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In [1]:



    


%matplotlib inline
from galaxy_analysis.plot.plot_styles import *
####
import numpy as np
import matplotlib.pyplot as plt
from galaxy_analysis.analysis import Galaxy
from sklearn.decomposition import PCA
import yt



    


















    






/home/aemerick/anaconda2/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
/home/aemerick/code/galaxy_analysis/particle_analysis/IMF.py:2: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py", line 16, in <module>
    app.launch_new_instance()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelapp.py", line 477, in start
    ioloop.IOLoop.instance().start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/ioloop.py", line 177, in start
    super(ZMQIOLoop, self).start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/ioloop.py", line 888, in start
    handler_func(fd_obj, events)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 440, in _handle_events
    self._handle_recv()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 472, in _handle_recv
    self._run_callback(callback, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 414, in _run_callback
    callback(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
    return self.dispatch_shell(stream, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
    handler(stream, idents, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
    user_expressions, allow_stdin)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/ipkernel.py", line 196, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2718, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2822, in run_ast_nodes
    if self.run_code(code, result):
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2882, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-5b2393a95dde>", line 1, in <module>
    get_ipython().magic(u'matplotlib inline')
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2160, in magic
    return self.run_line_magic(magic_name, magic_arg_s)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2081, in run_line_magic
    result = fn(*args,**kwargs)
  File "<decorator-gen-105>", line 2, in matplotlib
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magic.py", line 188, in <lambda>
    call = lambda f, *a, **k: f(*a, **k)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magics/pylab.py", line 100, in matplotlib
    gui, backend = self.shell.enable_matplotlib(args.gui)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2950, in enable_matplotlib
    pt.activate_matplotlib(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/pylabtools.py", line 308, in activate_matplotlib
    matplotlib.pyplot.switch_backend(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 229, in switch_backend
    matplotlib.use(newbackend, warn=False, force=True)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py", line 1305, in use
    reload(sys.modules['matplotlib.backends'])
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 14, in <module>
    line for line in traceback.format_stack()


  mpl.use('Agg')
/home/aemerick/code/galaxy_analysis/particle_analysis/sfrFromParticles.py:4: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py", line 16, in <module>
    app.launch_new_instance()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelapp.py", line 477, in start
    ioloop.IOLoop.instance().start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/ioloop.py", line 177, in start
    super(ZMQIOLoop, self).start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/ioloop.py", line 888, in start
    handler_func(fd_obj, events)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 440, in _handle_events
    self._handle_recv()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 472, in _handle_recv
    self._run_callback(callback, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 414, in _run_callback
    callback(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
    return self.dispatch_shell(stream, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
    handler(stream, idents, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
    user_expressions, allow_stdin)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/ipkernel.py", line 196, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2718, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2822, in run_ast_nodes
    if self.run_code(code, result):
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2882, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-5b2393a95dde>", line 1, in <module>
    get_ipython().magic(u'matplotlib inline')
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2160, in magic
    return self.run_line_magic(magic_name, magic_arg_s)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2081, in run_line_magic
    result = fn(*args,**kwargs)
  File "<decorator-gen-105>", line 2, in matplotlib
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magic.py", line 188, in <lambda>
    call = lambda f, *a, **k: f(*a, **k)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magics/pylab.py", line 100, in matplotlib
    gui, backend = self.shell.enable_matplotlib(args.gui)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2950, in enable_matplotlib
    pt.activate_matplotlib(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/pylabtools.py", line 308, in activate_matplotlib
    matplotlib.pyplot.switch_backend(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 229, in switch_backend
    matplotlib.use(newbackend, warn=False, force=True)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py", line 1305, in use
    reload(sys.modules['matplotlib.backends'])
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 14, in <module>
    line for line in traceback.format_stack()


  mpl.use('Agg')
/home/aemerick/code/galaxy_analysis/particle_analysis/sn_rate.py:4: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py", line 16, in <module>
    app.launch_new_instance()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelapp.py", line 477, in start
    ioloop.IOLoop.instance().start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/ioloop.py", line 177, in start
    super(ZMQIOLoop, self).start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/ioloop.py", line 888, in start
    handler_func(fd_obj, events)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 440, in _handle_events
    self._handle_recv()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 472, in _handle_recv
    self._run_callback(callback, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 414, in _run_callback
    callback(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
    return self.dispatch_shell(stream, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
    handler(stream, idents, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
    user_expressions, allow_stdin)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/ipkernel.py", line 196, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2718, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2822, in run_ast_nodes
    if self.run_code(code, result):
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2882, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-5b2393a95dde>", line 1, in <module>
    get_ipython().magic(u'matplotlib inline')
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2160, in magic
    return self.run_line_magic(magic_name, magic_arg_s)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2081, in run_line_magic
    result = fn(*args,**kwargs)
  File "<decorator-gen-105>", line 2, in matplotlib
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magic.py", line 188, in <lambda>
    call = lambda f, *a, **k: f(*a, **k)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magics/pylab.py", line 100, in matplotlib
    gui, backend = self.shell.enable_matplotlib(args.gui)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2950, in enable_matplotlib
    pt.activate_matplotlib(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/pylabtools.py", line 308, in activate_matplotlib
    matplotlib.pyplot.switch_backend(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 229, in switch_backend
    matplotlib.use(newbackend, warn=False, force=True)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py", line 1305, in use
    reload(sys.modules['matplotlib.backends'])
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 14, in <module>
    line for line in traceback.format_stack()


  mpl.use('Agg')
/home/aemerick/code/galaxy_analysis/particle_analysis/sfhFromParticles.py:4: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py", line 16, in <module>
    app.launch_new_instance()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelapp.py", line 477, in start
    ioloop.IOLoop.instance().start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/ioloop.py", line 177, in start
    super(ZMQIOLoop, self).start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/ioloop.py", line 888, in start
    handler_func(fd_obj, events)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 440, in _handle_events
    self._handle_recv()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 472, in _handle_recv
    self._run_callback(callback, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 414, in _run_callback
    callback(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
    return self.dispatch_shell(stream, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
    handler(stream, idents, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
    user_expressions, allow_stdin)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/ipkernel.py", line 196, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2718, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2822, in run_ast_nodes
    if self.run_code(code, result):
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2882, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-5b2393a95dde>", line 1, in <module>
    get_ipython().magic(u'matplotlib inline')
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2160, in magic
    return self.run_line_magic(magic_name, magic_arg_s)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2081, in run_line_magic
    result = fn(*args,**kwargs)
  File "<decorator-gen-105>", line 2, in matplotlib
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magic.py", line 188, in <lambda>
    call = lambda f, *a, **k: f(*a, **k)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magics/pylab.py", line 100, in matplotlib
    gui, backend = self.shell.enable_matplotlib(args.gui)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2950, in enable_matplotlib
    pt.activate_matplotlib(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/pylabtools.py", line 308, in activate_matplotlib
    matplotlib.pyplot.switch_backend(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 229, in switch_backend
    matplotlib.use(newbackend, warn=False, force=True)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py", line 1305, in use
    reload(sys.modules['matplotlib.backends'])
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 14, in <module>
    line for line in traceback.format_stack()


  mpl.use('Agg')
/home/aemerick/code/galaxy_analysis/plot/plot_styles.py:7: UserWarning: 
This call to matplotlib.use() has no effect because the backend has already
been chosen; matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

The backend was *originally* set to 'module://ipykernel.pylab.backend_inline' by the following code:
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/aemerick/anaconda2/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py", line 16, in <module>
    app.launch_new_instance()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelapp.py", line 477, in start
    ioloop.IOLoop.instance().start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/ioloop.py", line 177, in start
    super(ZMQIOLoop, self).start()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/ioloop.py", line 888, in start
    handler_func(fd_obj, events)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 440, in _handle_events
    self._handle_recv()
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 472, in _handle_recv
    self._run_callback(callback, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 414, in _run_callback
    callback(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper
    return fn(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher
    return self.dispatch_shell(stream, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
    handler(stream, idents, msg)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
    user_expressions, allow_stdin)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/ipkernel.py", line 196, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2718, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2822, in run_ast_nodes
    if self.run_code(code, result):
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2882, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-5b2393a95dde>", line 1, in <module>
    get_ipython().magic(u'matplotlib inline')
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2160, in magic
    return self.run_line_magic(magic_name, magic_arg_s)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2081, in run_line_magic
    result = fn(*args,**kwargs)
  File "<decorator-gen-105>", line 2, in matplotlib
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magic.py", line 188, in <lambda>
    call = lambda f, *a, **k: f(*a, **k)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/magics/pylab.py", line 100, in matplotlib
    gui, backend = self.shell.enable_matplotlib(args.gui)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2950, in enable_matplotlib
    pt.activate_matplotlib(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/IPython/core/pylabtools.py", line 308, in activate_matplotlib
    matplotlib.pyplot.switch_backend(backend)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 229, in switch_backend
    matplotlib.use(newbackend, warn=False, force=True)
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/__init__.py", line 1305, in use
    reload(sys.modules['matplotlib.backends'])
  File "/home/aemerick/anaconda2/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 14, in <module>
    line for line in traceback.format_stack()


  mpl.use('Agg')

















In [6]:



    


#
# Load the data set and get all defined abundance ratios
#
gal = Galaxy('DD0619', wdir="/home/aemerick/work/enzo_runs/sn_H2atten_H2sh/")
derived_fields = gal.ds.derived_field_list
all_abundance_fields = [x[1] for x in derived_fields if (('particle_' in x[1]) and ('_over_' in x[1]))]



    


















    






Parsing Hierarchy : 100%|██████████| 422/422 [00:00<00:00, 46235.73it/s]

















In [6]:



    


gal.df['particle_O_fraction']



    


















    
Out[6]:








YTArray([3.98402921e-28, 3.98402921e-28, 1.73634694e-11, ...,
         2.67069546e-09, 2.67069546e-09, 9.50525643e-06]) (dimensionless)

















In [7]:



    


#
# Now gather all of the particle data for all main sequence stars:
#
select = (gal.df['creation_time'] > 100.0*yt.units.Myr) * (gal.df['creation_time'] < 1000.0*yt.units.Myr)

# for testing
#abundance_fields = ['particle_O_over_Fe','particle_Mg_over_Fe','particle_N_over_Fe','particle_Ba_over_Fe']

abundance_fields = [x for x in all_abundance_fields if '_over_Fe' in x]

dtype = [ (x,'f8') for x in abundance_fields ]

get_field = lambda name : gal.df[('io',name)][select].value
all_data  = np.array( map( get_field, abundance_fields )) # , dtype = dtype)
#all_data = np.zeros( len(gal.df['particle_type'][select]) , dtype = {'names':abundance_fields, 'formats':['f8']*len(abundance_fields)})
#
#for field in abundance_fields:
#    all_data[field] = get_field(field)
print np.shape(all_data)



    


















    






(16, 19259)

















In [8]:



    


from sklearn.preprocessing import StandardScaler
scaled_data = StandardScaler().fit_transform(all_data)



    











In [9]:



    


pca = PCA(n_components=len(abundance_fields))
pca.fit(scaled_data)
print pca.explained_variance_ratio_



    


















    






[7.81560980e-01 1.62047757e-01 3.18037391e-02 1.55734024e-02
 3.89135457e-03 1.97210217e-03 1.10958169e-03 7.87511807e-04
 6.70461618e-04 3.00246758e-04 2.36360929e-04 2.57211760e-05
 1.75243110e-05 3.17111413e-06 8.55731294e-08 5.37435001e-32]

















In [104]:



    


pca.score(



    


















    






/home/aemerick/anaconda2/lib/python2.7/site-packages/sklearn/decomposition/base.py:73: RuntimeWarning: divide by zero encountered in divide
  precision = np.dot(components_, components_.T) / self.noise_variance_
/home/aemerick/anaconda2/lib/python2.7/site-packages/sklearn/decomposition/base.py:73: RuntimeWarning: invalid value encountered in divide
  precision = np.dot(components_, components_.T) / self.noise_variance_










    






---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-104-22f9e4890b4c> in <module>()
----> 1 pca.score(scaled_data)

/home/aemerick/anaconda2/lib/python2.7/site-packages/sklearn/decomposition/pca.pyc in score(self, X, y)
    562             Average log-likelihood of the samples under the current model
    563         """
--> 564         return np.mean(self.score_samples(X))
    565 
    566 

/home/aemerick/anaconda2/lib/python2.7/site-packages/sklearn/decomposition/pca.pyc in score_samples(self, X)
    537         n_features = X.shape[1]
    538         log_like = np.zeros(X.shape[0])
--> 539         precision = self.get_precision()
    540         log_like = -.5 * (Xr * (np.dot(Xr, precision))).sum(axis=1)
    541         log_like -= .5 * (n_features * log(2. * np.pi) -

/home/aemerick/anaconda2/lib/python2.7/site-packages/sklearn/decomposition/base.pyc in get_precision(self)
     74         precision.flat[::len(precision) + 1] += 1. / exp_var_diff
     75         precision = np.dot(components_.T,
---> 76                            np.dot(linalg.inv(precision), components_))
     77         precision /= -(self.noise_variance_ ** 2)
     78         precision.flat[::len(precision) + 1] += 1. / self.noise_variance_

/home/aemerick/anaconda2/lib/python2.7/site-packages/scipy/linalg/basic.pyc in inv(a, overwrite_a, check_finite)
    945 
    946     """
--> 947     a1 = _asarray_validated(a, check_finite=check_finite)
    948     if len(a1.shape) != 2 or a1.shape[0] != a1.shape[1]:
    949         raise ValueError('expected square matrix')

/home/aemerick/anaconda2/lib/python2.7/site-packages/scipy/_lib/_util.pyc in _asarray_validated(a, check_finite, sparse_ok, objects_ok, mask_ok, as_inexact)
    236             raise ValueError('masked arrays are not supported')
    237     toarray = np.asarray_chkfinite if check_finite else np.asarray
--> 238     a = toarray(a)
    239     if not objects_ok:
    240         if a.dtype is np.dtype('O'):

/home/aemerick/anaconda2/lib/python2.7/site-packages/numpy/lib/function_base.pyc in asarray_chkfinite(a, dtype, order)
   1231     if a.dtype.char in typecodes['AllFloat'] and not np.isfinite(a).all():
   1232         raise ValueError(
-> 1233             "array must not contain infs or NaNs")
   1234     return a
   1235 

ValueError: array must not contain infs or NaNs
















In [51]:



    


order = []
for i, x in enumerate(all_data):
    for y in top_five:
        if np.allclose(x,y):
            order += [i]



    











In [52]:



    


top_five



    


















    
Out[52]:








array([[ 1.86140727e-02,  1.86140727e-02, -7.67567152e-03, ...,
        -5.82941054e-03, -5.82941054e-03, -8.44704018e-03],
       [ 5.57655910e-03,  5.57655910e-03,  1.00452428e-02, ...,
         1.38801371e-02,  1.38801371e-02, -2.77208113e-03],
       [-1.06244542e-02, -1.06244542e-02, -4.58814744e-02, ...,
         1.80957185e-04,  1.80957185e-04, -4.82401029e-04],
       [-5.31198295e-01,  1.74699972e-02,  8.44005456e-01, ...,
        -5.93670436e-04,  1.03935126e-04, -1.38739042e-04]])

















In [54]:



    


PCA.transform?



    











In [ ]:

Content source: aemerick/galaxy_analysis

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