Fully updated workshop with clearer instructions

ptsa_plot/.gitignore

@@ -0,0 +1,100 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+.idea/

ptsa_plot/.travis.yml

@@ -0,0 +1,43 @@
+dist: trusty
+sudo: false
+language: python
+python:
+  # We don't actually use the Travis Python, but this keeps it organized.
+  - "2.7"
+  - "3.5"
+  - "3.6"
+notifications:
+  email: false
+env:
+  - CC=gcc-4.9 CXX=g++-4.9 NO_RHINO=1
+install:
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy xarray pywavelets h5py swig
+  - source activate test-environment
+  - conda install -y -c pennmem ptsa
+  - pip install pytest pytest-cov
+
+addons:
+  apt:
+    sources:
+      - ubuntu-toolchain-r-test
+    packages:
+      - gcc-4.9
+      - g++-4.9
+      - libfftw3-dev
+
+script:
+  - python -m ptsa_plot.test
+  - coverage report

ptsa_plot/CONTRIBUTING.md

@@ -0,0 +1,28 @@
+# Contributing to ptsa_plot
+
+## General guidelines
+
+- Always use docstrings for classes and functions.
+  [Numpy-style](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt)
+  doc strings are preferred.
+- It's nice to include demo usages whether in docstrings or as a standalone
+  example file.
+
+## How to contribute new code
+
+1. Fork this repository and create a new branch
+2. Add your new code to a sensible place
+3. Follow [PEP8][] guidelines as best as possible (it's OK to ignore the line
+   length limit of 80 characters)
+4. Add unit tests to ensure that everything works as expected. Test files should
+   be placed in the `ptsa_plot.test` package and be named `test_yournewmodule.py`
+   where `yournewmodule` is the name of your new module.
+5. Submit a pull request
+6. Make modifications as requested by the maintainers
+
+Your new code should run on Python 3 and legacy Python 2.7. Some exceptions may
+exist if dependencies for some reason are not compatible with certain Python
+versions (you should seriously consider if it's a necessary dependency if that
+is the case).
+
+[PEP8]: https://www.python.org/dev/peps/pep-0008/

ptsa_plot/README.rst

@@ -0,0 +1,14 @@
+ptsa_plot
+=========
+
+.. image:: https://travis-ci.org/pennmem/ptsa_plot.svg?branch=master
+    :target: https://travis-ci.org/pennmem/ptsa_plot
+
+Plotting and visualization utilities using all your favorite PTSA toppings.
+
+Contributing
+------------
+
+This is a collaborative project meant to collect useful plotting and
+visualization routines in one place. Please see ``CONTRIBUTING.md`` for
+guidelines on how to get your own code included.

ptsa_plot/ptsa_plot/coords.py

@@ -0,0 +1,52 @@
+"""Coordinate system conversion utilities."""
+
+import numpy as np
+
+
+def deg2rad(degrees):
+    """Convert degrees to radians."""
+    return degrees / 180. * np.pi
+
+
+def rad2deg(radians):
+    """Convert radians to degrees."""
+    return radians / np.pi * 180.
+
+
+def pol2cart(theta, radius, z=None, radians=True):
+    """Converts corresponding angles (theta), radii, and (optional) height (z)
+    from polar (or, when height is given, cylindrical) coordinates
+    to Cartesian coordinates x, y, and z.
+    Theta is assumed to be in radians, but will be converted
+    from degrees if radians==False.
+
+    """
+    if radians:
+        x = radius * np.cos(theta)
+        y = radius * np.sin(theta)
+    else:
+        x = radius * np.cos(deg2rad(theta))
+        y = radius * np.sin(deg2rad(theta))
+    if z is not None:
+        return x, y, z
+    else:
+        return x, y
+
+
+def cart2pol(x, y, z=None, radians=True):
+    """Converts corresponding Cartesian coordinates x, y, and (optional) z
+    to polar (or, when z is given, cylindrical) coordinates
+    angle (theta), radius, and z.
+    By default theta is returned in radians, but will be converted
+    to degrees if radians==False.
+
+    """
+    if radians:
+        theta = np.arctan2(y, x)
+    else:
+        theta = rad2deg(np.arctan2(y, x))
+    radius = np.hypot(x, y)
+    if z is not None:
+        return theta, radius, z
+    else:
+        return theta, radius

ptsa_plot/ptsa_plot/electrode_layouts/GSN129.dat

@@ -0,0 +1,2 @@
+   3.8241827e+01   3.3888206e+01   2.6304955e+01   1.8445913e+01   1.4506407e+01   0.0000000e+00  -3.9057101e+01   2.3656025e+01   1.8856055e+01   1.3994913e+01   0.0000000e+00  -1.4506407e+01  -3.6148575e+01   1.0592588e+01   6.4845245e+00   0.0000000e+00   0.0000000e+00  -6.4845245e+00  -1.3994913e+01  -1.8445913e+01  -3.3348566e+01  -1.0592588e+01  -1.8856055e+01  -2.6304955e+01  -3.4234344e+01  -2.3656025e+01  -3.3888206e+01  -4.2719008e+01  -5.3020925e+01  -5.9786194e+01  -7.5958075e+01  -1.1813245e+02  -3.8241827e+01  -4.7997295e+01  -6.1855338e+01  -7.2089465e+01  -8.7423024e+01  -1.1115585e+02  -5.5602412e+01  -6.9707597e+01  -7.9906235e+01  -9.1252163e+01  -1.1147459e+02  -6.5249879e+01  -7.7780619e+01  -8.8226249e+01  -1.0092497e+02  -1.1104064e+02  -8.3051033e+01  -1.1140607e+02  -1.1933948e+02  -1.2726362e+02  -1.3353332e+02  -1.4911757e+02   1.8000000e+02  -1.2022233e+02  -1.2024175e+02  -1.2880516e+02  -1.3654079e+02  -1.4505509e+02  -1.5702729e+02   1.8000000e+02  -1.3293845e+02  -1.3636909e+02  -1.4687303e+02  -1.5491284e+02  -1.6292934e+02   1.8000000e+02  -1.4987398e+02  -1.5601667e+02  -1.6275088e+02  -1.6793193e+02   1.8000000e+02  -1.6553625e+02  -1.6703238e+02   1.8000000e+02   1.6793193e+02   1.6292934e+02   1.5702729e+02   1.4911757e+02   1.1813245e+02   1.8000000e+02   1.6703238e+02   1.6275088e+02   1.5491284e+02   1.4505509e+02   1.3353332e+02   1.1115585e+02   1.6553625e+02   1.5601667e+02   1.4687303e+02   1.3654079e+02   1.2726362e+02   1.1147459e+02   1.4987398e+02   1.3636909e+02   1.2880516e+02   1.1933948e+02   1.1104064e+02   1.3293845e+02   1.2024175e+02   1.1140607e+02   1.0092497e+02   9.1252163e+01   8.7423024e+01   7.5958075e+01   3.9057101e+01   1.2022233e+02   8.8226249e+01   7.9906235e+01   7.2089465e+01   5.9786194e+01   3.6148575e+01   8.3051033e+01   7.7780619e+01   6.9707597e+01   6.1855338e+01   5.3020925e+01   3.3348566e+01   6.5249879e+01   5.5602412e+01   4.7997295e+01   4.2719008e+01   3.4234344e+01   4.7268792e+01   2.4970025e+01  -2.4970025e+01  -4.7268792e+01  -0.0000000e+00
+   5.7435555e-01   4.9211244e-01   4.1054770e-01   3.2178968e-01   2.3895219e-01   1.4198533e-01   8.2493070e-02   5.5329363e-01   4.7702561e-01   3.9148601e-01   3.0904334e-01   2.3895219e-01   1.7013032e-01   5.3636357e-01   4.6312362e-01   3.9400020e-01   5.8014881e-01   4.6312362e-01   3.9148601e-01   3.2178968e-01   2.6367691e-01   5.3636357e-01   4.7702561e-01   4.1054770e-01   3.4964389e-01   5.5329363e-01   4.9211244e-01   4.2583549e-01   3.4473021e-01   2.4517683e-01   1.5524645e-01   9.5851512e-02   5.7435555e-01   5.1224224e-01   4.2206600e-01   3.4627907e-01   2.5844969e-01   1.9592503e-01   6.2724444e-01   5.3625084e-01   4.4802495e-01   3.8089340e-01   2.9590146e-01   7.2583061e-01   6.4143205e-01   5.4563936e-01   4.5766663e-01   3.9773419e-01   7.4288762e-01   5.5534027e-01   4.7832833e-01   3.8447455e-01   2.8655722e-01   1.8228612e-01   1.1740025e-01   7.4541467e-01   6.3296406e-01   5.6050470e-01   4.7202527e-01   3.7322426e-01   2.8383293e-01   2.1310630e-01   7.3277406e-01   6.2251579e-01   5.5416077e-01   4.6633612e-01   3.7536174e-01   2.8985751e-01   7.1178026e-01   6.1282201e-01   5.4332190e-01   4.6577728e-01   4.0135547e-01   7.0192122e-01   6.2854804e-01   5.3094877e-01   4.6577728e-01   3.7536174e-01   2.8383293e-01   1.8228612e-01   9.5851512e-02   6.9093251e-01   6.2854804e-01   5.4332190e-01   4.6633612e-01   3.7322426e-01   2.8655722e-01   1.9592503e-01   7.0192122e-01   6.1282201e-01   5.5416077e-01   4.7202527e-01   3.8447455e-01   2.9590146e-01   7.1178026e-01   6.2251579e-01   5.6050470e-01   4.7832833e-01   3.9773419e-01   7.3277406e-01   6.3296406e-01   5.5534027e-01   4.5766663e-01   3.8089340e-01   2.5844969e-01   1.5524645e-01   8.2493070e-02   7.4541467e-01   5.4563936e-01   4.4802495e-01   3.4627907e-01   2.4517683e-01   1.7013032e-01   7.4288762e-01   6.4143205e-01   5.3625084e-01   4.2206600e-01   3.4473021e-01   2.6367691e-01   7.2583061e-01   6.2724444e-01   5.1224224e-01   4.2583549e-01   3.4964389e-01   6.9491142e-01   7.5332566e-01   7.5332566e-01   6.9491142e-01   0.0000000e+00

ptsa_plot/ptsa_plot/electrode_layouts/HCGSN128.dat

@@ -0,0 +1,2 @@
+   4.6351589e+01   3.8264632e+01   2.6846561e+01   2.1874325e+01   1.4581944e+01   0.0000000e+00  -3.8133998e+01   2.7825796e+01   1.6876327e+01   1.1872545e+01   0.0000000e+00  -1.4581944e+01  -3.6815100e+01   7.6337108e+00   0.0000000e+00   0.0000000e+00   0.0000000e+00  -1.1872545e+01  -2.1874325e+01  -3.6759195e+01  -7.6337108e+00  -1.6876327e+01  -2.6846561e+01  -3.6524362e+01  -2.7825796e+01  -3.8264632e+01  -4.6178909e+01  -5.3144352e+01  -6.0468013e+01  -7.5431834e+01  -1.0929177e+02  -4.6351589e+01  -5.7179011e+01  -6.6490962e+01  -7.6922594e+01  -8.7022947e+01  -1.1123182e+02  -6.1131219e+01  -8.3258549e+01  -8.9750790e+01  -9.6616476e+01  -1.1144028e+02  -6.9654787e+01  -7.9413888e+01  -1.0433176e+02  -1.0744971e+02  -1.1408635e+02  -6.9431184e+01  -8.6215277e+01  -1.2067732e+02  -1.2543764e+02  -1.2762566e+02  -1.3391069e+02  -1.4637742e+02   1.8000000e+02  -1.1170657e+02  -1.1960885e+02  -1.3364463e+02  -1.4104708e+02  -1.4581619e+02  -1.5683771e+02   1.8000000e+02  -1.2889243e+02  -1.3736791e+02  -1.4746039e+02  -1.5479273e+02  -1.6591948e+02  -1.4940375e+02  -1.5510218e+02  -1.6235024e+02  -1.7054614e+02   1.8000000e+02  -1.6556632e+02  -1.7241621e+02   1.8000000e+02   1.7054614e+02   1.6591948e+02   1.5683771e+02   1.4637742e+02   1.0929177e+02   1.8000000e+02   1.7241621e+02   1.6235024e+02   1.5479273e+02   1.4581619e+02   1.3391069e+02   1.1123182e+02   1.6556632e+02   1.5510218e+02   1.4746039e+02   1.4104708e+02   1.2762566e+02   1.1144028e+02   1.4940375e+02   1.3736791e+02   1.3364463e+02   1.2543764e+02   1.1408635e+02   1.2889243e+02   1.1960885e+02   1.2067732e+02   1.0744971e+02   9.6616476e+01   8.7022947e+01   7.5431834e+01   3.8133998e+01   1.1170657e+02   1.0433176e+02   8.9750790e+01   7.6922594e+01   6.0468013e+01   3.6815100e+01   8.6215277e+01   7.9413888e+01   8.3258549e+01   6.6490962e+01   5.3144352e+01   3.6759195e+01   6.9431184e+01   6.9654787e+01   6.1131219e+01   5.7179011e+01   4.6178909e+01   3.6524362e+01   5.3521492e+01   2.9379528e+01  -2.9379528e+01  -5.3521492e+01
+   5.9922820e-01   4.8855253e-01   3.9041997e-01   3.1698474e-01   2.2653740e-01   1.4307050e-01   7.3410787e-02   5.4732752e-01   4.6285863e-01   3.9053301e-01   3.2024325e-01   2.2653740e-01   1.5618491e-01   5.3142251e-01   4.5362720e-01   3.9506715e-01   5.7453604e-01   3.9053301e-01   3.1698474e-01   2.6160576e-01   5.3142251e-01   4.6285863e-01   3.9041997e-01   3.3208048e-01   5.4732752e-01   4.8855253e-01   3.8996261e-01   3.1263428e-01   2.2774343e-01   1.4772838e-01   7.5536205e-02   5.9922820e-01   5.1490639e-01   3.9953030e-01   3.0135425e-01   2.2599662e-01   1.5766893e-01   6.3413851e-01   5.3861906e-01   4.1015635e-01   3.1391888e-01   2.6014064e-01   7.0597474e-01   6.5034519e-01   5.2650286e-01   4.0397092e-01   3.3601109e-01   7.8543916e-01   7.4376018e-01   5.0936931e-01   3.9520726e-01   3.1143044e-01   2.2119107e-01   1.4754097e-01   7.5944155e-02   7.2391529e-01   6.1979607e-01   4.9802123e-01   3.8986307e-01   2.9880775e-01   2.2326320e-01   2.5512195e-01   7.1847315e-01   6.1067114e-01   4.9520376e-01   3.8735638e-01   3.0796634e-01   6.9596342e-01   6.0323681e-01   4.9156715e-01   3.8353311e-01   3.2828767e-01   6.8647567e-01   5.9529709e-01   4.8275277e-01   3.8353311e-01   3.0796634e-01   2.2326320e-01   1.4754097e-01   7.5536205e-02   6.7878336e-01   5.9529709e-01   4.9156715e-01   3.8735638e-01   2.9880775e-01   2.2119107e-01   1.5766893e-01   6.8647567e-01   6.0323681e-01   4.9520376e-01   3.8986307e-01   3.1143044e-01   2.6014064e-01   6.9596342e-01   6.1067114e-01   4.9802123e-01   3.9520726e-01   3.3601109e-01   7.1847315e-01   6.1979607e-01   5.0936931e-01   4.0397092e-01   3.1391888e-01   2.2599662e-01   1.4772838e-01   7.3410787e-02   7.2391529e-01   5.2650286e-01   4.1015635e-01   3.0135425e-01   2.2774343e-01   1.5618491e-01   7.4376018e-01   6.5034519e-01   5.3861906e-01   3.9953030e-01   3.1263428e-01   2.6160576e-01   7.8543916e-01   7.0597474e-01   6.3413851e-01   5.1490639e-01   3.8996261e-01   3.3208048e-01   6.6716702e-01   7.2531599e-01   7.2531599e-01   6.6716702e-01

ptsa_plot/ptsa_plot/electrode_layouts/HCGSN128.sfp

@@ -0,0 +1,132 @@
+FidNz	0	9.071585155	-2.359754454
+FidT9	-6.711765	0.040402876	-3.251600355
+FidT10	6.711765	0.040402876	-3.251600355
+E1	5.787677636	5.520863216	-2.577468644
+E2	5.291804727	6.709097557	0.307434896
+E3	3.864122447	7.63424051	3.067770143
+E4	2.868837559	7.145708546	4.989564557
+E5	1.479340453	5.68662139	6.812878187
+E6	0	3.806770224	7.891304964
+E7	-1.223800252	1.558864431	8.44043914
+E8	4.221901505	7.998817387	-1.354789681
+E9	2.695405558	8.884820317	1.088308144
+E10	1.830882336	8.708839134	3.18709115
+E11	0	7.96264703	5.044718001
+E12	-1.479340453	5.68662139	6.812878187
+E13	-2.435870762	3.254307219	7.608766206
+E14	1.270447661	9.479016328	-0.947183306
+E15	0	9.087440894	1.333345013
+E16	0	9.076490798	3.105438474
+E17	0	9.271139705	-2.211516434
+E18	-1.830882336	8.708839134	3.18709115
+E19	-2.868837559	7.145708546	4.989564557
+E20	-3.825797111	5.121648995	5.942844877
+E21	-1.270447661	9.479016328	-0.947183306
+E22	-2.695405558	8.884820317	1.088308144
+E23	-3.864122447	7.63424051	3.067770143
+E24	-4.459387187	6.021159964	4.365321482
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+E26	-5.291804727	6.709097557	0.307434896
+E27	-5.682547954	5.453384344	2.836565436
+E28	-5.546670402	4.157847823	4.627615703
+E29	-4.762196763	2.697832099	6.297663028
+E30	-3.695490968	0.960411022	7.627828134
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