Update/dash 3d image partitioning

apps/dash-3d-image-partitioning/.gitignore

@@ -2,3 +2,4 @@ tags
 *~
 venv*
 __pycache__
+.venv

apps/dash-3d-image-partitioning/README.md

@@ -2,22 +2,27 @@
 
 ## Setup
 
-run `./setup` to create the virtualenv and download the necessary libraries.
-This will also set up the git submodules.
+run `./setup` to install the cairo system library (via brew, apt or dnf),
+create the virtualenv and download the necessary libraries. Needs python 3.12
+or newer.
 
-To run programs in this directory, do `source venv/bin/activate` after running
+To run programs in this directory, do `source .venv/bin/activate` after running
 `./setup`.
 
+Alternatively, with [uv](https://docs.astral.sh/uv/), run `uv sync`. Note that
+this does not install cairo; run `./setup` first or install it yourself.
+
 ## Running
 
 A recommended command line is
 
 ```bash
-LOAD_SUPERPIXEL=assets/BraTS19_2013_10_1_flair_superpixels.npz.gz \
-PYTHONPATH=plotly-common \
-python app.py
+python run_dev.py
 ```
 
+This runs `app.py` with `LOAD_SUPERPIXEL` pointing at the precomputed
+superpixel file in `assets`.
+
 Then you can navigate to the displayed link in your browser. You can also run
 without specifying `LOAD_SUPERPIXEL`, in which case the segmentation will happen
 when the app loads.

apps/dash-3d-image-partitioning/app.py

@@ -1,7 +1,6 @@
 import dash
 from dash.dependencies import Input, Output, State, ClientsideFunction
-import dash_html_components as html
-import dash_core_components as dcc
+from dash import html, dcc
 import plotly.graph_objects as go
 from skimage import data, img_as_ubyte, segmentation, measure
 from dash_canvas.utils import array_to_data_url
@@ -53,7 +52,7 @@ def make_seg_image(img):
     is clear (alpha=0) where there are no boundaries. """
     segb = np.zeros_like(img).astype("uint8")
     seg = segmentation.slic(
-        img, start_label=1, multichannel=False, compactness=0.1, n_segments=300
+        img, start_label=1, channel_axis=None, compactness=0.1, n_segments=300
     )
     # Only keep superpixels with an average intensity greater than threshold
     # in order to remove superpixels of the background
@@ -122,7 +121,7 @@ def make_default_figure(
 
 
 img = image.load_img("assets/BraTS19_2013_10_1_flair.nii")
-img = img.get_data().transpose(2, 0, 1)[::-1].astype("float")
+img = img.get_fdata().transpose(2, 0, 1)[::-1].astype("float")
 img = img_as_ubyte((img - img.min()) / (img.max() - img.min()))
 
 
@@ -1023,4 +1022,4 @@ def update_click_output(button_click, close_click):
 
 
 if __name__ == "__main__":
-    app.run_server(debug=DEBUG)
+    app.run(debug=DEBUG)

apps/dash-3d-image-partitioning/plotly-common/plot_common.py

@@ -4,7 +4,7 @@
 import numpy as np
 import plotly.graph_objects as go
 import skimage.util
-from plotly.utils import ImageUriValidator
+from _plotly_utils.basevalidators import ImageUriValidator
 import re
 
 

apps/dash-3d-image-partitioning/pyproject.toml

@@ -0,0 +1,24 @@
+[project]
+name = "dash-3d-image-partitioning"
+version = "0.1.0"
+requires-python = ">=3.12"
+dependencies = [
+    "dash>=4.4.1",
+    "dash-canvas>=0.1.0",
+    "plotly>=7.0.0",
+    "scikit-image>=0.26.0",
+    "numpy>=2.5.2",
+    "nilearn>=0.14.1",
+    "nibabel>=5.4.2",
+    "cairosvg>=2.9.0",
+    "pillow>=12.3.0",
+    "gunicorn>=26.2.0",
+]
+
+[build-system]
+requires = ["setuptools>=80"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+package-dir = { "" = "plotly-common" }
+py-modules = ["plot_common", "image_utils", "shape_utils", "app_utils"]

apps/dash-3d-image-partitioning/requirements.txt

@@ -1,75 +1,57 @@
-appdirs==1.4.4
-attrs==19.3.0
-backcall==0.2.0
-black==19.10b0
-Brotli==1.0.7
-cairocffi==1.1.0
-CairoSVG==2.4.2
-cffi==1.14.0
-click==7.1.2
-cssselect2==0.3.0
-cycler==0.10.0
-dash==1.14.0
+-e .
+annotated-types==0.8.0
+blinker==1.9.0
+cairocffi==1.7.1
+cairosvg==2.9.0
+certifi==2026.7.22
+cffi==2.1.1
+charset-normalizer==3.5.1
+click==8.5.0
+cloudpickle==3.1.2
+comm==0.2.3
+cssselect2==0.10.1
+dash==4.4.1
 dash-canvas==0.1.0
-dash-core-components==1.10.2
-dash-html-components==1.0.3
-dash-renderer==1.6.0
-dash-table==4.9.0
-decorator==4.4.2
-defusedxml==0.6.0
-Flask==1.1.2
-Flask-Compress==1.5.0
-future==0.18.2
-gunicorn==20.0.4
-imageio==2.8.0
-importlib-metadata==1.6.1
-ipython==7.15.0
-ipython-genutils==0.2.0
-itsdangerous==1.1.0
-jedi==0.17.0
-Jinja2==2.11.2
-joblib==0.15.1
-jsonschema==3.2.0
-jupyter-core==4.6.3
-kiwisolver==1.2.0
-MarkupSafe==1.1.1
-matplotlib==3.2.1
-nbformat==5.0.7
-networkx==2.4
-nibabel==3.1.0
-nilearn==0.6.2
-numpy==1.18.5
-packaging==20.4
-pandas==1.0.4
-parso==0.7.0
-pathspec==0.8.0
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow==8.2.0
-plotly==4.8.2
-prompt-toolkit==3.0.5
-ptyprocess==0.6.0
-pycparser==2.20
-Pygments==2.6.1
-pyparsing==2.4.7
-pyrsistent==0.16.0
-python-dateutil==2.8.1
-pytz==2020.1
-PyWavelets==1.1.1
-regex==2020.6.8
-retrying==1.3.3
-scikit-image==0.17.2
-scikit-learn==0.23.1
-scipy==1.4.1
-six==1.15.0
-sklearn==0.0
-threadpoolctl==2.1.0
-tifffile==2020.6.3
-tinycss2==1.0.2
-toml==0.10.1
-traitlets==4.3.3
-typed-ast==1.4.1
-wcwidth==0.2.4
-webencodings==0.5.1
-Werkzeug==1.0.1
-zipp==3.1.0
+defusedxml==0.7.1
+flask==3.1.3
+gunicorn==26.2.0
+idna==3.19
+imageio==2.37.4
+importlib-metadata==9.0.1
+itsdangerous==2.2.0
+janus==2.0.0
+jinja2==3.1.6
+joblib==1.6.0
+lazy-loader==0.5
+markupsafe==3.0.3
+narwhals==2.25.0
+nest-asyncio==1.6.0
+networkx==3.6.1
+nibabel==5.4.2
+nilearn==0.14.1
+numpy==2.5.2
+packaging==26.3
+pandas==3.0.5
+pillow==12.3.0
+plotly==7.0.0
+pycparser==3.0 ; implementation_name != 'PyPy'
+pydantic==2.13.5
+pydantic-core==2.46.5
+python-dateutil==2.9.0.post0
+requests==2.34.2
+retrying==1.4.2
+scikit-image==0.26.0
+scikit-learn==1.8.0
+scipy==1.18.1
+setuptools==84.0.0
+six==1.17.0
+threadpoolctl==3.6.0
+tifffile==2026.8.23
+tinycss2==1.5.1
+typing-extensions==4.16.0
+typing-inspection==0.4.4
+tzdata==2026.3 ; sys_platform == 'emscripten' or sys_platform == 'win32'
+urllib3==2.7.0
+webencodings==0.6.1
+werkzeug==3.1.8
+zipp==4.1.0

apps/dash-3d-image-partitioning/run_app.sh

@@ -1,4 +1,8 @@
-gunicorn \
+# On Apple Silicon, Homebrew installs libcairo under /opt/homebrew/lib, which
+# macOS does not search by default. No-op elsewhere.
+[ -d /opt/homebrew/lib ] && export DYLD_FALLBACK_LIBRARY_PATH=/opt/homebrew/lib
+
+python -m gunicorn \
 --pythonpath plotly-common \
 -e LOAD_SUPERPIXEL=assets/BraTS19_2013_10_1_flair_superpixels.npz.gz \
 app:server

apps/dash-3d-image-partitioning/run_dev.py

@@ -0,0 +1,31 @@
+"""Start the Dash development server with the environment app.py expects.
+
+Works the same on macOS, Linux and Windows:
+
+    uv run run_dev.py        (or: python run_dev.py)
+
+Any environment variable you set yourself (LOAD_SUPERPIXEL, SAVE_SUPERPIXEL,
+DEBUG, ...) is passed through unchanged.
+"""
+
+import os
+import subprocess
+import sys
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+PRECOMPUTED = "assets/BraTS19_2013_10_1_flair_superpixels.npz.gz"
+
+env = dict(os.environ)
+
+# if no LOAD/SAVE path given: load the precomputed superpixels from assets/
+if not env.get("LOAD_SUPERPIXEL") and not env.get("SAVE_SUPERPIXEL"):
+    env["LOAD_SUPERPIXEL"] = PRECOMPUTED
+
+# On Apple Silicon, Homebrew installs libcairo under /opt/homebrew/lib, which
+# macOS does not search by default. No-op elsewhere.
+if sys.platform == "darwin" and os.path.isdir("/opt/homebrew/lib"):
+    env.setdefault("DYLD_FALLBACK_LIBRARY_PATH", "/opt/homebrew/lib")
+
+sys.exit(
+    subprocess.call([sys.executable, "app.py", *sys.argv[1:]], cwd=HERE, env=env)
+)

apps/dash-3d-image-partitioning/setup

@@ -1,22 +1,39 @@
 #!/bin/bash
 
 
-[ -d "venv" ] && (echo "venv already exisits, aborting..." && exit 1)
-[ "$VIRTUAL_ENV" == "" ] || (echo "virtual env already active, aborting..." && exit 2)
+[ -d ".venv" ] && { echo ".venv already exists, aborting..."; exit 1; }
+[ "$VIRTUAL_ENV" == "" ] || { echo "virtual env already active, aborting..."; exit 2; }
+
+# need python 3.12 or newer
+python3 -c 'import sys; sys.exit(sys.version_info < (3, 12))' 2> /dev/null \
+    || { echo "needs python 3.12 or newer, found: $(python3 --version 2>&1)"; exit 3; }
+
+# install the cairo library that cairosvg needs
+if [ "$(uname)" == "Darwin" ]; then
+    command -v brew > /dev/null || { echo "Homebrew is needed to install cairo: https://brew.sh"; exit 1; }
+    brew list cairo > /dev/null 2>&1 && echo "cairo already installed" || brew install cairo
+elif command -v apt-get > /dev/null; then
+    dpkg -s libcairo2 > /dev/null 2>&1 && echo "cairo already installed" || sudo apt-get install -y libcairo2
+elif command -v dnf > /dev/null; then
+    rpm -q cairo > /dev/null 2>&1 && echo "cairo already installed" || sudo dnf install -y cairo
+else
+    echo "install the cairo library with your package manager, then rerun ./setup"
+    exit 1
+fi
 
 # create virtual environment
-[ -d "venv" ] || virtualenv --prompt '(`basename $PWD`/`basename "$VIRTUAL_ENV"`)' venv
+python3 -m venv --prompt "$(basename "$PWD")" .venv
 
-source venv/bin/activate
+source .venv/bin/activate
 
 # install requirements
 [ "$VIRTUAL_ENV" == "" ] \
     && echo "Error starting virtual environment." \
-    || (pip install -r requirements.txt && cat <<DOC
+    || (python -m pip install -r requirements.txt && cat <<DOC
 
 setup successful
 don't forget to 
-  source venv/bin/activate
+  source .venv/bin/activate
 before getting to work :-)
 DOC
 )