Merge pull request #240 from stardist/dev

Changes for 0.8.4 release

.github/workflows/cibuildwheel.yml

@@ -22,8 +22,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-10.15]
-        py: [cp36, cp37, cp38, cp39, cp310]
+        os: [ubuntu-20.04, windows-2019, macos-11]
+        py: [cp36, cp37, cp38, cp39, cp310, cp311]
 
     steps:
       - uses: actions/checkout@v3
@@ -37,6 +37,7 @@ jobs:
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel
 
+        # https://scikit-learn.org/stable/developers/advanced_installation.html#macos
       - name: Setup OpenMP (macOS)
         if: startsWith(matrix.os, 'macos')
         shell: bash
@@ -47,9 +48,9 @@ jobs:
           tee -a $GITHUB_ENV << END
           CC=/usr/bin/clang
           CXX=/usr/bin/clang++
-          CFLAGS=${CFLAGS} -I${HOMEBREW_PREFIX}/include
-          CXXFLAGS=${CXXFLAGS} -I${HOMEBREW_PREFIX}/include
-          LDFLAGS=${LDFLAGS} -Wl,-rpath,${HOMEBREW_PREFIX}/lib -L${HOMEBREW_PREFIX}/lib -lomp
+          CFLAGS=${CFLAGS} -I${HOMEBREW_PREFIX}/opt/libomp/include
+          CXXFLAGS=${CXXFLAGS} -I${HOMEBREW_PREFIX}/opt/libomp/include
+          LDFLAGS=${LDFLAGS} -Wl,-rpath,${HOMEBREW_PREFIX}/opt/libomp/lib -L${HOMEBREW_PREFIX}/opt/libomp/lib -lomp
           END
 
       - name: Build wheels for CPython (macOS)
@@ -128,4 +129,4 @@ jobs:
           password: ${{ secrets.PYPI_API_TOKEN }}
           verbose: true
           # password: ${{ secrets.TESTPYPI_API_TOKEN }}
-          # repository_url: https://test.pypi.org/legacy/
+          # repository-url: https://test.pypi.org/legacy/

.github/workflows/tests.yml

@@ -19,16 +19,18 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04, windows-latest, macos-latest]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
         tensorflow: [1, 2]
         exclude:
-            # https://www.tensorflow.org/install/pip#system-requirements
+            # https://www.tensorflow.org/install/source#tested_build_configurations
           - python-version: '3.8'
             tensorflow: 1
           - python-version: '3.9'
             tensorflow: 1
           - python-version: '3.10'
             tensorflow: 1
+          - python-version: '3.11'
+            tensorflow: 1
           - os: windows-latest
             tensorflow: 1
 
@@ -51,7 +53,7 @@ jobs:
         if: matrix.python-version == 3.9
         run: pip install edt "numpy>=1.20"
 
-      # # should also work with clang, but there are
+      # # should also work with clang, but there are 
       # # openmp-related symbol issues just when using Python 3.6?
       # - name: Use GCC on macOS
       #   if: startsWith(matrix.os, 'macos')
@@ -66,8 +68,13 @@ jobs:
 
       - name: Install bioimage.io dependencies
         if: |
-          matrix.python-version >= 3.7 &&
+          matrix.python-version == 3.7 &&
           matrix.tensorflow == 1
         run: pip install ".[bioimageio]"
 
-      - run: pytest -v --durations=50 -m "not gpu"
+      - name: Disable PytestReturnNotNoneWarning (Python 3.7+)
+        if: matrix.python-version != 3.6
+        run: echo "PYTEST_ADDOPTS='-W ignore::pytest.PytestReturnNotNoneWarning'" >> $GITHUB_ENV
+        shell: bash
+
+      - run: pytest -m "not gpu"

.github/workflows/tests_cron.yml

@@ -14,16 +14,18 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04, windows-latest, macos-latest]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
         tensorflow: [1, 2]
         exclude:
-            # https://www.tensorflow.org/install/pip#system-requirements
+            # https://www.tensorflow.org/install/source#tested_build_configurations
           - python-version: '3.8'
             tensorflow: 1
           - python-version: '3.9'
             tensorflow: 1
           - python-version: '3.10'
             tensorflow: 1
+          - python-version: '3.11'
+            tensorflow: 1
           - os: windows-latest
             tensorflow: 1
 
@@ -65,8 +67,13 @@ jobs:
 
       - name: Install bioimage.io dependencies
         if: |
-          matrix.python-version >= 3.7 &&
+          matrix.python-version == 3.7 &&
           matrix.tensorflow == 1
         run: pip install "stardist[bioimageio]"
 
-      - run: pytest -v --durations=50 -m "not gpu"
+      - name: Disable PytestReturnNotNoneWarning (Python 3.7+)
+        if: matrix.python-version != 3.6
+        run: echo "PYTEST_ADDOPTS='-W ignore::pytest.PytestReturnNotNoneWarning'" >> $GITHUB_ENV
+        shell: bash
+
+      - run: pytest -m "not gpu"

README.md

@@ -3,6 +3,7 @@
 [![Test](https://github.com/stardist/stardist/workflows/Test/badge.svg)](https://github.com/stardist/stardist/actions?query=workflow%3ATest)
 [![Test (PyPI)](https://github.com/stardist/stardist/workflows/Test%20(PyPI)/badge.svg)](https://github.com/stardist/stardist/actions?query=workflow%3A%22Test+%28PyPI%29%22)
 [![Image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fstardist.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tags/stardist)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/stardist)](https://pypistats.org/packages/stardist)
 
 # *StarDist* - Object Detection with Star-convex Shapes
 

docker/Dockerfile

@@ -1,8 +1,8 @@
-FROM tensorflow/tensorflow:1.15.4-gpu-py3-jupyter
+FROM tensorflow/tensorflow:2.11.0-gpu-jupyter
 
 LABEL maintainer="ko.sugawara@ens-lyon.fr"
 
-ARG NVIDIA_DRIVER_VERSION=455
+ARG NVIDIA_DRIVER_VERSION=470
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     ocl-icd-dev \

docker/README.md

@@ -4,24 +4,26 @@ With this Docker image, you can run *StarDist* with [GPU support](https://www.te
 
 [gputools](https://github.com/maweigert/gputools) and [Multi-Label Anisotropic 3D Euclidean Distance Transform (MLAEDT-3D)](https://github.com/seung-lab/euclidean-distance-transform-3d) are also included.
 
-This Docker image is extended from `tensorflow/tensorflow:1.15.4-gpu-py3-jupyter`, which is based on `Ubuntu 18.04` with `CUDA 10.0` and `Python 3.6.9`.
+This Docker image is extended from `tensorflow/tensorflow:2.11.0-gpu-jupyter`, which is based on `Ubuntu 20.04.5 LTS` with `CUDA 11.2` and `Python 3.8.10`.
 
 ### Prerequisites
 
 - [Docker 19.03](https://docs.docker.com/install/)
 - NVIDIA Driver
 - [NVIDIA Container Toolkit](https://github.com/NVIDIA/nvidia-docker)
 
+For further information, see the [TensorFlow Docker documentation](https://www.tensorflow.org/install/docker).
+
 ### Building image
 
     # assuming that you are in the docker/ directory
-    docker build -t stardist --build-arg NVIDIA_DRIVER_VERSION=455 .
+    docker build -t stardist --build-arg NVIDIA_DRIVER_VERSION=470 .
 
 Please change the `NVIDIA_DRIVER_VERSION` depending on your environment.
 
-This argument is used to install an appropriate package for running OpenCL.
+Try `nvidia-smi | grep "Driver Version"` or `cat /proc/driver/nvidia/version` to find your driver version.
 
-The default value is `455` and `390`|`410`|`418`|`430`|`435`|`440`|`450`|`455`|`460` are available.
+This argument is used to install an appropriate package for running OpenCL.
 
 ### Usage example
 
@@ -32,6 +34,6 @@ This command will launch a jupyter notebook as root, binding the project root di
 
 ### Notes
 
-- Please see the [Dockerfile](Dockerfile) and [its parent image](https://hub.docker.com/layers/tensorflow/tensorflow/1.15.4-gpu-py3-jupyter/images/sha256-ef81875f4f24bec719e3b064ad8b83d8ed0e602981a19499d65d31f67424e645) for details.
+- Please see the [Dockerfile](Dockerfile) and [its parent image](https://hub.docker.com/layers/tensorflow/tensorflow/2.11.0-gpu-jupyter/images/sha256-fc519621eb9a54591721e9019f1606688c9abb329b16b00cc7107c23f14a6f24) for details.
 - Please follow the instructions for the usage of [Docker + NVIDIA Container Toolkit](https://github.com/NVIDIA/nvidia-docker).
-- Previous versions of Docker + nvidia-docker2 might work as well but we have not tested.
+- Previous versions of Docker + nvidia-docker2 might work as well but have not been tested.

pyproject.toml

@@ -1,3 +1,13 @@
 [build-system]
 requires = ["setuptools>=40.8.0", "wheel", "oldest-supported-numpy"]
-build-backend = "setuptools.build_meta"
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+addopts = "-v --durations=50"
+testpaths = [
+    "tests",
+]
+# only works for pytest >= 7.2.0, which isn't available for Python 3.6
+# filterwarnings = [
+#     "ignore::pytest.PytestReturnNotNoneWarning"
+# ]

setup.cfg

@@ -1,2 +1,2 @@
 [metadata]
-description-file = README.md
+description_file = README.md

setup.py

@@ -122,18 +122,22 @@ def compile_patched(obj, src, ext, cc_args, extra_postargs, pp_opts):
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
     ],
 
     install_requires=[
-        'csbdeep>=0.6.3',
+        'csbdeep>=0.7.4',
         'scikit-image',
         'numba',
         'imageio',
     ],
 
     extras_require={
-        "tf1":  ["csbdeep[tf1]>=0.6.3"],
-        "test": ["pytest"],
+        "tf1":  ["csbdeep[tf1]>=0.7.4"],
+        "test": [
+            "pytest;        python_version< '3.7'",
+            "pytest>=7.2.0; python_version>='3.7'",
+         ],
         "bioimageio": ["bioimageio.core>=0.5.0","importlib-metadata"],
     },
 

stardist/models/base.py

@@ -179,7 +179,7 @@ def __init__(self, X, Y, n_rays, grid, batch_size, patch_size, length,
             from gputools import max_filter
             self.max_filter = lambda y, patch_size: max_filter(y.astype(np.float32), patch_size)
         else:
-            from scipy.ndimage.filters import maximum_filter
+            from scipy.ndimage import maximum_filter
             self.max_filter = lambda y, patch_size: maximum_filter(y, patch_size, mode='constant')
 
         self.maxfilter_patch_size = maxfilter_patch_size if maxfilter_patch_size is not None else self.patch_size
@@ -467,6 +467,7 @@ def _predict_generator(self, img, axes=None, normalizer=None, n_tiles=None, show
 
         """
 
+        predict_kwargs.setdefault('verbose', 0)
         x, axes, axes_net, axes_net_div_by, _permute_axes, resizer, n_tiles, grid, grid_dict, channel, predict_direct, tiling_setup = \
             self._predict_setup(img, axes, normalizer, n_tiles, show_tile_progress, predict_kwargs)
 
@@ -534,6 +535,7 @@ def _predict_sparse_generator(self, img, prob_thresh=None, axes=None, normalizer
         """
         if prob_thresh is None: prob_thresh = self.thresholds.prob
 
+        predict_kwargs.setdefault('verbose', 0)
         x, axes, axes_net, axes_net_div_by, _permute_axes, resizer, n_tiles, grid, grid_dict, channel, predict_direct, tiling_setup = \
             self._predict_setup(img, axes, normalizer, n_tiles, show_tile_progress, predict_kwargs)
 
@@ -1066,8 +1068,8 @@ def _compute_receptive_field(self, img_size=None):
         x = np.zeros((1,)+img_size+(self.config.n_channel_in,), dtype=np.float32)
         z = np.zeros_like(x)
         x[(0,)+mid+(slice(None),)] = 1
-        y  = self.keras_model.predict(x)[0][0,...,0]
-        y0 = self.keras_model.predict(z)[0][0,...,0]
+        y  = self.keras_model.predict(x, verbose=0)[0][0,...,0]
+        y0 = self.keras_model.predict(z, verbose=0)[0][0,...,0]
         grid = tuple((np.array(x.shape[1:-1])/np.array(y.shape)).astype(int))
         assert grid == self.config.grid
         y  = zoom(y, grid,order=0)

stardist/models/model2d.py

@@ -234,7 +234,8 @@ def __init__(self, axes='YX', n_rays=32, n_channel_in=1, grid=(1,1), n_classes=N
         self.train_n_val_patches       = None
         self.train_tensorboard         = True
         # the parameter 'min_delta' was called 'epsilon' for keras<=2.1.5
-        min_delta_key = 'epsilon' if LooseVersion(keras.__version__)<=LooseVersion('2.1.5') else 'min_delta'
+        # keras.__version__ was removed in tensorflow 2.13.0
+        min_delta_key = 'epsilon' if LooseVersion(getattr(keras, '__version__', '9.9.9'))<=LooseVersion('2.1.5') else 'min_delta'
         self.train_reduce_lr           = {'factor': 0.5, 'patience': 40, min_delta_key: 0}
 
         self.use_gpu                   = False

stardist/models/model3d.py

@@ -272,7 +272,8 @@ def __init__(self, axes='ZYX', rays=None, n_channel_in=1, grid=(1,1,1), n_classe
         self.train_n_val_patches       = None
         self.train_tensorboard         = True
         # the parameter 'min_delta' was called 'epsilon' for keras<=2.1.5
-        min_delta_key = 'epsilon' if LooseVersion(keras.__version__)<=LooseVersion('2.1.5') else 'min_delta'
+        # keras.__version__ was removed in tensorflow 2.13.0
+        min_delta_key = 'epsilon' if LooseVersion(getattr(keras, '__version__', '9.9.9'))<=LooseVersion('2.1.5') else 'min_delta'
         self.train_reduce_lr           = {'factor': 0.5, 'patience': 40, min_delta_key: 0}
 
         self.use_gpu                   = False

stardist/utils.py

@@ -7,8 +7,8 @@
 from tqdm import tqdm
 from collections import defaultdict
 from zipfile import ZipFile, ZIP_DEFLATED
-from scipy.ndimage.morphology import distance_transform_edt, binary_fill_holes
-from scipy.ndimage.measurements import find_objects
+from scipy.ndimage import distance_transform_edt, binary_fill_holes
+from scipy.ndimage import find_objects
 from scipy.optimize import minimize_scalar
 from skimage.measure import regionprops
 from csbdeep.utils import _raise
@@ -365,9 +365,9 @@ def mask_to_categorical(y, n_classes, classes, return_cls_dict=False):
     for cls, labels in cls_dict.items():
         if cls is None:
             # prob == -1 will be used in the loss to ignore object
-            y_mask[np.isin(y, labels)] = -1
+            y_mask[np.isin(y, labels), :] = -1
         elif np.issubdtype(type(cls), np.integer) and 0 <= cls <= n_classes:
-            y_mask[...,cls] = np.isin(y, labels)
+            y_mask[np.isin(y, labels), cls] = 1
         else:
             raise ValueError(f"Wrong class id '{cls}' (for n_classes={n_classes})")
 

stardist/version.py

@@ -1 +1 @@
-__version__ = '0.8.3'
+__version__ = '0.8.4'

tests/utils.py

@@ -2,7 +2,7 @@
 import numpy as np
 from tifffile import imread
 from skimage.measure import label
-from scipy.ndimage.filters import gaussian_filter
+from scipy.ndimage import gaussian_filter
 from pathlib import Path
 from timeit import default_timer
 from csbdeep.utils.tf import keras_import