Merge pull request #47 from calum-chamberlain/develop

Merge develop for release 0.1.3

.gitignore

@@ -27,3 +27,6 @@ station.dat
 *L.S??????
 *R.S??????
 .idea
+.coverage.*
+eqcorrscan/core/subspace_statistic.c
+eqcorrscan/core/sliding_normxcorr.c

.travis.yml

@@ -6,16 +6,19 @@ matrix:
       env: PYTHON_VERSION=2.7
     - os: linux
       env: PYTHON_VERSION=3.5
+    - os: linux
+      env: PYTHON_VERSION=3.4
+    #    - os: linux
+    #      env: PYTHON_VERSION=3.3
+    # There isn't and openCV3 for python 3.3 on Conda
 
-#     Conda install on OSX is an issue - gives 0.238 xcorr when should give 1...
-#    - os: osx
-#      env: PYTHON_VERSION=2.7
-#    - os: osx
-#      env: PYTHON_VERSION=3.5
+    - os: osx
+      env: PYTHON_VERSION=2.7
+    - os: osx
+      env: PYTHON_VERSION=3.5
 
 sudo: false
 
-# Test with multiple obspy versions, allow some backwards compatability
 env:
   global:
     - OBSPY_VERSION=1.0.1
@@ -26,7 +29,7 @@ install:
       export py=$PYTHON_VERSION;
     else
       export OS="Linux";
-      export py=$TRAVIS_PYTHON_VERSION;
+      export py=$PYTHON_VERSION;
     fi
   - if [[ "$py" == "2.7_with_system_site_packages" ]]; then
       export py="2.7";
@@ -41,6 +44,7 @@ install:
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda config --add channels menpo
+  - conda config --add channels obspy
   - conda update -q conda
   # Useful for debugging any issues with conda
   - conda info -a
@@ -52,36 +56,47 @@ install:
         env_file="misc/py2_test_env.lis"
         PYFLAKES="pyflakes=0.9.0"
       fi
+  - echo $PYTHON_VERSION
   - |
       if [[ "$OS" == "MacOSX" ]]; then
-          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib basemap pyproj flake8 future lxml decorator sqlalchemy mock nose gdal docopt coverage requests
-      else
+          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib obspy flake8 mock coverage opencv3
+      elif [[ "$py" == "3.5" ]]; then
           conda create -q -n test-environment --file $env_file
+      elif [[ "$py" == "2.7" ]]; then
+          conda create -q -n test-environment --file $env_file
+      else
+          conda create -q -n test-environment python=$PYTHON_VERSION numpy scipy matplotlib obspy flake8 mock coverage opencv3
       fi
   - source activate test-environment
   - conda install $PYFLAKES
   - conda install pyproj
-  - |
-      if [[ "${py:0:1}" == "3" ]] && [[ "$OS" == "MacOSX" ]]; then
-        conda install -c menpo opencv3=3.1.0
-      elif [[ "$OS" == "MacOSX" ]]; then
-        conda install opencv
-      fi
+  - conda install h5py
+  #  - |
+  #      if [[ "${py:0:1}" == "3" ]] && [[ "$OS" == "MacOSX" ]]; then
+  #        conda install opencv3
+  #        conda install obspy
+  #      fi
+  #      elif [[ "$OS" == "MacOSX" ]]; then
+  #        conda install -c menpo opencv3=3.1.0
+  #      fi
   - pip install coveralls
   - pip install geographiclib
   - pip install https://github.com/megies/PyImgur/archive/py3.zip
   - pip install pep8-naming
   - pip install pytest
   - pip install pytest-cov
-  - pip install obspy==$OBSPY_VERSION
-  # - pip install obspy==$OBSPY_VERSION
+  - pip install Cython
+  #  - pip install obspy==$OBSPY_VERSION
   - pip freeze
   - conda list
   # done installing dependencies
   - git version
-  - pip install .
+  - python setup.py install
+
 script:
-  python setup.py test
+  # Need to ignore the files in current directory to ensure we find the
+  # installed version of EQcorrscan with compiled code.
+  - python setup.py test
 
 after_success:
   # Check how much code is actually tested and send this report to coveralls

CHANGES.md

@@ -1,3 +1,17 @@
+## 0.1.3
+* Now testing on OSX (python 2.7 and 3.5) - also added linux python 3.4;
+* Add lag-calculation and tests for it;
+* Change how lag-calc does the trace splitting to reduce memory usage;
+* Added pick-filtering utility to clean up tutorials;
+* Change template generation function names for clarity (wrappers for
+depreciated names);
+* Add more useful error messages when picks are not associated with
+waveforms;
+* Add example plots for more plotting functions;
+* Add subspace detector including docs and tutorial.
+* Add *delayed* option to all template_gen functions, set to True by
+default which retains old behaviour.
+
 ## 0.1.2
 * Add handling for empty location information in sfiles.
 * Added project setup script which creates a useful directory structure and copies

README.md

@@ -1,5 +1,5 @@
 # EQcorrscan
-## A python package to conduct matched-filter earthquake detections.
+## A python package for the detection and anlysis of repeating and near-repeating earthquakes.
 
 [![Join the chat at https://gitter.im/calum-chamberlain/EQcorrscan](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/calum-chamberlain/EQcorrscan?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![TravisCIStatus](https://travis-ci.org/calum-chamberlain/EQcorrscan.svg?branch=master)](https://travis-ci.org/calum-chamberlain/EQcorrscan)
@@ -9,10 +9,10 @@
 [![DocumentationStatus](http://readthedocs.org/projects/eqcorrscan/badge/?version=latest)](http://eqcorrscan.readthedocs.org/en/latest/?badge=latest)
 
 # Installation
-Installation has been tested on both OSX and Linux (Ubuntu), and now
-Windows systems.  We support Python versions 2.7 and 3.5.  The codes likely
-work on Py 3.4 too, but we currently don't test this and recommend users to
-work in Py 3.5.
+Installation has been tested on both OSX and Linux (Ubuntu), and
+Windows systems.  We support Python versions 2.7, 3.4 and 3.5.
+Note that, although we support Windows, EQcorrscan is optimized for
+linux style distributions.
 
 Instructions for installing EQcorrscan and the required dependency, openCV
 are linked from the [docs](http://eqcorrscan.readthedocs.io/en/latest/intro.html#installation)
@@ -56,13 +56,13 @@ the gh-pages branch.
 
 # Functionality
 
-This package contains routines to enable the user to conduct match-filter earthquake
+This package contains routines to enable the user to conduct matched-filter earthquake
 detections using [obspy](https://github.com/obspy/obspy/wiki) bindings when reading
 and writing seismic data, and the correlation routine in [openCV](http://opencv.org/).
-The OpendCV package is not installed by this software, due to a need to build from
+The OpenCV package is not installed by this software, due to a need to build from
 source.  The user should follow the instructions above for OpenCV install.
-This package was written to implement the Matlab routines
-used by Chamberlain et al. (2014) for the detection of low-frequency earthquakes.
+
+We have also added subspace detection and correlation derived pick adjustment.
 
 Also within this package are:
 * Clustering routines for seismic data;
@@ -74,10 +74,9 @@ Also within this package are:
 * Brightness based template creation based on the work of Frank et al. (2014);
 * Singular Value Decomposition derived magnitude calculations based on Rubinstein & Ellsworth (2010).
 
-We are currently hovering around 9,000 lines of code (including doc-strings) - it is probably worth
-having a look at the docs to check what functions we have.  We plan to write a series of tutorials to be
-included on the EQcorrscan API to highlight key functions, currently our tutorials only show
-how to do the core matched-filter detection.
+We are currently hovering around 15,000 lines of code (including doc-strings) - it is probably worth
+having a look at the docs to check what functions we have.  We are writing a series of tutorials
+included on the EQcorrscan API to highlight key functions.
 
 # Licence
 
@@ -100,18 +99,6 @@ Please document your functions following the other documentation within the
 functions, these doc-scripts will then be built into the main documentation
 using Sphinx.
 
-We are trying to implement a better branching model, following that found [here](http://nvie.com/posts/a-successful-git-branching-model/).
-To this end, please fork the development branch if you want to develop
-things, and flag issues in the master for us to bugfix.
-If you have a feature you want to develop please create a new branch
-from the development branch and work on it there, we can then merge
-it back in to the development branch when it is stable enough.
-
-This branching model (git-flow) is pretty well established, and I would recommend
-you to install [git-flow](https://github.com/nvie/gitflow/wiki/Installation) and
-read their [documentation](https://github.com/nvie/gitflow). It seems pretty intuitive and
-will keep us all branching in the same way.
-
 # References
 * CJ Chamberlain, DR Shelly, J Townend, TA Stern (2014) [Low‐frequency earthquakes reveal punctuated slow slip on the deep extent of the Alpine Fault, New Zealand](http://onlinelibrary.wiley.com/doi/10.1002/2014GC005436/full), __G-cubed__,doi:10.1002/2014GC005436
 * Thurber, C. H., Zeng, X., Thomas, A. M., & Audet, P. (2014). [Phase‐Weighted Stacking Applied to Low‐Frequency Earthquakes](http://www.bssaonline.org/content/early/2014/08/12/0120140077.abstract), __BSSA__, doi:10.1785/0120140077.

appveyor.yml

@@ -1,4 +1,5 @@
 
+
 # AppVeyor.com is a Continuous Integration service to build and run tests under Windows
 
 environment:
@@ -29,14 +30,16 @@ install:
   - "%CMD_IN_ENV% python --version"
   # Install the build and runtime dependencies of the project.
   - "conda update -q --yes conda"
+  - "conda config --add channels menpo"
+  - "conda config --add channels obspy"
   # Create a conda environment using the astropy bonus packages
   - "conda create -q --yes -n test python=%PYTHON_VERSION%"
   - "activate test"
   # Install default dependencies
-  - "conda install -q --yes pip numpy scipy matplotlib=1.3.1 lxml sqlalchemy flake8 mock nose gdal decorator requests basemap pytest pyflakes=0.9.0"
+  - "conda install -q --yes pip numpy scipy opencv3 matplotlib obspy mock flake8 pytest pyflakes=0.9.0 cython h5py"
   # additional dependecies
-  - "choco install opencv -version 2.4.9.20140518"
-  - "powershell copy-item C:\\OpenCV249\\opencv\\build\\python\\2.7\\x64\\cv2.pyd C:\\conda\\envs\\test\\lib\\site-packages\\."
+  #  - "choco install opencv"
+  #  - "powershell copy-item C:\\OpenCV\\opencv\\build\\python\\2.7\\x64\\cv2.pyd C:\\conda\\envs\\test\\lib\\site-packages\\."
   - "pip install pyimgur"
   - "pip install -U future"
   - "pip install pytest-cov"
@@ -49,4 +52,4 @@ build: false
 
 test_script:
   - "%CMD_IN_ENV% python setup.py develop"
-  - "%CMD_IN_ENV% py.test"
+  - "%CMD_IN_ENV% py.test"

eqcorrscan/__init__.py

@@ -34,9 +34,11 @@
 import importlib
 import warnings
 
-__all__ = ['core', 'utils', 'par']
+__all__ = ['core', 'utils']
+
+
+__version__ = '0.1.3'
 
-__version__ = '0.1.2'
 
 # Cope with changes to name-space to remove most of the camel-case
 _import_map = {

eqcorrscan/core/__init__.py

@@ -28,7 +28,8 @@
     python-pylab    - used for plotting
 """
 
-__all__ = ['template_gen', 'match_filter', 'bright_lights']
+__all__ = ['template_gen', 'match_filter', 'bright_lights', 'lag_calc',
+           'subspace', 'subspace_statistic']
 
 if __name__ == '__main__':
     import doctest