From 3c51413d36e52cda043bc8cd67d87342b25233fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Harri=20J=C3=A4=C3=A4linoja?= Date: Thu, 30 Jan 2025 17:43:02 +0200 Subject: [PATCH] fix cellpose GPU flags --- active_plugins/runcellpose.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/active_plugins/runcellpose.py b/active_plugins/runcellpose.py index 47426d2..6edc915 100644 --- a/active_plugins/runcellpose.py +++ b/active_plugins/runcellpose.py @@ -601,10 +601,13 @@ def run(self, workspace): # Save the image to the Docker mounted directory skimage.io.imsave(temp_img_path, x_data) - cmd = [docker_path, 'run', '--rm', '-v', f'{temp_dir}:/data', self.docker_image.value] + cmd = [docker_path, 'run', '--rm', '-v', f'{temp_dir}:/data',] if self.use_gpu.value: cmd += ['--gpus', 'all'] - cmd += ['cellpose', '--verbose', '--dir', '/data/img', '--pretrained_model'] + cmd += [self.docker_image.value, 'cellpose'] + if self.use_gpu.value: + cmd += ['--use_gpu'] + cmd += ['--verbose', '--dir', '/data/img', '--pretrained_model'] if self.mode.value !='custom': cmd += [self.mode.value] else: