Merge pull request #6 from simpeg/feat/em

Feat/em

.bumpversion.cfg

@@ -0,0 +1,4 @@
+[bumpversion]
+current_version = 0.0.1
+files = setup.py geoana/__init__.py docs/conf.py
+

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 python:
-  - 3.4
+  - 3.6
   - 2.7
 
 sudo: false
@@ -11,9 +11,8 @@ env:
 install:
   - pip install --upgrade pip;
   - pip install -r requirements.txt
-  - pip install sphinx_rtd_theme
-  - git clone https://github.com/3ptscience/vectormath;
-  - export PYTHONPATH=$PWD/geoana:$PWD/vectormath:$PYTHONPATH
+  - pip install -r requirements_dev.txt
+  - cd geoana; python setup.py install; cd ..
 
 # Run test
 script:

Makefile

@@ -0,0 +1,34 @@
+PACKAGE_NAME=geoana
+
+.PHONY: install coverage lint graphs tests docs clean deploy
+
+install:
+	python setup.py install
+
+coverage:
+	nosetests --logging-level=INFO --with-coverage --cover-package=geoana --cover-html
+	open cover/index.html
+
+lint:
+	pylint $(PACKAGE_NAME)
+
+lint-html:
+	pylint --output-format=html $(PACKAGE_NAME) > pylint.html
+
+graphs:
+	pyreverse -my -A -o pdf -p geoana geoana/**.py geoana/**/**.py
+
+tests:
+	nosetests --logging-level=INFO
+
+docs:
+	cd docs;make html
+
+clean_pyc:
+	find . -name "*.pyc" | xargs -I {} rm -v "{}"
+
+clean: clean_pyc
+	cd docs;make clean
+
+deploy:
+	python setup.py sdist upload

README.rst

@@ -1,10 +1,10 @@
-.. _index:
+.. _geoana:
 
 geoana
 ======
 
 .. image:: https://readthedocs.org/projects/geoana/badge/?version=latest
-    :target: http://geoana.readthedocs.io/en/latest/?badge=latest
+    :target: https://geoana.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
 .. image:: https://img.shields.io/github/license/simpeg/geoana.svg
@@ -13,15 +13,12 @@ geoana
 
 .. image:: https://travis-ci.org/simpeg/geoana.svg?branch=master
     :target: https://travis-ci.org/simpeg/geoana
-    :alt: travis status
-
-.. image:: https://www.quantifiedcode.com/api/v1/project/cb381a23f09245bd855f86eac295d8ec/badge.svg
-    :target: https://www.quantifiedcode.com/app/project/cb381a23f09245bd855f86eac295d8ec
-    :alt: Code issues
+    :alt: Travis status
 
 .. image:: https://api.codacy.com/project/badge/Grade/2e32cd28f4424dc1800f1590a64c244f
     :target: https://www.codacy.com/app/lindseyheagy/geoana?utm_source=github.com&utm_medium=referral&utm_content=simpeg/geoana&utm_campaign=Badge_Grade
     :alt: codacy status
 
-Interactive geoscience (mostly) analytic functions.
+
+Interactive geoscience (mostly) analytic functions in geophysics.
 

appveyor.yml

@@ -0,0 +1,45 @@
+# AppVeyor.com is a Continuous Integration service to build and run tests under Windows
+
+build: off
+
+environment:
+  matrix:
+    - PYTHON: 2.7
+      MINICONDA: C:\Miniconda
+      PYTHON_ARCH: 32
+
+    - PYTHON: 3.5
+      MINICONDA: C:\Miniconda3
+      PYTHON_ARCH: 32
+
+    - PYTHON: 3.6
+      MINICONDA: C:\Miniconda3
+      PYTHON_ARCH: 32
+
+    - PYTHON: 2.7
+      MINICONDA: C:\Miniconda
+      PYTHON_ARCH: 64
+
+    - PYTHON: 3.5
+      MINICONDA: C:\Miniconda3
+      PYTHON_ARCH: 64
+
+    - PYTHON: 3.6
+      MINICONDA: C:\Miniconda3
+      PYTHON_ARCH: 64
+
+init:
+  - "ECHO %PYTHON% %MINICONDA%"
+
+install:
+  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - "conda create -q -n test-environment python=%PYTHON% numpy scipy matplotlib cython jupyter ipython pillow wheel"
+  - activate test-environment
+  - pip install -r requirements_dev.txt
+  - python setup.py install
+
+test_script:
+  - nosetests tests -v -s

docs/conf.py

@@ -119,6 +119,14 @@
     html_theme = 'sphinx_rtd_theme'
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
+
+linkcheck_ignore = [
+    'https://readthedocs.org/projects/geoana/badge/?version=latest'
+]
+
+linkcheck_retries = 3
+linkcheck_timeout = 500
+
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
@@ -299,3 +307,20 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'https://docs.python.org/': None}
+
+
+def supress_nonlocal_image_warn():
+    import sphinx.environment
+    sphinx.environment.BuildEnvironment.warn_node = (
+        _supress_nonlocal_image_warn
+    )
+
+
+def _supress_nonlocal_image_warn(self, msg, node, **kwargs):
+    from docutils.utils import get_source_line
+
+    if not msg.startswith('nonlocal image URI found:'):
+        self._warnfunc(msg, '{0!s}:{1!s}'.format(*get_source_line(node)))
+
+supress_nonlocal_image_warn()
+

docs/content/earthquake.rst

@@ -0,0 +1,8 @@
+.. _earthquake:
+
+Earthquake
+==========
+
+.. autoclass:: geoana.earthquake
+    :members:
+    :undoc-members:

docs/content/em.rst

@@ -0,0 +1,8 @@
+.. _em:
+
+Electromagnetics
+================
+
+.. autoclass:: geoana.em
+    :members:
+    :undoc-members:

docs/index.rst

@@ -1,18 +1,13 @@
-.. _index:
+
 
 .. include:: ../README.rst
 
-Contents:
+
+**Contents:**
 
 .. toctree::
    :maxdepth: 2
 
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   content/earthquake
+   content/em
 

examples/README.txt

@@ -0,0 +1,2 @@
+Examples
+********

examples/em/README.txt

@@ -0,0 +1,2 @@
+Electromagnetics
+****************

examples/em/fdem_ElectricDipoleWholeSpace.py

@@ -0,0 +1,113 @@
+"""
+Electric Dipole in a Whole Space: Frequency Domain
+==================================================
+
+In this example, we plot electric and magnetic flux density due to an electric
+dipole in a whole space. Note that you can also examine the current density
+and magnetic field.
+
+We can vary the conductivity, magnetic permeability and dielectric permittivity
+of the wholespace, the frequency of the source and whether or not the
+quasistatic assumption is imposed.
+
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.colors import LogNorm
+from scipy.constants import mu_0, epsilon_0
+
+from geoana import utils, spatial
+from geoana.em import fdem
+
+# define frequencies that we want to look at
+frequencies = np.logspace(0, 4, 3)
+
+# Build the electric dipole object
+edipole = fdem.ElectricDipoleWholeSpace(
+    sigma=1.,  # conductivity of 1 S/m
+    mu=mu_0,  # permeability of free space (this is the default)
+    epsilon=epsilon_0,  # permittivity of free space (this is the default)
+    location=np.r_[0., 0., 0.],  # location of the dipole
+    orientation='Z',  # vertical dipole (can also be a unit-vector)
+    quasistatic=False  # don't use the quasistatic assumption
+)
+
+# construct a grid where we want to plot electric fields
+x = np.linspace(-50, 50, 100)
+z = np.linspace(-50, 50, 100)
+xyz = utils.ndgrid([x, np.r_[0], z])
+
+
+# plot amplitude
+def plot_amplitude(ax, v):
+    v = spatial.vector_magnitude(v)
+    plt.colorbar(
+        ax.pcolormesh(
+            x, z, v.reshape(len(x), len(z), order='F'), norm=LogNorm()
+        ), ax=ax
+    )
+    ax.axis('square')
+    ax.set_xlabel('x (m)')
+    ax.set_ylabel('z (m)')
+
+
+# plot streamlines
+def plot_streamlines(ax, v):
+    vx = v[:, 0].reshape(len(x), len(z), order='F')
+    vz = v[:, 2].reshape(len(x), len(z), order='F')
+    ax.streamplot(x, z, vx.T, vz.T, color='k')
+
+
+# create fig, ax for electric fields and magnetic flux
+fig_e, ax_e = plt.subplots(
+    2, len(frequencies), figsize=(5*len(frequencies), 7)
+)
+fig_b, ax_b = plt.subplots(
+    2, len(frequencies), figsize=(5*len(frequencies), 7)
+)
+
+# loop over frequencies and plot
+for i, frequency in enumerate(frequencies):
+
+    # set the frequency of the dipole
+    edipole.frequency = frequency
+
+    # evaluate the electric field and magnetic flux density
+    electric_field = edipole.electric_field(xyz)
+    magnetic_flux_density = edipole.magnetic_flux_density(xyz)
+
+    # plot amplitude of electric field
+    for ax, reim in zip(ax_e[:, i], ['real', 'imag']):
+        # grab real or imag component
+        e_plot = getattr(electric_field, reim)
+
+        # plot both amplitude and streamlines
+        plot_amplitude(ax, e_plot)
+        plot_streamlines(ax, e_plot)
+
+        # set the title
+        ax.set_title(
+            'E {} at {:1.1e} Hz'.format(reim, frequency)
+        )
+
+    # plot the amplitude of the magnetic field (note the magnetic field is into
+    # and out of the page in this geometry, so we don't plot vectors)
+    for ax, reim in zip(ax_b[:, i], ['real', 'imag']):
+        # grab real or imag component
+        b_plot = getattr(magnetic_flux_density, reim)
+
+        # plot amplitude
+        plot_amplitude(ax, b_plot)
+
+        # set the title
+        ax.set_title(
+            'B {} at {:1.1e} Hz'.format(reim, frequency)
+        )
+
+# format so text doesn't overlap
+fig_e.tight_layout()
+fig_b.tight_layout()
+plt.show()
+
+

geoana/__init__.py

@@ -1 +1,9 @@
+from . import earthquake
 from . import em
+from . import utils
+
+__version__ = '0.0.1'
+__author__ = 'SimPEG developers'
+__license__ = 'MIT'
+__copyright__ = 'Copyright 2017 SimPEG developers'
+

geoana/earthquake/oksar.py

@@ -23,7 +23,17 @@
 import matplotlib.pyplot as plt
 
 
-class EarthquakeInterferogram(properties.UidModel):
+class EarthquakeInterferogram(properties.HasProperties):
+    title = properties.String(
+        'name of the earthquake',
+        required=True
+    )
+
+    description = properties.String(
+        'description of the event',
+        required=False
+    )
+
     location = properties.Vector2(
         'interferogram location (bottom N, left E)',
         required=True
@@ -229,6 +239,8 @@ def get_LOS_vector(self, locations):
             calculate beta - the angle at earth center between reference point
             and satellite nadir
         """
+        if not isinstance(locations, list):
+            locations = [locations]
 
         utmZone = self.location_UTM_zone
         refPoint = vmath.Vector3(self.ref.x, self.ref.y, 0)
@@ -283,7 +295,7 @@ def get_LOS_vector(self, locations):
         los_y = -np.sin(satAzimuth * DEG2RAD) * np.cos(satIncidence * DEG2RAD)
         los_z = np.sin(satIncidence * DEG2RAD)
 
-        return vmath.Vector3(los_x, los_y, los_z)
+        return vmath.Vector3Array([los_x, los_y, los_z])
 
     @staticmethod
     def _ang_to_gc(x, y, origx, origy, satAzimuth):

geoana/em/__init__.py

@@ -1,2 +1,3 @@
 from . import static
 from . import fdem
+from . import tdem