Merge pull request #165 from GenevieveBuckley/napari-plugin

micro-sam napari plugin

MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

micro_sam/napari.yaml

@@ -0,0 +1,47 @@
+name: micro-sam
+display_name: SegmentAnything for Microscopy
+contributions:
+  commands:
+    - id: micro-sam.sample_data_image_series
+      python_name: micro_sam.sample_data:sample_data_image_series
+      title: Load image series sample data from micro-sam plugin
+    - id: micro-sam.sample_data_wholeslide
+      python_name: micro_sam.sample_data:sample_data_wholeslide
+      title: Load WholeSlide sample data from micro-sam plugin
+    - id: micro-sam.sample_data_livecell
+      python_name: micro_sam.sample_data:sample_data_livecell
+      title: Load LiveCell sample data from micro-sam plugin
+    - id: micro-sam.sample_data_hela_2d
+      python_name: micro_sam.sample_data:sample_data_hela_2d
+      title: Load 2D Hela sample data from micro-sam plugin
+    - id: micro-sam.sample_data_3d
+      python_name: micro_sam.sample_data:sample_data_3d
+      title: Load Lucchi++ 3D sample data from micro-sam plugin
+    - id: micro-sam.sample_data_tracking
+      python_name: micro_sam.sample_data:sample_data_tracking
+      title: Load tracking sample data from micro-sam plugin
+    - id: micro-sam.sample_data_segmentation
+      python_name: micro_sam.sample_data:sample_data_segmentation
+      title: Load segmentation sample data from micro-sam plugin
+  sample_data:
+    - command: micro-sam.sample_data_image_series
+      display_name: Image series example data
+      key: micro-sam-image-series
+    - command: micro-sam.sample_data_wholeslide
+      display_name: WholeSlide example data
+      key: micro-sam-wholeslide
+    - command: micro-sam.sample_data_livecell
+      display_name: LiveCell example data
+      key: micro-sam-livecell
+    - command: micro-sam.sample_data_hela_2d
+      display_name: HeLa 2d example data
+      key: micro-sam-hela2d
+    - command: micro-sam.sample_data_3d
+      display_name: Lucchi++ 3d dataset
+      key: micro-sam-lucchi
+    - command: micro-sam.sample_data_tracking
+      display_name: Tracking sample dataset
+      key: micro-sam-tracking
+    - command: micro-sam.sample_data_segmentation
+      display_name: Segmentation sample dataset
+      key: micro-sam-segmentation

micro_sam/sample_data.py

@@ -6,6 +6,8 @@
 from pathlib import Path
 from typing import Union
 
+import imageio.v3 as imageio
+import numpy as np
 import pooch
 
 
@@ -17,6 +19,9 @@ def fetch_image_series_example_data(save_directory: Union[str, os.PathLike]) ->
     Returns:
         The folder that contains the downloaded data.
     """
+    # This sample dataset is currently not provided to napari by the micro-sam
+    # plugin, because images are not all the same shape and cannot be combined
+    # into a single layer
     save_directory = Path(save_directory)
     os.makedirs(save_directory, exist_ok=True)
     print("Example data directory is:", save_directory.resolve())
@@ -36,6 +41,26 @@ def fetch_image_series_example_data(save_directory: Union[str, os.PathLike]) ->
     return data_folder
 
 
+def sample_data_image_series():
+    """Provides image series example image to napari.
+
+    Opens as three separate image layers in napari (one per image in series).
+    The third image in the series has a different size and modality.
+    """
+    # Return list of tuples
+    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
+    # Check the documentation for more information about the
+    # add_image_kwargs
+    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
+    default_base_data_dir = pooch.os_cache('micro-sam')
+    data_directory = fetch_image_series_example_data(default_base_data_dir)
+    fnames = os.listdir(data_directory)
+    full_filenames = [os.path.join(data_directory, f) for f in fnames]
+    full_filenames.sort()
+    data_and_image_kwargs = [(imageio.imread(f), {"name": f"img-{i}"}) for i, f in enumerate(full_filenames)]
+    return data_and_image_kwargs
+
+
 def fetch_wholeslide_example_data(save_directory: Union[str, os.PathLike]) -> str:
     """Download the sample data for the 2d annotator.
 
@@ -61,6 +86,20 @@ def fetch_wholeslide_example_data(save_directory: Union[str, os.PathLike]) -> st
     return os.path.join(save_directory, fname)
 
 
+def sample_data_wholeslide():
+    """Provides wholeslide 2d example image to napari."""
+    # Return list of tuples
+    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
+    # Check the documentation for more information about the
+    # add_image_kwargs
+    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
+    default_base_data_dir = pooch.os_cache('micro-sam')
+    filename = fetch_wholeslide_example_data(default_base_data_dir)
+    data = imageio.imread(filename)
+    add_image_kwargs = {"name": "wholeslide"}
+    return [(data, add_image_kwargs)]
+
+
 def fetch_livecell_example_data(save_directory: Union[str, os.PathLike]) -> str:
     """Download the sample data for the 2d annotator.
 
@@ -74,7 +113,6 @@ def fetch_livecell_example_data(save_directory: Union[str, os.PathLike]) -> str:
     """
     save_directory = Path(save_directory)
     os.makedirs(save_directory, exist_ok=True)
-    print("Example data directory is:", save_directory.resolve())
     fname = "livecell-2d-image.png"
     pooch.retrieve(
         url="https://owncloud.gwdg.de/index.php/s/fSaOJIOYjmFBjPM/download",
@@ -86,7 +124,21 @@ def fetch_livecell_example_data(save_directory: Union[str, os.PathLike]) -> str:
     return os.path.join(save_directory, fname)
 
 
-def fetch_hela_2d_example_data(save_directory: Union[str, os.PathLike]) -> str:
+def sample_data_livecell():
+    """Provides livecell 2d example image to napari."""
+    # Return list of tuples
+    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
+    # Check the documentation for more information about the
+    # add_image_kwargs
+    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
+    default_base_data_dir = pooch.os_cache('micro-sam')
+    filename = fetch_livecell_example_data(default_base_data_dir)
+    data = imageio.imread(filename)
+    add_image_kwargs = {"name": "livecell"}
+    return [(data, add_image_kwargs)]
+
+
+def fetch_hela_2d_example_data(save_directory: Union[str, os.PathLike]) -> Union[str, os.PathLike]:
     """Download the sample data for the 2d annotator.
 
     This downloads a single image from the HeLa CTC dataset.
@@ -110,6 +162,20 @@ def fetch_hela_2d_example_data(save_directory: Union[str, os.PathLike]) -> str:
     return os.path.join(save_directory, fname)
 
 
+def sample_data_hela_2d():
+    """Provides HeLa 2d example image to napari."""
+    # Return list of tuples
+    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
+    # Check the documentation for more information about the
+    # add_image_kwargs
+    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
+    default_base_data_dir = pooch.os_cache("micro-sam")
+    filename = fetch_hela_2d_example_data(default_base_data_dir)
+    data = imageio.imread(filename)
+    add_image_kwargs = {"name": "hela_2d"}
+    return [(data, add_image_kwargs)]
+
+
 def fetch_3d_example_data(save_directory: Union[str, os.PathLike]) -> str:
     """Download the sample data for the 3d annotator.
 
@@ -139,6 +205,23 @@ def fetch_3d_example_data(save_directory: Union[str, os.PathLike]) -> str:
     return str(lucchi_dir)
 
 
+def sample_data_3d():
+    """Provides Lucchi++ 3d example image to napari."""
+    # Return list of tuples
+    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
+    # Check the documentation for more information about the
+    # add_image_kwargs
+    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
+    default_base_data_dir = pooch.os_cache("micro-sam")
+    data_directory = fetch_3d_example_data(default_base_data_dir)
+    fnames = os.listdir(data_directory)
+    full_filenames = [os.path.join(data_directory, f) for f in fnames]
+    full_filenames.sort()
+    data = np.stack([imageio.imread(f) for f in full_filenames], axis=0)
+    add_image_kwargs = {"name": "lucchi++"}
+    return [(data, add_image_kwargs)]
+
+
 def fetch_tracking_example_data(save_directory: Union[str, os.PathLike]) -> str:
     """Download the sample data for the tracking annotator.
 
@@ -156,7 +239,6 @@ def fetch_tracking_example_data(save_directory: Union[str, os.PathLike]) -> str:
     """
     save_directory = Path(save_directory)
     os.makedirs(save_directory, exist_ok=True)
-    print("Example data directory is:", save_directory.resolve())
     unpack_filenames = [os.path.join("DIC-C2DH-HeLa", "01", f"t{str(i).zfill(3)}.tif") for i in range(84)]
     unpack = pooch.Unzip(members=unpack_filenames)
     fname = "DIC-C2DH-HeLa.zip"
@@ -173,6 +255,23 @@ def fetch_tracking_example_data(save_directory: Union[str, os.PathLike]) -> str:
     return str(cell_tracking_dir)
 
 
+def sample_data_tracking():
+    """Provides tracking example dataset to napari."""
+    # Return list of tuples
+    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
+    # Check the documentation for more information about the
+    # add_image_kwargs
+    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
+    default_base_data_dir = pooch.os_cache("micro-sam")
+    data_directory = fetch_tracking_example_data(default_base_data_dir)
+    fnames = os.listdir(data_directory)
+    full_filenames = [os.path.join(data_directory, f) for f in fnames]
+    full_filenames.sort()
+    data = np.stack([imageio.imread(f) for f in full_filenames], axis=0)
+    add_image_kwargs = {"name": "tracking"}
+    return [(data, add_image_kwargs)]
+
+
 def fetch_tracking_segmentation_data(save_directory: Union[str, os.PathLike]) -> str:
     """Download groundtruth segmentation for the tracking example data.
 
@@ -200,3 +299,20 @@ def fetch_tracking_segmentation_data(save_directory: Union[str, os.PathLike]) ->
     cell_tracking_dir = save_directory.joinpath(f"{fname}.unzip", "masks")
     assert os.path.exists(cell_tracking_dir)
     return str(cell_tracking_dir)
+
+
+def sample_data_segmentation():
+    """Provides segmentation example dataset to napari."""
+    # Return list of tuples
+    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
+    # Check the documentation for more information about the
+    # add_image_kwargs
+    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
+    default_base_data_dir = pooch.os_cache("micro-sam")
+    data_directory = fetch_tracking_segmentation_data(default_base_data_dir)
+    fnames = os.listdir(data_directory)
+    full_filenames = [os.path.join(data_directory, f) for f in fnames]
+    full_filenames.sort()
+    data = np.stack([imageio.imread(f) for f in full_filenames], axis=0)
+    add_image_kwargs = {"name": "segmentation"}
+    return [(data, add_image_kwargs)]

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.black]
+line-length = 79
+target-version = ['py38', 'py39', 'py310']
+
+
+[tool.ruff]
+line-length = 79
+select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py38"
+fix = true

setup.cfg

@@ -0,0 +1,56 @@
+[metadata]
+name = micro-sam
+version = attr: micro_sam.__version__
+description = SegmentAnything For Microscopy
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/computational-cell-analytics/micro-sam
+author = Anwai Archit, Constantin Pape
+author_email = [email protected]
+license = MIT
+license_files = LICENSE
+classifiers =
+    Development Status :: 2 - Pre-Alpha
+    Framework :: napari
+    Intended Audience :: Developers
+    License :: OSI Approved :: BSD License
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Topic :: Scientific/Engineering :: Image Processing
+project_urls =
+    Bug Tracker = https://github.com/computational-cell-analytics/micro-sam/issues
+    Documentation = https://computational-cell-analytics.github.io/micro-sam/micro_sam.html
+    Source Code = https://github.com/computational-cell-analytics/micro-sam
+    User Support = https://github.com/computational-cell-analytics/micro-sam/issues
+
+[options]
+packages = find:
+python_requires = >=3.8
+include_package_data = True
+package_dir =
+    = .
+
+[options.packages.find]
+where = .
+
+# tell napari where to find to your manifest
+[options.entry_points]
+napari.manifest =
+    micro-sam = micro_sam:napari.yaml
+
+# make sure it gets included in your package
+[options.package_data]
+* = *.yaml
+
+[project.scripts]
+micro_sam.annotator = "micro_sam.sam_annotator.annotator:main"
+micro_sam.annotator_2d = "micro_sam.sam_annotator.annotator_2d:main"
+micro_sam.annotator_3d = "micro_sam.sam_annotator.annotator_3d:main"
+micro_sam.annotator_tracking = "micro_sam.sam_annotator.annotator_tracking:main"
+micro_sam.image_series_annotator = "micro_sam.sam_annotator.image_series_annotator:main"
+micro_sam.precompute_embeddings = "micro_sam.util:main"