Version bump + black + inference test

Author: C-Achard

napari_cellseg3d/_tests/test_dock_widget.py

@@ -6,9 +6,7 @@
 
 
 def test_prepare(make_napari_viewer):
-    path_image = str(
-        Path(__file__).resolve().parent / "res/test.tif"
-    )
+    path_image = str(Path(__file__).resolve().parent / "res/test.tif")
     image = imread(str(path_image))
     viewer = make_napari_viewer()
     viewer.add_image(image)
@@ -18,4 +16,6 @@ def test_prepare(make_napari_viewer):
 
     assert widget.filetype == ".tif"
     assert widget.as_folder == False
-    assert Path(widget.csv_path) == (Path(__file__).resolve().parent / "res/_train0.csv")
+    assert Path(widget.csv_path) == (
+        Path(__file__).resolve().parent / "res/_train0.csv"
+    )

napari_cellseg3d/_tests/test_plugin_inference.py

@@ -0,0 +1,48 @@
+from tifffile import imread
+from pathlib import Path
+import warnings
+
+from qtpy.QtWidgets import QTextEdit
+
+from napari_cellseg3d.code_plugins.plugin_model_inference import Inferer
+
+
+class LogFixture(QTextEdit):
+    def __init__(self):
+        super(LogFixture, self).__init__()
+
+    def print_and_log(self, text, printing=None):
+        print(text)
+
+    def warn(self, warning):
+        warnings.warn(warning)
+
+
+def test_inference(make_napari_viewer, qtbot):
+
+    im_path = str(Path(__file__).resolve().parent / "res/test.tif")
+    image = imread(im_path)
+
+    assert image.shape == (6, 6, 6)
+
+    viewer = make_napari_viewer()
+    widget = Inferer(viewer)
+    widget.log = LogFixture()
+    viewer.window.add_dock_widget(widget)
+    viewer.add_image(image)
+
+    assert len(viewer.layers) == 1
+
+    widget.window_infer_box.setChecked(True)
+    widget.window_overlap_slider.setValue(0.0)
+    widget.keep_data_on_cpu_box.setChecked(True)
+
+    assert widget.check_ready()
+
+    widget.start()
+    assert widget.worker is not None
+
+    with qtbot.waitSignal(signal=widget.worker.finished) as blocker:
+        blocker.connect(widget.worker.errored)
+
+    assert len(viewer.layers) == 2

napari_cellseg3d/_tests/test_plugin_utils.py

@@ -1,12 +1,14 @@
 from napari_cellseg3d.code_plugins.plugin_utilities import Utilities
 from napari_cellseg3d.code_plugins.plugin_utilities import UTILITIES_WIDGETS
 
+
 def test_utils_plugin(make_napari_viewer):
     view = make_napari_viewer()
     widget = Utilities(view)
 
     view.window.add_dock_widget(widget)
     for i, utils_name in enumerate(UTILITIES_WIDGETS.keys()):
         widget.utils_choice.setCurrentIndex(i)
-        assert isinstance(widget.utils_widgets[i], UTILITIES_WIDGETS[utils_name])
-
+        assert isinstance(
+            widget.utils_widgets[i], UTILITIES_WIDGETS[utils_name]
+        )

napari_cellseg3d/_tests/test_review.py

@@ -15,7 +15,9 @@ def test_launch_review(make_napari_viewer):
     widget.folder_choice.setChecked(True)
     widget.image_filewidget.text_field = im_path
     widget.labels_filewidget.text_field = im_path
-    widget.results_filewidget.text_field = str(Path(__file__).resolve().parent / "res")
+    widget.results_filewidget.text_field = str(
+        Path(__file__).resolve().parent / "res"
+    )
 
     widget.run_review()
     widget._viewer.close()

napari_cellseg3d/_tests/test_weight_download.py

@@ -1,4 +1,7 @@
-from napari_cellseg3d.code_models.model_workers import WeightsDownloader, WEIGHTS_DIR
+from napari_cellseg3d.code_models.model_workers import (
+    WeightsDownloader,
+    WEIGHTS_DIR,
+)
 from napari_cellseg3d.config import ModelInfo
 
 
@@ -8,12 +11,7 @@ def test_weight_download():
 
     downloader = WeightsDownloader()
 
-    downloader.download_weights(
-        info.name,
-        info.get_model().get_weights_file()
-    )
+    downloader.download_weights(info.name, info.get_model().get_weights_file())
     result_path = WEIGHTS_DIR / str(info.get_model().get_weights_file())
 
     assert result_path.is_file()
-
-

napari_cellseg3d/code_models/model_framework.py

@@ -119,25 +119,29 @@ def __init__(
 
     def send_log(self, text):
         """Emit a signal to print in a Log"""
-        self.log.print_and_log(text)
+        if self.log is not None:
+            self.log.print_and_log(text)
 
     def save_log(self):
         """Saves the worker's log to disk at self.results_path when called"""
-        log = self.log.toPlainText()
-
-        path = self.results_path
-
-        if len(log) != 0:
-            with open(
-                path + f"/Log_report_{utils.get_date_time()}.txt",
-                "x",
-            ) as f:
-                f.write(log)
-                f.close()
+        if self.log is not None:
+            log = self.log.toPlainText()
+
+            path = self.results_path
+
+            if len(log) != 0:
+                with open(
+                    path + f"/Log_report_{utils.get_date_time()}.txt",
+                    "x",
+                ) as f:
+                    f.write(log)
+                    f.close()
+            else:
+                warnings.warn(
+                    "No job has been completed yet, please start one or re-open the log window."
+                )
         else:
-            warnings.warn(
-                "No job has been completed yet, please start one or re-open the log window."
-            )
+            warnings.warn(f"No logger defined : Log is {self.log}")
 
     def save_log_to_path(self, path):
         """Saves the worker log to a specific path. Cannot be used with connect.

napari_cellseg3d/code_models/model_workers.py

@@ -137,6 +137,7 @@ def show_progress(count, block_size, total_size):
                 url, reporthook=show_progress
             )
             with tarfile.open(filename, mode="r:gz") as tar:
+
                 def is_within_directory(directory, target):
 
                     abs_directory = Path(directory).resolve()
@@ -148,12 +149,16 @@ def is_within_directory(directory, target):
 
                     return abs_directory in abs_target.parents
 
-                def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
+                def safe_extract(
+                    tar, path=".", members=None, *, numeric_owner=False
+                ):
 
                     for member in tar.getmembers():
                         member_path = str(Path(path) / member.name)
                         if not is_within_directory(path, member_path):
-                            raise Exception("Attempted Path Traversal in Tar File")
+                            raise Exception(
+                                "Attempted Path Traversal in Tar File"
+                            )
 
                     tar.extractall(path, members, numeric_owner=numeric_owner)
 

napari_cellseg3d/code_plugins/plugin_crop.py

@@ -308,7 +308,7 @@ def _start(self):
         else:
             self.image_layer1.opacity = 0.7
             self.image_layer1.colormap = "inferno"
-            self.image_layer1.contrast_limits = [200, 1000] # TODO generalize
+            self.image_layer1.contrast_limits = [200, 1000]  # TODO generalize
 
             self.image_layer1.refresh()
 
@@ -334,7 +334,7 @@ def add_isotropic_layer(
         self,
         layer,
         colormap="inferno",
-        contrast_lim= [200, 1000],  # TODO generalize ?
+        contrast_lim=[200, 1000],  # TODO generalize ?
         opacity=0.7,
         visible=True,
     ):

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napari-cellseg3d
-version = 0.0.1rc4
+version = 0.0.2rc1
 author = Cyril Achard, Maxime Vidal, Jessy Lauer, Mackenzie Mathis
 author_email = [email protected], [email protected], [email protected]