bulid: initial commit

.github/workflows/ci.yml

@@ -2,8 +2,7 @@ name: CI
 
 on:
   push:
-    branches:
-      - main
+    branches: [main]
     tags:
       - "v*"
   pull_request:
@@ -24,48 +23,23 @@ jobs:
       - run: pipx run check-manifest
 
   test:
-    name: ${{ matrix.platform }} (${{ matrix.python-version }})
-    runs-on: ${{ matrix.platform }}
+    uses: pyapp-kit/workflows/.github/workflows/test-pyrepo.yml@v2
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      coverage-upload: artifact
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        platform: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: 🐍 Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache-dependency-path: "pyproject.toml"
-          cache: "pip"
-
-      - name: Install Dependencies
-        run: |
-          python -m pip install -U pip
-          # if running a cron job, we add the --pre flag to test against pre-releases
-          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
-
-      - name: 🧪 Run Tests
-        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
-
-      - name: 📝 Report --pre Failures
-        if: failure() && github.event_name == 'schedule'
-        uses: JasonEtco/create-an-issue@v2
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          PLATFORM: ${{ matrix.platform }}
-          PYTHON: ${{ matrix.python-version }}
-          RUN_ID: ${{ github.run_id }}
-          TITLE: "[test-bot] pip install --pre is failing"
-        with:
-          filename: .github/TEST_FAIL_TEMPLATE.md
-          update_existing: true
-
-      - name: Coverage
-        uses: codecov/codecov-action@v3
+  upload_coverage:
+    if: always()
+    needs: [test]
+    uses: pyapp-kit/workflows/.github/workflows/upload-coverage.yml@v2
+    secrets:
+      codecov_token: ${{ secrets.CODECOV_TOKEN }}
 
   deploy:
     name: Deploy
@@ -83,7 +57,7 @@ jobs:
           fetch-depth: 0
 
       - name: 🐍 Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
 
@@ -98,4 +72,4 @@ jobs:
       - uses: softprops/action-gh-release@v1
         with:
           generate_release_notes: true
-          files: './dist/*'
+          files: "./dist/*"

.pre-commit-config.yaml

@@ -1,7 +1,3 @@
-# enable pre-commit.ci at https://pre-commit.ci/
-# it adds:
-# 1. auto fixing pull requests
-# 2. auto updating the pre-commit configuration
 ci:
   autoupdate_schedule: monthly
   autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
@@ -17,20 +13,19 @@ repos:
     rev: typos-dict-v0.11.20
     hooks:
       - id: typos
-        args: [--force-exclude]  # omitting --write-changes
+        args: [--force-exclude] # omitting --write-changes
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.4.8
     hooks:
       - id: ruff
-        args: [--fix]  # may also add '--unsafe-fixes'
+        args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.10.0
     hooks:
       - id: mypy
         files: "^src/"
-        # # you have to add the things you want to type check against here
-        # additional_dependencies:
-        #   - numpy
+        additional_dependencies:
+          - numpy

examples/dask_arr.py

@@ -0,0 +1,32 @@
+from __future__ import annotations
+
+import numpy as np
+
+try:
+    from dask.array.core import map_blocks
+except ImportError:
+    raise ImportError("Please `pip install dask[array]` to run this example.")
+
+frame_size = (1024, 1024)
+
+
+def _dask_block(block_id: tuple[int, int, int, int, int]) -> np.ndarray | None:
+    if isinstance(block_id, np.ndarray):
+        return None
+    data = np.random.randint(0, 255, size=frame_size, dtype=np.uint8)
+    return data[(None,) * 3]
+
+
+chunks = [(1,) * x for x in (1000, 64, 3)]
+chunks += [(x,) for x in frame_size]
+dask_arr = map_blocks(_dask_block, chunks=chunks, dtype=np.uint8)
+
+if __name__ == "__main__":
+    from qtpy import QtWidgets
+
+    from ndv import NDViewer
+
+    qapp = QtWidgets.QApplication([])
+    v = NDViewer(dask_arr)
+    v.show()
+    qapp.exec()

examples/jax_arr.py

@@ -0,0 +1,20 @@
+from __future__ import annotations
+
+try:
+    import jax.numpy as jnp
+except ImportError:
+    raise ImportError("Please install jax to run this example")
+from numpy_arr import generate_5d_sine_wave
+from qtpy import QtWidgets
+
+from ndv import NDViewer
+
+# Example usage
+array_shape = (10, 3, 5, 512, 512)  # Specify the desired dimensions
+sine_wave_5d = jnp.asarray(generate_5d_sine_wave(array_shape))
+
+if __name__ == "__main__":
+    qapp = QtWidgets.QApplication([])
+    v = NDViewer(sine_wave_5d, channel_axis=1)
+    v.show()
+    qapp.exec()

examples/numpy_arr.py

@@ -0,0 +1,64 @@
+from __future__ import annotations
+
+import numpy as np
+
+
+def generate_5d_sine_wave(
+    shape: tuple[int, int, int, int, int],
+    amplitude: float = 240,
+    base_frequency: float = 5,
+) -> np.ndarray:
+    """5D dataset."""
+    # Unpack the dimensions
+    angle_dim, freq_dim, phase_dim, ny, nx = shape
+
+    # Create an empty array to hold the data
+    output = np.zeros(shape)
+
+    # Define spatial coordinates for the last two dimensions
+    half_per = base_frequency * np.pi
+    x = np.linspace(-half_per, half_per, nx)
+    y = np.linspace(-half_per, half_per, ny)
+    y, x = np.meshgrid(y, x)
+
+    # Iterate through each parameter in the higher dimensions
+    for phase_idx in range(phase_dim):
+        for freq_idx in range(freq_dim):
+            for angle_idx in range(angle_dim):
+                # Calculate phase and frequency
+                phase = np.pi / phase_dim * phase_idx
+                frequency = 1 + (freq_idx * 0.1)  # Increasing frequency with each step
+
+                # Calculate angle
+                angle = np.pi / angle_dim * angle_idx
+                # Rotate x and y coordinates
+                xr = np.cos(angle) * x - np.sin(angle) * y
+                np.sin(angle) * x + np.cos(angle) * y
+
+                # Compute the sine wave
+                sine_wave = (amplitude * 0.5) * np.sin(frequency * xr + phase)
+                sine_wave += amplitude * 0.5
+
+                # Assign to the output array
+                output[angle_idx, freq_idx, phase_idx] = sine_wave
+
+    return output
+
+
+try:
+    from skimage import data
+
+    img = data.cells3d()
+except Exception:
+    img = generate_5d_sine_wave((10, 3, 8, 512, 512))
+
+
+if __name__ == "__main__":
+    from qtpy import QtWidgets
+
+    from ndv import NDViewer
+
+    qapp = QtWidgets.QApplication([])
+    v = NDViewer(img)
+    v.show()
+    qapp.exec()

examples/tensorstore_arr.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+import numpy as np
+import tensorstore as ts
+from qtpy import QtWidgets
+
+from ndv import NDViewer
+
+shape = (10, 4, 3, 512, 512)
+ts_array = ts.open(
+    {"driver": "zarr", "kvstore": {"driver": "memory"}},
+    create=True,
+    shape=shape,
+    dtype=ts.uint8,
+).result()
+ts_array[:] = np.random.randint(0, 255, size=shape, dtype=np.uint8)
+ts_array = ts_array[ts.d[:].label["t", "c", "z", "y", "x"]]
+
+if __name__ == "__main__":
+    qapp = QtWidgets.QApplication([])
+    v = NDViewer(ts_array)
+    v.show()
+    qapp.exec()

examples/xarray_arr.py

@@ -0,0 +1,14 @@
+from __future__ import annotations
+
+import xarray as xr
+from qtpy import QtWidgets
+
+from ndv import NDViewer
+
+da = xr.tutorial.open_dataset("air_temperature").air
+
+if __name__ == "__main__":
+    qapp = QtWidgets.QApplication([])
+    v = NDViewer(da, colormaps=["thermal"], channel_mode="composite")
+    v.show()
+    qapp.exec()

examples/zarr_arr.py

@@ -0,0 +1,16 @@
+from __future__ import annotations
+
+import zarr
+import zarr.storage
+from qtpy import QtWidgets
+
+from ndv import NDViewer
+
+URL = "https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/tczyx.ome.zarr"
+zarr_arr = zarr.open(URL, mode="r")
+
+if __name__ == "__main__":
+    qapp = QtWidgets.QApplication([])
+    v = NDViewer(zarr_arr["s0"])
+    v.show()
+    qapp.exec()

pyproject.toml

@@ -17,33 +17,35 @@ sources = ["src"]
 [project]
 name = "ndv"
 dynamic = ["version"]
-description = "simple ndviewer"
+description = "simple nd image viewer"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = { text = "BSD-3-Clause" }
-authors = [{ name = "Talley Lambert", email = "talley.lambert@example.com" }]
+authors = [{ name = "Talley Lambert", email = "talley.lambert@gmail.com" }]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "License :: OSI Approved :: BSD License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Typing :: Typed",
 ]
-dependencies = []
+dependencies = ["qtpy", "numpy", "superqt[cmap,iconify]"]
 
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
-test = ["pytest", "pytest-cov"]
+pyqt = ["pyqt6"]
+vispy = ["vispy", "pyopengl"]
+pyside = ["pyside6"]
+test = ["pytest", "pytest-cov", "pytest-qt", "dask"]
 dev = [
     "ipython",
     "mypy",
-    "pdbpp",  # https://github.com/pdbpp/pdbpp
+    "pdbpp",      # https://github.com/pdbpp/pdbpp
     "pre-commit",
-    "rich",  # https://github.com/Textualize/rich
+    "rich",       # https://github.com/Textualize/rich
     "ruff",
 ]
 
@@ -81,11 +83,13 @@ ignore = [
 
 [tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
+"examples/*.py" = ["D", "B9"]
+
 
 # https://docs.astral.sh/ruff/formatter/
 [tool.ruff.format]
 docstring-code-format = true
-skip-magic-trailing-comma = false  # default is false
+skip-magic-trailing-comma = false # default is false
 
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]
@@ -119,8 +123,7 @@ exclude_lines = [
 source = ["ndv"]
 
 [tool.check-manifest]
-ignore = [
-    ".pre-commit-config.yaml",
-    ".ruff_cache/**/*",
-    "tests/**/*",
-]
+ignore = [".pre-commit-config.yaml", ".ruff_cache/**/*", "tests/**/*"]
+
+[tool.typos.default]
+extend-ignore-identifiers-re = ["(?i)nd2?.*", "(?i)ome", ".*ser_schema"]

src/ndv/__init__.py

@@ -8,3 +8,8 @@
     __version__ = "uninstalled"
 __author__ = "Talley Lambert"
 __email__ = "[email protected]"
+
+from .viewer._indexing import DataWrapper
+from .viewer._stack_viewer import NDViewer
+
+__all__ = ["NDViewer", "DataWrapper"]

src/ndv/viewer/__init__.py

@@ -0,0 +1 @@
+"""viewer source."""