Feature slide info

.travis.yml

@@ -5,7 +5,9 @@ python:
   - 3.8
   - 3.7
   - 3.6
-  - 3.5
+
+before_install:
+  - sudo apt-get -y install openslide-tools
 
 # Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
 install: pip install -U tox-travis
@@ -15,13 +17,13 @@ script: tox
 
 # Upload test coverage reports (codecov and deepsource)
 after_success:
-# Upload coverage to codecov
-- bash <(curl -s https://codecov.io/bash)
-# Install deepsource CLI
-- curl https://deepsource.io/cli | sh
-- export DEEPSOURCE_DSN=https://sampledsn@deepsource.io
-# Report coverage artifact to 'test-coverage' analyzer
--./bin/deepsource report --analyzer test-coverage --key python --value-file ./coverage.xml
+  # Upload coverage to codecov
+  - bash <(curl -s https://codecov.io/bash)
+  # Install deepsource CLI
+  - curl https://deepsource.io/cli | sh
+  - export DEEPSOURCE_DSN=https://sampledsn@deepsource.io
+  # Report coverage artifact to 'test-coverage' analyzer
+  - ./bin/deepsource report --analyzer test-coverage --key python --value-file ./coverage.xml
 
 # Assuming you have installed the travis-ci CLI tool, after you
 # create the Github repo and add it to Travis, run the

README.rst

@@ -1,25 +1,56 @@
+.. raw:: html
+
+   <p align="center">
+     <img width="450" height="200" src=https://warwick.ac.uk/fac/sci/dcs/research/tia/tiatoolbox/files/tialab_logo.png>
+   </p>
+
 ===========
 TIA Toolbox
 ===========
 
+Computational Pathology Toolbox developed by TIA Lab
+
+Please try
+
+::
+
+    python -m tiatoolbox -h
+
+Getting Started
+===============
 
+First, install OpenSlide `here <https://openslide.org/download/>`__. Then, create and
+activate the conda environment:
 
+pip
+----
 
+::
 
+    pip install -r requirements_dev.txt
 
-Computational pathology toolbox developed by TIA Lab.
+conda
+-----
+::
 
+    conda env create --name tiatoolbox --file requirements.conda.yml
+    conda activate tiatoolbox
 
+tiatoolbox --help
+=======================
 
-Features
---------
+::
 
-* TODO
+    usage: tiatoolbox [-h] [--version] [--verbose VERBOSE]
+                     {slide_info}
+                     ...
 
-Credits
--------
+    positional arguments:
+      {slide_info}
+        slide_info          usage: python -m tiatoolbox slide_info -h
 
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+    optional arguments:
+      -h, --help            show this help message and exit
+      --version             show program`s version number and exit
+      --verbose VERBOSE
 
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

docs/conf.py

@@ -32,7 +32,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode", "sphinx.ext.napoleon"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]

docs/index.rst

@@ -1,5 +1,5 @@
 Welcome to TIA Toolbox's documentation!
-======================================
+=======================================
 
 .. toctree::
    :maxdepth: 2

docs/usage.rst

@@ -5,3 +5,47 @@ Usage
 To use TIA Toolbox in a project::
 
     import tiatoolbox
+
+
+----------
+Dataloader
+----------
+.. automodule:: tiatoolbox.dataloader
+
+^^^^^^^^^^^^^^^^^^^^
+dataloader.wsireader
+^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: tiatoolbox.dataloader.wsireader
+    :members: WSIReader
+    :special-members: __init__
+
+^^^^^^^^^^^^^^^^^^^^^
+dataloader.slide_info
+^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: tiatoolbox.dataloader.slide_info
+    :members: slide_info
+
+----------
+Decorators
+----------
+.. automodule:: tiatoolbox.decorators
+
+^^^^^^^^^^^^^^^^^^^^
+decorators.multiproc
+^^^^^^^^^^^^^^^^^^^^
+.. automodule:: tiatoolbox.decorators.multiproc
+    :members: TIAMultiProcess
+    :special-members: __init__, __call__
+
+------
+Utils
+------
+.. automodule:: tiatoolbox.utils
+
+^^^^^^^^^^
+utils.misc
+^^^^^^^^^^
+.. automodule:: tiatoolbox.utils.misc
+    :members: save_yaml, split_path_name_ext, grab_files_from_dir

requirements.conda.yml

@@ -0,0 +1,22 @@
+name: tiatoolbox
+channels:
+  - conda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.6
+  - setuptools==45.1.0
+  - Click==7.0
+  - cython=0.29.15
+  - h5py=2.8.0
+  - matplotlib-base=3.1.3
+  - numpy=1.18.1
+  - opencv=4.2
+  - pillow=7.0.0
+  - pip=20.0.2
+  - pyyaml=5.3.1
+  - requests=2.23.0
+  - pathos==0.2.5
+  - pip:
+    - openslide-python==1.1.1
+

requirements_dev.txt

@@ -1,4 +1,4 @@
-pip==19.2.3
+pip==20.0.2
 bump2version==0.5.11
 wheel==0.33.6
 watchdog==0.9.0
@@ -8,6 +8,10 @@ coverage==5.1
 Sphinx==1.8.5
 twine==1.14.0
 Click==7.0
-pytest==4.6.5
-pytest-runner==5.1
+setuptools==45.1.0
+pytest==5.4.2
+pytest-runner==5.2
+opencv-python==4.2.0.34
+pathos==0.2.5
+openslide-python==1.1.1
 pytest-cov==2.9.0

setup.py

@@ -25,19 +25,18 @@
 setup(
     author="TIA Lab",
     author_email="tialab@dcs.warwick.ac.uk",
-    python_requires=">=3.5",
+    python_requires=">=3.6",
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
         "Intended Audience :: Developers",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.5",
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],
     description="Computational pathology toolbox developed by TIA Lab.",
-    entry_points={"console_scripts": ["tiatoolbox=tiatoolbox.cli:main",],},
+    entry_points={"console_scripts": ["tiatoolbox=tiatoolbox.cli:main", ], },
     install_requires=requirements,
     long_description=readme + "\n\n" + history,
     include_package_data=True,

tests/test_tiatoolbox.py

@@ -1,37 +1,108 @@
 #!/usr/bin/env python
 
 """Tests for `tiatoolbox` package."""
-
 import pytest
 
-from click.testing import CliRunner
-
-from tiatoolbox import tiatoolbox
+from tiatoolbox.dataloader.slide_info import slide_info
+from tiatoolbox import utils
 from tiatoolbox import cli
+from tiatoolbox import __version__
+
+from click.testing import CliRunner
+import requests
+import os
+import pathlib
 
 
 @pytest.fixture
-def response():
-    """Sample pytest fixture.
+def _response_ndpi(request):
+    """
+    Sample pytest fixture for ndpi images
+    Download ndpi image for pytest
+    """
+    ndpi_file_path = pathlib.Path(__file__).parent.joinpath("CMU-1.ndpi")
+    if not pathlib.Path.is_file(ndpi_file_path):
+        r = requests.get(
+            "http://openslide.cs.cmu.edu/download/openslide-testdata"
+            "/Hamamatsu/CMU-1.ndpi"
+        )
+        with open(ndpi_file_path, "wb") as f:
+            f.write(r.content)
+
+    def close_ndpi():
+        if pathlib.Path.is_file(ndpi_file_path):
+            os.remove(str(ndpi_file_path))
+
+    request.addfinalizer(close_ndpi)
+    return _response_ndpi
 
-    See more at: http://doc.pytest.org/en/latest/fixture.html
+
+@pytest.fixture
+def _response_svs(request):
     """
-    # import requests
-    # return requests.get('https://github.com/audreyr/cookiecutter-pypackage')
+    Sample pytest fixture for svs images
+    Download ndpi image for pytest
+    """
+    svs_file_path = pathlib.Path(__file__).parent.joinpath("CMU-1.svs")
+    if not pathlib.Path.is_file(svs_file_path):
+        r = requests.get(
+            "http://openslide.cs.cmu.edu/download/openslide-testdata"
+            "/Hamamatsu/CMU-1.ndpi"
+        )
+        with open(svs_file_path, "wb") as f:
+            f.write(r.content)
+
+    def close_ndpi():
+        if pathlib.Path.is_file(svs_file_path):
+            os.remove(str(svs_file_path))
+
+    request.addfinalizer(close_ndpi)
+    return _response_svs
 
 
-def test_content(response):
-    """Sample pytest test function with the pytest fixture as an argument."""
-    # from bs4 import BeautifulSoup
-    # assert 'GitHub' in BeautifulSoup(response.content).title.string
+def test_slide_info(_response_ndpi, _response_svs):
+    """pytest for slide_info as a python function"""
+    file_types = ("*.ndpi", "*.svs", "*.mrxs")
+    files_all = utils.misc.grab_files_from_dir(
+        input_path=str(pathlib.Path(r".")), file_types=file_types,
+    )
+    slide_params = slide_info(input_path=files_all, workers=2)
 
+    for slide_param in slide_params:
+        utils.misc.save_yaml(slide_param, slide_param["file_name"] + ".yaml")
 
-def test_command_line_interface():
-    """Test the CLI."""
+
+def test_command_line_help_interface():
+    """Test the CLI help"""
     runner = CliRunner()
     result = runner.invoke(cli.main)
     assert result.exit_code == 0
-    assert "tiatoolbox.cli.main" in result.output
     help_result = runner.invoke(cli.main, ["--help"])
     assert help_result.exit_code == 0
-    assert "--help  Show this message and exit." in help_result.output
+    assert help_result.output == result.output
+
+
+def test_command_line_version():
+    """pytest for version check"""
+    runner = CliRunner()
+    version_result = runner.invoke(cli.main, ["-V"])
+    assert __version__ in version_result.output
+
+
+def test_command_line_slide_info(_response_ndpi, _response_svs):
+    """Test the Slide information CLI."""
+    runner = CliRunner()
+    slide_info_result = runner.invoke(
+        cli.main,
+        [
+            "slide-info",
+            "--wsi_input",
+            ".",
+            "--file_types",
+            '"*.ndpi, *.svs"',
+            "--workers",
+            "2",
+        ],
+    )
+
+    assert slide_info_result.exit_code == 0

tiatoolbox/__init__.py

@@ -1,5 +1,12 @@
 """Top-level package for TIA Toolbox."""
+from tiatoolbox import tiatoolbox
+from tiatoolbox import dataloader
+from tiatoolbox import utils
+
 
 __author__ = """TIA Lab"""
 __email__ = "tialab@dcs.warwick.ac.uk"
 __version__ = "0.1.1"
+
+if __name__ == "__main__":
+    pass

tiatoolbox/__main__.py

@@ -0,0 +1,5 @@
+"""__main__ file invoked with `python -m tiatoolbox` command"""
+
+from tiatoolbox.cli import main
+
+main()