Merge pull request #36 from constantinpape/zarr-support

Zarr support

Author: constantinpape

.github/workflows/build.yml

@@ -0,0 +1,40 @@
+---
+name: build
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    name: ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: pybdv-build-env
+          auto-update-conda: true
+          channels: conda-forge
+          environment-file: .github/workflows/environment.yaml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+        env:
+          ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+
+      - name: Install pybdv
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: pip install -e .
+      
+      - name: Run tests
+        shell: bash -l {0}
+        run: python -m unittest discover -s test -v

.github/workflows/environment.yaml

@@ -0,0 +1,11 @@
+name: pybdv-build-env
+channels:
+  - conda-forge
+dependencies:
+  - imageio
+  - h5py
+  - scikit-image
+  - tqdm
+  - z5py
+  # zarr doesn't work yet, because it doesn't allow writing 'dataType' as group attribute
+  # - zarr

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/constantinpape/pybdv.svg?branch=master)](https://travis-ci.org/constantinpape/pybdv)
+[![Build Status](https://github.com/constantinpape/pybdv/workflows/build/badge.svg)](https://github.com/constantinpape/pybdv/actions)
 
 # pyBDV
 

pybdv/util.py

@@ -19,19 +19,29 @@
 
     try:
         import z5py
+        n5_file = z5py.File
     except ImportError:
-        z5py = None
+        n5_file = None
+
+    if n5_file is None:
+        try:
+            import zarr
+            n5_file = zarr.open
+        except ImportError:
+            n5_file = None
 
     def open_file(path, mode='r'):
         ext = os.path.splitext(path)[1].lower()
         if ext in HDF5_EXTENSIONS:
             return h5py.File(path, mode=mode)
         elif ext in N5_EXTENSIONS:
-            if z5py is None:
-                raise ValueError("Need z5py to open n5 files")
-            return z5py.File(path, mode=mode)
+            if n5_file is None:
+                raise ValueError("Need zarr or z5py to open n5 files")
+            return n5_file(path, mode=mode)
         else:
             raise ValueError(f"Invalid extension: {ext}")
+else:
+    n5_file = open_file
 
 
 def get_key(is_h5, timepoint=None, setup_id=None, scale=None):

test/test_bdv_datasets.py

@@ -5,12 +5,8 @@
 
 import numpy as np
 from pybdv import make_bdv, BdvDataset
-from pybdv.util import open_file, get_key, HDF5_EXTENSIONS
+from pybdv.util import open_file, get_key, HDF5_EXTENSIONS, n5_file
 
-try:
-    import z5py
-except ImportError:
-    z5py = None
 
 DOWNSCALE_MODE = 'mean'
 
@@ -174,7 +170,7 @@ class TestBdvDatasetH5(BdvDatasetTestMixin, unittest.TestCase):
     out_path = './tmp/test.h5'
 
 
-@unittest.skipUnless(z5py is not None, "Need z5py for n5 support")
+@unittest.skipIf(n5_file is None, "Need zarr or z5py for n5 support")
 class TestBdvDatasetN5(BdvDatasetTestMixin, unittest.TestCase):
     out_path = './tmp/test.n5'
 

test/test_convert_to_bdv.py

@@ -5,12 +5,7 @@
 from shutil import rmtree
 
 import numpy as np
-from pybdv.util import get_key, open_file
-
-try:
-    import z5py
-except ImportError:
-    z5py = None
+from pybdv.util import get_key, open_file, n5_file
 
 
 class ConvertToBdvTestMixin(ABC):
@@ -124,7 +119,7 @@ class TestConvertToBdvH5(ConvertToBdvTestMixin, unittest.TestCase):
     is_h5 = True
 
 
-@unittest.skipUnless(z5py is not None, "Need z5py for n5 support")
+@unittest.skipIf(n5_file is None, "Need zarr or z5py for n5 support")
 class TestConvertToBdvN5(ConvertToBdvTestMixin, unittest.TestCase):
     in_path = './tmp/in.n5'
     out_path = './tmp/test.n5'

test/test_external.py

@@ -5,12 +5,12 @@
 import imageio
 import h5py
 import numpy as np
-import skimage.data
 
 
 # dummy test data, needs to be converted to bdv/xml
 # with FIJI externally
 def make_test_data():
+    import skimage.data
     d = skimage.data.astronaut()
     d = d.transpose((2, 0, 1))
     d = np.concatenate(2 * [d], axis=0)
@@ -22,6 +22,14 @@ def make_test_data():
 
 class TestExternal(unittest.TestCase):
     tmp_folder = 'tmp'
+    inp_path = os.path.join(
+        os.path.split(__file__)[0],
+        '../data/example.tif'
+    )
+    exp_path = os.path.join(
+        os.path.split(__file__)[0],
+        '../data/example.h5'
+    )
 
     def setUp(self):
         os.makedirs(self.tmp_folder, exist_ok=True)
@@ -34,12 +42,11 @@ def tearDown(self):
 
     def test_external(self):
         from pybdv import make_bdv
-        d = imageio.volread('../data/example.tif')
+        d = imageio.volread(self.inp_path)
         res_path = os.path.join(self.tmp_folder, 'data.h5')
-        exp_path = '../data/example.h5'
         make_bdv(d, res_path, convert_dtype=True)
 
-        with h5py.File(exp_path, 'r') as f:
+        with h5py.File(self.exp_path, 'r') as f:
             ds = f['t00000/s00/0/cells']
             exp = ds[:]
         with h5py.File(res_path, 'r') as f:

test/test_make_bdv.py

@@ -4,12 +4,7 @@
 from shutil import rmtree
 
 import numpy as np
-from pybdv.util import get_key, open_file
-
-try:
-    import z5py
-except ImportError:
-    z5py = None
+from pybdv.util import get_key, open_file, n5_file
 
 
 class MakeBdvTestMixin(ABC):
@@ -329,7 +324,7 @@ class TestMakeBdvH5(MakeBdvTestMixin, unittest.TestCase):
     is_h5 = True
 
 
-@unittest.skipUnless(z5py is not None, "Need z5py for n5 support")
+@unittest.skipIf(n5_file is None, "Need zarr or z5py for n5 support")
 class TestMakeBdvN5(MakeBdvTestMixin, unittest.TestCase):
     out_path = './tmp/test.n5'
     is_h5 = False

test/test_metadata.py

@@ -5,13 +5,7 @@
 
 import numpy as np
 from pybdv import make_bdv
-from pybdv.util import open_file
-
-try:
-    import z5py
-except ImportError:
-    z5py = None
-
+from pybdv.util import n5_file
 
 
 class MetadataTestMixin(ABC):
@@ -69,12 +63,12 @@ def test_validate_attributes(self):
 
         attrs2 = {'channel': {'id': None, 'name': 'foo'}}
         attrs2_exp = {'channel': {'id': 0, 'name': 'foo'}}
-        attrs2_ = validate_attributes(self.xml_path, attrs1, 0, True)
+        attrs2_ = validate_attributes(self.xml_path, attrs2, 0, True)
         self.assertEqual(attrs2_exp, attrs2_)
 
         attrs3 = {'channel': {'name': 'bar'}}
         with self.assertRaises(ValueError):
-            validate_attributes(self.xml_path, attrs1, 1, True)
+            validate_attributes(self.xml_path, attrs3, 1, True)
 
         attrs4 = {'displaysettings': {'id': 0, 'name': 'baz', 'min': 0, 'max': 1, 'isset': True,
                                       'color': [255, 255, 255, 255]}}
@@ -96,7 +90,7 @@ class TestMetadataH5(MetadataTestMixin, unittest.TestCase):
     bdv_format = 'bdv.hdf5'
 
 
-@unittest.skipUnless(z5py is not None, "Need z5py for n5 support")
+@unittest.skipIf(n5_file is None, "Need zarr or z5py for n5 support")
 class TestMetadataN5(MetadataTestMixin, unittest.TestCase):
     out_path = './tmp/test.n5'
     out_path2 = './tmp/test2.n5'