From aa4cae89ada08370a3a82105ce2f6ae828e7372c Mon Sep 17 00:00:00 2001
From: Manuel Paez <79882298+mannypaeza@users.noreply.github.com>
Date: Thu, 23 Feb 2023 14:22:15 -0500
Subject: [PATCH 01/14] Add files via upload

---
 examples/config.yaml | 62 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 examples/config.yaml

diff --git a/examples/config.yaml b/examples/config.yaml
new file mode 100644
index 0000000..5b010d5
--- /dev/null
+++ b/examples/config.yaml
@@ -0,0 +1,62 @@
+system:
+  cpus: 1
+  gpus: 1
+  seed: 1
+  
+dataset:
+  training:
+    s3vol01700:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_01700/img.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_01700/label_v3.h5"
+    s3vol02299:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_02299/img.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_02299/label_v3.h5"
+    s3vol02400:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_02400/img_zyx_2400-2656_5700-5956_2770-3026.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_02400/label_v1_diane.h5"
+    # s3vol02684:
+    # images: ["~/dropbox/40_gt/13_wasp_sample3/vol_02284/img_zyx_2400-2656_5700-5956_2770-3026.h5",]
+    #  label: "~/dropbox/40_gt/13_wasp_sample3/vol_0684/label_v1_diane.h5"
+    s3vol02794:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_02794/img_zyx_2794-3050_5811-6067_8757-9013.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_02794/seg_v1_cropped.h5"
+    s3vol03290:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_03290/img_zyx_3290-3546_2375-2631_8450-8706.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_03290/label_v1.h5"
+    s3vol03700:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_03700/img_zyx_3700-3956_5000-5256_4250-4506.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_03700/label_v3.h5"
+    s3vol03998:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_03998/img.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_03998/label_v1.h5"
+    s3vol04900:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_04900/img.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_04900/label_v1.h5"
+    s3vol05250:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_05250/img_zyx_5250-5506_4600-4856_5500-5756.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_05250/label_v3_remove_contact.h5"
+    s3vol05450:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_05450/img_zyx_5450-5706_5350-5606_7000-7256.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_05450/label_v4_chiyip.h5"
+  validation:
+    s3vol04000:
+      images: ["~/dropbox/40_gt/13_wasp_sample3/vol_04000/img_zyx_4000-4256_3400-3656_8150-8406.h5",]
+      label: "~/dropbox/40_gt/13_wasp_sample3/vol_04000/label_v3.h5"
+model:
+  in_channels: 1
+  out_channels: 3
+
+train:
+  iter_start: 0
+  iter_stop: 1000000
+  class_rebalance: false
+  # batch size per GPU
+  # The dataprovider should provide nGPU*batch_size batches!
+  batch_size: 1
+  output_dir: "./"
+  patch_size: [128, 128, 128]
+  learning_rate: 0.001
+    #training_interval: 200
+    #validation_interval: 2000
+  training_interval: 2
+  validation_interval: 4
\ No newline at end of file

From c8076850f6b28dd6201ba447c44a2bdfda79198d Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Mon, 27 Feb 2023 19:52:59 -0500
Subject: [PATCH 02/14] boundary augmentation

---
 neutorch/train/affinity_map.py |  3 ++-
 neutorch/train/boundary_aug.py | 36 ++++++++++++++++++++++++++++++++++
 setup.py                       |  1 +
 3 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 neutorch/train/boundary_aug.py

diff --git a/neutorch/train/affinity_map.py b/neutorch/train/affinity_map.py
index b2a9daf..54b22e9 100644
--- a/neutorch/train/affinity_map.py
+++ b/neutorch/train/affinity_map.py
@@ -3,9 +3,10 @@
 import click
 from yacs.config import CfgNode
 
-from .base import TrainerBase
 from neutorch.data.dataset import AffinityMapDataset
 
+from .base import TrainerBase
+
 
 class AffinityMapTrainer(TrainerBase):
     def __init__(self, cfg: CfgNode) -> None:
diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
new file mode 100644
index 0000000..b8a552d
--- /dev/null
+++ b/neutorch/train/boundary_aug.py
@@ -0,0 +1,36 @@
+from functools import cached_property
+
+import click
+from yacs.config import CfgNode
+
+from neutorch.data.dataset import AffinityMapDataset
+
+from .base import TrainerBase
+
+
+class BoundaryAugTrainer(TrainerBase):
+    def __init__(self, cfg: CfgNode) -> None:
+        assert isinstance(cfg, CfgNode)
+        super().__init__(cfg)
+        self.cfg = cfg
+        breakpoint()
+
+    @cached_property
+    def training_dataset(self):
+        return AffinityMapDataset.from_config(self.cfg, is_train=True)
+       
+    @cached_property
+    def validation_dataset(self):
+        return AffinityMapDataset.from_config(self.cfg, is_train=False)
+
+@click.command()
+@click.option('--config-file', '-c',
+    type=click.Path(exists=True, dir_okay=False, file_okay=True, readable=True, resolve_path=True), 
+    default='./config.yaml', 
+    help = 'configuration file containing all the parameters.'
+)
+def main(config_file: str):
+    from neutorch.data.dataset import load_cfg
+    cfg = load_cfg(config_file)
+    trainer = BoundaryAugTrainer(cfg)
+    trainer()
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 4e9aff2..070a46a 100755
--- a/setup.py
+++ b/setup.py
@@ -18,6 +18,7 @@
         neutrain-denoise=neutorch.train.denoise:main
         neutrain-post=neutorch.train.post_synapses:main
         neutrain-affs=neutorch.train.affinity_map:main
+        neutrain-ba=neutorch.train.boundary_aug:main
     ''',
     classifiers=[
         'Development Status :: 4 - Beta',

From 0754d9cda152b22df6f007a88ad6652684838f75 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Mon, 13 Mar 2023 14:26:47 -0400
Subject: [PATCH 03/14] commented reneu

---
 neutorch/data/dataset.py   | 38 +++++++++++++++++++++++++++++++++-----
 neutorch/data/transform.py | 19 ++++++++++---------
 2 files changed, 43 insertions(+), 14 deletions(-)

diff --git a/neutorch/data/dataset.py b/neutorch/data/dataset.py
index a2883a9..389c0b9 100644
--- a/neutorch/data/dataset.py
+++ b/neutorch/data/dataset.py
@@ -1,15 +1,14 @@
+import math
 import random
 from functools import cached_property
-import math
 
 import numpy as np
 import torch
-from yacs.config import CfgNode
-
 from chunkflow.lib.cartesian_coordinate import Cartesian
+from yacs.config import CfgNode
 
-from neutorch.data.transform import *
 from neutorch.data.sample import SemanticSample
+from neutorch.data.transform import *
 
 DEFAULT_PATCH_SIZE = Cartesian(128, 128, 128)
 
@@ -273,6 +272,34 @@ def transform(self):
             Label2AffinityMap(probability=1.),
         ])
 
+class BoundaryAugmentationDataset(SemanticDataset):
+    def __initi__(self, samples: list):
+        super.__init__(samples)
+
+    @cached_property
+    def transform(self):
+        return Compose([
+            NormalizeTo01(probability=1.),
+            AdjustBrightness(),
+            AdjustContrast(),
+            Gamma(),
+            OneOf([
+                Noise(),
+                GaussianBlur2D(),
+            ]),
+            MaskBox(),
+            Perspective2D(),
+            # RotateScale(probability=1.),
+            # DropSection(),
+            Flip(),
+            Transpose(),
+            MissAlignment(),
+            # Tranform to affinity map
+            # there is a shrinking, so we put this transformation here
+            # rather than the label2target function.
+            Label2AffinityMap(probability=1.),
+        ])
+
 if __name__ == '__main__':
 
     from yacs.config import CfgNode
@@ -288,4 +315,5 @@ def transform(self):
         patch_size=Cartesian(128, 128, 128),
     )
     
-    # print(sd.samples)
\ No newline at end of file
+    # print(sd.samples)
+    
\ No newline at end of file
diff --git a/neutorch/data/transform.py b/neutorch/data/transform.py
index 945c275..c88a5a7 100644
--- a/neutorch/data/transform.py
+++ b/neutorch/data/transform.py
@@ -1,24 +1,25 @@
-from abc import ABC, abstractmethod
 import random
+from abc import ABC, abstractmethod
 from functools import cached_property
 
-
+import cv2
+import numpy as np
 from chunkflow.lib.cartesian_coordinate import Cartesian
+# from reneu.lib.segmentation import seg_to_affs
+from scipy.ndimage.filters import gaussian_filter
+from skimage.transform import swirl
+from skimage.util import random_noise
+
+from .patch import Patch
+
 # from copy import deepcopy
 
-import numpy as np
 
-from scipy.ndimage.filters import gaussian_filter
 # from scipy.ndimage import affine_transform
 
-import cv2
 
-from skimage.util import random_noise
-from skimage.transform import swirl
 
-from reneu.lib.segmentation import seg_to_affs
 
-from .patch import Patch
 
 
 DEFAULT_PROBABILITY = .5

From 4a8f876216ef611dda5d7641c9733b5de4c30493 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Mon, 13 Mar 2023 14:29:46 -0400
Subject: [PATCH 04/14] commentted reneu

---
 neutorch/data/transform.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/neutorch/data/transform.py b/neutorch/data/transform.py
index c88a5a7..3caa248 100644
--- a/neutorch/data/transform.py
+++ b/neutorch/data/transform.py
@@ -17,11 +17,6 @@
 
 # from scipy.ndimage import affine_transform
 
-
-
-
-
-
 DEFAULT_PROBABILITY = .5
 DEFAULT_SHRINK_SIZE = (0, 0, 0, 0, 0, 0)
 

From 5d659a58e7cce8ec854b934a7940f41baded6c04 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Mon, 13 Mar 2023 14:59:39 -0400
Subject: [PATCH 05/14] added

---
 examples/config.yaml           |  2 +-
 neutorch/data/patch.py         |  3 ++-
 neutorch/train/boundary_aug.py | 15 +++++++++++----
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/examples/config.yaml b/examples/config.yaml
index 5b010d5..e4259d0 100644
--- a/examples/config.yaml
+++ b/examples/config.yaml
@@ -43,7 +43,7 @@ dataset:
       images: ["~/dropbox/40_gt/13_wasp_sample3/vol_04000/img_zyx_4000-4256_3400-3656_8150-8406.h5",]
       label: "~/dropbox/40_gt/13_wasp_sample3/vol_04000/label_v3.h5"
 model:
-  in_channels: 1
+  in_channels: 3
   out_channels: 3
 
 train:
diff --git a/neutorch/data/patch.py b/neutorch/data/patch.py
index 1d3554f..8d6c829 100644
--- a/neutorch/data/patch.py
+++ b/neutorch/data/patch.py
@@ -1,8 +1,9 @@
 from functools import cached_property
-import numpy as np
 
+import numpy as np
 # from torch import tensor, device
 import torch
+
 # torch.multiprocessing.set_start_method('spawn')
 
 # from chunkflow.lib.cartesian_coordinate import Cartesian
diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
index b8a552d..a41fb2a 100644
--- a/neutorch/train/boundary_aug.py
+++ b/neutorch/train/boundary_aug.py
@@ -1,9 +1,11 @@
 from functools import cached_property
 
 import click
+import numpy as np
+import tensorflow as tf
 from yacs.config import CfgNode
 
-from neutorch.data.dataset import AffinityMapDataset
+from neutorch.data.dataset import BoundaryAugmentationDataset
 
 from .base import TrainerBase
 
@@ -17,11 +19,11 @@ def __init__(self, cfg: CfgNode) -> None:
 
     @cached_property
     def training_dataset(self):
-        return AffinityMapDataset.from_config(self.cfg, is_train=True)
+        return BoundaryAugmentationDataset.from_config(self.cfg, is_train=True)
        
     @cached_property
     def validation_dataset(self):
-        return AffinityMapDataset.from_config(self.cfg, is_train=False)
+        return BoundaryAugmentationDataset.from_config(self.cfg, is_train=False)
 
 @click.command()
 @click.option('--config-file', '-c',
@@ -29,8 +31,13 @@ def validation_dataset(self):
     default='./config.yaml', 
     help = 'configuration file containing all the parameters.'
 )
+
 def main(config_file: str):
     from neutorch.data.dataset import load_cfg
     cfg = load_cfg(config_file)
     trainer = BoundaryAugTrainer(cfg)
-    trainer()
\ No newline at end of file
+    trainer()
+
+    #Tensorboard configuration
+    #maybe not
+

From eb6da3ff094ea72162ebba400b7e1463c22e279c Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Mon, 13 Mar 2023 16:00:57 -0400
Subject: [PATCH 06/14] stuff

---
 neutorch/train/boundary_aug.py | 1 -
 requirements.txt               | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
index a41fb2a..4285ed6 100644
--- a/neutorch/train/boundary_aug.py
+++ b/neutorch/train/boundary_aug.py
@@ -2,7 +2,6 @@
 
 import click
 import numpy as np
-import tensorflow as tf
 from yacs.config import CfgNode
 
 from neutorch.data.dataset import BoundaryAugmentationDataset
diff --git a/requirements.txt b/requirements.txt
index 3269f25..bb52fe1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,6 +2,7 @@ torch
 torchvision
 yacs
 h5py
+tensorflow
 tensorboard
 opencv-python
 scikit-image

From dfb2500c5b1bf380e4e1bf55993a82ce343fb638 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Mon, 13 Mar 2023 16:11:03 -0400
Subject: [PATCH 07/14] made change

---
 neutorch/train/base.py | 21 +++++++++------------
 requirements.txt       |  1 -
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/neutorch/train/base.py b/neutorch/train/base.py
index cbae7a8..bad344c 100644
--- a/neutorch/train/base.py
+++ b/neutorch/train/base.py
@@ -1,25 +1,22 @@
+import os
+import random
 from abc import ABC, abstractproperty
 from functools import cached_property
 from glob import glob
-
-import random
-import os
 from time import time
 
-from yacs.config import CfgNode
 import numpy as np
-
-from chunkflow.lib.cartesian_coordinate import Cartesian
-
 import torch
-from torch.utils.tensorboard import SummaryWriter
+from chunkflow.lib.cartesian_coordinate import Cartesian
 from torch.utils.data import DataLoader
-from neutorch.data.patch import collate_batch
+from torch.utils.tensorboard import SummaryWriter
+from yacs.config import CfgNode
 
-from neutorch.model.IsoRSUNet import Model
-from neutorch.model.io import save_chkpt, load_chkpt, log_tensor
-from neutorch.loss import BinomialCrossEntropyWithLogits
 from neutorch.data.dataset import worker_init_fn
+from neutorch.data.patch import collate_batch
+from neutorch.loss import BinomialCrossEntropyWithLogits
+from neutorch.model.io import load_chkpt, log_tensor, save_chkpt
+from neutorch.model.IsoRSUNet import Model
 
 
 class TrainerBase(ABC):
diff --git a/requirements.txt b/requirements.txt
index bb52fe1..3269f25 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,7 +2,6 @@ torch
 torchvision
 yacs
 h5py
-tensorflow
 tensorboard
 opencv-python
 scikit-image

From f59b2faa09ab880f24b422cbcb6aab715ebc69a2 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Tue, 14 Mar 2023 11:40:37 -0400
Subject: [PATCH 08/14] tensorboard

---
 neutorch/data/dataset.py       |  4 +-
 neutorch/train/boundary_aug.py | 72 +++++++++++++++++++++++++++++++++-
 2 files changed, 73 insertions(+), 3 deletions(-)

diff --git a/neutorch/data/dataset.py b/neutorch/data/dataset.py
index 389c0b9..ea2859e 100644
--- a/neutorch/data/dataset.py
+++ b/neutorch/data/dataset.py
@@ -272,7 +272,7 @@ def transform(self):
             Label2AffinityMap(probability=1.),
         ])
 
-class BoundaryAugmentationDataset(SemanticDataset):
+class BoundaryAugmentationDataset(SemanticDataset): #for now
     def __initi__(self, samples: list):
         super.__init__(samples)
 
@@ -309,7 +309,7 @@ def transform(self):
         cfg = CfgNode.load_cfg(file)
     cfg.freeze()
 
-    sd = AffinityMapDataset(
+    sd = BoundaryAugmentationDataset(
         path_list=['/mnt/ceph/users/neuro/wasp_em/jwu/40_gt/13_wasp_sample3/vol_01700/rna_v1.h5'],
         sample_name_to_image_versions=cfg.dataset.sample_name_to_image_versions,
         patch_size=Cartesian(128, 128, 128),
diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
index 4285ed6..87e30a8 100644
--- a/neutorch/train/boundary_aug.py
+++ b/neutorch/train/boundary_aug.py
@@ -2,14 +2,18 @@
 
 import click
 import numpy as np
+import torch
 from yacs.config import CfgNode
 
+from torch.utils.tensorboard import SummaryWriter
+from .base import SemanticTrainer
 from neutorch.data.dataset import BoundaryAugmentationDataset
 
+from neutorch.model.io import log_tensor
 from .base import TrainerBase
 
 
-class BoundaryAugTrainer(TrainerBase):
+class BoundaryAugTrainer(SemanticTrainer):
     def __init__(self, cfg: CfgNode) -> None:
         assert isinstance(cfg, CfgNode)
         super().__init__(cfg)
@@ -24,6 +28,72 @@ def training_dataset(self):
     def validation_dataset(self):
         return BoundaryAugmentationDataset.from_config(self.cfg, is_train=False)
 
+    # def label_to_target(self, label: torch.Tensor):
+    #    return (label > 0).float
+
+"""
+    @catch_property
+    def loss(self):
+    #loss module for the training 
+"""
+"""
+    def call(self):
+        writer = SummaryWriter(log_dir=self.cfg.train.output_dir) 
+        accumulated_loss = 0. #floating point
+
+        for image, label in self.training_data_loader:
+            itder_idx += 1
+            if iter_idx> self.cfg.train.iter_stop:
+                print('exeeds maximum iteration:', self.cfg.train.iter_stop)
+                return
+            
+            pint = time()
+            predict = self.model(image)
+            loss = self.loss_module(predict, label)
+            assert not torch.isnan(loss), 'loss is NaN.'
+
+            self.optimizer #fix
+            loss.backward()
+            self.optimizer.step()
+            accumulated_loss += loss.tolist()
+
+            if iter_idx % self.cfg.train.training_interval == 0 and iter_idx > 0:
+                per_voxel_loss = accumulated_loss / \
+                    self.cfg.train.training_interval / \
+                    self.voxel_num
+
+                print(f'iteration {iter_idx} takes {round(time()-ping, 3)} seconds with loss: {per_voxel_loss}')
+                #print(f'training loss {round(per_voxel_loss, 3)}')
+                accumulated_loss = 0.
+                predict = self.post_processing(predict)
+                writer.add_scalar('loss/train', per_voxel_loss, iter_idx)
+                log_tensor(writer, 'train/image', image, 'image', iter_idx)
+                log_tensor(writer, 'train/prediction', predict.detach(), 'image', iter_idx)
+                log_tensor(writer, 'train/label', label, 'segmentation', iter_idx)
+
+            if iter_idx % self.cfg.train.validation_interval == 0 and iter_idx > 0:
+                fname = os.path.join(self.cfg.train.output_dir, f'model_{iter_idx}.chkpt')
+                print(f'save model to {fname}')
+                save_chkpt(self.model, self.cfg.train.output_dir, iter_idx, self.optimizer)
+
+                print('evaluate prediction: ')
+                validation_image, validation_label = next(self.validation_data_iter)
+
+                with torch.no_grad():
+                    validation_predict = self.model(validation_image)
+                    validation_loss = self.loss_module(validation_predict, validation_label)
+                    validation_predict = self.post_processing(validation_predict)
+                    per_voxel_loss = validation_loss.tolist() / self.voxel_num
+                    print(f'iteration {iter_idx} takes {round(time()-ping, 3)} seconds with loss: {per_voxel_loss}')
+                    # print(f'iter {iter_idx}: validation loss: {round(per_voxel_loss, 3)}')
+                    writer.add_scalar('loss/validation', per_voxel_loss, iter_idx)
+                    log_tensor(writer, 'validation/image', validation_image, 'image', iter_idx)
+                    log_tensor(writer, 'validation/prediction', validation_predict, 'image', iter_idx)
+                    log_tensor(writer, 'validation/label', validation_label, 'segmentation', iter_idx)
+
+        writer.close()
+"""
+
 @click.command()
 @click.option('--config-file', '-c',
     type=click.Path(exists=True, dir_okay=False, file_okay=True, readable=True, resolve_path=True), 

From 11a2e15aa39797a4bcb3eafeb890f48a33576fd5 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Tue, 14 Mar 2023 12:27:16 -0400
Subject: [PATCH 09/14] here

---
 neutorch/train/boundary_aug.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
index 87e30a8..60e8aef 100644
--- a/neutorch/train/boundary_aug.py
+++ b/neutorch/train/boundary_aug.py
@@ -3,14 +3,13 @@
 import click
 import numpy as np
 import torch
+from torch.utils.tensorboard import SummaryWriter
 from yacs.config import CfgNode
 
-from torch.utils.tensorboard import SummaryWriter
-from .base import SemanticTrainer
 from neutorch.data.dataset import BoundaryAugmentationDataset
-
 from neutorch.model.io import log_tensor
-from .base import TrainerBase
+
+from .base import SemanticTrainer, TrainerBase
 
 
 class BoundaryAugTrainer(SemanticTrainer):

From b96d84cb96a27ad64eeb08ce847b4e4c96f69c1b Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Tue, 21 Mar 2023 13:33:04 -0400
Subject: [PATCH 10/14] changes

---
 neutorch/data/dataset.py       | 16 +++++++---------
 neutorch/data/sample.py        |  7 ++++++-
 neutorch/train/boundary_aug.py | 27 ++++++++++-----------------
 3 files changed, 23 insertions(+), 27 deletions(-)

diff --git a/neutorch/data/dataset.py b/neutorch/data/dataset.py
index ea2859e..4a553cb 100644
--- a/neutorch/data/dataset.py
+++ b/neutorch/data/dataset.py
@@ -266,12 +266,10 @@ def transform(self):
             Flip(),
             Transpose(),
             MissAlignment(),
-            # Tranform to affinity map
-            # there is a shrinking, so we put this transformation here
-            # rather than the label2target function.
             Label2AffinityMap(probability=1.),
         ])
 
+
 class BoundaryAugmentationDataset(SemanticDataset): #for now
     def __initi__(self, samples: list):
         super.__init__(samples)
@@ -294,11 +292,13 @@ def transform(self):
             Flip(),
             Transpose(),
             MissAlignment(),
-            # Tranform to affinity map
-            # there is a shrinking, so we put this transformation here
-            # rather than the label2target function.
-            Label2AffinityMap(probability=1.),
+            # Label2AffinityMap(probability=1.),
         ])
+    
+    """ binarization of the dataset
+    
+    
+    """
 
 if __name__ == '__main__':
 
@@ -314,6 +314,4 @@ def transform(self):
         sample_name_to_image_versions=cfg.dataset.sample_name_to_image_versions,
         patch_size=Cartesian(128, 128, 128),
     )
-    
-    # print(sd.samples)
     
\ No newline at end of file
diff --git a/neutorch/data/sample.py b/neutorch/data/sample.py
index 00692b4..3e11835 100644
--- a/neutorch/data/sample.py
+++ b/neutorch/data/sample.py
@@ -7,7 +7,12 @@
 
 from chunkflow.lib.cartesian_coordinate import BoundingBox, Cartesian 
 from chunkflow.chunk import Chunk
-from chunkflow.chunk.utils import load_chunk_or_volume
+try:
+    import chunkflow.chunk.utils
+    has_chunkflowchunkutils = True
+except ImportError:
+    has_chunkflowchunkutils = False
+
 from chunkflow.lib.synapses import Synapses
 
 from neutorch.data.patch import Patch
diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
index 60e8aef..dfc81a6 100644
--- a/neutorch/train/boundary_aug.py
+++ b/neutorch/train/boundary_aug.py
@@ -5,9 +5,10 @@
 import torch
 from torch.utils.tensorboard import SummaryWriter
 from yacs.config import CfgNode
+from time import time
 
 from neutorch.data.dataset import BoundaryAugmentationDataset
-from neutorch.model.io import log_tensor
+from neutorch.model.io import save_chkpt, log_tensor
 
 from .base import SemanticTrainer, TrainerBase
 
@@ -27,22 +28,17 @@ def training_dataset(self):
     def validation_dataset(self):
         return BoundaryAugmentationDataset.from_config(self.cfg, is_train=False)
 
-    # def label_to_target(self, label: torch.Tensor):
-    #    return (label > 0).float
+    """ -> binarization/skeletonization
+    def label_to_target(self, label: torch.Tensor):
+        return (label > 0).float
 
-"""
-    @catch_property
-    def loss(self):
-    #loss module for the training 
-"""
-"""
     def call(self):
         writer = SummaryWriter(log_dir=self.cfg.train.output_dir) 
         accumulated_loss = 0. #floating point
 
         for image, label in self.training_data_loader:
-            itder_idx += 1
-            if iter_idx> self.cfg.train.iter_stop:
+            iter_idx += 1
+            if iter_idx > self.cfg.train.iter_stop:
                 print('exeeds maximum iteration:', self.cfg.train.iter_stop)
                 return
             
@@ -51,18 +47,18 @@ def call(self):
             loss = self.loss_module(predict, label)
             assert not torch.isnan(loss), 'loss is NaN.'
 
-            self.optimizer #fix
+            self.optimizer #
             loss.backward()
             self.optimizer.step()
             accumulated_loss += loss.tolist()
 
+            #fix
             if iter_idx % self.cfg.train.training_interval == 0 and iter_idx > 0:
                 per_voxel_loss = accumulated_loss / \
                     self.cfg.train.training_interval / \
                     self.voxel_num
 
                 print(f'iteration {iter_idx} takes {round(time()-ping, 3)} seconds with loss: {per_voxel_loss}')
-                #print(f'training loss {round(per_voxel_loss, 3)}')
                 accumulated_loss = 0.
                 predict = self.post_processing(predict)
                 writer.add_scalar('loss/train', per_voxel_loss, iter_idx)
@@ -84,14 +80,13 @@ def call(self):
                     validation_predict = self.post_processing(validation_predict)
                     per_voxel_loss = validation_loss.tolist() / self.voxel_num
                     print(f'iteration {iter_idx} takes {round(time()-ping, 3)} seconds with loss: {per_voxel_loss}')
-                    # print(f'iter {iter_idx}: validation loss: {round(per_voxel_loss, 3)}')
                     writer.add_scalar('loss/validation', per_voxel_loss, iter_idx)
                     log_tensor(writer, 'validation/image', validation_image, 'image', iter_idx)
                     log_tensor(writer, 'validation/prediction', validation_predict, 'image', iter_idx)
                     log_tensor(writer, 'validation/label', validation_label, 'segmentation', iter_idx)
 
         writer.close()
-"""
+    """
 
 @click.command()
 @click.option('--config-file', '-c',
@@ -106,6 +101,4 @@ def main(config_file: str):
     trainer = BoundaryAugTrainer(cfg)
     trainer()
 
-    #Tensorboard configuration
-    #maybe not
 

From 9831eadb8a37972bcd2d4b7f64d0cf41a3235dc6 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Tue, 21 Mar 2023 14:05:07 -0400
Subject: [PATCH 11/14] changes

---
 neutorch/data/dataset.py       |  7 -------
 neutorch/data/sample.py        |  1 +
 neutorch/train/boundary_aug.py | 11 +++--------
 3 files changed, 4 insertions(+), 15 deletions(-)

diff --git a/neutorch/data/dataset.py b/neutorch/data/dataset.py
index 4a553cb..6f81900 100644
--- a/neutorch/data/dataset.py
+++ b/neutorch/data/dataset.py
@@ -245,7 +245,6 @@ def __next__(self):
 
 class AffinityMapDataset(SemanticDataset):
     def __init__(self, samples: list):
-            #patch_size: Cartesian = DEFAULT_PATCH_SIZE):
         super().__init__(samples)
     
     @cached_property
@@ -292,13 +291,7 @@ def transform(self):
             Flip(),
             Transpose(),
             MissAlignment(),
-            # Label2AffinityMap(probability=1.),
         ])
-    
-    """ binarization of the dataset
-    
-    
-    """
 
 if __name__ == '__main__':
 
diff --git a/neutorch/data/sample.py b/neutorch/data/sample.py
index 3e11835..40c09ca 100644
--- a/neutorch/data/sample.py
+++ b/neutorch/data/sample.py
@@ -7,6 +7,7 @@
 
 from chunkflow.lib.cartesian_coordinate import BoundingBox, Cartesian 
 from chunkflow.chunk import Chunk
+
 try:
     import chunkflow.chunk.utils
     has_chunkflowchunkutils = True
diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
index dfc81a6..27764be 100644
--- a/neutorch/train/boundary_aug.py
+++ b/neutorch/train/boundary_aug.py
@@ -1,14 +1,15 @@
+import os
 from functools import cached_property
+from time import time
 
 import click
 import numpy as np
 import torch
 from torch.utils.tensorboard import SummaryWriter
 from yacs.config import CfgNode
-from time import time
 
 from neutorch.data.dataset import BoundaryAugmentationDataset
-from neutorch.model.io import save_chkpt, log_tensor
+from neutorch.model.io import log_tensor, save_chkpt
 
 from .base import SemanticTrainer, TrainerBase
 
@@ -28,10 +29,6 @@ def training_dataset(self):
     def validation_dataset(self):
         return BoundaryAugmentationDataset.from_config(self.cfg, is_train=False)
 
-    """ -> binarization/skeletonization
-    def label_to_target(self, label: torch.Tensor):
-        return (label > 0).float
-
     def call(self):
         writer = SummaryWriter(log_dir=self.cfg.train.output_dir) 
         accumulated_loss = 0. #floating point
@@ -52,7 +49,6 @@ def call(self):
             self.optimizer.step()
             accumulated_loss += loss.tolist()
 
-            #fix
             if iter_idx % self.cfg.train.training_interval == 0 and iter_idx > 0:
                 per_voxel_loss = accumulated_loss / \
                     self.cfg.train.training_interval / \
@@ -86,7 +82,6 @@ def call(self):
                     log_tensor(writer, 'validation/label', validation_label, 'segmentation', iter_idx)
 
         writer.close()
-    """
 
 @click.command()
 @click.option('--config-file', '-c',

From 4687fe258be332bd9550a008efb903d847954156 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Tue, 21 Mar 2023 14:17:11 -0400
Subject: [PATCH 12/14] change

---
 neutorch/data/sample.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/neutorch/data/sample.py b/neutorch/data/sample.py
index 40c09ca..3ba5614 100644
--- a/neutorch/data/sample.py
+++ b/neutorch/data/sample.py
@@ -8,12 +8,7 @@
 from chunkflow.lib.cartesian_coordinate import BoundingBox, Cartesian 
 from chunkflow.chunk import Chunk
 
-try:
-    import chunkflow.chunk.utils
-    has_chunkflowchunkutils = True
-except ImportError:
-    has_chunkflowchunkutils = False
-
+from chunkflow.chunk.utils import load_chunk_or_volume
 from chunkflow.lib.synapses import Synapses
 
 from neutorch.data.patch import Patch

From 0feb0b44ded7977a16ea579ea796dbdcc2b2cf1a Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Tue, 21 Mar 2023 14:21:22 -0400
Subject: [PATCH 13/14] yes

---
 neutorch/data/sample.py        | 1 -
 neutorch/train/boundary_aug.py | 3 ++-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/neutorch/data/sample.py b/neutorch/data/sample.py
index 3ba5614..00692b4 100644
--- a/neutorch/data/sample.py
+++ b/neutorch/data/sample.py
@@ -7,7 +7,6 @@
 
 from chunkflow.lib.cartesian_coordinate import BoundingBox, Cartesian 
 from chunkflow.chunk import Chunk
-
 from chunkflow.chunk.utils import load_chunk_or_volume
 from chunkflow.lib.synapses import Synapses
 
diff --git a/neutorch/train/boundary_aug.py b/neutorch/train/boundary_aug.py
index 27764be..76c8450 100644
--- a/neutorch/train/boundary_aug.py
+++ b/neutorch/train/boundary_aug.py
@@ -13,7 +13,6 @@
 
 from .base import SemanticTrainer, TrainerBase
 
-
 class BoundaryAugTrainer(SemanticTrainer):
     def __init__(self, cfg: CfgNode) -> None:
         assert isinstance(cfg, CfgNode)
@@ -29,6 +28,7 @@ def training_dataset(self):
     def validation_dataset(self):
         return BoundaryAugmentationDataset.from_config(self.cfg, is_train=False)
 
+    """
     def call(self):
         writer = SummaryWriter(log_dir=self.cfg.train.output_dir) 
         accumulated_loss = 0. #floating point
@@ -82,6 +82,7 @@ def call(self):
                     log_tensor(writer, 'validation/label', validation_label, 'segmentation', iter_idx)
 
         writer.close()
+    """
 
 @click.command()
 @click.option('--config-file', '-c',

From 56d2c69576b365ffc82ce6931bea9325ff986466 Mon Sep 17 00:00:00 2001
From: Manuel Paez <mannypaezjr@comcast.net>
Date: Tue, 21 Mar 2023 14:35:31 -0400
Subject: [PATCH 14/14] changes

---
 neutorch/data/dataset.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/neutorch/data/dataset.py b/neutorch/data/dataset.py
index 6f81900..0c3f795 100644
--- a/neutorch/data/dataset.py
+++ b/neutorch/data/dataset.py
@@ -268,8 +268,7 @@ def transform(self):
             Label2AffinityMap(probability=1.),
         ])
 
-
-class BoundaryAugmentationDataset(SemanticDataset): #for now
+class BoundaryAugmentationDataset(SemanticDataset): 
     def __initi__(self, samples: list):
         super.__init__(samples)