restructure data

.gitignore

@@ -1,5 +1,10 @@
 __pycache__/
+data/
+out/
+src/
+GroundingDINO/
 *.jpg
+*.gif
 *.png
 *.pt
 *.pth

README.md

@@ -20,18 +20,22 @@ To use SST, the following setup must be ran on a GPU enabled machine. The code r
 
 Example Conda Environment Setup:
 ```bash
+# clone repo
+(git clone https://github.com/Imageomics/SST.git && cd SST)
 # Create conda environment
 conda create --name sst python=3.10.14
 conda activate sst
-# Download corresponding torch torchvision version
+# Download PyTorch corresponding to the CUDA version of the GPU
 ...
+# Download and setup GroundingDINO
+(git clone https://github.com/IDEA-Research/GroundingDINO.git && cd GroundingDINO/ && pip install -e .)
 # Download required python packages
 pip install -r requirements.txt --no-dependencies
 # Download model checkpoints
 (cd checkpoints && ./download_ckpts.sh)
 (cd checkpoints && wget -q https://github.com/IDEA-Research/GroundingDINO/releases/download/v0.1.0-alpha/groundingdino_swint_ogc.pth)
 # Install SAM 2
-(cd sam2 && pip install -e .)
+(cd segment-anything-2 && pip install -e .)
 ```
 
 ## 🧑‍💻 Usage

code/sam_utils.py

@@ -147,7 +147,7 @@ def show_anns(anns, color=None, borders=True):
 
     ax.imshow(img)
 
-def build_sam2_predictor(checkpoint="../../checkpoints/sam2_hiera_large.pt", model_cfg="../../sam2_configs/sam2_hiera_l.yaml"):
+def build_sam2_predictor(checkpoint="checkpoints/sam2_hiera_large.pt", model_cfg="sam2_hiera_l"):
     device = "cuda" if torch.cuda.is_available() else "cpu"
     video_predictor = build_sam2_video_predictor(model_cfg, checkpoint, device=device, apply_postprocessing=False)
     return video_predictor

code/segment.py

@@ -1,4 +1,3 @@
-#%%
 import os
 import numpy as np
 import matplotlib.pyplot as plt
@@ -24,6 +23,7 @@
 output_format = args.output_format
 
 # load the support image and mask
+print ("Loading support image and mask...")
 support_image = cv2.imread(support_image_path)[..., ::-1]
 support_mask = cv2.imread(support_mask_path, cv2.IMREAD_GRAYSCALE)
 support_masks = [support_mask == i for i in range(1, support_mask.max()+1)]
@@ -36,11 +36,13 @@
 video_predictor = sam_utils.build_sam2_predictor()
 
 # load the support image and mask
+print ("Inferring the masks...")
 state = sam_utils.load_masks(video_predictor, query_images, support_image, support_masks, verbose=True)
 frames_info = sam_utils.propagate_masks(video_predictor, state, verbose=True)
 
 # visualize the results
 output_imgs = []
+print ("Visualizing the results...")
 for i, frame in enumerate(frames_info):
     plt.clf()
     plt.figure(figsize=(10, 10))
@@ -61,8 +63,10 @@
 if not os.path.exists(output_folder):
     os.makedirs(output_folder)
 if output_format == 'gif':
-    output_imgs[0].save(output_folder, save_all=True, append_images=output_imgs[1:], loop=0, duration=1000)
+    output_imgs[0].save(os.path.join(output_folder, "out.gif"), save_all=True, append_images=output_imgs[1:], loop=0, duration=1000)
 else:
     for i, img in enumerate(output_imgs):
         img.save(os.path.join(output_folder, f"{i:06d}.png"))
 
+print ("Done! The output is saved in", output_folder)
+

requirements.txt

@@ -69,7 +69,6 @@ GitPython==3.1.43
 google-pasta==0.2.0
 gradio==3.32.0
 gradio_client==0.2.5
--e git+https://github.com/IDEA-Research/GroundingDINO.git@856dde20aee659246248e20734ef9ba5214f5e44#egg=groundingdino
 grpcio==1.66.1
 h11==0.14.0
 h5py==3.11.0

segment-anything-2/.clang-format

@@ -0,0 +1,85 @@
+AccessModifierOffset: -1
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands:   false
+AlignTrailingComments: false
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: false
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ForEachMacros:   [ FOR_EACH, FOR_EACH_R, FOR_EACH_RANGE, ]
+IncludeCategories:
+  - Regex:           '^<.*\.h(pp)?>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IndentCaseLabels: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never

segment-anything-2/.gitignore

@@ -0,0 +1,24 @@
+.vscode/
+.DS_Store
+__pycache__/
+*-checkpoint.ipynb
+.venv
+*.egg*
+build/*
+_C.*
+outputs/*
+*.pt
+*.sh
+data/*
+*.jpg
+*.png
+results/*
+sav_dataset/*
+*.gz
+*.zip
+*.out
+*.log
+*.pkl
+*.pdf
+*.gif
+

segment-anything-2/LICENSE

@@ -0,0 +1,20 @@
+Copyright (c) 2023-2024 Imageomics Institute
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

segment-anything-2/README.md

@@ -0,0 +1,3 @@
+# SST
+
+Repository for the paper Static Segmentation by Tracking: A Frustratingly Label-Efficient Approach to Fine-Grained Segmentation.

segment-anything-2/pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = [
+    "setuptools>=61.0",  
+    "torch>=2.3.1",
+    ]
+build-backend = "setuptools.build_meta"