From 1c84c258c1e4167d4e6864abb3d399703894464d Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Mon, 14 Nov 2022 10:11:18 +0800 Subject: [PATCH] MIN Replace http:// links with https:// --- CITATION | 4 ++-- CITATION.cff | 2 +- INSTALL | 6 +++--- README.md | 30 +++++++++++++++--------------- mahotas/__init__.py | 8 ++++---- mahotas/_histogram.cpp | 2 +- mahotas/_labeled.cpp | 4 ++-- mahotas/colors.py | 10 +++++----- mahotas/distance.py | 2 +- mahotas/euler.py | 2 +- mahotas/features/_surf.cpp | 2 +- mahotas/features/tas.py | 6 +++--- mahotas/features/texture.py | 4 ++-- mahotas/io/__init__.py | 4 ++-- mahotas/labeled.py | 4 ++-- mahotas/morph.py | 4 ++-- mahotas/polygon.py | 6 +++--- mahotas/thresholding.py | 2 +- setup.py | 2 +- 19 files changed, 52 insertions(+), 52 deletions(-) diff --git a/CITATION b/CITATION index 8bebbb5c..5e3d2848 100644 --- a/CITATION +++ b/CITATION @@ -2,7 +2,7 @@ If you use mahotas on a scientific publication, please cite: **Luis Pedro Coelho** Mahotas: Open source software for scriptable computer vision in Journal of Open Research Software, vol 1, 2013. [`DOI - `__] + `__] In Bibtex format:: @@ -12,7 +12,7 @@ In Bibtex format:: title = {Mahotas: Open source software for scriptable computer vision}, journal = {Journal of Open Research Software}, year = {2013}, - doi = {http://dx.doi.org/10.5334/jors.ac}, + doi = {https://dx.doi.org/10.5334/jors.ac}, month = {July}, volume = {1} } diff --git a/CITATION.cff b/CITATION.cff index c7a41a13..fc148613 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,7 +4,7 @@ title: 'Mahotas: Open source software for scriptable computer vision' authors: - family-names: Coelho given-names: Luis Pedro - orcid: http://orcid.org/0000-0002-9280-7885 + orcid: https://orcid.org/0000-0002-9280-7885 doi: 10.5334/jors.ac date-released: 2013-7-29 version: 0.0.0 diff --git a/INSTALL b/INSTALL index 8aa16873..6e4f71ad 100644 --- a/INSTALL +++ b/INSTALL @@ -8,10 +8,10 @@ From binary packages There are a few binary packages. For **Windows**: Christoph Gohlke maintains binary packages at -http://www.lfd.uci.edu/~gohlke/pythonlibs/ +https://www.lfd.uci.edu/~gohlke/pythonlibs/ For FreeBSD, there are ports packages at -http://www.freshports.org/graphics/mahotas/ Unfortunately, they may be slightly +https://www.freshports.org/graphics/mahotas/ Unfortunately, they may be slightly out of date. On NixOS, there are up-to-date packages available as ``pythonPackages.mahotas`` @@ -46,7 +46,7 @@ Only **numpy** is required, except: You will need a way to load images into numpy arrays. Try one of the following packages -1. `imread `__ +1. `imread `__ 2. matplotlib 3. Freeimage diff --git a/README.md b/README.md index 257eda99..3b8147f4 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ in C++ for speed) operating over numpy arrays. ![GH Actions Status](https://github.com/luispedro/mahotas/workflows/Python%20Package%20using%20Conda/badge.svg) [![Coverage Status](https://coveralls.io/repos/github/luispedro/mahotas/badge.svg?branch=master)](https://coveralls.io/github/luispedro/mahotas?branch=master) -[![License](https://img.shields.io/badge/License-MIT-blue)](http://opensource.org/licenses/MIT) +[![License](https://img.shields.io/badge/License-MIT-blue)](https://opensource.org/licenses/MIT) [![Downloads](https://pepy.tech/badge/mahotas/month)](https://pepy.tech/project/mahotas/month) [![Install with Conda](https://anaconda.org/conda-forge/mahotas/badges/downloads.svg)](https://anaconda.org/conda-forge/mahotas) [![Install with Anaconda](https://anaconda.org/conda-forge/mahotas/badges/installer/conda.svg)](https://anaconda.org/conda-forge/mahotas) @@ -16,14 +16,14 @@ Python versions 2.7, 3.4+, are supported. Notable algorithms: -- [watershed](http://mahotas.readthedocs.io/en/latest/distance.html) -- [convex points calculations](http://mahotas.readthedocs.io/en/latest/polygon.html). +- [watershed](https://mahotas.readthedocs.io/en/latest/distance.html) +- [convex points calculations](https://mahotas.readthedocs.io/en/latest/polygon.html). - hit & miss, thinning. - Zernike & Haralick, LBP, and TAS features. - [Speeded-Up Robust Features - (SURF)](http://mahotas.readthedocs.io/en/latest/surf.html), a form of local + (SURF)](https://mahotas.readthedocs.io/en/latest/surf.html), a form of local features. -- [thresholding](http://mahotas.readthedocs.io/en/latest/thresholding.html). +- [thresholding](https://mahotas.readthedocs.io/en/latest/thresholding.html). - convolution. - Sobel edge detection. - spline interpolation @@ -41,7 +41,7 @@ years, but in the meanwhile, you only get a warning). In a few unfortunate cases, there was a bug in the old code and your results will change for the better. -Please cite [the mahotas paper](http://dx.doi.org/10.5334/jors.ac) (see +Please cite [the mahotas paper](https://dx.doi.org/10.5334/jors.ac) (see details below under [Citation](#Citation)) if you use it in a publication. ## Examples @@ -117,7 +117,7 @@ As you can see, we rely on numpy/matplotlib for many operations. ## Install -If you are using [conda](http://anaconda.org/), you can install mahotas from +If you are using [conda](https://anaconda.org/), you can install mahotas from [conda-forge](https://conda-forge.github.io/) using the following commands: conda config --add channels conda-forge @@ -145,7 +145,7 @@ If you use mahotas on a published publication, please cite: > **Luis Pedro Coelho** Mahotas: Open source software for scriptable > computer vision in Journal of Open Research Software, vol 1, 2013. -> [[DOI](http://dx.doi.org/10.5334/jors.ac)] +> [[DOI](https://dx.doi.org/10.5334/jors.ac)] In Bibtex format: @@ -154,7 +154,7 @@ In Bibtex format: > title = {Mahotas: Open source software for scriptable computer vision}, > journal = {Journal of Open Research Software}, > year = {2013}, -> doi = {http://dx.doi.org/10.5334/jors.ac}, +> doi = {https://dx.doi.org/10.5334/jors.ac}, > month = {July}, > volume = {1} > } @@ -164,7 +164,7 @@ You can access this information using the `mahotas.citation()` function. ## Development Development happens on github -([http://github.com/luispedro/mahotas](https://github.com/luispedro/mahotas)). +([https://github.com/luispedro/mahotas](https://github.com/luispedro/mahotas)). You can set the `DEBUG` environment variable before compilation to get a debug version: @@ -194,11 +194,11 @@ run the test suite. issues](https://github.com/luispedro/mahotas/issues) *Mailing List*: Use the [pythonvision mailing -list](http://groups.google.com/group/pythonvision?pli=1) for questions, +list](https://groups.google.com/group/pythonvision?pli=1) for questions, bug submissions, etc. Or ask on [stackoverflow (tag -mahotas)](http://stackoverflow.com/questions/tagged/mahotas) +mahotas)](https://stackoverflow.com/questions/tagged/mahotas) -*Main Author & Maintainer*: [Luis Pedro Coelho](http://luispedro.org) +*Main Author & Maintainer*: [Luis Pedro Coelho](https://luispedro.org) (follow on [twitter](https://twitter.com/luispedrocoelho) or [github](https://github.com/luispedro)). @@ -208,11 +208,11 @@ Gohlke, as well as [others](https://github.com/luispedro/mahotas/graphs/contributors). [Presentation about mahotas for bioimage -informatics](http://luispedro.org/files/talks/2013/EuBIAS/mahotas.html) +informatics](https://luispedro.org/files/talks/2013/EuBIAS/mahotas.html) For more general discussion of computer vision in Python, the [pythonvision mailing -list](http://groups.google.com/group/pythonvision?pli=1) is a much +list](https://groups.google.com/group/pythonvision?pli=1) is a much better venue and generates a public discussion log for others in the future. You can use it for mahotas or general computer vision in Python questions. diff --git a/mahotas/__init__.py b/mahotas/__init__.py index 54eb560a..34ab2e55 100644 --- a/mahotas/__init__.py +++ b/mahotas/__init__.py @@ -25,7 +25,7 @@ Coelho, Luis Pedro, 2013. Mahotas: Open source software for scriptable computer vision. Journal of Open Research Software, 1:e3, DOI: - http://dx.doi.org/10.5334/jors.ac + https://dx.doi.org/10.5334/jors.ac ''' try: from .bbox import bbox, croptobbox @@ -102,7 +102,7 @@ Coelho, Luis Pedro, 2013. Mahotas: Open source software for scriptable computer vision. Journal of Open Research Software, 1:e3, DOI: - http://dx.doi.org/10.5334/jors.ac + https://dx.doi.org/10.5334/jors.ac In BibTex format: @@ -114,13 +114,13 @@ 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} } ''' short_citation_text = \ '''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 ''' def citation(print_out=True, short=False): diff --git a/mahotas/_histogram.cpp b/mahotas/_histogram.cpp index f68fd14e..98abb63f 100644 --- a/mahotas/_histogram.cpp +++ b/mahotas/_histogram.cpp @@ -63,7 +63,7 @@ PyObject* py_histogram(PyObject* self, PyObject* args) { int otsu(const double* hist, const int n) { // Otsu calculated according to CVonline: -// http://homepages.inf.ed.ac.uk/rbf/CVonline/LOCAL_COPIES/MORSE/threshold.pdf +// https://homepages.inf.ed.ac.uk/rbf/CVonline/LOCAL_COPIES/MORSE/threshold.pdf gil_release nogil; std::vector nB, nO; if (n <= 1) return 0; diff --git a/mahotas/_labeled.cpp b/mahotas/_labeled.cpp index 19bced80..c568d0d8 100644 --- a/mahotas/_labeled.cpp +++ b/mahotas/_labeled.cpp @@ -233,8 +233,8 @@ void labeled_foldl(const numpy::aligned_array array, const numpy::aligned_arr // In certain versions of g++, in certain environments, // multiple versions of std::min & std::max are in scope and the compiler is // unable to resolve them. Therefore, based on -// http://www.cplusplus.com/reference/algorithm/min/ & -// http://www.cplusplus.com/reference/algorithm/max/ I implemented equivalents +// https://www.cplusplus.com/reference/algorithm/min/ & +// https://www.cplusplus.com/reference/algorithm/max/ I implemented equivalents // here: template diff --git a/mahotas/colors.py b/mahotas/colors.py index 9432fe47..03a4f8af 100644 --- a/mahotas/colors.py +++ b/mahotas/colors.py @@ -58,12 +58,12 @@ def rgb2xyz(rgb, dtype=None): The input is interpreted as sRGB. See Wikipedia for more details: - http://en.wikipedia.org/wiki/SRGB + https://en.wikipedia.org/wiki/SRGB Parameters ---------- rgb : ndarray - dtype : dtype, optional + dtype : dtype, optional What dtype to return Returns @@ -95,7 +95,7 @@ def xyz2rgb(xyz, dtype=None): The output should be interpreted as sRGB. See Wikipedia for more details: - http://en.wikipedia.org/wiki/SRGB + https://en.wikipedia.org/wiki/SRGB Parameters ---------- @@ -132,7 +132,7 @@ def xyz2lab(xyz, dtype=None): Convert CIE XYZ to L*a*b* coordinates - http://en.wikipedia.org/wiki/CIELAB + https://en.wikipedia.org/wiki/CIELAB Parameters ---------- @@ -168,7 +168,7 @@ def rgb2lab(rgb, dtype=None): Convert sRGB to L*a*b* coordinates - http://en.wikipedia.org/wiki/CIELAB + https://en.wikipedia.org/wiki/CIELAB Parameters ---------- diff --git a/mahotas/distance.py b/mahotas/distance.py index e9dbcb1d..3fa9a254 100644 --- a/mahotas/distance.py +++ b/mahotas/distance.py @@ -46,7 +46,7 @@ def distance(bw, metric='euclidean2'): Cornell Computing and Information.* 2004. Available at: - http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.1647&rep=rep1&type=pdf. + https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.1647&rep=rep1&type=pdf. For n-D images (with n > 2), a slower hand-craft method is used. ''' diff --git a/mahotas/euler.py b/mahotas/euler.py index 7325a41e..2f30aa01 100644 --- a/mahotas/euler.py +++ b/mahotas/euler.py @@ -49,7 +49,7 @@ def euler(f, n=8, mode='constant'): References ---------- - http://en.wikipedia.org/wiki/Euler_characteristic + https://en.wikipedia.org/wiki/Euler_characteristic References ---------- diff --git a/mahotas/features/_surf.cpp b/mahotas/features/_surf.cpp index 88a73731..00b71201 100644 --- a/mahotas/features/_surf.cpp +++ b/mahotas/features/_surf.cpp @@ -441,7 +441,7 @@ void build_pyramid(numpy::aligned_array integral, // Survey."by Tuytelaars T and Mikolajczyk K.; Foundations // and Trends® in Computer Graphics and Vision. // 2007;3(3):177-280. Available at: - // http://www.nowpublishers.com/product.aspx?product=CGV&doi=0600000017. + // https://www.nowpublishers.com/product.aspx?product=CGV&doi=0600000017. // // Also uses 0.6 double determinant = Dxx*Dyy - 0.36*Dxy*Dxy; diff --git a/mahotas/features/tas.py b/mahotas/features/tas.py index 76201988..b8ac99bd 100644 --- a/mahotas/features/tas.py +++ b/mahotas/features/tas.py @@ -60,7 +60,7 @@ def tas(img): Compute Threshold Adjacency Statistics TAS were presented by Hamilton et al. in "Fast automated cell phenotype - image classification" (http://www.biomedcentral.com/1471-2105/8/110) + image classification" (https://www.biomedcentral.com/1471-2105/8/110) Also returns a version computed on the negative of the binarisation defined by Hamilton et al. @@ -90,7 +90,7 @@ def pftas(img, T=None): Compute parameter free Threshold Adjacency Statistics TAS were presented by Hamilton et al. in "Fast automated cell phenotype - image classification" (http://www.biomedcentral.com/1471-2105/8/110) + image classification" (https://www.biomedcentral.com/1471-2105/8/110) The current version is an adapted version which is free of parameters. The thresholding is done by using Otsu's algorithm (or can be pre-computed and @@ -98,7 +98,7 @@ def pftas(img, T=None): included is the standard deviation. This was first published by Coelho et al. in "Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature" - (http://www.springerlink.com/content/60634778710577t0/) + (https://www.springerlink.com/content/60634778710577t0/) Also returns a version computed on the negative of the binarisation defined by Hamilton et al. diff --git a/mahotas/features/texture.py b/mahotas/features/texture.py index 87830373..96bdf8d7 100644 --- a/mahotas/features/texture.py +++ b/mahotas/features/texture.py @@ -78,7 +78,7 @@ def haralick(f, pages = {610--621}, publisher = {IEEE}, title = {Textural features for image classification}, - url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4309314}, + url = {https://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4309314}, volume = {3}, year = {1973} } @@ -190,7 +190,7 @@ def haralick_features(cmats, pages = {610--621}, publisher = {IEEE}, title = {Textural features for image classification}, - url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4309314}, + url = {https://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4309314}, volume = {3}, year = {1973} } diff --git a/mahotas/io/__init__.py b/mahotas/io/__init__.py index 36a6201f..3c0537c3 100644 --- a/mahotas/io/__init__.py +++ b/mahotas/io/__init__.py @@ -25,7 +25,7 @@ On **Windows**, use Christoph Gohlke's packages. See: -http://www.lfd.uci.edu/~gohlke/pythonlibs/#imread +https://www.lfd.uci.edu/~gohlke/pythonlibs/#imread @@ -41,7 +41,7 @@ actually called `libfreeimage3` in debian/ubuntu, for example). Under Windows, consider using the third-party mahotas packages at -http://www.lfd.uci.edu/~gohlke/pythonlibs/ (kindly maintained by Christoph +https://www.lfd.uci.edu/~gohlke/pythonlibs/ (kindly maintained by Christoph Gohlke), which already package freeimage. Full error was: %s''' diff --git a/mahotas/labeled.py b/mahotas/labeled.py index 27691e2a..729f0dc2 100644 --- a/mahotas/labeled.py +++ b/mahotas/labeled.py @@ -38,7 +38,7 @@ def label(array, Bc=None, out=None, output=None): This is also called *connected component labeled*, where the connectivity is defined by the structuring element ``Bc``. - See: http://en.wikipedia.org/wiki/Connected-component_labeling + See: https://en.wikipedia.org/wiki/Connected-component_labeling Parameters ---------- @@ -524,7 +524,7 @@ def perimeter(bwimage, n=4, mode="constant"): ---------- .. [1] K. Benkrid, D. Crookes. Design and FPGA Implementation of a Perimeter Estimator. The Queen's University of Belfast. - http://www.cs.qub.ac.uk/~d.crookes/webpubs/papers/perimeter.doc + https://www.cs.qub.ac.uk/~d.crookes/webpubs/papers/perimeter.doc """ global _perimeter_values perim = bwperim(bwimage, n, mode) diff --git a/mahotas/morph.py b/mahotas/morph.py index 9e2d683e..ebf45b7f 100644 --- a/mahotas/morph.py +++ b/mahotas/morph.py @@ -747,7 +747,7 @@ def tophat_close(f, Bc=None, out=None): This returns objects that are smaller than ``Bc`` and contain lower values than their surroundings. - See: http://en.wikipedia.org/wiki/Top-hat_transform + See: https://en.wikipedia.org/wiki/Top-hat_transform Parameters ---------- @@ -781,7 +781,7 @@ def tophat_open(f, Bc=None, out=None): This returns objects that are smaller than ``Bc`` and contain higher values than their surroundings. - See: http://en.wikipedia.org/wiki/Top-hat_transform + See: https://en.wikipedia.org/wiki/Top-hat_transform Parameters ---------- diff --git a/mahotas/polygon.py b/mahotas/polygon.py index 0e81eea3..ab1051dc 100644 --- a/mahotas/polygon.py +++ b/mahotas/polygon.py @@ -34,7 +34,7 @@ def line(p0, p1, canvas, color=1): notes ----- - `Implementation Reference `__ + `Implementation Reference `__ ''' y0,x0 = p0 y1,x1 = p1 @@ -76,7 +76,7 @@ def fill_polygon(polygon, canvas, color=1): color : integer, optional which colour to use (default: 1) ''' -# algorithm adapted from: http://www.alienryderflex.com/polygon_fill/ +# algorithm adapted from: https://www.alienryderflex.com/polygon_fill/ if not len(polygon): return min_y = min(y for y,x in polygon) @@ -108,7 +108,7 @@ def convexhull(bwimg): Compute the convex hull as a polygon This is an implementation of the Graham Scan: - http://en.wikipedia.org/wiki/Graham_scan + https://en.wikipedia.org/wiki/Graham_scan Parameters ---------- diff --git a/mahotas/thresholding.py b/mahotas/thresholding.py index 6b4c2c7a..d4b2de44 100644 --- a/mahotas/thresholding.py +++ b/mahotas/thresholding.py @@ -77,7 +77,7 @@ def otsu(img, ignore_zeros=False): bin = (im > t) See Wikipedia for details on methods: - http://en.wikipedia.org/wiki/Otsu's_method + https://en.wikipedia.org/wiki/Otsu's_method Parameters ---------- diff --git a/setup.py b/setup.py index b5982f4d..7d6fb20d 100644 --- a/setup.py +++ b/setup.py @@ -138,7 +138,7 @@ def build_extensions(self): license = 'MIT', platforms = ['Any'], classifiers = classifiers, - url = 'http://luispedro.org/software/mahotas', + url = 'https://luispedro.org/software/mahotas', packages = packages, ext_modules = ext_modules, package_dir = package_dir,