redo

LICENSE.txt

@@ -0,0 +1,19 @@
+ PyHum
+
+ Written by Daniel Buscombe
+ while at
+ Grand Canyon Monitoring and Research Center, U.G. Geological Survey, Flagstaff, AZ 
+ please contact:
+ [email protected]
+ for latest code version please visit:
+ https://github.com/dbuscombe-usgs
+
+====================================
+   This function is part of PyHum software
+   This software is in the public domain because it contains materials that originally came 
+   from the United States Geological Survey, an agency of the United States Department of Interior. 
+   For more information, see the official USGS copyright policy at 
+   http://www.usgs.gov/visual-id/credit_usgs.html#copyright
+
+Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. government. 
+====================================

MANIFEST

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+# file GENERATED by distutils, do NOT edit
+setup.cfg
+setup.py
+PyHum/B000.IDX
+PyHum/B000.SON
+PyHum/B001.IDX
+PyHum/B001.SON
+PyHum/B002.IDX
+PyHum/B002.SON
+PyHum/B003.IDX
+PyHum/B003.SON
+PyHum/RunningStats.cpp
+PyHum/RunningStats.h
+PyHum/RunningStats.py
+PyHum/RunningStats_wrap.cxx
+PyHum/__init__.py
+PyHum/_gui.py
+PyHum/_pyhum_correct.py
+PyHum/_pyhum_e1e2.py
+PyHum/_pyhum_map.py
+PyHum/_pyhum_map_texture.py
+PyHum/_pyhum_mosaic.py
+PyHum/_pyhum_mosaic_texture.py
+PyHum/_pyhum_read.py
+PyHum/_pyhum_rmshadows.py
+PyHum/_pyhum_texture.py
+PyHum/cwt.pyx
+PyHum/d_conc.txt
+PyHum/dat2mat.py
+PyHum/getxy.pyx
+PyHum/io.py
+PyHum/ppdrc.pyx
+PyHum/pyhum_logo_white_sm.png
+PyHum/pyread.pyx
+PyHum/pyread_single.pyx
+PyHum/replace_nans.pyx
+PyHum/spec_noise.pyx
+PyHum/stdev.pyx
+PyHum/test.DAT
+PyHum/test.py
+PyHum/utils.py
+PyHum/write.pyx

PKG-INFO

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+Metadata-Version: 1.0
+Name: PyHum
+Version: 1.0
+Summary: a description
+Home-page: https://github.com/dbuscombe-usgs/PyHum
+Author: Daniel Buscombe
+Author-email: [email protected]
+License: GPL
+Description: PyHum
+
+Keywords: meshing
+Platform: UNKNOWN
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.2
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Topic :: Scientific/Engineering :: Mathematics

PyHum/RunningStats.cpp

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+/* http://www.johndcook.com/blog/skewness_kurtosis/ */
+#include "RunningStats.h"
+#include <cmath>
+#include <vector>
+
+RunningStats::RunningStats() 
+{
+    Clear();
+}
+
+void RunningStats::Clear()
+{
+    n = 0;
+    M1 = M2 = M3 = M4 = 0.0;
+}
+
+void RunningStats::Push(double x)
+{
+    double delta, delta_n, delta_n2, term1;
+
+    long long n1 = n;
+    n++;
+    delta = x - M1;
+    delta_n = delta / n;
+    delta_n2 = delta_n * delta_n;
+    term1 = delta * delta_n * n1;
+    M1 += delta_n;
+    M4 += term1 * delta_n2 * (n*n - 3*n + 3) + 6 * delta_n2 * M2 - 4 * delta_n * M3;
+    M3 += term1 * delta_n * (n - 2) - 3 * delta_n * M2;
+    M2 += term1;
+}
+
+long long RunningStats::NumDataValues() const
+{
+    return n;
+}
+
+double RunningStats::Mean() const
+{
+    return M1;
+}
+
+double RunningStats::Variance() const
+{
+    return M2/(n-1.0);
+}
+
+double RunningStats::StandardDeviation() const
+{
+    return sqrt( Variance() );
+}
+
+double RunningStats::Skewness() const
+{
+    return sqrt(double(n)) * M3/ pow(M2, 1.5);
+}
+
+double RunningStats::Kurtosis() const
+{
+    return double(n)*M4 / (M2*M2) - 3.0;
+}
+
+RunningStats operator+(const RunningStats a, const RunningStats b)
+{
+    RunningStats combined;
+
+    combined.n = a.n + b.n;
+
+    double delta = b.M1 - a.M1;
+    double delta2 = delta*delta;
+    double delta3 = delta*delta2;
+    double delta4 = delta2*delta2;
+
+    combined.M1 = (a.n*a.M1 + b.n*b.M1) / combined.n;
+
+    combined.M2 = a.M2 + b.M2 + 
+                  delta2 * a.n * b.n / combined.n;
+
+    combined.M3 = a.M3 + b.M3 + 
+                  delta3 * a.n * b.n * (a.n - b.n)/(combined.n*combined.n);
+    combined.M3 += 3.0*delta * (a.n*b.M2 - b.n*a.M2) / combined.n;
+
+    combined.M4 = a.M4 + b.M4 + delta4*a.n*b.n * (a.n*a.n - a.n*b.n + b.n*b.n) / 
+                  (combined.n*combined.n*combined.n);
+    combined.M4 += 6.0*delta2 * (a.n*a.n*b.M2 + b.n*b.n*a.M2)/(combined.n*combined.n) + 
+                  4.0*delta*(a.n*b.M3 - b.n*a.M3) / combined.n;
+
+    return combined;
+}
+
+RunningStats& RunningStats::operator+=(const RunningStats& rhs)
+{ 
+        RunningStats combined = *this + rhs;
+        *this = combined;
+        return *this;
+}

PyHum/RunningStats.h

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+/* http://www.johndcook.com/blog/skewness_kurtosis/ */
+#ifndef RUNNINGSTATS_H
+#define RUNNINGSTATS_H
+
+class RunningStats
+{
+public:
+    RunningStats();
+    void Clear();
+    void Push(double x);
+    long long NumDataValues() const;
+    double Mean() const;
+    double Variance() const;
+    double StandardDeviation() const;
+    double Skewness() const;
+    double Kurtosis() const;
+
+    friend RunningStats operator+(const RunningStats a, const RunningStats b);
+    RunningStats& operator+=(const RunningStats &rhs);
+
+private:
+    long long n;
+    double M1, M2, M3, M4;
+};
+
+#endif

PyHum/RunningStats.i

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+/* File: RunningStats.i */
+%module RunningStats
+
+%{
+#define SWIG_FILE_WITH_INIT
+#include "RunningStats.h"
+%}
+
+%include "RunningStats.h"

PyHum/RunningStats.py

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+# This file was automatically generated by SWIG (http://www.swig.org).
+# Version 2.0.11
+#
+# Do not make changes to this file unless you know what you are doing--modify
+# the SWIG interface file instead.
+
+
+
+
+
+from sys import version_info
+if version_info >= (2,6,0):
+    def swig_import_helper():
+        from os.path import dirname
+        import imp
+        fp = None
+        try:
+            fp, pathname, description = imp.find_module('_RunningStats', [dirname(__file__)])
+        except ImportError:
+            import _RunningStats
+            return _RunningStats
+        if fp is not None:
+            try:
+                _mod = imp.load_module('_RunningStats', fp, pathname, description)
+            finally:
+                fp.close()
+            return _mod
+    _RunningStats = swig_import_helper()
+    del swig_import_helper
+else:
+    import _RunningStats
+del version_info
+try:
+    _swig_property = property
+except NameError:
+    pass # Python < 2.2 doesn't have 'property'.
+def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
+    if (name == "thisown"): return self.this.own(value)
+    if (name == "this"):
+        if type(value).__name__ == 'SwigPyObject':
+            self.__dict__[name] = value
+            return
+    method = class_type.__swig_setmethods__.get(name,None)
+    if method: return method(self,value)
+    if (not static):
+        self.__dict__[name] = value
+    else:
+        raise AttributeError("You cannot add attributes to %s" % self)
+
+def _swig_setattr(self,class_type,name,value):
+    return _swig_setattr_nondynamic(self,class_type,name,value,0)
+
+def _swig_getattr(self,class_type,name):
+    if (name == "thisown"): return self.this.own()
+    method = class_type.__swig_getmethods__.get(name,None)
+    if method: return method(self)
+    raise AttributeError(name)
+
+def _swig_repr(self):
+    try: strthis = "proxy of " + self.this.__repr__()
+    except: strthis = ""
+    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
+
+try:
+    _object = object
+    _newclass = 1
+except AttributeError:
+    class _object : pass
+    _newclass = 0
+
+
+class RunningStats(_object):
+    __swig_setmethods__ = {}
+    __setattr__ = lambda self, name, value: _swig_setattr(self, RunningStats, name, value)
+    __swig_getmethods__ = {}
+    __getattr__ = lambda self, name: _swig_getattr(self, RunningStats, name)
+    __repr__ = _swig_repr
+    def __init__(self): 
+        this = _RunningStats.new_RunningStats()
+        try: self.this.append(this)
+        except: self.this = this
+    def Clear(self): return _RunningStats.RunningStats_Clear(self)
+    def Push(self, *args): return _RunningStats.RunningStats_Push(self, *args)
+    def NumDataValues(self): return _RunningStats.RunningStats_NumDataValues(self)
+    def Mean(self): return _RunningStats.RunningStats_Mean(self)
+    def Variance(self): return _RunningStats.RunningStats_Variance(self)
+    def StandardDeviation(self): return _RunningStats.RunningStats_StandardDeviation(self)
+    def Skewness(self): return _RunningStats.RunningStats_Skewness(self)
+    def Kurtosis(self): return _RunningStats.RunningStats_Kurtosis(self)
+    def __iadd__(self, *args): return _RunningStats.RunningStats___iadd__(self, *args)
+    __swig_destroy__ = _RunningStats.delete_RunningStats
+    __del__ = lambda self : None;
+RunningStats_swigregister = _RunningStats.RunningStats_swigregister
+RunningStats_swigregister(RunningStats)
+
+# This file is compatible with both classic and new-style classes.
+
+