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Generation_Pipeline_filter/Atlas_X_1k.txt

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Generation_Pipeline_filter/best_metric_model_classification3d_dict.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:331395112f91825f17114067c7218c6c9bd727378cbe4c43a1d47edb140b7282
+size 45594067

Generation_Pipeline_filter/get_syn_list.py

@@ -0,0 +1,26 @@
+import os
+
+organ = 'colon'
+real_organ = []
+with open(f'real_set/{organ}.txt', 'r') as f:
+    real_organ=f.readlines()
+real_organ = [i.split('\n')[0] for i in real_organ]
+
+
+total_case = []
+with open(f'real_total.txt', 'r') as f:
+    total_case=f.readlines()
+total_case = [i.split('\n')[0] for i in total_case]
+
+
+absence2= list(set(total_case) - set(real_organ))
+absence2 = [i for i in absence2]
+# breakpoint()
+
+filename = open(f'syn_{organ}/healthy_{organ}_1k.txt','a+')#dict转txt
+for i in absence2:
+    filename.write(i)
+    filename.write('\n')
+filename.close()
+
+

Generation_Pipeline_filter/get_training_list.py

@@ -0,0 +1,45 @@
+import os
+
+total_case = []
+with open(f'real_total.txt', 'r') as f:
+    total_case=f.readlines()
+total_case = [i.split('\n')[0] for i in total_case]
+
+
+real_organ = []
+with open(f'val_set/bodymap_liver.txt', 'r') as f:
+    real_organ=f.readlines()
+real_organ = [i.split('\n')[0] for i in real_organ]
+total_case= list(set(total_case) - set(real_organ))
+total_case = [i for i in total_case]
+
+real_organ = []
+with open(f'val_set/bodymap_pancreas.txt', 'r') as f:
+    real_organ=f.readlines()
+real_organ = [i.split('\n')[0] for i in real_organ]
+total_case= list(set(total_case) - set(real_organ))
+total_case = [i for i in total_case]
+
+real_organ = []
+with open(f'val_set/bodymap_kidney.txt', 'r') as f:
+    real_organ=f.readlines()
+real_organ = [i.split('\n')[0] for i in real_organ]
+total_case= list(set(total_case) - set(real_organ))
+total_case = [i for i in total_case]
+
+real_organ = []
+with open(f'val_set/bodymap_colon.txt', 'r') as f:
+    real_organ=f.readlines()
+real_organ = [i.split('\n')[0] for i in real_organ]
+total_case= list(set(total_case) - set(real_organ))
+total_case = [i for i in total_case]
+
+
+
+filename = open(f'Atlas_X_1k.txt','a+')#dict转txt
+for i in total_case:
+    filename.write(i)
+    filename.write('\n')
+filename.close()
+
+

Generation_Pipeline_filter/real_set/colon.txt

@@ -0,0 +1,126 @@
+BDMAP_00001078
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Generation_Pipeline_filter/real_set/kidney.txt

@@ -0,0 +1,489 @@
+BDMAP_00000245
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Generation_Pipeline_filter/real_set/liver.txt

@@ -0,0 +1,159 @@
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Generation_Pipeline_filter/real_set/pancreas.txt

@@ -0,0 +1,281 @@
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Generation_Pipeline_filter/real_total.txt

@@ -0,0 +1,1054 @@
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Generation_Pipeline_filter/resample.py

@@ -0,0 +1,120 @@
+import os, time, csv
+import numpy as np
+import torch
+from sklearn.metrics import confusion_matrix
+from scipy import ndimage
+from scipy.ndimage import label
+from functools import partial
+import monai
+from monai.transforms import AsDiscrete,AsDiscreted,Compose,Invertd,SaveImaged
+from monai import transforms, data
+import nibabel as nib
+
+import warnings
+warnings.filterwarnings("ignore")
+
+import argparse
+parser = argparse.ArgumentParser(description='colon tumor validation')
+
+# file dir
+parser.add_argument('--data_root', default=None, type=str)
+parser.add_argument('--organ_type', default='colon', type=str)
+parser.add_argument('--save_dir', default='out', type=str)
+parser.add_argument('--data_file', default='out', type=str)
+parser.add_argument('--ddim_ts', default=50, type=int)
+parser.add_argument('--fg_thresh', default=30, type=int)
+parser.add_argument('--start', default=0, type=int)
+parser.add_argument('--end', default=1000, type=int)
+
+def voxel2R(A):
+    return (np.array(A)/4*3/np.pi)**(1/3)
+    
+def _get_loader(args):
+    # val_data_dir = args.val_dir
+    # datalist_json = args.json_dir 
+    val_org_transform = transforms.Compose(
+        [
+            transforms.LoadImaged(keys=["image"], dtype=np.int16),
+            transforms.AddChanneld(keys=["image"]),
+            transforms.Orientationd(keys=["image"], axcodes="RAS"),
+            transforms.Spacingd(keys=["image"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear")),
+            # transforms.ScaleIntensityRanged(keys=["image"], a_min=-175, a_max=250, b_min=0.0, b_max=1.0, clip=True),
+            transforms.ToTensord(keys=["image"]),
+        ]
+    )
+
+    val_img=[]
+    val_name=[]
+    
+    for line in open(args.data_file):
+        # name = line.strip().split()[1].split('.')[0]
+        # val_img.append(args.data_root + line.strip().split()[0])
+        # val_lbl.append(args.data_root + line.strip().split()[1])
+        # breakpoint()
+        name = line.strip()
+        val_img.append(os.path.join(args.data_root, name, 'ct.nii.gz'))
+        val_name.append(name)
+    data_dicts_val = [{'image': image, 'name': name}
+                for image, name in zip(val_img, val_name)]
+    
+    if args.end < len(data_dicts_val):
+        data_dicts_val = data_dicts_val[args.start:args.end]
+    else:
+        data_dicts_val = data_dicts_val[args.start:]
+    print('val len {}'.format(len(data_dicts_val)))
+    val_org_ds = data.Dataset(data_dicts_val, transform=val_org_transform)
+    val_org_loader = data.DataLoader(val_org_ds, batch_size=1, shuffle=False, num_workers=4, sampler=None, pin_memory=True)
+
+    post_transforms = Compose([
+        Invertd(
+            keys=['image'],
+            transform=val_org_transform,
+            orig_keys="image",
+            nearest_interp=False,
+            # nearest_interp=True,
+            to_tensor=True,
+        )
+    ])
+    return val_org_loader, post_transforms
+
+def main():
+    args = parser.parse_args()
+    output_dir = args.save_dir
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+    print("MAIN Argument values:")
+    for k, v in vars(args).items():
+        print(k, '=>', v)
+    print('-----------------')
+
+    ## loader and post_transform
+    val_loader, post_transforms = _get_loader(args)
+
+    start_time=0
+    with torch.no_grad():
+        for idx, val_data in enumerate(val_loader):
+            print('idx',idx)
+            if idx == 0:
+                start_time = time.time()
+
+            data_names = val_data['name']
+            case_name = data_names[0].split('/')[-1]
+            print('case_name', case_name)
+            original_affine = val_data["image_meta_dict"]["original_affine"][0].numpy()
+
+            val_data = [post_transforms(i) for i in data.decollate_batch(val_data)]
+            synt_data = val_data[0]['image'][0]
+            final_data = synt_data.cpu().numpy()
+
+            # synt_data = val_data['image']
+            # final_data = synt_data.cpu().numpy()[0,0]
+            # breakpoint()
+            os.makedirs(os.path.join(output_dir, f'{case_name}'), exist_ok=True)
+            nib.save(nib.Nifti1Image(final_data, original_affine), os.path.join(output_dir, f'{case_name}/ct.nii.gz'))
+            # breakpoint()
+            print('time = ', time.time()-start_time)
+            start_time = time.time()
+
+
+if __name__ == "__main__":
+    main()

Generation_Pipeline_filter/syn_colon/CT_syn_colon_data_new.py

@@ -0,0 +1,230 @@
+import os, time, csv
+import numpy as np
+import torch
+from sklearn.metrics import confusion_matrix
+from scipy import ndimage
+from scipy.ndimage import label
+from functools import partial
+import monai
+from monai.transforms import AsDiscrete,AsDiscreted,Compose,Invertd,SaveImaged
+from monai import transforms, data
+from TumorGeneration.utils import synthesize_colon_tumor, synt_model_prepare
+import nibabel as nib
+
+import warnings
+warnings.filterwarnings("ignore")
+
+import argparse
+parser = argparse.ArgumentParser(description='colon tumor validation')
+
+# file dir
+parser.add_argument('--data_root', default=None, type=str)
+parser.add_argument('--organ_type', default='colon', type=str)
+parser.add_argument('--save_dir', default='out', type=str)
+parser.add_argument('--data_file', default='out', type=str)
+parser.add_argument('--ddim_ts', default=50, type=int)
+parser.add_argument('--fg_thresh', default=30, type=int)
+parser.add_argument('--start', default=0, type=int)
+parser.add_argument('--end', default=1000, type=int)
+
+def voxel2R(A):
+    return (np.array(A)/4*3/np.pi)**(1/3)
+
+class RandCropByPosNegLabeld_select(transforms.RandCropByPosNegLabeld):
+    def __init__(self, keys, label_key, spatial_size, 
+                 pos=1.0, neg=1.0, num_samples=1, 
+                 image_key=None, image_threshold=0.0, allow_missing_keys=True,
+                   fg_thresh=0):
+        super().__init__(keys=keys, label_key=label_key, spatial_size=spatial_size, 
+                 pos=pos, neg=neg, num_samples=num_samples, 
+                 image_key=image_key, image_threshold=image_threshold, allow_missing_keys=allow_missing_keys)
+        self.fg_thresh = fg_thresh
+
+    def R2voxel(self,R):
+        return (4/3*np.pi)*(R)**(3)
+
+    def __call__(self, data):
+        d = dict(data)
+        data_name = d['name']
+        d.pop('name')
+
+        if '10_Decathlon' in data_name or '05_KiTS' in data_name:
+            d_crop = super().__call__(d)
+
+        else:
+            flag=0
+            while 1:
+                flag+=1
+
+                d_crop = super().__call__(d)
+                pixel_num = (d_crop[0]['label']>0).sum()
+                
+                if pixel_num > self.R2voxel(self.fg_thresh):
+                    break
+                if flag>5 and pixel_num > self.R2voxel(max(self.fg_thresh-5, 5)):
+                    break
+                if flag>10 and pixel_num > self.R2voxel(max(self.fg_thresh-10, 5)):
+                    break
+                if flag>15 and pixel_num > self.R2voxel(max(self.fg_thresh-15, 5)):
+                    break
+                if flag>20 and pixel_num > self.R2voxel(max(self.fg_thresh-20, 5)):
+                    break
+                if flag>25 and pixel_num > self.R2voxel(max(self.fg_thresh-25, 5)):
+                    break
+                if flag>50:
+                    break
+            
+        d_crop[0]['name'] = data_name
+        
+        return d_crop
+    
+def _get_loader(args):
+    # val_data_dir = args.val_dir
+    # datalist_json = args.json_dir 
+    val_org_transform = transforms.Compose(
+        [
+            transforms.LoadImaged(keys=["image", "label", "raw_image"]),
+            transforms.AddChanneld(keys=["image", "label", "raw_image"]),
+            transforms.Orientationd(keys=["image", "label"], axcodes="RAS"),
+            transforms.Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear", "bilinear")),
+            transforms.ScaleIntensityRanged(keys=["image"], a_min=-175, a_max=250, b_min=0.0, b_max=1.0, clip=True),
+            transforms.SpatialPadd(keys=["image", "label"], mode=["minimum", "constant"], spatial_size=[96, 96, 96]),
+            RandCropByPosNegLabeld_select(
+                keys=["image", "label", "name"],
+                label_key="label",
+                spatial_size=(96, 96, 96),
+                pos=1,
+                neg=0,
+                num_samples=1,
+                image_key="image",
+                image_threshold=0,
+                fg_thresh = args.fg_thresh,
+            ),
+            transforms.ToTensord(keys=["image", "label", "raw_image"]),
+        ]
+    )
+
+    val_img=[]
+    val_lbl=[]
+    val_name=[]
+    
+    for line in open(args.data_file):
+        # name = line.strip().split()[1].split('.')[0]
+        # val_img.append(args.data_root + line.strip().split()[0])
+        # val_lbl.append(args.data_root + line.strip().split()[1])
+        # breakpoint()
+        name = line.strip()
+        val_img.append(os.path.join(args.data_root, name, 'ct.nii.gz'))
+        val_lbl.append(os.path.join(args.data_root, name, 'segmentations/colon.nii.gz'))
+        val_name.append(name)
+    data_dicts_val = [{'image': image, 'raw_image':image, 'label': label, 'name': name}
+                for image, label, name in zip(val_img, val_lbl, val_name)]
+    
+    if args.end < len(data_dicts_val):
+        data_dicts_val = data_dicts_val[args.start:args.end]
+    else:
+        data_dicts_val = data_dicts_val[args.start:]
+    print('val len {}'.format(len(data_dicts_val)))
+    val_org_ds = data.Dataset(data_dicts_val, transform=val_org_transform)
+    val_org_loader = data.DataLoader(val_org_ds, batch_size=1, shuffle=False, num_workers=4, sampler=None, pin_memory=True)
+
+    post_transforms = Compose([
+        Invertd(
+            keys=['image'],
+            transform=val_org_transform,
+            orig_keys="image",
+            nearest_interp=False,
+            # nearest_interp=True,
+            to_tensor=True,
+        ),
+        Invertd(
+            keys=['label'],
+            transform=val_org_transform,
+            orig_keys="label",
+            nearest_interp=False,
+            # nearest_interp=True,
+            to_tensor=True,
+        )
+    ])
+    return val_org_loader, post_transforms
+
+def main():
+    args = parser.parse_args()
+    output_dir = args.save_dir
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+    print("MAIN Argument values:")
+    for k, v in vars(args).items():
+        print(k, '=>', v)
+    print('-----------------')
+
+    ## loader and post_transform
+    val_loader, post_transforms = _get_loader(args)
+
+    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+    model = monai.networks.nets.DenseNet121(spatial_dims=3, in_channels=1, out_channels=2).to(device)
+    model.load_state_dict(torch.load("../best_metric_model_classification3d_dict.pth"))
+    model.eval()
+
+    start_time=0
+    with torch.no_grad():
+        for idx, val_data in enumerate(val_loader):
+            print('idx',idx)
+            if idx == 0:
+                start_time = time.time()
+            # val_inputs = val_data["image"]
+            # name = val_data['label_meta_dict']['filename_or_obj'][0].split('/')[-1].split('.')[0]
+            
+            vqgan, noearly_sampler= synt_model_prepare(device = torch.device("cuda"), fold=0, organ=args.organ_type)
+            
+            healthy_data, healthy_target, data_names, raw_data = val_data['image'], val_data['label'], val_data['name'], val_data['raw_image']
+            case_name = data_names[0].split('/')[-1]
+            print('case_name', case_name)
+            original_affine = val_data["label_meta_dict"]["original_affine"][0].numpy()
+
+            if healthy_target.sum() == 0:
+                val_data = [post_transforms(i) for i in data.decollate_batch(val_data)]
+                tumor_mask = val_data[0]['label'][0].cpu().numpy().astype(np.uint8)
+                tumor_mask_ = np.zeros_like(tumor_mask)
+                nib.save(nib.Nifti1Image(tumor_mask_, original_affine), os.path.join(output_dir, f'{case_name}/segmentations/colon_tumor.nii.gz'))
+                continue
+            
+            healthy_data, healthy_target = healthy_data.cuda(), healthy_target.cuda()
+            healthy_target = (healthy_target>0).to(healthy_target)
+            flag=0
+            while 1:
+                flag+=1
+                synt_data, synt_target = synthesize_colon_tumor(healthy_data, healthy_target, vqgan, noearly_sampler, ddim_ts=args.ddim_ts)
+
+                syn_confidence = model(synt_data).sigmoid()[:,1]
+                if syn_confidence>0.01:
+                    break
+                elif flag > 40 and syn_confidence>0.005:
+                    break
+                elif flag > 60 and syn_confidence>0.001:
+                    break
+                
+            val_data['image'] = synt_data.detach()
+            val_data['label'] = synt_target.detach()
+
+            val_data = [post_transforms(i) for i in data.decollate_batch(val_data)]
+            synt_data = val_data[0]['image'][0]
+            synt_target = val_data[0]['label'][0]
+            final_data = raw_data[0,0]
+
+            synt_data = (synt_data*(250+175)-175)
+            final_data[synt_target>1] = synt_data[synt_target>1]
+            final_data = final_data.cpu().numpy()
+            final_label = (synt_target>=1.5).cpu().numpy().astype(np.uint8)
+
+            os.makedirs(os.path.join(output_dir, f'{case_name}'), exist_ok=True)
+            os.makedirs(os.path.join(output_dir, f'{case_name}/segmentations'), exist_ok=True)
+            nib.save(nib.Nifti1Image(final_data, original_affine), os.path.join(output_dir, f'{case_name}/ct.nii.gz'))
+            nib.save(nib.Nifti1Image(final_label, original_affine), os.path.join(output_dir, f'{case_name}/segmentations/colon_tumor.nii.gz'))
+
+            print('time = ', time.time()-start_time)
+            start_time = time.time()
+
+
+if __name__ == "__main__":
+    main()

Generation_Pipeline_filter/syn_colon/TumorGeneration/README.md

@@ -0,0 +1,5 @@
+```bash
+wget https://www.dropbox.com/scl/fi/k856fhk60kck8uqxtxazw/model_weight.tar.gz?rlkey=hrcn4cbt690dzern1bkbfejll
+mv model_weight.tar.gz?rlkey=hrcn4cbt690dzern1bkbfejll model_weight.tar.gz
+tar -xzvf model_weight.tar.gz
+```

Generation_Pipeline_filter/syn_colon/TumorGeneration/TumorGenerated.py

@@ -0,0 +1,39 @@
+import random
+from typing import Hashable, Mapping, Dict
+
+from monai.config import KeysCollection
+from monai.config.type_definitions import NdarrayOrTensor
+from monai.transforms.transform import MapTransform, RandomizableTransform
+
+from .utils_ import SynthesisTumor
+import numpy as np
+
+class TumorGenerated(RandomizableTransform, MapTransform):
+    def __init__(self, 
+    keys: KeysCollection, 
+    prob: float = 0.1,
+    tumor_prob = [0.2, 0.2, 0.2, 0.2, 0.2],
+    allow_missing_keys: bool = False
+    ) -> None:
+        MapTransform.__init__(self, keys, allow_missing_keys)
+        RandomizableTransform.__init__(self, prob)
+        random.seed(0)
+        np.random.seed(0)
+
+        self.tumor_types = ['tiny', 'small', 'medium', 'large', 'mix']
+        
+        assert len(tumor_prob) == 5
+        self.tumor_prob = np.array(tumor_prob)
+
+
+
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Dict[Hashable, NdarrayOrTensor]:
+        d = dict(data)
+        self.randomize(None)
+
+        if self._do_transform and (np.max(d['label']) <= 1):  
+            tumor_type = np.random.choice(self.tumor_types, p=self.tumor_prob.ravel())
+
+            d['image'][0], d['label'][0] = SynthesisTumor(d['image'][0], d['label'][0], tumor_type)
+            # print(tumor_type, d['image'].shape, np.max(d['label']))
+        return d

Generation_Pipeline_filter/syn_colon/TumorGeneration/__init__.py

@@ -0,0 +1,5 @@
+### Online Version TumorGeneration ###
+
+from .TumorGenerated import TumorGenerated
+
+# from .utils import synthesize_early_tumor, synthesize_medium_tumor, synthesize_large_tumor

Generation_Pipeline_filter/syn_colon/TumorGeneration/diffusion_config/ddpm.yaml

@@ -0,0 +1,29 @@
+vqgan_ckpt: None
+
+# Have to be derived from VQ-GAN Latent space dimensions
+diffusion_img_size: 24
+diffusion_depth_size: 24
+diffusion_num_channels: 17 # 17
+out_dim: 8
+dim_mults: [1,2,4,8]
+results_folder: checkpoints/ddpm/
+results_folder_postfix: 'own_dataset_t2'
+load_milestone: False # False
+
+batch_size: 2 # 40
+num_workers: 20
+logger: wandb
+objective: pred_x0
+save_and_sample_every: 1000
+denoising_fn: Unet3D
+train_lr: 1e-4
+timesteps: 2 # number of steps
+sampling_timesteps: 250 # number of sampling timesteps (using ddim for faster inference [see citation for ddim paper])
+loss_type: l1 # L1 or L2
+train_num_steps: 700000 # total training steps
+gradient_accumulate_every: 2 # gradient accumulation steps
+ema_decay: 0.995 # exponential moving average decay
+amp: False # turn on mixed precision
+num_sample_rows: 1
+gpus: 0
+

Generation_Pipeline_filter/syn_colon/TumorGeneration/diffusion_config/vq_gan_3d.yaml

@@ -0,0 +1,37 @@
+seed: 1234
+batch_size: 2 # 30
+num_workers: 32 # 30
+
+gpus: 1
+accumulate_grad_batches: 1
+default_root_dir: checkpoints/vq_gan/
+default_root_dir_postfix: 'flair'
+resume_from_checkpoint:
+max_steps: -1
+max_epochs: -1
+precision: 16
+gradient_clip_val: 1.0
+
+
+embedding_dim: 8 # 256
+n_codes: 16384 # 2048
+n_hiddens: 16
+lr: 3e-4
+downsample: [2, 2, 2] # [4, 4, 4]
+disc_channels: 64
+disc_layers: 3
+discriminator_iter_start: 10000 # 50000
+disc_loss_type: hinge
+image_gan_weight: 1.0
+video_gan_weight: 1.0
+l1_weight: 4.0
+gan_feat_weight: 4.0 # 0.0
+perceptual_weight: 4.0 # 0.0
+i3d_feat: False
+restart_thres: 1.0
+no_random_restart: False
+norm_type: group
+padding_type: replicate
+num_groups: 32
+
+

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/ddpm/__init__.py

@@ -0,0 +1 @@
+from .diffusion import Unet3D, GaussianDiffusion, Tester

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/ddpm/ddim.py

@@ -0,0 +1,206 @@
+"""SAMPLING ONLY."""
+
+import torch
+import numpy as np
+from tqdm import tqdm
+from functools import partial
+
+from .util import make_ddim_sampling_parameters, make_ddim_timesteps, noise_like
+
+
+class DDIMSampler(object):
+    def __init__(self, model, schedule="linear", **kwargs):
+        super().__init__()
+        self.model = model
+        self.ddpm_num_timesteps = model.num_timesteps
+        self.schedule = schedule
+
+    def register_buffer(self, name, attr):
+        if type(attr) == torch.Tensor:
+            if attr.device != torch.device("cuda"):
+                attr = attr.to(torch.device("cuda"))
+        setattr(self, name, attr)
+
+    def make_schedule(self, ddim_num_steps, ddim_discretize="uniform", ddim_eta=0., verbose=True): # "uniform" 'quad'
+        self.ddim_timesteps = make_ddim_timesteps(ddim_discr_method=ddim_discretize, num_ddim_timesteps=ddim_num_steps,
+                                                  num_ddpm_timesteps=self.ddpm_num_timesteps,verbose=verbose)
+        
+        alphas_cumprod = self.model.alphas_cumprod
+        assert alphas_cumprod.shape[0] == self.ddpm_num_timesteps, 'alphas have to be defined for each timestep'
+        to_torch = lambda x: x.clone().detach().to(torch.float32).to(self.model.device)
+
+        self.register_buffer('betas', to_torch(self.model.betas))
+        self.register_buffer('alphas_cumprod', to_torch(alphas_cumprod))
+        self.register_buffer('alphas_cumprod_prev', to_torch(self.model.alphas_cumprod_prev))
+
+        # calculations for diffusion q(x_t | x_{t-1}) and others
+        self.register_buffer('sqrt_alphas_cumprod', to_torch(np.sqrt(alphas_cumprod.cpu())))
+        self.register_buffer('sqrt_one_minus_alphas_cumprod', to_torch(np.sqrt(1. - alphas_cumprod.cpu())))
+        self.register_buffer('log_one_minus_alphas_cumprod', to_torch(np.log(1. - alphas_cumprod.cpu())))
+        self.register_buffer('sqrt_recip_alphas_cumprod', to_torch(np.sqrt(1. / alphas_cumprod.cpu())))
+        self.register_buffer('sqrt_recipm1_alphas_cumprod', to_torch(np.sqrt(1. / alphas_cumprod.cpu() - 1)))
+        # breakpoint()
+        # ddim sampling parameters
+        ddim_sigmas, ddim_alphas, ddim_alphas_prev = make_ddim_sampling_parameters(alphacums=alphas_cumprod.cpu(),
+                                                                                   ddim_timesteps=self.ddim_timesteps,
+                                                                                   eta=ddim_eta,verbose=verbose)
+        self.register_buffer('ddim_sigmas', ddim_sigmas)
+        self.register_buffer('ddim_alphas', ddim_alphas)
+        self.register_buffer('ddim_alphas_prev', ddim_alphas_prev)
+        self.register_buffer('ddim_sqrt_one_minus_alphas', np.sqrt(1. - ddim_alphas))
+        sigmas_for_original_sampling_steps = ddim_eta * torch.sqrt(
+            (1 - self.alphas_cumprod_prev) / (1 - self.alphas_cumprod) * (
+                        1 - self.alphas_cumprod / self.alphas_cumprod_prev))
+        self.register_buffer('ddim_sigmas_for_original_num_steps', sigmas_for_original_sampling_steps)
+
+    @torch.no_grad()
+    def sample(self,
+               S,
+               batch_size,
+               shape,
+               conditioning=None,
+               callback=None,
+               normals_sequence=None,
+               img_callback=None,
+               quantize_x0=False,
+               eta=0.,
+               mask=None,
+               x0=None,
+               temperature=1.,
+               noise_dropout=0.,
+               score_corrector=None,
+               corrector_kwargs=None,
+               verbose=True,
+               x_T=None,
+               log_every_t=100,
+               unconditional_guidance_scale=1.,
+               unconditional_conditioning=None,
+               # this has to come in the same format as the conditioning, # e.g. as encoded tokens, ...
+               **kwargs
+               ):
+        if conditioning is not None:
+            if isinstance(conditioning, dict):
+                cbs = conditioning[list(conditioning.keys())[0]].shape[0]
+                if cbs != batch_size:
+                    print(f"Warning: Got {cbs} conditionings but batch-size is {batch_size}")
+            else:
+                if conditioning.shape[0] != batch_size:
+                    print(f"Warning: Got {conditioning.shape[0]} conditionings but batch-size is {batch_size}")
+
+        self.make_schedule(ddim_num_steps=S, ddim_eta=eta, verbose=verbose)
+        # sampling
+        C, T, H, W = shape
+        # breakpoint()
+        size = (batch_size, C, T, H, W)
+        # print(f'Data shape for DDIM sampling is {size}, eta {eta}')
+
+        samples, intermediates = self.ddim_sampling(conditioning, size,
+                                                    callback=callback,
+                                                    img_callback=img_callback,
+                                                    quantize_denoised=quantize_x0,
+                                                    mask=mask, x0=x0,
+                                                    ddim_use_original_steps=False,
+                                                    noise_dropout=noise_dropout,
+                                                    temperature=temperature,
+                                                    score_corrector=score_corrector,
+                                                    corrector_kwargs=corrector_kwargs,
+                                                    x_T=x_T,
+                                                    log_every_t=log_every_t,
+                                                    unconditional_guidance_scale=unconditional_guidance_scale,
+                                                    unconditional_conditioning=unconditional_conditioning,
+                                                    )
+        return samples, intermediates
+
+    @torch.no_grad()
+    def ddim_sampling(self, cond, shape,
+                      x_T=None, ddim_use_original_steps=False,
+                      callback=None, timesteps=None, quantize_denoised=False,
+                      mask=None, x0=None, img_callback=None, log_every_t=100,
+                      temperature=1., noise_dropout=0., score_corrector=None, corrector_kwargs=None,
+                      unconditional_guidance_scale=1., unconditional_conditioning=None,):
+        device = self.model.betas.device
+        b = shape[0]
+        if x_T is None:
+            img = torch.randn(shape, device=device)
+        else:
+            img = x_T
+
+        if timesteps is None:
+            timesteps = self.ddpm_num_timesteps if ddim_use_original_steps else self.ddim_timesteps
+        elif timesteps is not None and not ddim_use_original_steps:
+            subset_end = int(min(timesteps / self.ddim_timesteps.shape[0], 1) * self.ddim_timesteps.shape[0]) - 1
+            timesteps = self.ddim_timesteps[:subset_end]
+
+        intermediates = {'x_inter': [img], 'pred_x0': [img]}
+        time_range = reversed(range(0,timesteps)) if ddim_use_original_steps else np.flip(timesteps)
+        total_steps = timesteps if ddim_use_original_steps else timesteps.shape[0]
+        # print(f"Running DDIM Sampling with {total_steps} timesteps")
+
+        # iterator = tqdm(time_range, desc='DDIM Sampler', total=total_steps)
+
+        for i, step in enumerate(time_range):
+            index = total_steps - i - 1
+            ts = torch.full((b,), step, device=device, dtype=torch.long)
+
+            if mask is not None:
+                assert x0 is not None
+                img_orig = self.model.q_sample(x0, ts)  # TODO: deterministic forward pass?
+                img = img_orig * mask + (1. - mask) * img
+
+            outs = self.p_sample_ddim(img, cond, ts, index=index, use_original_steps=ddim_use_original_steps,
+                                      quantize_denoised=quantize_denoised, temperature=temperature,
+                                      noise_dropout=noise_dropout, score_corrector=score_corrector,
+                                      corrector_kwargs=corrector_kwargs,
+                                      unconditional_guidance_scale=unconditional_guidance_scale,
+                                      unconditional_conditioning=unconditional_conditioning)
+            img, pred_x0 = outs
+            if callback: callback(i)
+            if img_callback: img_callback(pred_x0, i)
+
+            if index % log_every_t == 0 or index == total_steps - 1:
+                intermediates['x_inter'].append(img)
+                intermediates['pred_x0'].append(pred_x0)
+
+        return img, intermediates
+
+    @torch.no_grad()
+    def p_sample_ddim(self, x, c, t, index, repeat_noise=False, use_original_steps=False, quantize_denoised=False,
+                      temperature=1., noise_dropout=0., score_corrector=None, corrector_kwargs=None,
+                      unconditional_guidance_scale=1., unconditional_conditioning=None):
+        b, *_, device = *x.shape, x.device
+
+        if unconditional_conditioning is None or unconditional_guidance_scale == 1.:
+            # breakpoint()
+            e_t = self.model.denoise_fn(x, t, c)
+        else:
+            x_in = torch.cat([x] * 2)
+            t_in = torch.cat([t] * 2)
+            c_in = torch.cat([unconditional_conditioning, c])
+            e_t_uncond, e_t = self.model.denoise_fn(x_in, t_in, c_in).chunk(2)
+            e_t = e_t_uncond + unconditional_guidance_scale * (e_t - e_t_uncond)
+
+        if score_corrector is not None:
+            assert self.model.parameterization == "eps"
+            e_t = score_corrector.modify_score(self.model, e_t, x, t, c, **corrector_kwargs)
+
+        alphas = self.model.alphas_cumprod if use_original_steps else self.ddim_alphas
+        alphas_prev = self.model.alphas_cumprod_prev if use_original_steps else self.ddim_alphas_prev
+        sqrt_one_minus_alphas = self.model.sqrt_one_minus_alphas_cumprod if use_original_steps else self.ddim_sqrt_one_minus_alphas
+        sigmas = self.ddim_sigmas_for_original_num_steps if use_original_steps else self.ddim_sigmas
+        # select parameters corresponding to the currently considered timestep
+        a_t = torch.full((b, 1, 1, 1), alphas[index], device=device)
+        a_prev = torch.full((b, 1, 1, 1), alphas_prev[index], device=device)
+        sigma_t = torch.full((b, 1, 1, 1), sigmas[index], device=device)
+        sqrt_one_minus_at = torch.full((b, 1, 1, 1), sqrt_one_minus_alphas[index],device=device)
+
+        # current prediction for x_0
+        pred_x0 = (x - sqrt_one_minus_at * e_t) / a_t.sqrt()
+        if quantize_denoised:
+            pred_x0, _, *_ = self.model.first_stage_model.quantize(pred_x0)
+        # direction pointing to x_t
+        dir_xt = (1. - a_prev - sigma_t**2).sqrt() * e_t
+        noise = sigma_t * noise_like(x.shape, device, repeat_noise) * temperature
+        if noise_dropout > 0.:
+            noise = torch.nn.functional.dropout(noise, p=noise_dropout)
+        x_prev = a_prev.sqrt() * pred_x0 + dir_xt + noise
+        return x_prev, pred_x0

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/ddpm/diffusion.py

@@ -0,0 +1,1016 @@
+"Largely taken and adapted from https://github.com/lucidrains/video-diffusion-pytorch"
+
+import math
+import copy
+import torch
+from torch import nn, einsum
+import torch.nn.functional as F
+from functools import partial
+
+from torch.utils import data
+from pathlib import Path
+from torch.optim import Adam
+from torchvision import transforms as T, utils
+from torch.cuda.amp import autocast, GradScaler
+from PIL import Image
+
+from tqdm import tqdm
+from einops import rearrange
+from einops_exts import check_shape, rearrange_many
+
+from rotary_embedding_torch import RotaryEmbedding
+
+from .text import tokenize, bert_embed, BERT_MODEL_DIM
+from torch.utils.data import Dataset, DataLoader
+from ..vq_gan_3d.model.vqgan import VQGAN
+
+import matplotlib.pyplot as plt
+
+# helpers functions
+
+
+def exists(x):
+    return x is not None
+
+
+def noop(*args, **kwargs):
+    pass
+
+
+def is_odd(n):
+    return (n % 2) == 1
+
+
+def default(val, d):
+    if exists(val):
+        return val
+    return d() if callable(d) else d
+
+
+def cycle(dl):
+    while True:
+        for data in dl:
+            yield data
+
+
+def num_to_groups(num, divisor):
+    groups = num // divisor
+    remainder = num % divisor
+    arr = [divisor] * groups
+    if remainder > 0:
+        arr.append(remainder)
+    return arr
+
+
+def prob_mask_like(shape, prob, device):
+    if prob == 1:
+        return torch.ones(shape, device=device, dtype=torch.bool)
+    elif prob == 0:
+        return torch.zeros(shape, device=device, dtype=torch.bool)
+    else:
+        return torch.zeros(shape, device=device).float().uniform_(0, 1) < prob
+
+
+def is_list_str(x):
+    if not isinstance(x, (list, tuple)):
+        return False
+    return all([type(el) == str for el in x])
+
+# relative positional bias
+
+
+class RelativePositionBias(nn.Module):
+    def __init__(
+        self,
+        heads=8,
+        num_buckets=32,
+        max_distance=128
+    ):
+        super().__init__()
+        self.num_buckets = num_buckets
+        self.max_distance = max_distance
+        self.relative_attention_bias = nn.Embedding(num_buckets, heads)
+
+    @staticmethod
+    def _relative_position_bucket(relative_position, num_buckets=32, max_distance=128):
+        ret = 0
+        n = -relative_position
+
+        num_buckets //= 2
+        ret += (n < 0).long() * num_buckets
+        n = torch.abs(n)
+
+        max_exact = num_buckets // 2
+        is_small = n < max_exact
+
+        val_if_large = max_exact + (
+            torch.log(n.float() / max_exact) / math.log(max_distance /
+                                                        max_exact) * (num_buckets - max_exact)
+        ).long()
+        val_if_large = torch.min(
+            val_if_large, torch.full_like(val_if_large, num_buckets - 1))
+
+        ret += torch.where(is_small, n, val_if_large)
+        return ret
+
+    def forward(self, n, device):
+        q_pos = torch.arange(n, dtype=torch.long, device=device)
+        k_pos = torch.arange(n, dtype=torch.long, device=device)
+        rel_pos = rearrange(k_pos, 'j -> 1 j') - rearrange(q_pos, 'i -> i 1')
+        rp_bucket = self._relative_position_bucket(
+            rel_pos, num_buckets=self.num_buckets, max_distance=self.max_distance)
+        values = self.relative_attention_bias(rp_bucket)
+        return rearrange(values, 'i j h -> h i j')
+
+# small helper modules
+
+
+class EMA():
+    def __init__(self, beta):
+        super().__init__()
+        self.beta = beta
+
+    def update_model_average(self, ma_model, current_model):
+        for current_params, ma_params in zip(current_model.parameters(), ma_model.parameters()):
+            old_weight, up_weight = ma_params.data, current_params.data
+            ma_params.data = self.update_average(old_weight, up_weight)
+
+    def update_average(self, old, new):
+        if old is None:
+            return new
+        return old * self.beta + (1 - self.beta) * new
+
+
+class Residual(nn.Module):
+    def __init__(self, fn):
+        super().__init__()
+        self.fn = fn
+
+    def forward(self, x, *args, **kwargs):
+        return self.fn(x, *args, **kwargs) + x
+
+
+class SinusoidalPosEmb(nn.Module):
+    def __init__(self, dim):
+        super().__init__()
+        self.dim = dim
+
+    def forward(self, x):
+        device = x.device
+        half_dim = self.dim // 2
+        emb = math.log(10000) / (half_dim - 1)
+        emb = torch.exp(torch.arange(half_dim, device=device) * -emb)
+        emb = x[:, None] * emb[None, :]
+        emb = torch.cat((emb.sin(), emb.cos()), dim=-1)
+        return emb
+
+
+def Upsample(dim):
+    return nn.ConvTranspose3d(dim, dim, (1, 4, 4), (1, 2, 2), (0, 1, 1))
+
+
+def Downsample(dim):
+    return nn.Conv3d(dim, dim, (1, 4, 4), (1, 2, 2), (0, 1, 1))
+
+
+class LayerNorm(nn.Module):
+    def __init__(self, dim, eps=1e-5):
+        super().__init__()
+        self.eps = eps
+        self.gamma = nn.Parameter(torch.ones(1, dim, 1, 1, 1))
+
+    def forward(self, x):
+        var = torch.var(x, dim=1, unbiased=False, keepdim=True)
+        mean = torch.mean(x, dim=1, keepdim=True)
+        return (x - mean) / (var + self.eps).sqrt() * self.gamma
+
+
+class PreNorm(nn.Module):
+    def __init__(self, dim, fn):
+        super().__init__()
+        self.fn = fn
+        self.norm = LayerNorm(dim)
+
+    def forward(self, x, **kwargs):
+        x = self.norm(x)
+        return self.fn(x, **kwargs)
+
+# building block modules
+
+
+class Block(nn.Module):
+    def __init__(self, dim, dim_out, groups=8):
+        super().__init__()
+        self.proj = nn.Conv3d(dim, dim_out, (1, 3, 3), padding=(0, 1, 1))
+        self.norm = nn.GroupNorm(groups, dim_out)
+        self.act = nn.SiLU()
+
+    def forward(self, x, scale_shift=None):
+        x = self.proj(x)
+        x = self.norm(x)
+
+        if exists(scale_shift):
+            scale, shift = scale_shift
+            x = x * (scale + 1) + shift
+
+        return self.act(x)
+
+
+class ResnetBlock(nn.Module):
+    def __init__(self, dim, dim_out, *, time_emb_dim=None, groups=8):
+        super().__init__()
+        self.mlp = nn.Sequential(
+            nn.SiLU(),
+            nn.Linear(time_emb_dim, dim_out * 2)
+        ) if exists(time_emb_dim) else None
+
+        self.block1 = Block(dim, dim_out, groups=groups)
+        self.block2 = Block(dim_out, dim_out, groups=groups)
+        self.res_conv = nn.Conv3d(
+            dim, dim_out, 1) if dim != dim_out else nn.Identity()
+
+    def forward(self, x, time_emb=None):
+
+        scale_shift = None
+        if exists(self.mlp):
+            assert exists(time_emb), 'time emb must be passed in'
+            time_emb = self.mlp(time_emb)
+            time_emb = rearrange(time_emb, 'b c -> b c 1 1 1')
+            scale_shift = time_emb.chunk(2, dim=1)
+
+        h = self.block1(x, scale_shift=scale_shift)
+
+        h = self.block2(h)
+        return h + self.res_conv(x)
+
+
+class SpatialLinearAttention(nn.Module):
+    def __init__(self, dim, heads=4, dim_head=32):
+        super().__init__()
+        self.scale = dim_head ** -0.5
+        self.heads = heads
+        hidden_dim = dim_head * heads
+        self.to_qkv = nn.Conv2d(dim, hidden_dim * 3, 1, bias=False)
+        self.to_out = nn.Conv2d(hidden_dim, dim, 1)
+
+    def forward(self, x):
+        b, c, f, h, w = x.shape
+        x = rearrange(x, 'b c f h w -> (b f) c h w')
+
+        qkv = self.to_qkv(x).chunk(3, dim=1)
+        q, k, v = rearrange_many(
+            qkv, 'b (h c) x y -> b h c (x y)', h=self.heads)
+
+        q = q.softmax(dim=-2)
+        k = k.softmax(dim=-1)
+
+        q = q * self.scale
+        context = torch.einsum('b h d n, b h e n -> b h d e', k, v)
+
+        out = torch.einsum('b h d e, b h d n -> b h e n', context, q)
+        out = rearrange(out, 'b h c (x y) -> b (h c) x y',
+                        h=self.heads, x=h, y=w)
+        out = self.to_out(out)
+        return rearrange(out, '(b f) c h w -> b c f h w', b=b)
+
+# attention along space and time
+
+
+class EinopsToAndFrom(nn.Module):
+    def __init__(self, from_einops, to_einops, fn):
+        super().__init__()
+        self.from_einops = from_einops
+        self.to_einops = to_einops
+        self.fn = fn
+
+    def forward(self, x, **kwargs):
+        shape = x.shape
+        reconstitute_kwargs = dict(
+            tuple(zip(self.from_einops.split(' '), shape)))
+        x = rearrange(x, f'{self.from_einops} -> {self.to_einops}')
+        x = self.fn(x, **kwargs)
+        x = rearrange(
+            x, f'{self.to_einops} -> {self.from_einops}', **reconstitute_kwargs)
+        return x
+
+
+class Attention(nn.Module):
+    def __init__(
+        self,
+        dim,
+        heads=4,
+        dim_head=32,
+        rotary_emb=None
+    ):
+        super().__init__()
+        self.scale = dim_head ** -0.5
+        self.heads = heads
+        hidden_dim = dim_head * heads
+
+        self.rotary_emb = rotary_emb
+        self.to_qkv = nn.Linear(dim, hidden_dim * 3, bias=False)
+        self.to_out = nn.Linear(hidden_dim, dim, bias=False)
+
+    def forward(
+        self,
+        x,
+        pos_bias=None,
+        focus_present_mask=None
+    ):
+        n, device = x.shape[-2], x.device
+
+        qkv = self.to_qkv(x).chunk(3, dim=-1)
+
+        if exists(focus_present_mask) and focus_present_mask.all():
+            # if all batch samples are focusing on present
+            # it would be equivalent to passing that token's values through to the output
+            values = qkv[-1]
+            return self.to_out(values)
+
+        # split out heads
+
+        q, k, v = rearrange_many(qkv, '... n (h d) -> ... h n d', h=self.heads)
+
+        # scale
+
+        q = q * self.scale
+
+        # rotate positions into queries and keys for time attention
+
+        if exists(self.rotary_emb):
+            q = self.rotary_emb.rotate_queries_or_keys(q)
+            k = self.rotary_emb.rotate_queries_or_keys(k)
+
+        # similarity
+
+        sim = einsum('... h i d, ... h j d -> ... h i j', q, k)
+
+        # relative positional bias
+
+        if exists(pos_bias):
+            sim = sim + pos_bias
+
+        if exists(focus_present_mask) and not (~focus_present_mask).all():
+            attend_all_mask = torch.ones(
+                (n, n), device=device, dtype=torch.bool)
+            attend_self_mask = torch.eye(n, device=device, dtype=torch.bool)
+
+            mask = torch.where(
+                rearrange(focus_present_mask, 'b -> b 1 1 1 1'),
+                rearrange(attend_self_mask, 'i j -> 1 1 1 i j'),
+                rearrange(attend_all_mask, 'i j -> 1 1 1 i j'),
+            )
+
+            sim = sim.masked_fill(~mask, -torch.finfo(sim.dtype).max)
+
+        # numerical stability
+
+        sim = sim - sim.amax(dim=-1, keepdim=True).detach()
+        attn = sim.softmax(dim=-1)
+
+        # aggregate values
+
+        out = einsum('... h i j, ... h j d -> ... h i d', attn, v)
+        out = rearrange(out, '... h n d -> ... n (h d)')
+        return self.to_out(out)
+
+# model
+
+
+class Unet3D(nn.Module):
+    def __init__(
+        self,
+        dim,
+        cond_dim=None,
+        out_dim=None,
+        dim_mults=(1, 2, 4, 8),
+        channels=3,
+        attn_heads=8,
+        attn_dim_head=32,
+        use_bert_text_cond=False,
+        init_dim=None,
+        init_kernel_size=7,
+        use_sparse_linear_attn=True,
+        block_type='resnet',
+        resnet_groups=8
+    ):
+        super().__init__()
+        self.channels = channels
+
+        # temporal attention and its relative positional encoding
+
+        rotary_emb = RotaryEmbedding(min(32, attn_dim_head))
+
+        def temporal_attn(dim): return EinopsToAndFrom('b c f h w', 'b (h w) f c', Attention(
+            dim, heads=attn_heads, dim_head=attn_dim_head, rotary_emb=rotary_emb))
+
+        # realistically will not be able to generate that many frames of video... yet
+        self.time_rel_pos_bias = RelativePositionBias(
+            heads=attn_heads, max_distance=32)
+
+        # initial conv
+
+        init_dim = default(init_dim, dim)
+        assert is_odd(init_kernel_size)
+
+        init_padding = init_kernel_size // 2
+        self.init_conv = nn.Conv3d(channels, init_dim, (1, init_kernel_size,
+                                   init_kernel_size), padding=(0, init_padding, init_padding))
+
+        self.init_temporal_attn = Residual(
+            PreNorm(init_dim, temporal_attn(init_dim)))
+
+        # dimensions
+
+        dims = [init_dim, *map(lambda m: dim * m, dim_mults)]
+        in_out = list(zip(dims[:-1], dims[1:]))
+
+        # time conditioning
+
+        time_dim = dim * 4
+        self.time_mlp = nn.Sequential(
+            SinusoidalPosEmb(dim),
+            nn.Linear(dim, time_dim),
+            nn.GELU(),
+            nn.Linear(time_dim, time_dim)
+        )
+
+        # text conditioning
+
+        self.has_cond = exists(cond_dim) or use_bert_text_cond
+        cond_dim = BERT_MODEL_DIM if use_bert_text_cond else cond_dim
+
+        self.null_cond_emb = nn.Parameter(
+            torch.randn(1, cond_dim)) if self.has_cond else None
+
+        cond_dim = time_dim + int(cond_dim or 0)
+
+        # layers
+
+        self.downs = nn.ModuleList([])
+        self.ups = nn.ModuleList([])
+
+        num_resolutions = len(in_out)
+        # block type
+
+        block_klass = partial(ResnetBlock, groups=resnet_groups)
+        block_klass_cond = partial(block_klass, time_emb_dim=cond_dim)
+
+        # modules for all layers
+        for ind, (dim_in, dim_out) in enumerate(in_out):
+            is_last = ind >= (num_resolutions - 1)
+
+            self.downs.append(nn.ModuleList([
+                block_klass_cond(dim_in, dim_out),
+                block_klass_cond(dim_out, dim_out),
+                Residual(PreNorm(dim_out, SpatialLinearAttention(
+                    dim_out, heads=attn_heads))) if use_sparse_linear_attn else nn.Identity(),
+                Residual(PreNorm(dim_out, temporal_attn(dim_out))),
+                Downsample(dim_out) if not is_last else nn.Identity()
+            ]))
+
+        mid_dim = dims[-1]
+        self.mid_block1 = block_klass_cond(mid_dim, mid_dim)
+
+        spatial_attn = EinopsToAndFrom(
+            'b c f h w', 'b f (h w) c', Attention(mid_dim, heads=attn_heads))
+
+        self.mid_spatial_attn = Residual(PreNorm(mid_dim, spatial_attn))
+        self.mid_temporal_attn = Residual(
+            PreNorm(mid_dim, temporal_attn(mid_dim)))
+
+        self.mid_block2 = block_klass_cond(mid_dim, mid_dim)
+
+        for ind, (dim_in, dim_out) in enumerate(reversed(in_out)):
+            is_last = ind >= (num_resolutions - 1)
+
+            self.ups.append(nn.ModuleList([
+                block_klass_cond(dim_out * 2, dim_in),
+                block_klass_cond(dim_in, dim_in),
+                Residual(PreNorm(dim_in, SpatialLinearAttention(
+                    dim_in, heads=attn_heads))) if use_sparse_linear_attn else nn.Identity(),
+                Residual(PreNorm(dim_in, temporal_attn(dim_in))),
+                Upsample(dim_in) if not is_last else nn.Identity()
+            ]))
+
+        out_dim = default(out_dim, channels)
+        self.final_conv = nn.Sequential(
+            block_klass(dim * 2, dim),
+            nn.Conv3d(dim, out_dim, 1)
+        )
+
+    def forward_with_cond_scale(
+        self,
+        *args,
+        cond_scale=2.,
+        **kwargs
+    ):
+        logits = self.forward(*args, null_cond_prob=0., **kwargs)
+        if cond_scale == 1 or not self.has_cond:
+            return logits
+
+        null_logits = self.forward(*args, null_cond_prob=1., **kwargs)
+        return null_logits + (logits - null_logits) * cond_scale
+
+    def forward(
+        self,
+        x,
+        time,
+        cond=None,
+        null_cond_prob=0.,
+        focus_present_mask=None,
+        # probability at which a given batch sample will focus on the present (0. is all off, 1. is completely arrested attention across time)
+        prob_focus_present=0.
+    ):
+        assert not (self.has_cond and not exists(cond)
+                    ), 'cond must be passed in if cond_dim specified'
+        x = torch.cat([x, cond], dim=1)
+
+        batch, device = x.shape[0], x.device
+
+        focus_present_mask = default(focus_present_mask, lambda: prob_mask_like(
+            (batch,), prob_focus_present, device=device))
+
+        time_rel_pos_bias = self.time_rel_pos_bias(x.shape[2], device=x.device)
+
+        x = self.init_conv(x)
+        r = x.clone()
+
+        x = self.init_temporal_attn(x, pos_bias=time_rel_pos_bias)
+
+        t = self.time_mlp(time) if exists(self.time_mlp) else None # [2, 128]
+
+        # classifier free guidance
+
+        if self.has_cond:
+            batch, device = x.shape[0], x.device
+            mask = prob_mask_like((batch,), null_cond_prob, device=device)
+            cond = torch.where(rearrange(mask, 'b -> b 1'),
+                               self.null_cond_emb, cond)
+            t = torch.cat((t, cond), dim=-1)
+
+        h = []
+        
+        for block1, block2, spatial_attn, temporal_attn, downsample in self.downs:
+            x = block1(x, t)
+            x = block2(x, t)
+            x = spatial_attn(x)
+            x = temporal_attn(x, pos_bias=time_rel_pos_bias,
+                              focus_present_mask=focus_present_mask)
+            h.append(x)
+            x = downsample(x)
+
+        # [2, 256, 32, 4, 4]
+        x = self.mid_block1(x, t) 
+        x = self.mid_spatial_attn(x)
+        x = self.mid_temporal_attn(
+            x, pos_bias=time_rel_pos_bias, focus_present_mask=focus_present_mask)
+        x = self.mid_block2(x, t)
+
+        for block1, block2, spatial_attn, temporal_attn, upsample in self.ups:
+            x = torch.cat((x, h.pop()), dim=1)
+            x = block1(x, t)
+            x = block2(x, t)
+            x = spatial_attn(x)
+            x = temporal_attn(x, pos_bias=time_rel_pos_bias,
+                              focus_present_mask=focus_present_mask)
+            x = upsample(x)
+
+        x = torch.cat((x, r), dim=1)
+        return self.final_conv(x)
+
+# gaussian diffusion trainer class
+
+
+def extract(a, t, x_shape):
+    b, *_ = t.shape
+    out = a.gather(-1, t)
+    return out.reshape(b, *((1,) * (len(x_shape) - 1)))
+
+
+def cosine_beta_schedule(timesteps, s=0.008):
+    """
+    cosine schedule
+    as proposed in https://openreview.net/forum?id=-NEXDKk8gZ
+    """
+    steps = timesteps + 1
+    x = torch.linspace(0, timesteps, steps, dtype=torch.float64)
+    alphas_cumprod = torch.cos(
+        ((x / timesteps) + s) / (1 + s) * torch.pi * 0.5) ** 2
+    alphas_cumprod = alphas_cumprod / alphas_cumprod[0]
+    betas = 1 - (alphas_cumprod[1:] / alphas_cumprod[:-1])
+    return torch.clip(betas, 0, 0.9999)
+
+
+class GaussianDiffusion(nn.Module):
+    def __init__(
+        self,
+        denoise_fn,
+        *,
+        image_size,
+        num_frames,
+        text_use_bert_cls=False,
+        channels=3,
+        timesteps=1000,
+        loss_type='l1',
+        use_dynamic_thres=False,  # from the Imagen paper
+        dynamic_thres_percentile=0.9,
+        vqgan_ckpt=None,
+        device=None
+    ):
+        super().__init__()
+        self.channels = channels
+        self.image_size = image_size
+        self.num_frames = num_frames
+        self.denoise_fn = denoise_fn
+        self.device = device
+            
+        if vqgan_ckpt:
+            self.vqgan = VQGAN.load_from_checkpoint(vqgan_ckpt).cuda()
+            self.vqgan.eval()
+        else:
+            self.vqgan = None
+
+        betas = cosine_beta_schedule(timesteps)
+
+        alphas = 1. - betas
+        alphas_cumprod = torch.cumprod(alphas, axis=0)
+        alphas_cumprod_prev = F.pad(alphas_cumprod[:-1], (1, 0), value=1.)
+
+        timesteps, = betas.shape
+        self.num_timesteps = int(timesteps)
+        self.loss_type = loss_type
+
+        # register buffer helper function that casts float64 to float32
+
+        def register_buffer(name, val): return self.register_buffer(
+            name, val.to(torch.float32))
+
+        register_buffer('betas', betas)
+        register_buffer('alphas_cumprod', alphas_cumprod)
+        register_buffer('alphas_cumprod_prev', alphas_cumprod_prev)
+
+        # calculations for diffusion q(x_t | x_{t-1}) and others
+
+        register_buffer('sqrt_alphas_cumprod', torch.sqrt(alphas_cumprod))
+        register_buffer('sqrt_one_minus_alphas_cumprod',
+                        torch.sqrt(1. - alphas_cumprod))
+        register_buffer('log_one_minus_alphas_cumprod',
+                        torch.log(1. - alphas_cumprod))
+        register_buffer('sqrt_recip_alphas_cumprod',
+                        torch.sqrt(1. / alphas_cumprod))
+        register_buffer('sqrt_recipm1_alphas_cumprod',
+                        torch.sqrt(1. / alphas_cumprod - 1))
+
+        # calculations for posterior q(x_{t-1} | x_t, x_0)
+
+        posterior_variance = betas * \
+            (1. - alphas_cumprod_prev) / (1. - alphas_cumprod)
+
+        # above: equal to 1. / (1. / (1. - alpha_cumprod_tm1) + alpha_t / beta_t)
+
+        register_buffer('posterior_variance', posterior_variance)
+
+        # below: log calculation clipped because the posterior variance is 0 at the beginning of the diffusion chain
+
+        register_buffer('posterior_log_variance_clipped',
+                        torch.log(posterior_variance.clamp(min=1e-20)))
+        register_buffer('posterior_mean_coef1', betas *
+                        torch.sqrt(alphas_cumprod_prev) / (1. - alphas_cumprod))
+        register_buffer('posterior_mean_coef2', (1. - alphas_cumprod_prev)
+                        * torch.sqrt(alphas) / (1. - alphas_cumprod))
+
+        # text conditioning parameters
+
+        self.text_use_bert_cls = text_use_bert_cls
+
+        # dynamic thresholding when sampling
+
+        self.use_dynamic_thres = use_dynamic_thres
+        self.dynamic_thres_percentile = dynamic_thres_percentile
+
+    def q_mean_variance(self, x_start, t):
+        mean = extract(self.sqrt_alphas_cumprod, t, x_start.shape) * x_start
+        variance = extract(1. - self.alphas_cumprod, t, x_start.shape)
+        log_variance = extract(
+            self.log_one_minus_alphas_cumprod, t, x_start.shape)
+        return mean, variance, log_variance
+
+    def predict_start_from_noise(self, x_t, t, noise):
+        return (
+            extract(self.sqrt_recip_alphas_cumprod, t, x_t.shape) * x_t -
+            extract(self.sqrt_recipm1_alphas_cumprod, t, x_t.shape) * noise
+        )
+
+    def q_posterior(self, x_start, x_t, t):
+        posterior_mean = (
+            extract(self.posterior_mean_coef1, t, x_t.shape) * x_start +
+            extract(self.posterior_mean_coef2, t, x_t.shape) * x_t
+        )
+        posterior_variance = extract(self.posterior_variance, t, x_t.shape)
+        posterior_log_variance_clipped = extract(
+            self.posterior_log_variance_clipped, t, x_t.shape)
+        return posterior_mean, posterior_variance, posterior_log_variance_clipped
+
+    def p_mean_variance(self, x, t, clip_denoised: bool, cond=None, cond_scale=1.):
+        x_recon = self.predict_start_from_noise(
+            x, t=t, noise=self.denoise_fn.forward_with_cond_scale(x, t, cond=cond, cond_scale=cond_scale))
+
+        if clip_denoised:
+            s = 1.
+            if self.use_dynamic_thres:
+                s = torch.quantile(
+                    rearrange(x_recon, 'b ... -> b (...)').abs(),
+                    self.dynamic_thres_percentile,
+                    dim=-1
+                )
+
+                s.clamp_(min=1.)
+                s = s.view(-1, *((1,) * (x_recon.ndim - 1)))
+
+            # clip by threshold, depending on whether static or dynamic
+            x_recon = x_recon.clamp(-s, s) / s
+
+        model_mean, posterior_variance, posterior_log_variance = self.q_posterior(
+            x_start=x_recon, x_t=x, t=t)
+        return model_mean, posterior_variance, posterior_log_variance
+
+    @torch.inference_mode()
+    def p_sample(self, x, t, cond=None, cond_scale=1., clip_denoised=True):
+        b, *_, device = *x.shape, x.device
+        model_mean, _, model_log_variance = self.p_mean_variance(
+            x=x, t=t, clip_denoised=clip_denoised, cond=cond, cond_scale=cond_scale)
+        noise = torch.randn_like(x)
+        # no noise when t == 0
+        nonzero_mask = (1 - (t == 0).float()).reshape(b,
+                                                      *((1,) * (len(x.shape) - 1)))
+        return model_mean + nonzero_mask * (0.5 * model_log_variance).exp() * noise
+
+    @torch.inference_mode()
+    def p_sample_loop(self, shape, cond=None, cond_scale=1.):
+        device = self.betas.device
+
+        b = shape[0]
+        img = torch.randn(shape, device=device)
+        # print('cond', cond.shape)
+        for i in reversed(range(0, self.num_timesteps)):
+            img = self.p_sample(img, torch.full(
+                (b,), i, device=device, dtype=torch.long), cond=cond, cond_scale=cond_scale)
+
+        return img
+
+    @torch.inference_mode()
+    def sample(self, cond=None, cond_scale=1., batch_size=16):
+        device = next(self.denoise_fn.parameters()).device
+
+        if is_list_str(cond):
+            cond = bert_embed(tokenize(cond)).to(device)
+
+        # batch_size = cond.shape[0] if exists(cond) else batch_size
+        batch_size = batch_size 
+        image_size = self.image_size
+        channels = 8 # self.channels
+        num_frames = self.num_frames
+        # print((batch_size, channels, num_frames, image_size, image_size))
+        # print('cond_',cond.shape)
+        _sample = self.p_sample_loop(
+            (batch_size, channels, num_frames, image_size, image_size), cond=cond, cond_scale=cond_scale)
+
+        if isinstance(self.vqgan, VQGAN):
+            # denormalize TODO: Remove eventually
+            _sample = (((_sample + 1.0) / 2.0) * (self.vqgan.codebook.embeddings.max() -
+                                                  self.vqgan.codebook.embeddings.min())) + self.vqgan.codebook.embeddings.min()
+
+            _sample = self.vqgan.decode(_sample, quantize=True)
+        else:
+            unnormalize_img(_sample)
+
+        return _sample
+
+    @torch.inference_mode()
+    def interpolate(self, x1, x2, t=None, lam=0.5):
+        b, *_, device = *x1.shape, x1.device
+        t = default(t, self.num_timesteps - 1)
+
+        assert x1.shape == x2.shape
+
+        t_batched = torch.stack([torch.tensor(t, device=device)] * b)
+        xt1, xt2 = map(lambda x: self.q_sample(x, t=t_batched), (x1, x2))
+
+        img = (1 - lam) * xt1 + lam * xt2
+        for i in reversed(range(0, t)):
+            img = self.p_sample(img, torch.full(
+                (b,), i, device=device, dtype=torch.long))
+
+        return img
+
+    def q_sample(self, x_start, t, noise=None):
+        noise = default(noise, lambda: torch.randn_like(x_start))
+
+        return (
+            extract(self.sqrt_alphas_cumprod, t, x_start.shape) * x_start +
+            extract(self.sqrt_one_minus_alphas_cumprod,
+                    t, x_start.shape) * noise
+        )
+
+    def p_losses(self, x_start, t, cond=None, noise=None, **kwargs):
+        b, c, f, h, w, device = *x_start.shape, x_start.device
+        noise = default(noise, lambda: torch.randn_like(x_start))
+        # breakpoint()
+        x_noisy = self.q_sample(x_start=x_start, t=t, noise=noise) # [2, 8, 32, 32, 32]
+
+        if is_list_str(cond):
+            cond = bert_embed(
+                tokenize(cond), return_cls_repr=self.text_use_bert_cls)
+            cond = cond.to(device)
+
+        x_recon = self.denoise_fn(x_noisy, t, cond=cond, **kwargs)
+
+        if self.loss_type == 'l1':
+            loss = F.l1_loss(noise, x_recon)
+        elif self.loss_type == 'l2':
+            loss = F.mse_loss(noise, x_recon)
+        else:
+            raise NotImplementedError()
+
+        return loss
+
+    def forward(self, x, *args, **kwargs):
+        bs = int(x.shape[0]/2)
+        img=x[:bs,...]
+        mask=x[bs:,...]
+        mask_=(1-mask).detach()
+        masked_img = (img*mask_).detach()
+        masked_img=masked_img.permute(0,1,-1,-3,-2)
+        img=img.permute(0,1,-1,-3,-2)
+        mask=mask.permute(0,1,-1,-3,-2)
+        # breakpoint()
+        if isinstance(self.vqgan, VQGAN):
+            with torch.no_grad():
+                img = self.vqgan.encode(
+                    img, quantize=False, include_embeddings=True)
+                # normalize to -1 and 1
+                img = ((img - self.vqgan.codebook.embeddings.min()) /
+                     (self.vqgan.codebook.embeddings.max() -
+                      self.vqgan.codebook.embeddings.min())) * 2.0 - 1.0
+                
+                masked_img = self.vqgan.encode(
+                    masked_img, quantize=False, include_embeddings=True)
+                # normalize to -1 and 1
+                masked_img = ((masked_img - self.vqgan.codebook.embeddings.min()) /
+                     (self.vqgan.codebook.embeddings.max() -
+                      self.vqgan.codebook.embeddings.min())) * 2.0 - 1.0
+        else:
+            print("Hi")
+            img = normalize_img(img)
+            masked_img = normalize_img(masked_img)
+        mask = mask*2.0 - 1.0
+        cc = torch.nn.functional.interpolate(mask, size=masked_img.shape[-3:])
+        cond = torch.cat((masked_img, cc), dim=1)
+
+        b, device, img_size, = img.shape[0], img.device, self.image_size
+        t = torch.randint(0, self.num_timesteps, (b,), device=device).long()
+        # breakpoint()
+        return self.p_losses(img, t, cond=cond, *args, **kwargs)
+
+# trainer class
+
+
+CHANNELS_TO_MODE = {
+    1: 'L',
+    3: 'RGB',
+    4: 'RGBA'
+}
+
+
+def seek_all_images(img, channels=3):
+    assert channels in CHANNELS_TO_MODE, f'channels {channels} invalid'
+    mode = CHANNELS_TO_MODE[channels]
+
+    i = 0
+    while True:
+        try:
+            img.seek(i)
+            yield img.convert(mode)
+        except EOFError:
+            break
+        i += 1
+
+# tensor of shape (channels, frames, height, width) -> gif
+
+
+def video_tensor_to_gif(tensor, path, duration=120, loop=0, optimize=True):
+    tensor = ((tensor - tensor.min()) / (tensor.max() - tensor.min())) * 1.0
+    images = map(T.ToPILImage(), tensor.unbind(dim=1))
+    first_img, *rest_imgs = images
+    first_img.save(path, save_all=True, append_images=rest_imgs,
+                   duration=duration, loop=loop, optimize=optimize)
+    return images
+
+# gif -> (channels, frame, height, width) tensor
+
+
+def gif_to_tensor(path, channels=3, transform=T.ToTensor()):
+    img = Image.open(path)
+    tensors = tuple(map(transform, seek_all_images(img, channels=channels)))
+    return torch.stack(tensors, dim=1)
+
+
+def identity(t, *args, **kwargs):
+    return t
+
+
+def normalize_img(t):
+    return t * 2 - 1
+
+
+def unnormalize_img(t):
+    return (t + 1) * 0.5
+
+
+def cast_num_frames(t, *, frames):
+    f = t.shape[1]
+
+    if f == frames:
+        return t
+
+    if f > frames:
+        return t[:, :frames]
+
+    return F.pad(t, (0, 0, 0, 0, 0, frames - f))
+
+
+class Dataset(data.Dataset):
+    def __init__(
+        self,
+        folder,
+        image_size,
+        channels=3,
+        num_frames=16,
+        horizontal_flip=False,
+        force_num_frames=True,
+        exts=['gif']
+    ):
+        super().__init__()
+        self.folder = folder
+        self.image_size = image_size
+        self.channels = channels
+        self.paths = [p for ext in exts for p in Path(
+            f'{folder}').glob(f'**/*.{ext}')]
+
+        self.cast_num_frames_fn = partial(
+            cast_num_frames, frames=num_frames) if force_num_frames else identity
+
+        self.transform = T.Compose([
+            T.Resize(image_size),
+            T.RandomHorizontalFlip() if horizontal_flip else T.Lambda(identity),
+            T.CenterCrop(image_size),
+            T.ToTensor()
+        ])
+
+    def __len__(self):
+        return len(self.paths)
+
+    def __getitem__(self, index):
+        path = self.paths[index]
+        tensor = gif_to_tensor(path, self.channels, transform=self.transform)
+        return self.cast_num_frames_fn(tensor)
+
+# trainer class
+
+
+class Tester(object):
+    def __init__(
+        self,
+        diffusion_model,
+    ):
+        super().__init__()
+        self.model = diffusion_model
+        self.ema_model = copy.deepcopy(self.model)
+        self.step=0
+        self.image_size = diffusion_model.image_size
+
+        self.reset_parameters()
+
+    def reset_parameters(self):
+        self.ema_model.load_state_dict(self.model.state_dict())
+
+
+    def load(self, milestone, map_location=None, **kwargs):
+        if milestone == -1:
+            all_milestones = [int(p.stem.split('-')[-1])
+                              for p in Path(self.results_folder).glob('**/*.pt')]
+            assert len(
+                all_milestones) > 0, 'need to have at least one milestone to load from latest checkpoint (milestone == -1)'
+            milestone = max(all_milestones)
+
+        if map_location:
+            data = torch.load(milestone, map_location=map_location)
+        else:
+            data = torch.load(milestone)
+
+        self.step = data['step']
+        self.model.load_state_dict(data['model'], **kwargs)
+        self.ema_model.load_state_dict(data['ema'], **kwargs)
+
+

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/ddpm/text.py

@@ -0,0 +1,94 @@
+"Taken and adapted from https://github.com/lucidrains/video-diffusion-pytorch"
+
+import torch
+from einops import rearrange
+
+
+def exists(val):
+    return val is not None
+
+# singleton globals
+
+
+MODEL = None
+TOKENIZER = None
+BERT_MODEL_DIM = 768
+
+
+def get_tokenizer():
+    global TOKENIZER
+    if not exists(TOKENIZER):
+        TOKENIZER = torch.hub.load(
+            'huggingface/pytorch-transformers', 'tokenizer', 'bert-base-cased')
+    return TOKENIZER
+
+
+def get_bert():
+    global MODEL
+    if not exists(MODEL):
+        MODEL = torch.hub.load(
+            'huggingface/pytorch-transformers', 'model', 'bert-base-cased')
+        if torch.cuda.is_available():
+            MODEL = MODEL.cuda()
+
+    return MODEL
+
+# tokenize
+
+
+def tokenize(texts, add_special_tokens=True):
+    if not isinstance(texts, (list, tuple)):
+        texts = [texts]
+
+    tokenizer = get_tokenizer()
+
+    encoding = tokenizer.batch_encode_plus(
+        texts,
+        add_special_tokens=add_special_tokens,
+        padding=True,
+        return_tensors='pt'
+    )
+
+    token_ids = encoding.input_ids
+    return token_ids
+
+# embedding function
+
+
+@torch.no_grad()
+def bert_embed(
+    token_ids,
+    return_cls_repr=False,
+    eps=1e-8,
+    pad_id=0.
+):
+    model = get_bert()
+    mask = token_ids != pad_id
+
+    if torch.cuda.is_available():
+        token_ids = token_ids.cuda()
+        mask = mask.cuda()
+
+    outputs = model(
+        input_ids=token_ids,
+        attention_mask=mask,
+        output_hidden_states=True
+    )
+
+    hidden_state = outputs.hidden_states[-1]
+
+    if return_cls_repr:
+        # return [cls] as representation
+        return hidden_state[:, 0]
+
+    if not exists(mask):
+        return hidden_state.mean(dim=1)
+
+    # mean all tokens excluding [cls], accounting for length
+    mask = mask[:, 1:]
+    mask = rearrange(mask, 'b n -> b n 1')
+
+    numer = (hidden_state[:, 1:] * mask).sum(dim=1)
+    denom = mask.sum(dim=1)
+    masked_mean = numer / (denom + eps)
+    return

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/ddpm/time_embedding.py

@@ -0,0 +1,75 @@
+import math
+import torch
+import torch.nn as nn
+
+from monai.networks.layers.utils import get_act_layer
+
+
+class SinusoidalPosEmb(nn.Module):
+    def __init__(self, emb_dim=16, downscale_freq_shift=1, max_period=10000, flip_sin_to_cos=False):
+        super().__init__()
+        self.emb_dim = emb_dim
+        self.downscale_freq_shift = downscale_freq_shift
+        self.max_period = max_period
+        self.flip_sin_to_cos = flip_sin_to_cos
+
+    def forward(self, x):
+        device = x.device
+        half_dim = self.emb_dim // 2
+        emb = math.log(self.max_period) / \
+            (half_dim - self.downscale_freq_shift)
+        emb = torch.exp(-emb*torch.arange(half_dim, device=device))
+        emb = x[:, None] * emb[None, :]
+        emb = torch.cat((emb.sin(), emb.cos()), dim=-1)
+
+        if self.flip_sin_to_cos:
+            emb = torch.cat([emb[:, half_dim:], emb[:, :half_dim]], dim=-1)
+
+        if self.emb_dim % 2 == 1:
+            emb = torch.nn.functional.pad(emb, (0, 1, 0, 0))
+        return emb
+
+
+class LearnedSinusoidalPosEmb(nn.Module):
+    """ following @crowsonkb 's lead with learned sinusoidal pos emb """
+    """ https://github.com/crowsonkb/v-diffusion-jax/blob/master/diffusion/models/danbooru_128.py#L8 """
+
+    def __init__(self, emb_dim):
+        super().__init__()
+        self.emb_dim = emb_dim
+        half_dim = emb_dim // 2
+        self.weights = nn.Parameter(torch.randn(half_dim))
+
+    def forward(self, x):
+        x = x[:, None]
+        freqs = x * self.weights[None, :] * 2 * math.pi
+        fouriered = torch.cat((freqs.sin(), freqs.cos()), dim=-1)
+        fouriered = torch.cat((x, fouriered), dim=-1)
+        if self.emb_dim % 2 == 1:
+            fouriered = torch.nn.functional.pad(fouriered, (0, 1, 0, 0))
+        return fouriered
+
+
+class TimeEmbbeding(nn.Module):
+    def __init__(
+        self,
+        emb_dim=64,
+        pos_embedder=SinusoidalPosEmb,
+        pos_embedder_kwargs={},
+        act_name=("SWISH", {})  # Swish = SiLU
+    ):
+        super().__init__()
+        self.emb_dim = emb_dim
+        self.pos_emb_dim = pos_embedder_kwargs.get('emb_dim', emb_dim//4)
+        pos_embedder_kwargs['emb_dim'] = self.pos_emb_dim
+        self.pos_embedder = pos_embedder(**pos_embedder_kwargs)
+
+        self.time_emb = nn.Sequential(
+            self.pos_embedder,
+            nn.Linear(self.pos_emb_dim, self.emb_dim),
+            get_act_layer(act_name),
+            nn.Linear(self.emb_dim, self.emb_dim)
+        )
+
+    def forward(self, time):
+        return self.time_emb(time)

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/ddpm/unet.py

@@ -0,0 +1,226 @@
+from ddpm.time_embedding import TimeEmbbeding
+
+import monai.networks.nets as nets
+import torch
+import torch.nn as nn
+from einops import rearrange
+
+from monai.networks.blocks import UnetBasicBlock, UnetResBlock, UnetUpBlock, Convolution, UnetOutBlock
+from monai.networks.layers.utils import get_act_layer
+
+
+class DownBlock(nn.Module):
+    def __init__(
+            self,
+            spatial_dims,
+            in_ch,
+            out_ch,
+            time_emb_dim,
+            cond_emb_dim,
+            act_name=("swish", {}),
+            **kwargs):
+        super(DownBlock, self).__init__()
+        self.loca_time_embedder = nn.Sequential(
+            get_act_layer(name=act_name),
+            nn.Linear(time_emb_dim, in_ch)  # in_ch * 2
+        )
+        if cond_emb_dim is not None:
+            self.loca_cond_embedder = nn.Sequential(
+                get_act_layer(name=act_name),
+                nn.Linear(cond_emb_dim, in_ch),
+            )
+        self.down_op = UnetBasicBlock(
+            spatial_dims, in_ch, out_ch, act_name=act_name, **kwargs)
+
+    def forward(self, x, time_emb, cond_emb):
+        b, c, *_ = x.shape
+        sp_dim = x.ndim-2
+
+        # ------------ Time ----------
+        time_emb = self.loca_time_embedder(time_emb)
+        time_emb = time_emb.reshape(b, c, *((1,)*sp_dim))
+        # scale, shift = time_emb.chunk(2, dim = 1)
+
+        # ------------ Combine ------------
+        # x = x * (scale + 1) + shift
+        x = x + time_emb
+
+        # ----------- Condition ------------
+        if cond_emb is not None:
+            cond_emb = self.loca_cond_embedder(cond_emb)
+            cond_emb = cond_emb.reshape(b, c, *((1,)*sp_dim))
+            x = x + cond_emb
+
+        # ----------- Image ---------
+        y = self.down_op(x)
+        return y
+
+
+class UpBlock(nn.Module):
+    def __init__(
+            self,
+            spatial_dims,
+            skip_ch,
+            enc_ch,
+            time_emb_dim,
+            cond_emb_dim,
+            act_name=("swish", {}),
+            **kwargs):
+        super(UpBlock, self).__init__()
+        self.up_op = UnetUpBlock(spatial_dims, enc_ch,
+                                 skip_ch, act_name=act_name, **kwargs)
+        self.loca_time_embedder = nn.Sequential(
+            get_act_layer(name=act_name),
+            nn.Linear(time_emb_dim, skip_ch * 2),
+        )
+        if cond_emb_dim is not None:
+            self.loca_cond_embedder = nn.Sequential(
+                get_act_layer(name=act_name),
+                nn.Linear(cond_emb_dim, skip_ch * 2),
+            )
+
+    def forward(self, x_skip, x_enc, time_emb, cond_emb):
+        b, c, *_ = x_enc.shape
+        sp_dim = x_enc.ndim-2
+
+        # ----------- Time --------------
+        time_emb = self.loca_time_embedder(time_emb)
+        time_emb = time_emb.reshape(b, c, *((1,)*sp_dim))
+        # scale, shift = time_emb.chunk(2, dim = 1)
+
+        # -------- Combine -------------
+        # y = x * (scale + 1) + shift
+        x_enc = x_enc + time_emb
+
+        # ----------- Condition ------------
+        if cond_emb is not None:
+            cond_emb = self.loca_cond_embedder(cond_emb)
+            cond_emb = cond_emb.reshape(b, c, *((1,)*sp_dim))
+            x_enc = x_enc + cond_emb
+
+        # ----------- Image -------------
+        y = self.up_op(x_enc, x_skip)
+
+        # -------- Combine -------------
+        # y = y * (scale + 1) + shift
+
+        return y
+
+
+class UNet(nn.Module):
+
+    def __init__(self,
+                 in_ch=1,
+                 out_ch=1,
+                 spatial_dims=3,
+                 hid_chs=[32,       64,      128,      256,  512],
+                 kernel_sizes=[(1, 3, 3), (1, 3, 3), (1, 3, 3),    3,   3],
+                 strides=[1,     (1, 2, 2), (1, 2, 2),    2,   2],
+                 upsample_kernel_sizes=None,
+                 act_name=("SWISH", {}),
+                 norm_name=("INSTANCE", {"affine": True}),
+                 time_embedder=TimeEmbbeding,
+                 time_embedder_kwargs={},
+                 cond_embedder=None,
+                 cond_embedder_kwargs={},
+                 # True = all but last layer, 0/False=disable, 1=only first layer, ...
+                 deep_ver_supervision=True,
+                 estimate_variance=False,
+                 use_self_conditioning=False,
+                 **kwargs
+                 ):
+        super().__init__()
+        if upsample_kernel_sizes is None:
+            upsample_kernel_sizes = strides[1:]
+
+        # ------------- Time-Embedder-----------
+        self.time_embedder = time_embedder(**time_embedder_kwargs)
+
+        # ------------- Condition-Embedder-----------
+        if cond_embedder is not None:
+            self.cond_embedder = cond_embedder(**cond_embedder_kwargs)
+            cond_emb_dim = self.cond_embedder.emb_dim
+        else:
+            self.cond_embedder = None
+            cond_emb_dim = None
+
+        # ----------- In-Convolution ------------
+        in_ch = in_ch*2 if use_self_conditioning else in_ch
+        self.inc = UnetBasicBlock(spatial_dims, in_ch, hid_chs[0], kernel_size=kernel_sizes[0], stride=strides[0],
+                                  act_name=act_name, norm_name=norm_name, **kwargs)
+
+        # ----------- Encoder ----------------
+        self.encoders = nn.ModuleList([
+            DownBlock(spatial_dims, hid_chs[i-1], hid_chs[i],  time_emb_dim=self.time_embedder.emb_dim,
+                      cond_emb_dim=cond_emb_dim,  kernel_size=kernel_sizes[
+                          i], stride=strides[i], act_name=act_name,
+                      norm_name=norm_name, **kwargs)
+            for i in range(1, len(strides))
+        ])
+
+        # ------------ Decoder ----------
+        self.decoders = nn.ModuleList([
+            UpBlock(spatial_dims, hid_chs[i], hid_chs[i+1], time_emb_dim=self.time_embedder.emb_dim,
+                    cond_emb_dim=cond_emb_dim, kernel_size=kernel_sizes[i +
+                                                                        1], stride=strides[i+1], act_name=act_name,
+                    norm_name=norm_name, upsample_kernel_size=upsample_kernel_sizes[i], **kwargs)
+            for i in range(len(strides)-1)
+        ])
+
+        # --------------- Out-Convolution ----------------
+        out_ch_hor = out_ch*2 if estimate_variance else out_ch
+        self.outc = UnetOutBlock(
+            spatial_dims, hid_chs[0], out_ch_hor, dropout=None)
+        if isinstance(deep_ver_supervision, bool):
+            deep_ver_supervision = len(
+                strides)-2 if deep_ver_supervision else 0
+        self.outc_ver = nn.ModuleList([
+            UnetOutBlock(spatial_dims, hid_chs[i], out_ch, dropout=None)
+            for i in range(1, deep_ver_supervision+1)
+        ])
+
+    def forward(self, x_t, t, cond=None, self_cond=None, **kwargs):
+        condition = cond
+        # x_t [B, C, (D), H, W]
+        # t [B,]
+
+        # -------- In-Convolution --------------
+        x = [None for _ in range(len(self.encoders)+1)]
+        x_t = torch.cat([x_t, self_cond],
+                        dim=1) if self_cond is not None else x_t
+        x[0] = self.inc(x_t)
+
+        # -------- Time Embedding (Gloabl) -----------
+        time_emb = self.time_embedder(t)  # [B, C]
+
+        # -------- Condition Embedding (Gloabl) -----------
+        if (condition is None) or (self.cond_embedder is None):
+            cond_emb = None
+        else:
+            cond_emb = self.cond_embedder(condition)  # [B, C]
+
+        # --------- Encoder --------------
+        for i in range(len(self.encoders)):
+            x[i+1] = self.encoders[i](x[i], time_emb, cond_emb)
+
+        # -------- Decoder -----------
+        for i in range(len(self.decoders), 0, -1):
+            x[i-1] = self.decoders[i-1](x[i-1], x[i], time_emb, cond_emb)
+
+        # ---------Out-Convolution ------------
+        y_hor = self.outc(x[0])
+        y_ver = [outc_ver_i(x[i+1])
+                 for i, outc_ver_i in enumerate(self.outc_ver)]
+
+        return y_hor  # , y_ver
+
+    def forward_with_cond_scale(self, *args, cond_scale=0., **kwargs):
+        return self.forward(*args, **kwargs)
+
+
+if __name__ == '__main__':
+    model = UNet(in_ch=3)
+    input = torch.randn((1, 3, 16, 128, 128))
+    time = torch.randn((1,))
+    out_hor, out_ver = model(input, time)
+    print(out_hor[0].shape)

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/ddpm/util.py

@@ -0,0 +1,271 @@
+# adopted from
+# https://github.com/openai/improved-diffusion/blob/main/improved_diffusion/gaussian_diffusion.py
+# and
+# https://github.com/lucidrains/denoising-diffusion-pytorch/blob/7706bdfc6f527f58d33f84b7b522e61e6e3164b3/denoising_diffusion_pytorch/denoising_diffusion_pytorch.py
+# and
+# https://github.com/openai/guided-diffusion/blob/0ba878e517b276c45d1195eb29f6f5f72659a05b/guided_diffusion/nn.py
+#
+# thanks!
+
+
+import os
+import math
+import torch
+import torch.nn as nn
+import numpy as np
+from einops import repeat
+
+# from ldm.util import instantiate_from_config
+
+
+def make_beta_schedule(schedule, n_timestep, linear_start=1e-4, linear_end=2e-2, cosine_s=8e-3):
+    if schedule == "linear":
+        betas = (
+                torch.linspace(linear_start ** 0.5, linear_end ** 0.5, n_timestep, dtype=torch.float64) ** 2
+        )
+
+    elif schedule == "cosine":
+        timesteps = (
+                torch.arange(n_timestep + 1, dtype=torch.float64) / n_timestep + cosine_s
+        )
+        alphas = timesteps / (1 + cosine_s) * np.pi / 2
+        alphas = torch.cos(alphas).pow(2)
+        alphas = alphas / alphas[0]
+        betas = 1 - alphas[1:] / alphas[:-1]
+        betas = np.clip(betas, a_min=0, a_max=0.999)
+
+    elif schedule == "sqrt_linear":
+        betas = torch.linspace(linear_start, linear_end, n_timestep, dtype=torch.float64)
+    elif schedule == "sqrt":
+        betas = torch.linspace(linear_start, linear_end, n_timestep, dtype=torch.float64) ** 0.5
+    else:
+        raise ValueError(f"schedule '{schedule}' unknown.")
+    return betas.numpy()
+
+
+def make_ddim_timesteps(ddim_discr_method, num_ddim_timesteps, num_ddpm_timesteps, verbose=True):
+    if ddim_discr_method == 'uniform':
+        c = num_ddpm_timesteps // num_ddim_timesteps
+        ddim_timesteps = np.asarray(list(range(0, num_ddpm_timesteps, c)))
+    elif ddim_discr_method == 'quad':
+        ddim_timesteps = ((np.linspace(0, np.sqrt(num_ddpm_timesteps * .8), num_ddim_timesteps)) ** 2).astype(int)
+    else:
+        raise NotImplementedError(f'There is no ddim discretization method called "{ddim_discr_method}"')
+
+    # assert ddim_timesteps.shape[0] == num_ddim_timesteps
+    # add one to get the final alpha values right (the ones from first scale to data during sampling)
+    if c != 1:
+        steps_out = ddim_timesteps + 1
+    else:
+        steps_out = ddim_timesteps
+    if verbose:
+        print(f'Selected timesteps for ddim sampler: {steps_out}')
+    return steps_out
+
+
+def make_ddim_sampling_parameters(alphacums, ddim_timesteps, eta, verbose=True):
+    # select alphas for computing the variance schedule
+
+    alphas = alphacums[ddim_timesteps]
+    alphas_prev = np.asarray([alphacums[0]] + alphacums[ddim_timesteps[:-1]].tolist())
+
+    # according the the formula provided in https://arxiv.org/abs/2010.02502
+    sigmas = eta * np.sqrt((1 - alphas_prev) / (1 - alphas) * (1 - alphas / alphas_prev))
+    if verbose:
+        print(f'Selected alphas for ddim sampler: a_t: {alphas}; a_(t-1): {alphas_prev}')
+        print(f'For the chosen value of eta, which is {eta}, '
+              f'this results in the following sigma_t schedule for ddim sampler {sigmas}')
+    return sigmas, alphas, alphas_prev
+
+
+def betas_for_alpha_bar(num_diffusion_timesteps, alpha_bar, max_beta=0.999):
+    """
+    Create a beta schedule that discretizes the given alpha_t_bar function,
+    which defines the cumulative product of (1-beta) over time from t = [0,1].
+    :param num_diffusion_timesteps: the number of betas to produce.
+    :param alpha_bar: a lambda that takes an argument t from 0 to 1 and
+                      produces the cumulative product of (1-beta) up to that
+                      part of the diffusion process.
+    :param max_beta: the maximum beta to use; use values lower than 1 to
+                     prevent singularities.
+    """
+    betas = []
+    for i in range(num_diffusion_timesteps):
+        t1 = i / num_diffusion_timesteps
+        t2 = (i + 1) / num_diffusion_timesteps
+        betas.append(min(1 - alpha_bar(t2) / alpha_bar(t1), max_beta))
+    return np.array(betas)
+
+
+def extract_into_tensor(a, t, x_shape):
+    b, *_ = t.shape
+    out = a.gather(-1, t)
+    return out.reshape(b, *((1,) * (len(x_shape) - 1)))
+
+
+def checkpoint(func, inputs, params, flag):
+    """
+    Evaluate a function without caching intermediate activations, allowing for
+    reduced memory at the expense of extra compute in the backward pass.
+    :param func: the function to evaluate.
+    :param inputs: the argument sequence to pass to `func`.
+    :param params: a sequence of parameters `func` depends on but does not
+                   explicitly take as arguments.
+    :param flag: if False, disable gradient checkpointing.
+    """
+    if flag:
+        args = tuple(inputs) + tuple(params)
+        return CheckpointFunction.apply(func, len(inputs), *args)
+    else:
+        return func(*inputs)
+
+
+class CheckpointFunction(torch.autograd.Function):
+    @staticmethod
+    def forward(ctx, run_function, length, *args):
+        ctx.run_function = run_function
+        ctx.input_tensors = list(args[:length])
+        ctx.input_params = list(args[length:])
+
+        with torch.no_grad():
+            output_tensors = ctx.run_function(*ctx.input_tensors)
+        return output_tensors
+
+    @staticmethod
+    def backward(ctx, *output_grads):
+        ctx.input_tensors = [x.detach().requires_grad_(True) for x in ctx.input_tensors]
+        with torch.enable_grad():
+            # Fixes a bug where the first op in run_function modifies the
+            # Tensor storage in place, which is not allowed for detach()'d
+            # Tensors.
+            shallow_copies = [x.view_as(x) for x in ctx.input_tensors]
+            output_tensors = ctx.run_function(*shallow_copies)
+        input_grads = torch.autograd.grad(
+            output_tensors,
+            ctx.input_tensors + ctx.input_params,
+            output_grads,
+            allow_unused=True,
+        )
+        del ctx.input_tensors
+        del ctx.input_params
+        del output_tensors
+        return (None, None) + input_grads
+
+
+def timestep_embedding(timesteps, dim, max_period=10000, repeat_only=False):
+    """
+    Create sinusoidal timestep embeddings.
+    :param timesteps: a 1-D Tensor of N indices, one per batch element.
+                      These may be fractional.
+    :param dim: the dimension of the output.
+    :param max_period: controls the minimum frequency of the embeddings.
+    :return: an [N x dim] Tensor of positional embeddings.
+    """
+    if not repeat_only:
+        half = dim // 2
+        freqs = torch.exp(
+            -math.log(max_period) * torch.arange(start=0, end=half, dtype=torch.float32) / half
+        ).to(device=timesteps.device)
+        args = timesteps[:, None].float() * freqs[None]
+        embedding = torch.cat([torch.cos(args), torch.sin(args)], dim=-1)
+        if dim % 2:
+            embedding = torch.cat([embedding, torch.zeros_like(embedding[:, :1])], dim=-1)
+    else:
+        embedding = repeat(timesteps, 'b -> b d', d=dim)
+    return embedding
+
+
+def zero_module(module):
+    """
+    Zero out the parameters of a module and return it.
+    """
+    for p in module.parameters():
+        p.detach().zero_()
+    return module
+
+
+def scale_module(module, scale):
+    """
+    Scale the parameters of a module and return it.
+    """
+    for p in module.parameters():
+        p.detach().mul_(scale)
+    return module
+
+
+def mean_flat(tensor):
+    """
+    Take the mean over all non-batch dimensions.
+    """
+    return tensor.mean(dim=list(range(1, len(tensor.shape))))
+
+
+def normalization(channels):
+    """
+    Make a standard normalization layer.
+    :param channels: number of input channels.
+    :return: an nn.Module for normalization.
+    """
+    return GroupNorm32(32, channels)
+
+
+# PyTorch 1.7 has SiLU, but we support PyTorch 1.5.
+class SiLU(nn.Module):
+    def forward(self, x):
+        return x * torch.sigmoid(x)
+
+
+class GroupNorm32(nn.GroupNorm):
+    def forward(self, x):
+        return super().forward(x.float()).type(x.dtype)
+
+def conv_nd(dims, *args, **kwargs):
+    """
+    Create a 1D, 2D, or 3D convolution module.
+    """
+    if dims == 1:
+        return nn.Conv1d(*args, **kwargs)
+    elif dims == 2:
+        return nn.Conv2d(*args, **kwargs)
+    elif dims == 3:
+        return nn.Conv3d(*args, **kwargs)
+    raise ValueError(f"unsupported dimensions: {dims}")
+
+
+def linear(*args, **kwargs):
+    """
+    Create a linear module.
+    """
+    return nn.Linear(*args, **kwargs)
+
+
+def avg_pool_nd(dims, *args, **kwargs):
+    """
+    Create a 1D, 2D, or 3D average pooling module.
+    """
+    if dims == 1:
+        return nn.AvgPool1d(*args, **kwargs)
+    elif dims == 2:
+        return nn.AvgPool2d(*args, **kwargs)
+    elif dims == 3:
+        return nn.AvgPool3d(*args, **kwargs)
+    raise ValueError(f"unsupported dimensions: {dims}")
+
+
+class HybridConditioner(nn.Module):
+
+    def __init__(self, c_concat_config, c_crossattn_config):
+        super().__init__()
+        self.concat_conditioner = instantiate_from_config(c_concat_config)
+        self.crossattn_conditioner = instantiate_from_config(c_crossattn_config)
+
+    def forward(self, c_concat, c_crossattn):
+        c_concat = self.concat_conditioner(c_concat)
+        c_crossattn = self.crossattn_conditioner(c_crossattn)
+        return {'c_concat': [c_concat], 'c_crossattn': [c_crossattn]}
+
+
+def noise_like(shape, device, repeat=False):
+    repeat_noise = lambda: torch.randn((1, *shape[1:]), device=device).repeat(shape[0], *((1,) * (len(shape) - 1)))
+    noise = lambda: torch.randn(shape, device=device)
+    return repeat_noise() if repeat else noise()

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/vq_gan_3d/model/__init__.py

@@ -0,0 +1,3 @@
+from .vqgan import VQGAN
+from .codebook import Codebook
+from .lpips import LPIPS

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/vq_gan_3d/model/cache/vgg.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a78928a0af1e5f0fcb1f3b9e8f8c3a2a5a3de244d830ad5c1feddc79b8432868
+size 7289

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/vq_gan_3d/model/codebook.py

@@ -0,0 +1,109 @@
+""" Adapted from https://github.com/SongweiGe/TATS"""
+# Copyright (c) Meta Platforms, Inc. All Rights Reserved
+
+import numpy as np
+
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import torch.distributed as dist
+
+from ..utils import shift_dim
+
+
+class Codebook(nn.Module):
+    def __init__(self, n_codes, embedding_dim, no_random_restart=False, restart_thres=1.0):
+        super().__init__()
+        self.register_buffer('embeddings', torch.randn(n_codes, embedding_dim))
+        self.register_buffer('N', torch.zeros(n_codes))
+        self.register_buffer('z_avg', self.embeddings.data.clone())
+
+        self.n_codes = n_codes
+        self.embedding_dim = embedding_dim
+        self._need_init = True
+        self.no_random_restart = no_random_restart
+        self.restart_thres = restart_thres
+
+    def _tile(self, x):
+        d, ew = x.shape
+        if d < self.n_codes:
+            n_repeats = (self.n_codes + d - 1) // d
+            std = 0.01 / np.sqrt(ew)
+            x = x.repeat(n_repeats, 1)
+            x = x + torch.randn_like(x) * std
+        return x
+
+    def _init_embeddings(self, z):
+        # z: [b, c, t, h, w]
+        self._need_init = False
+        breakpoint()
+        flat_inputs = shift_dim(z, 1, -1).flatten(end_dim=-2) # [65536, 8] [2, 8, 32, 32, 32]
+        y = self._tile(flat_inputs) # [65536, 8]
+
+        d = y.shape[0]
+        _k_rand = y[torch.randperm(y.shape[0])][:self.n_codes]
+        if dist.is_initialized():
+            dist.broadcast(_k_rand, 0)
+        self.embeddings.data.copy_(_k_rand)
+        self.z_avg.data.copy_(_k_rand)
+        self.N.data.copy_(torch.ones(self.n_codes))
+
+    def forward(self, z):
+        # z: [b, c, t, h, w]
+        if self._need_init and self.training:
+            self._init_embeddings(z)
+        flat_inputs = shift_dim(z, 1, -1).flatten(end_dim=-2)  # [bthw, c] [65536, 8]
+        distances = (flat_inputs ** 2).sum(dim=1, keepdim=True) \
+            - 2 * flat_inputs @ self.embeddings.t() \
+            + (self.embeddings.t() ** 2).sum(dim=0, keepdim=True)  # [bthw, c] [65536, 8]
+
+        encoding_indices = torch.argmin(distances, dim=1) # [65536]
+        encode_onehot = F.one_hot(encoding_indices, self.n_codes).type_as(
+            flat_inputs)  # [bthw, ncode] [65536, 16384]
+        encoding_indices = encoding_indices.view(
+            z.shape[0], *z.shape[2:])  # [b, t, h, w, ncode] [2, 32, 32, 32]
+
+        embeddings = F.embedding(
+            encoding_indices, self.embeddings)  # [b, t, h, w, c] self.embeddings [16384, 8]
+        embeddings = shift_dim(embeddings, -1, 1)  # [b, c, t, h, w] [2, 8, 32, 32, 32]
+
+        commitment_loss = 0.25 * F.mse_loss(z, embeddings.detach())
+
+        # EMA codebook update
+        if self.training:
+            n_total = encode_onehot.sum(dim=0) # [16384]
+            encode_sum = flat_inputs.t() @ encode_onehot # [8, 16384]
+            if dist.is_initialized():
+                dist.all_reduce(n_total)
+                dist.all_reduce(encode_sum)
+
+            self.N.data.mul_(0.99).add_(n_total, alpha=0.01)
+            self.z_avg.data.mul_(0.99).add_(encode_sum.t(), alpha=0.01)
+
+            n = self.N.sum()
+            weights = (self.N + 1e-7) / (n + self.n_codes * 1e-7) * n
+            encode_normalized = self.z_avg / weights.unsqueeze(1)
+            self.embeddings.data.copy_(encode_normalized)
+
+            y = self._tile(flat_inputs)
+            _k_rand = y[torch.randperm(y.shape[0])][:self.n_codes]
+            if dist.is_initialized():
+                dist.broadcast(_k_rand, 0)
+
+            if not self.no_random_restart:
+                usage = (self.N.view(self.n_codes, 1)
+                         >= self.restart_thres).float()
+                self.embeddings.data.mul_(usage).add_(_k_rand * (1 - usage))
+
+        embeddings_st = (embeddings - z).detach() + z
+
+        avg_probs = torch.mean(encode_onehot, dim=0)
+        perplexity = torch.exp(-torch.sum(avg_probs *
+                               torch.log(avg_probs + 1e-10)))
+
+        return dict(embeddings=embeddings_st, encodings=encoding_indices,
+                    commitment_loss=commitment_loss, perplexity=perplexity)
+
+    def dictionary_lookup(self, encodings):
+        embeddings = F.embedding(encodings, self.embeddings)
+        return embeddings

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/vq_gan_3d/model/lpips.py

@@ -0,0 +1,181 @@
+"""Adapted from https://github.com/SongweiGe/TATS"""
+
+"""Stripped version of https://github.com/richzhang/PerceptualSimilarity/tree/master/models"""
+
+
+from collections import namedtuple
+from torchvision import models
+import torch.nn as nn
+import torch
+from tqdm import tqdm
+import requests
+import os
+import hashlib
+URL_MAP = {
+    "vgg_lpips": "https://heibox.uni-heidelberg.de/f/607503859c864bc1b30b/?dl=1"
+}
+
+CKPT_MAP = {
+    "vgg_lpips": "vgg.pth"
+}
+
+MD5_MAP = {
+    "vgg_lpips": "d507d7349b931f0638a25a48a722f98a"
+}
+
+
+def download(url, local_path, chunk_size=1024):
+    os.makedirs(os.path.split(local_path)[0], exist_ok=True)
+    with requests.get(url, stream=True) as r:
+        total_size = int(r.headers.get("content-length", 0))
+        with tqdm(total=total_size, unit="B", unit_scale=True) as pbar:
+            with open(local_path, "wb") as f:
+                for data in r.iter_content(chunk_size=chunk_size):
+                    if data:
+                        f.write(data)
+                        pbar.update(chunk_size)
+
+
+def md5_hash(path):
+    with open(path, "rb") as f:
+        content = f.read()
+    return hashlib.md5(content).hexdigest()
+
+
+def get_ckpt_path(name, root, check=False):
+    assert name in URL_MAP
+    path = os.path.join(root, CKPT_MAP[name])
+    if not os.path.exists(path) or (check and not md5_hash(path) == MD5_MAP[name]):
+        print("Downloading {} model from {} to {}".format(
+            name, URL_MAP[name], path))
+        download(URL_MAP[name], path)
+        md5 = md5_hash(path)
+        assert md5 == MD5_MAP[name], md5
+    return path
+
+
+class LPIPS(nn.Module):
+    # Learned perceptual metric
+    def __init__(self, use_dropout=True):
+        super().__init__()
+        self.scaling_layer = ScalingLayer()
+        self.chns = [64, 128, 256, 512, 512]  # vg16 features
+        self.net = vgg16(pretrained=True, requires_grad=False)
+        self.lin0 = NetLinLayer(self.chns[0], use_dropout=use_dropout)
+        self.lin1 = NetLinLayer(self.chns[1], use_dropout=use_dropout)
+        self.lin2 = NetLinLayer(self.chns[2], use_dropout=use_dropout)
+        self.lin3 = NetLinLayer(self.chns[3], use_dropout=use_dropout)
+        self.lin4 = NetLinLayer(self.chns[4], use_dropout=use_dropout)
+        # self.load_from_pretrained()
+        for param in self.parameters():
+            param.requires_grad = False
+
+    def load_from_pretrained(self, name="vgg_lpips"):
+        ckpt = get_ckpt_path(name, os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "cache"))
+        self.load_state_dict(torch.load(
+            ckpt, map_location=torch.device("cpu")), strict=False)
+        print("loaded pretrained LPIPS loss from {}".format(ckpt))
+
+    @classmethod
+    def from_pretrained(cls, name="vgg_lpips"):
+        if name is not "vgg_lpips":
+            raise NotImplementedError
+        model = cls()
+        ckpt = get_ckpt_path(name, os.path.join(
+            os.path.dirname(os.path.abspath(__file__)), "cache"))
+        model.load_state_dict(torch.load(
+            ckpt, map_location=torch.device("cpu")), strict=False)
+        return model
+
+    def forward(self, input, target):
+        in0_input, in1_input = (self.scaling_layer(
+            input), self.scaling_layer(target))
+        outs0, outs1 = self.net(in0_input), self.net(in1_input)
+        feats0, feats1, diffs = {}, {}, {}
+        lins = [self.lin0, self.lin1, self.lin2, self.lin3, self.lin4]
+        for kk in range(len(self.chns)):
+            feats0[kk], feats1[kk] = normalize_tensor(
+                outs0[kk]), normalize_tensor(outs1[kk])
+            diffs[kk] = (feats0[kk] - feats1[kk]) ** 2
+
+        res = [spatial_average(lins[kk].model(diffs[kk]), keepdim=True)
+               for kk in range(len(self.chns))]
+        val = res[0]
+        for l in range(1, len(self.chns)):
+            val += res[l]
+        return val
+
+
+class ScalingLayer(nn.Module):
+    def __init__(self):
+        super(ScalingLayer, self).__init__()
+        self.register_buffer('shift', torch.Tensor(
+            [-.030, -.088, -.188])[None, :, None, None])
+        self.register_buffer('scale', torch.Tensor(
+            [.458, .448, .450])[None, :, None, None])
+
+    def forward(self, inp):
+        return (inp - self.shift) / self.scale
+
+
+class NetLinLayer(nn.Module):
+    """ A single linear layer which does a 1x1 conv """
+
+    def __init__(self, chn_in, chn_out=1, use_dropout=False):
+        super(NetLinLayer, self).__init__()
+        layers = [nn.Dropout(), ] if (use_dropout) else []
+        layers += [nn.Conv2d(chn_in, chn_out, 1, stride=1,
+                             padding=0, bias=False), ]
+        self.model = nn.Sequential(*layers)
+
+
+class vgg16(torch.nn.Module):
+    def __init__(self, requires_grad=False, pretrained=True):
+        super(vgg16, self).__init__()
+        vgg_pretrained_features = models.vgg16(pretrained=pretrained).features
+        self.slice1 = torch.nn.Sequential()
+        self.slice2 = torch.nn.Sequential()
+        self.slice3 = torch.nn.Sequential()
+        self.slice4 = torch.nn.Sequential()
+        self.slice5 = torch.nn.Sequential()
+        self.N_slices = 5
+        for x in range(4):
+            self.slice1.add_module(str(x), vgg_pretrained_features[x])
+        for x in range(4, 9):
+            self.slice2.add_module(str(x), vgg_pretrained_features[x])
+        for x in range(9, 16):
+            self.slice3.add_module(str(x), vgg_pretrained_features[x])
+        for x in range(16, 23):
+            self.slice4.add_module(str(x), vgg_pretrained_features[x])
+        for x in range(23, 30):
+            self.slice5.add_module(str(x), vgg_pretrained_features[x])
+        if not requires_grad:
+            for param in self.parameters():
+                param.requires_grad = False
+
+    def forward(self, X):
+        h = self.slice1(X)
+        h_relu1_2 = h
+        h = self.slice2(h)
+        h_relu2_2 = h
+        h = self.slice3(h)
+        h_relu3_3 = h
+        h = self.slice4(h)
+        h_relu4_3 = h
+        h = self.slice5(h)
+        h_relu5_3 = h
+        vgg_outputs = namedtuple(
+            "VggOutputs", ['relu1_2', 'relu2_2', 'relu3_3', 'relu4_3', 'relu5_3'])
+        out = vgg_outputs(h_relu1_2, h_relu2_2,
+                          h_relu3_3, h_relu4_3, h_relu5_3)
+        return out
+
+
+def normalize_tensor(x, eps=1e-10):
+    norm_factor = torch.sqrt(torch.sum(x**2, dim=1, keepdim=True))
+    return x/(norm_factor+eps)
+
+
+def spatial_average(x, keepdim=True):
+    return x.mean([2, 3], keepdim=keepdim)

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/vq_gan_3d/model/vqgan.py

@@ -0,0 +1,561 @@
+"""Adapted from https://github.com/SongweiGe/TATS"""
+# Copyright (c) Meta Platforms, Inc. All Rights Reserved
+
+import math
+import argparse
+import numpy as np
+import pickle as pkl
+
+import pytorch_lightning as pl
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+import torch.distributed as dist
+
+from ..utils import shift_dim, adopt_weight, comp_getattr
+from .lpips import LPIPS
+from .codebook import Codebook
+
+
+def silu(x):
+    return x*torch.sigmoid(x)
+
+
+class SiLU(nn.Module):
+    def __init__(self):
+        super(SiLU, self).__init__()
+
+    def forward(self, x):
+        return silu(x)
+
+
+def hinge_d_loss(logits_real, logits_fake):
+    loss_real = torch.mean(F.relu(1. - logits_real))
+    loss_fake = torch.mean(F.relu(1. + logits_fake))
+    d_loss = 0.5 * (loss_real + loss_fake)
+    return d_loss
+
+
+def vanilla_d_loss(logits_real, logits_fake):
+    d_loss = 0.5 * (
+        torch.mean(torch.nn.functional.softplus(-logits_real)) +
+        torch.mean(torch.nn.functional.softplus(logits_fake)))
+    return d_loss
+
+
+class VQGAN(pl.LightningModule):
+    def __init__(self, cfg):
+        super().__init__()
+        self.cfg = cfg
+        self.embedding_dim = cfg.model.embedding_dim # 8
+        self.n_codes = cfg.model.n_codes # 16384
+
+        self.encoder = Encoder(cfg.model.n_hiddens, # 16
+                               cfg.model.downsample, # [2, 2, 2]
+                               cfg.dataset.image_channels, # 1
+                               cfg.model.norm_type, # group
+                               cfg.model.padding_type, # replicate
+                               cfg.model.num_groups, # 32
+                               )
+        self.decoder = Decoder(
+            cfg.model.n_hiddens, cfg.model.downsample, cfg.dataset.image_channels, cfg.model.norm_type, cfg.model.num_groups)
+        self.enc_out_ch = self.encoder.out_channels
+        self.pre_vq_conv = SamePadConv3d(
+            self.enc_out_ch, cfg.model.embedding_dim, 1, padding_type=cfg.model.padding_type)
+        self.post_vq_conv = SamePadConv3d(
+            cfg.model.embedding_dim, self.enc_out_ch, 1)
+
+        self.codebook = Codebook(cfg.model.n_codes, cfg.model.embedding_dim,
+                                 no_random_restart=cfg.model.no_random_restart, restart_thres=cfg.model.restart_thres)
+
+        self.gan_feat_weight = cfg.model.gan_feat_weight
+        # TODO: Changed batchnorm from sync to normal
+        self.image_discriminator = NLayerDiscriminator(
+            cfg.dataset.image_channels, cfg.model.disc_channels, cfg.model.disc_layers, norm_layer=nn.BatchNorm2d)
+        self.video_discriminator = NLayerDiscriminator3D(
+            cfg.dataset.image_channels, cfg.model.disc_channels, cfg.model.disc_layers, norm_layer=nn.BatchNorm3d)
+
+        if cfg.model.disc_loss_type == 'vanilla':
+            self.disc_loss = vanilla_d_loss
+        elif cfg.model.disc_loss_type == 'hinge':
+            self.disc_loss = hinge_d_loss
+
+        self.perceptual_model = LPIPS().eval()
+
+        self.image_gan_weight = cfg.model.image_gan_weight
+        self.video_gan_weight = cfg.model.video_gan_weight
+
+        self.perceptual_weight = cfg.model.perceptual_weight
+
+        self.l1_weight = cfg.model.l1_weight
+        self.save_hyperparameters()
+
+    def encode(self, x, include_embeddings=False, quantize=True):
+        h = self.pre_vq_conv(self.encoder(x))
+        if quantize:
+            vq_output = self.codebook(h)
+            if include_embeddings:
+                return vq_output['embeddings'], vq_output['encodings']
+            else:
+                return vq_output['encodings']
+        return h
+
+    def decode(self, latent, quantize=False):
+        if quantize:
+            vq_output = self.codebook(latent)
+            latent = vq_output['encodings']
+        h = F.embedding(latent, self.codebook.embeddings)
+        h = self.post_vq_conv(shift_dim(h, -1, 1))
+        return self.decoder(h)
+
+    def forward(self, x, optimizer_idx=None, log_image=False):
+        B, C, T, H, W = x.shape
+        z = self.pre_vq_conv(self.encoder(x)) # [2, 32, 32, 32, 32] [2, 8, 32, 32, 32]
+        vq_output = self.codebook(z) # ['embeddings', 'encodings', 'commitment_loss', 'perplexity']
+        x_recon = self.decoder(self.post_vq_conv(vq_output['embeddings'])) # [2, 8, 32, 32, 32] [2, 32, 32, 32, 32]
+
+        recon_loss = F.l1_loss(x_recon, x) * self.l1_weight
+
+        # Selects one random 2D image from each 3D Image
+        frame_idx = torch.randint(0, T, [B]).cuda()
+        frame_idx_selected = frame_idx.reshape(-1,
+                                               1, 1, 1, 1).repeat(1, C, 1, H, W) # [2, 1, 1, 64, 64]
+        frames = torch.gather(x, 2, frame_idx_selected).squeeze(2) # [2, 1, 64, 64]
+        frames_recon = torch.gather(x_recon, 2, frame_idx_selected).squeeze(2) # [2, 1, 64, 64]
+
+        if log_image:
+            return frames, frames_recon, x, x_recon
+
+        if optimizer_idx == 0:
+            # Autoencoder - train the "generator"
+
+            # Perceptual loss
+            perceptual_loss = 0
+            if self.perceptual_weight > 0:
+                perceptual_loss = self.perceptual_model(
+                    frames, frames_recon).mean() * self.perceptual_weight
+
+            # Discriminator loss (turned on after a certain epoch)
+            logits_image_fake, pred_image_fake = self.image_discriminator(
+                frames_recon)
+            logits_video_fake, pred_video_fake = self.video_discriminator(
+                x_recon)
+            g_image_loss = -torch.mean(logits_image_fake)
+            g_video_loss = -torch.mean(logits_video_fake)
+            g_loss = self.image_gan_weight*g_image_loss + self.video_gan_weight*g_video_loss
+            disc_factor = adopt_weight(
+                self.global_step, threshold=self.cfg.model.discriminator_iter_start)
+            aeloss = disc_factor * g_loss
+
+            # GAN feature matching loss - tune features such that we get the same prediction result on the discriminator
+            image_gan_feat_loss = 0
+            video_gan_feat_loss = 0
+            feat_weights = 4.0 / (3 + 1)
+            if self.image_gan_weight > 0:
+                logits_image_real, pred_image_real = self.image_discriminator(
+                    frames)
+                for i in range(len(pred_image_fake)-1):
+                    image_gan_feat_loss += feat_weights * \
+                        F.l1_loss(pred_image_fake[i], pred_image_real[i].detach(
+                        )) * (self.image_gan_weight > 0)
+            if self.video_gan_weight > 0:
+                logits_video_real, pred_video_real = self.video_discriminator(
+                    x)
+                for i in range(len(pred_video_fake)-1):
+                    video_gan_feat_loss += feat_weights * \
+                        F.l1_loss(pred_video_fake[i], pred_video_real[i].detach(
+                        )) * (self.video_gan_weight > 0)
+            gan_feat_loss = disc_factor * self.gan_feat_weight * \
+                (image_gan_feat_loss + video_gan_feat_loss)
+
+            self.log("train/g_image_loss", g_image_loss,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/g_video_loss", g_video_loss,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/image_gan_feat_loss", image_gan_feat_loss,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/video_gan_feat_loss", video_gan_feat_loss,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/perceptual_loss", perceptual_loss,
+                     prog_bar=True, logger=True, on_step=True, on_epoch=True)
+            self.log("train/recon_loss", recon_loss, prog_bar=True,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/aeloss", aeloss, prog_bar=True,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/commitment_loss", vq_output['commitment_loss'],
+                     prog_bar=True, logger=True, on_step=True, on_epoch=True)
+            self.log('train/perplexity', vq_output['perplexity'],
+                     prog_bar=True, logger=True, on_step=True, on_epoch=True)
+            return recon_loss, x_recon, vq_output, aeloss, perceptual_loss, gan_feat_loss
+
+        if optimizer_idx == 1:
+            # Train discriminator
+            logits_image_real, _ = self.image_discriminator(frames.detach())
+            logits_video_real, _ = self.video_discriminator(x.detach())
+
+            logits_image_fake, _ = self.image_discriminator(
+                frames_recon.detach())
+            logits_video_fake, _ = self.video_discriminator(x_recon.detach())
+
+            d_image_loss = self.disc_loss(logits_image_real, logits_image_fake)
+            d_video_loss = self.disc_loss(logits_video_real, logits_video_fake)
+            disc_factor = adopt_weight(
+                self.global_step, threshold=self.cfg.model.discriminator_iter_start)
+            discloss = disc_factor * \
+                (self.image_gan_weight*d_image_loss +
+                 self.video_gan_weight*d_video_loss)
+
+            self.log("train/logits_image_real", logits_image_real.mean().detach(),
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/logits_image_fake", logits_image_fake.mean().detach(),
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/logits_video_real", logits_video_real.mean().detach(),
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/logits_video_fake", logits_video_fake.mean().detach(),
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/d_image_loss", d_image_loss,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/d_video_loss", d_video_loss,
+                     logger=True, on_step=True, on_epoch=True)
+            self.log("train/discloss", discloss, prog_bar=True,
+                     logger=True, on_step=True, on_epoch=True)
+            return discloss
+
+        perceptual_loss = self.perceptual_model(
+            frames, frames_recon) * self.perceptual_weight
+        return recon_loss, x_recon, vq_output, perceptual_loss
+
+    def training_step(self, batch, batch_idx, optimizer_idx):
+        x = batch['image']
+        if optimizer_idx == 0:
+            recon_loss, _, vq_output, aeloss, perceptual_loss, gan_feat_loss = self.forward(
+                x, optimizer_idx)
+            commitment_loss = vq_output['commitment_loss']
+            loss = recon_loss + commitment_loss + aeloss + perceptual_loss + gan_feat_loss
+        if optimizer_idx == 1:
+            discloss = self.forward(x, optimizer_idx)
+            loss = discloss
+        return loss
+
+    def validation_step(self, batch, batch_idx):
+        x = batch['image']  # TODO: batch['stft']
+        recon_loss, _, vq_output, perceptual_loss = self.forward(x)
+        self.log('val/recon_loss', recon_loss, prog_bar=True)
+        self.log('val/perceptual_loss', perceptual_loss, prog_bar=True)
+        self.log('val/perplexity', vq_output['perplexity'], prog_bar=True)
+        self.log('val/commitment_loss',
+                 vq_output['commitment_loss'], prog_bar=True)
+
+    def configure_optimizers(self):
+        lr = self.cfg.model.lr
+        opt_ae = torch.optim.Adam(list(self.encoder.parameters()) +
+                                  list(self.decoder.parameters()) +
+                                  list(self.pre_vq_conv.parameters()) +
+                                  list(self.post_vq_conv.parameters()) +
+                                  list(self.codebook.parameters()),
+                                  lr=lr, betas=(0.5, 0.9))
+        opt_disc = torch.optim.Adam(list(self.image_discriminator.parameters()) +
+                                    list(self.video_discriminator.parameters()),
+                                    lr=lr, betas=(0.5, 0.9))
+        return [opt_ae, opt_disc], []
+
+    def log_images(self, batch, **kwargs):
+        log = dict()
+        x = batch['image']
+        x = x.to(self.device)
+        frames, frames_rec, _, _ = self(x, log_image=True)
+        log["inputs"] = frames
+        log["reconstructions"] = frames_rec
+        #log['mean_org'] = batch['mean_org']
+        #log['std_org'] = batch['std_org']
+        return log
+
+    def log_videos(self, batch, **kwargs):
+        log = dict()
+        x = batch['image']
+        _, _, x, x_rec = self(x, log_image=True)
+        log["inputs"] = x
+        log["reconstructions"] = x_rec
+        #log['mean_org'] = batch['mean_org']
+        #log['std_org'] = batch['std_org']
+        return log
+
+
+def Normalize(in_channels, norm_type='group', num_groups=32):
+    assert norm_type in ['group', 'batch']
+    if norm_type == 'group':
+        # TODO Changed num_groups from 32 to 8
+        return torch.nn.GroupNorm(num_groups=num_groups, num_channels=in_channels, eps=1e-6, affine=True)
+    elif norm_type == 'batch':
+        return torch.nn.SyncBatchNorm(in_channels)
+
+
+class Encoder(nn.Module):
+    def __init__(self, n_hiddens, downsample, image_channel=3, norm_type='group', padding_type='replicate', num_groups=32):
+        super().__init__()
+        n_times_downsample = np.array([int(math.log2(d)) for d in downsample])
+        self.conv_blocks = nn.ModuleList()
+        max_ds = n_times_downsample.max()
+
+        self.conv_first = SamePadConv3d(
+            image_channel, n_hiddens, kernel_size=3, padding_type=padding_type)
+
+        for i in range(max_ds):
+            block = nn.Module()
+            in_channels = n_hiddens * 2**i
+            out_channels = n_hiddens * 2**(i+1)
+            stride = tuple([2 if d > 0 else 1 for d in n_times_downsample])
+            block.down = SamePadConv3d(
+                in_channels, out_channels, 4, stride=stride, padding_type=padding_type)
+            block.res = ResBlock(
+                out_channels, out_channels, norm_type=norm_type, num_groups=num_groups)
+            self.conv_blocks.append(block)
+            n_times_downsample -= 1
+
+        self.final_block = nn.Sequential(
+            Normalize(out_channels, norm_type, num_groups=num_groups),
+            SiLU()
+        )
+
+        self.out_channels = out_channels
+
+    def forward(self, x):
+        h = self.conv_first(x)
+        for block in self.conv_blocks:
+            h = block.down(h)
+            h = block.res(h)
+        h = self.final_block(h)
+        return h
+
+
+class Decoder(nn.Module):
+    def __init__(self, n_hiddens, upsample, image_channel, norm_type='group', num_groups=32):
+        super().__init__()
+
+        n_times_upsample = np.array([int(math.log2(d)) for d in upsample])
+        max_us = n_times_upsample.max()
+
+        in_channels = n_hiddens*2**max_us
+        self.final_block = nn.Sequential(
+            Normalize(in_channels, norm_type, num_groups=num_groups),
+            SiLU()
+        )
+
+        self.conv_blocks = nn.ModuleList()
+        for i in range(max_us):
+            block = nn.Module()
+            in_channels = in_channels if i == 0 else n_hiddens*2**(max_us-i+1)
+            out_channels = n_hiddens*2**(max_us-i)
+            us = tuple([2 if d > 0 else 1 for d in n_times_upsample])
+            block.up = SamePadConvTranspose3d(
+                in_channels, out_channels, 4, stride=us)
+            block.res1 = ResBlock(
+                out_channels, out_channels, norm_type=norm_type, num_groups=num_groups)
+            block.res2 = ResBlock(
+                out_channels, out_channels, norm_type=norm_type, num_groups=num_groups)
+            self.conv_blocks.append(block)
+            n_times_upsample -= 1
+
+        self.conv_last = SamePadConv3d(
+            out_channels, image_channel, kernel_size=3)
+
+    def forward(self, x):
+        h = self.final_block(x)
+        for i, block in enumerate(self.conv_blocks):
+            h = block.up(h)
+            h = block.res1(h)
+            h = block.res2(h)
+        h = self.conv_last(h)
+        return h
+
+
+class ResBlock(nn.Module):
+    def __init__(self, in_channels, out_channels=None, conv_shortcut=False, dropout=0.0, norm_type='group', padding_type='replicate', num_groups=32):
+        super().__init__()
+        self.in_channels = in_channels
+        out_channels = in_channels if out_channels is None else out_channels
+        self.out_channels = out_channels
+        self.use_conv_shortcut = conv_shortcut
+
+        self.norm1 = Normalize(in_channels, norm_type, num_groups=num_groups)
+        self.conv1 = SamePadConv3d(
+            in_channels, out_channels, kernel_size=3, padding_type=padding_type)
+        self.dropout = torch.nn.Dropout(dropout)
+        self.norm2 = Normalize(in_channels, norm_type, num_groups=num_groups)
+        self.conv2 = SamePadConv3d(
+            out_channels, out_channels, kernel_size=3, padding_type=padding_type)
+        if self.in_channels != self.out_channels:
+            self.conv_shortcut = SamePadConv3d(
+                in_channels, out_channels, kernel_size=3, padding_type=padding_type)
+
+    def forward(self, x):
+        h = x
+        h = self.norm1(h)
+        h = silu(h)
+        h = self.conv1(h)
+        h = self.norm2(h)
+        h = silu(h)
+        h = self.conv2(h)
+
+        if self.in_channels != self.out_channels:
+            x = self.conv_shortcut(x)
+
+        return x+h
+
+
+# Does not support dilation
+class SamePadConv3d(nn.Module):
+    def __init__(self, in_channels, out_channels, kernel_size, stride=1, bias=True, padding_type='replicate'):
+        super().__init__()
+        if isinstance(kernel_size, int):
+            kernel_size = (kernel_size,) * 3
+        if isinstance(stride, int):
+            stride = (stride,) * 3
+
+        # assumes that the input shape is divisible by stride
+        total_pad = tuple([k - s for k, s in zip(kernel_size, stride)])
+        pad_input = []
+        for p in total_pad[::-1]:  # reverse since F.pad starts from last dim
+            pad_input.append((p // 2 + p % 2, p // 2))
+        pad_input = sum(pad_input, tuple())
+        self.pad_input = pad_input
+        self.padding_type = padding_type
+
+        self.conv = nn.Conv3d(in_channels, out_channels, kernel_size,
+                              stride=stride, padding=0, bias=bias)
+
+    def forward(self, x):
+        return self.conv(F.pad(x, self.pad_input, mode=self.padding_type))
+
+
+class SamePadConvTranspose3d(nn.Module):
+    def __init__(self, in_channels, out_channels, kernel_size, stride=1, bias=True, padding_type='replicate'):
+        super().__init__()
+        if isinstance(kernel_size, int):
+            kernel_size = (kernel_size,) * 3
+        if isinstance(stride, int):
+            stride = (stride,) * 3
+
+        total_pad = tuple([k - s for k, s in zip(kernel_size, stride)])
+        pad_input = []
+        for p in total_pad[::-1]:  # reverse since F.pad starts from last dim
+            pad_input.append((p // 2 + p % 2, p // 2))
+        pad_input = sum(pad_input, tuple())
+        self.pad_input = pad_input
+        self.padding_type = padding_type
+
+        self.convt = nn.ConvTranspose3d(in_channels, out_channels, kernel_size,
+                                        stride=stride, bias=bias,
+                                        padding=tuple([k - 1 for k in kernel_size]))
+
+    def forward(self, x):
+        return self.convt(F.pad(x, self.pad_input, mode=self.padding_type))
+
+
+class NLayerDiscriminator(nn.Module):
+    def __init__(self, input_nc, ndf=64, n_layers=3, norm_layer=nn.SyncBatchNorm, use_sigmoid=False, getIntermFeat=True):
+        # def __init__(self, input_nc, ndf=64, n_layers=3, norm_layer=nn.BatchNorm2d, use_sigmoid=False, getIntermFeat=True):
+        super(NLayerDiscriminator, self).__init__()
+        self.getIntermFeat = getIntermFeat
+        self.n_layers = n_layers
+
+        kw = 4
+        padw = int(np.ceil((kw-1.0)/2))
+        sequence = [[nn.Conv2d(input_nc, ndf, kernel_size=kw,
+                               stride=2, padding=padw), nn.LeakyReLU(0.2, True)]]
+
+        nf = ndf
+        for n in range(1, n_layers):
+            nf_prev = nf
+            nf = min(nf * 2, 512)
+            sequence += [[
+                nn.Conv2d(nf_prev, nf, kernel_size=kw, stride=2, padding=padw),
+                norm_layer(nf), nn.LeakyReLU(0.2, True)
+            ]]
+
+        nf_prev = nf
+        nf = min(nf * 2, 512)
+        sequence += [[
+            nn.Conv2d(nf_prev, nf, kernel_size=kw, stride=1, padding=padw),
+            norm_layer(nf),
+            nn.LeakyReLU(0.2, True)
+        ]]
+
+        sequence += [[nn.Conv2d(nf, 1, kernel_size=kw,
+                                stride=1, padding=padw)]]
+
+        if use_sigmoid:
+            sequence += [[nn.Sigmoid()]]
+
+        if getIntermFeat:
+            for n in range(len(sequence)):
+                setattr(self, 'model'+str(n), nn.Sequential(*sequence[n]))
+        else:
+            sequence_stream = []
+            for n in range(len(sequence)):
+                sequence_stream += sequence[n]
+            self.model = nn.Sequential(*sequence_stream)
+
+    def forward(self, input):
+        if self.getIntermFeat:
+            res = [input]
+            for n in range(self.n_layers+2):
+                model = getattr(self, 'model'+str(n))
+                res.append(model(res[-1]))
+            return res[-1], res[1:]
+        else:
+            return self.model(input), _
+
+
+class NLayerDiscriminator3D(nn.Module):
+    def __init__(self, input_nc, ndf=64, n_layers=3, norm_layer=nn.SyncBatchNorm, use_sigmoid=False, getIntermFeat=True):
+        super(NLayerDiscriminator3D, self).__init__()
+        self.getIntermFeat = getIntermFeat
+        self.n_layers = n_layers
+
+        kw = 4
+        padw = int(np.ceil((kw-1.0)/2))
+        sequence = [[nn.Conv3d(input_nc, ndf, kernel_size=kw,
+                               stride=2, padding=padw), nn.LeakyReLU(0.2, True)]]
+
+        nf = ndf
+        for n in range(1, n_layers):
+            nf_prev = nf
+            nf = min(nf * 2, 512)
+            sequence += [[
+                nn.Conv3d(nf_prev, nf, kernel_size=kw, stride=2, padding=padw),
+                norm_layer(nf), nn.LeakyReLU(0.2, True)
+            ]]
+
+        nf_prev = nf
+        nf = min(nf * 2, 512)
+        sequence += [[
+            nn.Conv3d(nf_prev, nf, kernel_size=kw, stride=1, padding=padw),
+            norm_layer(nf),
+            nn.LeakyReLU(0.2, True)
+        ]]
+
+        sequence += [[nn.Conv3d(nf, 1, kernel_size=kw,
+                                stride=1, padding=padw)]]
+
+        if use_sigmoid:
+            sequence += [[nn.Sigmoid()]]
+
+        if getIntermFeat:
+            for n in range(len(sequence)):
+                setattr(self, 'model'+str(n), nn.Sequential(*sequence[n]))
+        else:
+            sequence_stream = []
+            for n in range(len(sequence)):
+                sequence_stream += sequence[n]
+            self.model = nn.Sequential(*sequence_stream)
+
+    def forward(self, input):
+        if self.getIntermFeat:
+            res = [input]
+            for n in range(self.n_layers+2):
+                model = getattr(self, 'model'+str(n))
+                res.append(model(res[-1]))
+            return res[-1], res[1:]
+        else:
+            return self.model(input), _

Generation_Pipeline_filter/syn_colon/TumorGeneration/ldm/vq_gan_3d/utils.py

@@ -0,0 +1,177 @@
+""" Adapted from https://github.com/SongweiGe/TATS"""
+# Copyright (c) Meta Platforms, Inc. All Rights Reserved
+
+import warnings
+import torch
+import imageio
+
+import math
+import numpy as np
+
+import sys
+import pdb as pdb_original
+import logging
+
+import imageio.core.util
+logging.getLogger("imageio_ffmpeg").setLevel(logging.ERROR)
+
+
+class ForkedPdb(pdb_original.Pdb):
+    """A Pdb subclass that may be used
+    from a forked multiprocessing child
+
+    """
+
+    def interaction(self, *args, **kwargs):
+        _stdin = sys.stdin
+        try:
+            sys.stdin = open('/dev/stdin')
+            pdb_original.Pdb.interaction(self, *args, **kwargs)
+        finally:
+            sys.stdin = _stdin
+
+
+# Shifts src_tf dim to dest dim
+# i.e. shift_dim(x, 1, -1) would be (b, c, t, h, w) -> (b, t, h, w, c)
+def shift_dim(x, src_dim=-1, dest_dim=-1, make_contiguous=True):
+    n_dims = len(x.shape)
+    if src_dim < 0:
+        src_dim = n_dims + src_dim
+    if dest_dim < 0:
+        dest_dim = n_dims + dest_dim
+
+    assert 0 <= src_dim < n_dims and 0 <= dest_dim < n_dims
+
+    dims = list(range(n_dims))
+    del dims[src_dim]
+
+    permutation = []
+    ctr = 0
+    for i in range(n_dims):
+        if i == dest_dim:
+            permutation.append(src_dim)
+        else:
+            permutation.append(dims[ctr])
+            ctr += 1
+    x = x.permute(permutation)
+    if make_contiguous:
+        x = x.contiguous()
+    return x
+
+
+# reshapes tensor start from dim i (inclusive)
+# to dim j (exclusive) to the desired shape
+# e.g. if x.shape = (b, thw, c) then
+# view_range(x, 1, 2, (t, h, w)) returns
+# x of shape (b, t, h, w, c)
+def view_range(x, i, j, shape):
+    shape = tuple(shape)
+
+    n_dims = len(x.shape)
+    if i < 0:
+        i = n_dims + i
+
+    if j is None:
+        j = n_dims
+    elif j < 0:
+        j = n_dims + j
+
+    assert 0 <= i < j <= n_dims
+
+    x_shape = x.shape
+    target_shape = x_shape[:i] + shape + x_shape[j:]
+    return x.view(target_shape)
+
+
+def accuracy(output, target, topk=(1,)):
+    """Computes the accuracy over the k top predictions for the specified values of k"""
+    with torch.no_grad():
+        maxk = max(topk)
+        batch_size = target.size(0)
+
+        _, pred = output.topk(maxk, 1, True, True)
+        pred = pred.t()
+        correct = pred.eq(target.reshape(1, -1).expand_as(pred))
+
+        res = []
+        for k in topk:
+            correct_k = correct[:k].reshape(-1).float().sum(0, keepdim=True)
+            res.append(correct_k.mul_(100.0 / batch_size))
+        return res
+
+
+def tensor_slice(x, begin, size):
+    assert all([b >= 0 for b in begin])
+    size = [l - b if s == -1 else s
+            for s, b, l in zip(size, begin, x.shape)]
+    assert all([s >= 0 for s in size])
+
+    slices = [slice(b, b + s) for b, s in zip(begin, size)]
+    return x[slices]
+
+
+def adopt_weight(global_step, threshold=0, value=0.):
+    weight = 1
+    if global_step < threshold:
+        weight = value
+    return weight
+
+
+def save_video_grid(video, fname, nrow=None, fps=6):
+    b, c, t, h, w = video.shape
+    video = video.permute(0, 2, 3, 4, 1)
+    video = (video.cpu().numpy() * 255).astype('uint8')
+    if nrow is None:
+        nrow = math.ceil(math.sqrt(b))
+    ncol = math.ceil(b / nrow)
+    padding = 1
+    video_grid = np.zeros((t, (padding + h) * nrow + padding,
+                           (padding + w) * ncol + padding, c), dtype='uint8')
+    for i in range(b):
+        r = i // ncol
+        c = i % ncol
+        start_r = (padding + h) * r
+        start_c = (padding + w) * c
+        video_grid[:, start_r:start_r + h, start_c:start_c + w] = video[i]
+    video = []
+    for i in range(t):
+        video.append(video_grid[i])
+    imageio.mimsave(fname, video, fps=fps)
+    ## skvideo.io.vwrite(fname, video_grid, inputdict={'-r': '5'})
+    #print('saved videos to', fname)
+
+
+def comp_getattr(args, attr_name, default=None):
+    if hasattr(args, attr_name):
+        return getattr(args, attr_name)
+    else:
+        return default
+
+
+def visualize_tensors(t, name=None, nest=0):
+    if name is not None:
+        print(name, "current nest: ", nest)
+    print("type: ", type(t))
+    if 'dict' in str(type(t)):
+        print(t.keys())
+        for k in t.keys():
+            if t[k] is None:
+                print(k, "None")
+            else:
+                if 'Tensor' in str(type(t[k])):
+                    print(k, t[k].shape)
+                elif 'dict' in str(type(t[k])):
+                    print(k, 'dict')
+                    visualize_tensors(t[k], name, nest + 1)
+                elif 'list' in str(type(t[k])):
+                    print(k, len(t[k]))
+                    visualize_tensors(t[k], name, nest + 1)
+    elif 'list' in str(type(t)):
+        print("list length: ", len(t))
+        for t2 in t:
+            visualize_tensors(t2, name, nest + 1)
+    elif 'Tensor' in str(type(t)):
+        print(t.shape)
+    else:
+        print(t)
+    return ""

Generation_Pipeline_filter/syn_colon/TumorGeneration/utils.py

@@ -0,0 +1,233 @@
+### Tumor Generateion
+import random
+import cv2
+import elasticdeform
+import numpy as np
+from scipy.ndimage import gaussian_filter
+from TumorGeneration.ldm.ddpm.ddim import DDIMSampler
+import skimage
+
+def im2col(A, BSZ, stepsize=1):
+    # Parameters
+    M, N = A.shape
+    # Get Starting block indices
+    start_idx = np.arange(
+        0, M-BSZ[0]+1, stepsize)[:, None]*N + np.arange(0, N-BSZ[1]+1, stepsize)
+    # Get offsetted indices across the height and width of input array
+    offset_idx = np.arange(BSZ[0])[:, None]*N + np.arange(BSZ[1])
+    # Get all actual indices & index into input array for final output
+    return np.take(A, start_idx.ravel()[:, None] + offset_idx.ravel())
+
+def seg_to_instance_bd(seg: np.ndarray,
+                       tsz_h: int = 1) -> np.ndarray:
+    """Generate instance contour map from segmentation masks.
+    """
+
+    tsz = tsz_h*2+1
+    tsz=int(tsz)
+    kernel = np.ones((tsz, tsz, tsz), np.uint8)
+    dilated_seg_mask = skimage.morphology.binary_erosion(seg.astype('uint8'), kernel)
+
+    dilated_seg_mask = dilated_seg_mask.astype(np.uint8)
+    bd = seg-dilated_seg_mask
+    bd = (bd>0).astype('uint8')
+
+    return bd
+
+def sector_mask(shape,centre,radius,angle_range):
+    """
+    Return a boolean mask for a circular sector. The start/stop angles in  
+    `angle_range` should be given in clockwise order.
+    """
+
+    x,y = np.ogrid[:shape[0],:shape[1]]
+    cx,cy = centre
+    tmin,tmax = np.deg2rad(angle_range)
+
+    # ensure stop angle > start angle
+    if tmax < tmin:
+            tmax += 2*np.pi
+
+    # convert cartesian --> polar coordinates
+    r2 = (x-cx)*(x-cx) + (y-cy)*(y-cy)
+    theta = np.arctan2(x-cx,y-cy) - tmin
+
+    # wrap angles between 0 and 2*pi
+    theta %= (2*np.pi)
+
+    # circular mask
+    circmask = r2 <= radius*radius
+
+    # angular mask
+    anglemask = theta <= (tmax-tmin)
+
+    return circmask*anglemask
+
+from scipy.ndimage import label
+import elasticdeform
+def generate_random_mask(organ_mask):
+    # initialize tumor mask
+    tumor_mask = np.zeros_like(organ_mask)
+
+    # randowm mask angle
+    start_angle = random.randint(0, 360)
+    angle_range = random.randint(90, 360)
+
+    # generate organ boundary
+    erode_sz = angle_range//45 * 1 + 3
+    # select_size = [3.5, 4, 4.5, 5.0, 5.5, 6.0]
+    # erode_sz = np.random.choice(select_size)
+    # print('erode_sz', erode_sz)
+    organ_bd = seg_to_instance_bd(organ_mask, tsz_h=erode_sz)
+    
+    # organ mask range
+    z_valid_list = np.where(np.any(organ_bd, axis=(0, 1)))[0]
+    valid_num = len(z_valid_list)
+    z_valid_list = z_valid_list[round(valid_num*0.25):round(valid_num*0.75)]
+    # print(z_valid_list)
+    z =  random.choice(z_valid_list)
+
+    # sample thickness
+    z_thickness = random.randint(10, 20) # 10-20
+    # print('z, z_thickness', z, z_thickness)
+    # crop
+    tumor_mask[:,:,max(0,z-z_thickness):min(95,z+z_thickness)] = organ_bd[:,:,max(0,z-z_thickness):min(95,z+z_thickness)]
+
+    # random select one 
+    tumor_mask, nb = label(tumor_mask)
+    sample_id = random.randint(1, nb)
+    sample_tumor_mask = (tumor_mask==sample_id).astype(np.uint8)
+
+    z_valid = np.where(np.any(sample_tumor_mask, axis=(0, 1)))[0]
+    z = z_valid[round(0.5 * len(z_valid))]
+    
+    # randowm mask region
+    selected_slice = sample_tumor_mask[..., z]
+    coordinates = np.argwhere(selected_slice == 1)
+    center_x, center_y = int(coordinates[:,0].mean()), int(coordinates[:,1].mean())
+    # start_angle = random.randint(0, 360)
+    # angle_range = random.randint(90, 360)
+    mask_region = sector_mask(selected_slice.shape,(center_x,center_y), 48, (start_angle,start_angle+angle_range))
+    mask_region = np.repeat(mask_region[:,:,np.newaxis], axis=-1, repeats=96)
+
+    # elasticdeform
+    # sigma = random.uniform(1,2)
+    sigma = random.uniform(2,5)
+    # sigma = random.uniform(5,10)
+    deform_tumor_mask = elasticdeform.deform_random_grid(sample_tumor_mask, sigma=sigma, points=3, order=0, axis=(0,1))
+    # deform_tumor_mask = elasticdeform.deform_random_grid(deform_tumor_mask, sigma=sigma, points=3, order=0, axis=(1,2))
+    # deform_tumor_mask = elasticdeform.deform_random_grid(deform_tumor_mask, sigma=sigma, points=3, order=0, axis=(0,2))
+
+    # final_tumor_mask = deform_tumor_mask*mask_region*organ_mask
+    final_tumor_mask = deform_tumor_mask*mask_region
+
+    return final_tumor_mask
+    
+
+from .ldm.vq_gan_3d.model.vqgan import VQGAN
+import matplotlib.pyplot as plt
+import SimpleITK as sitk
+from .ldm.ddpm import Unet3D, GaussianDiffusion, Tester
+from hydra import initialize, compose
+import torch
+import yaml
+def synt_model_prepare(device, vqgan_ckpt='TumorGeneration/model_weight/recon_colon.ckpt', diffusion_ckpt='TumorGeneration/model_weight/', fold=0, organ='colon'):
+    with initialize(config_path="diffusion_config/"):
+        cfg=compose(config_name="ddpm.yaml")
+    vqgan_ckpt = 'TumorGeneration/model_weight/recon_colon.ckpt'
+    diffusion_ckpt = 'TumorGeneration/model_weight/diffusion_colon.pt'
+    print('diffusion_ckpt',diffusion_ckpt)
+    vqgan = VQGAN.load_from_checkpoint(vqgan_ckpt)
+    vqgan = vqgan.to(device)
+    vqgan.eval()
+
+    
+    noearly_Unet3D = Unet3D(
+            dim=cfg.diffusion_img_size,
+            dim_mults=cfg.dim_mults,
+            channels=cfg.diffusion_num_channels,
+            out_dim=cfg.out_dim
+            ).to(device)
+    
+    noearly_diffusion = GaussianDiffusion(
+            noearly_Unet3D,
+            vqgan_ckpt= vqgan_ckpt, # cfg.vqgan_ckpt,
+            image_size=cfg.diffusion_img_size,
+            num_frames=cfg.diffusion_depth_size,
+            channels=cfg.diffusion_num_channels,
+            timesteps=200, # cfg.timesteps,
+            loss_type=cfg.loss_type,
+            device=device
+            ).to(device)
+
+    noearly_checkpoint = torch.load(diffusion_ckpt, map_location=device)
+
+    noearly_diffusion.load_state_dict(noearly_checkpoint['ema'])
+
+    noearly_sampler = DDIMSampler(noearly_diffusion, schedule="cosine")
+    # breakpoint()
+    return vqgan, noearly_sampler
+
+def synthesize_colon_tumor(ct_volume, organ_mask, vqgan, sampler, ddim_ts=50):
+    device=ct_volume.device
+
+    # generate tumor mask
+    total_tumor_mask = []
+    organ_mask_np = organ_mask.cpu().numpy()
+    with torch.no_grad():
+        # get model input
+        for bs in range(organ_mask_np.shape[0]):
+            tumor_mask = generate_random_mask(organ_mask_np[bs,0])
+            # tumor_mask = organ_mask_np[bs,0]
+            total_tumor_mask.append(torch.from_numpy(tumor_mask)[None,:])
+        total_tumor_mask = torch.stack(total_tumor_mask, dim=0).to(dtype=torch.float32, device=device)
+        # breakpoint()
+        volume = ct_volume*2.0 - 1.0
+        mask = total_tumor_mask*2.0 - 1.0
+        mask_ = 1-total_tumor_mask
+        masked_volume = (volume*mask_).detach()
+        
+        volume = volume.permute(0,1,-1,-3,-2)
+        masked_volume = masked_volume.permute(0,1,-1,-3,-2)
+        mask = mask.permute(0,1,-1,-3,-2)
+
+        # vqgan encoder inference
+        masked_volume_feat = vqgan.encode(masked_volume, quantize=False, include_embeddings=True)
+        masked_volume_feat = ((masked_volume_feat - vqgan.codebook.embeddings.min()) /
+                (vqgan.codebook.embeddings.max() - vqgan.codebook.embeddings.min())) * 2.0 - 1.0
+        
+        cc = torch.nn.functional.interpolate(mask, size=masked_volume_feat.shape[-3:])
+        cond = torch.cat((masked_volume_feat, cc), dim=1)
+
+        # diffusion inference and decoder
+        shape = masked_volume_feat.shape[-4:]
+        samples_ddim, _ = sampler.sample(S=ddim_ts,
+                                        conditioning=cond,
+                                        batch_size=1,
+                                        shape=shape,
+                                        verbose=False)
+        samples_ddim = (((samples_ddim + 1.0) / 2.0) * (vqgan.codebook.embeddings.max() -
+                                                        vqgan.codebook.embeddings.min())) + vqgan.codebook.embeddings.min()
+
+        sample = vqgan.decode(samples_ddim, quantize=True)
+
+        # post-process
+        mask_01 = torch.clamp((mask+1.0)/2.0, min=0.0, max=1.0)
+        sigma = np.random.uniform(1, 2) # (1, 2)
+        mask_01_np_blur = gaussian_filter(mask_01.cpu().numpy()*1.0, sigma=[0,0,sigma,sigma,sigma])
+        # mask_01_np_blur = mask_01_np_blur*mask_01.cpu().numpy()
+
+        volume_ = torch.clamp((volume+1.0)/2.0, min=0.0, max=1.0)
+        sample_ = torch.clamp((sample+1.0)/2.0, min=0.0, max=1.0)
+
+        mask_01_blur = torch.from_numpy(mask_01_np_blur).to(device=device)
+        final_volume_ = (1-mask_01_blur)*volume_ +mask_01_blur*sample_
+        final_volume_ = torch.clamp(final_volume_, min=0.0, max=1.0)
+
+        # final_volume_ = (sample+1.0)/2.0
+        final_volume_ = final_volume_.permute(0,1,-2,-1,-3)
+        organ_tumor_mask = torch.zeros_like(organ_mask)
+        organ_tumor_mask[organ_mask==1] = 1
+        organ_tumor_mask[total_tumor_mask==1] = 2
+
+    return final_volume_, organ_tumor_mask

Generation_Pipeline_filter/syn_colon/TumorGeneration/utils_.py

@@ -0,0 +1,298 @@
+### Tumor Generateion
+import random
+import cv2
+import elasticdeform
+import numpy as np
+from scipy.ndimage import gaussian_filter
+
+# Step 1: Random select (numbers) location for tumor.
+def random_select(mask_scan):
+    # we first find z index and then sample point with z slice
+    z_start, z_end = np.where(np.any(mask_scan, axis=(0, 1)))[0][[0, -1]]
+
+    # we need to strict number z's position (0.3 - 0.7 in the middle of liver)
+    z = round(random.uniform(0.3, 0.7) * (z_end - z_start)) + z_start
+
+    liver_mask = mask_scan[..., z]
+
+    # erode the mask (we don't want the edge points)
+    kernel = np.ones((5,5), dtype=np.uint8)
+    liver_mask = cv2.erode(liver_mask, kernel, iterations=1)
+
+    coordinates = np.argwhere(liver_mask == 1)
+    random_index = np.random.randint(0, len(coordinates))
+    xyz = coordinates[random_index].tolist() # get x,y
+    xyz.append(z)
+    potential_points = xyz
+
+    return potential_points
+
+# Step 2 : generate the ellipsoid
+def get_ellipsoid(x, y, z):
+    """"
+    x, y, z is the radius of this ellipsoid in x, y, z direction respectly.
+    """
+    sh = (4*x, 4*y, 4*z)
+    out = np.zeros(sh, int)
+    aux = np.zeros(sh)
+    radii = np.array([x, y, z])
+    com = np.array([2*x, 2*y, 2*z])  # center point
+
+    # calculate the ellipsoid 
+    bboxl = np.floor(com-radii).clip(0,None).astype(int)
+    bboxh = (np.ceil(com+radii)+1).clip(None, sh).astype(int)
+    roi = out[tuple(map(slice,bboxl,bboxh))]
+    roiaux = aux[tuple(map(slice,bboxl,bboxh))]
+    logrid = *map(np.square,np.ogrid[tuple(
+            map(slice,(bboxl-com)/radii,(bboxh-com-1)/radii,1j*(bboxh-bboxl)))]),
+    dst = (1-sum(logrid)).clip(0,None)
+    mask = dst>roiaux
+    roi[mask] = 1
+    np.copyto(roiaux,dst,where=mask)
+
+    return out
+
+def get_fixed_geo(mask_scan, tumor_type):
+
+    enlarge_x, enlarge_y, enlarge_z = 160, 160, 160
+    geo_mask = np.zeros((mask_scan.shape[0] + enlarge_x, mask_scan.shape[1] + enlarge_y, mask_scan.shape[2] + enlarge_z), dtype=np.int8)
+    tiny_radius, small_radius, medium_radius, large_radius = 4, 8, 16, 32
+
+    if tumor_type == 'tiny':
+        num_tumor = random.randint(3,10)
+        for _ in range(num_tumor):
+            # Tiny tumor
+            x = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
+            y = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
+            z = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
+            sigma = random.uniform(0.5,1)
+            
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste small tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+
+    if tumor_type == 'small':
+        num_tumor = random.randint(3,10)
+        for _ in range(num_tumor):
+            # Small tumor
+            x = random.randint(int(0.75*small_radius), int(1.25*small_radius))
+            y = random.randint(int(0.75*small_radius), int(1.25*small_radius))
+            z = random.randint(int(0.75*small_radius), int(1.25*small_radius))
+            sigma = random.randint(1, 2)
+            
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            # texture = get_texture((4*x, 4*y, 4*z))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste small tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture
+
+    if tumor_type == 'medium':
+        num_tumor = random.randint(2, 5)
+        for _ in range(num_tumor):
+            # medium tumor
+            x = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
+            y = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
+            z = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
+            sigma = random.randint(3, 6)
+            
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            # texture = get_texture((4*x, 4*y, 4*z))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste medium tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture
+
+    if tumor_type == 'large':
+        num_tumor = random.randint(1,3)
+        for _ in range(num_tumor):
+            # Large tumor
+            x = random.randint(int(0.75*large_radius), int(1.25*large_radius))
+            y = random.randint(int(0.75*large_radius), int(1.25*large_radius))
+            z = random.randint(int(0.75*large_radius), int(1.25*large_radius))
+            sigma = random.randint(5, 10)
+            
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            # texture = get_texture((4*x, 4*y, 4*z))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste small tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture
+
+    if tumor_type == "mix":
+        # tiny
+        num_tumor = random.randint(3,10)
+        for _ in range(num_tumor):
+            # Tiny tumor
+            x = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
+            y = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
+            z = random.randint(int(0.75*tiny_radius), int(1.25*tiny_radius))
+            sigma = random.uniform(0.5,1)
+            
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste small tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+
+        # small
+        num_tumor = random.randint(5,10)
+        for _ in range(num_tumor):
+            # Small tumor
+            x = random.randint(int(0.75*small_radius), int(1.25*small_radius))
+            y = random.randint(int(0.75*small_radius), int(1.25*small_radius))
+            z = random.randint(int(0.75*small_radius), int(1.25*small_radius))
+            sigma = random.randint(1, 2)
+        
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            # texture = get_texture((4*x, 4*y, 4*z))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste small tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture
+            
+        # medium
+        num_tumor = random.randint(2, 5)
+        for _ in range(num_tumor):
+            # medium tumor
+            x = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
+            y = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
+            z = random.randint(int(0.75*medium_radius), int(1.25*medium_radius))
+            sigma = random.randint(3, 6)
+            
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            # texture = get_texture((4*x, 4*y, 4*z))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste medium tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture
+
+        # large
+        num_tumor = random.randint(1,3)
+        for _ in range(num_tumor):
+            # Large tumor
+            x = random.randint(int(0.75*large_radius), int(1.25*large_radius))
+            y = random.randint(int(0.75*large_radius), int(1.25*large_radius))
+            z = random.randint(int(0.75*large_radius), int(1.25*large_radius))
+            sigma = random.randint(5, 10)
+            geo = get_ellipsoid(x, y, z)
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,1))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(1,2))
+            geo = elasticdeform.deform_random_grid(geo, sigma=sigma, points=3, order=0, axis=(0,2))
+            # texture = get_texture((4*x, 4*y, 4*z))
+            point = random_select(mask_scan)
+            new_point = [point[0] + enlarge_x//2, point[1] + enlarge_y//2, point[2] + enlarge_z//2]
+            x_low, x_high = new_point[0] - geo.shape[0]//2, new_point[0] + geo.shape[0]//2 
+            y_low, y_high = new_point[1] - geo.shape[1]//2, new_point[1] + geo.shape[1]//2 
+            z_low, z_high = new_point[2] - geo.shape[2]//2, new_point[2] + geo.shape[2]//2 
+            
+            # paste small tumor geo into test sample
+            geo_mask[x_low:x_high, y_low:y_high, z_low:z_high] += geo
+            # texture_map[x_low:x_high, y_low:y_high, z_low:z_high] = texture
+
+    geo_mask = geo_mask[enlarge_x//2:-enlarge_x//2, enlarge_y//2:-enlarge_y//2, enlarge_z//2:-enlarge_z//2]
+    # texture_map = texture_map[enlarge_x//2:-enlarge_x//2, enlarge_y//2:-enlarge_y//2, enlarge_z//2:-enlarge_z//2]
+    geo_mask = (geo_mask * mask_scan) >=1
+    
+    return geo_mask
+
+
+def get_tumor(volume_scan, mask_scan, tumor_type):
+    tumor_mask = get_fixed_geo(mask_scan, tumor_type)
+
+    sigma = np.random.uniform(1, 2)
+    # difference = np.random.uniform(65, 145)
+    difference = 1
+
+    # blur the boundary
+    tumor_mask_blur = gaussian_filter(tumor_mask*1.0, sigma)
+    
+    
+    abnormally_full = volume_scan * (1 - mask_scan) + abnormally
+    abnormally_mask = mask_scan + geo_mask
+
+    return abnormally_full, abnormally_mask
+
+def SynthesisTumor(volume_scan, mask_scan, tumor_type):
+    # for speed_generate_tumor, we only send the liver part into the generate program
+    x_start, x_end = np.where(np.any(mask_scan, axis=(1, 2)))[0][[0, -1]]
+    y_start, y_end = np.where(np.any(mask_scan, axis=(0, 2)))[0][[0, -1]]
+    z_start, z_end = np.where(np.any(mask_scan, axis=(0, 1)))[0][[0, -1]]
+
+    # shrink the boundary
+    x_start, x_end = max(0, x_start+1), min(mask_scan.shape[0], x_end-1)
+    y_start, y_end = max(0, y_start+1), min(mask_scan.shape[1], y_end-1)
+    z_start, z_end = max(0, z_start+1), min(mask_scan.shape[2], z_end-1)
+
+    ct_volume = volume_scan[x_start:x_end, y_start:y_end, z_start:z_end]
+    organ_mask   = mask_scan[x_start:x_end, y_start:y_end, z_start:z_end]
+
+    # input texture shape: 420, 300, 320
+    # we need to cut it into the shape of liver_mask
+    # for examples, the liver_mask.shape = 286, 173, 46; we should change the texture shape
+    x_length, y_length, z_length = 64, 64, 64
+    crop_x = random.randint(x_start, x_end - x_length - 1) # random select the start point, -1 is to avoid boundary check
+    crop_y = random.randint(y_start, y_end - y_length - 1) 
+    crop_z = random.randint(z_start, z_end - z_length - 1) 
+
+    ct_volume, organ_tumor_mask = get_tumor(ct_volume, organ_mask, tumor_type)
+    volume_scan[x_start:x_end, y_start:y_end, z_start:z_end] = ct_volume
+    mask_scan[x_start:x_end, y_start:y_end, z_start:z_end] = organ_tumor_mask
+
+    return volume_scan, mask_scan

Generation_Pipeline_filter/syn_colon/healthy_colon_1k.txt

@@ -0,0 +1,928 @@
+BDMAP_00001823
+BDMAP_00003074
+BDMAP_00001305
+BDMAP_00001635
+BDMAP_00002359
+BDMAP_00001265
+BDMAP_00000701
+BDMAP_00000771
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+BDMAP_00004198
+BDMAP_00003514
+BDMAP_00000432
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+BDMAP_00002244
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+BDMAP_00000926
+BDMAP_00002849
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+BDMAP_00003920
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+BDMAP_00000831
+BDMAP_00000855
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+BDMAP_00003749
+BDMAP_00000245
+BDMAP_00000989
+BDMAP_00001247
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+BDMAP_00002278
+BDMAP_00004841
+BDMAP_00001602
+BDMAP_00001464
+BDMAP_00001712
+BDMAP_00003815
+BDMAP_00002407
+BDMAP_00003150
+BDMAP_00001711
+BDMAP_00002273
+BDMAP_00002751
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+BDMAP_00004447
+BDMAP_00000977
+BDMAP_00004297
+BDMAP_00000812
+BDMAP_00004641
+BDMAP_00001422
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+BDMAP_00002475
+BDMAP_00002166
+BDMAP_00004232
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+BDMAP_00000159
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+BDMAP_00004943
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+BDMAP_00003329
+BDMAP_00001597
+BDMAP_00002172
+BDMAP_00000833
+BDMAP_00004187
+BDMAP_00004744
+BDMAP_00001676
+BDMAP_00003558
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+BDMAP_00004128
+BDMAP_00005140
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+BDMAP_00001001
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+BDMAP_00000607
+BDMAP_00002940
+BDMAP_00002930
+BDMAP_00003377
+BDMAP_00004509
+BDMAP_00000923
+BDMAP_00001413
+BDMAP_00001636
+BDMAP_00001705
+BDMAP_00000273
+BDMAP_00003840
+BDMAP_00001333
+BDMAP_00005092
+BDMAP_00001368
+BDMAP_00003994
+BDMAP_00004925
+BDMAP_00001370
+BDMAP_00003455
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+BDMAP_00005174
+BDMAP_00005009
+BDMAP_00001549
+BDMAP_00001941
+BDMAP_00000154
+BDMAP_00001521
+BDMAP_00002653
+BDMAP_00001148
+BDMAP_00000774
+BDMAP_00005105
+BDMAP_00002421
+BDMAP_00000139
+BDMAP_00003867
+BDMAP_00003479
+BDMAP_00004741
+BDMAP_00001516
+BDMAP_00002396
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+BDMAP_00000324
+BDMAP_00002841
+BDMAP_00003326
+BDMAP_00002437
+BDMAP_00000100
+BDMAP_00004586
+BDMAP_00004867
+BDMAP_00001040
+BDMAP_00001185
+BDMAP_00001461
+BDMAP_00000692
+BDMAP_00001563
+BDMAP_00002289
+BDMAP_00004901
+BDMAP_00001632
+BDMAP_00000558
+BDMAP_00000469
+BDMAP_00001966
+BDMAP_00003315
+BDMAP_00002313
+BDMAP_00005006
+BDMAP_00000439
+BDMAP_00004551
+BDMAP_00003294
+BDMAP_00001807
+BDMAP_00004579
+BDMAP_00002057
+BDMAP_00002060
+BDMAP_00004508
+BDMAP_00004104
+BDMAP_00000052
+BDMAP_00003439
+BDMAP_00001502
+BDMAP_00005186
+BDMAP_00002529
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Generation_Pipeline_filter/syn_colon/requirements.txt

@@ -0,0 +1,94 @@
+absl-py==1.1.0
+accelerate==0.11.0
+aiohttp==3.8.1
+aiosignal==1.2.0
+antlr4-python3-runtime==4.9.3
+async-timeout==4.0.2
+attrs==21.4.0
+autopep8==1.6.0
+cachetools==5.2.0
+certifi==2022.6.15
+charset-normalizer==2.0.12
+click==8.1.3
+cycler==0.11.0
+Deprecated==1.2.13
+docker-pycreds==0.4.0
+einops==0.4.1
+einops-exts==0.0.3
+ema-pytorch==0.0.8
+fonttools==4.34.4
+frozenlist==1.3.0
+fsspec==2022.5.0
+ftfy==6.1.1
+future==0.18.2
+gitdb==4.0.9
+GitPython==3.1.27
+google-auth==2.9.0
+google-auth-oauthlib==0.4.6
+grpcio==1.47.0
+h5py==3.7.0
+humanize==4.2.2
+hydra-core==1.2.0
+idna==3.3
+imageio==2.19.3
+imageio-ffmpeg==0.4.7
+importlib-metadata==4.12.0
+importlib-resources==5.9.0
+joblib==1.1.0
+kiwisolver==1.4.3
+lxml==4.9.1
+Markdown==3.3.7
+matplotlib==3.5.2
+multidict==6.0.2
+networkx==2.8.5
+nibabel==4.0.1
+nilearn==0.9.1
+numpy==1.23.0
+oauthlib==3.2.0
+omegaconf==2.2.3
+pandas==1.4.3
+Pillow==9.1.1
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+pycodestyle==2.8.0
+pyDeprecate==0.3.1
+pydicom==2.3.0
+pytorch-lightning==1.6.4
+pytz==2022.1
+PyWavelets==1.3.0
+PyYAML==6.0
+pyzmq==19.0.2
+regex==2022.6.2
+requests==2.28.0
+requests-oauthlib==1.3.1
+rotary-embedding-torch==0.1.5
+rsa==4.8
+scikit-image==0.19.3
+scikit-learn==1.1.2
+scikit-video==1.1.11
+scipy==1.8.1
+seaborn==0.11.2
+sentry-sdk==1.7.2
+setproctitle==1.2.3
+shortuuid==1.0.9
+SimpleITK==2.1.1.2
+smmap==5.0.0
+tensorboard==2.9.1
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+threadpoolctl==3.1.0
+tifffile==2022.8.3
+toml==0.10.2
+torch-tb-profiler==0.4.0
+torchio==0.18.80
+torchmetrics==0.9.1
+tqdm==4.64.0
+typing_extensions==4.2.0
+urllib3==1.26.9
+wandb==0.12.21
+Werkzeug==2.1.2
+wrapt==1.14.1
+yarl==1.7.2
+zipp==3.8.0
+wandb
+tensorboardX==2.4.1

Generation_Pipeline_filter/syn_kidney/CT_syn_kidney_data_new.py

@@ -0,0 +1,241 @@
+import os, time, csv
+import numpy as np
+import torch
+from sklearn.metrics import confusion_matrix
+from scipy import ndimage
+from scipy.ndimage import label
+from functools import partial
+import monai
+from monai.transforms import AsDiscrete,AsDiscreted,Compose,Invertd,SaveImaged
+from monai import transforms, data
+from TumorGeneration.utils import synthesize_early_tumor, synthesize_medium_tumor, synthesize_large_tumor, synt_model_prepare
+import nibabel as nib
+
+import warnings
+warnings.filterwarnings("ignore")
+
+import argparse
+parser = argparse.ArgumentParser(description='kidney tumor validation')
+
+# file dir
+parser.add_argument('--data_root', default=None, type=str)
+parser.add_argument('--organ_type', default='kidney', type=str)
+parser.add_argument('--save_dir', default='out', type=str)
+parser.add_argument('--data_file', default='out', type=str)
+parser.add_argument('--ddim_ts', default=50, type=int)
+parser.add_argument('--fg_thresh', default=30, type=int)
+parser.add_argument('--start', default=0, type=int)
+parser.add_argument('--end', default=1000, type=int)
+
+def voxel2R(A):
+    return (np.array(A)/4*3/np.pi)**(1/3)
+
+class RandCropByPosNegLabeld_select(transforms.RandCropByPosNegLabeld):
+    def __init__(self, keys, label_key, spatial_size, 
+                 pos=1.0, neg=1.0, num_samples=1, 
+                 image_key=None, image_threshold=0.0, allow_missing_keys=True,
+                   fg_thresh=0):
+        super().__init__(keys=keys, label_key=label_key, spatial_size=spatial_size, 
+                 pos=pos, neg=neg, num_samples=num_samples, 
+                 image_key=image_key, image_threshold=image_threshold, allow_missing_keys=allow_missing_keys)
+        self.fg_thresh = fg_thresh
+
+    def R2voxel(self,R):
+        return (4/3*np.pi)*(R)**(3)
+
+    def __call__(self, data):
+        d = dict(data)
+        data_name = d['name']
+        d.pop('name')
+
+        if '10_Decathlon' in data_name or '05_KiTS' in data_name:
+            d_crop = super().__call__(d)
+
+        else:
+            flag=0
+            while 1:
+                flag+=1
+
+                d_crop = super().__call__(d)
+                pixel_num = (d_crop[0]['label']>0).sum()
+                
+                if pixel_num > self.R2voxel(self.fg_thresh):
+                    break
+                if flag>5 and pixel_num > self.R2voxel(max(self.fg_thresh-5, 5)):
+                    break
+                if flag>10 and pixel_num > self.R2voxel(max(self.fg_thresh-10, 5)):
+                    break
+                if flag>15 and pixel_num > self.R2voxel(max(self.fg_thresh-15, 5)):
+                    break
+                if flag>20 and pixel_num > self.R2voxel(max(self.fg_thresh-20, 5)):
+                    break
+                if flag>25 and pixel_num > self.R2voxel(max(self.fg_thresh-25, 5)):
+                    break
+                if flag>50:
+                    break
+            
+        d_crop[0]['name'] = data_name
+        
+        return d_crop
+    
+def _get_loader(args):
+    # val_data_dir = args.val_dir
+    # datalist_json = args.json_dir 
+    val_org_transform = transforms.Compose(
+        [
+            transforms.LoadImaged(keys=["image", "label", "raw_image"]),
+            transforms.AddChanneld(keys=["image", "label", "raw_image"]),
+            transforms.Orientationd(keys=["image", "label"], axcodes="RAS"),
+            transforms.Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear", "bilinear")),
+            transforms.ScaleIntensityRanged(keys=["image"], a_min=-175, a_max=250, b_min=0.0, b_max=1.0, clip=True),
+            transforms.SpatialPadd(keys=["image", "label"], mode=["minimum", "constant"], spatial_size=[96, 96, 96]),
+            RandCropByPosNegLabeld_select(
+                keys=["image", "label", "name"],
+                label_key="label",
+                spatial_size=(96, 96, 96),
+                pos=1,
+                neg=0,
+                num_samples=1,
+                image_key="image",
+                image_threshold=0,
+                fg_thresh = args.fg_thresh,
+            ),
+            transforms.ToTensord(keys=["image", "label", "raw_image"]),
+        ]
+    )
+
+    val_img=[]
+    val_lbl=[]
+    val_name=[]
+    
+    for line in open(args.data_file):
+        # name = line.strip().split()[1].split('.')[0]
+        # val_img.append(args.data_root + line.strip().split()[0])
+        # val_lbl.append(args.data_root + line.strip().split()[1])
+        # breakpoint()
+        name = line.strip()
+        val_img.append(os.path.join(args.data_root, name, 'ct.nii.gz'))
+        val_lbl.append(os.path.join(args.data_root, name, 'segmentations/kidney_left.nii.gz'))
+        val_name.append(name)
+    data_dicts_val = [{'image': image, 'raw_image':image, 'label': label, 'name': name}
+                for image, label, name in zip(val_img, val_lbl, val_name)]
+    
+    if args.end < len(data_dicts_val):
+        data_dicts_val = data_dicts_val[args.start:args.end]
+    else:
+        data_dicts_val = data_dicts_val[args.start:]
+    print('val len {}'.format(len(data_dicts_val)))
+    val_org_ds = data.Dataset(data_dicts_val, transform=val_org_transform)
+    val_org_loader = data.DataLoader(val_org_ds, batch_size=1, shuffle=False, num_workers=4, sampler=None, pin_memory=True)
+
+    post_transforms = Compose([
+        Invertd(
+            keys=['image'],
+            transform=val_org_transform,
+            orig_keys="image",
+            nearest_interp=False,
+            # nearest_interp=True,
+            to_tensor=True,
+        ),
+        Invertd(
+            keys=['label'],
+            transform=val_org_transform,
+            orig_keys="label",
+            nearest_interp=False,
+            # nearest_interp=True,
+            to_tensor=True,
+        )
+    ])
+    return val_org_loader, post_transforms
+
+def main():
+    args = parser.parse_args()
+    output_dir = args.save_dir
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+    print("MAIN Argument values:")
+    for k, v in vars(args).items():
+        print(k, '=>', v)
+    print('-----------------')
+
+    ## loader and post_transform
+    val_loader, post_transforms = _get_loader(args)
+
+    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+    model = monai.networks.nets.DenseNet121(spatial_dims=3, in_channels=1, out_channels=2).to(device)
+    model.load_state_dict(torch.load("../best_metric_model_classification3d_dict.pth"))
+    model.eval()
+    
+    start_time=0
+    with torch.no_grad():
+        for idx, val_data in enumerate(val_loader):
+            print('idx',idx)
+            if idx == 0:
+                start_time = time.time()
+            # val_inputs = val_data["image"]
+            # name = val_data['label_meta_dict']['filename_or_obj'][0].split('/')[-1].split('.')[0]
+            
+            vqgan, early_sampler, noearly_sampler= synt_model_prepare(device = torch.device("cuda"), fold=0, organ=args.organ_type)
+            
+            healthy_data, healthy_target, data_names, raw_data = val_data['image'], val_data['label'], val_data['name'], val_data['raw_image']
+            case_name = data_names[0].split('/')[-1]
+            print('case_name', case_name)
+            original_affine = val_data["label_meta_dict"]["original_affine"][0].numpy()
+
+            if healthy_target.sum() == 0:
+                val_data = [post_transforms(i) for i in data.decollate_batch(val_data)]
+                tumor_mask = val_data[0]['label'][0].cpu().numpy().astype(np.uint8)
+                tumor_mask_ = np.zeros_like(tumor_mask)
+                nib.save(nib.Nifti1Image(tumor_mask_, original_affine), os.path.join(output_dir, f'{case_name}/segmentations/kidney_tumor.nii.gz'))
+                continue
+            
+            healthy_data, healthy_target = healthy_data.cuda(), healthy_target.cuda()
+            healthy_target = (healthy_target>0).to(healthy_target)
+
+            tumor_types = ['early', 'medium', 'large']
+            # tumor_probs = np.array([0.45, 0.45, 0.1])
+            # tumor_probs = np.array([1.0, 0.0, 0.0])
+            tumor_probs = np.array([0.5, 0.4, 0.1])
+            synthetic_tumor_type = np.random.choice(tumor_types, p=tumor_probs.ravel())
+            print('synthetic_tumor_type',synthetic_tumor_type)
+            flag=0
+            while 1:
+                flag+=1
+                if synthetic_tumor_type == 'early':
+                    synt_data, synt_target = synthesize_early_tumor(healthy_data, healthy_target, args.organ_type, vqgan, early_sampler)
+                elif synthetic_tumor_type == 'medium':
+                    synt_data, synt_target = synthesize_medium_tumor(healthy_data, healthy_target, args.organ_type, vqgan, noearly_sampler, ddim_ts=args.ddim_ts)
+                elif synthetic_tumor_type == 'large':
+                    synt_data, synt_target = synthesize_large_tumor(healthy_data, healthy_target, args.organ_type, vqgan, noearly_sampler, ddim_ts=args.ddim_ts)
+                
+                syn_confidence = model(synt_data).sigmoid()[:,1]
+                if syn_confidence>0.01:
+                    break
+                elif flag > 40 and syn_confidence>0.005:
+                    break
+                elif flag > 60 and syn_confidence>0.001:
+                    break
+            val_data['image'] = synt_data.detach()
+            val_data['label'] = synt_target.detach()
+
+            val_data = [post_transforms(i) for i in data.decollate_batch(val_data)]
+            synt_data = val_data[0]['image'][0]
+            synt_target = val_data[0]['label'][0]
+            final_data = raw_data[0,0]
+
+            synt_data = (synt_data*(250+175)-175)
+            final_data[synt_target>1] = synt_data[synt_target>1]
+            final_data = final_data.cpu().numpy()
+            final_label = (synt_target>=1.5).cpu().numpy().astype(np.uint8)
+
+            os.makedirs(os.path.join(output_dir, f'{case_name}'), exist_ok=True)
+            os.makedirs(os.path.join(output_dir, f'{case_name}/segmentations'), exist_ok=True)
+            nib.save(nib.Nifti1Image(final_data, original_affine), os.path.join(output_dir, f'{case_name}/ct.nii.gz'))
+            nib.save(nib.Nifti1Image(final_label, original_affine), os.path.join(output_dir, f'{case_name}/segmentations/kidney_tumor.nii.gz'))
+
+            print('time = ', time.time()-start_time)
+            start_time = time.time()
+
+
+if __name__ == "__main__":
+    main()

Generation_Pipeline_filter/syn_kidney/CT_syn_kidney_data_new2.py

@@ -0,0 +1,251 @@
+import os, time, csv
+import numpy as np
+import torch
+from sklearn.metrics import confusion_matrix
+from scipy import ndimage
+from scipy.ndimage import label
+from functools import partial
+import monai
+from monai.transforms import AsDiscrete,AsDiscreted,Compose,Invertd,SaveImaged
+from monai import transforms, data
+from TumorGeneration.utils import synthesize_early_tumor, synthesize_medium_tumor, synthesize_large_tumor, synt_model_prepare
+import nibabel as nib
+
+import warnings
+warnings.filterwarnings("ignore")
+
+import argparse
+parser = argparse.ArgumentParser(description='kidney tumor validation')
+
+# file dir
+parser.add_argument('--data_root', default=None, type=str)
+parser.add_argument('--organ_type', default='kidney', type=str)
+parser.add_argument('--save_dir', default='out', type=str)
+parser.add_argument('--data_file', default='out', type=str)
+parser.add_argument('--ddim_ts', default=50, type=int)
+parser.add_argument('--fg_thresh', default=30, type=int)
+parser.add_argument('--start', default=0, type=int)
+parser.add_argument('--end', default=1000, type=int)
+
+def voxel2R(A):
+    return (np.array(A)/4*3/np.pi)**(1/3)
+
+class RandCropByPosNegLabeld_select(transforms.RandCropByPosNegLabeld):
+    def __init__(self, keys, label_key, spatial_size, 
+                 pos=1.0, neg=1.0, num_samples=1, 
+                 image_key=None, image_threshold=0.0, allow_missing_keys=True,
+                   fg_thresh=0):
+        super().__init__(keys=keys, label_key=label_key, spatial_size=spatial_size, 
+                 pos=pos, neg=neg, num_samples=num_samples, 
+                 image_key=image_key, image_threshold=image_threshold, allow_missing_keys=allow_missing_keys)
+        self.fg_thresh = fg_thresh
+
+    def R2voxel(self,R):
+        return (4/3*np.pi)*(R)**(3)
+
+    def __call__(self, data):
+        d = dict(data)
+        data_name = d['name']
+        d.pop('name')
+
+        if '10_Decathlon' in data_name or '05_KiTS' in data_name:
+            d_crop = super().__call__(d)
+
+        else:
+            flag=0
+            while 1:
+                flag+=1
+
+                d_crop = super().__call__(d)
+                pixel_num = (d_crop[0]['label']>0).sum()
+                
+                if pixel_num > self.R2voxel(self.fg_thresh):
+                    break
+                if flag>5 and pixel_num > self.R2voxel(max(self.fg_thresh-5, 5)):
+                    break
+                if flag>10 and pixel_num > self.R2voxel(max(self.fg_thresh-10, 5)):
+                    break
+                if flag>15 and pixel_num > self.R2voxel(max(self.fg_thresh-15, 5)):
+                    break
+                if flag>20 and pixel_num > self.R2voxel(max(self.fg_thresh-20, 5)):
+                    break
+                if flag>25 and pixel_num > self.R2voxel(max(self.fg_thresh-25, 5)):
+                    break
+                if flag>50:
+                    break
+            
+        d_crop[0]['name'] = data_name
+        
+        return d_crop
+    
+def _get_loader(args):
+    # val_data_dir = args.val_dir
+    # datalist_json = args.json_dir 
+    val_org_transform = transforms.Compose(
+        [
+            transforms.LoadImaged(keys=["image", "label", 'tumor_label', "raw_image"]),
+            transforms.AddChanneld(keys=["image", "label", 'tumor_label', "raw_image"]),
+            transforms.Orientationd(keys=["image", "label", 'tumor_label'], axcodes="RAS"),
+            transforms.Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear", "bilinear")),
+            transforms.ScaleIntensityRanged(keys=["image"], a_min=-175, a_max=250, b_min=0.0, b_max=1.0, clip=True),
+            transforms.SpatialPadd(keys=["image", "label"], mode=["minimum", "constant"], spatial_size=[96, 96, 96]),
+            RandCropByPosNegLabeld_select(
+                keys=["image", "label", "name"],
+                label_key="label",
+                spatial_size=(96, 96, 96),
+                pos=1,
+                neg=0,
+                num_samples=1,
+                image_key="image",
+                image_threshold=0,
+                fg_thresh = args.fg_thresh,
+            ),
+            transforms.ToTensord(keys=["image", "label", 'tumor_label', "raw_image"]),
+        ]
+    )
+
+    val_img=[]
+    val_lbl=[]
+    val_name=[]
+    tumor_lbl=[]
+    for line in open(args.data_file):
+        # name = line.strip().split()[1].split('.')[0]
+        # val_img.append(args.data_root + line.strip().split()[0])
+        # val_lbl.append(args.data_root + line.strip().split()[1])
+        # breakpoint()
+        name = line.strip()
+        val_img.append(os.path.join(args.data_root, name, 'ct.nii.gz'))
+        val_lbl.append(os.path.join(args.data_root, name, 'segmentations/kidney_right.nii.gz'))
+        tumor_lbl.append(os.path.join(args.data_root, name, 'segmentations/kidney_tumor.nii.gz'))
+        val_name.append(name)
+    data_dicts_val = [{'image': image, 'raw_image':image, 'label': label, 'tumor_label':tumor_label,'name': name}
+                for image, label, tumor_label, name in zip(val_img, val_lbl, tumor_lbl, val_name)]
+    
+    if args.end < len(data_dicts_val):
+        data_dicts_val = data_dicts_val[args.start:args.end]
+    else:
+        data_dicts_val = data_dicts_val[args.start:]
+    print('val len {}'.format(len(data_dicts_val)))
+    val_org_ds = data.Dataset(data_dicts_val, transform=val_org_transform)
+    val_org_loader = data.DataLoader(val_org_ds, batch_size=1, shuffle=False, num_workers=4, sampler=None, pin_memory=True)
+
+    post_transforms = Compose([
+        Invertd(
+            keys=['image'],
+            transform=val_org_transform,
+            orig_keys="image",
+            nearest_interp=False,
+            # nearest_interp=True,
+            to_tensor=True,
+        ),
+        Invertd(
+            keys=['label'],
+            transform=val_org_transform,
+            orig_keys="label",
+            nearest_interp=False,
+            # nearest_interp=True,
+            to_tensor=True,
+        ),
+        Invertd(
+            keys=['tumor_label'],
+            transform=val_org_transform,
+            orig_keys="tumor_label",
+            nearest_interp=False,
+            to_tensor=True,
+        )
+    ])
+    return val_org_loader, post_transforms
+
+def main():
+    args = parser.parse_args()
+    output_dir = args.save_dir
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+    print("MAIN Argument values:")
+    for k, v in vars(args).items():
+        print(k, '=>', v)
+    print('-----------------')
+
+    ## loader and post_transform
+    val_loader, post_transforms = _get_loader(args)
+
+    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+    model = monai.networks.nets.DenseNet121(spatial_dims=3, in_channels=1, out_channels=2).to(device)
+    model.load_state_dict(torch.load("../best_metric_model_classification3d_dict.pth"))
+    model.eval()
+    
+    start_time=0
+    with torch.no_grad():
+        for idx, val_data in enumerate(val_loader):
+            print('idx',idx)
+            if idx == 0:
+                start_time = time.time()
+            # val_inputs = val_data["image"]
+            # name = val_data['label_meta_dict']['filename_or_obj'][0].split('/')[-1].split('.')[0]
+            
+            vqgan, early_sampler, noearly_sampler= synt_model_prepare(device = torch.device("cuda"), fold=0, organ=args.organ_type)
+            
+            healthy_data, healthy_target, data_names, raw_data = val_data['image'], val_data['label'], val_data['name'], val_data['raw_image']
+            case_name = data_names[0].split('/')[-1]
+            print('case_name', case_name)
+            original_affine = val_data["label_meta_dict"]["original_affine"][0].numpy()
+
+            if healthy_target.sum() == 0:
+                # val_data = [post_transforms(i) for i in data.decollate_batch(val_data)]
+                # tumor_mask = val_data[0]['label'][0].cpu().numpy().astype(np.uint8)
+                # tumor_mask_ = np.zeros_like(tumor_mask)
+                # nib.save(nib.Nifti1Image(tumor_mask_, original_affine), os.path.join(output_dir, f'{case_name}/segmentations/kidney_tumor.nii.gz'))
+                continue
+            
+            healthy_data, healthy_target = healthy_data.cuda(), healthy_target.cuda()
+            healthy_target = (healthy_target>0).to(healthy_target)
+
+            tumor_types = ['early', 'medium', 'large']
+            # tumor_probs = np.array([0.45, 0.45, 0.1])
+            # tumor_probs = np.array([1.0, 0.0, 0.0])
+            tumor_probs = np.array([0.5, 0.4, 0.1])
+            synthetic_tumor_type = np.random.choice(tumor_types, p=tumor_probs.ravel())
+            print('synthetic_tumor_type',synthetic_tumor_type)
+            flag=0
+            while 1:
+                flag+=1
+                if synthetic_tumor_type == 'early':
+                    synt_data, synt_target = synthesize_early_tumor(healthy_data, healthy_target, args.organ_type, vqgan, early_sampler)
+                elif synthetic_tumor_type == 'medium':
+                    synt_data, synt_target = synthesize_medium_tumor(healthy_data, healthy_target, args.organ_type, vqgan, noearly_sampler, ddim_ts=args.ddim_ts)
+                elif synthetic_tumor_type == 'large':
+                    synt_data, synt_target = synthesize_large_tumor(healthy_data, healthy_target, args.organ_type, vqgan, noearly_sampler, ddim_ts=args.ddim_ts)
+                
+                syn_confidence = model(synt_data).sigmoid()[:,1]
+                if syn_confidence>0.01:
+                    break
+                elif flag > 40 and syn_confidence>0.005:
+                    break
+                elif flag > 60 and syn_confidence>0.001:
+                    break
+            val_data['image'] = synt_data.detach()
+            val_data['label'] = synt_target.detach()
+
+            val_data = [post_transforms(i) for i in data.decollate_batch(val_data)]
+            synt_data = val_data[0]['image'][0]
+            synt_target = val_data[0]['label'][0]
+            tumor_mask = val_data[0]['tumor_label'][0]
+            final_data = raw_data[0,0]
+
+            synt_data = (synt_data*(250+175)-175)
+            final_data[synt_target>1] = synt_data[synt_target>1]
+            final_data = final_data.cpu().numpy()
+            final_label = (synt_target>=1.5).cpu().numpy().astype(np.uint8)
+            final_label[tumor_mask==1] = 1
+
+            os.makedirs(os.path.join(output_dir, f'{case_name}'), exist_ok=True)
+            os.makedirs(os.path.join(output_dir, f'{case_name}/segmentations'), exist_ok=True)
+            nib.save(nib.Nifti1Image(final_data, original_affine), os.path.join(output_dir, f'{case_name}/ct.nii.gz'))
+            nib.save(nib.Nifti1Image(final_label, original_affine), os.path.join(output_dir, f'{case_name}/segmentations/kidney_tumor.nii.gz'))
+
+            print('time = ', time.time()-start_time)
+            start_time = time.time()
+
+
+if __name__ == "__main__":
+    main()