From b3c589b2960158d3c02a1bc694817ddccdfec872 Mon Sep 17 00:00:00 2001 From: Can-Zhao Date: Wed, 2 Apr 2025 22:16:00 +0000 Subject: [PATCH 1/2] fix Error in MAISI Signed-off-by: Can-Zhao --- generation/maisi/maisi_train_vae_tutorial.ipynb | 2 +- generation/maisi/scripts/augmentation.py | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/generation/maisi/maisi_train_vae_tutorial.ipynb b/generation/maisi/maisi_train_vae_tutorial.ipynb index 26343a6a9..780e215a5 100644 --- a/generation/maisi/maisi_train_vae_tutorial.ipynb +++ b/generation/maisi/maisi_train_vae_tutorial.ipynb @@ -326,7 +326,7 @@ } ], "source": [ - "config_file = \"./configs/config_maisi.json\"\n", + "config_file = \"./configs/config_maisi3d-rflow.json\"\n", "config_dict = json.load(open(config_file, \"r\"))\n", "for k, v in config_dict.items():\n", " setattr(args, k, v)\n", diff --git a/generation/maisi/scripts/augmentation.py b/generation/maisi/scripts/augmentation.py index 64469403a..c406c48ef 100644 --- a/generation/maisi/scripts/augmentation.py +++ b/generation/maisi/scripts/augmentation.py @@ -60,7 +60,7 @@ def dilate3d(input_tensor, erosion=3): return output.squeeze(0).squeeze(0) -def augmentation_tumor_bone(pt_nda, output_size, random_seed): +def augmentation_tumor_bone(pt_nda, output_size, random_seed = None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 128] = 1 @@ -113,7 +113,7 @@ def augmentation_tumor_bone(pt_nda, output_size, random_seed): return pt_nda -def augmentation_tumor_liver(pt_nda, output_size, random_seed): +def augmentation_tumor_liver(pt_nda, output_size, random_seed = None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 1] = 1 @@ -163,7 +163,7 @@ def augmentation_tumor_liver(pt_nda, output_size, random_seed): return pt_nda -def augmentation_tumor_lung(pt_nda, output_size, random_seed): +def augmentation_tumor_lung(pt_nda, output_size, random_seed = None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 23] = 1 @@ -227,7 +227,7 @@ def augmentation_tumor_lung(pt_nda, output_size, random_seed): return pt_nda -def augmentation_tumor_pancreas(pt_nda, output_size, random_seed): +def augmentation_tumor_pancreas(pt_nda, output_size, random_seed = None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 4] = 1 @@ -277,7 +277,7 @@ def augmentation_tumor_pancreas(pt_nda, output_size, random_seed): return pt_nda -def augmentation_tumor_colon(pt_nda, output_size, random_seed): +def augmentation_tumor_colon(pt_nda, output_size, random_seed = None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 27] = 1 @@ -335,7 +335,7 @@ def augmentation_tumor_colon(pt_nda, output_size, random_seed): return pt_nda -def augmentation_body(pt_nda, random_seed): +def augmentation_body(pt_nda, random_seed = None): volume = pt_nda.squeeze(0) zoom = RandZoom(min_zoom=0.99, max_zoom=1.01, mode="nearest", align_corners=None, prob=1.0) @@ -347,7 +347,7 @@ def augmentation_body(pt_nda, random_seed): return pt_nda -def augmentation(pt_nda, output_size, random_seed): +def augmentation(pt_nda, output_size, random_seed = None): label_list = torch.unique(pt_nda) label_list = list(label_list.cpu().numpy()) From b32390c4d973731078540d13d570f43f69653e1b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 2 Apr 2025 22:18:20 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- generation/maisi/scripts/augmentation.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/generation/maisi/scripts/augmentation.py b/generation/maisi/scripts/augmentation.py index c406c48ef..55f586594 100644 --- a/generation/maisi/scripts/augmentation.py +++ b/generation/maisi/scripts/augmentation.py @@ -60,7 +60,7 @@ def dilate3d(input_tensor, erosion=3): return output.squeeze(0).squeeze(0) -def augmentation_tumor_bone(pt_nda, output_size, random_seed = None): +def augmentation_tumor_bone(pt_nda, output_size, random_seed=None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 128] = 1 @@ -113,7 +113,7 @@ def augmentation_tumor_bone(pt_nda, output_size, random_seed = None): return pt_nda -def augmentation_tumor_liver(pt_nda, output_size, random_seed = None): +def augmentation_tumor_liver(pt_nda, output_size, random_seed=None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 1] = 1 @@ -163,7 +163,7 @@ def augmentation_tumor_liver(pt_nda, output_size, random_seed = None): return pt_nda -def augmentation_tumor_lung(pt_nda, output_size, random_seed = None): +def augmentation_tumor_lung(pt_nda, output_size, random_seed=None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 23] = 1 @@ -227,7 +227,7 @@ def augmentation_tumor_lung(pt_nda, output_size, random_seed = None): return pt_nda -def augmentation_tumor_pancreas(pt_nda, output_size, random_seed = None): +def augmentation_tumor_pancreas(pt_nda, output_size, random_seed=None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 4] = 1 @@ -277,7 +277,7 @@ def augmentation_tumor_pancreas(pt_nda, output_size, random_seed = None): return pt_nda -def augmentation_tumor_colon(pt_nda, output_size, random_seed = None): +def augmentation_tumor_colon(pt_nda, output_size, random_seed=None): volume = pt_nda.squeeze(0) real_l_volume_ = torch.zeros_like(volume) real_l_volume_[volume == 27] = 1 @@ -335,7 +335,7 @@ def augmentation_tumor_colon(pt_nda, output_size, random_seed = None): return pt_nda -def augmentation_body(pt_nda, random_seed = None): +def augmentation_body(pt_nda, random_seed=None): volume = pt_nda.squeeze(0) zoom = RandZoom(min_zoom=0.99, max_zoom=1.01, mode="nearest", align_corners=None, prob=1.0) @@ -347,7 +347,7 @@ def augmentation_body(pt_nda, random_seed = None): return pt_nda -def augmentation(pt_nda, output_size, random_seed = None): +def augmentation(pt_nda, output_size, random_seed=None): label_list = torch.unique(pt_nda) label_list = list(label_list.cpu().numpy())