Merge pull request #9 from SiLab-Bonn/development

GIT: merge Development

.coveragerc

@@ -9,4 +9,9 @@ exclude_lines =
 
 omit = 
     */__init__.py
-    tests/*
+    testbeam_analysis/testing/*
+    testbeam_analysis/converter/*
+    testbeam_analysis/tools/residuals.py
+    testbeam_analysis/tools/test_tools.py
+    testbeam_analysis/tools/deprecated.py
+    testbeam_analysis/tools/data_selection.py

.gitignore

@@ -49,6 +49,8 @@ data_clusterizer.cpp
 # PyDev files
 .project
 .pydevproject
+# Examples output data
+examples/data/output*
 # Example data
 TestBeamData_FEI4_DUT0_cluster.h5
 TestBeamData_FEI4_DUT1_cluster.h5
@@ -69,14 +71,4 @@ Correlation.h5
 TrackCandidates.h5
 Tracklets.h5
 Tracklets_corr.h5
-Tracks.h5
-tmp
-*.h5
-!data/
-!test_hit_analysis/
-!test_track_analysis/
-!test_result_analysis/
-!test_correlation_fixing/
-*.pdf
-*tmp*.*
-.coverage*
+Tracks.h5

.travis.yml

@@ -1,13 +1,14 @@
 language: python
 python:
   - 2.7
-  - 3.4
+  - 3.5
 
 sudo: false
 
-branches:
-  only:
-    - master
+addons:
+  apt:
+    packages:
+    - gfortran
 
 notifications:
   email:
@@ -29,8 +30,8 @@ before_install:
   - export PATH="$HOME/miniconda/bin:$PATH"
   - conda update --yes conda
   - conda info -a
-  - conda install --yes numpy cython pytables scipy matplotlib pandas nose
-  - pip install progressbar-latest xvfbwrapper coverage coveralls
+  - conda install --yes numpy cython pytables scipy matplotlib nose numba mock
+  - pip install progressbar-latest xvfbwrapper coverage coveralls pixel_clusterizer pykalman pylandau
   - python setup.py develop
 
 # Run test
@@ -40,7 +41,7 @@ script:
   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
       touch $HOME/miniconda/lib/python2.7/site-packages/converage.pth && printf "import coverage; coverage.process_startup()" > $HOME/miniconda/lib/python2.7/site-packages/converage.pth;
     else
-      touch $HOME/miniconda/lib/python3.4/site-packages/converage.pth && printf "import coverage; coverage.process_startup()" > $HOME/miniconda/lib/python3.4/site-packages/converage.pth;
+      touch $HOME/miniconda/lib/python3.5/site-packages/converage.pth && printf "import coverage; coverage.process_startup()" > $HOME/miniconda/lib/python3.5/site-packages/converage.pth;
     fi
   - nosetests --with-coverage --cover-package=testbeam_analysis
 

MANIFEST.in

@@ -1,7 +1,6 @@
 include LICENSE
 include README.*
 include requirements.*
-#recursive-include docs *
-recursive-include examples *
-recursive-include tests *
+include requirements_docs.*
+recursive-include docs *
 recursive-include testbeam_analysis *

README.rst

@@ -0,0 +1,68 @@
+===============================================
+Introduction
+===============================================
+
+|travis-status|  |appveyor-status|  |rtd-status|  |coverage|
+
+Testbeam analysis is a simple analysis of pixel-sensor data in particle beams. All steps of a complete analysis
+are implemented with a few independent python functions. If you want to understand the basics of telescope data
+reconstruction this code might help. 
+If you want to have something fancy to account for thick devices in combination with low energetic beams
+use e.g. _EUTelescope_. Depending on the setup a resolution that is only ~ 15% worse can be archieved with this code.
+For a quick first impression check the examples in the documentation.
+
+In future releases it is forseen to make the code more readable and to implement a Kalman Filter to have the best
+possible track fit results.
+
+Installation
+============
+You have to have Python 2/3 with the following modules installed:
+- cython
+- tables
+- scipy
+- matplotlib
+- numba
+
+If you are new to Python please look at the installation guide in the wiki.
+Since it is recommended to change example files according to your needs you should install the module with
+
+.. code-block:: bash
+
+   python setup.py develop
+
+This does not copy the code to a new location, but just links to it.
+Uninstall:
+
+.. code-block:: bash
+
+   pip uninstall testbeam_analysis
+
+
+Example usage
+==============
+Check the examples folder with data and examples of a Mimosa26 and a FE-I4 telescope analysis.
+Run eutelescope_example.py or fei4_telescope_example.py in the example folder and check the text output to
+the console as well as the plot and data files that are created to understand what is going on.
+In the examples folder type e.g.:
+
+.. code-block:: bash
+   
+   python fei4_telescope_example.py
+
+.. |travis-status| image:: https://travis-ci.org/SiLab-Bonn/testbeam_analysis.svg?branch=development
+    :target: https://travis-ci.org/SiLab-Bonn/testbeam_analysis
+    :alt: Build status
+
+.. |appveyor-status| image:: https://ci.appveyor.com/api/projects/status/github/SiLab-Bonn/testbeam_analysis
+    :target: https://ci.appveyor.com/project/DavidLP/testbeam-analysis
+    :alt: Build status
+
+.. |rtd-status| image:: https://readthedocs.org/projects/testbeam_analysis/badge/?version=latest
+    :target: http://testbeam_analysis.rtfd.org
+    :alt: Documentation
+
+.. |coverage| image:: https://coveralls.io/repos/SiLab-Bonn/testbeam_analysis/badge.svg?branch=development
+    :target: https://coveralls.io/github/SiLab-Bonn/testbeam_analysis?branch=development
+    :alt: Coverage
+
+

appveyor.yml

@@ -5,16 +5,15 @@ environment:
     - PYTHON: 2.7
 
 platform:
-  - x86
   - x64
 
 init:
   - "ECHO %PYTHON%"
   - ps: Start-FileDownload 'http://download.microsoft.com/download/7/9/6/796EF2E4-801B-4FC4-AB28-B59FBF6D907B/VCForPython27.msi' C:\VCForPython27.msi; echo "Done"
   - cmd: msiexec /i C:\VCForPython27.msi /quiet /qn
-  - set PATH=C:\Miniconda;C:\Miniconda\Scripts;%PATH%  # miniconda is already installed on appveyor: https://github.com/appveyor/ci/issues/359
-  - conda install --yes numpy cython pytables scipy matplotlib pandas nose
-  - pip install progressbar-latest
+  - set PATH=C:\Miniconda-x64;C:\Miniconda-x64\\Scripts;%PATH%  # Miniconda is already installed on appveyor: https://github.com/appveyor/ci/issues/359
+  - conda install --yes numpy cython pytables scipy matplotlib nose numba mock
+  - pip install progressbar-latest pixel_clusterizer pykalman pylandau
   - conda info -a
   - conda list
 

docs/Examples.rst

@@ -0,0 +1,33 @@
+.. toctree::
+   :numbered:
+
+Examples
+********
+
+There are plenty of examples available that cover different setups.
+These examples are a good starting point to get to know `Testbeam Analysis`.
+
+ATLAS FE-I4 telescope
+=====================
+.. automodule:: testbeam_analysis.examples.fei4_telescope
+.. image:: _static/example_fei4/CorrelationColumn.png
+.. image:: _static/example_fei4/CorrelationRow.png
+
+Original correlation :download:`pdf output <_static/example_fei4/Correlation.pdf>`
+
+.. image:: _static/example_fei4/AlignmentCorrSlice.png
+.. image:: _static/example_fei4/AlignmentCorrFit.png
+
+Original pre-alignment :download:`pdf output <_static/example_fei4/Prealignment.pdf>`
+
+.. image:: _static/example_fei4/Track_chi2.png
+
+Original track fitting :download:`pdf output <_static/example_fei4/Correlation.pdf>`
+
+.. image:: _static/example_fei4/EventMonitor.png
+
+Original event plot :download:`pdf output <_static/example_fei4/Event.pdf>`
+
+.. image:: _static/example_fei4/Efficiency.png
+
+Original efficiency :download:`pdf output <_static/example_fei4/Efficiency.pdf>`