added saving as zip

Author: C-Achard

napari_cellseg3d/_tests/test_utils.py

@@ -67,12 +67,12 @@ def test_get_padding_dim():
 
     assert pad == [2048, 32, 64]
 
-    tensor = torch.randn(65,70,80)
+    tensor = torch.randn(65, 70, 80)
     size = tensor.size()
 
     pad = utils.get_padding_dim(size)
 
-    assert pad == [128,128,128]
+    assert pad == [128, 128, 128]
 
 
 def test_normalize_x():

napari_cellseg3d/interface.py

@@ -1,5 +1,5 @@
-from qtpy.QtCore import QUrl
 from qtpy.QtCore import Qt
+from qtpy.QtCore import QUrl
 from qtpy.QtGui import QDesktopServices
 from qtpy.QtWidgets import QCheckBox
 from qtpy.QtWidgets import QComboBox

napari_cellseg3d/model_framework.py

@@ -13,10 +13,10 @@
 from napari_cellseg3d import interface as ui
 from napari_cellseg3d import utils
 from napari_cellseg3d.log_utility import Log
-from napari_cellseg3d.models import TRAILMAP_test as TMAP
 from napari_cellseg3d.models import model_SegResNet as SegResNet
 from napari_cellseg3d.models import model_TRAILMAP as TRAILMAP
 from napari_cellseg3d.models import model_VNet as VNet
+from napari_cellseg3d.models import TRAILMAP_test as TMAP
 from napari_cellseg3d.plugin_base import BasePluginFolder
 
 warnings.formatwarning = utils.format_Warning

napari_cellseg3d/model_workers.py

@@ -9,9 +9,9 @@
 from monai.data import CacheDataset
 from monai.data import DataLoader
 from monai.data import Dataset
-from monai.data import PatchDataset
 from monai.data import decollate_batch
 from monai.data import pad_list_data_collate
+from monai.data import PatchDataset
 from monai.inferers import sliding_window_inference
 from monai.metrics import DiceMetric
 from monai.transforms import AsDiscrete

napari_cellseg3d/models/unet/model.py

@@ -1,10 +1,8 @@
 import torch.nn as nn
 
-from napari_cellseg3d.models.unet.buildingblocks import (
-    DoubleConv,
-    create_encoders,
-    create_decoders,
-)
+from napari_cellseg3d.models.unet.buildingblocks import create_decoders
+from napari_cellseg3d.models.unet.buildingblocks import create_encoders
+from napari_cellseg3d.models.unet.buildingblocks import DoubleConv
 
 
 def number_of_features_per_level(init_channel_number, num_levels):

napari_cellseg3d/plugin_convert.py

@@ -4,11 +4,9 @@
 
 import napari_cellseg3d.interface as ui
 from napari_cellseg3d import utils
-from napari_cellseg3d.model_instance_seg import (
-    to_semantic,
-    to_instance,
-    clear_small_objects,
-)
+from napari_cellseg3d.model_instance_seg import clear_small_objects
+from napari_cellseg3d.model_instance_seg import to_instance
+from napari_cellseg3d.model_instance_seg import to_semantic
 from napari_cellseg3d.plugin_base import BasePluginFolder
 
 

napari_cellseg3d/plugin_metrics.py

@@ -4,7 +4,8 @@
     FigureCanvasQTAgg as FigureCanvas,
 )
 from matplotlib.figure import Figure
-from monai.transforms import SpatialPad, ToTensor
+from monai.transforms import SpatialPad
+from monai.transforms import ToTensor
 from tifffile import imread
 
 from napari_cellseg3d import interface as ui

napari_cellseg3d/plugin_model_inference.py

@@ -1,8 +1,8 @@
 import os
 import warnings
-import numpy as np
 
 import napari
+import numpy as np
 
 # Qt
 from qtpy.QtWidgets import QLabel

napari_cellseg3d/plugin_model_training.py

@@ -1,12 +1,13 @@
 import os
+import shutil
 import warnings
-import torch
-from torch import nn
+import zipfile
 from pathlib import Path
 
 import matplotlib.pyplot as plt
 import napari
 import numpy as np
+import torch
 from matplotlib.backends.backend_qt5agg import (
     FigureCanvasQTAgg as FigureCanvas,
 )
@@ -866,9 +867,21 @@ def on_finish(self):
 
         del self.worker
         self.worker = None
-        self.results_path_folder = ""
         self.empty_cuda_cache()
 
+        shutil.make_archive(
+            self.results_path_folder, "zip", self.results_path_folder
+        )
+
+        # if zipfile.is_zipfile(self.results_path_folder+".zip"):
+
+        # if not shutil.rmtree.avoids_symlink_attacks:
+        #     raise RuntimeError("shutil.rmtree is not safe on this platform")
+
+        # shutil.rmtree(self.results_path_folder)
+
+        self.results_path_folder = ""
+
         # self.clean_cache() # trying to fix memory leak
 
     def on_error(self):
@@ -958,6 +971,7 @@ def plot_loss(self, loss, dice_metric):
 
             plot_path = self.results_path_folder + "/Loss_plots"
             os.makedirs(plot_path, exist_ok=True)
+
             if self.canvas is not None:
                 self.canvas.figure.savefig(
                     (

napari_cellseg3d/plugin_utilities.py

@@ -1,8 +1,8 @@
 import napari
 
 # Qt
-from qtpy.QtWidgets import QTabWidget
 from qtpy.QtWidgets import QSizePolicy
+from qtpy.QtWidgets import QTabWidget
 
 from napari_cellseg3d.plugin_convert import ConvertUtils