From ece832f6d3cd3f2582ea6fd37ecd2bf6d302205f Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 09:14:43 -0700
Subject: [PATCH 01/36] Add batch_c15n for [0,1] image input and
 imagenet-normalized input.

---
 mart/configs/batch_c15n/image_01.yaml           |  6 ++++++
 .../configs/batch_c15n/imagenet_normalized.yaml |  6 ++++++
 .../batch_c15n/transform/255_to_imagenet.yaml   |  4 ++++
 .../batch_c15n/transform/divided_by_255.yaml    |  3 +++
 .../batch_c15n/transform/imagenet_to_255.yaml   | 17 +++++++++++++++++
 .../transform/times_255_and_round.yaml          | 13 +++++++++++++
 6 files changed, 49 insertions(+)
 create mode 100644 mart/configs/batch_c15n/image_01.yaml
 create mode 100644 mart/configs/batch_c15n/imagenet_normalized.yaml
 create mode 100644 mart/configs/batch_c15n/transform/255_to_imagenet.yaml
 create mode 100644 mart/configs/batch_c15n/transform/divided_by_255.yaml
 create mode 100644 mart/configs/batch_c15n/transform/imagenet_to_255.yaml
 create mode 100644 mart/configs/batch_c15n/transform/times_255_and_round.yaml

diff --git a/mart/configs/batch_c15n/image_01.yaml b/mart/configs/batch_c15n/image_01.yaml
new file mode 100644
index 00000000..f3f8e758
--- /dev/null
+++ b/mart/configs/batch_c15n/image_01.yaml
@@ -0,0 +1,6 @@
+defaults:
+  - list
+  - transform: times_255_and_round
+  - transform@untransform: divided_by_255
+
+input_key: 0
diff --git a/mart/configs/batch_c15n/imagenet_normalized.yaml b/mart/configs/batch_c15n/imagenet_normalized.yaml
new file mode 100644
index 00000000..e41fb3ff
--- /dev/null
+++ b/mart/configs/batch_c15n/imagenet_normalized.yaml
@@ -0,0 +1,6 @@
+defaults:
+  - dict
+  - transform: imagenet_to_255
+  - transform@untransform: 255_to_imagenet
+
+input_key: image
diff --git a/mart/configs/batch_c15n/transform/255_to_imagenet.yaml b/mart/configs/batch_c15n/transform/255_to_imagenet.yaml
new file mode 100644
index 00000000..9bb9ebef
--- /dev/null
+++ b/mart/configs/batch_c15n/transform/255_to_imagenet.yaml
@@ -0,0 +1,4 @@
+_target_: torchvision.transforms.Normalize
+# from 0-1 scale statistics: mean=[0.485, 0.456, 0.406]*255 std=[0.229, 0.224, 0.225]*255
+mean: [123.6750, 116.2800, 103.5300]
+std: [58.3950, 57.1200, 57.3750]
diff --git a/mart/configs/batch_c15n/transform/divided_by_255.yaml b/mart/configs/batch_c15n/transform/divided_by_255.yaml
new file mode 100644
index 00000000..92a63b7c
--- /dev/null
+++ b/mart/configs/batch_c15n/transform/divided_by_255.yaml
@@ -0,0 +1,3 @@
+_target_: torchvision.transforms.Normalize
+mean: 0
+std: 255
diff --git a/mart/configs/batch_c15n/transform/imagenet_to_255.yaml b/mart/configs/batch_c15n/transform/imagenet_to_255.yaml
new file mode 100644
index 00000000..66a4ef53
--- /dev/null
+++ b/mart/configs/batch_c15n/transform/imagenet_to_255.yaml
@@ -0,0 +1,17 @@
+_target_: torchvision.transforms.Compose
+transforms:
+  - _target_: mart.transforms.Denormalize
+    # from 0-1 scale statistics: mean=[0.485, 0.456, 0.406]*255 std=[0.229, 0.224, 0.225]*255
+    center:
+      _target_: torch.as_tensor
+      data: [123.6750, 116.2800, 103.5300]
+    scale:
+      _target_: torch.as_tensor
+      data: [58.3950, 57.1200, 57.3750]
+  - _target_: torch.fake_quantize_per_tensor_affine
+    _partial_: true
+    # (x/1+0).round().clamp(0, 255) * 1
+    scale: 1
+    zero_point: 0
+    quant_min: 0
+    quant_max: 255
diff --git a/mart/configs/batch_c15n/transform/times_255_and_round.yaml b/mart/configs/batch_c15n/transform/times_255_and_round.yaml
new file mode 100644
index 00000000..dbeff64d
--- /dev/null
+++ b/mart/configs/batch_c15n/transform/times_255_and_round.yaml
@@ -0,0 +1,13 @@
+_target_: torchvision.transforms.Compose
+transforms:
+  - _target_: mart.transforms.Denormalize
+    center: 0
+    scale: 255
+  # Fix potential numeric error.
+  - _target_: torch.fake_quantize_per_tensor_affine
+    _partial_: true
+    # (x/1+0).round().clamp(0, 255) * 1
+    scale: 1
+    zero_point: 0
+    quant_min: 0
+    quant_max: 255

From 726a0af0cc93120d7acf329cf841e49566d2b583 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 09:18:27 -0700
Subject: [PATCH 02/36] Turn off inference mode before creating perturbations.

---
 mart/attack/adversary.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/mart/attack/adversary.py b/mart/attack/adversary.py
index 9fbdec75..1555620b 100644
--- a/mart/attack/adversary.py
+++ b/mart/attack/adversary.py
@@ -151,6 +151,8 @@ def configure_gradient_clipping(
             for group in optimizer.param_groups:
                 self.gradient_modifier(group["params"])
 
+    # Turn off the inference mode, so we will create perturbation that requires gradient.
+    @torch.inference_mode(False)
     @silent()
     def fit(self, input, target, *, model: Callable):
         # The attack also needs access to the model at every iteration.

From b0c307970a07264a2125595d02c9b0b6256982e1 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 09:18:51 -0700
Subject: [PATCH 03/36] Switch to training mode before running
 LightningModule.training_step().

---
 mart/callbacks/adversary_connector.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/mart/callbacks/adversary_connector.py b/mart/callbacks/adversary_connector.py
index a35b225b..db8fe7b0 100644
--- a/mart/callbacks/adversary_connector.py
+++ b/mart/callbacks/adversary_connector.py
@@ -7,7 +7,7 @@
 from __future__ import annotations
 
 import types
-from typing import Callable
+from typing import Any, Callable
 
 from lightning.pytorch.callbacks import Callback
 
@@ -16,6 +16,20 @@
 __all__ = ["AdversaryConnector"]
 
 
+class training_mode:
+    """A context that switches a torch.nn.Module object to the training mode."""
+
+    def __init__(self, module):
+        self.module = module
+        self.training = self.module.training
+
+    def __enter__(self):
+        self.module.train(True)
+
+    def __exit__(self, exc_type: Any, exc_value: Any, traceback: Any):
+        self.module.train(self.training)
+
+
 class AdversaryConnector(Callback):
     """Perturbs inputs to be adversarial."""
 
@@ -81,7 +95,9 @@ def model(input, target):
                 # LightningModule must have "training_step".
                 # Disable logging if we have to reuse training_step() of the target model.
                 with MonkeyPatch(pl_module, "log", lambda *args, **kwargs: None):
-                    outputs = pl_module.training_step(batch, dataloader_idx)
+                    # Switch the model to the training mode so traing_step works as expected.
+                    with training_mode(pl_module):
+                        outputs = pl_module.training_step(batch, dataloader_idx)
             return outputs
 
         # Canonicalize the batch to work with Adversary.

From eba3c2bb6ca988ebc7f1ea9171a2f4f28238ee44 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 09:21:16 -0700
Subject: [PATCH 04/36] Add utils for config instantiation.

---
 mart/utils/config.py | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/mart/utils/config.py b/mart/utils/config.py
index 36dbb6e6..3a4268ad 100644
--- a/mart/utils/config.py
+++ b/mart/utils/config.py
@@ -8,14 +8,17 @@
 
 import os
 
+import hydra
 from hydra import compose as hydra_compose
 from hydra import initialize_config_dir
+from lightning.pytorch.callbacks.callback import Callback
+from omegaconf import OmegaConf
 
 DEFAULT_VERSION_BASE = "1.2"
 DEFAULT_CONFIG_DIR = "."
 DEFAULT_CONFIG_NAME = "lightning.yaml"
 
-__all__ = ["compose"]
+__all__ = ["compose", "instantiate", "Instantiator", "CallbackInstantiator"]
 
 
 def compose(
@@ -40,3 +43,28 @@ def compose(
             cfg = cfg[key]
 
     return cfg
+
+
+def instantiate(cfg_path):
+    """Instantiate an object from a Hydra yaml config file."""
+    config = OmegaConf.load(cfg_path)
+    obj = hydra.utils.instantiate(config)
+    return obj
+
+
+class Instantiator:
+    def __new__(cls, cfg_path):
+        return instantiate(cfg_path)
+
+
+class CallbackInstantiator(Callback):
+    """Type checking for Lightning Callback."""
+
+    def __new__(cls, cfg_path):
+        obj = instantiate(cfg_path)
+        if isinstance(obj, Callback):
+            return obj
+        else:
+            raise ValueError(
+                f"We expect to instantiate a lightning Callback from {cfg_path}, but we get {type(obj)} instead."
+            )

From dd10c795b4a7101796c1803dde21816c01f4de37 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 09:27:44 -0700
Subject: [PATCH 05/36] Add mart.utils.Get() to extract a value from kwargs
 dict.

---
 mart/utils/utils.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/mart/utils/utils.py b/mart/utils/utils.py
index f4a0a4ec..dbf3fb21 100644
--- a/mart/utils/utils.py
+++ b/mart/utils/utils.py
@@ -28,6 +28,7 @@
     "save_file",
     "task_wrapper",
     "flatten_dict",
+    "Get",
 ]
 
 log = pylogger.get_pylogger(__name__)
@@ -293,3 +294,13 @@ def get_dottedpath_items(d: dict, parent: Optional[str] = None):
         ret[key] = value
 
     return ret
+
+
+class Get:
+    """Get a value from the kwargs dictionary by key."""
+
+    def __init__(self, key):
+        self.key = key
+
+    def __call__(self, **kwargs):
+        return kwargs[self.key]

From 43d63f54adb0c596c80eb2a49d577b8430892485 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 09:35:55 -0700
Subject: [PATCH 06/36] Upgrade Lightning from 2.0 to 2.1.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6599ba3a..cce09539 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ requires-python = ">=3.9"
 dependencies = [
   "torch >= 2.0.1",
   "torchvision >= 0.15.2",
-  "lightning[extra] ~= 2.0.5", # Full functionality including TensorboardX.
+  "lightning[extra] ~= 2.1.4", # Full functionality including TensorboardX.
   "pydantic == 1.10.11", # https://github.com/Lightning-AI/lightning/pull/18022/files
   "torchmetrics == 1.0.1",
   "numpy == 1.23.5", # https://github.com/pytorch/pytorch/issues/91516

From f4f1f1aa89776d23eab6c042a5e6e1bd8fc8637c Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 11:18:51 -0700
Subject: [PATCH 07/36] Move most dependencies to optional groups.

---
 pyproject.toml | 45 ++++++++++++++++++++++++++-------------------
 1 file changed, 26 insertions(+), 19 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index cce09539..7703d776 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,32 +11,13 @@ authors = [
 requires-python = ">=3.9"
 
 dependencies = [
-  "torch >= 2.0.1",
-  "torchvision >= 0.15.2",
-  "lightning[extra] ~= 2.1.4", # Full functionality including TensorboardX.
-  "pydantic == 1.10.11", # https://github.com/Lightning-AI/lightning/pull/18022/files
-  "torchmetrics == 1.0.1",
-  "numpy == 1.23.5", # https://github.com/pytorch/pytorch/issues/91516
-
   # --------- hydra --------- #
   "hydra-core ~= 1.2.0",
   "hydra-colorlog ~= 1.2.0",
   "hydra-optuna-sweeper ~= 1.2.0",
 
-  # --------- loggers --------- #
-  # wandb
-  # neptune-client
-  # mlflow
-  # comet-ml
-
   # --------- others --------- #
   "pyrootutils ~= 1.0.4",      # standardizing the project root setup
-  "rich ~= 12.6.0",            # beautiful text formatting in terminal
-  "timm ~= 0.6.11",            # pytorch image models
-
-  # ----- object detection----- #
-  "pycocotools ~= 2.0.5",
-
   "fire == 0.5.0",
 ]
 
@@ -47,6 +28,31 @@ Source = "https://github.com/IntelLabs/MART"
 mart = "mart.__main__:main"
 
 [project.optional-dependencies]
+core = [
+  "torch >= 2.0.1",
+  "torchvision >= 0.15.2",
+  "lightning[extra] ~= 2.1.4", # Full functionality including TensorboardX.
+  "pydantic == 1.10.11", # https://github.com/Lightning-AI/lightning/pull/18022/files
+  "torchmetrics >= 1.3.2",
+  "numpy == 1.23.5", # https://github.com/pytorch/pytorch/issues/91516
+]
+
+loggers = [
+  "wandb",
+  "neptune-client",
+  "mlflow",
+  "comet-ml",
+]
+
+models = [
+  "timm ~= 0.6.11", # pytorch image models
+]
+
+objdet = [
+  # ----- object detection----- #
+  "pycocotools ~= 2.0.5",
+]
+
 developer = [
   "pre-commit ~= 2.20.0",      # hooks for applying linters on commit
   "pytest ~= 7.2.0",           # tests
@@ -61,6 +67,7 @@ fiftyone = [
 ]
 
 extras = [
+  "rich ~= 12.6.0",            # beautiful text formatting in terminal
 ]
 
 [tool.setuptools]

From a18b691303d783e4eb5f1c28bc155a154dcd18be Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 13:18:01 -0700
Subject: [PATCH 08/36] Avoid importing everything in mart.

---
 mart/__init__.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/mart/__init__.py b/mart/__init__.py
index 85181105..2c02b644 100644
--- a/mart/__init__.py
+++ b/mart/__init__.py
@@ -1,11 +1,3 @@
-import importlib
-
-from mart import attack as attack
-from mart import datamodules as datamodules
-from mart import models as models
-from mart import nn as nn
-from mart import optim as optim
-from mart import transforms as transforms
-from mart import utils as utils
+import importlib.metadata
 
 __version__ = importlib.metadata.version(__package__ or __name__)

From 6c8a99dcd3a8598f273f656e7bbd1a93e1ec8d7a Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 2 May 2024 13:21:21 -0700
Subject: [PATCH 09/36] Make a separate naming space mart.transforms.objdet for
 object detection transforms.

---
 mart/transforms/__init__.py |  3 ++
 mart/transforms/extended.py | 74 ------------------------------
 mart/transforms/objdet.py   | 91 +++++++++++++++++++++++++++++++++++++
 3 files changed, 94 insertions(+), 74 deletions(-)
 create mode 100644 mart/transforms/objdet.py

diff --git a/mart/transforms/__init__.py b/mart/transforms/__init__.py
index 8f30723a..19acd8c7 100644
--- a/mart/transforms/__init__.py
+++ b/mart/transforms/__init__.py
@@ -7,3 +7,6 @@
 from .batch_c15n import *  # noqa: F403
 from .extended import *  # noqa: F403
 from .transforms import *  # noqa: F403
+
+# We don't import .objdet here, because we may not install the object detection related packages, such as pycocotools.
+# from .objdet import *
diff --git a/mart/transforms/extended.py b/mart/transforms/extended.py
index ba827865..41595383 100644
--- a/mart/transforms/extended.py
+++ b/mart/transforms/extended.py
@@ -6,19 +6,12 @@
 
 import logging
 import os
-from typing import Dict, Optional, Tuple
 
 import numpy as np
 import torch
 from PIL import Image, ImageOps
-from torch import Tensor
-from torchvision.transforms import functional as F
 from torchvision.transforms import transforms as T
 
-# FIXME: We really shouldn't be importing private functions
-from .torchvision_ref import ConvertCocoPolysToMask as ConvertCocoPolysToMask_
-from .torchvision_ref import _flip_coco_person_keypoints
-
 logger = logging.getLogger(__name__)
 
 __all__ = [
@@ -28,9 +21,6 @@
     "SplitLambda",
     "LoadPerturbableMask",
     "LoadCoords",
-    "ConvertInstanceSegmentationToPerturbable",
-    "RandomHorizontalFlip",
-    "ConvertCocoPolysToMask",
 ]
 
 
@@ -113,17 +103,6 @@ def __call__(self, tensor, **kwargs):
         return tensor
 
 
-class ConvertInstanceSegmentationToPerturbable(ExTransform):
-    """Merge all instance masks and reverse."""
-
-    def __call__(self, image, target):
-        perturbable_mask = torch.sum(target["masks"], dim=0) == 0
-        # Convert to float to be differentiable.
-        target["perturbable_mask"] = perturbable_mask.float()
-
-        return image, target
-
-
 class LoadPerturbableMask(ExTransform):
     """Load perturbable masks and add to target."""
 
@@ -158,56 +137,3 @@ def __call__(self, image, target):
         # Convert to float to be differentiable.
         target["coords"] = coords
         return image, target
-
-
-class RandomHorizontalFlip(T.RandomHorizontalFlip, ExTransform):
-    """Flip the image and annotations including boxes, masks, keypoints and the
-    perturable_masks."""
-
-    @staticmethod
-    def flip_boxes(image, target):
-        width, _ = F.get_image_size(image)
-        target["boxes"][:, [0, 2]] = width - target["boxes"][:, [2, 0]]
-        return image, target
-
-    @staticmethod
-    def flip_masks(image, target):
-        target["masks"] = target["masks"].flip(-1)
-        return image, target
-
-    @staticmethod
-    def flip_keypoints(image, target):
-        width, _ = F.get_image_size(image)
-        keypoints = target["keypoints"]
-        keypoints = _flip_coco_person_keypoints(keypoints, width)
-        target["keypoints"] = keypoints
-        return image, target
-
-    @staticmethod
-    def flip_perturable_masks(image, target):
-        target["masks"] = target["masks"].flip(-1)
-        return image, target
-
-    @staticmethod
-    def flip_perturbable_mask(image, target):
-        target["perturbable_mask"] = target["perturbable_mask"].flip(-1)
-        return image, target
-
-    def forward(
-        self, image: Tensor, target: Optional[Dict[str, Tensor]] = None
-    ) -> Tuple[Tensor, Optional[Dict[str, Tensor]]]:
-        if torch.rand(1) < self.p:
-            image = F.hflip(image)
-            if target is not None:
-                image, target = self.flip_boxes(image, target)
-                if "masks" in target:
-                    image, target = self.flip_masks(image, target)
-                if "keypoints" in target:
-                    image, target = self.flip_keypoints(image, target)
-                if "perturbable_mask" in target:
-                    image, target = self.flip_perturable_masks(image, target)
-        return image, target
-
-
-class ConvertCocoPolysToMask(ConvertCocoPolysToMask_, ExTransform):
-    pass
diff --git a/mart/transforms/objdet.py b/mart/transforms/objdet.py
new file mode 100644
index 00000000..68a7686f
--- /dev/null
+++ b/mart/transforms/objdet.py
@@ -0,0 +1,91 @@
+#
+# Copyright (C) 2022 Intel Corporation
+#
+# SPDX-License-Identifier: BSD-3-Clause
+#
+
+import logging
+from typing import Dict, Optional, Tuple
+
+import torch
+from torch import Tensor
+from torchvision.transforms import functional as F
+from torchvision.transforms import transforms as T
+
+from .extended import ExTransform
+
+# FIXME: We really shouldn't be importing private functions
+from .torchvision_ref import ConvertCocoPolysToMask as ConvertCocoPolysToMask_
+from .torchvision_ref import _flip_coco_person_keypoints
+
+logger = logging.getLogger(__name__)
+
+__all__ = [
+    "ConvertInstanceSegmentationToPerturbable",
+    "RandomHorizontalFlip",
+    "ConvertCocoPolysToMask",
+]
+
+
+class ConvertInstanceSegmentationToPerturbable(ExTransform):
+    """Merge all instance masks and reverse."""
+
+    def __call__(self, image, target):
+        perturbable_mask = torch.sum(target["masks"], dim=0) == 0
+        # Convert to float to be differentiable.
+        target["perturbable_mask"] = perturbable_mask.float()
+
+        return image, target
+
+
+class RandomHorizontalFlip(T.RandomHorizontalFlip, ExTransform):
+    """Flip the image and annotations including boxes, masks, keypoints and the
+    perturable_masks."""
+
+    @staticmethod
+    def flip_boxes(image, target):
+        width, _ = F.get_image_size(image)
+        target["boxes"][:, [0, 2]] = width - target["boxes"][:, [2, 0]]
+        return image, target
+
+    @staticmethod
+    def flip_masks(image, target):
+        target["masks"] = target["masks"].flip(-1)
+        return image, target
+
+    @staticmethod
+    def flip_keypoints(image, target):
+        width, _ = F.get_image_size(image)
+        keypoints = target["keypoints"]
+        keypoints = _flip_coco_person_keypoints(keypoints, width)
+        target["keypoints"] = keypoints
+        return image, target
+
+    @staticmethod
+    def flip_perturable_masks(image, target):
+        target["masks"] = target["masks"].flip(-1)
+        return image, target
+
+    @staticmethod
+    def flip_perturbable_mask(image, target):
+        target["perturbable_mask"] = target["perturbable_mask"].flip(-1)
+        return image, target
+
+    def forward(
+        self, image: Tensor, target: Optional[Dict[str, Tensor]] = None
+    ) -> Tuple[Tensor, Optional[Dict[str, Tensor]]]:
+        if torch.rand(1) < self.p:
+            image = F.hflip(image)
+            if target is not None:
+                image, target = self.flip_boxes(image, target)
+                if "masks" in target:
+                    image, target = self.flip_masks(image, target)
+                if "keypoints" in target:
+                    image, target = self.flip_keypoints(image, target)
+                if "perturbable_mask" in target:
+                    image, target = self.flip_perturable_masks(image, target)
+        return image, target
+
+
+class ConvertCocoPolysToMask(ConvertCocoPolysToMask_, ExTransform):
+    pass

From e0dc984b59d948c10cb786f351a4f0358a5f3183 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Tue, 14 May 2024 11:59:34 -0700
Subject: [PATCH 10/36] Comment

---
 mart/utils/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mart/utils/config.py b/mart/utils/config.py
index 3a4268ad..578b4351 100644
--- a/mart/utils/config.py
+++ b/mart/utils/config.py
@@ -58,7 +58,7 @@ def __new__(cls, cfg_path):
 
 
 class CallbackInstantiator(Callback):
-    """Type checking for Lightning Callback."""
+    """Satisfying type checking for Lightning Callback."""
 
     def __new__(cls, cfg_path):
         obj = instantiate(cfg_path)

From f4e9acc3a88d2bf08d69a3bc322f789ae80201ce Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Tue, 14 May 2024 22:22:31 -0700
Subject: [PATCH 11/36] Clean up.

---
 mart/configs/batch_c15n/image_01.yaml            | 6 ------
 mart/configs/batch_c15n/imagenet_normalized.yaml | 6 ------
 2 files changed, 12 deletions(-)
 delete mode 100644 mart/configs/batch_c15n/image_01.yaml
 delete mode 100644 mart/configs/batch_c15n/imagenet_normalized.yaml

diff --git a/mart/configs/batch_c15n/image_01.yaml b/mart/configs/batch_c15n/image_01.yaml
deleted file mode 100644
index f3f8e758..00000000
--- a/mart/configs/batch_c15n/image_01.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-defaults:
-  - list
-  - transform: times_255_and_round
-  - transform@untransform: divided_by_255
-
-input_key: 0
diff --git a/mart/configs/batch_c15n/imagenet_normalized.yaml b/mart/configs/batch_c15n/imagenet_normalized.yaml
deleted file mode 100644
index e41fb3ff..00000000
--- a/mart/configs/batch_c15n/imagenet_normalized.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-defaults:
-  - dict
-  - transform: imagenet_to_255
-  - transform@untransform: 255_to_imagenet
-
-input_key: image

From b283bf1d126d09f1aaf5d16d7e81e07cdb6c4a63 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 09:37:10 -0700
Subject: [PATCH 12/36] Move to mart.nn.Get().

---
 mart/nn/nn.py       | 12 +++++++++++-
 mart/utils/utils.py | 11 -----------
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/mart/nn/nn.py b/mart/nn/nn.py
index 02113899..147a4773 100644
--- a/mart/nn/nn.py
+++ b/mart/nn/nn.py
@@ -13,7 +13,7 @@
 
 import torch
 
-__all__ = ["GroupNorm32", "SequentialDict", "ReturnKwargs", "CallWith", "Sum"]
+__all__ = ["GroupNorm32", "SequentialDict", "ReturnKwargs", "CallWith", "Sum", "Get"]
 
 logger = logging.getLogger(__name__)
 
@@ -300,3 +300,13 @@ def __init__(self):
 
     def forward(self, *args):
         return sum(args)
+
+
+class Get:
+    """Get a value from the kwargs dictionary by key."""
+
+    def __init__(self, key):
+        self.key = key
+
+    def __call__(self, **kwargs):
+        return kwargs[self.key]
diff --git a/mart/utils/utils.py b/mart/utils/utils.py
index dbf3fb21..f4a0a4ec 100644
--- a/mart/utils/utils.py
+++ b/mart/utils/utils.py
@@ -28,7 +28,6 @@
     "save_file",
     "task_wrapper",
     "flatten_dict",
-    "Get",
 ]
 
 log = pylogger.get_pylogger(__name__)
@@ -294,13 +293,3 @@ def get_dottedpath_items(d: dict, parent: Optional[str] = None):
         ret[key] = value
 
     return ret
-
-
-class Get:
-    """Get a value from the kwargs dictionary by key."""
-
-    def __init__(self, key):
-        self.key = key
-
-    def __call__(self, **kwargs):
-        return kwargs[self.key]

From b96a99a2928ed40c1b90ab3b8de6530b737d6f30 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 10:06:58 -0700
Subject: [PATCH 13/36] Revert changes in transforms.

---
 mart/transforms/objdet.py                 | 91 -----------------------
 mart/transforms/vision/objdet/extended.py | 74 ++++++++++++++++++
 2 files changed, 74 insertions(+), 91 deletions(-)
 delete mode 100644 mart/transforms/objdet.py

diff --git a/mart/transforms/objdet.py b/mart/transforms/objdet.py
deleted file mode 100644
index 68a7686f..00000000
--- a/mart/transforms/objdet.py
+++ /dev/null
@@ -1,91 +0,0 @@
-#
-# Copyright (C) 2022 Intel Corporation
-#
-# SPDX-License-Identifier: BSD-3-Clause
-#
-
-import logging
-from typing import Dict, Optional, Tuple
-
-import torch
-from torch import Tensor
-from torchvision.transforms import functional as F
-from torchvision.transforms import transforms as T
-
-from .extended import ExTransform
-
-# FIXME: We really shouldn't be importing private functions
-from .torchvision_ref import ConvertCocoPolysToMask as ConvertCocoPolysToMask_
-from .torchvision_ref import _flip_coco_person_keypoints
-
-logger = logging.getLogger(__name__)
-
-__all__ = [
-    "ConvertInstanceSegmentationToPerturbable",
-    "RandomHorizontalFlip",
-    "ConvertCocoPolysToMask",
-]
-
-
-class ConvertInstanceSegmentationToPerturbable(ExTransform):
-    """Merge all instance masks and reverse."""
-
-    def __call__(self, image, target):
-        perturbable_mask = torch.sum(target["masks"], dim=0) == 0
-        # Convert to float to be differentiable.
-        target["perturbable_mask"] = perturbable_mask.float()
-
-        return image, target
-
-
-class RandomHorizontalFlip(T.RandomHorizontalFlip, ExTransform):
-    """Flip the image and annotations including boxes, masks, keypoints and the
-    perturable_masks."""
-
-    @staticmethod
-    def flip_boxes(image, target):
-        width, _ = F.get_image_size(image)
-        target["boxes"][:, [0, 2]] = width - target["boxes"][:, [2, 0]]
-        return image, target
-
-    @staticmethod
-    def flip_masks(image, target):
-        target["masks"] = target["masks"].flip(-1)
-        return image, target
-
-    @staticmethod
-    def flip_keypoints(image, target):
-        width, _ = F.get_image_size(image)
-        keypoints = target["keypoints"]
-        keypoints = _flip_coco_person_keypoints(keypoints, width)
-        target["keypoints"] = keypoints
-        return image, target
-
-    @staticmethod
-    def flip_perturable_masks(image, target):
-        target["masks"] = target["masks"].flip(-1)
-        return image, target
-
-    @staticmethod
-    def flip_perturbable_mask(image, target):
-        target["perturbable_mask"] = target["perturbable_mask"].flip(-1)
-        return image, target
-
-    def forward(
-        self, image: Tensor, target: Optional[Dict[str, Tensor]] = None
-    ) -> Tuple[Tensor, Optional[Dict[str, Tensor]]]:
-        if torch.rand(1) < self.p:
-            image = F.hflip(image)
-            if target is not None:
-                image, target = self.flip_boxes(image, target)
-                if "masks" in target:
-                    image, target = self.flip_masks(image, target)
-                if "keypoints" in target:
-                    image, target = self.flip_keypoints(image, target)
-                if "perturbable_mask" in target:
-                    image, target = self.flip_perturable_masks(image, target)
-        return image, target
-
-
-class ConvertCocoPolysToMask(ConvertCocoPolysToMask_, ExTransform):
-    pass
diff --git a/mart/transforms/vision/objdet/extended.py b/mart/transforms/vision/objdet/extended.py
index 41595383..ba827865 100644
--- a/mart/transforms/vision/objdet/extended.py
+++ b/mart/transforms/vision/objdet/extended.py
@@ -6,12 +6,19 @@
 
 import logging
 import os
+from typing import Dict, Optional, Tuple
 
 import numpy as np
 import torch
 from PIL import Image, ImageOps
+from torch import Tensor
+from torchvision.transforms import functional as F
 from torchvision.transforms import transforms as T
 
+# FIXME: We really shouldn't be importing private functions
+from .torchvision_ref import ConvertCocoPolysToMask as ConvertCocoPolysToMask_
+from .torchvision_ref import _flip_coco_person_keypoints
+
 logger = logging.getLogger(__name__)
 
 __all__ = [
@@ -21,6 +28,9 @@
     "SplitLambda",
     "LoadPerturbableMask",
     "LoadCoords",
+    "ConvertInstanceSegmentationToPerturbable",
+    "RandomHorizontalFlip",
+    "ConvertCocoPolysToMask",
 ]
 
 
@@ -103,6 +113,17 @@ def __call__(self, tensor, **kwargs):
         return tensor
 
 
+class ConvertInstanceSegmentationToPerturbable(ExTransform):
+    """Merge all instance masks and reverse."""
+
+    def __call__(self, image, target):
+        perturbable_mask = torch.sum(target["masks"], dim=0) == 0
+        # Convert to float to be differentiable.
+        target["perturbable_mask"] = perturbable_mask.float()
+
+        return image, target
+
+
 class LoadPerturbableMask(ExTransform):
     """Load perturbable masks and add to target."""
 
@@ -137,3 +158,56 @@ def __call__(self, image, target):
         # Convert to float to be differentiable.
         target["coords"] = coords
         return image, target
+
+
+class RandomHorizontalFlip(T.RandomHorizontalFlip, ExTransform):
+    """Flip the image and annotations including boxes, masks, keypoints and the
+    perturable_masks."""
+
+    @staticmethod
+    def flip_boxes(image, target):
+        width, _ = F.get_image_size(image)
+        target["boxes"][:, [0, 2]] = width - target["boxes"][:, [2, 0]]
+        return image, target
+
+    @staticmethod
+    def flip_masks(image, target):
+        target["masks"] = target["masks"].flip(-1)
+        return image, target
+
+    @staticmethod
+    def flip_keypoints(image, target):
+        width, _ = F.get_image_size(image)
+        keypoints = target["keypoints"]
+        keypoints = _flip_coco_person_keypoints(keypoints, width)
+        target["keypoints"] = keypoints
+        return image, target
+
+    @staticmethod
+    def flip_perturable_masks(image, target):
+        target["masks"] = target["masks"].flip(-1)
+        return image, target
+
+    @staticmethod
+    def flip_perturbable_mask(image, target):
+        target["perturbable_mask"] = target["perturbable_mask"].flip(-1)
+        return image, target
+
+    def forward(
+        self, image: Tensor, target: Optional[Dict[str, Tensor]] = None
+    ) -> Tuple[Tensor, Optional[Dict[str, Tensor]]]:
+        if torch.rand(1) < self.p:
+            image = F.hflip(image)
+            if target is not None:
+                image, target = self.flip_boxes(image, target)
+                if "masks" in target:
+                    image, target = self.flip_masks(image, target)
+                if "keypoints" in target:
+                    image, target = self.flip_keypoints(image, target)
+                if "perturbable_mask" in target:
+                    image, target = self.flip_perturable_masks(image, target)
+        return image, target
+
+
+class ConvertCocoPolysToMask(ConvertCocoPolysToMask_, ExTransform):
+    pass

From 89eea7718342b13a76b24b2db9cca3a82c198fb0 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 10:07:22 -0700
Subject: [PATCH 14/36] Revert changes in __init__.py

---
 mart/__init__.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/mart/__init__.py b/mart/__init__.py
index 2c02b644..85181105 100644
--- a/mart/__init__.py
+++ b/mart/__init__.py
@@ -1,3 +1,11 @@
-import importlib.metadata
+import importlib
+
+from mart import attack as attack
+from mart import datamodules as datamodules
+from mart import models as models
+from mart import nn as nn
+from mart import optim as optim
+from mart import transforms as transforms
+from mart import utils as utils
 
 __version__ = importlib.metadata.version(__package__ or __name__)

From 9491cc43cd96454ac87786a9da86882a37537dc9 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 10:08:20 -0700
Subject: [PATCH 15/36] Revert changes in pyproject.toml.

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 47ebfbce..3e614550 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -74,7 +74,6 @@ full = [
 ]
 
 extras = [
-  "rich ~= 12.6.0",            # beautiful text formatting in terminal
 ]
 
 [tool.setuptools]

From ec63b73403c78fe752c947b337bf07ecdeabe5b2 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 10:33:41 -0700
Subject: [PATCH 16/36] Skip object detection tests if pycocotools is not
 installed.

---
 tests/conftest.py         |  7 ++++++-
 tests/test_experiments.py | 17 +++++++++++++----
 2 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 74ce8433..f5745d66 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -14,7 +14,7 @@
 from hydra.core.global_hydra import GlobalHydra
 from omegaconf import DictConfig, open_dict
 
-from mart.utils.imports import _HAS_TIMM, _HAS_TORCHVISION
+from mart.utils.imports import _HAS_PYCOCOTOOLS, _HAS_TIMM, _HAS_TORCHVISION
 
 root = Path(os.getcwd())
 pyrootutils.set_root(path=root, dotenv=True, pythonpath=True)
@@ -22,6 +22,9 @@
 experiments_require_torchvision = [
     "CIFAR10_CNN",
     "CIFAR10_CNN_Adv",
+]
+
+experiments_require_torchvision_pycocotools = [
     "COCO_TorchvisionFasterRCNN",
     "COCO_TorchvisionFasterRCNN_Adv",
     "COCO_TorchvisionRetinaNet",
@@ -35,6 +38,8 @@
 experiments_names = []
 if _HAS_TORCHVISION:
     experiments_names += experiments_require_torchvision
+if _HAS_TORCHVISION and _HAS_PYCOCOTOOLS:
+    experiments_names += experiments_require_torchvision_pycocotools
 if _HAS_TIMM and _HAS_TORCHVISION:
     experiments_names += experiments_require_torchvision_and_timm
 
diff --git a/tests/test_experiments.py b/tests/test_experiments.py
index e1f1ff01..637660ea 100644
--- a/tests/test_experiments.py
+++ b/tests/test_experiments.py
@@ -4,7 +4,7 @@
 import pytest
 from hydra.core.global_hydra import GlobalHydra
 
-from mart.utils.imports import _HAS_TIMM, _HAS_TORCHVISION
+from mart.utils.imports import _HAS_PYCOCOTOOLS, _HAS_TIMM, _HAS_TORCHVISION
 from tests.helpers.dataset_generator import FakeCOCODataset
 from tests.helpers.run_if import RunIf
 from tests.helpers.run_sh_command import run_sh_command
@@ -131,7 +131,10 @@ def test_imagenet_timm_experiment(classification_cfg, tmp_path):
 
 @RunIf(sh=True)
 @pytest.mark.slow
-@pytest.mark.skipif(not _HAS_TORCHVISION, reason="test requires that torchvision is installed")
+@pytest.mark.skipif(
+    not _HAS_TORCHVISION or not _HAS_PYCOCOTOOLS,
+    reason="test requires that torchvision and pycocotools are installed",
+)
 def test_coco_fasterrcnn_experiment(coco_cfg, tmp_path):
     """Test TorchVision FasterRCNN experiment."""
     overrides = coco_cfg["trainer"] + coco_cfg["datamodel"]
@@ -147,7 +150,10 @@ def test_coco_fasterrcnn_experiment(coco_cfg, tmp_path):
 
 @RunIf(sh=True)
 @pytest.mark.slow
-@pytest.mark.skipif(not _HAS_TORCHVISION, reason="test requires that torchvision is installed")
+@pytest.mark.skipif(
+    not _HAS_TORCHVISION or not _HAS_PYCOCOTOOLS,
+    reason="test requires that torchvision and pycocotools are installed",
+)
 def test_coco_fasterrcnn_adv_experiment(coco_cfg, tmp_path):
     """Test TorchVision FasterRCNN Adv experiment."""
     overrides = coco_cfg["trainer"] + coco_cfg["datamodel"]
@@ -163,7 +169,10 @@ def test_coco_fasterrcnn_adv_experiment(coco_cfg, tmp_path):
 
 @RunIf(sh=True)
 @pytest.mark.slow
-@pytest.mark.skipif(not _HAS_TORCHVISION, reason="test requires that torchvision is installed")
+@pytest.mark.skipif(
+    not _HAS_TORCHVISION or not _HAS_PYCOCOTOOLS,
+    reason="test requires that torchvision and pycocotools  installed",
+)
 def test_coco_retinanet_experiment(coco_cfg, tmp_path):
     """Test TorchVision RetinaNet experiment."""
     overrides = coco_cfg["trainer"] + coco_cfg["datamodel"]

From e063944052f8dded87b6c85d78a62eefbbe20e93 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 11:25:32 -0700
Subject: [PATCH 17/36] Simplify dependency with newer lightning 2.1+.

---
 pyproject.toml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3e614550..378b2a57 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,8 +36,11 @@ core = [
   "lightning[extra] ~= 2.1.4", # Full functionality including TensorboardX.
   "torchmetrics == 1.0.1",
   # TODO: Remove pydantic and numpy constraints with newer lightning.
-  "pydantic == 1.10.14",       # https://github.com/Lightning-AI/lightning/pull/18022/files
-  "numpy == 1.23.5",           # https://github.com/pytorch/pytorch/issues/91516
+  # Fixed in Lightning 2.1.0+: https://github.com/Lightning-AI/pytorch-lightning/commit/df959aeb4fd454d515a74b0553ad7018b73d1f15
+  # "pydantic == 1.10.14",       # https://github.com/Lightning-AI/lightning/pull/18022/files
+  # Fixed in PyTorch 2.0+: https://github.com/pytorch/pytorch/pull/96452
+  # "numpy == 1.23.5",           # https://github.com/pytorch/pytorch/issues/91516
+  # numpy 1.26.4
 ]
 
 vision = [
@@ -46,7 +49,8 @@ vision = [
 ]
 
 objdet = [
-  "pycocotools ~= 2.0.5",      # data format for object detection.
+  # pycocotools<2.0.6 use np.float that is deprecated since numpy 1.20.0 with a warning, later with an error.
+  "pycocotools ~= 2.0.6",      # data format for object detection.
   "fiftyone ~= 0.21.4",        # visualization for object detection
 ]
 

From 63286d016077cffb7525cc4186bf9c1f757b914b Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 11:26:11 -0700
Subject: [PATCH 18/36] Clean up comments.

---
 pyproject.toml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 378b2a57..25153293 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,12 +35,6 @@ core = [
   "torch >= 2.0.1",
   "lightning[extra] ~= 2.1.4", # Full functionality including TensorboardX.
   "torchmetrics == 1.0.1",
-  # TODO: Remove pydantic and numpy constraints with newer lightning.
-  # Fixed in Lightning 2.1.0+: https://github.com/Lightning-AI/pytorch-lightning/commit/df959aeb4fd454d515a74b0553ad7018b73d1f15
-  # "pydantic == 1.10.14",       # https://github.com/Lightning-AI/lightning/pull/18022/files
-  # Fixed in PyTorch 2.0+: https://github.com/pytorch/pytorch/pull/96452
-  # "numpy == 1.23.5",           # https://github.com/pytorch/pytorch/issues/91516
-  # numpy 1.26.4
 ]
 
 vision = [
@@ -49,7 +43,6 @@ vision = [
 ]
 
 objdet = [
-  # pycocotools<2.0.6 use np.float that is deprecated since numpy 1.20.0 with a warning, later with an error.
   "pycocotools ~= 2.0.6",      # data format for object detection.
   "fiftyone ~= 0.21.4",        # visualization for object detection
 ]

From d725ea3e9b36ed82025fc03dd9bb5aa93b81b363 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 12:08:10 -0700
Subject: [PATCH 19/36] Remove the version constraint on rich, due to the
 conflict with Anomalib.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 25153293..a9b5626b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,7 +18,7 @@ dependencies = [
 
   # --------- basics --------- #
   "pyrootutils ~= 1.0.4",      # standardizing the project root setup
-  "rich ~= 12.6.0",            # beautiful text formatting in terminal
+  "rich",                      # beautiful text formatting in terminal
   "fire == 0.5.0",
 ]
 

From 8d19d9bbd472707cdaead80924e623d03613ac90 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 12:13:19 -0700
Subject: [PATCH 20/36] Make a package anomalib_adversary

---
 examples/anomalib_adversary/.gitignore       | 2 ++
 examples/anomalib_adversary/requirements.txt | 2 ++
 examples/anomalib_adversary/setup.py         | 8 ++++++++
 3 files changed, 12 insertions(+)
 create mode 100644 examples/anomalib_adversary/.gitignore
 create mode 100644 examples/anomalib_adversary/requirements.txt
 create mode 100644 examples/anomalib_adversary/setup.py

diff --git a/examples/anomalib_adversary/.gitignore b/examples/anomalib_adversary/.gitignore
new file mode 100644
index 00000000..3747c7e1
--- /dev/null
+++ b/examples/anomalib_adversary/.gitignore
@@ -0,0 +1,2 @@
+results
+datasets
diff --git a/examples/anomalib_adversary/requirements.txt b/examples/anomalib_adversary/requirements.txt
new file mode 100644
index 00000000..ae34b0f9
--- /dev/null
+++ b/examples/anomalib_adversary/requirements.txt
@@ -0,0 +1,2 @@
+anomalib[full] @ git+https://github.com/openvinotoolkit/anomalib.git@v1.0.1
+mart @ git+https://github.com/IntelLabs/MART@mzweilin/upgrade_lightning_2.1.4
diff --git a/examples/anomalib_adversary/setup.py b/examples/anomalib_adversary/setup.py
new file mode 100644
index 00000000..d9986611
--- /dev/null
+++ b/examples/anomalib_adversary/setup.py
@@ -0,0 +1,8 @@
+import setuptools
+
+setuptools.setup(
+    name="anomalib_adversary",
+    version="0.1.0a",
+    description="Evaluating robustness of anomaly detection models in Anomalib.",
+    packages=["anomalib_adversary"],
+)

From 94d4d4485a9ddd89a2bbc6b31f4ee9fe0a39e750 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 12:14:02 -0700
Subject: [PATCH 21/36] Add two model configs for Anomalib.

---
 .../configs/anomalib/stfpm.yaml               | 21 ++++++++++++++++
 .../configs/anomalib/stfpm_mart.yaml          | 24 +++++++++++++++++++
 2 files changed, 45 insertions(+)
 create mode 100644 examples/anomalib_adversary/configs/anomalib/stfpm.yaml
 create mode 100644 examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml

diff --git a/examples/anomalib_adversary/configs/anomalib/stfpm.yaml b/examples/anomalib_adversary/configs/anomalib/stfpm.yaml
new file mode 100644
index 00000000..c5e783ba
--- /dev/null
+++ b/examples/anomalib_adversary/configs/anomalib/stfpm.yaml
@@ -0,0 +1,21 @@
+model:
+  class_path: anomalib.models.Stfpm
+  init_args:
+    backbone: resnet18
+    layers:
+      - layer1
+      - layer2
+      - layer3
+
+metrics:
+  pixel:
+    - AUROC
+
+trainer:
+  max_epochs: 100
+  callbacks:
+    - class_path: lightning.pytorch.callbacks.EarlyStopping
+      init_args:
+        patience: 5
+        monitor: pixel_AUROC
+        mode: max
diff --git a/examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml b/examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml
new file mode 100644
index 00000000..f83b1494
--- /dev/null
+++ b/examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml
@@ -0,0 +1,24 @@
+model:
+  class_path: anomalib.models.Stfpm
+  init_args:
+    backbone: resnet18
+    layers:
+      - layer1
+      - layer2
+      - layer3
+
+metrics:
+  pixel:
+    - AUROC
+
+trainer:
+  max_epochs: 100
+  callbacks:
+    - class_path: lightning.pytorch.callbacks.EarlyStopping
+      init_args:
+        patience: 5
+        monitor: pixel_AUROC
+        mode: max
+    - class_path: mart.utils.CallbackInstantiator
+      init_args:
+        cfg_path: ./anomalib_fgsm_linf_10.yaml

From b85aaf1c3a09e5f9315da8213aa9f8b0a1874acb Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 12:14:37 -0700
Subject: [PATCH 22/36] Add README.

---
 examples/anomalib_adversary/README.md | 88 +++++++++++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 examples/anomalib_adversary/README.md

diff --git a/examples/anomalib_adversary/README.md b/examples/anomalib_adversary/README.md
new file mode 100644
index 00000000..f826c225
--- /dev/null
+++ b/examples/anomalib_adversary/README.md
@@ -0,0 +1,88 @@
+# Adversarial Robustness of Anomaly Detection
+
+This project demonstrates how to generate adversarial examples against anomaly detection models in [Anomalib](https://github.com/openvinotoolkit/anomalib).
+
+## Installation
+
+Anomalib requires Python 3.10+.
+
+```sh
+pip install -r requirements.txt
+```
+
+## Experiment
+
+0. \[Optional\] Soft link the existing datasets folder from Anomalib if you have downloaded datasets before with Anomalib.
+
+```sh
+ln -s {PATH_TO_ANOMALIB_REPO}/datasets .
+```
+
+1. Train a model. The config file [configs/anomalib/stfpm.yaml](configs/anomalib/stfpm.yaml) adds an EarlyStopping Callback with maximal 100 epochs.
+
+```sh
+CUDA_VISIBLE_DEVICES=0 anomalib train \
+--data anomalib.data.MVTec \
+--data.category transistor \
+--config configs/anomalib/stfpm.yaml
+```
+
+2. Evaluate the trained model without adversary as baseline.
+
+```sh
+CUDA_VISIBLE_DEVICES=0 anomalib test \
+--data anomalib.data.MVTec \
+--data.category transistor \
+--config configs/anomalib/stfpm.yaml \
+--ckpt_path=results/Stfpm/MVTec/transistor/latest/weights/lightning/model.ckpt
+```
+
+```console
+┏━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
+┃        Test metric        ┃       DataLoader 0        ┃
+┡━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
+│        image_AUROC        │    0.8733333349227905     │
+│       image_F1Score       │    0.7945205569267273     │
+│        pixel_AUROC        │    0.7860202789306641     │
+└───────────────────────────┴───────────────────────────┘
+```
+
+2. Generate an adversary config from MART.
+
+```sh
+python -m mart.generate_config \
+--config_dir="configs" \
+--export_node=callbacks.adversary_connector \
+--resolve=True \
+callbacks=adversary_connector \
+batch_c15n@callbacks.adversary_connector.batch_c15n=dict_imagenet_normalized \
+callbacks.adversary_connector.adversary=$\{attack\} \
++attack=classification_fgsm_linf \
+~attack.gain \
++attack.gain._target_=mart.nn.Get \
++attack.gain.key=loss \
+attack.objective=null \
+attack.eps=10 \
+attack.callbacks.progress_bar.enable=true \
+> anomalib_fgsm_linf_10.yaml
+```
+
+3. Run attack. The config file [configs/anomalib/stfpm_mart.yaml](configs/anomalib/stfpm_mart.yaml) adds a MART callback that loads the attack config file we just generated [./anomalib_fgsm_linf_10.yaml](./anomalib_fgsm_linf_10.yaml).
+
+```sh
+CUDA_VISIBLE_DEVICES=0 anomalib test \
+--data anomalib.data.MVTec \
+--data.category transistor \
+--config configs/anomalib/stfpm_mart.yaml \
+--ckpt_path=results/Stfpm/MVTec/transistor/latest/weights/lightning/model.ckpt
+```
+
+```console
+┏━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
+┃        Test metric        ┃       DataLoader 0        ┃
+┡━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
+│        image_AUROC        │    0.5979167222976685     │
+│       image_F1Score       │    0.5714285969734192     │
+│        pixel_AUROC        │    0.6867808699607849     │
+└───────────────────────────┴───────────────────────────┘
+```

From 3c0f172821de0b35be0930775e2874a12638a0c3 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 15 May 2024 12:19:00 -0700
Subject: [PATCH 23/36] Update README

---
 examples/anomalib_adversary/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/anomalib_adversary/README.md b/examples/anomalib_adversary/README.md
index f826c225..732dd2b4 100644
--- a/examples/anomalib_adversary/README.md
+++ b/examples/anomalib_adversary/README.md
@@ -47,7 +47,7 @@ CUDA_VISIBLE_DEVICES=0 anomalib test \
 └───────────────────────────┴───────────────────────────┘
 ```
 
-2. Generate an adversary config from MART.
+3. Generate an adversary config from MART.
 
 ```sh
 python -m mart.generate_config \
@@ -67,7 +67,7 @@ attack.callbacks.progress_bar.enable=true \
 > anomalib_fgsm_linf_10.yaml
 ```
 
-3. Run attack. The config file [configs/anomalib/stfpm_mart.yaml](configs/anomalib/stfpm_mart.yaml) adds a MART callback that loads the attack config file we just generated [./anomalib_fgsm_linf_10.yaml](./anomalib_fgsm_linf_10.yaml).
+4. Run attack. The config file [configs/anomalib/stfpm_mart.yaml](configs/anomalib/stfpm_mart.yaml) adds a MART callback that loads the attack config file we just generated [./anomalib_fgsm_linf_10.yaml](./anomalib_fgsm_linf_10.yaml).
 
 ```sh
 CUDA_VISIBLE_DEVICES=0 anomalib test \

From 101940d4e04002eaf344fcf61de7e60da663964d Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 16 May 2024 08:45:15 -0700
Subject: [PATCH 24/36] Replace Anomalib config files with command lines.

---
 examples/anomalib_adversary/README.md         | 22 +++++++++++------
 .../configs/anomalib/stfpm.yaml               | 21 ----------------
 .../configs/anomalib/stfpm_mart.yaml          | 24 -------------------
 3 files changed, 15 insertions(+), 52 deletions(-)
 delete mode 100644 examples/anomalib_adversary/configs/anomalib/stfpm.yaml
 delete mode 100644 examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml

diff --git a/examples/anomalib_adversary/README.md b/examples/anomalib_adversary/README.md
index 732dd2b4..3bcb6e28 100644
--- a/examples/anomalib_adversary/README.md
+++ b/examples/anomalib_adversary/README.md
@@ -18,13 +18,17 @@ pip install -r requirements.txt
 ln -s {PATH_TO_ANOMALIB_REPO}/datasets .
 ```
 
-1. Train a model. The config file [configs/anomalib/stfpm.yaml](configs/anomalib/stfpm.yaml) adds an EarlyStopping Callback with maximal 100 epochs.
+1. Train a model. We add an EarlyStopping callback in command line.
 
 ```sh
 CUDA_VISIBLE_DEVICES=0 anomalib train \
 --data anomalib.data.MVTec \
 --data.category transistor \
---config configs/anomalib/stfpm.yaml
+--model Stfpm \
+--trainer.callbacks lightning.pytorch.callbacks.EarlyStopping \
+--trainer.callbacks.patience 5 \
+--trainer.callbacks.monitor pixel_AUROC \
+--trainer.callbacks.mode max
 ```
 
 2. Evaluate the trained model without adversary as baseline.
@@ -33,7 +37,7 @@ CUDA_VISIBLE_DEVICES=0 anomalib train \
 CUDA_VISIBLE_DEVICES=0 anomalib test \
 --data anomalib.data.MVTec \
 --data.category transistor \
---config configs/anomalib/stfpm.yaml \
+--model Stfpm \
 --ckpt_path=results/Stfpm/MVTec/transistor/latest/weights/lightning/model.ckpt
 ```
 
@@ -44,10 +48,11 @@ CUDA_VISIBLE_DEVICES=0 anomalib test \
 │        image_AUROC        │    0.8733333349227905     │
 │       image_F1Score       │    0.7945205569267273     │
 │        pixel_AUROC        │    0.7860202789306641     │
+│       pixel_F1Score       │    0.46384868025779724    │
 └───────────────────────────┴───────────────────────────┘
 ```
 
-3. Generate an adversary config from MART.
+3. Generate an adversary config file from MART.
 
 ```sh
 python -m mart.generate_config \
@@ -67,13 +72,15 @@ attack.callbacks.progress_bar.enable=true \
 > anomalib_fgsm_linf_10.yaml
 ```
 
-4. Run attack. The config file [configs/anomalib/stfpm_mart.yaml](configs/anomalib/stfpm_mart.yaml) adds a MART callback that loads the attack config file we just generated [./anomalib_fgsm_linf_10.yaml](./anomalib_fgsm_linf_10.yaml).
+4. Run attack. We add a MART callback that loads the attack config file we just generated [./anomalib_fgsm_linf_10.yaml](./anomalib_fgsm_linf_10.yaml).
 
 ```sh
 CUDA_VISIBLE_DEVICES=0 anomalib test \
 --data anomalib.data.MVTec \
 --data.category transistor \
---config configs/anomalib/stfpm_mart.yaml \
+--model Stfpm \
+--trainer.callbacks mart.utils.CallbackInstantiator \
+--trainer.callbacks.cfg_path ./anomalib_fgsm_linf_10.yaml \
 --ckpt_path=results/Stfpm/MVTec/transistor/latest/weights/lightning/model.ckpt
 ```
 
@@ -83,6 +90,7 @@ CUDA_VISIBLE_DEVICES=0 anomalib test \
 ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
 │        image_AUROC        │    0.5979167222976685     │
 │       image_F1Score       │    0.5714285969734192     │
-│        pixel_AUROC        │    0.6867808699607849     │
+│        pixel_AUROC        │     0.686780571937561     │
+│       pixel_F1Score       │    0.0955422893166542     │
 └───────────────────────────┴───────────────────────────┘
 ```
diff --git a/examples/anomalib_adversary/configs/anomalib/stfpm.yaml b/examples/anomalib_adversary/configs/anomalib/stfpm.yaml
deleted file mode 100644
index c5e783ba..00000000
--- a/examples/anomalib_adversary/configs/anomalib/stfpm.yaml
+++ /dev/null
@@ -1,21 +0,0 @@
-model:
-  class_path: anomalib.models.Stfpm
-  init_args:
-    backbone: resnet18
-    layers:
-      - layer1
-      - layer2
-      - layer3
-
-metrics:
-  pixel:
-    - AUROC
-
-trainer:
-  max_epochs: 100
-  callbacks:
-    - class_path: lightning.pytorch.callbacks.EarlyStopping
-      init_args:
-        patience: 5
-        monitor: pixel_AUROC
-        mode: max
diff --git a/examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml b/examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml
deleted file mode 100644
index f83b1494..00000000
--- a/examples/anomalib_adversary/configs/anomalib/stfpm_mart.yaml
+++ /dev/null
@@ -1,24 +0,0 @@
-model:
-  class_path: anomalib.models.Stfpm
-  init_args:
-    backbone: resnet18
-    layers:
-      - layer1
-      - layer2
-      - layer3
-
-metrics:
-  pixel:
-    - AUROC
-
-trainer:
-  max_epochs: 100
-  callbacks:
-    - class_path: lightning.pytorch.callbacks.EarlyStopping
-      init_args:
-        patience: 5
-        monitor: pixel_AUROC
-        mode: max
-    - class_path: mart.utils.CallbackInstantiator
-      init_args:
-        cfg_path: ./anomalib_fgsm_linf_10.yaml

From ed21be6ced76065edc10351a40efc9682f3c3116 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 16 May 2024 21:37:51 -0700
Subject: [PATCH 25/36] Add an empty configs folder, because
 mart.generate_config requires a local configs folder.

---
 examples/anomalib_adversary/configs/.gitkeep | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 examples/anomalib_adversary/configs/.gitkeep

diff --git a/examples/anomalib_adversary/configs/.gitkeep b/examples/anomalib_adversary/configs/.gitkeep
new file mode 100644
index 00000000..e69de29b

From f74c293a938f0c785bb62dbba410e53efd4b35ed Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Thu, 16 May 2024 21:41:47 -0700
Subject: [PATCH 26/36] Point dependency to MART@main.

---
 examples/anomalib_adversary/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/anomalib_adversary/requirements.txt b/examples/anomalib_adversary/requirements.txt
index ae34b0f9..d7e474c8 100644
--- a/examples/anomalib_adversary/requirements.txt
+++ b/examples/anomalib_adversary/requirements.txt
@@ -1,2 +1,2 @@
 anomalib[full] @ git+https://github.com/openvinotoolkit/anomalib.git@v1.0.1
-mart @ git+https://github.com/IntelLabs/MART@mzweilin/upgrade_lightning_2.1.4
+mart @ git+https://github.com/IntelLabs/MART@main

From 061b50288a796902fe9e6041c9385caafbfe6fc9 Mon Sep 17 00:00:00 2001
From: Cory Cornelius <cory.cornelius@intel.com>
Date: Fri, 17 May 2024 18:26:52 -0700
Subject: [PATCH 27/36] Parameterize module step function in AdversaryConnector

---
 mart/callbacks/adversary_connector.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/mart/callbacks/adversary_connector.py b/mart/callbacks/adversary_connector.py
index 006fbe1f..f5a95d13 100644
--- a/mart/callbacks/adversary_connector.py
+++ b/mart/callbacks/adversary_connector.py
@@ -62,6 +62,7 @@ def __init__(
         val_adversary: Callable = None,
         test_adversary: Callable = None,
         batch_c15n: Callable = None,
+        module_step_fn: str = "training_step",
     ):
         """A pl.Trainer callback which perturbs input to be adversarial in training/validation/test
         phase.
@@ -77,6 +78,7 @@ def __init__(
         self.val_adversary = val_adversary or adversary
         self.test_adversary = test_adversary or adversary
         self.batch_c15n = batch_c15n
+        self.module_step_fn = module_step_fn
 
     def setup(self, trainer, pl_module, stage=None):
         self._on_after_batch_transfer = pl_module.on_after_batch_transfer
@@ -123,7 +125,8 @@ def model(input, target):
                         pl_module,
                         excludes=["torch.nn.modules.dropout", "torch.nn.modules.batchnorm"],
                     ):
-                        outputs = pl_module.training_step(batch, dataloader_idx)
+                        pl_module_step_fn = getattr(pl_module, self.module_step_fn)
+                        outputs = pl_module_step_fn(batch, dataloader_idx)
             return outputs
 
         # Canonicalize the batch to work with Adversary.

From ceb7ccbcdbb9bda76570868250c42b6293a42fdf Mon Sep 17 00:00:00 2001
From: Cory Cornelius <cory.cornelius@intel.com>
Date: Fri, 17 May 2024 18:27:22 -0700
Subject: [PATCH 28/36] HACK: Gain function that clones it target

---
 mart/attack/gain.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/mart/attack/gain.py b/mart/attack/gain.py
index 93317dd7..9169fa8a 100644
--- a/mart/attack/gain.py
+++ b/mart/attack/gain.py
@@ -84,3 +84,10 @@ def forward(self, rpn_objectness: torch.Tensor) -> torch.Tensor:
         else:
             # Encourage foreground.
             return probs
+
+
+from torch.nn import BCELoss as BCELoss_
+class BCELoss(BCELoss_):
+    def forward(self, input, target):
+        # We clone target because that tensor can be made in inference mode.
+        return super().forward(input, target.clone())

From 310186e98a301cf47fcc9c7b5f127ca2be58adcc Mon Sep 17 00:00:00 2001
From: Cory Cornelius <cory.cornelius@intel.com>
Date: Fri, 17 May 2024 18:29:20 -0700
Subject: [PATCH 29/36] Update README with WinClip example

---
 examples/anomalib_adversary/README.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/examples/anomalib_adversary/README.md b/examples/anomalib_adversary/README.md
index 3bcb6e28..17952953 100644
--- a/examples/anomalib_adversary/README.md
+++ b/examples/anomalib_adversary/README.md
@@ -52,6 +52,10 @@ CUDA_VISIBLE_DEVICES=0 anomalib test \
 └───────────────────────────┴───────────────────────────┘
 ```
 
+```sh
+anomalib test --data anomalib.data.MVTec  --data.category hazelnut --model WinClip --data.init_args.image_size 240 --data.init_args.eval_batch_size 16 "--metrics.pixel=[F1Score,AUROC]"
+```
+
 3. Generate an adversary config file from MART.
 
 ```sh
@@ -72,6 +76,10 @@ attack.callbacks.progress_bar.enable=true \
 > anomalib_fgsm_linf_10.yaml
 ```
 
+```sh
+python -m mart.generate_config --config_dir="configs" --export_node=callbacks.adversary_connector --resolve=True  callbacks=adversary_connector batch_c15n@callbacks.adversary_connector.batch_c15n=dict_imagenet_normalized callbacks.adversary_connector.adversary=$\{attack\} +attack=classification_fgsm_linf attack.objective=null attack.eps=10 attack.callbacks.progress_bar.enable=true +callbacks.adversary_connector.module_step_fn=validation_step attack.gain._call_with_args_.0=anomaly_maps attack.gain._call_with_args_.1=mask > anomalib_fgsm_linf_10.yaml
+```
+
 4. Run attack. We add a MART callback that loads the attack config file we just generated [./anomalib_fgsm_linf_10.yaml](./anomalib_fgsm_linf_10.yaml).
 
 ```sh
@@ -94,3 +102,7 @@ CUDA_VISIBLE_DEVICES=0 anomalib test \
 │       pixel_F1Score       │    0.0955422893166542     │
 └───────────────────────────┴───────────────────────────┘
 ```
+
+```sh
+anomalib test --data anomalib.data.MVTec  --data.category hazelnut --model WinClip --data.init_args.image_size 240 --data.init_args.eval_batch_size 16 "--metrics.pixel=[F1Score,AUROC]" --trainer.callbacks mart.utils.CallbackInstantiator --trainer.callbacks.cfg_path ./anomalib_fgsm_linf_10.yaml
+```

From 187ac53c2e937aac902ee056f95cbb8729227474 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 5 Jun 2024 10:15:47 -0700
Subject: [PATCH 30/36] Update MART dependency.

---
 examples/anomalib_adversary/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/anomalib_adversary/requirements.txt b/examples/anomalib_adversary/requirements.txt
index d7e474c8..2fe868c7 100644
--- a/examples/anomalib_adversary/requirements.txt
+++ b/examples/anomalib_adversary/requirements.txt
@@ -1,2 +1,2 @@
 anomalib[full] @ git+https://github.com/openvinotoolkit/anomalib.git@v1.0.1
-mart @ git+https://github.com/IntelLabs/MART@main
+mart @ git+https://github.com/IntelLabs/MART@v0.6.1

From e0117ae8a07d242267e53cb443ff3abcf5b48c69 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 5 Jun 2024 10:40:41 -0700
Subject: [PATCH 31/36] Mordenize packaging with pyproject.toml.

---
 examples/anomalib_adversary/pyproject.toml   | 15 +++++++++++++++
 examples/anomalib_adversary/requirements.txt |  2 --
 examples/anomalib_adversary/setup.py         |  8 --------
 3 files changed, 15 insertions(+), 10 deletions(-)
 create mode 100644 examples/anomalib_adversary/pyproject.toml
 delete mode 100644 examples/anomalib_adversary/requirements.txt
 delete mode 100644 examples/anomalib_adversary/setup.py

diff --git a/examples/anomalib_adversary/pyproject.toml b/examples/anomalib_adversary/pyproject.toml
new file mode 100644
index 00000000..8caea066
--- /dev/null
+++ b/examples/anomalib_adversary/pyproject.toml
@@ -0,0 +1,15 @@
+[project]
+name = "anomalib_adversary"
+version = "0.1.0a"
+description = "Evaluating robustness of anomaly detection models in Anomalib."
+authors = [
+  {name = "Intel Corporation"}
+]
+
+dependencies = [
+    "anomalib[full]==1.0.1",
+    "mart @ https://github.com/IntelLabs/MART/archive/refs/tags/v0.6.1.zip"
+]
+
+[tool.setuptools.packages.find]
+include = ["anomalib_adversary*"]
diff --git a/examples/anomalib_adversary/requirements.txt b/examples/anomalib_adversary/requirements.txt
deleted file mode 100644
index 2fe868c7..00000000
--- a/examples/anomalib_adversary/requirements.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-anomalib[full] @ git+https://github.com/openvinotoolkit/anomalib.git@v1.0.1
-mart @ git+https://github.com/IntelLabs/MART@v0.6.1
diff --git a/examples/anomalib_adversary/setup.py b/examples/anomalib_adversary/setup.py
deleted file mode 100644
index d9986611..00000000
--- a/examples/anomalib_adversary/setup.py
+++ /dev/null
@@ -1,8 +0,0 @@
-import setuptools
-
-setuptools.setup(
-    name="anomalib_adversary",
-    version="0.1.0a",
-    description="Evaluating robustness of anomaly detection models in Anomalib.",
-    packages=["anomalib_adversary"],
-)

From 3b016d0a60f8c16da77a7b7bc6b8531fe664ab40 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 5 Jun 2024 11:36:29 -0700
Subject: [PATCH 32/36] Revert "Parameterize module step function in
 AdversaryConnector"

This reverts commit 061b50288a796902fe9e6041c9385caafbfe6fc9.
---
 mart/callbacks/adversary_connector.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/mart/callbacks/adversary_connector.py b/mart/callbacks/adversary_connector.py
index f5a95d13..006fbe1f 100644
--- a/mart/callbacks/adversary_connector.py
+++ b/mart/callbacks/adversary_connector.py
@@ -62,7 +62,6 @@ def __init__(
         val_adversary: Callable = None,
         test_adversary: Callable = None,
         batch_c15n: Callable = None,
-        module_step_fn: str = "training_step",
     ):
         """A pl.Trainer callback which perturbs input to be adversarial in training/validation/test
         phase.
@@ -78,7 +77,6 @@ def __init__(
         self.val_adversary = val_adversary or adversary
         self.test_adversary = test_adversary or adversary
         self.batch_c15n = batch_c15n
-        self.module_step_fn = module_step_fn
 
     def setup(self, trainer, pl_module, stage=None):
         self._on_after_batch_transfer = pl_module.on_after_batch_transfer
@@ -125,8 +123,7 @@ def model(input, target):
                         pl_module,
                         excludes=["torch.nn.modules.dropout", "torch.nn.modules.batchnorm"],
                     ):
-                        pl_module_step_fn = getattr(pl_module, self.module_step_fn)
-                        outputs = pl_module_step_fn(batch, dataloader_idx)
+                        outputs = pl_module.training_step(batch, dataloader_idx)
             return outputs
 
         # Canonicalize the batch to work with Adversary.

From 4fb06906ecf4d639b4d6e82030727b5beb4da604 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 5 Jun 2024 11:36:37 -0700
Subject: [PATCH 33/36] Revert "HACK: Gain function that clones it target"

This reverts commit ceb7ccbcdbb9bda76570868250c42b6293a42fdf.
---
 mart/attack/gain.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/mart/attack/gain.py b/mart/attack/gain.py
index 9169fa8a..93317dd7 100644
--- a/mart/attack/gain.py
+++ b/mart/attack/gain.py
@@ -84,10 +84,3 @@ def forward(self, rpn_objectness: torch.Tensor) -> torch.Tensor:
         else:
             # Encourage foreground.
             return probs
-
-
-from torch.nn import BCELoss as BCELoss_
-class BCELoss(BCELoss_):
-    def forward(self, input, target):
-        # We clone target because that tensor can be made in inference mode.
-        return super().forward(input, target.clone())

From 75005395577c3424921da0ca53d5c9f32560f192 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 5 Jun 2024 11:36:43 -0700
Subject: [PATCH 34/36] Revert "Update README with WinClip example"

This reverts commit 310186e98a301cf47fcc9c7b5f127ca2be58adcc.
---
 examples/anomalib_adversary/README.md | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/examples/anomalib_adversary/README.md b/examples/anomalib_adversary/README.md
index 17952953..3bcb6e28 100644
--- a/examples/anomalib_adversary/README.md
+++ b/examples/anomalib_adversary/README.md
@@ -52,10 +52,6 @@ CUDA_VISIBLE_DEVICES=0 anomalib test \
 └───────────────────────────┴───────────────────────────┘
 ```
 
-```sh
-anomalib test --data anomalib.data.MVTec  --data.category hazelnut --model WinClip --data.init_args.image_size 240 --data.init_args.eval_batch_size 16 "--metrics.pixel=[F1Score,AUROC]"
-```
-
 3. Generate an adversary config file from MART.
 
 ```sh
@@ -76,10 +72,6 @@ attack.callbacks.progress_bar.enable=true \
 > anomalib_fgsm_linf_10.yaml
 ```
 
-```sh
-python -m mart.generate_config --config_dir="configs" --export_node=callbacks.adversary_connector --resolve=True  callbacks=adversary_connector batch_c15n@callbacks.adversary_connector.batch_c15n=dict_imagenet_normalized callbacks.adversary_connector.adversary=$\{attack\} +attack=classification_fgsm_linf attack.objective=null attack.eps=10 attack.callbacks.progress_bar.enable=true +callbacks.adversary_connector.module_step_fn=validation_step attack.gain._call_with_args_.0=anomaly_maps attack.gain._call_with_args_.1=mask > anomalib_fgsm_linf_10.yaml
-```
-
 4. Run attack. We add a MART callback that loads the attack config file we just generated [./anomalib_fgsm_linf_10.yaml](./anomalib_fgsm_linf_10.yaml).
 
 ```sh
@@ -102,7 +94,3 @@ CUDA_VISIBLE_DEVICES=0 anomalib test \
 │       pixel_F1Score       │    0.0955422893166542     │
 └───────────────────────────┴───────────────────────────┘
 ```
-
-```sh
-anomalib test --data anomalib.data.MVTec  --data.category hazelnut --model WinClip --data.init_args.image_size 240 --data.init_args.eval_batch_size 16 "--metrics.pixel=[F1Score,AUROC]" --trainer.callbacks mart.utils.CallbackInstantiator --trainer.callbacks.cfg_path ./anomalib_fgsm_linf_10.yaml
-```

From 6cc6df6ab28519ff9f9f515748d34ca523b3e943 Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 5 Jun 2024 11:39:08 -0700
Subject: [PATCH 35/36] Update README.

---
 examples/anomalib_adversary/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/anomalib_adversary/README.md b/examples/anomalib_adversary/README.md
index 3bcb6e28..1432b107 100644
--- a/examples/anomalib_adversary/README.md
+++ b/examples/anomalib_adversary/README.md
@@ -7,7 +7,7 @@ This project demonstrates how to generate adversarial examples against anomaly d
 Anomalib requires Python 3.10+.
 
 ```sh
-pip install -r requirements.txt
+pip install -e .
 ```
 
 ## Experiment

From 26214600c403981ee9b1af53ef1994d20b179b7c Mon Sep 17 00:00:00 2001
From: Weilin Xu <weilin.xu@intel.com>
Date: Wed, 5 Jun 2024 13:57:49 -0700
Subject: [PATCH 36/36] Add a comma to make consistent lines.

---
 examples/anomalib_adversary/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/anomalib_adversary/pyproject.toml b/examples/anomalib_adversary/pyproject.toml
index 8caea066..0444dabe 100644
--- a/examples/anomalib_adversary/pyproject.toml
+++ b/examples/anomalib_adversary/pyproject.toml
@@ -8,7 +8,7 @@ authors = [
 
 dependencies = [
     "anomalib[full]==1.0.1",
-    "mart @ https://github.com/IntelLabs/MART/archive/refs/tags/v0.6.1.zip"
+    "mart @ https://github.com/IntelLabs/MART/archive/refs/tags/v0.6.1.zip",
 ]
 
 [tool.setuptools.packages.find]