From 8c116107549cf70e691ba7c00059d11f100cdfc1 Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Tue, 28 Jun 2022 01:55:40 +0200 Subject: [PATCH] DOC Use HTTPS links in docs --- docs/source/_templates/sidebar.html | 14 +++++++------- docs/source/classification.rst | 4 ++-- docs/source/color.rst | 4 ++-- docs/source/contributing.rst | 2 +- docs/source/faq.rst | 10 +++++----- docs/source/features.rst | 4 ++-- docs/source/index.rst | 16 ++++++++-------- docs/source/install.rst | 16 ++++++++-------- docs/source/io.rst | 4 ++-- docs/source/labeled.rst | 2 +- docs/source/lbp.rst | 2 +- docs/source/mahotas-features.rst | 2 +- docs/source/morphology.rst | 4 ++-- docs/source/polygon.rst | 2 +- docs/source/surfref.rst | 2 +- docs/source/tasks.rst | 18 +++++++++--------- docs/source/wally.rst | 2 +- 17 files changed, 54 insertions(+), 54 deletions(-) diff --git a/docs/source/_templates/sidebar.html b/docs/source/_templates/sidebar.html index 58747ec3..9cf65905 100644 --- a/docs/source/_templates/sidebar.html +++ b/docs/source/_templates/sidebar.html @@ -4,21 +4,21 @@

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C++) operates over numpy arrays for convenience.

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@@ -26,7 +26,7 @@

Cite

If you use mahotas in a publication, please cite:

- Luis Pedro Coelho. Mahotas: + Luis Pedro Coelho. Mahotas: Open source software for scriptable computer vision in Journal of Open Research Software, vol 1, 2013. [DOI:10.5334/jors.ac]
diff --git a/docs/source/classification.rst b/docs/source/classification.rst index 3a8b2652..c183576a 100644 --- a/docs/source/classification.rst +++ b/docs/source/classification.rst @@ -15,7 +15,7 @@ Here is the simple algorithm: 2. learn a classifier 3. use that classifier on the unlabeled images -In the code below I used `jug `_ to give you +In the code below I used `jug `_ to give you the possibility of running it on multiple processors, but the code also works if you remove every line which mentions ``TaskGenerator``. @@ -74,6 +74,6 @@ with other features in ``mahotas.features`` if you'd like (or try ``mahotas.surf``, but that gets more complicated). (This was motivated by `a question on Stackoverflow -`__). +`__). diff --git a/docs/source/color.rst b/docs/source/color.rst index 3243c96e..f94eb9c4 100644 --- a/docs/source/color.rst +++ b/docs/source/color.rst @@ -52,7 +52,7 @@ Other Colour Spaces ------------------- Mahotas can also convert to `XYZ space -`__ and to the `Lab space -`__ with ``rgb2xyz`` and +`__ and to the `Lab space +`__ with ``rgb2xyz`` and ``rgb2lab``, respectively. diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 59e123c2..e70ec06e 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -47,7 +47,7 @@ the ``fast`` Make target to get the non-debug build:: Using make will not change your environment. The ``DEBUG`` variable is set internally only. -If you don't know about it, check out `ccache `__ +If you don't know about it, check out `ccache `__ which is a great tool if you are developing in compiled languages (this is not specific to mahotas or even Python). It will allow you to quickly perform ``make clean; make debug`` and ``make clean; make fast`` so you never get your diff --git a/docs/source/faq.rst b/docs/source/faq.rst index ffb65165..6778c52e 100644 --- a/docs/source/faq.rst +++ b/docs/source/faq.rst @@ -5,7 +5,7 @@ Frequently Asked Questions How do I install mahotas with anaconda? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -If you are using `conda `__, you can +If you are using `conda `__, you can install mahotas from `conda-forge `__ using the following commands:: @@ -19,7 +19,7 @@ Who uses mahotas? In June 2016, there were `34 papers `__ citing the `mahotas paper -`__ +`__ Why did you not simply contribute to ``scipy.ndimage`` or ``scikits.image``? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -76,7 +76,7 @@ If you use mahotas in a scientific publication, please cite: Coelho, L.P. 2013. Mahotas: Open source software for scriptable computer vision. Journal of Open Research Software 1(1), DOI: - http://dx.doi.org/10.5334/jors.ac + https://dx.doi.org/10.5334/jors.ac In BibTeX format:: @@ -87,7 +87,7 @@ In BibTeX format:: year = {2013}, volume = {1}, doi = {10.5334/jors.ac}, - url = {http://dx.doi.org/10.5334/jors.ac} + url = {https://dx.doi.org/10.5334/jors.ac} } This is accessible in Python using ``mahotas.citation()``. @@ -109,5 +109,5 @@ as it uses other packages itself. Thus, depending on what you had installed, the resulting images would be different. If you are running on Windows, you may wish to try `Christoph Gohlke's packages -`__. +`__. diff --git a/docs/source/features.rst b/docs/source/features.rst index c18a83d5..30a4fbe3 100644 --- a/docs/source/features.rst +++ b/docs/source/features.rst @@ -42,7 +42,7 @@ They can be computed for 2-D or 3-D images and are available in the Only the first 13 features are implemented. The last (14th) feature is normally considered to be *unstable*, although it is not clear to me why this is. -(`See this unanswered question on Cross-validated `__). +(`See this unanswered question on Cross-validated `__). Local Binary Patterns ~~~~~~~~~~~~~~~~~~~~~ @@ -62,7 +62,7 @@ Threshold adjacency statistics (TAS) are a recent innovation too. In the original version, they have fixed parameters, but we have adapted them to *parameter-free* versions (see `Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature -`__ by Coelho +`__ by Coelho et al. for a reference). Mahotas supports both. Zernike Moments diff --git a/docs/source/index.rst b/docs/source/index.rst index 4316e636..ba4a5507 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -6,7 +6,7 @@ Mahotas: Computer Vision in Python Coelho, L.P. 2013. Mahotas: Open source software for scriptable computer vision. Journal of Open Research Software 1(1):e3, DOI: - http://dx.doi.org/10.5334/jors.ac + https://dx.doi.org/10.5334/jors.ac Mahotas is a computer vision and image processing library for Python. @@ -16,14 +16,14 @@ numpy arrays and with a very clean Python interface. Mahotas currently has over 100 functions for image processing and computer vision and it keeps growing. Some examples of mahotas functionality: - - `watershed `__ + - `watershed `__ - convex points calculations. - - `hit & miss. thinning `__ + - `hit & miss. thinning `__ - Zernike & Haralick, `local binary patterns - `__, and TAS features. - - `morphological processing `__ - - `Speeded-Up Robust Features (SURF), a form of local features `__ - - `thresholding `__ + `__, and TAS features. + - `morphological processing `__ + - `Speeded-Up Robust Features (SURF), a form of local features `__ + - `thresholding `__ - convolution. - Sobel edge detection. @@ -38,7 +38,7 @@ Bug reports with test cases typically get fixed in 24 hours. .. seealso:: - `mahotas-imread `__ is side + `mahotas-imread `__ is side project which includes code to read/write images to files Examples diff --git a/docs/source/install.rst b/docs/source/install.rst index 84562107..2702e359 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -3,7 +3,7 @@ How To Install Mahotas .. image:: https://anaconda.org/conda-forge/mahotas/badges/installer/conda.svg :target: https://conda.anaconda.org/conda-forge -The simplest way to install mahotas is to use `conda `__. +The simplest way to install mahotas is to use `conda `__. If you have conda installed, you can install mahotas using the following pair of commands:: @@ -26,7 +26,7 @@ You can get the released version using pip:: pip install mahotas If you prefer, you can download the source from `PyPI -`__ and run:: +`__ and run:: python setup.py install @@ -55,22 +55,22 @@ On Windows ~~~~~~~~~~ On Windows, Christoph Gohlke does an excellent job maintaining `binary packages -of mahotas `__ (and several other +of mahotas `__ (and several other packages). WinPython ~~~~~~~~~ -`WinPython `__ ships with `mahotas as a -standard package `__ +`WinPython `__ ships with `mahotas as a +standard package `__ Python(x, y) ~~~~~~~~~~~~ -If you use `Python(x, y) `__, which is often a good +If you use `Python(x, y) `__, which is often a good solution, then you probably have it already as `mahotas is a standard plugin -`__. +`__. Enthought Canopy ~~~~~~~~~~~~~~~~ @@ -82,7 +82,7 @@ FreeBSD ~~~~~~~ Mahotas is available for FreeBSD as `graphics/mahotas -`__. +`__. MacPorts ~~~~~~~~ diff --git a/docs/source/io.rst b/docs/source/io.rst index 8fbd9347..a6302f95 100644 --- a/docs/source/io.rst +++ b/docs/source/io.rst @@ -16,7 +16,7 @@ It can use the following backends (it tries them in the following order): arrays. It supports PNG, JPEG, TIFF, WEBP, BMP, and a few TIFF-based microscopy formats (LSM and STK). -2. It also looks for `freeimage `__. +2. It also looks for `freeimage `__. Freeimage can read and write many formats. Unfortunately, it is harder to install and it is not as well-maintained as imread. @@ -29,4 +29,4 @@ Thus, depending on what you had installed, the resulting images would be different. If you are running on Windows, you may wish to try `Christoph Gohlke's packages -`__. +`__. diff --git a/docs/source/labeled.rst b/docs/source/labeled.rst index cdb5b14e..f9330fe8 100644 --- a/docs/source/labeled.rst +++ b/docs/source/labeled.rst @@ -68,7 +68,7 @@ Here is a slightly more complex example. The full code is in the `demos directory `__ as ``nuclear.py``. We are going to use this image, a fluorescent microscopy image from a `nuclear segmentation benchmark -`__ +`__ This image is available as ``mahotas.demos.nuclear_image()`` diff --git a/docs/source/lbp.rst b/docs/source/lbp.rst index e9f21baa..0ed99901 100644 --- a/docs/source/lbp.rst +++ b/docs/source/lbp.rst @@ -8,7 +8,7 @@ diagram below: .. image:: LBP.svg :alt: Neighbourhood illustration -(Image reference: `Wikipedia `__) +(Image reference: `Wikipedia `__) The reference pixel is in red, at the centre. A number of points are defined at a distance ``r`` from it. These are the green points. As you go from left to diff --git a/docs/source/mahotas-features.rst b/docs/source/mahotas-features.rst index 93fadfe7..8d7c0626 100644 --- a/docs/source/mahotas-features.rst +++ b/docs/source/mahotas-features.rst @@ -26,7 +26,7 @@ You can obtain help on all the options by running ``mahotas-features.py --help``:: If you use mahotas in a scientific publication, please cite - Coelho, LP (2013). http://dx.doi.org/10.5334/jors.ac + Coelho, LP (2013). https://dx.doi.org/10.5334/jors.ac usage: mahotas-features.py [-h] [--output OUTPUT] [--clobber] diff --git a/docs/source/morphology.rst b/docs/source/morphology.rst index 165f1579..c97e80bc 100644 --- a/docs/source/morphology.rst +++ b/docs/source/morphology.rst @@ -38,8 +38,8 @@ After Oct 2013, you can get this image with mahotas as:: Dilation & Erosion ------------------ -`Dilation `__ and `erosion -`__ are two very basic +`Dilation `__ and `erosion +`__ are two very basic operators (mathematically, you only need one of them as you can define the erosion as dilation of the negative or vice-versa). diff --git a/docs/source/polygon.rst b/docs/source/polygon.rst index 048b4cee..93886bcd 100644 --- a/docs/source/polygon.rst +++ b/docs/source/polygon.rst @@ -15,7 +15,7 @@ for many complex usage. The main purpose of these utilities is to aid debugging and visualisation. If you need to generate fancy graphs, look for packages such as `matplotlib -`__. +`__. Convex Hull ----------- diff --git a/docs/source/surfref.rst b/docs/source/surfref.rst index 3b4402dc..0d5c891d 100644 --- a/docs/source/surfref.rst +++ b/docs/source/surfref.rst @@ -4,7 +4,7 @@ Implementing SURF-ref With Mahotas This is a companion to the paper `Determining the subcellular location of new proteins from microscope images using local features -`__ +`__ by Coelho et al. (2013). :: diff --git a/docs/source/tasks.rst b/docs/source/tasks.rst index 81e77bf5..2eedef52 100644 --- a/docs/source/tasks.rst +++ b/docs/source/tasks.rst @@ -8,20 +8,20 @@ Here are a few ideas for improving mahotas. New Features ------------ -- `HOG `__ -- `BRISK `__ -- `Canny edge detection `__ -- `Hough Transform `__ -- `bilateral filtering `__ -- `Non Local Filtering `__ -- `Wiener filtering `__ +- `HOG `__ +- `BRISK `__ +- `Canny edge detection `__ +- `Hough Transform `__ +- `bilateral filtering `__ +- `Non Local Filtering `__ +- `Wiener filtering `__ Small Improvements ------------------ -- something like the ``overlay`` function from `pymorph `__ (or even just copy it over and adapt it to mahotas style). +- something like the ``overlay`` function from `pymorph `__ (or even just copy it over and adapt it to mahotas style). - H-maxima transform (again, pymorph can provide a basis) -- `entropy thresholding `__ +- `entropy thresholding `__ Internals --------- diff --git a/docs/source/wally.rst b/docs/source/wally.rst index 8ad21dee..6143338e 100644 --- a/docs/source/wally.rst +++ b/docs/source/wally.rst @@ -3,7 +3,7 @@ Finding Wally ============= This was originally an `answer on stackoverflow -`__ +`__ We can use it as a simple tutorial example. The problem is to find Wally (who goes by Waldo in the US) in the following