.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## 0.14.6 - 2022-11-13
+
+### Bug Fixes
+
+-   Fix bug when loading already created project causing hide of ROI layer (#787)
+
+### Features
+
+-   Improve error message if segmentation do not fit in ROI Mask (#788)
+
 ## 0.14.5 - 2022-11-09
 
 ### Bug Fixes

package/PartSeg/common_gui/napari_image_view.py

@@ -17,7 +17,7 @@
 from napari.utils.colormaps.colormap import ColormapInterpolationMode
 from nme import register_class
 from packaging.version import parse as parse_version
-from qtpy.QtCore import QEvent, QObject, QPoint, Qt, QTimer, Signal
+from qtpy.QtCore import QEvent, QPoint, Qt, QTimer, Signal, Slot
 from qtpy.QtWidgets import QApplication, QCheckBox, QHBoxLayout, QLabel, QMenu, QSpinBox, QToolTip, QVBoxLayout, QWidget
 from scipy.ndimage import binary_dilation
 from superqt import QEnumComboBox, ensure_main_thread
@@ -582,36 +582,44 @@ def calculate_filter(array: np.ndarray, parameters: Tuple[NoiseFilterType, float
             return bilateral(array, parameters[1])
         return median(array, int(parameters[1]))
 
-    def _remove_worker(self, sender):
+    def _remove_worker(self, sender=None):
+        if sender is None:
+            sender = self.sender()
         for worker in self.worker_list:
             if hasattr(worker, "signals") and sender is worker.signals:
                 self.worker_list.remove(worker)
                 break
         else:
-            logging.debug(f"[_remove_worker] {sender}")
+            logging.debug("[_remove_worker] %s", sender)
 
     def _add_layer_util(self, index, layer, filters):
         if layer not in self.viewer.layers:
             self.viewer.add_layer(layer)
 
-        set_data_obj = _SetData(self)
-
-        @thread_worker(connect={"returned": set_data_obj.set_data})
-        def calc_filter(j, layer_):
-            if filters[j][0] == NoiseFilterType.No or filters[j][1] == 0:
-                return None, layer_
-            return self.calculate_filter(layer_.data, parameters=filters[j]), layer_
+        if filters[index][0] == NoiseFilterType.No or filters[index][1] == 0:
+            return
 
-        set_data_obj.worker = calc_filter(index, layer)
+        worker = calc_layer_filter(layer, filters[index][0], filters[index][1])
+        worker.returned.connect(self._add_layer_util_end)
+        worker.finished.connect(self._remove_worker)
+        self.worker_list.append(worker)
+        worker.start()
 
-        self.worker_list.append(set_data_obj)
+    @Slot(object)
+    def _add_layer_util_end(self, val):
+        data_, layer_ = val
+        if data_ is not None:
+            layer_.data = data_
 
     def _add_image(self, image_data: Tuple[ImageInfo, bool]):
-        self._remove_worker(self.sender())
-
-        image_info, _replace = image_data
+        image_info, replace = image_data
         image = image_info.image
 
+        if replace:
+            for layer in list(reversed(self.viewer.layers)):
+                self.viewer.layers.remove(layer)
+            QApplication.instance().processEvents()
+
         filters = self.channel_control.get_filter()
         for i, layer in enumerate(image_info.layers):
             try:
@@ -658,11 +666,6 @@ def add_image(self, image: Optional[Image], replace=False):
         if image.file_path in self.image_info:
             raise ValueError("Image already added")
 
-        if replace:
-            for layer in list(reversed(self.viewer.layers)):
-                self.viewer.layers.remove(layer)
-            QApplication.instance().processEvents()
-
         self.image_info[image.file_path] = ImageInfo(image, [])
 
         channels = image.channels
@@ -687,6 +690,7 @@ def add_image(self, image: Optional[Image], replace=False):
     def _prepare_layers(self, image, parameters, replace):
         worker = prepare_layers(image, parameters, replace)
         worker.returned.connect(self._add_image)
+        worker.finished.connect(self._remove_worker)
         self.worker_list.append(worker)
         worker.start()
 
@@ -1012,6 +1016,15 @@ def _prepare_layers(image: Image, param: ImageParameters, replace: bool) -> Tupl
 prepare_layers = thread_worker(_prepare_layers)
 
 
+def _calc_layer_filter(layer: NapariImage, filter_type: NoiseFilterType, radius: float):
+    if filter_type == NoiseFilterType.No or radius == 0:
+        return None, layer
+    return ImageView.calculate_filter(layer.data, parameters=(filter_type, radius)), layer
+
+
+calc_layer_filter = thread_worker(_calc_layer_filter)
+
+
 def _print_dict(dkt: MutableMapping, indent="") -> str:
     if not isinstance(dkt, MutableMapping):
         logging.error(f"{type(dkt)} instead of dict passed to _print_dict")
@@ -1023,22 +1036,3 @@ def _print_dict(dkt: MutableMapping, indent="") -> str:
         else:
             res.append(f"{indent}{k}: {v}")
     return "\n".join(res)
-
-
-class _SetData(QObject):
-    def __init__(self, viewer: ImageView):
-        super().__init__()
-        self.viewer = viewer
-        self.worker = None
-
-    def set_data(self, val):
-        self._set_data(val)
-        self.viewer.worker_list.remove(self)
-
-    def _set_data(self, val):
-        data_, layer_ = val
-        if data_ is None:
-            return
-        if layer_ not in self.viewer.viewer.layers:
-            return
-        layer_.data = data_

package/tests/test_PartSeg/conftest.py

@@ -45,15 +45,18 @@ def part_settings_with_project(image, analysis_segmentation2, tmp_path):
 
 
 @pytest.fixture(autouse=True)
-def disable_threads_viewer(monkeypatch, request):
-    if "no_viewer_patch" in request.keywords:
-        return
-
+def disable_threads_viewer_patch_prepare_leyers(monkeypatch):
     def _prepare_layers(self, image, parameters, replace):
         self._add_image(napari_image_view._prepare_layers(image, parameters, replace))
 
     monkeypatch.setattr(napari_image_view.ImageView, "_prepare_layers", _prepare_layers)
 
+
+@pytest.fixture(autouse=True)
+def disable_threads_viewer_patch_add_layer(monkeypatch, request):
+    if "no_patch_add_layer" in request.keywords:
+        return
+
     def _add_layer_util(self, index, layer, filters):
         if layer not in self.viewer.layers:
             self.viewer.add_layer(layer)
@@ -153,7 +156,7 @@ def __init__(self, *args, **kwargs):
         self._call_list = []
 
     def setTimeout(self, *args, **kwargs):
-        pass
+        pass  # as it is dummy throttler then timeout is obsolete.
 
     def throttle(self, *args, **kwargs):
         for cl in self._call_list:

package/tests/test_PartSeg/test_napari_image_view.py

@@ -1,7 +1,6 @@
 # pylint: disable=R0201
 import gc
 import platform
-import sys
 from functools import partial
 from unittest.mock import MagicMock
 
@@ -21,6 +20,7 @@
     QMenu,
     SearchComponentModal,
     SearchType,
+    _calc_layer_filter,
     _print_dict,
 )
 from PartSegCore.image_operations import NoiseFilterType
@@ -296,19 +296,36 @@ def test_roi_removed_add_image_restore(self, base_settings, image_view):
         assert "ROI" in image_view.viewer.layers
         assert "Mask" in image_view.viewer.layers
 
-    @pytest.mark.no_viewer_patch
-    @pytest.mark.skipif(sys.platform == "darwin", reason="fails on macos because of SIGILL")
+    @pytest.mark.parametrize("filter_type", NoiseFilterType.__members__.values())
+    @pytest.mark.parametrize("radius", [1, 2, 3.5])
+    def test_calculate_filter(self, filter_type, radius, image):
+        ch = image.get_channel(0)
+        filtered = ImageView.calculate_filter(ch, (filter_type, radius))
+        assert filtered.shape == ch.shape
+        assert (filter_type == NoiseFilterType.No) != (filtered is not ch)
+
+    @pytest.mark.no_patch_add_layer
+    @pytest.mark.enablethread
+    def test_add_layer_util_check_init(self, base_settings, image_view, qtbot):
+        def has_layers():
+            return len(image_view.viewer.layers) > 0
+
+        qtbot.waitUntil(has_layers)
+
+    @pytest.mark.no_patch_add_layer
     def test_add_layer_util(self, base_settings, image_view, qtbot):
         def has_layers():
             return len(image_view.viewer.layers) > 0
 
         qtbot.waitUntil(has_layers)
 
         layer = image_view.viewer.layers[0]
+        del image_view.viewer.layers[layer.name]
         assert isinstance(layer, NapariImage)
+        layer.visible = False
 
         def no_worker():
-            return not image_view.worker_list
+            return len(image_view.worker_list) == 0
 
         prev_data = layer.data
 
@@ -317,10 +334,13 @@ def no_worker():
         qtbot.waitUntil(no_worker)
         assert layer.data is prev_data
 
+        del image_view.viewer.layers[layer.name]
+
         image_view._add_layer_util(0, layer, [(NoiseFilterType.Median, 1)])
 
         qtbot.waitUntil(no_worker)
         assert layer.data is not prev_data
+        qtbot.wait(50)
 
 
 def test_search_component_modal(qtbot, image_view, monkeypatch):
@@ -340,3 +360,14 @@ def test_search_component_modal(qtbot, image_view, monkeypatch):
     image_view.component_zoom.assert_called_with(1)
     modal.close()
     image_view.component_unmark.assert_called_once()
+
+
+def test_calc_layer_filter():
+    layer = NapariImage(np.zeros((10, 10)), name="test")
+
+    assert _calc_layer_filter(layer, NoiseFilterType.No, 0)[0] is None
+    assert _calc_layer_filter(layer, NoiseFilterType.No, 1)[0] is None
+    assert _calc_layer_filter(layer, NoiseFilterType.Gauss, 0)[0] is None
+
+    assert _calc_layer_filter(layer, NoiseFilterType.Gauss, 1)[0] is not None
+    assert _calc_layer_filter(layer, NoiseFilterType.Gauss, 1)[0] is not layer.data

package/tests/test_PartSegCore/test_measurements.py

@@ -2334,7 +2334,7 @@ def test_per_component(method, area):
     )
     assert len(result["Measurement per component"][0]) == 1
     assert isinstance(result["Measurement"][0], (float, int))
-    assert result["Measurement per component"][0][0] == result["Measurement"][0]
+    assert isclose(result["Measurement per component"][0][0], result["Measurement"][0])
 
 
 @pytest.mark.parametrize("method", CorrelationEnum.__members__.values())

setup.cfg

@@ -144,7 +144,7 @@ filterwarnings =
 markers =
     enablethread: Allow to use thread in test
     enabledialog: Allow to use dialog in test
-    no_viewer_patch: Do not patch napari viewer
+    no_patch_add_layer: Do not patch napari viewer
 
 [coverage:paths]
 source =