Week 07 exercises

.gitignore

@@ -0,0 +1,153 @@
+
+# Created by https://www.toptal.com/developers/gitignore/api/python,vscode
+# Edit at https://www.toptal.com/developers/gitignore?templates=python,vscode
+
+### 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
+
+### 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/python,vscode

command.py

@@ -0,0 +1,16 @@
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
+from sagital_brain import run_averages
+
+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()
+
+    run_averages(arguments.file_input, arguments.file_output)
+
+if __name__ == "__main__":
+    process()

sagital_brain.py

@@ -1,5 +1,3 @@
-from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
-
 import numpy as np
 
 
@@ -16,19 +14,7 @@ def run_averages(file_input='brain_sample.csv', file_output='brain_average.csv')
 
     # Calculates the averages through the sagital/horizontal planes
     # and makes it as a row vector
-    averages = planes.mean(axis=0)[np.newaxis, :]
+    averages = planes.mean(axis=1)[np.newaxis, :]
 
     # write it out on my file
     np.savetxt(file_output, averages, fmt='%.1f', delimiter=',')
-
-
-if __name__ == "__main__":
-    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()
-
-    run_averages(arguments.file_input, arguments.file_output)

setup.py

@@ -0,0 +1,12 @@
+from setuptools import setup, find_packages
+
+setup(
+    name = "sagital_average",
+    version = "0.1.0",
+    packages=find_packages(exclude=['*test']),
+    install_requires=['numpy'],
+    entry_points={
+        'console_scripts': [
+            'run_averages = command:main'
+        ]}
+)