- base & view model for imread

- transforms bugfix
- implement (nan)var and (nan)std
- add tests

.github/workflows/pytest.yml

@@ -0,0 +1,22 @@
+name: PyTest
+
+on: [workflow_call, push, pull_request]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install pytest
+      - name: Test with pytest
+        run: pytest

README.md

@@ -1,3 +1,5 @@
+[![Pytest](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml)
+
 # ndbioimage - Work in progress
 
 Exposes (bio) images as a numpy ndarray-like-object, but without loading the whole
@@ -55,9 +57,9 @@ with Imread('image_file.tif', axes='cztxy') as im:
 ```
 
 ## Adding more formats
-Readers for image formats subclass Imread. When an image reader is imported, Imread will
+Readers for image formats subclass AbstractReader. When an image reader is imported, Imread will
 automatically recognize it and use it to open the appropriate file format. Image readers
-subclass Imread and are required to implement the following methods:
+are required to implement the following methods:
 
 - staticmethod _can_open(path): return True if path can be opened by this reader
 - property ome: reads metadata from file and adds them to an OME object imported
@@ -65,7 +67,7 @@ from the ome-types library
 - \_\_frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file
 
 Optional methods:
-- open(self): maybe open some file
+- open(self): maybe open some file handle
 - close(self): close any file handles
 
 Optional fields:

ndbioimage/readers/bfread.py

@@ -3,7 +3,7 @@ import numpy as np
 from abc import ABC
 from multiprocessing import queues
 from traceback import print_exc
-from .. import Imread, JVM
+from .. import AbstractReader, JVM
 
 
 jars = {'bioformats_package.jar':
@@ -174,7 +174,7 @@ def can_open(path):
         jvm.kill_vm()
 
 
-class Reader(Imread, ABC):
+class Reader(AbstractReader, ABC):
     """ This class is used as a last resort, when we don't have another way to open the file. We don't like it
         because it requires the java vm.
     """

ndbioimage/readers/cziread.py

@@ -7,10 +7,10 @@ from abc import ABC
 from functools import cached_property
 from itertools import product
 from pathlib import Path
-from .. import Imread
+from .. import AbstractReader
 
 
-class Reader(Imread, ABC):
+class Reader(AbstractReader, ABC):
     priority = 0
     do_not_pickle = 'reader', 'filedict'
 
@@ -69,7 +69,7 @@ class Reader(Imread, ABC):
 
         instrument = information.find("Instrument")
         for _ in instrument.find("Microscopes"):
-            ome.instruments.append(model.Instrument())
+            ome.instruments.append(model.Instrument(id='Instrument:0'))
 
         for detector in instrument.find("Detectors"):
             try:
@@ -414,7 +414,7 @@ class Reader(Imread, ABC):
         return ome
 
     def __frame__(self, c=0, z=0, t=0):
-        f = np.zeros(self.file_shape[:2], self.dtype)
+        f = np.zeros(self.base.shape['xy'], self.dtype)
         directory_entries = self.filedict[c, z, t]
         x_min = min([f.start[f.axes.index('X')] for f in directory_entries])
         y_min = min([f.start[f.axes.index('Y')] for f in directory_entries])

ndbioimage/readers/fijiread.py

@@ -7,10 +7,10 @@ from pathlib import Path
 from struct import unpack
 from warnings import warn
 import numpy as np
-from .. import Imread
+from .. import AbstractReader
 
 
-class Reader(Imread, ABC):
+class Reader(AbstractReader, ABC):
     """ Can read some tif files written with Fiji which are broken because Fiji didn't finish writing. """
     priority = 90
     do_not_pickle = 'reader'

ndbioimage/readers/ndread.py

@@ -2,11 +2,11 @@ import numpy as np
 from ome_types import model
 from functools import cached_property
 from abc import ABC
-from .. import Imread
+from .. import AbstractReader
 from itertools import product
 
 
-class Reader(Imread, ABC):
+class Reader(AbstractReader, ABC):
     priority = 20
 
     @staticmethod

ndbioimage/readers/seqread.py

@@ -8,7 +8,7 @@ from ome_types._base_type import quantity_property
 from itertools import product
 from datetime import datetime
 from abc import ABC
-from .. import Imread
+from .. import AbstractReader
 
 
 def lazy_property(function, field, *arg_fields):
@@ -36,7 +36,7 @@ class Plane(model.Plane):
         return float((datetime.strptime(info["Time"], "%Y-%m-%d %H:%M:%S %z") - t0).seconds)
 
 
-class Reader(Imread, ABC):
+class Reader(AbstractReader, ABC):
     priority = 10
 
     @staticmethod

ndbioimage/readers/tifread.py

@@ -6,10 +6,10 @@ from functools import cached_property
 from ome_types import model
 from pathlib import Path
 from itertools import product
-from .. import Imread
+from .. import AbstractReader
 
 
-class Reader(Imread, ABC):
+class Reader(AbstractReader, ABC):
     priority = 0
     do_not_pickle = 'reader'
 
@@ -67,6 +67,6 @@ class Reader(Imread, ABC):
 
     def __frame__(self, c, z, t):
         if self.p_ndim == 3:
-            return np.transpose(self.reader.asarray(z + t * self.file_shape[3]), self.p_transpose)[c]
+            return np.transpose(self.reader.asarray(z + t * self.base.shape['z']), self.p_transpose)[c]
         else:
-            return self.reader.asarray(c + z * self.file_shape[2] + t * self.file_shape[2] * self.file_shape[3])
+            return self.reader.asarray(c + z * self.base.shape['c'] + t * self.base.shape['c'] * self.base.shape['z'])

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ndbioimage"
-version = "2023.7.4"
+version = "2023.8.0"
 description = "Bio image reading, metadata and some affine registration."
 authors = ["W. Pomp <w.pomp@nki.nl>"]
 license = "GPLv3"
@@ -22,7 +22,7 @@ pint = "*"
 tqdm = "*"
 lxml = "*"
 pyyaml = "*"
-parfor = "*"
+parfor = ">=2023.8.2"
 JPype1 = "*"
 SimpleITK-SimpleElastix = "*"
 pytest = { version = "*", optional = true }

tests/test_open.py

@@ -1,12 +1,25 @@
+import pickle
 import pytest
 from pathlib import Path
+from multiprocessing import active_children
 from ndbioimage import Imread, ReaderNotFoundError
 
 
-@pytest.mark.parametrize("file", (Path(__file__).parent / 'files').iterdir())
+@pytest.mark.parametrize('file', (Path(__file__).parent / 'files').iterdir())
 def test_open(file):
     try:
         with Imread(file) as im:
-            print(im[dict(c=0, z=0, t=0)].mean())
+            mean = im[dict(c=0, z=0, t=0)].mean()
+            b = pickle.dumps(im)
+            jm = pickle.loads(b)
+            assert jm[dict(c=0, z=0, t=0)].mean() == mean
+            v = im.view()
+            assert v[dict(c=0, z=0, t=0)].mean() == mean
+            b = pickle.dumps(v)
+            w = pickle.loads(b)
+            assert w[dict(c=0, z=0, t=0)].mean() == mean
     except ReaderNotFoundError:
-        assert len(Imread.__subclasses__()), "No subclasses for Imread found."
+        assert len(Imread.__subclasses__()), 'No subclasses for Imread found.'
+
+    for child in active_children():
+        child.kill()

tests/test_ufuncs.py

@@ -0,0 +1,18 @@
+import pytest
+import numpy as np
+from ndbioimage import Imread
+from itertools import product
+
+
+r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
+im = Imread(r)
+a = np.array(im)
+
+
+@pytest.mark.parametrize('fun_and_axis', product(
+    (np.sum, np.nansum, np.min, np.nanmin, np.max, np.nanmax, np.argmin, np.argmax,
+     np.mean, np.nanmean, np.var, np.nanvar, np.std, np.nanstd), (None, 0, 1, 2, 3, 4)))
+def test_ufuncs(fun_and_axis):
+    fun, axis = fun_and_axis
+    assert np.all(np.isclose(fun(im, axis), fun(a, axis))), \
+        f'function {fun.__name__} over axis {axis} does not give the correct result'