spacr 0.4.60__py3-none-any.whl → 0.9.0__py3-none-any.whl

spacr/resources/MEDIAR/config/mediar_example.json

@@ -1,72 +0,0 @@
-{
-    "data_setups":{
-        "labeled":{
-            "root": "/home/gihun/data/CellSeg/",
-            "mapping_file": "./train_tools/data_utils/mapping_labeled.json",
-            "amplified": false,
-            "batch_size": 8, 
-            "valid_portion": 0.1
-        },
-        "public":{
-            "enabled": true,
-            "params":{
-                "root": "/home/gihun/data/CellSeg/",
-                "mapping_file": "./train_tools/data_utils/mapping_public.json",
-                "batch_size": 1
-            }
-        },
-        "unlabeled":{
-            "enabled": false
-        }        
-    },
-    "train_setups":{
-        "model":{
-            "name": "mediar-former",
-            "params": {
-                "encoder_name": "mit_b5",
-                "encoder_weights": "imagenet",
-                "decoder_channels": [1024, 512, 256, 128, 64],
-                "decoder_pab_channels": 256,
-                "in_channels": 3,
-                "classes": 3
-            },
-            "pretrained":{
-                "enabled": false,
-                "weights": "./weights/pretrained/phase2.pth",
-                "strict": false
-            }
-        },
-        "trainer": {
-            "name": "mediar",
-            "params": {            
-                "num_epochs": 200,
-                "valid_frequency": 1,
-                "device": "cuda:0",
-                "amp": true,
-                "algo_params": {"with_public": false}
-            }
-        },
-        "optimizer":{
-            "name": "adamw",
-            "params": {"lr": 5e-5}
-        },
-        "scheduler":{
-            "enabled": true,
-            "name": "cosine",
-            "params": {"T_max": 100, "eta_min": 1e-7}
-        },
-        "seed": 19940817
-    },
-    "pred_setups":{
-        "input_path":"/home/gihun/data/CellSeg/Official/TuningSet",
-        "output_path": "./mediar_example",
-        "make_submission": true,
-        "exp_name": "mediar_example",
-        "algo_params": {"use_tta": false}
-    },
-    "wandb_setups":{
-        "project": "CellSeg",
-        "group": "MEDIAR",
-        "name": "mediar_example"
-    }
-}

spacr/resources/MEDIAR/config/pred/pred_mediar.json

@@ -1,17 +0,0 @@
-{
-    "pred_setups":{
-        "name": "medair",
-        "input_path":"input_path",
-        "output_path": "./test",
-        "make_submission": true,
-        "model_path": "model_path",
-        "device": "cuda:0",
-        "model":{
-            "name": "mediar-former",
-            "params": {},
-            "pretrained":{
-                "enabled": false
-            }
-        }
-    }
-}

spacr/resources/MEDIAR/config/step1_pretraining/phase1.json

@@ -1,55 +0,0 @@
-{
-    "data_setups":{
-        "labeled":{
-            "root": "/home/gihun/MEDIAR/",
-            "mapping_file": "./train_tools/data_utils/mapping_public.json",
-            "mapping_file_tuning": "/home/gihun/MEDIAR/train_tools/data_utils/mapping_tuning.json",
-            "batch_size": 9, 
-            "valid_portion": 0
-        },
-        "public":{
-            "enabled": false,
-            "params":{}
-        }     
-    },
-    "train_setups":{
-        "model":{
-            "name": "mediar-former",
-            "params": {},
-            "pretrained":{
-                "enabled": false
-            }
-        },
-        "trainer": {
-            "name": "mediar",
-            "params": {            
-                "num_epochs": 80,
-                "valid_frequency": 10,
-                "device": "cuda:0",
-                "amp": true,
-                "algo_params": {"with_public": false}
-            }
-        },
-        "optimizer":{
-            "name": "adamw",
-            "ft_rate": 1.0,
-            "params": {"lr": 5e-5}
-        },
-        "scheduler":{
-            "enabled": true,
-            "name": "cosine",
-            "params": {"T_max": 80, "eta_min": 1e-6}
-        },
-        "seed": 19940817
-    },
-    "pred_setups":{
-        "input_path":"/home/gihun/MEDIAR/data/Official/Tuning/images",
-        "output_path": "./mediar_pretrained_phase1",
-        "make_submission": false
-    },
-    "wandb_setups":{
-        "project": "CellSeg",
-        "group": "Pretraining",
-        "name": "phase1"
-    }
-}

spacr/resources/MEDIAR/config/step1_pretraining/phase2.json

@@ -1,58 +0,0 @@
-{
-    "data_setups":{
-        "labeled":{
-            "root": "/home/gihun/MEDIAR/",
-            "mapping_file": "./train_tools/data_utils/mapping_labeled.json",
-            "mapping_file_tuning": "/home/gihun/MEDIAR/train_tools/data_utils/mapping_tuning.json",
-            "join_mapping_file": "./train_tools/data_utils/mapping_public.json",
-            "batch_size": 9, 
-            "valid_portion": 0
-        },
-        "unlabeled":{
-            "enabled": false
-        },
-        "public":{
-            "enabled": false
-        }        
-    },
-    "train_setups":{
-        "model":{
-            "name": "mediar-former",
-            "params": {},
-            "pretrained":{
-                "enabled": false
-            }
-        },
-        "trainer": {
-            "name": "mediar",
-            "params": {            
-                "num_epochs": 60,
-                "valid_frequency": 10,
-                "device": "cuda:0",
-                "amp": true,
-                "algo_params": {"with_public": false}
-            }
-        },
-        "optimizer":{
-            "name": "adamw",
-            "ft_rate": 1.0,
-            "params": {"lr": 5e-5}
-        },
-        "scheduler":{
-            "enabled": true,
-            "name": "cosine",
-            "params": {"T_max": 60, "eta_min": 1e-6}
-        },
-        "seed": 19940817
-    },
-    "pred_setups":{
-        "input_path":"/home/gihun/MEDIAR/data/Official/Tuning/images",
-        "output_path": "./mediar_pretrain_phase2",
-        "make_submission": false
-    },
-    "wandb_setups":{
-        "project": "CellSeg",
-        "group": "Pretraining",
-        "name": "phase2"
-    }
-}

spacr/resources/MEDIAR/config/step2_finetuning/finetuning1.json

@@ -1,66 +0,0 @@
-{
-    "data_setups":{
-        "labeled":{
-            "root": "/home/gihun/MEDIAR/",
-            "mapping_file": "./train_tools/data_utils/mapping_labeled.json",
-            "mapping_file_tuning": "/home/gihun/MEDIAR/train_tools/data_utils/mapping_tuning.json",
-            "amplified": true,
-            "batch_size": 8, 
-            "valid_portion": 0.0
-        },
-        "public":{
-            "enabled": false,
-            "params":{
-                "root": "/home/gihun/MEDIAR/",
-                "mapping_file": "./train_tools/data_utils/mapping_public.json",
-                "batch_size": 1
-            }
-        },
-        "unlabeled":{
-            "enabled": false
-        }
-    },
-    "train_setups":{
-        "model":{
-            "name": "mediar-former",
-            "params": {},
-            "pretrained":{
-                "enabled": true,
-                "weights": "./weights/pretrained/phase1.pth",
-                "strict": false
-            }
-        },
-        "trainer": {
-            "name": "mediar",
-            "params": {            
-                "num_epochs": 200,
-                "valid_frequency": 1,
-                "device": "cuda:7",
-                "amp": true,
-                "algo_params": {"with_public": false}
-            }
-        },
-        "optimizer":{
-            "name": "adamw",
-            "params": {"lr": 2e-5}
-        },
-        "scheduler":{
-            "enabled": true,
-            "name": "cosine",
-            "params": {"T_max": 100, "eta_min": 1e-7}
-        },
-        "seed": 19940817
-    },
-    "pred_setups":{
-        "input_path":"/home/gihun/MEDIAR/data/Official/Tuning/images",
-        "output_path": "./results/",
-        "make_submission": true,
-        "exp_name": "mediar_from_phase1",
-        "algo_params": {"use_tta": false}
-    },
-    "wandb_setups":{
-        "project": "CellSeg",
-        "group": "Fine-tuning",
-        "name": "from_phase1"
-    }
-}

spacr/resources/MEDIAR/config/step2_finetuning/finetuning2.json

@@ -1,66 +0,0 @@
-{
-    "data_setups":{
-        "labeled":{
-            "root": "/home/gihun/MEDIAR/",
-            "mapping_file": "./train_tools/data_utils/mapping_labeled.json",
-            "mapping_file_tuning": "/home/gihun/MEDIAR/train_tools/data_utils/mapping_tuning.json",
-            "amplified": true,
-            "batch_size": 8, 
-            "valid_portion": 0.0
-        },
-        "public":{
-            "enabled": true,
-            "params":{
-                "root": "/home/gihun/MEDIAR/",
-                "mapping_file": "./train_tools/data_utils/mapping_public.json",
-                "batch_size": 1
-            }
-        },
-        "unlabeled":{
-            "enabled": false
-        }     
-    },
-    "train_setups":{
-        "model":{
-            "name": "mediar-former",
-            "params": {},
-            "pretrained":{
-                "enabled": true,
-                "weights": "./weights/pretrained/phase2.pth",
-                "strict": false
-            }
-        },
-        "trainer": {
-            "name": "mediar",
-            "params": {            
-                "num_epochs": 50,
-                "valid_frequency": 1,
-                "device": "cuda:0",
-                "amp": true,
-                "algo_params": {"with_public": true}
-            }
-        },
-        "optimizer":{
-            "name": "adamw",
-            "params": {"lr": 2e-5}
-        },
-        "scheduler":{
-            "enabled": true,
-            "name": "cosine",
-            "params": {"T_max": 100, "eta_min": 1e-7}
-        },
-        "seed": 19940817
-    },
-    "pred_setups":{
-        "input_path":"/home/gihun/MEDIAR/data/Official/Tuning/images",
-        "output_path": "./results/from_phase2",
-        "make_submission": true,
-        "exp_name": "mediar_from_phase2",
-        "algo_params": {"use_tta": false}
-    },
-    "wandb_setups":{
-        "project": "CellSeg",
-        "group": "Fine-tuning",
-        "name": "from_phase2"
-    }
-}

spacr/resources/MEDIAR/config/step3_prediction/base_prediction.json

@@ -1,16 +0,0 @@
-{
-    "pred_setups":{
-        "name": "mediar",
-        "input_path":"/home/gihun/MEDIAR/data/Official/Tuning/images",
-        "output_path": "./results/mediar_base_prediction",
-        "make_submission": true,
-        "model_path": "./weights/finetuned/from_phase1.pth",
-        "device": "cuda:7",
-        "model":{
-            "name": "mediar-former",
-            "params": {}
-        },
-        "exp_name": "mediar_p1_base",
-        "algo_params": {"use_tta": false}
-    }
-}

spacr/resources/MEDIAR/config/step3_prediction/ensemble_tta.json

@@ -1,23 +0,0 @@
-{
-    "pred_setups":{
-        "name": "ensemble_mediar",
-        "input_path":"/home/gihun/MEDIAR/data/Official/Tuning/images",
-        "output_path": "./results/mediar_ensemble_tta",
-        "make_submission": true,
-        "model_path1": "./weights/finetuned/from_phase1.pth",
-        "model_path2": "./weights/finetuned/from_phase2.pth",
-        "device": "cuda:0",
-        "model":{
-            "name": "mediar-former",
-            "params": {
-                    "encoder_name":"mit_b5",        
-                    "decoder_channels": [1024, 512, 256, 128, 64],
-                    "decoder_pab_channels": 256,
-                    "in_channels":3, 
-                    "classes":3
-            }
-        },
-        "exp_name": "mediar_ensemble_tta",
-        "algo_params": {"use_tta": true}
-    }
-}

spacr/resources/MEDIAR/core/BasePredictor.py

@@ -1,120 +0,0 @@
-import torch
-import numpy as np
-import time, os
-import tifffile as tif
-
-from datetime import datetime
-from zipfile import ZipFile
-from pytz import timezone
-
-from train_tools.data_utils.transforms import get_pred_transforms
-
-
-class BasePredictor:
-    def __init__(
-        self,
-        model,
-        device,
-        input_path,
-        output_path,
-        make_submission=False,
-        exp_name=None,
-        algo_params=None,
-    ):
-        self.model = model
-        self.device = device
-        self.input_path = input_path
-        self.output_path = output_path
-        self.make_submission = make_submission
-        self.exp_name = exp_name
-
-        # Assign algoritm-specific arguments
-        if algo_params:
-            self.__dict__.update((k, v) for k, v in algo_params.items())
-
-        # Prepare inference environments
-        self._setups()
-
-    @torch.no_grad()
-    def conduct_prediction(self):
-        self.model.to(self.device)
-        self.model.eval()
-        total_time = 0
-        total_times = []
-
-        for img_name in self.img_names:
-            img_data = self._get_img_data(img_name)
-            img_data = img_data.to(self.device)
-
-            start = time.time()
-
-            pred_mask = self._inference(img_data)
-            pred_mask = self._post_process(pred_mask.squeeze(0).cpu().numpy())
-            self.write_pred_mask(
-                pred_mask, self.output_path, img_name, self.make_submission
-            )
-
-            end = time.time()
-
-            time_cost = end - start
-            total_times.append(time_cost)
-            total_time += time_cost
-            print(
-                f"Prediction finished: {img_name}; img size = {img_data.shape}; costing: {time_cost:.2f}s"
-            )
-
-        print(f"\n Total Time Cost: {total_time:.2f}s")
-
-        if self.make_submission:
-            fname = "%s.zip" % self.exp_name
-
-            os.makedirs("./submissions", exist_ok=True)
-            submission_path = os.path.join("./submissions", fname)
-
-            with ZipFile(submission_path, "w") as zipObj2:
-                pred_names = sorted(os.listdir(self.output_path))
-                for pred_name in pred_names:
-                    pred_path = os.path.join(self.output_path, pred_name)
-                    zipObj2.write(pred_path)
-
-            print("\n>>>>> Submission file is saved at: %s\n" % submission_path)
-
-        return time_cost
-
-    def write_pred_mask(self, pred_mask, output_dir, image_name, submission=False):
-
-        # All images should contain at least 5 cells
-        if submission:
-            if not (np.max(pred_mask) > 5):
-                print("[!Caution] Only %d Cells Detected!!!\n" % np.max(pred_mask))
-
-        file_name = image_name.split(".")[0]
-        file_name = file_name + "_label.tiff"
-        file_path = os.path.join(output_dir, file_name)
-
-        tif.imwrite(file_path, pred_mask, compression="zlib")
-
-    def _setups(self):
-        self.pred_transforms = get_pred_transforms()
-        os.makedirs(self.output_path, exist_ok=True)
-
-        now = datetime.now(timezone("Asia/Seoul"))
-        dt_string = now.strftime("%m%d_%H%M")
-        self.exp_name = (
-            self.exp_name + dt_string if self.exp_name is not None else dt_string
-        )
-
-        self.img_names = sorted(os.listdir(self.input_path))
-
-    def _get_img_data(self, img_name):
-        img_path = os.path.join(self.input_path, img_name)
-        img_data = self.pred_transforms(img_path)
-        img_data = img_data.unsqueeze(0)
-
-        return img_data
-
-    def _inference(self, img_data):
-        raise NotImplementedError
-
-    def _post_process(self, pred_mask):
-        raise NotImplementedError