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Commit d2eb0ac3 authored by Russell Luke's avatar Russell Luke
Browse files

Merge remote-tracking branch 'refs/remotes/origin/master'

parents f8beafda 26391979
......@@ -6,4 +6,5 @@ build
dist
.vscode/launch.json
.vscode/settings.json
tests/orb_tomog_regression_tests.py
\ No newline at end of file
tests/orb_tomog_regression_tests.py
/env
# Build with
#
# nix-build env.nix -o env
#
# VSCode will see the generated ./env as a virtualenv and offer it as an
# interpreter in the ‘Python: Select Interpreter’ command.
#
# To run Python with all dependencies available, use the wrapper script
# env/bin/python.
{ nixpkgs ? <nixpkgs>, pkgs ? import nixpkgs {} }:
with pkgs;
poetry2nix.mkPoetryEnv {
projectDir = ./.;
preferWheels = true;
overrides = poetry2nix.overrides.withDefaults (self: super: {
# We need to explicityly specify the dependency on the plotting backend.
# Use tkinter for simplicity.
matplotlib = super.matplotlib.overridePythonAttrs (attrs: {
propagatedBuildInputs = attrs.propagatedBuildInputs ++ [
self.tkinter
];
});
});
}
......@@ -43,6 +43,18 @@ optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*"
version = "4.4.2"
[[package]]
category = "main"
description = "Read and write HDF5 files from Python"
name = "h5py"
optional = false
python-versions = "*"
version = "2.10.0"
[package.dependencies]
numpy = ">=1.7"
six = "*"
[[package]]
category = "main"
description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
......@@ -68,7 +80,7 @@ description = "A Python utility / library to sort Python imports."
name = "isort"
optional = false
python-versions = ">=3.6,<4.0"
version = "5.6.4"
version = "5.7.0"
[package.extras]
colors = ["colorama (>=0.4.3,<0.5.0)"]
......@@ -145,7 +157,7 @@ description = "NumPy is the fundamental package for array computing with Python.
name = "numpy"
optional = false
python-versions = ">=3.6"
version = "1.19.4"
version = "1.19.5"
[[package]]
category = "main"
......@@ -153,7 +165,7 @@ description = "Python Imaging Library (Fork)"
name = "pillow"
optional = false
python-versions = ">=3.6"
version = "8.0.1"
version = "8.1.0"
[[package]]
category = "dev"
......@@ -228,11 +240,11 @@ category = "main"
description = "SciPy: Scientific Library for Python"
name = "scipy"
optional = false
python-versions = ">=3.6"
version = "1.5.4"
python-versions = ">=3.7"
version = "1.6.0"
[package.dependencies]
numpy = ">=1.14.5"
numpy = ">=1.16.5"
[[package]]
category = "main"
......@@ -248,13 +260,13 @@ description = "Read and write TIFF(r) files"
name = "tifffile"
optional = false
python-versions = ">=3.7"
version = "2020.10.1"
version = "2021.1.14"
[package.dependencies]
numpy = ">=1.15.1"
[package.extras]
all = ["imagecodecs (>=2020.5.30)", "matplotlib (>=3.2)", "lxml"]
all = ["imagecodecs (>=2021.1.11)", "matplotlib (>=3.2)", "lxml"]
[[package]]
category = "dev"
......@@ -271,7 +283,7 @@ marker = "implementation_name == \"cpython\" and python_version < \"3.8\""
name = "typed-ast"
optional = false
python-versions = "*"
version = "1.4.1"
version = "1.4.2"
[[package]]
category = "dev"
......@@ -282,7 +294,8 @@ python-versions = "*"
version = "1.12.1"
[metadata]
content-hash = "0855986c7d442a22ca518a7cdd507ad39a8d094b277bf740cb0bc1cd098c24a3"
content-hash = "c811618ab8deee6479acf39bce6364056c4bdd071f35ea56848bbc0a168891c9"
lock-version = "1.0"
python-versions = "^3.7"
[metadata.files]
......@@ -302,13 +315,44 @@ decorator = [
{file = "decorator-4.4.2-py2.py3-none-any.whl", hash = "sha256:41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760"},
{file = "decorator-4.4.2.tar.gz", hash = "sha256:e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7"},
]
h5py = [
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{file = "h5py-2.10.0-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:86868dc07b9cc8cb7627372a2e6636cdc7a53b7e2854ad020c9e9d8a4d3fd0f5"},
{file = "h5py-2.10.0-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:aac4b57097ac29089f179bbc2a6e14102dd210618e94d77ee4831c65f82f17c0"},
{file = "h5py-2.10.0-cp27-cp27m-win32.whl", hash = "sha256:7be5754a159236e95bd196419485343e2b5875e806fe68919e087b6351f40a70"},
{file = "h5py-2.10.0-cp27-cp27m-win_amd64.whl", hash = "sha256:13c87efa24768a5e24e360a40e0bc4c49bcb7ce1bb13a3a7f9902cec302ccd36"},
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{file = "h5py-2.10.0.tar.gz", hash = "sha256:84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d"},
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imageio = [
{file = "imageio-2.9.0-py3-none-any.whl", hash = "sha256:3604d751f03002e8e0e7650aa71d8d9148144a87daf17cb1f3228e80747f2e6b"},
{file = "imageio-2.9.0.tar.gz", hash = "sha256:52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0"},
]
isort = [
{file = "isort-5.6.4-py3-none-any.whl", hash = "sha256:dcab1d98b469a12a1a624ead220584391648790275560e1a43e54c5dceae65e7"},
{file = "isort-5.6.4.tar.gz", hash = "sha256:dcaeec1b5f0eca77faea2a35ab790b4f3680ff75590bfcb7145986905aab2f58"},
{file = "isort-5.7.0-py3-none-any.whl", hash = "sha256:fff4f0c04e1825522ce6949973e83110a6e907750cd92d128b0d14aaaadbffdc"},
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]
kiwisolver = [
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......@@ -403,70 +447,74 @@ networkx = [
{file = "networkx-2.5.tar.gz", hash = "sha256:7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602"},
]
numpy = [
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......
......@@ -121,7 +121,7 @@ class P_Sparsity_Superpixel(P_Sparsity):
# Set the superpixel size:
self.superpixel_size = experiment.superpixel_size
# Bin the support:
if self.support is not 1:
if self.support != 1:
self.support = bin_array(self.support, self.superpixel_size)
self.support = self.support / max(self.support)
# Assert that the binning+upsampling conserves the array size
......
......@@ -72,7 +72,7 @@ def procrustes(X, Y, scaling=True, reflection='best'):
V = Vt.T
T = np.dot(V, U.T)
if reflection is not 'best':
if reflection != 'best':
# does the current solution use a reflection?
have_reflection = np.linalg.det(T) < 0
......
......@@ -10,6 +10,7 @@ numpy = "^1.19.2"
scikit-image = "^0.17.2"
matplotlib = "^3.3.2"
scipy = "^1.5.2"
h5py = "^2.10.0"
[tool.poetry.dev-dependencies]
pylint = "^2.6.0"
......
......@@ -105,11 +105,11 @@ setup(
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and allow
# pip to create the appropriate form of executable for the target platform.
entry_points={
'console_scripts': [
'sample=sample:main',
],
},
#entry_points={
# 'console_scripts': [
# 'sample=sample:main',
# ],
#},
# Some packages which are required for the good operation of ProxPython
install_requires=['numpy', 'scikit-image', 'matplotlib', 'scipy']
......
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