Merge pull request #5 from BMCV/dev/fix-4

`giatools.io.imread` will automatically use `tifffile` for loading TIFF images, when available

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+
+omit = tests/*

.flake8

@@ -1,3 +1,5 @@
 [flake8]
 
-extend-ignore = E221,E211,E222,E202,F541,E201,E203,E501
+max-line-length = 120
+
+extend-ignore = E221,E211,E222,E202,F541,E201,E203

.gitignore

@@ -5,4 +5,5 @@ __pycache__
 /build
 *.swp
 tests/*-out-*
-/.venv
+/.venv
+/.coverage

.isort.cfg

@@ -0,0 +1,9 @@
+[settings]
+
+multi_line_output = 3
+
+force_grid_wrap = 2
+
+include_trailing_comma = true
+
+skip_glob = docs/source/conf.py

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+    "[git-commit]": {
+        "editor.rulers": [50]
+    },
+
+    "[python]": {
+        "editor.rulers": [119]
+    }
+}

README.rst

@@ -15,3 +15,5 @@
 Galaxy Image Analysis: https://github.com/BMCV/galaxy-image-analysis
 
 Use ``python -m unittest`` in the root directory of the repository to run the test suite.
+
+Use ``coverage run -m unittest && coverage html`` to generate a coverage report.

giatools/__init__.py

@@ -1,5 +1,5 @@
 VERSION_MAJOR = 0
-VERSION_MINOR = 1
-VERSION_PATCH = 2
+VERSION_MINOR = 2
+VERSION_PATCH = 0
 
 VERSION = '%d.%d%s' % (VERSION_MAJOR, VERSION_MINOR, '.%d' % VERSION_PATCH if VERSION_PATCH > 0 else '')

giatools/io.py

@@ -5,26 +5,36 @@
 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
 """
 
-import contextlib
-
 import skimage.io
 
+import giatools.util
+
+try:
+    import tifffile
+except ImportError:
+    tifffile = None
 
-def imread(*args, impl=skimage.io.imread, **kwargs):
-    """
-    Wrapper around ``skimage.io.imread`` which mutes non-fatal errors.
 
-    When using ``skimage.io.imread`` to read an image file, sometimes errors can be reported although the image file will be read successfully.
-    In those cases, Galaxy might detect the errors and assume that the tool has failed: https://docs.galaxyproject.org/en/latest/dev/schema.html#error-detection
-    To prevent this, this wrapper around ``skimage.io.imread`` will mute all non-fatal errors.
+@giatools.util.silent
+def imread(*args, **kwargs):
     """
-    try:
+    Wrapper for loading images which mutes non-fatal errors.
 
-        # Mute stderr unless an error occurs
-        with contextlib.redirect_stderr(None):
-            return impl(*args, **kwargs)
+    When using ``skimage.io.imread`` to read an image file, sometimes errors can be reported although the image file
+    will be read successfully. In those cases, Galaxy might detect the errors on stdout or stderr, and assume that the
+    tool has failed: https://docs.galaxyproject.org/en/latest/dev/schema.html#error-detection To prevent this, this
+    wrapper around ``skimage.io.imread`` will mute all non-fatal errors.
+
+    Image loading is first attempted using `tifffile` (if available, more reliable for loading TIFF files), and if
+    that fails (e.g., because the file is not a TIFF file), falls back to ``skimage.io.imread``.
+    """
 
-    except:  # noqa: E722
+    # First, try to read the image using `tifffile` (will only succeed if it is a TIFF file)
+    if tifffile is not None:
+        try:
+            return tifffile.imread(*args, **kwargs)
+        except tifffile.TiffFileError:
+            pass  # not a TIFF file
 
-        # Raise the error outside of the contextlib redirection
-        raise
+    # If the image is not a TIFF file, or `tifffile is not available`, fall back to `skimage.io.imread`
+    return skimage.io.imread(*args, **kwargs)

giatools/util.py

@@ -5,10 +5,26 @@
 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
 """
 
+import contextlib
+import os
+
 import numpy as np
 import skimage.util
 
 
+def silent(func):
+    """
+    Decorator that mutes the standard error stream of the decorated function.
+    """
+
+    def wrapper(*args, **kwargs):
+        with open(os.devnull, 'w') as fnull:
+            with contextlib.redirect_stderr(fnull):
+                return func(*args, **kwargs)
+
+    return wrapper
+
+
 def convert_image_to_format_of(image, format_image):
     """
     Convert the first image to the format of the second image.

setup.py

@@ -6,12 +6,12 @@
 
 
 setup(
-    name = 'giatools',
-    version = giatools.VERSION,
-    description = 'Tools required for Galaxy Image Analysis',
-    author = 'Leonid Kostrykin',
-    author_email = '[email protected]',
-    url = 'https://kostrykin.com',
-    license = 'MIT',
-    packages = ['giatools'],
+    name='giatools',
+    version=giatools.VERSION,
+    description='Tools required for Galaxy Image Analysis',
+    author='Leonid Kostrykin',
+    author_email='[email protected]',
+    url='https://kostrykin.com',
+    license='MIT',
+    packages=['giatools'],
 )

tests/test_io.py

@@ -1,7 +1,11 @@
 import unittest
+import unittest.mock
 
 import giatools.io
 
+# This tests require that the `tifffile` package is installed.
+assert giatools.io.tifffile is not None
+
 
 class imread(unittest.TestCase):
 
@@ -12,3 +16,32 @@ def test_input1(self):
     def test_input2(self):
         img = giatools.io.imread('tests/data/input2.tif')
         self.assertEqual(img.mean(), 9.543921821305842)
+
+    def test_input3(self):
+        """
+        This is a multi-page TIFF, that sometimes fails to load properly with ``skimage.io.imread``, but works with
+        `tifffile`.
+
+        For details see: https://github.com/BMCV/galaxy-image-analysis/pull/132#issuecomment-2371561435
+        """
+        img = giatools.io.imread('tests/data/input3.tif')
+        self.assertEqual(img.shape, (5, 198, 356))
+        self.assertEqual(img.mean(), 1259.6755334241288)
+
+    def test_input4(self):
+        """
+        This is an RGB PNG file, that cannot be loaded with `tifffile`, but works with ``skimage.io.imread``.
+        """
+        img = giatools.io.imread('tests/data/input4.png')
+        self.assertEqual(img.shape, (10, 10, 3))
+        self.assertEqual(img.mean(), 130.04)
+
+    @unittest.mock.patch('skimage.io.imread')
+    @unittest.mock.patch('giatools.io.tifffile', None)
+    def test_without_tifffile(self, mock_skimage_io_imread):
+        """
+        Test that loading an image without `tifffile` installed falls back to ``skimage.io.imread``.
+        """
+        img = giatools.io.imread('tests/data/input1.tif')
+        mock_skimage_io_imread.assert_called_once_with('tests/data/input1.tif')
+        self.assertIs(img, mock_skimage_io_imread.return_value)

tests/test_util.py

@@ -1,10 +1,25 @@
 import itertools
+import sys
 import unittest
 
 import numpy as np
 import skimage.util
 
 import giatools.util
+import tests.tools
+
+
+class silent(unittest.TestCase):
+
+    def test_silent(self):
+        @giatools.util.silent
+        def func():
+            print('Test', file=sys.stderr)
+            raise ValueError('This is a test error message')
+        with tests.tools.CaptureStderr() as stderr:
+            with self.assertRaises(ValueError):
+                func()
+        self.assertEqual(str(stderr), '')
 
 
 class convert_image_to_format_of(unittest.TestCase):

tests/tools.py

@@ -0,0 +1,19 @@
+import contextlib
+import io
+
+
+class CaptureStderr:
+
+    def __init__(self):
+        self.stdout_buf = io.StringIO()
+
+    def __enter__(self):
+        self.redirect = contextlib.redirect_stderr(self.stdout_buf)
+        self.redirect.__enter__()
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        self.redirect.__exit__(exc_type, exc_value, traceback)
+
+    def __str__(self):
+        return self.stdout_buf.getvalue()