Make this program into a module

.devcontainer/Dockerfile

@@ -0,0 +1,22 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.148.1/containers/python-3/.devcontainer/base.Dockerfile
+
+# [Choice] Python version: 3, 3.9, 3.8, 3.7, 3.6
+ARG VARIANT="3"
+FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT}
+
+# [Option] Install Node.js
+ARG INSTALL_NODE="true"
+ARG NODE_VERSION="lts/*"
+RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "source /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
+# COPY requirements.txt /tmp/pip-tmp/
+# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
+#    && rm -rf /tmp/pip-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

.devcontainer/devcontainer.json

@@ -0,0 +1,44 @@
+{
+	"name": "Python 3",
+	"build": {
+		"dockerfile": "Dockerfile",
+		"context": "..",
+		"args": { 
+			// Update 'VARIANT' to pick a Python version: 3, 3.6, 3.7, 3.8, 3.9
+			"VARIANT": "3",
+			// Options
+			"INSTALL_NODE": "false"
+		}
+	},
+
+	// Set *default* container specific settings.json values on container create.
+	"settings": { 
+		"terminal.integrated.shell.linux": "/bin/bash",
+		"python.pythonPath": "/usr/local/bin/python",
+		"python.linting.enabled": true,
+		"python.linting.pylintEnabled": true,
+		"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
+		"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+		"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
+		"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
+		"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
+		"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
+		"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
+		"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
+		"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
+	},
+
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": [
+		"ms-python.python"
+	],
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "pip3 install --user -r requirements.txt",
+
+	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "vscode"
+}

.gitignore

@@ -0,0 +1,203 @@
+
+# Created by https://www.toptal.com/developers/gitignore/api/vscode,python,macos,vim
+# Edit at https://www.toptal.com/developers/gitignore?templates=vscode,python,macos,vim
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Python ###
+# 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/
+pip-wheel-metadata/
+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/
+pytestdebug.log
+
+# 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/
+doc/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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/
+pythonenv*
+
+# 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/
+
+# profiling data
+.prof
+
+### Vim ###
+# Swap
+[._]*.s[a-v][a-z]
+!*.svg  # comment out if you don't need vector files
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+Sessionx.vim
+
+# Temporary
+.netrwhist
+*~
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
+
+### vscode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+*.code-workspace
+
+# End of https://www.toptal.com/developers/gitignore/api/vscode,python,macos,vim

.vscode/launch.json

@@ -0,0 +1,15 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal"
+        }
+    ]
+}

brain_sample.csv

@@ -1,20 +1,20 @@
-1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20
-2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21
-3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
-4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
-5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24
-6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25
-7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26
-8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
-9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28
-10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29
-11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30
-12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31
-13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32
-14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33
-15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34
-16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35
-17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36
-18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37
-19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38
-20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1

sagital_average/__init__.py

@@ -0,0 +1 @@
+from .sagital_brain import run_averages

sagital_average/brain_average.csv

@@ -0,0 +1 @@
+0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0

sagital_average/brain_sample.csv

@@ -0,0 +1,20 @@
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1

sagital_average/command.py

@@ -0,0 +1,12 @@
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
+import sagital_brain
+
+def process():
+    parser = ArgumentParser(description="Calculates the average for each sagital-horizontal plane.",
+                            formatter_class=ArgumentDefaultsHelpFormatter)
+    parser.add_argument('file_input', nargs='?', default="brain_sample.csv",
+                        help="Input CSV file with the results from scikit-brain binning algorithm.")
+    parser.add_argument('--file_output', '-o', default="brain_average.csv",
+                        help="Name of the output CSV file.")
+    arguments = parser.parse_args()
+    sagital_brain.run_averages(arguments.file_input, arguments.file_output)

sagital_average/requirements.txt

@@ -0,0 +1 @@
+numpy

sagital_average/sagital_brain.py

@@ -0,0 +1,21 @@
+import numpy as np
+
+def run_averages(file_input='brain_sample.csv', file_output='brain_average.csv'):
+    """
+    Calculates the average through the coronal planes
+    The input file should has as many columns as coronal planes
+    The rows are intersections of the sagital/horizontal planes
+
+    The result is the average for each sagital/horizontal plane (rows)
+    """
+    # Open the file to analyse
+    planes = np.loadtxt(file_input, dtype=int,  delimiter=',')
+
+    # Calculates the averages through the sagital/horizontal planes
+    # and makes it as a row vector
+    averages = planes.mean(axis=1)[np.newaxis, :]
+
+    # write it out on my file
+    np.savetxt(file_output, averages, fmt='%.1f', delimiter=',')
+
+