Merge remote-tracking branch 'upstream/master' into attribute_operators

.github/ISSUE_TEMPLATE.md

@@ -1,15 +1,25 @@
 ## Description
-[Please provide a general introduction to the issue/proposal.]
-
-[If reporting a bug, attach the entire traceback from Python.]
-[If proposing an enhancement/new feature, provide links to related articles, reference examples, etc.]
 
 
 ## Way to reproduce
-[If reporting a bug, please include the following important information:]
-- [ ] Code example
-- [ ] Relevant images (if any)
-- [ ] Operating system and version
-- [ ] Python version
-- [ ] scikit-image version (run `skimage.__version__`)
+```python
+# Place the full code we need to recreate your issue here
+# upload all necessary images to github too!
+```
+
+
+## Version information
+```python
+# Paste the output of the following python commands
+from __future__ import print_function
+import sys; print(sys.version)
+import platform; print(platform.platform())
+import skimage; print("scikit-image version: {}".format(skimage.__version__))
+import numpy; print("numpy version: {}".format(numpy.__version__))
+```
+
+```python
+# your output here
+
+```
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,27 +1,27 @@
 ## Description
-[Tell us about your new feature, improvement, or fix! If relevant, please supplement the PR with images.]
+
+<!-- If this is a bug-fix or enhancement, state the issue # it closes -->
+<!-- If this is a new feature, reference what paper it implements. -->
 
 
 ## Checklist
-[It's fine to submit PRs which are a work in progress! But before they are merged, all PRs should provide:]
-- [ ] Clean style in [the spirit of PEP8](https://www.python.org/dev/peps/pep-0008/)
+
+<!-- It's fine to submit PRs which are a work in progress! -->
+<!-- But before they are merged, all PRs should provide: -->
 - [ ] [Docstrings for all functions](https://github.com/numpy/numpy/blob/master/doc/example.py)
 - [ ] Gallery example in `./doc/examples` (new features only)
 - [ ] Benchmark in `./benchmarks`, if your changes aren't covered by an
   existing benchmark
 - [ ] Unit tests
+- [ ] Clean style in [the spirit of PEP8](https://www.python.org/dev/peps/pep-0008/)
 
-[For detailed information on these and other aspects see [scikit-image contribution guidelines](https://scikit-image.org/docs/dev/contribute.html)]
-
-
-## References
-[If this is a bug-fix or enhancement, it closes issue # ]
-[If this is a new feature, it implements the following paper: ]
+<!-- For detailed information on these and other aspects see -->
+<!-- the scikit-image contribution guidelines. -->
+<!-- https://scikit-image.org/docs/dev/contribute.html -->
 
 ## For reviewers
 
-(Don't remove the checklist below.)
-
+<!-- Don't remove the checklist below. -->
 - [ ] Check that the PR title is short, concise, and will make sense 1 year
   later.
 - [ ] Check that new functions are imported in corresponding `__init__.py`.

.gitignore

@@ -28,7 +28,7 @@ doc/source/auto_examples/**/*
 doc/source/_static/random.js
 .idea/
 *.log
-doc/release/_release_notes_for_docs.txt
+doc/release/_release_notes_for_docs.rst
 doc/gh-pages
 wheels
 skimage/morphology/_skeletonize_3d_cy.pyx

.travis.yml

@@ -20,6 +20,9 @@ addons:
     - texlive
     - texlive-latex-extra
     - dvipng
+    # this became necessary to use matplotlib and qt5.12
+    # https://github.com/matplotlib/matplotlib/pull/13412
+    - qtbase5-dev
 
 env:
   global:
@@ -38,7 +41,7 @@ matrix:
   include:
     - os: linux
       python: 3.5
-      env: OPTIONAL_DEPS=1 WITH_PYSIDE=1 BUILD_DOCS=1
+      env: OPTIONAL_DEPS=1 WITH_PYSIDE=1 BUILD_DOCS=1 INSTALL_FROM_SDIST=1
     - os: linux
       python: 3.5
       env: QT=PyQt5 MINIMUM_REQUIREMENTS=1
@@ -53,19 +56,25 @@ matrix:
       dist: xenial # Required for Python 3.7
       sudo: true   # travis-ci/travis-ci#9069
       env: QT=PyQt5 OPTIONAL_DEPS=1 BUILD_DOCS=1
+      services:
+        - xvfb
     - os: linux
       python: 3.6
       env: QT=PyQt5 OPTIONAL_DEPS=1 PIP_FLAGS="--pre"
+    # For smooth deployment, the osx_image here should match
+    # what we set in the wheel generation travis images.
+    # If not set, it will use the default version from Travis
+    # https://docs.travis-ci.com/user/reference/osx/#xcode-version
     - os: osx
-      osx_image: xcode10.1
+      osx_image: xcode9.4
       language: objective-c
       env: TRAVIS_PYTHON_VERSION=3.5
     - os: osx
-      osx_image: xcode10.1
+      osx_image: xcode9.4
       language: objective-c
       env: TRAVIS_PYTHON_VERSION=3.6 OPTIONAL_DEPS=1
     - os: osx
-      osx_image: xcode10.1
+      osx_image: xcode9.4
       language: objective-c
       env: TRAVIS_PYTHON_VERSION=3.7
 
@@ -87,8 +96,18 @@ before_install:
     - tools/check_sdist.py $SDIST_NAME
 
 install:
-    - python setup.py develop
     - ccache --show-stats
+    # Test installing without cython using the sdist
+    # --no-build-isolation ensures even in the presense of a pyproject.toml
+    # pip will not create a virtual environment, just for building the package
+    # This is problematic because the version of numpy of that virtual environment
+    # may be higher than the version we want to test with.
+    - if [[ $INSTALL_FROM_SDIST ]]; then
+        pip uninstall cython -y;
+        pip install dist/scikit-image-*.tar.gz;
+      else
+        pip install --no-build-isolation .;
+      fi
     # Install testing requirements
     - pip install --retries 3 -q $PIP_FLAGS -r requirements/test.txt
     # Matplotlib settings - do not show figures during doc examples

CONTRIBUTING.txt

@@ -170,6 +170,50 @@ Once you've fixed all merge conflicts, do::
    <https://scikit-image.org/docs/dev/gitwash/development_workflow.html#rebasing-on-trunk>`__,
    but we squash and merge most PRs either way.
 
+Build environment setup
+-----------------------
+
+Once you've cloned your fork of the scikit-image repository,
+you should setup a Python development environment tailored for scikit-image.
+You may choose the environment manager of your choice.
+Here we provide instructions for two popular environment managers:
+``venv`` (pip based) and ``conda`` (Anaconda or Miniconda).
+
+venv
+====
+When using ``venv``, you may find the following bash commands useful::
+
+  # Create a virtualenv named ``skimage-dev`` that lives in the directory of
+  # the same name
+  python -m venv skimage-dev
+  # Activate it
+  source skimage-dev/bin/activate
+  # Install all development and runtime dependencies of scikit-image
+  pip install -r <(cat requirements/*.txt)
+  # Build and install scikit-image from source
+  pip install -e .
+  # Test your installation
+  pytest skimage
+
+conda
+=====
+
+When using conda, you may find the following bash commands useful::
+
+  # Create a conda environment named ``skimage-dev``
+  conda create --name skimage-dev
+  # Activate it
+  conda activate skimage-dev
+  # Install major development and runtime dependencies of scikit-image
+  # (the rest can be installed from conda-forge or pip, if needed)
+  conda install `for i in requirements/{default,build}.txt; do echo -n " --file $i "; done`
+  # Install minimal testing dependencies
+  conda install pytest
+  # Install scikit-image from source
+  pip install -e . --no-deps
+  # Test your installation
+  pytest skimage
+
 Guidelines
 ----------
 

CONTRIBUTORS.txt

@@ -269,3 +269,6 @@
 - Mark Harfouche
   Enabled GIL free operation of many algorithms implemented in Cython.
   Maintenance of the build and test infrastructure.
+
+- Taylor D. Scott
+  Simplified _upsampled_dft and extended register_translation to nD images.

MANIFEST.in

@@ -1,12 +1,10 @@
 include setup*.py
-include conftest.py
 include MANIFEST.in
 include *.txt
 include *.rst
 recursive-include requirements *.txt
 include requirements/README.md
 include Makefile
-include pyproject.toml
 include skimage/scripts/skivi
 recursive-include skimage *.pyx *.pxd *.pxi *.py *.c *.h *.ini *.npy *.txt *.in *.cpp *.md
 recursive-include skimage/data *

README.md

@@ -1,4 +1,5 @@
 # scikit-image: Image processing in Python
+[![Image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fscikit-image.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tags/scikit-image)
 [![Stackoverflow](https://img.shields.io/badge/stackoverflow-Ask%20questions-blue.svg)](https://stackoverflow.com/questions/tagged/scikit-image)
 [![project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://skimage.zulipchat.com)
 [![codecov.io](https://codecov.io/github/scikit-image/scikit-image/coverage.svg?branch=master)](https://codecov.io/github/scikit-image/scikit-image?branch=master)

TODO.txt

@@ -33,6 +33,9 @@ Version 0.16
 * In ``skimage.morphology.remove_small_holes``, remove ``min_size`` argument.
 * In ``skimage.filters.median``, change default from ``behavior='rank'`` to
   ``behavior='ndimage'``.
+* Remove ``skimage.transform.seam_carve``, including the source code file, the
+  import and ``__all__`` listing in ``skimage/transform/__init__.py``, and
+  the test file in ``skimage/transform/tests``.
 
 Version 0.17
 ------------

benchmarks/benchmark_feature.py

@@ -2,7 +2,8 @@
 # https://asv.readthedocs.io/en/latest/writing_benchmarks.html
 import numpy as np
 from scipy import ndimage as ndi
-from skimage import feature, util
+from skimage import feature, util, img_as_float
+from skimage.data import binary_blobs
 
 
 class FeatureSuite:
@@ -24,3 +25,41 @@ def time_glcm(self):
         pi = np.pi
         result = feature.greycomatrix(self.image_ubyte, distances=[1, 2],
                                       angles=[0, pi/4, pi/2, 3*pi/4])
+
+
+class RegisterTranslation:
+    """Benchmarks for feature.register_translation in scikit-image"""
+    param_names = ["ndims", "image_size", "upscale_factor"]
+    params = [(2, 3), (32, 100), (1, 5, 10)]
+
+    def setup(self, ndims, image_size, upscale_factor, *args):
+        shifts = (-2.3, 1.7, 5.4, -3.2)[:ndims]
+        phantom = img_as_float(binary_blobs(length=image_size, n_dim=ndims))
+        self.reference_image = np.fft.fftn(phantom)
+        self.shifted_image = ndi.fourier_shift(self.reference_image, shifts)
+
+    def time_register_translation(self, ndims, image_size, upscale_factor):
+        result = feature.register_translation(self.reference_image,
+                                              self.shifted_image,
+                                              upscale_factor,
+                                              space="fourier")
+
+    def peakmem_reference(self, *args):
+        """Provide reference for memory measurement with empty benchmark.
+        Peakmem benchmarks measure the maximum amount of RAM used by a
+        function. However, this maximum also includes the memory used
+        during the setup routine (as of asv 0.2.1; see [1]_).
+        Measuring an empty peakmem function might allow us to disambiguate
+        between the memory used by setup and the memory used by target (see
+        other ``peakmem_`` functions below).
+        References
+        ----------
+        .. [1]: https://asv.readthedocs.io/en/stable/writing_benchmarks.html#peak-memory
+        """
+        pass
+
+    def peakmem_register_translation(self, ndims, image_size, upscale_factor):
+        result = feature.register_translation(self.reference_image,
+                                              self.shifted_image,
+                                              upscale_factor,
+                                              space="fourier")

doc/examples/data/plot_scientific.py

@@ -16,6 +16,7 @@
 images = ('hubble_deep_field',
           'immunohistochemistry',
           'moon',
+          'retina',
           )