Merge pull request #62 from MStarmans91/development

Release version 3.4.5

.github/workflows/unit_test.yml

@@ -0,0 +1,89 @@
+name: Unit test
+
+on:
+  push:
+    branches: [master, development]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: [3.7]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8
+          pip install -r requirements.txt
+      - name: Additional dependency for MaxOSX for XGBoost
+        run: |
+            brew install libomp
+        if: matrix.os == 'macos-latest'
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=WORC_config.py
+          # exit-zero treats all errors as warnings.
+          flake8 . --count --exit-zero --statistics --max-line-length=1000 --exclude=WORC_config.py,*elastixtools*
+      - name: Install WORC package itself
+        run: python setup.py -q install
+      - name: Clone the WORC Tutorial and run as test
+        run: |
+          git clone --single-branch --branch develop https://github.com/MStarmans91/WORCTutorial
+          python WORCTutorial/WORCTutorialSimple.py
+        env:
+          WORCDEBUG: true
+      - name: Debugging on Linux
+        run: |
+            fastr trace /tmp/WORC_Example_STWStrategyHN/__sink_data__.json --sinks features_train_CT_0_predict --samples HN1331
+            fastr trace /tmp/WORC_Example_STWStrategyHN/__sink_data__.json --sinks classification --samples all
+            fastr trace /tmp/WORC_Example_STWStrategyHN/__sink_data__.json --sinks performance --samples all
+            fastr trace /tmp/GS/DEBUG_0/tmp/__sink_data__.json --sinks output --samples id_0__0000__0000
+        if: matrix.os == 'ubuntu-latest'
+      - name: Debugging on Windows
+        run: |
+            fastr trace "C:\Users\RUNNER~1\AppData\Local\Temp\WORC_Example_STWStrategyHN\__sink_data__.json" --sinks features_train_CT_0_predict --samples HN1331
+            fastr trace "C:\Users\RUNNER~1\AppData\Local\Temp\WORC_Example_STWStrategyHN\__sink_data__.json" --sinks classification --samples all
+            fastr trace "C:\Users\RUNNER~1\AppData\Local\Temp\WORC_Example_STWStrategyHN\__sink_data__.json" --sinks performance --samples all
+            fastr trace "C:\Users\RUNNER~1\AppData\Local\Temp\GS\DEBUG_0\tmp\__sink_data__.json" --sinks output --samples id_0__0000__0000
+        if: matrix.os == 'windows-latest'
+      - name: Debugging on MaxOSX
+        run: |
+            fastr trace WORCTutorial/WORC_Example_STWStrategyHN/__sink_data__.json --sinks features_train_CT_0_predict --samples HN1331
+            fastr trace WORCTutorial/WORC_Example_STWStrategyHN/__sink_data__.json --sinks classification --samples all
+            fastr trace WORCTutorial/WORC_Example_STWStrategyHN/__sink_data__.json --sinks performance --samples all
+            fastr trace WORCTutorial/GS/DEBUG_0/tmp/__sink_data__.json --sinks output --samples id_0__0000__0000
+        if: matrix.os == 'macos-latest'
+      - name: Run additional test for regression on Linux
+        run: |
+            rm -r /tmp/GS/DEBUG_0
+            python WORC/tests/WORCTutorialSimple_unittest_regression.py
+            fastr trace /tmp/WORC_Example_STWStrategyHN_Regression/__sink_data__.json --sinks classification --samples all
+            fastr trace /tmp/WORC_Example_STWStrategyHN_Regression/__sink_data__.json --sinks performance --samples all
+            fastr trace /tmp/GS/DEBUG_0/tmp/__sink_data__.json --sinks output --samples id_0__0000__0000
+        env:
+          WORCDEBUG: true
+        if: matrix.os == 'ubuntu-latest'
+      - name: Run additional tests for multiclass on Linux
+        run: |
+            rm -r /tmp/GS/DEBUG_0
+            python WORC/tests/WORCTutorialSimple_unittest_multiclass.py
+            fastr trace /tmp/WORC_Example_STWStrategyHN_Multiclass/__sink_data__.json --sinks classification --samples all
+            fastr trace /tmp/WORC_Example_STWStrategyHN_Multiclass/__sink_data__.json --sinks performance --samples all
+            fastr trace /tmp/GS/DEBUG_0/tmp/__sink_data__.json --sinks output --samples id_0__0000__0000
+        env:
+          WORCDEBUG: true
+        if: matrix.os == 'ubuntu-latest'

CHANGELOG

@@ -6,6 +6,20 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <http://keepachangelog.com/>`_
 and this project adheres to `Semantic Versioning <http://semver.org/>`_
 
+
+3.4.5 - 2021-07-09
+------------------
+ Unit tests moved from Travis to Github Workflow from this verion on.
+
+Fixed
+~~~~~
+- Bug in plotting images when ranking the posteriors or percentages.
+- Linting issues.
+
+Changed
+~~~~~~~
+- Removed deprecated scatterplot, RankedSVM functions.
+
 3.4.4 - 2021-07-01
 ------------------
 

README.md

@@ -1,17 +1,14 @@
-# WORC v3.4.4
+# WORC v3.4.5
 ## Workflow for Optimal Radiomics Classification
 
 ## Information
 
-| Linux                          | Windows                       | Documentation                 | PyPi                          |Citing WORC          |
-|--------------------------------|-------------------------------|-------------------------------|-------------------------------|---------------------|
-| [![][tci-linx]][tci-linx-lnk]  | [![][tci-wind]][tci-wind-lnk] | [![][doc]][doc-lnk]           | [![][pypi]][pypi-lnk]         | [![][DOI]][DOI-lnk] |
+| Unit test                      | Documentation                 | PyPi                          |Citing WORC          |
+|--------------------------------|-------------------------------|-------------------------------|---------------------|
+| [![][gi-workflow]][gi-workflow-lnk]  | [![][doc]][doc-lnk]           | [![][pypi]][pypi-lnk]         | [![][DOI]][DOI-lnk] |
 
-[tci-linx]: https://travis-ci.com/MStarmans91/WORC.svg?token=qyvaeq7Cpwu7hJGB98Gp&branch=master&job=1
-[tci-linx-lnk]: https://travis-ci.com/MStarmans91/WORC
-
-[tci-wind]: https://travis-ci.com/MStarmans91/WORC.svg?token=qyvaeq7Cpwu7hJGB98Gp&branch=master&job=2
-[tci-wind-lnk]: https://travis-ci.com/MStarmans91/WORC
+[gi-workflow]: https://github.com/MStarmans91/WORC/workflows/Unit%20test/badge.svg
+[gi-workflow-lnk]: https://github.com/MStarmans91/WORC/actions?query=workflow%3A%22Unit+test%22
 
 [doc]:https://readthedocs.org/projects/worc/badge/?version=latest
 [doc-lnk]: https://worc.readthedocs.io/en/latest/?badge=latest
@@ -54,8 +51,8 @@ The official documentation can be found at [https://worc.readthedocs.io](https:/
 
 ## Installation
 
-WORC currently only supports Unix with Python 3.6+ (tested on 3.7.2 - 3.7.4) systems and
-has been tested on Ubuntu 16.04 and 18.04, and Windows 10. For detailed installation
+WORC supports Unix and Windows systems with Python 3.6+: the [unit tests](https://github.com/MStarmans91/WORC/actions?query=workflow%3A%22Unit+test%22)
+are performed on the latest Ubuntu and Windows versions with Python 3.7. For detailed installation
 instructions, please check  [the ReadTheDocs installation guidelines](https://worc.readthedocs.io/en/latest/static/quick_start.html#installation).
 
 The package can be installed through pip:
@@ -70,10 +67,6 @@ Make sure you install the requirements first:
 
       pip install -r requirements.txt
 
-NOTE: The version of PyRadiomics which WORC currently uses requires numpy to be installed beforehand. Make sure you do so, e.g.
-
-      pip install numpy
-
 ## 3rd-party packages used in WORC:
 
  - SimpleITK (Image loading and preprocessing)

README.rst

@@ -1,4 +1,4 @@
-WORC v3.4.4
+WORC v3.4.5
 ===========
 
 Workflow for Optimal Radiomics Classification
@@ -7,12 +7,11 @@ Workflow for Optimal Radiomics Classification
 Information
 -----------
 
-+-----------------+-----------------+-----------------+-----------------+------------+
-| Linux           | Windows         | Documentation   | PyPi            | Citing     |
-|                 |                 |                 |                 | WORC       |
-+=================+=================+=================+=================+============+
-| |image0|        | |image1|        | |image2|        | |image3|        | |image4|   |
-+-----------------+-----------------+-----------------+-----------------+------------+
++---------------------+---------------------+---------------------+---------------+
+| Unit test           | Documentation       | PyPi                | Citing WORC   |
++=====================+=====================+=====================+===============+
+| |image0|            | |image1|            | |image2|            | |image3|      |
++---------------------+---------------------+---------------------+---------------+
 
 Introduction
 ============
@@ -38,7 +37,7 @@ When using WORC, please cite this repository as following:
 
 ``Martijn P.A. Starmans, Sebastian R. van der Voort, Thomas Phil and Stefan Klein. Workflow for Optimal Radiomics Classification (WORC). Zenodo (2018). Available from:  https://github.com/MStarmans91/WORC. DOI: http://doi.org/10.5281/zenodo.3840534.``
 
-For the DOI, visit |image5|.
+For the DOI, visit |image4|.
 
 Disclaimer
 ----------
@@ -60,10 +59,11 @@ The official documentation can be found at https://worc.readthedocs.io.
 Installation
 ------------
 
-WORC currently only supports Unix with Python 3.6+ (tested on 3.7.2 -
-3.7.4) systems and has been tested on Ubuntu 16.04 and 18.04, and
-Windows 10. For detailed installation instructions, please check `the
-ReadTheDocs installation
+WORC supports Unix and Windows systems with Python 3.6+: the `unit
+tests <https://github.com/MStarmans91/WORC/actions?query=workflow%3A%22Unit+test%22>`__
+are performed on the latest Ubuntu and Windows versions with Python 3.7.
+For detailed installation instructions, please check `the ReadTheDocs
+installation
 guidelines <https://worc.readthedocs.io/en/latest/static/quick_start.html#installation>`__.
 
 The package can be installed through pip:
@@ -84,13 +84,6 @@ Make sure you install the requirements first:
 
       pip install -r requirements.txt
 
-NOTE: The version of PyRadiomics which WORC currently uses requires
-numpy to be installed beforehand. Make sure you do so, e.g.
-
-::
-
-      pip install numpy
-
 3rd-party packages used in WORC:
 --------------------------------
 
@@ -182,15 +175,13 @@ to XNAT. We advise you to specify your account settings in a .netrc file
 when using this feature for your own datasets, such that you do not need
 to input them on every request.
 
-.. |image0| image:: https://travis-ci.com/MStarmans91/WORC.svg?token=qyvaeq7Cpwu7hJGB98Gp&branch=master&job=1
-   :target: https://travis-ci.com/MStarmans91/WORC
-.. |image1| image:: https://travis-ci.com/MStarmans91/WORC.svg?token=qyvaeq7Cpwu7hJGB98Gp&branch=master&job=2
-   :target: https://travis-ci.com/MStarmans91/WORC
-.. |image2| image:: https://readthedocs.org/projects/worc/badge/?version=latest
+.. |image0| image:: https://github.com/MStarmans91/WORC/workflows/Unit%20test/badge.svg
+   :target: https://github.com/MStarmans91/WORC/actions?query=workflow%3A%22Unit+test%22
+.. |image1| image:: https://readthedocs.org/projects/worc/badge/?version=latest
    :target: https://worc.readthedocs.io/en/latest/?badge=latest
-.. |image3| image:: https://badge.fury.io/py/WORC.svg
+.. |image2| image:: https://badge.fury.io/py/WORC.svg
    :target: https://badge.fury.io/py/WORC
-.. |image4| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3840534.svg
+.. |image3| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3840534.svg
    :target: https://zenodo.org/badge/latestdoi/92295542
-.. |image5| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3840534.svg
+.. |image4| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3840534.svg
    :target: https://zenodo.org/badge/latestdoi/92295542

WORC/classification/AdvancedSampler.py

@@ -162,8 +162,10 @@ def __iter__(self):
         # Generate the sequence generator
         if self.method == 'Halton':
             sequence = self.Halton.get(self.n_iter)
-        elif self.method == 'Sobol':
-            sequence = Sobol(len(self.param_distributions.keys()), self.n_iter)
+            # elif self.method == 'Sobol':
+            #     sequence = Sobol(len(self.param_distributions.keys()), self.n_iter)
+        else:
+            raise KeyError(f'Methods {self.method} not known!')
 
         # Always sort the keys of a dictionary, for reproducibility
         items = sorted(self.param_distributions.items())
@@ -206,7 +208,7 @@ def __len__(self):
 
     n_iter = 6
 
-    method = 'Sobol'
+    method = 'Halton'
     sampled_params = AdvancedSampler(param_distributions,
                                      n_iter,
                                      random_state)