astrofrog · astrofrog · Sep 3, 2013 · Dec 22, 2012 · Dec 22, 2012 · Dec 22, 2012
diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,2 @@
+[run]
+omit = sedfitter/*/tests/*.py
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,37 @@
+# Compiled files
+*.py[co]
+*.a
+*.o
+*.so
+__pycache__
+
+# Ignore .c files by default to avoid including generated code. If you want to
+# add a non-generated .c extension, use `git add -f filename.c`.
+*.c
+
+# Other generated files
+*/version.py
+
+# Sphinx
+_build
+
+# Packages/installer info
+*.egg
+*.egg-info
+dist
 build
-*.pyc
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+distribute-*.tar.gz
+
+# Other
+.*.swp
+*~
+
+# Mac OSX
+.DS_Store
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,55 @@
+language: python
+
+python:
+    - 2.6
+    - 2.7
+    - 3.2
+    - 3.3
+
+env:
+    global:
+        - PIP_WHEEL_COMMAND="pip install --find-links http://wheels.astropy.org/ --find-links http://wheels2.astropy.org/ --use-wheel --upgrade --use-mirrors"
+    matrix:
+        - NUMPY_VERSION=1.7.1 SETUP_CMD='test'
+
+matrix:
+    include:
+        # try alternate Numpy versions
+        # disabled for now, because the SciPy wheels only work for Numpy 1.7.1
+        # - python: 2.7
+        #   env: NUMPY_VERSION=1.6.2 SETUP_CMD='test'
+        # - python: 2.7
+        #   env: NUMPY_VERSION=1.5.1 SETUP_CMD='test'
+        # - python: 3.2
+        #   env: NUMPY_VERSION=1.6.2 SETUP_CMD='test'
+        - python: 2.7
+          env: NUMPY_VERSION=1.7.1 SETUP_CMD='cov'
+
+before_install:
+
+   # Install the pip that supports wheel
+   - pip install setuptools --upgrade
+   - pip install pip --upgrade
+   - pip install wheel
+
+   - sudo apt-get update -qq
+   - sudo apt-get install -qq python-numpy python-scipy
+
+install:
+   - export PYTHONIOENCODING=UTF8 # just in case
+   - $PIP_WHEEL_COMMAND "Cython>=0.18"
+   - $PIP_WHEEL_COMMAND "numpy==$NUMPY_VERSION"
+   - $PIP_WHEEL_COMMAND "scipy>=0.12"
+   - $PIP_WHEEL_COMMAND "matplotlib>=1.3.0"
+   - pip install git+http://github.com/astropy/astropy.git#egg=astropy
+   - pip install atpy
+   - if [[ $SETUP_CMD == cov ]]; then pip install pytest --use-mirrors; fi
+   - if [[ $SETUP_CMD == cov ]]; then pip install pytest-cov --use-mirrors; fi
+   - if [[ $SETUP_CMD == cov ]]; then pip install coveralls --use-mirrors; fi
+
+script:
+   - if [[ $SETUP_CMD == test ]]; then python setup.py test ; fi
+   - if [[ $SETUP_CMD == cov ]]; then py.test --cov sedfitter; fi
+
+after_success:
+  - if [[ $SETUP_CMD == cov ]]; then coveralls; fi
diff --git a/README.md b/README.md
@@ -0,0 +1,13 @@
+About
+-----
+
+This is a Python port of the SED fitter from Robitaille et al. (2006).
+
+It is highly experimental - if you are interested in using it, please contact me.
+
+Status
+------
+
+[![Build Status](https://travis-ci.org/astrofrog/sedfitter.png?branch=refactor-non-affiliated)](https://travis-ci.org/astrofrog/sedfitter)
+
+[![Coverage Status](https://coveralls.io/repos/astrofrog/sedfitter/badge.png)](https://coveralls.io/r/astrofrog/sedfitter)
diff --git a/examples/data_glimpse_ex.par → examples/cli/data_glimpse_ex.par b/examples/data_glimpse_ex.par → examples/cli/data_glimpse_ex.par
diff --git a/examples/ex_law_gl.par → examples/cli/ex_law_gl.par b/examples/ex_law_gl.par → examples/cli/ex_law_gl.par
diff --git a/examples/fitter_stellar_ex.par → examples/cli/fitter_stellar_ex.par b/examples/fitter_stellar_ex.par → examples/cli/fitter_stellar_ex.par
diff --git a/examples/fitter_yso_ex.par → examples/cli/fitter_yso_ex.par b/examples/fitter_yso_ex.par → examples/cli/fitter_yso_ex.par
diff --git a/examples/plot_stellar_ex.par → examples/cli/plot_stellar_ex.par b/examples/plot_stellar_ex.par → examples/cli/plot_stellar_ex.par
diff --git a/examples/plot_yso_ex.par → examples/cli/plot_yso_ex.par b/examples/plot_yso_ex.par → examples/cli/plot_yso_ex.par
diff --git a/examples/python/data_glimpse b/examples/python/data_glimpse
@@ -0,0 +1,10 @@
+SSTGLMC_G009.8925-00.3420        9.89250  -0.34200 1 1 1 1 0 1 0   6.869e+01   6.869e+00   1.512e+02   1.512e+01   1.626e+02   1.626e+01   9.015e+01   9.015e+00  -9.999e+02  -9.999e+02   4.098e+01   4.098e+00  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.8940-00.3367        9.89408  -0.33675 0 0 1 1 0 1 0  -9.999e+02  -9.999e+02  -9.999e+02  -9.999e+02   7.412e+00   7.412e-01   1.199e+01   1.199e+00  -9.999e+02  -9.999e+02   7.582e+00   7.582e-01  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.8943-00.3378        9.89430  -0.33783 0 0 1 1 0 1 0  -9.999e+02  -9.999e+02  -9.999e+02  -9.999e+02   4.462e+00   4.462e-01   6.927e+00   6.927e-01  -9.999e+02  -9.999e+02   4.156e+00   4.156e-01  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.8972-00.3327        9.89720  -0.33274 1 1 1 1 0 0 0   3.099e+00   3.099e-01   5.464e+00   5.464e-01   5.622e+00   5.622e-01   3.237e+00   3.237e-01  -9.999e+02  -9.999e+02   0.000e+00   3.299e-01  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.8989-00.3400        9.89890  -0.34006 0 1 1 1 0 1 0  -9.999e+02  -9.999e+02   2.374e+00   2.374e-01   1.270e+01   1.270e+00   2.234e+01   2.234e+00  -9.999e+02  -9.999e+02   1.525e+01   1.525e+00  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.9005-00.3300        9.90054  -0.33008 0 1 1 1 0 1 0  -9.999e+02  -9.999e+02   4.462e+00   4.462e-01   1.541e+01   1.541e+00   1.875e+01   1.875e+00  -9.999e+02  -9.999e+02   1.198e+01   1.198e+00  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.9006-00.3398        9.90065  -0.33982 0 0 1 1 0 1 0  -9.999e+02  -9.999e+02  -9.999e+02  -9.999e+02   3.203e+00   3.203e-01   4.412e+00   4.412e-01  -9.999e+02  -9.999e+02   3.467e+00   3.467e-01  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.9009-00.3410        9.90098  -0.34107 1 1 1 1 0 1 0   1.562e+00   1.562e-01   5.638e+00   5.638e-01   7.942e+00   7.942e-01   5.876e+00   5.876e-01  -9.999e+02  -9.999e+02   2.579e+00   2.579e-01  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.9047-00.3437        9.90477  -0.34370 0 1 1 1 0 1 0  -9.999e+02  -9.999e+02   2.664e+00   2.664e-01   9.254e+00   9.254e-01   1.137e+01   1.137e+00  -9.999e+02  -9.999e+02   7.529e+00   7.529e-01  -9.999e+02  -9.999e+02 
+SSTGLMC_G009.9048-00.3418        9.90482  -0.34180 1 1 1 1 0 1 0   1.433e+00   1.433e-01   5.359e+00   5.359e-01   7.467e+00   7.467e-01   5.900e+00   5.900e-01  -9.999e+02  -9.999e+02   3.300e+00   3.300e-01  -9.999e+02  -9.999e+02 
diff --git a/examples/python/fit_glimpse.py b/examples/python/fit_glimpse.py
@@ -0,0 +1,51 @@
+import os
+import glob
+
+import matplotlib
+matplotlib.use('Agg')
+
+import sedfitter
+from sedfitter.extinction import Extinction
+
+model_dir = '/Users/tom/Models/models_r06'
+
+# Read in extinction law
+
+extinction = Extinction.from_file('kmh94.par')
+
+# Define filters and apertures
+
+filters = ['2J', '2H', '2K', 'I1', 'I2', 'I3', 'I4']
+
+apertures = [3., 3., 3., 3., 3., 3., 3.]
+
+# Run the fitting
+
+sedfitter.fit('data_glimpse', filters, apertures, model_dir,
+              'output_glimpse.fitinfo',
+              extinction_law=extinction,
+              distance_range=[1., 2.],
+              av_range=[0., 40.],
+              output_format=('F', 3.),
+              output_convolved=False,
+              remove_resolved=True)
+
+sedfitter.plot('output_glimpse.fitinfo',
+               plot_mode='A',
+               output_dir='plots_glimpse',
+               select_format=('F', 2.),
+               format='png',
+               show_convolved=False, show_sed=True,
+               x_mode='M', x_range=(0.1, 2000),
+               y_mode='M', y_range=(1.e-14, 2e-8),
+               plot_max=100)
+
+sedfitter.plot_params_1d('output_glimpse.fitinfo', 'TSTAR',
+                         log_x=True,
+                         output_dir='plots_glimpse_1d',
+                         select_format=('F', 2.), format='png')
+
+sedfitter.plot_params_2d('output_glimpse.fitinfo', 'RSTAR', 'TSTAR',
+                         log_x=True, log_y=True,
+                         output_dir='plots_glimpse_2d',
+                         select_format=('F', 2.), format='png')
diff --git a/examples/python/kmh94.par b/examples/python/kmh94.par
@@ -0,0 +1,95 @@
+  1.1000e-02  1.6907e-13  6.3083e-14  7.0866e+02  7.2517e-01  8.7469e-01  8.4000e+01
+  2.1000e-02  1.6907e-13  6.3083e-14  7.0866e+02  7.2517e-01  8.7469e-01  8.4000e+01
+  3.1000e-02  1.6907e-13  6.3083e-14  7.0866e+02  7.2517e-01  8.7469e-01  8.4000e+01
+  4.1000e-02  1.6907e-13  6.3083e-14  7.0866e+02  7.2517e-01  8.7469e-01  8.4000e+01
+  5.1000e-02  1.6907e-13  6.3083e-14  7.0866e+02  7.2517e-01  8.7469e-01  8.4000e+01
+  6.0000e-02  2.1593e-13  7.8234e-14  9.0510e+02  6.3716e-01  8.5677e-01  8.1000e+01
+  8.0000e-02  3.1374e-13  9.6018e-14  1.3151e+03  5.2803e-01  7.7429e-01  8.0000e+01
+  1.0000e-01  2.5518e-13  8.6322e-14  1.0696e+03  5.2214e-01  6.6856e-01  8.6000e+01
+  1.2000e-01  1.8035e-13  6.8978e-14  7.5594e+02  5.9813e-01  5.2693e-01  9.3000e+01
+  1.5000e-01  1.3558e-13  5.4897e-14  5.6828e+02  6.0663e-01  3.2117e-01  8.9000e+01
+  2.0000e-01  1.4598e-13  6.1280e-14  6.1190e+02  5.4295e-01  3.5688e-01  8.4000e+01
+  2.5000e-01  1.1772e-13  5.9357e-14  4.9343e+02  4.6616e-01  3.5351e-01  8.2000e+01
+  3.0000e-01  9.2127e-14  4.7900e-14  3.8616e+02  4.7858e-01  3.3468e-01  8.8000e+01
+  3.6000e-01  7.9016e-14  4.1493e-14  3.3121e+02  4.8287e-01  3.2713e-01  9.0000e+01
+  4.4000e-01  6.6839e-14  3.5457e-14  2.8016e+02  4.6618e-01  3.6226e-01  9.5000e+01
+  5.5000e-01  5.2771e-14  2.8329e-14  2.2119e+02  4.4278e-01  4.0421e-01  9.5000e+01
+  7.0000e-01  3.8502e-14  2.0279e-14  1.6139e+02  4.0630e-01  4.7766e-01  9.6000e+01
+  8.5000e-01  2.8667e-14  1.4552e-14  1.2016e+02  3.7345e-01  5.3806e-01  9.6000e+01
+  1.0000e+00  2.1881e-14  1.0649e-14  9.1717e+01  3.4632e-01  5.7488e-01  9.6000e+01
+  1.1500e+00  1.7139e-14  7.9881e-15  7.1840e+01  3.2591e-01  5.9122e-01  9.5000e+01
+  1.3000e+00  1.3770e-14  6.1480e-15  5.7718e+01  3.0981e-01  5.9650e-01  9.5000e+01
+  1.7000e+00  8.4820e-15  3.4043e-15  3.5553e+01  2.7907e-01  5.9373e-01  9.4000e+01
+  2.0000e+00  6.3230e-15  2.3542e-15  2.6503e+01  2.5877e-01  5.9986e-01  9.3000e+01
+  2.2000e+00  5.3215e-15  1.8843e-15  2.2306e+01  2.4442e-01  6.0965e-01  9.3000e+01
+  2.7000e+00  3.6806e-15  1.1483e-15  1.5428e+01  2.0745e-01  6.5235e-01  9.2000e+01
+  3.0000e+00  3.0434e-15  8.7778e-16  1.2757e+01  1.8444e-01  6.8078e-01  9.1000e+01
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+  4.5000e+00  1.4706e-15  2.7539e-16  6.1644e+00  8.4705e-02  7.9493e-01  8.9000e+01
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