Clean up

bob/ip/binseg/configs/datasets/chasedb11024all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.chasedb1 import Database as CHASEDB1
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,Crop(0,18,960,960)
-                        ,Resize(1024)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = CHASEDB1(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/chasedb11168all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.chasedb1 import Database as CHASEDB1
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,Crop(140,18,680,960)
-                        ,Resize(1168)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = CHASEDB1(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/drive1024all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.drive import Database as DRIVE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,CenterCrop((540,540))
-                        ,Resize(1024)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/drive1168all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.drive import Database as DRIVE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,Crop(75,10,416,544)
-                        ,Pad((21,0,22,0))
-                        ,Resize(1168)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/drive960all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.drive import Database as DRIVE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,CenterCrop((544,544))
-                        ,Resize(960)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = DRIVE(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/drivestarechasedb1hrfl1024_all.py

-from bob.ip.binseg.configs.datasets.drive1024all import dataset as drive
-from bob.ip.binseg.configs.datasets.stare1024all import dataset as stare
-from bob.ip.binseg.configs.datasets.hrf1024all import dataset as hrf
-from bob.ip.binseg.configs.datasets.chasedb11024all import dataset as chasedb
-from bob.db.iostar import Database as IOSTAR
-from bob.ip.binseg.data.transforms import *
-import torch
-
-
-#### Config ####
-
-# PyTorch dataset
-dataset = torch.utils.data.ConcatDataset([drive,stare,hrf,chasedb])
-

bob/ip/binseg/configs/datasets/drivestarechasedb1hrfl1024_all_ssliostar.py

-from bob.ip.binseg.configs.datasets.drive1024all import dataset as drive
-from bob.ip.binseg.configs.datasets.stare1024all import dataset as stare
-from bob.ip.binseg.configs.datasets.hrf1024all import dataset as hrf
-from bob.ip.binseg.configs.datasets.chasedb11024all import dataset as chasedb
-from bob.db.iostar import Database as IOSTAR
-from bob.ip.binseg.data.transforms import *
-import torch
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-
-
-#### Config ####
-
-# PyTorch dataset
-labeled_dataset = torch.utils.data.ConcatDataset([drive,stare,hrf,chasedb])
-
-#### Unlabeled IOSTAR Train ####
-unlabeled_transforms = Compose([  
-                        RandomHFlip()
-                        ,RandomVFlip()
-                        ,RandomRotation()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-iostarbobdb = IOSTAR(protocol='default_vessel')
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(iostarbobdb, split='train', transform=unlabeled_transforms)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file

bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168_all.py

-from bob.ip.binseg.configs.datasets.drive1168all import dataset as drive
-from bob.ip.binseg.configs.datasets.stare1168all import dataset as stare
-from bob.ip.binseg.configs.datasets.chasedb11168all import dataset as chasedb
-from bob.ip.binseg.configs.datasets.iostarvessel1168all import dataset as iostar
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-import torch
-
-
-#### Config ####
-
-# PyTorch dataset
-dataset = torch.utils.data.ConcatDataset([drive,stare,iostar,chasedb])
\ No newline at end of file

bob/ip/binseg/configs/datasets/drivestarechasedb1iostar1168_all_sslhrf.py

-from bob.ip.binseg.configs.datasets.drive1168all import dataset as drive
-from bob.ip.binseg.configs.datasets.stare1168all import dataset as stare
-from bob.ip.binseg.configs.datasets.chasedb11168all import dataset as chasedb
-from bob.ip.binseg.configs.datasets.iostarvessel1168all import dataset as iostar
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-import torch
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-
-
-#### Config ####
-
-# PyTorch dataset
-labeled_dataset = torch.utils.data.ConcatDataset([drive,stare,iostar,chasedb])
-
-#### Unlabeled HRF TRAIN ####
-unlabeled_transforms = Compose([  
-                        RandomRotation()
-                        ,Crop(0,108,2336,3296)
-                        ,Resize((1168))
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-hrfbobdb = HRF(protocol='default')
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(hrfbobdb, split='train', transform=unlabeled_transforms)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file

bob/ip/binseg/configs/datasets/drivestareiostarhrf960_all.py

-from bob.ip.binseg.configs.datasets.drive960all import dataset as drive
-from bob.ip.binseg.configs.datasets.stare960all import dataset as stare
-from bob.ip.binseg.configs.datasets.hrf960all import dataset as hrf
-from bob.ip.binseg.configs.datasets.iostarvessel960all import dataset as iostar
-from bob.db.chasedb1 import Database as CHASE
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-import torch
-
-
-#### Config ####
-
-# PyTorch dataset
-dataset = torch.utils.data.ConcatDataset([drive,stare,hrf,iostar])
\ No newline at end of file

bob/ip/binseg/configs/datasets/drivestareiostarhrf960_all_sslchase.py

-from bob.ip.binseg.configs.datasets.drive960all import dataset as drive
-from bob.ip.binseg.configs.datasets.stare960all import dataset as stare
-from bob.ip.binseg.configs.datasets.hrf960all import dataset as hrf
-from bob.ip.binseg.configs.datasets.iostarvessel960all import dataset as iostar
-from bob.db.chasedb1 import Database as CHASE
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-import torch
-from bob.ip.binseg.data.binsegdataset import BinSegDataset, SSLBinSegDataset, UnLabeledBinSegDataset
-
-
-#### Config ####
-
-# PyTorch dataset
-labeled_dataset = torch.utils.data.ConcatDataset([drive,stare,hrf,iostar])
-
-#### Unlabeled CHASE TRAIN ####
-unlabeled_transforms = Compose([  
-                        Crop(0,18,960,960)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,RandomRotation()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-chasebobdb = CHASE(protocol = 'default')
-
-# PyTorch dataset
-unlabeled_dataset = UnLabeledBinSegDataset(chasebobdb, split='train', transform=unlabeled_transforms)
-
-# SSL Dataset
-
-dataset = SSLBinSegDataset(labeled_dataset, unlabeled_dataset)
\ No newline at end of file

bob/ip/binseg/configs/datasets/hrf1024all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        Pad((0,584,0,584))                    
-                        ,Resize((1024))
-                        ,RandomRotation()
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = HRF(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])

bob/ip/binseg/configs/datasets/hrf960all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.hrf import Database as HRF
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        Pad((0,584,0,584))                    
-                        ,Resize((960))
-                        ,RandomRotation()
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = HRF(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])

bob/ip/binseg/configs/datasets/iostarvessel1168all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.iostar import Database as IOSTAR
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,Crop(144,0,768,1024)
-                        ,Pad((30,0,30,0))
-                        ,Resize(1168)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = IOSTAR(protocol='default_vessel')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/iostarvessel960all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.iostar import Database as IOSTAR
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        Resize(960)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,RandomRotation()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = IOSTAR(protocol='default_vessel')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/stare1024all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.stare import Database as STARE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,Pad((0,32,0,32))
-                        ,Resize(1024)
-                        ,CenterCrop(1024)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = STARE(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/stare1168all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.stare import Database as STARE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,Crop(50,0,500,705)
-                        ,Resize(1168)
-                        ,Pad((1,0,1,0))
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = STARE(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/configs/datasets/stare960all.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from bob.db.stare import Database as STARE
-from bob.ip.binseg.data.transforms import *
-from bob.ip.binseg.data.binsegdataset import BinSegDataset
-import torch
-
-#### Config ####
-
-transforms = Compose([  
-                        RandomRotation()
-                        ,Pad((0,32,0,32))
-                        ,Resize(960)
-                        ,CenterCrop(960)
-                        ,RandomHFlip()
-                        ,RandomVFlip()
-                        ,ColorJitter()
-                        ,ToTensor()
-                    ])
-
-# bob.db.dataset init
-bobdb = STARE(protocol = 'default')
-
-# PyTorch dataset
-train = BinSegDataset(bobdb, split='train', transform=transforms)
-test = BinSegDataset(bobdb, split='test', transform=transforms)
-
-dataset = torch.utils.data.ConcatDataset([train,test])
\ No newline at end of file

bob/ip/binseg/script/binseg.py

@@ -240,70 +240,6 @@ def test(model
     do_inference(model, data_loader, device, output_path)
 
 
-# Inference all checkpoints
-@binseg.command(entry_point_group='bob.ip.binseg.config', cls=ConfigCommand)
-@click.option(
-    '--output-path',
-    '-o',
-    required=True,
-    default="output",
-    cls=ResourceOption
-    )
-@click.option(
-    '--model',
-    '-m',
-    required=True,
-    cls=ResourceOption
-    )
-@click.option(
-    '--dataset',
-    '-d',
-    required=True,
-    cls=ResourceOption
-    )
-@click.option(
-    '--batch-size',
-    '-b',
-    required=True,
-    default=2,
-    cls=ResourceOption)
-@click.option(
-    '--device',
-    '-d',
-    help='A string indicating the device to use (e.g. "cpu" or "cuda:0"',
-    show_default=True,
-    required=True,
-    default='cpu',
-    cls=ResourceOption)
-@verbosity_option(cls=ResourceOption)
-def testcheckpoints(model
-        ,output_path
-        ,device
-        ,batch_size
-        ,dataset
-        , **kwargs):
-
-    """ Run inference and evaluate all checkpoints saved for a model"""
-    # PyTorch dataloader
-    data_loader = DataLoader(
-        dataset = dataset
-        ,batch_size = batch_size
-        ,shuffle= False
-        ,pin_memory = torch.cuda.is_available()
-        )
-    
-    # list checkpoints
-    ckpts = glob.glob(os.path.join(output_path,"*.pth"))
-    # output
-    for checkpoint in ckpts:
-        ckpts_name = os.path.basename(checkpoint).split('.')[0]
-        logger.info("Testing checkpoint: {}".format(ckpts_name))
-        output_subfolder = os.path.join(output_path, ckpts_name)
-        if not os.path.exists(output_subfolder): os.makedirs(output_subfolder)
-        # checkpointer, load last model in dir
-        checkpointer = DetectronCheckpointer(model, save_dir = output_subfolder, save_to_disk=False)
-        checkpointer.load(checkpoint)
-        do_inference(model, data_loader, device, output_subfolder)
 
 # Plot comparison
 @binseg.command(entry_point_group='bob.ip.binseg.config', cls=ConfigCommand)

setup.py

@@ -49,8 +49,6 @@ setup(
           'train = bob.ip.binseg.script.binseg:train',
           'test = bob.ip.binseg.script.binseg:test',
           'compare =  bob.bin.binseg.script.binseg:compare',
-          'testcheckpoints = bob.ip.binseg.script.binseg:testcheckpoints',
-          'pdfoverview = bob.ip.binseg.script.binseg:testcheckpoints',
           'gridtable = bob.ip.binseg.script.binseg:testcheckpoints',
           'visualize = bob.ip.binseg.script.binseg:visualize',
         ],