def __init__(self, gui=False, thd=False):
'''
Create a link with netlogo. Underneath, the netlogo jvm is started
throuhg jpype.
:param gui: boolean, if true run netlogo with gui, otherwise run in
headless mode. Defaults to false.
:param thd: boolean, if thrue start netlogo in 3d mode. Defaults to
false
'''
if not jpype.isJVMStarted():
# netlogo jars
jars = [NETLOGO_HOME + r'/lib/scala-library.jar',
NETLOGO_HOME + r'/lib/asm-all-3.3.1.jar',
NETLOGO_HOME + r'/lib/picocontainer-2.13.6.jar',
NETLOGO_HOME + r'/lib/log4j-1.2.16.jar',
NETLOGO_HOME + r'/lib/jmf-2.1.1e.jar',
NETLOGO_HOME + r'/lib/pegdown-1.1.0.jar',
NETLOGO_HOME + r'/lib/parboiled-core-1.0.2.jar',
NETLOGO_HOME + r'/lib/parboiled-java-1.0.2.jar',
NETLOGO_HOME + r'/lib/mrjadapter-1.2.jar',
NETLOGO_HOME + r'/lib/jhotdraw-6.0b1.jar',
NETLOGO_HOME + r'/lib/quaqua-7.3.4.jar',
NETLOGO_HOME + r'/lib/swing-layout-7.3.4.jar',
NETLOGO_HOME + r'/lib/jogl-1.1.1.jar',
NETLOGO_HOME + r'/lib/gluegen-rt-1.1.1.jar',
NETLOGO_HOME + r'/NetLogo.jar',
PYNETLOGO_HOME + r'/external_files/netlogoLink.jar']
# format jars in right format for starting java virtual machine
# TODO the use of the jre here is only relevant under windows
# apparently
# might be solvable by setting netlogo home user.dir
joined_jars = jar_separator.join(jars)
jarpath = '-Djava.class.path={}'.format(joined_jars)
jvm_handle = jpype.getDefaultJVMPath()
jpype.startJVM(jvm_handle, jarpath, "-Xms128M","-Xmx1024m")
jpype.java.lang.System.setProperty('user.dir', NETLOGO_HOME)
if sys.platform=='darwin':
jpype.java.lang.System.setProperty("java.awt.headless", "true");
debug("jvm started")
link = jpype.JClass('netlogoLink.NetLogoLink')
debug('NetLogoLink class found')
if sys.platform == 'darwin' and gui:
info('on mac only headless mode is supported')
gui=False
self.link = link(gui, thd)
debug('NetLogoLink class instantiated')
def find_box(self):
'''
Execute one iteration of the PRIM algorithm. That is, find one
box, starting from the current state of Prim.
'''
# set the indices
self._update_yi_remaining()
if self.yi_remaining.shape[0] == 0:
info("no data remaining")
return
# log how much data and how many coi are remaining
info(self.message.format(self.yi_remaining.shape[0],
self.determine_coi(self.yi_remaining)))
# make a new box that contains all the remaining data points
box = PrimBox(self, self.box_init, self.yi_remaining[:])
# perform peeling phase
box = self._peel(box)
debug("peeling completed")
# perform pasting phase
box = self._paste(box)
debug("pasting completed")
message = "mean: {0}, mass: {1}, coverage: {2}, density: {3} restricted_dimensions: {4}"
message = message.format(box.mean[-1],
box.mass[-1],
box.coverage[-1],
box.density[-1],
box.res_dim[-1])
if (self.threshold_type==ABOVE) &\
(box.mean[-1] >= self.threshold):
info(message)
self.boxes.append(box)
return box
elif (self.threshold_type==BELOW) &\
(box.mean[-1] <= self.threshold):
info(message)
self.boxes.append(box)
return box
else:
# make a dump box
info('box does not meet threshold criteria, value is {}, returning dump box'.format(box.mean[-1]))
box = PrimBox(self, self.box_init, self.yi_remaining[:])
self.boxes.append(box)
return box
def __filter(boxes, uncertainties=[]):
dump_box=boxes[-1]
boxes=boxes[0:-1]
uv=uncertainties
#iterate over uncertainties
names = []
if uncertainties:
uv=uncertainties
else:
uv = [entry[0] for entry in dump_box.dtype.descr]
for name in uv:
#determine whether to show
for box in boxes:
minimum = box[name][0]
maximum = box[name][1]
value = box.dtype.fields.get(name)[0]
if value == 'object':
a = dump_box[name][0]
if len(a) != len(minimum):
ans = False
else:
ans = np.all(np.equal(a, minimum))
if not ans:
names.append(name)
break
elif (minimum > dump_box[name][0]) or\
(maximum < dump_box[name][1]):
names.append(name)
break
a = set(uv) -set(names)
a = list(a)
a.sort()
string_list = ", ".join(a)
info(string_list + " are not not visualized because they are not restricted")
uv = names
return uv
def perform_prim(results,
classify,
peel_alpha = 0.05,
paste_alpha = 0.05,
mass_min = 0.05,
threshold = None,
pasting=True,
threshold_type=1,
obj_func=def_obj_func):
r'''
perform Patient Rule Induction Method (PRIM). This function performs
the PRIM algorithm on the data. It uses a Python implementation of PRIM
inspired by the `R <http://www.oga-lab.net/RGM2/func.php?rd_id=prim:prim-package>`_
algorithm. Compared to the R version, the Python version is data type aware.
That is, real valued, ordinal, and categorical data are treated
differently. Moreover, the pasting phase of PRIM in the R algorithm is
not consistent with the literature. The Python version is.
the PRIM algorithm tries to find subspaces of the input space that share
some characteristic in the output space. The characteristic that the
current implementation looks at is the mean of the results. Thus, the
output space is 1-D, and the characteristic is assumed to be continuous.
As a work around, to deal with classes, the user can supply a classify
function. This function should return a binary classification
(i.e. 1 or 0). Then, the mean of the box is indicative of the concentration
of cases of class 1. That is, if the specified threshold is say 0.8 and the
threshold_type is 1, PRIM looks for subspaces of the input space that
contains at least 80\% cases of class 1.
:param results: the return from :meth:`perform_experiments`.
:param classify: either a string denoting the outcome of interest to use
or a function. In case of a string and time series data,
the end state is used.
:param peel_alpha: parameter controlling the peeling stage (default = 0.05).
:param paste_alpha: parameter controlling the pasting stage (default = 0.05).
:param mass_min: minimum mass of a box (default = 0.05).
:param threshold: the threshold of the output space that boxes should meet.
:param pasting: perform pasting stage (default=True)
:param threshold_type: If 1, the boxes should go above the threshold, if -1
the boxes should go below the threshold, if 0, the
algorithm looks for both +1 and -1.
:param obj_func: The objective function to use. Default is
:func:`def_obj_func`
:return: a list of PRIM objects.
for each box, the scenario discovery metrics *coverage* and *density*
are also calculated:
.. math::
coverage=\frac
{{\displaystyle\sum_{y_{i}\in{B}}y_{i}{'}}}
{{\displaystyle\sum_{y_{i}\in{B^I}}y_{i}{'}}}
where :math:`y_{i}{'}=1` if :math:`x_{i}\in{B}` and :math:`y_{i}{'}=0`
otherwise.
.. math::
density=\frac
{{\displaystyle\sum_{y_{i}\in{B}}y_{i}{'}}}
{{\displaystyle\left|{y_{i}}\right|\in{B}}}
where :math:`y_{i}{'}=1` if :math:`x_{i}\in{B}` and :math:`y_{i}{'}=0`
otherwise, and :math:`{\displaystyle\left|{y_{i}}\right|\in{B}}` is the
cardinality of :math:`y_{i}`.
Density is the ratio of the cases of interest in a box to the
total number of cases in that box. *density* is identical to the mean
in case of a binary classification. For more detail on these metrics see
`Bryant and Lempert (2010) <http://www.sciencedirect.com/science/article/pii/S004016250900105X>`_
.. rubric:: references to relevant papers
* `original PRIM paper <http://www.springerlink.com/content/x3gpv05t34620878/>`_
* `paper on ordinal data and PRIM <http://www.sciencedirect.com/science/article/pii/S095741740700231X>`_
**ema application**
* `Lempert et al. (2006) <http://mansci.journal.informs.org/content/52/4/514>`_
* `Groves and Lempert (2007) <http://www.sciencedirect.com/science/article/pii/S0959378006000896#ref_bib19>`_
* `Bryant and Lempert (2010) <http://www.sciencedirect.com/science/article/pii/S004016250900105X>`_
'''
experiments, results = results
#make y
if type(classify) == StringType:
results = results.get(classify)
if len(results.shape) == 2:
y = results[:, -1]
else:
y = results
count = np.zeros(y.shape)
count[y*threshold_type > threshold*threshold_type] = 1
cases_of_interest = np.sum(count)
info("number of cases of interest is %d" % (np.sum(count)))
elif callable(classify):
y = classify(results)
cases_of_interest = np.sum(y)
info("number of cases of interest is %d" % (np.sum(y)))
else:
raise EMAError("incorrect specification of classify, this should be a function or a string")
x = experiments
#perform prim
boxes = recursivePrim.perform_prim(x, y, box_init=None, peel_alpha=peel_alpha,
paste_alpha=paste_alpha, mass_min=mass_min,
threshold=threshold, pasting=pasting,
threshold_type=threshold_type,obj_func=obj_func,
cases_of_interest=cases_of_interest)
#calculate scenario discovery metrics and add these to boxes
boxes = calculate_sd_metrics(boxes, y, threshold, threshold_type)
#return prim
return boxes