initial commit

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
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+target/
+
+# Jupyter Notebook
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+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
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+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
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+
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+
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+/site
+
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+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

README.md

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+# Transferring Relative Monocular Depth to Surgical Vision with Temporal Consistency
+This is the official repository for our state-of-the-art approach to monocular depth in surgical vision as presented in our paper...
+<ul><b>Transferring Relative Monocular Depth to Surgical Vision with Temporal Consistency</b><br>
+    Charlie Budd, Tom Vercauteren.<br>
+    [ <a href="https://arxiv.org/abs/2403.06683">arXiv</a> ] 
+</ul>
+
+# Using Our Models
+First, install our package...
+```
+pip install git+https://github.com/charliebudd/transferring-relative-monocular-depth-to-surgical-vision
+```
+Then download one of our models weights from the [release tab]() in this repo. We would reccomend our best performer, `da-sup-temp.pt`. The model may then be used as follows...
+```python
+import torch
+from torchvision.io import read_image
+from torchvision.transforms.functional import resize
+import matplotlib.pyplot as plt
+
+from trmdsv import load_model
+
+model, resize_for_model, normalise_for_model = load_model("midas", "weights/path.pt", "cuda")
+model.eval()
+
+image = read_image("surgical_image.png").cuda() / 255.0
+original_size = image.shape[-2:]
+image_for_model = normalise_for_model(resize_for_model(image.unsqueeze(0)))
+
+with torch.no_grad():
+    depth = model(image_for_model)
+
+depth = resize(depth, original_size)
+
+plt.subplot(121).axis("off")
+plt.imshow(image.cpu().permute(1, 2, 0))
+plt.subplot(122).axis("off")
+plt.imshow(depth.cpu().permute(1, 2, 0))
+plt.show()
+
+```
+
+# Recreating Our Results
+\### awaiting publication \###

requirements.txt

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+torch==2.2.0
+torchvision==0.17.0
+timm

setup.py

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+from setuptools import setup
+
+setup(
+    name='trmdsv',
+    author='Charlie Budd',
+    author_email='[email protected]',
+    url='https://github.com/charliebudd/transferring-relative-monocular-depth-to-surgical-vision',
+    license='MIT',
+    package_dir={'':'src'},
+    packages=['trmdsv'],
+)

src/trmdsv/__init__.py

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+from .trmdsv import load_model

src/trmdsv/third_party/depthanything/blocks.py

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+import torch.nn as nn
+
+
+def _make_scratch(in_shape, out_shape, groups=1, expand=False):
+    scratch = nn.Module()
+
+    out_shape1 = out_shape
+    out_shape2 = out_shape
+    out_shape3 = out_shape
+    if len(in_shape) >= 4:
+        out_shape4 = out_shape
+
+    if expand:
+        out_shape1 = out_shape
+        out_shape2 = out_shape*2
+        out_shape3 = out_shape*4
+        if len(in_shape) >= 4:
+            out_shape4 = out_shape*8
+
+    scratch.layer1_rn = nn.Conv2d(
+        in_shape[0], out_shape1, kernel_size=3, stride=1, padding=1, bias=False, groups=groups
+    )
+    scratch.layer2_rn = nn.Conv2d(
+        in_shape[1], out_shape2, kernel_size=3, stride=1, padding=1, bias=False, groups=groups
+    )
+    scratch.layer3_rn = nn.Conv2d(
+        in_shape[2], out_shape3, kernel_size=3, stride=1, padding=1, bias=False, groups=groups
+    )
+    if len(in_shape) >= 4:
+        scratch.layer4_rn = nn.Conv2d(
+            in_shape[3], out_shape4, kernel_size=3, stride=1, padding=1, bias=False, groups=groups
+        )
+
+    return scratch
+
+
+class ResidualConvUnit(nn.Module):
+    """Residual convolution module.
+    """
+
+    def __init__(self, features, activation, bn):
+        """Init.
+
+        Args:
+            features (int): number of features
+        """
+        super().__init__()
+
+        self.bn = bn
+
+        self.groups=1
+
+        self.conv1 = nn.Conv2d(
+            features, features, kernel_size=3, stride=1, padding=1, bias=True, groups=self.groups
+        )
+
+        self.conv2 = nn.Conv2d(
+            features, features, kernel_size=3, stride=1, padding=1, bias=True, groups=self.groups
+        )
+
+        if self.bn==True:
+            self.bn1 = nn.BatchNorm2d(features)
+            self.bn2 = nn.BatchNorm2d(features)
+
+        self.activation = activation
+
+        self.skip_add = nn.quantized.FloatFunctional()
+
+    def forward(self, x):
+        """Forward pass.
+
+        Args:
+            x (tensor): input
+
+        Returns:
+            tensor: output
+        """
+
+        out = self.activation(x)
+        out = self.conv1(out)
+        if self.bn==True:
+            out = self.bn1(out)
+
+        out = self.activation(out)
+        out = self.conv2(out)
+        if self.bn==True:
+            out = self.bn2(out)
+
+        if self.groups > 1:
+            out = self.conv_merge(out)
+
+        return self.skip_add.add(out, x)
+
+
+class FeatureFusionBlock(nn.Module):
+    """Feature fusion block.
+    """
+
+    def __init__(self, features, activation, deconv=False, bn=False, expand=False, align_corners=True, size=None):
+        """Init.
+
+        Args:
+            features (int): number of features
+        """
+        super(FeatureFusionBlock, self).__init__()
+
+        self.deconv = deconv
+        self.align_corners = align_corners
+
+        self.groups=1
+
+        self.expand = expand
+        out_features = features
+        if self.expand==True:
+            out_features = features//2
+
+        self.out_conv = nn.Conv2d(features, out_features, kernel_size=1, stride=1, padding=0, bias=True, groups=1)
+
+        self.resConfUnit1 = ResidualConvUnit(features, activation, bn)
+        self.resConfUnit2 = ResidualConvUnit(features, activation, bn)
+
+        self.skip_add = nn.quantized.FloatFunctional()
+
+        self.size=size
+
+    def forward(self, *xs, size=None):
+        """Forward pass.
+
+        Returns:
+            tensor: output
+        """
+        output = xs[0]
+
+        if len(xs) == 2:
+            res = self.resConfUnit1(xs[1])
+            output = self.skip_add.add(output, res)
+
+        output = self.resConfUnit2(output)
+
+        if (size is None) and (self.size is None):
+            modifier = {"scale_factor": 2}
+        elif size is None:
+            modifier = {"size": self.size}
+        else:
+            modifier = {"size": size}
+
+        output = nn.functional.interpolate(
+            output, **modifier, mode="bilinear", align_corners=self.align_corners
+        )
+
+        output = self.out_conv(output)
+
+        return output

src/trmdsv/third_party/depthanything/dinov2/__init__.py

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+# Copyright (c) Meta Platforms, Inc. and affiliates.
+#
+# This source code is licensed under the Apache License, Version 2.0
+# found in the LICENSE file in the root directory of this source tree.
+
+__version__ = "0.0.1"