get around the windows gooey issue chriskiehl/Gooey#907

deepfinder/commands/convert_tiff_to_h5.py

@@ -6,6 +6,8 @@
 from deepfinder.commands import utils
 from gooey import Gooey
 
+utils.run_with_python_on_windows(__file__)
+
 def get_tiff_files(path):
     return sorted([f for f in path.iterdir() if f.suffix.lower() in ['.tif', '.tiff']])
 

deepfinder/commands/detect_spots.py

@@ -6,6 +6,8 @@
 from deepfinder.commands.convert_tiff_to_h5 import convert_tiff_to_h5
 from gooey import Gooey
 
+utils.run_with_python_on_windows(__file__)
+
 def detect_spots(tiffs_path, detector_path, command, output_path):
     output_folder = output_path.with_suffix('')
     output_folder.mkdir(exist_ok=True, parents=True)

deepfinder/commands/exodeepfinder.py

@@ -11,6 +11,8 @@
 import inspect
 from gooey import Gooey, GooeyParser
 
+deepfinder.commands.utils.run_with_python_on_windows(__file__)
+
 deepfinder.commands.utils.ignore_gooey_if_args()
 
 def get_description(function):

deepfinder/commands/generate_annotation.py

@@ -12,6 +12,8 @@
 import deepfinder.utils.objl as ol
 from gooey import Gooey
 
+utils.run_with_python_on_windows(__file__)
+
 def cluster(segmentation_path, cluster_radius, output_path=None):
     output_path.parent.mkdir(exist_ok=True, parents=True)
 

deepfinder/commands/generate_segmentation.py

@@ -7,6 +7,8 @@
 import deepfinder.utils.objl as ol
 from gooey import Gooey
 
+utils.run_with_python_on_windows(__file__)
+
 # path_output.mkdir(exist_ok=True, parents=True)
 
 # First, define the (t,y,x) mask for exocytosis event:

deepfinder/commands/merge_detector_expert.py

@@ -7,6 +7,8 @@
 from deepfinder.commands import utils
 from gooey import Gooey
 
+utils.run_with_python_on_windows(__file__)
+
 def objlist2motl(objlist_path):
     """Translate function from MATLAB. Returns the motive list filled up with particle information from xml file.
 

deepfinder/commands/segment.py

@@ -4,11 +4,8 @@
 import deepfinder.utils.common as cm
 import deepfinder.utils.smap as sm
 from gooey import Gooey
-import platform, sys, subprocess
 
-if platform.system() == 'Windows' and len(sys.argv) == 1:
-    subprocess.call([sys.executable, __file__])
-    sys.exit()
+utils.run_with_python_on_windows(__file__)
 
 def segment(image_path, weights_path, output_path=None, visualization=False, patch_size=160):
     if output_path is None:

deepfinder/commands/structure_training_dataset.py

@@ -5,6 +5,8 @@
 from deepfinder.commands import utils
 from gooey import Gooey
 
+utils.run_with_python_on_windows(__file__)
+
 def structure_training_dataset(input_path:Path, output_path:Path, movie:Path, merged_segmentation:Path, merged_annotation:Path, split:float):
     if output_path.exists() and len(list(output_path.iterdir()))>0:
 

deepfinder/commands/train.py

@@ -2,6 +2,8 @@
 from deepfinder.commands import utils
 from gooey import Gooey
 
+utils.run_with_python_on_windows(__file__)
+
 def train(dataset_path, output_path, n_epochs, steps_per_epoch):
     from deepfinder.training import Train
     from deepfinder.utils.dataloader import Dataloader

deepfinder/commands/utils.py

@@ -1,6 +1,13 @@
-import sys, argparse
+import sys, argparse, platform, subprocess
 from gooey import GooeyParser
 
+# On windows, the command GUIs cannot be used directly, they must be called with python and full path to the command (because of [a known Gooey issue](https://github.com/chriskiehl/Gooey/issues/907))
+# So, if called from the command: rerun the same file but with python and full path
+def run_with_python_on_windows(file):
+    if platform.system() == 'Windows' and len(sys.argv) == 1 and not sys.argv[0].endswith('.py'):
+        subprocess.call([sys.executable, file])
+        sys.exit()
+
 def ignore_gooey_if_args():
     if len(sys.argv) > 1 and '--ignore-gooey' not in sys.argv:
         sys.argv.append('--ignore-gooey')