Merge branch 'update/repo' into 'master'

Sort repository and add an installation setup

See merge request uhlmann-group/python-spline-fitting-toolbox!1

.flake8

+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 79
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

.gitignore

+.idea
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

.gitlab-ci.yml

+image: continuumio/miniconda3:latest
+
+before_script:
+  # Setup of the conda virtual environment
+  - export PIP_CACHE_DIR="/opt/cache/pip"
+  - conda env create -f environment.yml
+  - source activate sft
+
+tests :
+  stage: test
+  script:
+    - pip install -e .
+    - pip install pytest pytest-cov
+    - pytest --cov=sft/ tests/
+    - coverage xml
+  artifacts:
+    reports:
+      cobertura: coverage.xml

.ipynb_checkpoints/playground2-checkpoint.ipynb

-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import numpy as np\n",
-    "import splineToolbox as st\n",
-    "import matplotlib.pyplot as plt\n",
-    "import imp\n",
-    "import tifffile\n",
-    "from skimage import measure\n",
-    "import time\n",
-    "import cv2"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "<module 'splineToolbox' from '/Users/uhlmann/git/python-spline-fitting-toolbox/splineToolbox.py'>"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "imp.reload(st)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "img=tifffile.imread('data/catMask.tif')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "M=30\n",
-    "splineCurve=st.SplineCurve(M,st.B3(),True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "splineCurve.getCoefsFromBinaryMask(img)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "image/png": "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\n",
-      "text/plain": [
-       "<Figure size 432x288 with 1 Axes>"
-      ]
-     },
-     "metadata": {
-      "needs_background": "light"
-     },
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "samplingRate=1000\n",
-    "splineContour=splineCurve.sampleParallel(samplingRate)\n",
-    "\n",
-    "fig, ax = plt.subplots()\n",
-    "ax.imshow(img, cmap=plt.cm.gray)\n",
-    "ax.scatter(splineContour[:,1],splineContour[:,0],s=1)\n",
-    "#plt.scatter(splineCurve.coefs[:,1],splineCurve.coefs[:,0])\n",
-    "plt.show()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "t0=0\n",
-    "tf=M"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "387.52339202920655\n",
-      "0.16715598106384277\n"
-     ]
-    }
-   ],
-   "source": [
-    "startTime=time.time()\n",
-    "samples, step = np.linspace(t0,tf,1000,endpoint=False,retstep=True)\n",
-    "print(sum([((splineCurve.parameterToWorldDerivative(i)[0]**2+splineCurve.parameterToWorldDerivative(i)[1]**2)**(1/2))*step for i in samples]))\n",
-    "print(str(time.time()-startTime))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "387.5234010126442\n",
-      "0.0008037090301513672\n"
-     ]
-    }
-   ],
-   "source": [
-    "startTime=time.time()\n",
-    "print(cv2.arcLength(np.float32(splineContour), True))\n",
-    "print(str(time.time()-startTime))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "387.52338843966817\n",
-      "0.17393994331359863\n"
-     ]
-    }
-   ],
-   "source": [
-    "startTime=time.time()\n",
-    "print(splineCurve.arcLength(t0,tf))\n",
-    "print(str(time.time()-startTime))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.7.3"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}

.ipynb_checkpoints/playgroundShapeSpace-checkpoint.ipynb

-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import splineToolbox as st\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "import math"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "numAnchors=8"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "II = np.repeat(np.arange(numAnchors)[:,None],numAnchors,axis = 1)\n",
-    "JJ = np.repeat(np.arange(numAnchors)[None,:],numAnchors,axis = 0)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([[ 0, -1, -2, -3, -4, -5, -6, -7],\n",
-       "       [ 1,  0, -1, -2, -3, -4, -5, -6],\n",
-       "       [ 2,  1,  0, -1, -2, -3, -4, -5],\n",
-       "       [ 3,  2,  1,  0, -1, -2, -3, -4],\n",
-       "       [ 4,  3,  2,  1,  0, -1, -2, -3],\n",
-       "       [ 5,  4,  3,  2,  1,  0, -1, -2],\n",
-       "       [ 6,  5,  4,  3,  2,  1,  0, -1],\n",
-       "       [ 7,  6,  5,  4,  3,  2,  1,  0]])"
-      ]
-     },
-     "execution_count": 7,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "II-JJ"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "M=numAnchors\n",
-    "I=II-JJ"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 23,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([0.])"
-      ]
-     },
-     "execution_count": 23,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "A = np.mod(I,M)\n",
-    "Phi11 = np.zeros(I.shape)\n",
-    "Phi11[A == 0] = 26.0/(35*M)\n",
-    "Phi11[A == 1] = 9.0/(70*M)\n",
-    "Phi11[A == M-1] = 9.0/(70*M)\n",
-    "Phi11ref=Phi11\n",
-    "\n",
-    "Phi11comp=np.array([[st.H3().h31PeriodicAutocorrelation(el,M) for el in row] for row in I])\n",
-    "\n",
-    "np.unique(Phi11ref-Phi11comp)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 34,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([-3.46944695e-18,  0.00000000e+00])"
-      ]
-     },
-     "execution_count": 34,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "A = np.mod(I,M)\n",
-    "Phi11 = np.zeros(I.shape)\n",
-    "Phi11[A == 0] = 26.0/(35*M)\n",
-    "Phi11[A == 1] = 9.0/(70*M)\n",
-    "Phi11[A == M-1] = 9.0/(70*M)\n",
-    "Phi11 = M/(M-1)*Phi11\n",
-    "Phi11[0,0] = .5*Phi11[0,0]\n",
-    "Phi11[-1,-1] = .5*Phi11[-1,-1]\n",
-    "Phi11[-1,0] = 0\n",
-    "Phi11[0,-1] = 0\n",
-    "Phi11ref=Phi11\n",
-    "\n",
-    "Phi11comp=np.array([[st.H3().h31Autocorrelation(II[j,i],JJ[j,i],M) for i in range(0,len(II[j]))] for j in range(0,len(II))])\n",
-    "\n",
-    "np.unique(Phi11ref-Phi11comp)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 22,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([0.])"
-      ]
-     },
-     "execution_count": 22,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "A = np.mod(I,M)\n",
-    "Phi22 = np.zeros(I.shape)\n",
-    "Phi22[A == 0] = 2.0/(105*M)\n",
-    "Phi22[A == 1] = -1.0/(140*M)\n",
-    "Phi22[A == M-1] = -1.0/(140*M)\n",
-    "Phi22ref=Phi22\n",
-    "\n",
-    "Phi22comp=np.array([[st.H3().h32PeriodicAutocorrelation(el,M) for el in row] for row in I])\n",
-    "\n",
-    "np.unique(Phi22ref-Phi22comp)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 35,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([0.00000000e+00, 2.16840434e-19, 4.33680869e-19])"
-      ]
-     },
-     "execution_count": 35,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "A = np.mod(I,M)\n",
-    "Phi22 = np.zeros(I.shape)\n",
-    "Phi22[A == 0] = 2.0/(105*M)\n",
-    "Phi22[A == 1] = -1.0/(140*M)\n",
-    "Phi22[A == M-1] = -1.0/(140*M)\n",
-    "Phi22 = M/(M-1)*Phi22\n",
-    "Phi22[0,0] = .5*Phi22[0,0]\n",
-    "Phi22[-1,-1] = .5*Phi22[-1,-1]\n",
-    "Phi22[-1,0] = 0\n",
-    "Phi22[0,-1] = 0\n",
-    "Phi22ref=Phi22\n",
-    "\n",
-    "Phi22comp=np.array([[st.H3().h32Autocorrelation(II[j,i],JJ[j,i],M) for i in range(0,len(II[j]))] for j in range(0,len(II))])\n",
-    "\n",
-    "np.unique(Phi22ref-Phi22comp)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 27,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([0.])"
-      ]
-     },
-     "execution_count": 27,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "A = np.mod(I,M)\n",
-    "Phi12 = np.zeros(I.shape)\n",
-    "Phi12[A == 1] = 13./(420*M)\n",
-    "Phi12[A == M-1] = -13./(420*M)\n",
-    "Phi12ref=Phi12\n",
-    "\n",
-    "Phi12comp=np.array([[st.H3().h3PeriodicCrosscorrelation(el,M) for el in row] for row in I])\n",
-    "\n",
-    "np.unique(Phi12ref-Phi12comp)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 37,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "array([-8.67361738e-19,  0.00000000e+00,  8.67361738e-19])"
-      ]
-     },
-     "execution_count": 37,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "A = np.mod(I,M)\n",
-    "Phi12 = np.zeros(I.shape)\n",
-    "Phi12[A == 1] = 13./(420*M)\n",
-    "Phi12[A == M-1] = -13./(420*M)\n",
-    "Phi12 = M/(M-1)*Phi12\n",
-    "Phi12[0,0] = 11./(210*(M-1))\n",
-    "Phi12[-1,-1] = -11./(210*(M-1))\n",
-    "Phi12[0,-1] = 0\n",
-    "Phi12[-1,0] = 0\n",
-    "Phi12ref=Phi12\n",
-    "\n",
-    "Phi12comp=np.array([[st.H3().h3Crosscorrelation(II[j,i],JJ[j,i],M) for i in range(0,len(II[j]))] for j in range(0,len(II))])\n",
-    "\n",
-    "np.unique(Phi12ref-Phi12comp)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,