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[yoda-svn] r509 - in trunk: . include/YODA pyext/yoda pyext/yoda/include
blackhole at projects.hepforge.org
blackhole at projects.hepforge.org
Fri Jul 20 00:22:40 BST 2012
Author: buckley
Date: Fri Jul 20 00:22:40 2012
New Revision: 509
Log:
Bin, Dbn, and Point improvements
Modified:
trunk/TODO
trunk/include/YODA/ProfileBin1D.h
trunk/pyext/yoda/Makefile.am
trunk/pyext/yoda/include/20-Dbn1D.pyx
trunk/pyext/yoda/include/20-Dbn2D.pyx
trunk/pyext/yoda/include/20-Point2D.pyx
trunk/pyext/yoda/include/20-Point3D.pyx
trunk/pyext/yoda/include/30-HistoBin1D.pyx
trunk/pyext/yoda/include/30-ProfileBin1D.pyx
trunk/pyext/yoda/include/40-Histo2D.pyx
Modified: trunk/TODO
==============================================================================
--- trunk/TODO Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/TODO Fri Jul 20 00:22:40 2012 (r509)
@@ -10,34 +10,44 @@
Ignore anything after "#" on data lines -- use this to write convenience
height & error info for each bin since not obvious from sumWX2 etc.
-* Add nice constructor behaviour and docstrings to the Scatter2D Python interface. (AB)
-
* Remove nasty Cython shims (DM)
- Does inheritance work automatically in Cython now?
+ Does inheritance work automatically in Cython now? Add operator support
+ everywhere it's needed.
-* Complete basic Histo2D and Profile2D functionality. (AB)
- Axis2D is working
+* Add Axis2D -> Histo2D/Profile2D bin adding and erasing. (AB)
* Make Python interface test scripts (DM)
-* Add copy assignment to Point/Scatter3D (AB)
+* Add copy assignment to both C++ and Cython (AB)
-* Improve tests Makefile setup to work out the path to the Python build dir. (AB)
+* Docstrings for Points, Dbns and Bins (AB)
+
+* Add stdErr to HistoBinXD (AB)
+
+* Add Dbn3D, ProfileBin2D, Profile2D and Scatter3D in Cython (AB)
+
+* Test Histo2D and Scatter2D from Python (AB)
+* Sort out _dealloc treatment (AB, DM)
+
+* Adding 2D operator support and bin-adding/erasing
NEXT
-* Add "official" counter and bar-chart types (AB)
- Need better names!
+* Auto-determine input and output formats (= readers/writers) from file extn (AB)
+
+* Improve tests Makefile setup to work out the path to the Python build dir. (AB)
-* Add a merge() method in Bin2D. Add a constructor that takes Dbns.
+* Add a merge() method in Bin2D. Add a constructor that takes Dbns (AB)
+ Use merge() to implement merging/rebinning in Axis2D -> Histo2D & Profile2D.
-* Rebinning: global rebinning of Axis2D -> Histo2D by integer factor(s) --
- different factors in x and y directions.
+* Detecting perfect/imperfect 2D grids (AB)
-* Automatically determine input and output formats (= readers/writers) from file extn.
+* 2D bin merging and rebinning (AB)
+ Only rebin perfect grids? Global rebinning of Axis2D -> Histo2D by generally
+ different integer factors in x and y directions.
* Test negative- and mixed-weighted stat calculations, and scaling.
@@ -48,12 +58,16 @@
* Add Scatter1D/Point1D (AB)
* Transform 1D differential to integral histos and vice versa.
- Bins have to be contiguous. (AB)
+ Bins have to be contiguous. (AB)
* Add a Counter type (mostly a UI/persistency wrapper on Dbn1D) (AB)
+ "Binning"/"axis" option on arbitrary types, particularly strings? ->
+ generalised bar charts.
+
+* "BinnedValues" type: use Axis behaviour to look up fixed values.
-* Multiple errors on Scatter2D -- via a vector of Error2D? How to implement
- flexible error combination? Error correlations?
+* Multiple errors on Scatters -- via a vector of Errors?
+ Flexible error combination? Error correlations? Max/min?
* WriterFlat and ReaderFlat, for Scatter2D representations only. (HH)
Modified: trunk/include/YODA/ProfileBin1D.h
==============================================================================
--- trunk/include/YODA/ProfileBin1D.h Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/include/YODA/ProfileBin1D.h Fri Jul 20 00:22:40 2012 (r509)
@@ -100,6 +100,10 @@
return _dbn.yStdErr();
}
+ double rms() const {
+ return _dbn.yRMS();
+ }
+
//@}
Modified: trunk/pyext/yoda/Makefile.am
==============================================================================
--- trunk/pyext/yoda/Makefile.am Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/Makefile.am Fri Jul 20 00:22:40 2012 (r509)
@@ -5,15 +5,18 @@
$(PYTHON) -m cython --cplus yoda.pyx
yoda.pyx: include/00-imports.pyx include/10-AnalysisObject.pyx \
- include/20-Dbn1D.pyx include/20-Dbn2D.pyx include/20-Point2D.pyx include/20-Point3D.pyx \
- include/30-HistoBin1D.pyx include/30-ProfileBin1D.pyx include/30-HistoBin2D.pyx \
- include/30-Reader.pyx \
+ include/20-Dbn1D.pyx include/20-Dbn2D.pyx \
+ include/20-Point2D.pyx include/20-Point3D.pyx \
+ include/30-HistoBin1D.pyx include/30-ProfileBin1D.pyx \
+ include/30-HistoBin2D.pyx \
+ include/30-Reader.pyx include/30-Writer.pyx \
include/30-Scatter2D.pyx \
include/40-Histo1D.pyx include/40-Profile1D.pyx \
include/40-Histo2D.pyx \
include/40-WriterYODA.pyx include/40-WriterAIDA.pyx \
include/99-ReaderYODA.pyx include/99-ReaderAIDA.pyx
cat $+ > yoda.pyx
+#include/30-ProfileBin2D.pyx
#include/30-Scatter3D.pyx
#include/40-Profile2D.pyx
Modified: trunk/pyext/yoda/include/20-Dbn1D.pyx
==============================================================================
--- trunk/pyext/yoda/include/20-Dbn1D.pyx Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/include/20-Dbn1D.pyx Fri Jul 20 00:22:40 2012 (r509)
@@ -26,9 +26,17 @@
cdef class Dbn1D:
+ """
+ A 1D distribution 'counter', used and exposed by 1D histograms and their bins.
+
+ TODO: Allow no-arg construction?
+ TODO: map operator+ and operator-, both internal and external
+ """
+
cdef cDbn1D *thisptr
cdef bool _dealloc
+
def __cinit__(self):
self._dealloc = False
@@ -59,67 +67,101 @@
def fill(self, double x, double weight=1.0):
+ "Fill the distribution with the given weight at given x."
self.ptr().fill(x, weight)
def reset(self):
+ "Reset the distribution counters to the unfilled state."
self.ptr().reset()
def scaleW(self, scalefactor):
+ "Scale the fill weights by the given factor"
self.ptr().scaleW(scalefactor)
def scaleX(self, factor):
+ "Scale the x variable by the given factor"
self.ptr().scaleX(factor)
+ @property
def mean(self):
+ "Get the weighted mean x (synonym for xMean)"
return self.ptr().mean()
+ @property
def xMean(self):
+ "Get the weighted mean x"
return self.ptr().xMean()
+ @property
def variance(self):
+ "Get the weighted variance of x (synonym for xVariance)"
return self.ptr().variance()
+ @property
def xVariance(self):
+ "Get the weighted variance of x"
return self.ptr().xVariance()
+ @property
def stdDev(self):
+ "Get the weighted standard deviation of x (synonym for xStdDev)"
return self.ptr().stdDev()
+ @property
def xStdDev(self):
+ "Get the weighted standard deviation of x"
return self.ptr().xStdDev()
+ @property
def stdErr(self):
+ "Get the weighted standard error on <x> (synonym for xStdErr)"
return self.ptr().stdDev()
+ @property
def xStdErr(self):
+ "Get the weighted standard error on <x>"
return self.ptr().xStdDev()
+ @property
def rms(self):
+ "Get the weighted RMS of x (synonym for xRMS)"
return self.ptr().rms()
+ @property
def xRMS(self):
+ "Get the weighted RMS of x"
return self.ptr().xRMS()
+ @property
def numEntries(self):
+ "Get the number of entries"
return self.ptr().numEntries()
+ @property
def effNumEntries(self):
+ "Get the effective number of entries (for weighted events)"
return self.ptr().effNumEntries()
+ @property
def sumW(self):
+ "Get the sum of weights"
return self.ptr().sumW()
+ @property
def sumW2(self):
+ "Get the sum of squared-weights"
return self.ptr().sumW2()
+ @property
def sumWX(self):
+ "Get the sum of weighted xs"
return self.ptr().sumWX()
+ @property
def sumWX2(self):
+ "Get the sum of weighted squared-xs"
return self.ptr().sumWX2()
- # TODO: map operator+ and operator-, both internal and external
-
cdef Dbn1D Dbn1D_fromptr(cDbn1D *ptr, dealloc=False):
Modified: trunk/pyext/yoda/include/20-Dbn2D.pyx
==============================================================================
--- trunk/pyext/yoda/include/20-Dbn2D.pyx Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/include/20-Dbn2D.pyx Fri Jul 20 00:22:40 2012 (r509)
@@ -31,7 +31,14 @@
cdef class Dbn2D:
- cdef cDbn2D *thisptr
+ """
+ A 2D distribution 'counter', used and exposed by 1D histograms and their bins.
+
+ TODO: Allow no-arg construction?
+ TODO: map operator+ and operator-, both internal and external
+ """
+
+ cdef cDbn2D* thisptr
cdef bool _dealloc
def __cinit__(self):
@@ -64,79 +71,120 @@
def fill(self, double x, double y, double weight=1.0):
+ "Fill the distribution with the given weight at given x and y."
self.ptr().fill(x, y, weight)
def reset(self):
+ "Reset the distribution counters to the unfilled state."
self.ptr().reset()
def scaleW(self, scalefactor):
+ "Scale the fill weights by the given factor"
self.ptr().scaleW(scalefactor)
def scaleX(self, factor):
+ "Scale the x variable by the given factor"
self.ptr().scaleX(factor)
def scaleY(self, factor):
+ "Scale the y variable by the given factor"
self.ptr().scaleY(factor)
+ @property
def xMean(self):
+ "Get the weighted mean x"
return self.ptr().xMean()
+ @property
def yMean(self):
+ "Get the weighted mean y"
return self.ptr().yMean()
+ @property
def xVariance(self):
+ "Get the weighted variance of x"
return self.ptr().xVariance()
+ @property
def yVariance(self):
+ "Get the weighted variance of y"
return self.ptr().yVariance()
+ @property
def xStdDev(self):
+ "Get the weighted standard deviation of x"
return self.ptr().xStdDev()
+ @property
def yStdDev(self):
+ "Get the weighted standard deviation of y"
return self.ptr().yStdDev()
+ @property
def xStdErr(self):
+ "Get the weighted standard error on <x>"
return self.ptr().xStdDev()
+ @property
def yStdErr(self):
+ "Get the weighted standard error on <y>"
return self.ptr().yStdDev()
+ @property
def xRMS(self):
+ "Get the weighted RMS of x"
return self.ptr().xRMS()
+ @property
def yRMS(self):
+ "Get the weighted RMS of y"
return self.ptr().yRMS()
+ @property
def numEntries(self):
+ "Get the number of entries"
return self.ptr().numEntries()
+ @property
def effNumEntries(self):
+ "Get the effective number of entries (for weighted events)"
return self.ptr().effNumEntries()
+ @property
def sumW(self):
+ "Get the sum of weights"
return self.ptr().sumW()
+ @property
def sumW2(self):
+ "Get the sum of squared-weights"
return self.ptr().sumW2()
+ @property
def sumWX(self):
+ "Get the sum of weighted xs"
return self.ptr().sumWX()
+ @property
def sumWX2(self):
+ "Get the sum of weighted squared-xs"
return self.ptr().sumWX2()
+ @property
def sumWY(self):
+ "Get the sum of weighted ys"
return self.ptr().sumWY()
+ @property
def sumWY2(self):
+ "Get the sum of weighted squared-ys"
return self.ptr().sumWY2()
+ @property
def sumWXY(self):
+ "Get the sum of weighted (x*y)s"
return self.ptr().sumWXY()
- # TODO: map operator+ and operator-, both internal and external
-
cdef Dbn2D Dbn2D_fromptr(cDbn2D *ptr, dealloc=False):
Modified: trunk/pyext/yoda/include/20-Point2D.pyx
==============================================================================
--- trunk/pyext/yoda/include/20-Point2D.pyx Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/include/20-Point2D.pyx Fri Jul 20 00:22:40 2012 (r509)
@@ -20,8 +20,18 @@
cdef class Point2D:
- cdef cPoint2D* thisptr
+ """
+ A 2D point, as contained in Scatter2D.
+
+ Several constructor forms are supported:
+ * Point2D() - default point construction at (0,0)
+ * Point2D(x, y) - point construction at (x,y)
+ * Point2D(x, y, ex, ey) - point construction at (x,y) with errors. ex and ey can be pairs.
+ * Point2D(x, y, ex-, ex+, ey-, ey+) - point construction at (x,y) with asymm errors.
+ """
+
+ cdef cPoint2D* thisptr
cdef bool _dealloc
cdef cPoint2D* ptr(self):
Modified: trunk/pyext/yoda/include/20-Point3D.pyx
==============================================================================
--- trunk/pyext/yoda/include/20-Point3D.pyx Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/include/20-Point3D.pyx Fri Jul 20 00:22:40 2012 (r509)
@@ -29,10 +29,21 @@
cdef class Point3D:
- cdef cPoint3D* thisptr
+ """
+ A 3D point, as contained in Scatter3D.
+
+ Several constructor forms are supported:
+
+ * Point3D() - default point construction at (0,0,0)
+ * Point3D(x, y, z) - point construction at (x,y,z)
+ * Point3D(x, y, z, ex, ey, ez) - point construction at (x,y,z) with errors. ex and ey can be pairs.
+ * Point3D(x, y, z, ex-, ex+, ey-, ey+, ez-, ez+) - point construction at (x,y,z) with asymm errors.
+ """
+ cdef cPoint3D* thisptr
cdef bool _dealloc
+
cdef cPoint3D* ptr(self):
return self.thisptr
@@ -44,6 +55,7 @@
self._dealloc = dealloc
return self
+
def __cinit__(self):
self._dealloc = False
@@ -52,7 +64,7 @@
self._dealloc = True
if len(args) == 0:
- self.pos = 0, 0
+ self.pos = 0, 0, 0
elif len(args) == 3:
self.pos = args
elif len(args) == 6:
Modified: trunk/pyext/yoda/include/30-HistoBin1D.pyx
==============================================================================
--- trunk/pyext/yoda/include/30-HistoBin1D.pyx Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/include/30-HistoBin1D.pyx Fri Jul 20 00:22:40 2012 (r509)
@@ -1,14 +1,15 @@
cdef extern from "YODA/HistoBin1D.h" namespace "YODA":
cdef cppclass cHistoBin1D "YODA::HistoBin1D":
- cHistoBin1D (cHistoBin1D &h)
- cHistoBin1D (double, double)
+ cHistoBin1D(cHistoBin1D &h)
+ cHistoBin1D(double, double)
double area()
double height()
double areaErr()
double heightErr()
void reset()
+ # TODO
# These are inherited methods from Bin1D... I can't seem to find a nice
# way to make Cython acknowledge these (it seems to be a typedef parsing
# issue rather than a technical issue).
@@ -25,6 +26,7 @@
double xVariance()
double xStdDev()
double xStdErr()
+ double xRMS()
double numEntries()
double effNumEntries()
double sumW()
@@ -33,16 +35,25 @@
double sumWX2()
-#Ugly hack using shim header for Cython 0.13
+# TODO: Ugly hack using shim header for Cython 0.13
cdef extern from "shims.h":
cHistoBin1D add_HistoBin1D (cHistoBin1D &, cHistoBin1D &)
cHistoBin1D subtract_HistoBin1D (cHistoBin1D &, cHistoBin1D &)
cdef class HistoBin1D:
- cdef cHistoBin1D *thisptr
+ """
+ A 1D histogram bin, as stored inside Histo1D.
+
+ Only one Python constructor:
+
+ * HistoBin1D(xlow, xhigh)
+ """
+
+ cdef cHistoBin1D* thisptr
cdef bool _dealloc
+
def __cinit__(self):
self._dealloc = False
@@ -50,7 +61,13 @@
if self._dealloc:
del self.thisptr
- cdef HistoBin1D setptr(self, cHistoBin1D *ptr, bool dealloc):
+
+ # TODO: Why does Cython hate this?!?
+ # def __init__(self, double xlow, double xhigh):
+ # self.setptr(new cHistoBin1D(xlow, xhigh), dealloc=True)
+
+
+ cdef HistoBin1D setptr(self, cHistoBin1D* ptr, bool dealloc):
if self._dealloc:
del self.thisptr
@@ -61,6 +78,11 @@
cdef cHistoBin1D* ptr(self):
return self.thisptr
+
+ ##############################
+ # THIS IS ALL BIN1D STUFF: CAN WE INHERIT THE PY MAPPING?
+
+
@property
def lowEdge(self):
"""The lower of the two bin edges."""
@@ -68,6 +90,7 @@
xMin = lowEdge
+
@property
def highEdge(self):
"""The higher of the two bin edges."""
@@ -75,6 +98,7 @@
xMax = highEdge
+
@property
def width(self):
"""The width of the bin."""
@@ -90,6 +114,7 @@
"""The point half-way between the bin edges."""
return self.ptr().midpoint()
+
@property
def xMean(self):
"""The mean of the x-values that have filled the bin."""
@@ -106,6 +131,16 @@
return self.ptr().xStdDev()
@property
+ def xStdErr(self):
+ """The standard error of the x-values that have filled the bin."""
+ return self.ptr().xStdErr()
+
+ @property
+ def xRMS(self):
+ """The RMS of the x-values that have filled the bin."""
+ return self.ptr().xRMS()
+
+ @property
def numEntries(self):
"""The number of entries in the bin."""
return self.ptr().numEntries()
@@ -136,6 +171,10 @@
"""Sum of the products of x-values squared and their weights."""
return self.ptr().sumWX2()
+
+ ########################
+
+
@property
def area(self):
"""
Modified: trunk/pyext/yoda/include/30-ProfileBin1D.pyx
==============================================================================
--- trunk/pyext/yoda/include/30-ProfileBin1D.pyx Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/include/30-ProfileBin1D.pyx Fri Jul 20 00:22:40 2012 (r509)
@@ -25,10 +25,12 @@
double xVariance()
double xStdDev()
double xStdErr()
+ double xRMS()
double mean()
double variance()
double stdDev()
double stdErr()
+ double rms()
double numEntries()
double effNumEntries()
double sumW()
@@ -46,7 +48,15 @@
cdef class ProfileBin1D:
- cdef cProfileBin1D *thisptr
+ """
+ A 1D profile histogram bin, as stored inside Histo1D.
+
+ Only one Python constructor:
+
+ * ProfileBin1D(xlow, xhigh)
+ """
+
+ cdef cProfileBin1D* thisptr
cdef bool _dealloc
def __cinit__(self):
@@ -56,7 +66,13 @@
if self._dealloc:
del self.thisptr
- cdef ProfileBin1D setptr(self, cProfileBin1D *ptr, bool dealloc):
+
+ # TODO: Why does Cython hate this?!?
+ # def __init__(self, double xlow, double xhigh):
+ # self.setptr(new cHistoBin1D(xlow, xhigh), dealloc=True)
+
+
+ cdef ProfileBin1D setptr(self, cProfileBin1D* ptr, bool dealloc):
if self._dealloc:
del self.thisptr
@@ -67,6 +83,10 @@
cdef cProfileBin1D* ptr(self):
return self.thisptr
+
+ ##############################
+ # THIS IS ALL BIN1D STUFF: CAN WE INHERIT THE PY MAPPING?
+
@property
def lowEdge(self):
"""The lower of the two bin edges."""
@@ -115,6 +135,14 @@
return self.ptr().xStdErr()
@property
+ def xRMS(self):
+ """The RMS of the x-values that have filled the bin."""
+ return self.ptr().xRMS()
+
+ ####################################
+
+
+ @property
def mean(self):
"""The mean of the y-values that have filled the bin."""
return self.ptr().mean()
@@ -135,6 +163,11 @@
return self.ptr().stdErr()
@property
+ def rms(self):
+ """The RMS of the y-values that have filled the bin."""
+ return self.ptr().rms()
+
+ @property
def numEntries(self):
"""The number of entries in the bin."""
return self.ptr().numEntries()
Modified: trunk/pyext/yoda/include/40-Histo2D.pyx
==============================================================================
--- trunk/pyext/yoda/include/40-Histo2D.pyx Thu Jul 19 09:51:13 2012 (r508)
+++ trunk/pyext/yoda/include/40-Histo2D.pyx Fri Jul 20 00:22:40 2012 (r509)
@@ -83,12 +83,10 @@
TODO: Add constructors from Scatter and Profile
TODO: Support adding and erasing bins
+ TODO: Support add, mul, div operators
"""
- # cdef tuple _bins
-
def __cinit__(self):
- # self._bins = None
self._dealloc = False
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