Fixed filepaths

Author: C-Achard

napari_cellseg3d/code_plugins/plugin_convert.py

@@ -46,7 +46,7 @@ def __init__(self, viewer: "napari.Viewer.viewer", parent=None):
         self.aniso_widgets = ui.AnisotropyWidgets(self, always_visible=True)
         self.start_btn = ui.Button("Start", self._start)
 
-        self.results_path = str(Path.home() / Path("cellseg3d/anisotropy"))
+        self.results_path = str(Path.home() / "cellseg3d" / "anisotropy")
         self.results_filewidget.text_field.setText(str(self.results_path))
         self.results_filewidget.check_ready()
 
@@ -145,7 +145,7 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
             text_label="Remove all smaller than (pxs):",
         )
 
-        self.results_path = Path.home() / Path("cellseg3d/small_removed")
+        self.results_path = Path.home() / "cellseg3d" / "small_removed"
         self.results_filewidget.text_field.setText(str(self.results_path))
         self.results_filewidget.check_ready()
 
@@ -233,9 +233,7 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
 
         self.start_btn = ui.Button("Start", self._start)
 
-        self.results_path = str(
-            Path.home() / Path("cellseg3d/instance_labels")
-        )
+        self.results_path = str(Path.home() / "cellseg3d" / "instance_labels")
         self.results_filewidget.text_field.setText(self.results_path)
         self.results_filewidget.check_ready()
 
@@ -326,7 +324,7 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
 
         self.start_btn = ui.Button("Start", self._start)
 
-        self.results_path = Path.home() / Path("cellseg3d/instance")
+        self.results_path = Path.home() / "cellseg3d" / "instance"
         self.results_filewidget.text_field.setText(str(self.results_path))
         self.results_filewidget.check_ready()
 
@@ -417,7 +415,7 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
             text_label="Remove all smaller than (value):",
         )
 
-        self.results_path = str(Path.home() / Path("cellseg3d/threshold"))
+        self.results_path = str(Path.home() / "cellseg3d" / "threshold")
         self.results_filewidget.text_field.setText(self.results_path)
         self.results_filewidget.check_ready()
 

napari_cellseg3d/code_plugins/plugin_crf.py

@@ -138,7 +138,7 @@ def __init__(self, viewer, parent=None):
         self.result_name = None
         self.crf_results = []
 
-        self.results_path = Path.home() / Path("cellseg3d/crf")
+        self.results_path = Path.home() / "cellseg3d" / "crf"
         self.results_filewidget.text_field.setText(str(self.results_path))
         self.results_filewidget.check_ready()
 

napari_cellseg3d/code_plugins/plugin_crop.py

@@ -38,7 +38,7 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
 
         super().__init__(viewer)
         self.docked_widgets = []
-        self.results_path = Path.home() / Path("cellseg3d/cropped")
+        self.results_path = Path.home() / "cellseg3d" / "cropped"
 
         self.btn_start = ui.Button("Start", self._start)
 

napari_cellseg3d/code_plugins/plugin_review.py

@@ -144,7 +144,7 @@ def _build(self):
         # self._show_io_element(self.results_filewidget)
 
         self.results_filewidget.text_field.setText(
-            str(Path.home() / Path("cellseg3d/review"))
+            str(Path.home() / "cellseg3d" / "review")
         )
 
         csv_param_w.setLayout(csv_param_l)

napari_cellseg3d/config.py

@@ -45,7 +45,7 @@
 class ReviewConfig:
     image: np.array = None
     labels: np.array = None
-    csv_path: str = Path.home() / Path("cellseg3d/review")
+    csv_path: str = Path.home() / "cellseg3d" / "review"
     model_name: str = ""
     new_csv: bool = True
     filetype: str = ".tif"
@@ -210,7 +210,7 @@ class InferenceWorkerConfig:
     device: str = "cpu"
     model_info: ModelInfo = ModelInfo()
     weights_config: WeightsInfo = WeightsInfo()
-    results_path: str = str(Path.home() / Path("cellseg3d/inference"))
+    results_path: str = str(Path.home() / "cellseg3d/inference")
     filetype: str = ".tif"
     keep_on_cpu: bool = False
     compute_stats: bool = False
@@ -258,7 +258,7 @@ class TrainingWorkerConfig:
     scheduler_patience: int = 10
     weights_info: WeightsInfo = WeightsInfo()
     # data params
-    results_path_folder: str = str(Path.home() / Path("cellseg3d/training"))
+    results_path_folder: str = str(Path.home() / "cellseg3d" / "training")
     sampling: bool = False
     num_samples: int = 2
     sample_size: List[int] = None