From d7b910fe4252937360e95fce9197b074da28e2b9 Mon Sep 17 00:00:00 2001
From: am <am>
Date: Thu, 1 Aug 2024 19:11:39 -0700
Subject: [PATCH 01/11] cell_sam_wrapper net

Signed-off-by: am <am>
---
 monai/networks/nets/cell_sam_wrapper.py | 87 +++++++++++++++++++++++++
 1 file changed, 87 insertions(+)
 create mode 100644 monai/networks/nets/cell_sam_wrapper.py

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
new file mode 100644
index 0000000000..3da0e0b5e4
--- /dev/null
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -0,0 +1,87 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import torch
+from torch import nn
+from torch.nn import functional as F
+
+try:
+    from segment_anything.build_sam import build_sam_vit_b
+except ImportError:
+    raise AssertionError("SAM is not installed, please run: pip install git+https://github.com/facebookresearch/segment-anything.git")
+
+
+_all__ = ["CellSamWrapper"]
+
+class CellSamWrapper(torch.nn.Module):
+    """
+    CellSamWrapper is thin wrapper around SAM model https://github.com/facebookresearch/segment-anything
+    with an image only decoder, that can be used for segmentation tasks.
+
+
+    Args:
+        auto_resize_inputs: whether to resize inputs before passing to the network.
+        network_resize_roi: expected input size for the network.
+        checkpoint: checkpoint file to load the SAM weights from.
+        return_features: whether to return features 
+
+    """
+        
+    def __init__(
+        self,
+        auto_resize_inputs=True,
+        network_resize_roi=[1024, 1024],
+        checkpoint="sam_vit_b_01ec64.pth",
+        return_features=False,
+        *args,
+        **kwargs,
+    ) -> None:
+        super().__init__(*args, **kwargs)
+
+        print(
+            f"CellSamWrapper auto_resize_inputs {auto_resize_inputs} network_resize_roi {network_resize_roi} checkpoint {checkpoint}"
+        )
+        self.network_resize_roi = network_resize_roi
+        self.auto_resize_inputs = auto_resize_inputs
+        self.return_features = return_features
+
+        model = build_sam_vit_b(checkpoint=checkpoint)
+
+        model.prompt_encoder = None
+        model.mask_decoder = None
+
+        model.mask_decoder = nn.Sequential(
+            nn.BatchNorm2d(num_features=256),
+            nn.ReLU(inplace=True),
+            nn.ConvTranspose2d(256, 128, kernel_size=3, stride=2, padding=1, output_padding=1, bias=False),
+            nn.BatchNorm2d(num_features=128),
+            nn.ReLU(inplace=True),
+            nn.ConvTranspose2d(128, 3, kernel_size=3, stride=2, padding=1, output_padding=1, bias=True),
+        )
+
+        self.model = model
+
+    def forward(self, x):
+        sh = x.shape[2:]
+
+        if self.auto_resize_inputs:
+            x = F.interpolate(x, size=self.network_resize_roi, mode="bilinear")
+
+        x = self.model.image_encoder(x)  
+
+        if not self.return_features:
+            x = self.model.mask_decoder(x)
+            if self.auto_resize_inputs:
+                x = F.interpolate(x, size=sh, mode="bilinear")
+
+        return x

From 51d63c91185a0b7609212d37b142e73ec5312825 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 2 Aug 2024 02:15:40 +0000
Subject: [PATCH 02/11] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Signed-off-by: am <am>
---
 monai/networks/nets/cell_sam_wrapper.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
index 3da0e0b5e4..ccca07dee2 100644
--- a/monai/networks/nets/cell_sam_wrapper.py
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -33,10 +33,10 @@ class CellSamWrapper(torch.nn.Module):
         auto_resize_inputs: whether to resize inputs before passing to the network.
         network_resize_roi: expected input size for the network.
         checkpoint: checkpoint file to load the SAM weights from.
-        return_features: whether to return features 
+        return_features: whether to return features
 
     """
-        
+
     def __init__(
         self,
         auto_resize_inputs=True,
@@ -77,7 +77,7 @@ def forward(self, x):
         if self.auto_resize_inputs:
             x = F.interpolate(x, size=self.network_resize_roi, mode="bilinear")
 
-        x = self.model.image_encoder(x)  
+        x = self.model.image_encoder(x)
 
         if not self.return_features:
             x = self.model.mask_decoder(x)

From 0c605db9a5f7db9dcae0cdf1d7ab1f0ab779ac65 Mon Sep 17 00:00:00 2001
From: myron <amyronenko@nvidia.com>
Date: Mon, 5 Aug 2024 22:44:01 -0700
Subject: [PATCH 03/11] unit test

Signed-off-by: myron <amyronenko@nvidia.com>
---
 monai/networks/nets/cell_sam_wrapper.py | 13 ++---
 tests/test_cell_sam_wrapper.py          | 63 +++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 8 deletions(-)
 create mode 100644 tests/test_cell_sam_wrapper.py

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
index ccca07dee2..b721756461 100644
--- a/monai/networks/nets/cell_sam_wrapper.py
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -15,11 +15,8 @@
 from torch import nn
 from torch.nn import functional as F
 
-try:
-    from segment_anything.build_sam import build_sam_vit_b
-except ImportError:
-    raise AssertionError("SAM is not installed, please run: pip install git+https://github.com/facebookresearch/segment-anything.git")
-
+from monai.utils import optional_import
+build_sam_vit_b, has_sam = optional_import("segment_anything.build_sam", name="build_sam_vit_b")
 
 _all__ = ["CellSamWrapper"]
 
@@ -48,13 +45,13 @@ def __init__(
     ) -> None:
         super().__init__(*args, **kwargs)
 
-        print(
-            f"CellSamWrapper auto_resize_inputs {auto_resize_inputs} network_resize_roi {network_resize_roi} checkpoint {checkpoint}"
-        )
         self.network_resize_roi = network_resize_roi
         self.auto_resize_inputs = auto_resize_inputs
         self.return_features = return_features
 
+        if not has_sam:
+            raise ValueError("SAM is not installed, please run: pip install git+https://github.com/facebookresearch/segment-anything.git")
+        
         model = build_sam_vit_b(checkpoint=checkpoint)
 
         model.prompt_encoder = None
diff --git a/tests/test_cell_sam_wrapper.py b/tests/test_cell_sam_wrapper.py
new file mode 100644
index 0000000000..fa88b311d3
--- /dev/null
+++ b/tests/test_cell_sam_wrapper.py
@@ -0,0 +1,63 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import torch
+from parameterized import parameterized
+
+from monai.networks import eval_mode
+from monai.networks.nets.cell_sam_wrapper import CellSamWrapper
+from tests.utils import SkipIfBeforePyTorchVersion, test_script_save
+
+from monai.utils import optional_import
+build_sam_vit_b, has_sam = optional_import("segment_anything.build_sam", name="build_sam_vit_b")
+
+device = "cuda" if torch.cuda.is_available() else "cpu"
+TEST_CASE_CELLSEGWRAPPER = []
+for auto_resize_inputs in [True, False]:
+    for dims in [128, 256, 512, 1024]:
+            test_case = [
+                {
+                    "auto_resize_inputs": True,
+                    "network_resize_roi": [1024, 1024],
+                    "checkpoint": None,
+                },
+                (1, 3, *([dims] * 2)),
+                (1, 3, *([dims] * 2)),
+            ]
+            TEST_CASE_CELLSEGWRAPPER.append(test_case)
+
+
+@unittest.skipUnless(has_sam, "Requires SAM installation")
+class TestResNetDS(unittest.TestCase):
+
+    @parameterized.expand(TEST_CASE_CELLSEGWRAPPER)
+    def test_shape(self, input_param, input_shape, expected_shape):
+        net = CellSamWrapper(**input_param).to(device)
+        with eval_mode(net):
+            result = net(torch.randn(input_shape).to(device))
+            self.assertEqual(result.shape, expected_shape, msg=str(input_param))
+    
+    def test_ill_arg0(self):
+        with self.assertRaises(RuntimeError):
+            net = CellSamWrapper(auto_resize_inputs=False, checkpoint=None).to(device)
+            net(torch.randn([1, 3, 256, 256]))
+
+    def test_ill_arg1(self):
+        with self.assertRaises(RuntimeError):
+            net = CellSamWrapper(network_resize_roi=[256,256], checkpoint=None).to(device)
+            net(torch.randn([1, 3, 1024, 1024]))
+
+if __name__ == "__main__":
+    unittest.main()

From 14cae5f5e6514e7f9231b3ecec8400f0eda86ac6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 6 Aug 2024 05:45:06 +0000
Subject: [PATCH 04/11] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 monai/networks/nets/cell_sam_wrapper.py | 2 +-
 tests/test_cell_sam_wrapper.py          | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
index b721756461..3bc5db2414 100644
--- a/monai/networks/nets/cell_sam_wrapper.py
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -51,7 +51,7 @@ def __init__(
 
         if not has_sam:
             raise ValueError("SAM is not installed, please run: pip install git+https://github.com/facebookresearch/segment-anything.git")
-        
+
         model = build_sam_vit_b(checkpoint=checkpoint)
 
         model.prompt_encoder = None
diff --git a/tests/test_cell_sam_wrapper.py b/tests/test_cell_sam_wrapper.py
index fa88b311d3..867f8e7d20 100644
--- a/tests/test_cell_sam_wrapper.py
+++ b/tests/test_cell_sam_wrapper.py
@@ -18,7 +18,6 @@
 
 from monai.networks import eval_mode
 from monai.networks.nets.cell_sam_wrapper import CellSamWrapper
-from tests.utils import SkipIfBeforePyTorchVersion, test_script_save
 
 from monai.utils import optional_import
 build_sam_vit_b, has_sam = optional_import("segment_anything.build_sam", name="build_sam_vit_b")
@@ -48,7 +47,7 @@ def test_shape(self, input_param, input_shape, expected_shape):
         with eval_mode(net):
             result = net(torch.randn(input_shape).to(device))
             self.assertEqual(result.shape, expected_shape, msg=str(input_param))
-    
+
     def test_ill_arg0(self):
         with self.assertRaises(RuntimeError):
             net = CellSamWrapper(auto_resize_inputs=False, checkpoint=None).to(device)

From d7d624b9fdf57a2e231a1632e9a9555c80bb2822 Mon Sep 17 00:00:00 2001
From: myron <amyronenko@nvidia.com>
Date: Fri, 9 Aug 2024 10:49:13 -0700
Subject: [PATCH 05/11] edits

Signed-off-by: myron <amyronenko@nvidia.com>
---
 monai/networks/nets/cell_sam_wrapper.py | 6 +++++-
 requirements-dev.txt                    | 1 +
 tests/test_cell_sam_wrapper.py          | 4 ++--
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
index 3bc5db2414..250146554f 100644
--- a/monai/networks/nets/cell_sam_wrapper.py
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -28,9 +28,13 @@ class CellSamWrapper(torch.nn.Module):
 
     Args:
         auto_resize_inputs: whether to resize inputs before passing to the network.
+            (usually they need be resized, unless they are already at the expected size)
         network_resize_roi: expected input size for the network.
+            (currently SAM expects 1024x1024)
         checkpoint: checkpoint file to load the SAM weights from.
-        return_features: whether to return features
+            (this can be downloaded from SAM repo https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth)
+        return_features: whether to return features from SAM encoder 
+            (without using decoder/upsampling to the original input size)
 
     """
 
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 72ba210093..76f1952345 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -59,3 +59,4 @@ nvidia-ml-py
 huggingface_hub
 pyamg>=5.0.0
 git+https://github.com/Project-MONAI/GenerativeModels.git@7428fce193771e9564f29b91d29e523dd1b6b4cd
+git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588
diff --git a/tests/test_cell_sam_wrapper.py b/tests/test_cell_sam_wrapper.py
index 867f8e7d20..d2be6880bf 100644
--- a/tests/test_cell_sam_wrapper.py
+++ b/tests/test_cell_sam_wrapper.py
@@ -51,12 +51,12 @@ def test_shape(self, input_param, input_shape, expected_shape):
     def test_ill_arg0(self):
         with self.assertRaises(RuntimeError):
             net = CellSamWrapper(auto_resize_inputs=False, checkpoint=None).to(device)
-            net(torch.randn([1, 3, 256, 256]))
+            net(torch.randn([1, 3, 256, 256]).to(device))
 
     def test_ill_arg1(self):
         with self.assertRaises(RuntimeError):
             net = CellSamWrapper(network_resize_roi=[256,256], checkpoint=None).to(device)
-            net(torch.randn([1, 3, 1024, 1024]))
+            net(torch.randn([1, 3, 1024, 1024]).to(device))
 
 if __name__ == "__main__":
     unittest.main()

From a41a615962bded7969abb6f06cf42aad7d0ffe26 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 9 Aug 2024 17:51:48 +0000
Subject: [PATCH 06/11] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 monai/networks/nets/cell_sam_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
index 250146554f..b849d5f259 100644
--- a/monai/networks/nets/cell_sam_wrapper.py
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -33,7 +33,7 @@ class CellSamWrapper(torch.nn.Module):
             (currently SAM expects 1024x1024)
         checkpoint: checkpoint file to load the SAM weights from.
             (this can be downloaded from SAM repo https://dl.fbaipublicfiles.com/segment_anything/sam_vit_b_01ec64.pth)
-        return_features: whether to return features from SAM encoder 
+        return_features: whether to return features from SAM encoder
             (without using decoder/upsampling to the original input size)
 
     """

From 24afcb46887a054feabaa320649258940fbaa5b8 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Sat, 10 Aug 2024 16:57:23 +0800
Subject: [PATCH 07/11] format fix

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/networks/nets/cell_sam_wrapper.py |  6 +++++-
 tests/test_cell_sam_wrapper.py          | 21 +++++++++------------
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
index b849d5f259..c984929147 100644
--- a/monai/networks/nets/cell_sam_wrapper.py
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -16,10 +16,12 @@
 from torch.nn import functional as F
 
 from monai.utils import optional_import
+
 build_sam_vit_b, has_sam = optional_import("segment_anything.build_sam", name="build_sam_vit_b")
 
 _all__ = ["CellSamWrapper"]
 
+
 class CellSamWrapper(torch.nn.Module):
     """
     CellSamWrapper is thin wrapper around SAM model https://github.com/facebookresearch/segment-anything
@@ -54,7 +56,9 @@ def __init__(
         self.return_features = return_features
 
         if not has_sam:
-            raise ValueError("SAM is not installed, please run: pip install git+https://github.com/facebookresearch/segment-anything.git")
+            raise ValueError(
+                "SAM is not installed, please run: pip install git+https://github.com/facebookresearch/segment-anything.git"
+            )
 
         model = build_sam_vit_b(checkpoint=checkpoint)
 
diff --git a/tests/test_cell_sam_wrapper.py b/tests/test_cell_sam_wrapper.py
index d2be6880bf..d0f3b1bc9e 100644
--- a/tests/test_cell_sam_wrapper.py
+++ b/tests/test_cell_sam_wrapper.py
@@ -18,24 +18,20 @@
 
 from monai.networks import eval_mode
 from monai.networks.nets.cell_sam_wrapper import CellSamWrapper
-
 from monai.utils import optional_import
+
 build_sam_vit_b, has_sam = optional_import("segment_anything.build_sam", name="build_sam_vit_b")
 
 device = "cuda" if torch.cuda.is_available() else "cpu"
 TEST_CASE_CELLSEGWRAPPER = []
 for auto_resize_inputs in [True, False]:
     for dims in [128, 256, 512, 1024]:
-            test_case = [
-                {
-                    "auto_resize_inputs": True,
-                    "network_resize_roi": [1024, 1024],
-                    "checkpoint": None,
-                },
-                (1, 3, *([dims] * 2)),
-                (1, 3, *([dims] * 2)),
-            ]
-            TEST_CASE_CELLSEGWRAPPER.append(test_case)
+        test_case = [
+            {"auto_resize_inputs": True, "network_resize_roi": [1024, 1024], "checkpoint": None},
+            (1, 3, *([dims] * 2)),
+            (1, 3, *([dims] * 2)),
+        ]
+        TEST_CASE_CELLSEGWRAPPER.append(test_case)
 
 
 @unittest.skipUnless(has_sam, "Requires SAM installation")
@@ -55,8 +51,9 @@ def test_ill_arg0(self):
 
     def test_ill_arg1(self):
         with self.assertRaises(RuntimeError):
-            net = CellSamWrapper(network_resize_roi=[256,256], checkpoint=None).to(device)
+            net = CellSamWrapper(network_resize_roi=[256, 256], checkpoint=None).to(device)
             net(torch.randn([1, 3, 1024, 1024]).to(device))
 
+
 if __name__ == "__main__":
     unittest.main()

From 8ee636fb900d2df4b398e4f2509a391dabbdce48 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Sat, 10 Aug 2024 17:22:19 +0800
Subject: [PATCH 08/11] fix format issue

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/networks/nets/cell_sam_wrapper.py |  2 +-
 tests/test_cell_sam_wrapper.py          | 15 +++++++--------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/monai/networks/nets/cell_sam_wrapper.py b/monai/networks/nets/cell_sam_wrapper.py
index c984929147..308c3a6bcb 100644
--- a/monai/networks/nets/cell_sam_wrapper.py
+++ b/monai/networks/nets/cell_sam_wrapper.py
@@ -43,7 +43,7 @@ class CellSamWrapper(torch.nn.Module):
     def __init__(
         self,
         auto_resize_inputs=True,
-        network_resize_roi=[1024, 1024],
+        network_resize_roi=(1024, 1024),
         checkpoint="sam_vit_b_01ec64.pth",
         return_features=False,
         *args,
diff --git a/tests/test_cell_sam_wrapper.py b/tests/test_cell_sam_wrapper.py
index d0f3b1bc9e..2f1ee2b901 100644
--- a/tests/test_cell_sam_wrapper.py
+++ b/tests/test_cell_sam_wrapper.py
@@ -24,14 +24,13 @@
 
 device = "cuda" if torch.cuda.is_available() else "cpu"
 TEST_CASE_CELLSEGWRAPPER = []
-for auto_resize_inputs in [True, False]:
-    for dims in [128, 256, 512, 1024]:
-        test_case = [
-            {"auto_resize_inputs": True, "network_resize_roi": [1024, 1024], "checkpoint": None},
-            (1, 3, *([dims] * 2)),
-            (1, 3, *([dims] * 2)),
-        ]
-        TEST_CASE_CELLSEGWRAPPER.append(test_case)
+for dims in [128, 256, 512, 1024]:
+    test_case = [
+        {"auto_resize_inputs": True, "network_resize_roi": [1024, 1024], "checkpoint": None},
+        (1, 3, *([dims] * 2)),
+        (1, 3, *([dims] * 2)),
+    ]
+    TEST_CASE_CELLSEGWRAPPER.append(test_case)
 
 
 @unittest.skipUnless(has_sam, "Requires SAM installation")

From b5c79f1b5924da134008d17e9950f50342c20beb Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Sat, 10 Aug 2024 17:42:37 +0800
Subject: [PATCH 09/11] try add it in setup.cfg

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 setup.cfg | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/setup.cfg b/setup.cfg
index dfa94fcfa1..657039c71a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -85,6 +85,7 @@ all =
     nvidia-ml-py
     huggingface_hub
     pyamg>=5.0.0
+    segment-anything
 nibabel =
     nibabel
 ninja =
@@ -167,6 +168,8 @@ huggingface_hub =
     huggingface_hub
 pyamg =
     pyamg>=5.0.0
+segment-anything =
+    git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588
 
 [flake8]
 select = B,C,E,F,N,P,T4,W,B9

From 6d4a047e20da8c93a98529bf541dc3a05c75b122 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Sat, 10 Aug 2024 17:47:00 +0800
Subject: [PATCH 10/11] add it in setup.cfg

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 setup.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 657039c71a..e240445e36 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -163,13 +163,13 @@ pynvml =
     nvidia-ml-py
 # # workaround https://github.com/Project-MONAI/MONAI/issues/5882
 # MetricsReloaded =
-#     MetricsReloaded @ git+https://github.com/Project-MONAI/MetricsReloaded@monai-support#egg=MetricsReloaded
+    # MetricsReloaded @ git+https://github.com/Project-MONAI/MetricsReloaded@monai-support#egg=MetricsReloaded
 huggingface_hub =
     huggingface_hub
 pyamg =
     pyamg>=5.0.0
 segment-anything =
-    git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588
+    segment-anything @ git+https://github.com/facebookresearch/segment-anything@6fdee8f2727f4506cfbbe553e23b895e27956588#egg=segment-anything
 
 [flake8]
 select = B,C,E,F,N,P,T4,W,B9

From 53ac8e1e38e2bf94cf01c776ae5b762cc68b24ba Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Sat, 10 Aug 2024 17:51:43 +0800
Subject: [PATCH 11/11] update installation md

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 docs/source/installation.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/installation.md b/docs/source/installation.md
index 4308a07647..70a8b6f1d4 100644
--- a/docs/source/installation.md
+++ b/docs/source/installation.md
@@ -254,10 +254,10 @@ Since MONAI v0.2.0, the extras syntax such as `pip install 'monai[nibabel]'` is
 - The options are
 
 ```
-[nibabel, skimage, scipy, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, clearml, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna, onnx, onnxruntime, zarr, lpips, pynvml, huggingface_hub]
+[nibabel, skimage, scipy, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, clearml, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna, onnx, onnxruntime, zarr, lpips, pynvml, huggingface_hub, segment-anything]
 ```
 
 which correspond to `nibabel`, `scikit-image`,`scipy`, `pillow`, `tensorboard`,
-`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `clearml`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, `onnx`, `onnxruntime`, `zarr`, `lpips`, `nvidia-ml-py`, `huggingface_hub` and `pyamg` respectively.
+`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `clearml`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, `onnx`, `onnxruntime`, `zarr`, `lpips`, `nvidia-ml-py`, `huggingface_hub`, `pyamg` and `segment-anything` respectively.
 
 - `pip install 'monai[all]'` installs all the optional dependencies.