refactoring

Author: matley

.gitignore

@@ -1,2 +1,5 @@
 *.pyc
 *.DS_Store
+\#*\#
+last_test_run.log
+.coverage

pylintrc

@@ -0,0 +1,210 @@
+[MASTER]
+
+# Specify a configuration file.
+#rcfile=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+init-hook=import sys; sys.path.append('/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/')
+
+# Profiled execution.
+profile=no
+
+# Add <file or directory> to the black list. It should be a base name, not a
+# path. You may set this option multiple times.
+ignore=CVS
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+
+[MESSAGES CONTROL]
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time.
+#enable=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifier separated by comma (,) or put this option
+# multiple time.
+#disable=
+
+
+[REPORTS]
+
+# Set the output format. Available formats are text, parseable, colorized, msvs
+# (visual studio) and html
+output-format=text
+
+# Include message's id in output
+include-ids=yes
+
+# Put messages in a separate file for each module / package specified on the
+# command line instead of printing them on stdout. Reports (if any) will be
+# written in a file name "pylint_global.[txt|html]".
+files-output=no
+
+# Tells whether to display a full report or only the messages
+reports=yes
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (R0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Add a comment according to your evaluation note. This is used by the global
+# evaluation report (R0004).
+comment=no
+
+
+[BASIC]
+
+# Variable names can be 1 to 31 characters long, with lowercase and underscores
+variable-rgx=[a-z_][a-z0-9_]{0,30}$
+
+# Argument names can be 2 to 31 characters long, with lowercase and underscores
+argument-rgx=[a-z_][a-z0-9_]{1,30}$
+
+# Method names should be at least 3 characters long
+# and be lowecased with underscores
+method-rgx=[a-z_][a-z0-9_]{2,50}$
+
+# Module names matching nova-* are ok (files in bin/)
+#module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+)|(nova-[a-z0-9_-]+))$
+
+# Don't require docstrings on tests.
+no-docstring-rgx=((__.*__)|([tT]est.*)|setUp|tearDown)$
+
+
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+max-line-length=100
+
+# Maximum number of lines in a module
+max-module-lines=1000
+
+# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
+# tab).
+indent-string='    '
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,XXX,TODO
+
+
+[SIMILARITIES]
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+
+[TYPECHECK]
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+#ignore-mixin-members=yes
+
+# List of classes names for which member attributes should not be checked
+# (useful for classes with attributes dynamically set).
+ignored-classes=SQLObject
+
+# When zope mode is activated, add a predefined set of Zope acquired attributes
+# to generated-members.
+zope=no
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E0201 when accessed.
+generated-members=REQUEST,acl_users,aq_parent
+
+
+[VARIABLES]
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# A regular expression matching names used for dummy variables (i.e. not used).
+dummy-variables-rgx=_|dummy
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+additional-builtins=
+
+
+[CLASSES]
+
+# List of interface methods to ignore, separated by a comma. This is used for
+# instance to not check methods defines in Zope's Interface base class.
+ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,__new__,setUp
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method
+max-args=5
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names=_.*
+
+# Maximum number of locals for function / method body
+max-locals=15
+
+# Maximum number of return / yield for function / method body
+max-returns=6
+
+# Maximum number of branch for function / method body
+max-branchs=12
+
+# Maximum number of statements in function / method body
+max-statements=50
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=0
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+
+[IMPORTS]
+
+# Deprecated modules which should not be used, separated by a comma
+deprecated-modules=regsub,string,TERMIOS,Bastion,rexec
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled)
+import-graph=import-graph.png
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled)
+ext-import-graph=ext-graph.png
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled)
+int-import-graph=int-graph.png

risklib/scenario_damage/fragility_function.py

@@ -0,0 +1,59 @@
+# coding=utf-8
+# Copyright (c) 2010-2012, GEM Foundation.
+#
+# OpenQuake is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# OpenQuake is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with OpenQuake.  If not, see <http://www.gnu.org/licenses/>.
+
+
+from scipy.stats import lognorm
+from scipy.interpolate import interp1d
+import math
+
+
+def poe(fragility_function, iml):
+    """
+    Compute the Probability of Exceedance (PoE) for the given
+    Intensity Measure Level (IML).
+    """
+    if fragility_function.is_discrete:
+        return poe_discrete(fragility_function, iml)
+    else:
+        return poe_continuous(fragility_function, iml)
+
+
+def poe_discrete(fragility_function, iml):
+    fm = fragility_function.fragility_model
+
+    highest_iml = fm.imls[-1]
+    no_damage_limit = fm.no_damage_limit
+
+    # when the intensity measure level is above
+    # the range, we use the highest one
+    if iml > highest_iml:
+        iml = highest_iml
+
+    imls = [no_damage_limit] + fm.imls
+    poes = [0.0] + fragility_function.poes
+
+    return interp1d(imls, poes)(iml)
+
+
+def poe_continuous(fragility_function, iml):
+    variance = fragility_function.stddev ** 2.0
+    sigma = math.sqrt(math.log(
+        (variance / fragility_function.mean ** 2.0) + 1.0))
+
+    mu = fragility_function.mean ** 2.0 / math.sqrt(
+        variance + fragility_function.mean ** 2.0)
+
+    return lognorm.cdf(iml, sigma, scale=mu)

risklib/scenario_damage/fragility_model.py

@@ -0,0 +1,52 @@
+# coding=utf-8
+# Copyright (c) 2010-2012, GEM Foundation.
+#
+# OpenQuake is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# OpenQuake is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with OpenQuake.  If not, see <http://www.gnu.org/licenses/>.
+
+
+NO_DAMAGE_STATE = "no_damage"
+
+
+def damage_states(fragility_model):
+    """
+    Return the damage states from the given limit states.
+
+    For N limit states in the fragility model, we always
+    define N+1 damage states. The first damage state
+    should always be 'no_damage'.
+
+    :param fragility_model A Fragility Model object which support a
+      property `lss` containing an iterator over limit states
+    """
+
+    dmg_states = list(fragility_model.lss)
+    dmg_states.insert(0, NO_DAMAGE_STATE)
+
+    return dmg_states
+
+
+def no_damage(fragility_model, gmv):
+    """
+    There is no damage when ground motions values are less
+    than the first iml or when the no damage limit value
+    is greater than the ground motions value.
+    """
+
+    discrete = fragility_model.format == "discrete"
+    no_damage_limit = fragility_model.no_damage_limit is not None
+
+    return ((discrete and not no_damage_limit and
+             gmv < fragility_model.imls[0]) or
+            (discrete and no_damage_limit and
+             gmv < fragility_model.no_damage_limit))