celldetective 1.5.0b3__py3-none-any.whl → 1.5.0b4__py3-none-any.whl

celldetective/_version.py

@@ -1 +1 @@
-__version__ = "1.5.0b3"
+__version__ = "1.5.0b4"

celldetective/gui/measure_annotator.py

@@ -950,9 +950,9 @@ class MeasureAnnotator(BaseAnnotator):
                 ].to_numpy()
             )
             self.colors.append(
-                self.df_tracks.loc[
-                    self.df_tracks["FRAME"] == t, ["group_color"]
-                ].to_numpy()
+                self.df_tracks.loc[self.df_tracks["FRAME"] == t, ["group_color"]]
+                .to_numpy()
+                .copy()
             )
             if "TRACK_ID" in self.df_tracks.columns:
                 self.tracks.append(

celldetective/gui/settings/_settings_segmentation_model_training.py

@@ -84,6 +84,12 @@ class SettingsSegmentationModelTraining(CelldetectiveSettingsPanel):
         self.bg_loader = BackgroundLoader()
         self.bg_loader.start()
 
+    def closeEvent(self, event):
+        if self.bg_loader.isRunning():
+            logger.info("Waiting for background loader to finish...")
+            self.bg_loader.wait()
+        super().closeEvent(event)
+
     def _add_to_layout(self):
 
         self._layout.addWidget(self.model_frame)

celldetective/gui/viewers/base_viewer.py

@@ -111,6 +111,11 @@ class StackLoader(QThread):
                 # If nothing to load, wait
                 self.mutex.lock()
                 self.condition.wait(self.mutex, 500)  # Wait 500ms or until new priority
+
+                if not self.running:
+                    self.mutex.unlock()
+                    break
+
                 self.mutex.unlock()
 
 

celldetective/utils/cellpose_utils/__init__.py

@@ -113,13 +113,29 @@ def _prep_cellpose_model(
 
     from cellpose.models import CellposeModel
 
-    model = CellposeModel(
-        gpu=use_gpu,
-        device=device,
-        pretrained_model=path + model_name,
-        model_type=None,
-        nchan=n_channels,
-    )  # diam_mean=30.0,
+    try:
+        model = CellposeModel(
+            gpu=use_gpu,
+            device=device,
+            pretrained_model=path + model_name,
+            model_type=None,
+            nchan=n_channels,
+        )  # diam_mean=30.0,
+    except AssertionError as e:
+        if use_gpu:
+            print(
+                f"[WARNING] Could not load Cellpose model with GPU ({e}). Retrying with CPU..."
+            )
+            device = torch.device("cpu")
+            model = CellposeModel(
+                gpu=False,
+                device=device,
+                pretrained_model=path + model_name,
+                model_type=None,
+                nchan=n_channels,
+            )
+        else:
+            raise e
     if scale is None:
         scale_model = model.diam_mean / model.diam_labels
     else:

{celldetective-1.5.0b3.dist-info → celldetective-1.5.0b4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b3
+Version: 1.5.0b4
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.5.0b3.dist-info → celldetective-1.5.0b4.dist-info}/RECORD

@@ -1,6 +1,6 @@
 celldetective/__init__.py,sha256=LfnOyfUnYPGDc8xcsF_PfYEL7-CqAb7BMBPBIWGv84o,666
 celldetective/__main__.py,sha256=Rzzu9ArxZSgfBVjV-lyn-3oanQB2MumQR6itK5ZaRpA,2597
-celldetective/_version.py,sha256=xyBMhGEXnWbOInuedgW565vK5NILuhG2r2EYCw9E9eU,24
+celldetective/_version.py,sha256=i0XQAcqdHCcwV-JF_A_FeVVfTjXROj_WnqM2Ktzzq1Q,24
 celldetective/events.py,sha256=n15R53c7QZ2wT8gjb0oeNikQbuRBrVVbyNsRCqXjzXA,8166
 celldetective/exceptions.py,sha256=f3VmIYOthWTiqMEV5xQCox2rw5c5e7yog88h-CcV4oI,356
 celldetective/extra_properties.py,sha256=s_2R4_El2p-gQNZ_EpgDxgrN3UnRitN7KDKHhyLuoHc,21681
@@ -30,7 +30,7 @@ celldetective/gui/gui_utils.py,sha256=t6SjEfjcaRH9a0TlbTGEiVRpCgocaCh4lgkIvRgRRw
 celldetective/gui/interactions_block.py,sha256=34VaHFrdKsq1hYuXrosmpP15JU26dSfbyx4lyt1jxNg,28440
 celldetective/gui/interactive_timeseries_viewer.py,sha256=u_amAhLdEHRpYSRwPDtVm5v-JZIz0ANTcG4YGksX1Vo,16079
 celldetective/gui/json_readers.py,sha256=t5rhtIxACj0pdwLrnPs-QjyhQo3P25UGWGgOCIBhQxs,4572
-celldetective/gui/measure_annotator.py,sha256=HdhrU3N207evB9s-pqZNfzJC2Jswx3yHdPPLR8CRILc,38354
+celldetective/gui/measure_annotator.py,sha256=ljNbsKmFXQk0R9zEfBZ6XfBHzFmlL7Gt6QyPHyqh08g,38357
 celldetective/gui/pair_event_annotator.py,sha256=QJHaM-z0K2I36sLf6XCMFMymfw-nFhzfGJ8oxrMfZco,124091
 celldetective/gui/plot_measurements.py,sha256=a_Mks-5XUTn2QEYih0PlXGp2lX3C34zuhK9ozzE1guM,56593
 celldetective/gui/plot_signals_ui.py,sha256=9VmA1yaTcNf1jY7drtK41R1q87dhEk7bXBCq_cQ94fs,28133
@@ -76,7 +76,7 @@ celldetective/gui/settings/_settings_event_model_training.py,sha256=TVPnnYPmdAF6
 celldetective/gui/settings/_settings_measurements.py,sha256=nrVR1dG3B7iyJayRql1yierhKvgXZiu6qVtfkxI1ABA,47947
 celldetective/gui/settings/_settings_neighborhood.py,sha256=ws6H99bKU4NYd2IYyaJj7g9-MScr5W6UB2raP88ytfE,23767
 celldetective/gui/settings/_settings_segmentation.py,sha256=6DihD1mk-dN4Sstdth1iJ-0HR34rTVlTHP-pXUh_rY0,1901
-celldetective/gui/settings/_settings_segmentation_model_training.py,sha256=XxqSCxLHOvn1w8V8ZEEfPAvdwfS0IKz107ox4yll7AA,30229
+celldetective/gui/settings/_settings_segmentation_model_training.py,sha256=6Ftih-_1VaICHBFLs6BPO8kf5ZDohwvDF4dEnhYC19M,30440
 celldetective/gui/settings/_settings_signal_annotator.py,sha256=Mvvre-yHJvRoR-slbkLNwEemuGgiMCQQ4H1BHjFk3r4,12412
 celldetective/gui/settings/_settings_tracking.py,sha256=5ZxJp3o3stD2NKdhqZofIgsUNp73oAN_pIi_bDFAd0Y,53293
 celldetective/gui/settings/_stardist_model_params.py,sha256=dEKhaLcJ4r8VxgBU2DI-hcTaTk5S181O-_CN0j7JSgE,4020
@@ -87,7 +87,7 @@ celldetective/gui/table_ops/_merge_one_hot.py,sha256=gKRgem-u_-JENkVkbjRobsH4TkS
 celldetective/gui/table_ops/_query_table.py,sha256=K-XHSZ1I4v2wwqWjyQAgyFRZJbem3CmTfHmO0vijh9g,1345
 celldetective/gui/table_ops/_rename_col.py,sha256=UAgDSpXJo_h4pLJpHaNc2w2VhbaW4D2JZTgJ3cYC4-g,1457
 celldetective/gui/viewers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-celldetective/gui/viewers/base_viewer.py,sha256=1U936rVnRqevXtyqlZnu_1o_VbWx3BJVofKh_oKG1jM,29857
+celldetective/gui/viewers/base_viewer.py,sha256=gHe9QBX6Lrn567Kc-9T6KoGuLqEP_1q4RROFBd9qLWE,29962
 celldetective/gui/viewers/channel_offset_viewer.py,sha256=aQpxrJX9qM_xX848XnFrxrhTqE22DIshtD-uKL8e4gU,12423
 celldetective/gui/viewers/contour_viewer.py,sha256=riHj03LKXLoa-Ys2o2EhCE5nULfcHMohx9LFoXbI6zU,14720
 celldetective/gui/viewers/size_viewer.py,sha256=uXITjaxg5dhQ09Q6TNUxwLxi-ZglyGFcxEH1RtGIZWw,6020
@@ -161,13 +161,14 @@ celldetective/utils/parsing.py,sha256=1zpIH9tyULCRmO5Kwzy6yA01fqm5uE_mZKYtondy-V
 celldetective/utils/resources.py,sha256=3Fz_W0NYWl_Ixc2AjEmkOv5f7ejXerCLJ2z1iWhGWUI,1153
 celldetective/utils/stats.py,sha256=4TVHRqi38Y0sed-izaMI51sMP0fd5tC5M68EYyfJjkE,3636
 celldetective/utils/types.py,sha256=lRfWSMVzTkxgoctGGp0NqD551akuxu0ygna7zVGonTg,397
-celldetective/utils/cellpose_utils/__init__.py,sha256=grsglxR29vj42tlgsBoXnVnjrIJWsBXqbtkjFjzqH7A,4898
+celldetective/utils/cellpose_utils/__init__.py,sha256=MeRDojrAkBSXe-wlLu5KIih5wXP9B2aPdP39JLYpoGE,5417
 celldetective/utils/event_detection/__init__.py,sha256=KX20PwPTevdbZ-25otDy_QTmealcDx5xNCfH2SOVIZM,323
 celldetective/utils/plots/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/utils/plots/regression.py,sha256=oUCn29-hp7PxMqC-R0yoL60KMw5ZWpZAIoCDh2ErlcY,1764
 celldetective/utils/stardist_utils/__init__.py,sha256=e9s3DEaTKCUOGZb5k_DgShBTl4B0U-Jmg3Ioo8D5PyE,3978
-celldetective-1.5.0b3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.5.0b4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/test_cellpose_fallback.py,sha256=BJZTDFF8sFR1x7rDbvZQ2RQOB1OP6wuFBRfc8zbl5zw,3513
 tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
 tests/test_filters.py,sha256=uj4NVyUnKXa18EpTSiWCetGKI1VFopDyNSJSUxX44wA,1689
 tests/test_io.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
@@ -181,10 +182,11 @@ tests/test_tracking.py,sha256=_YLjwQ3EChQssoHDfEnUJ7fI1yC5KEcJsFnAVR64L70,18909
 tests/test_utils.py,sha256=aSB_eMw9fzTsnxxdYoNmdQQRrXkWqBXB7Uv4TGU6kYE,4778
 tests/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/gui/test_enhancements.py,sha256=3x9au_rkQtMZ94DRj3OaEHKPr511RrWqBAUAcNQn1ys,13453
+tests/gui/test_measure_annotator_bugfix.py,sha256=tPfgWNKC0UkvrVssSrUcVDC1qgpzx6l2yCqvKtKYkM4,4544
 tests/gui/test_new_project.py,sha256=wRjW2vEaZb0LWT-f8G8-Ptk8CW9z8-FDPLpV5uqj6ck,8778
 tests/gui/test_project.py,sha256=KzAnodIc0Ovta0ARL5Kr5PkOR5euA6qczT_GhEZpyE4,4710
-celldetective-1.5.0b3.dist-info/METADATA,sha256=D4LkOtPQrdeuX4zW5_OKXlN1dxkxaZx_zqdILC36-Hk,10947
-celldetective-1.5.0b3.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
-celldetective-1.5.0b3.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.5.0b3.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.5.0b3.dist-info/RECORD,,
+celldetective-1.5.0b4.dist-info/METADATA,sha256=VgzQFDS1ExiiQdY4MjqmWfrRTC-MJQR1meL7t0Q8eMY,10947
+celldetective-1.5.0b4.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
+celldetective-1.5.0b4.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.5.0b4.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.5.0b4.dist-info/RECORD,,

tests/gui/test_measure_annotator_bugfix.py

@@ -0,0 +1,130 @@
+import pytest
+import os
+import pandas as pd
+import numpy as np
+import logging
+from PyQt5 import QtCore
+from celldetective.gui.InitWindow import AppInitWindow
+from celldetective.gui.measure_annotator import MeasureAnnotator
+from celldetective import get_software_location
+from unittest.mock import patch
+import shutil
+import tifffile
+
+software_location = get_software_location()
+
+
+@pytest.fixture(autouse=True)
+def disable_logging():
+    """Disable all logging to avoid Windows OSError with pytest capture."""
+    logger = logging.getLogger()
+    try:
+        logging.disable(logging.CRITICAL)
+        yield
+    finally:
+        logging.disable(logging.NOTSET)
+
+
+@pytest.fixture
+def app(qtbot):
+    test_app = AppInitWindow(software_location=software_location)
+    qtbot.addWidget(test_app)
+    return test_app
+
+
+def create_dummy_movie(exp_dir, well="W1", pos="100", prefix="sample", frames=5):
+    movie_dir = os.path.join(exp_dir, well, pos, "movie")
+    os.makedirs(movie_dir, exist_ok=True)
+    # Use a single multi-page TIF as expected by locate_stack
+    movie_path = os.path.join(movie_dir, f"{prefix}.tif")
+    img = np.zeros((frames, 100, 100), dtype=np.uint16)
+    tifffile.imwrite(movie_path, img)
+
+
+def test_measure_annotator_colors_writable(app, qtbot, tmp_path):
+    """
+    Test that self.colors in MeasureAnnotator contains writable arrays.
+    This verifies the fix for 'ValueError: assignment destination is read-only'.
+    """
+    exp_dir = str(tmp_path / "ExperimentColors")
+    os.makedirs(os.path.join(exp_dir, "W1", "100", "output", "tables"), exist_ok=True)
+    os.makedirs(os.path.join(exp_dir, "configs"), exist_ok=True)
+
+    with open(os.path.join(exp_dir, "config.ini"), "w") as f:
+        f.write(
+            "[MovieSettings]\nmovie_prefix = sample\nlen_movie = 10\nshape_x = 100\nshape_y = 100\npxtoum = 1.0\nframetomin = 1.0\n"
+        )
+        f.write(
+            "[Labels]\nconcentrations = 0\ncell_types = dummy\nantibodies = none\npharmaceutical_agents = none\n[Channels]\nChannel1 = 0\n"
+        )
+
+    create_dummy_movie(exp_dir, well="W1", pos="100", prefix="sample", frames=10)
+
+    # DataFrame with tracks
+    df = pd.DataFrame(
+        {
+            "TRACK_ID": [1, 1],
+            "FRAME": [0, 1],
+            "group_experimental": ["A", "A"],
+            "area": [100.0, 110.0],
+            "POSITION_X": [10, 12],
+            "POSITION_Y": [10, 12],
+            "status": [0, 0],  # Ensure status column exists
+        }
+    )
+    # The 'group_color' column is usually generated inside MeasureAnnotator,
+    # but let's see if we need to let it generate it.
+    # MeasureAnnotator calls 'color_from_state', then assigns 'group_color'.
+
+    traj_path = os.path.join(
+        exp_dir, "W1", "100", "output", "tables", "trajectories_effectors.csv"
+    )
+    df.to_csv(traj_path, index=False)
+
+    app.experiment_path_selection.setText(exp_dir)
+    qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+    qtbot.waitUntil(lambda: hasattr(app, "control_panel"), timeout=30000)
+
+    cp = app.control_panel
+    p0 = cp.ProcessPopulations[0]
+
+    qtbot.waitUntil(lambda: cp.well_list.count() > 0, timeout=30000)
+
+    with patch.object(cp.well_list, "getSelectedIndices", return_value=[0]):
+        with patch.object(cp.position_list, "getSelectedIndices", return_value=[0]):
+
+            cp.update_position_options()
+            qtbot.wait(500)
+
+            qtbot.mouseClick(p0.check_measurements_btn, QtCore.Qt.LeftButton)
+
+            try:
+                qtbot.waitUntil(lambda: hasattr(p0, "measure_annotator"), timeout=15000)
+            except Exception:
+                print("DEBUG: measure_annotator not found on p0.")
+                raise
+
+            annotator = p0.measure_annotator
+            qtbot.wait(1000)
+            assert annotator is not None
+
+            # Verify that self.colors arrays are writable
+            # extract_scatter_from_trajectories should have been called during init
+            assert hasattr(annotator, "colors")
+            assert len(annotator.colors) > 0
+
+            # Check the first frame's colors
+            colors_frame_0 = annotator.colors[0]
+
+            # Check flags
+            assert colors_frame_0.flags[
+                "WRITEABLE"
+            ], "self.colors arrays must be writable"
+
+            # Try to modify (should not raise ValueError)
+            try:
+                colors_frame_0[0] = "lime"
+            except ValueError as e:
+                pytest.fail(f"Could not modify colors array: {e}")
+
+            annotator.close()

tests/test_cellpose_fallback.py

@@ -0,0 +1,101 @@
+import unittest
+from unittest.mock import MagicMock, patch
+import sys
+
+# Do not import torch here to avoid WinError 1114 if environment is broken.
+# We will mock it in setUp.
+
+
+class TestCellposeFallback(unittest.TestCase):
+
+    def setUp(self):
+        # Create a mock for torch
+        self.mock_torch = MagicMock()
+        self.mock_torch.device = MagicMock(return_value="cpu")
+        self.mock_torch.cuda = MagicMock()
+        self.mock_torch.cuda.is_available.return_value = (
+            False  # Default to CPU environment simulation
+        )
+
+        # Patch modules so that 'import torch' and 'import cellpose' work with our mocks
+        # We need to patch 'torch' in sys.modules BEFORE importing code that uses it.
+        self.modules_patcher = patch.dict(
+            sys.modules,
+            {
+                "torch": self.mock_torch,
+                "cellpose": MagicMock(),
+                "cellpose.models": MagicMock(),
+            },
+        )
+        self.modules_patcher.start()
+
+        # Define a mock CellposeModel that we can control
+        self.MockCellposeModel = MagicMock()
+        sys.modules["cellpose.models"].CellposeModel = self.MockCellposeModel
+
+    def tearDown(self):
+        self.modules_patcher.stop()
+
+    def test_gpu_fallback_on_assertion_error(self):
+        """
+        Test that _prep_cellpose_model falls back to CPU if GPU init fails with AssertionError.
+        """
+        # Lazy import inside the test method/patch context
+        from celldetective.utils.cellpose_utils import _prep_cellpose_model
+
+        # Side effect for CellposeModel constructor
+        def side_effect(gpu=False, **kwargs):
+            if gpu:
+                raise AssertionError("Torch not compiled with CUDA enabled")
+
+            # Return a mock model object
+            model = MagicMock()
+            model.diam_mean = 30.0
+            model.diam_labels = 30.0
+            return model
+
+        self.MockCellposeModel.side_effect = side_effect
+
+        # Call the function with use_gpu=True
+        # We expect it to try with gpu=True, fail, print warning, and retry with gpu=False
+        model, scale = _prep_cellpose_model(
+            model_name="fake_model", path="fake_path/", use_gpu=True, n_channels=2
+        )
+
+        # Check call history
+        self.assertEqual(self.MockCellposeModel.call_count, 2)
+
+        args1, kwargs1 = self.MockCellposeModel.call_args_list[0]
+        self.assertTrue(kwargs1.get("gpu"), "First call should try gpu=True")
+
+        args2, kwargs2 = self.MockCellposeModel.call_args_list[1]
+        self.assertFalse(kwargs2.get("gpu"), "Second call should retry with gpu=False")
+
+        self.assertIsNotNone(model)
+
+    def test_gpu_success(self):
+        """
+        Test that _prep_cellpose_model works normally if GPU init succeeds.
+        """
+        from celldetective.utils.cellpose_utils import _prep_cellpose_model
+
+        # Side effect for success
+        def side_effect(gpu=False, **kwargs):
+            model = MagicMock()
+            model.diam_mean = 30.0
+            model.diam_labels = 30.0
+            return model
+
+        self.MockCellposeModel.side_effect = side_effect
+
+        model, scale = _prep_cellpose_model(
+            model_name="fake_model", path="fake_path/", use_gpu=True, n_channels=2
+        )
+
+        self.assertEqual(self.MockCellposeModel.call_count, 1)
+        args, kwargs = self.MockCellposeModel.call_args
+        self.assertTrue(kwargs.get("gpu"))
+
+
+if __name__ == "__main__":
+    unittest.main()