mirror of
https://github.com/titanscouting/tra-analysis.git
synced 2025-09-09 00:07:20 +00:00
tra-analysis v 3.0.0 aggregate PR (#73)
* reflected doc changes to README.md
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* tra_analysis v 2.1.0-alpha.1
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* changed setup.py to use __version__ from source
added Topic and keywords
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* updated Supported Platforms in README.md
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* moved required files back to parent
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* moved security back to parent
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* moved security back to parent
moved contributing back to parent
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* add PR template
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* moved to parent folder
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* moved meta files to .github folder
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* Analysis.py v 3.0.1
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* updated test_analysis for submodules, and added missing numpy import in Sort.py
* fixed item one of Issue #58
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* readded cache searching in postCreateCommand
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* added myself as an author
* feat: created kivy gui boilerplate
* added Kivy to requirements.txt
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* feat: gui with placeholders
* fix: changed config.json path
* migrated docker base image to debian
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* style: spaces to tabs
* migrated to ubuntu
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* fixed issues
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* fix: docker build?
* fix: use ubuntu bionic
* fix: get kivy installed
* @ltcptgeneral can't spell
* optim dockerfile for not installing unused packages
* install basic stuff while building the container
* use prebuilt image for development
* install pylint on base image
* rename and use new kivy
* tests: added tests for Array and CorrelationTest
Both are not working due to errors
* use new thing
* use 20.04 base
* symlink pip3 to pip
* use pip instead of pip3
* equation.Expression.py v 0.0.1-alpha
added corresponding .pyc to .gitignore
* parser.py v 0.0.2-alpha
* added pyparsing to requirements.txt
* parser v 0.0.4-alpha
* Equation v 0.0.1-alpha
* added Equation to tra_analysis imports
* tests: New unit tests for submoduling (#66)
* feat: created kivy gui boilerplate
* migrated docker base image to debian
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* migrated to ubuntu
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* fixed issues
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* fix: docker build?
* fix: use ubuntu bionic
* fix: get kivy installed
* @ltcptgeneral can't spell
* optim dockerfile for not installing unused packages
* install basic stuff while building the container
* use prebuilt image for development
* install pylint on base image
* rename and use new kivy
* tests: added tests for Array and CorrelationTest
Both are not working due to errors
* fix: Array no longer has *args and CorrelationTest functions no longer have self in the arguments
* use new thing
* use 20.04 base
* symlink pip3 to pip
* use pip instead of pip3
* tra_analysis v 2.1.0-alpha.2
SVM v 1.0.1
added unvalidated SVM unit tests
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* fixed version number
Signed-off-by: ltcptgeneral <learthurgo@gmail.com>
* tests: added tests for ClassificationMetric
* partially fixed and commented out svm unit tests
* fixed some SVM unit tests
* added installing pytest to devcontainer.json
* fix: small fixes to KNN
Namely, removing self from parameters and passing correct arguments to KNeighborsClassifier constructor
* fix, test: Added tests for KNN and NaiveBayes.
Also made some small fixes in KNN, NaiveBayes, and RegressionMetric
* test: finished unit tests except for StatisticalTest
Also made various small fixes and style changes
* StatisticalTest v 1.0.1
* fixed RegressionMetric unit test
temporarily disabled CorrelationTest unit tests
* tra_analysis v 2.1.0-alpha.3
* readded __all__
* fix: floating point issues in unit tests for CorrelationTest
Co-authored-by: AGawde05 <agawde05@gmail.com>
Co-authored-by: ltcptgeneral <learthurgo@gmail.com>
Co-authored-by: Dev Singh <dev@devksingh.com>
Co-authored-by: jzpan1 <panzhenyu2014@gmail.com>
* fixed depreciated escape sequences
* ficed tests, indent, import in test_analysis
* changed version to 3.0.0
added backwards compatibility
* ficed pytest install in container
* removed GUI changes
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* incremented version to rc.1 (release candidate 1)
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* fixed NaiveBayes __changelog__
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* fix: __setitem__ == to single =
* Array v 1.0.1
* Revert "Array v 1.0.1"
This reverts commit 59783b79f7.
* Array v 1.0.1
* Array.py v 1.0.2
added more Array unit tests
* cleaned .gitignore
tra_analysis v 3.0.0-rc2
Signed-off-by: Arthur Lu <learthurgo@gmail.com>
* added *.pyc to gitignore
finished subdividing test_analysis
* feat: gui layout + basic func
* Froze and removed superscript (data-analysis)
* remove data-analysis deps install for devcontainer
* tukey pairwise comparison and multicomparison but no critical q-values
* quick patch for devcontainer.json
* better fix for devcontainer.json
* fixed some styling in StatisticalTest
removed print statement in StatisticalTest unit tests
* update analysis tests to be more effecient
* don't use loop for test_nativebayes
* removed useless secondary docker files
* tra-analysis v 3.0.0
Co-authored-by: James Pan <panzhenyu2014@gmail.com>
Co-authored-by: AGawde05 <agawde05@gmail.com>
Co-authored-by: zpan1 <72054510+zpan1@users.noreply.github.com>
Co-authored-by: Dev Singh <dev@devksingh.com>
Co-authored-by: = <=>
Co-authored-by: Dev Singh <dsingh@imsa.edu>
Co-authored-by: zpan1 <zpan@imsa.edu>
This commit is contained in:
Arthur Lu
GitHub
@@ -0,0 +1,237 @@
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import math
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import sys
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import re
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if sys.version_info >= (3,):
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xrange = range
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basestring = str
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|
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class ExpressionObject(object):
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def __init__(self,*args,**kwargs):
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super(ExpressionObject,self).__init__(*args,**kwargs)
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def toStr(self,args,expression):
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return ""
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def toRepr(self,args,expression):
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return ""
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def __call__(self,args,expression):
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pass
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class ExpressionValue(ExpressionObject):
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def __init__(self,value,*args,**kwargs):
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super(ExpressionValue,self).__init__(*args,**kwargs)
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self.value = value
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def toStr(self,args,expression):
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if (isinstance(self.value,complex)):
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V = [self.value.real,self.value.imag]
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E = [0,0]
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B = [0,0]
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out = ["",""]
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for i in xrange(2):
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if V[i] == 0:
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E[i] = 0
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B[i] = 0
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else:
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E[i] = int(math.floor(math.log10(abs(V[i]))))
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B[i] = V[i]*10**-E[i]
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if E[i] in [0,1,2,3] and str(V[i])[-2:] == ".0":
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B[i] = int(V[i])
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E[i] = 0
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if E[i] in [-1,-2] and len(str(V[i])) <= 7:
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B[i] = V[i]
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E[i] = 0
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if i == 1:
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fmt = "{{0:+{0:s}}}"
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else:
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fmt = "{{0:-{0:s}}}"
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if type(B[i]) == int:
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out[i] += fmt.format('d').format(B[i])
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else:
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out[i] += fmt.format('.5f').format(B[i]).rstrip("0.")
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if i == 1:
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out[i] += "\\imath"
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if E[i] != 0:
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out[i] += "\\times10^{{{0:d}}}".format(E[i])
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return "\\left(" + ''.join(out) + "\\right)"
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elif (isinstance(self.value,float)):
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V = self.value
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E = 0
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B = 0
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out = ""
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if V == 0:
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E = 0
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B = 0
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else:
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E = int(math.floor(math.log10(abs(V))))
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B = V*10**-E
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if E in [0,1,2,3] and str(V)[-2:] == ".0":
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B = int(V)
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E = 0
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if E in [-1,-2] and len(str(V)) <= 7:
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B = V
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E = 0
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if type(B) == int:
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out += "{0:-d}".format(B)
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else:
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out += "{0:-.5f}".format(B).rstrip("0.")
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if E != 0:
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out += "\\times10^{{{0:d}}}".format(E)
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return "\\left(" + out + "\\right)"
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else:
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return out
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else:
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return str(self.value)
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def toRepr(self,args,expression):
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return str(self.value)
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def __call__(self,args,expression):
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return self.value
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def __repr__(self):
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return "<{0:s}.{1:s}({2:s}) object at {3:0=#10x}>".format(type(self).__module__,type(self).__name__,str(self.value),id(self))
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class ExpressionFunction(ExpressionObject):
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def __init__(self,function,nargs,form,display,id,isfunc,*args,**kwargs):
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super(ExpressionFunction,self).__init__(*args,**kwargs)
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self.function = function
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self.nargs = nargs
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self.form = form
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self.display = display
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self.id = id
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self.isfunc = isfunc
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def toStr(self,args,expression):
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params = []
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for i in xrange(self.nargs):
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params.append(args.pop())
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if self.isfunc:
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return str(self.display.format(','.join(params[::-1])))
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else:
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return str(self.display.format(*params[::-1]))
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def toRepr(self,args,expression):
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params = []
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for i in xrange(self.nargs):
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params.append(args.pop())
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if self.isfunc:
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return str(self.form.format(','.join(params[::-1])))
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else:
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return str(self.form.format(*params[::-1]))
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def __call__(self,args,expression):
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params = []
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for i in xrange(self.nargs):
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params.append(args.pop())
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return self.function(*params[::-1])
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def __repr__(self):
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return "<{0:s}.{1:s}({2:s},{3:d}) object at {4:0=#10x}>".format(type(self).__module__,type(self).__name__,str(self.id),self.nargs,id(self))
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class ExpressionVariable(ExpressionObject):
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def __init__(self,name,*args,**kwargs):
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super(ExpressionVariable,self).__init__(*args,**kwargs)
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self.name = name
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def toStr(self,args,expression):
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return str(self.name)
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def toRepr(self,args,expression):
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return str(self.name)
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def __call__(self,args,expression):
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if self.name in expression.variables:
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return expression.variables[self.name]
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else:
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return 0 # Default variables to return 0
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def __repr__(self):
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return "<{0:s}.{1:s}({2:s}) object at {3:0=#10x}>".format(type(self).__module__,type(self).__name__,str(self.name),id(self))
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class Core():
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constants = {}
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unary_ops = {}
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ops = {}
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functions = {}
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smatch = re.compile(r"\s*,")
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vmatch = re.compile(r"\s*"
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"(?:"
|
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"(?P<oct>"
|
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"(?P<octsign>[+-]?)"
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r"\s*0o"
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"(?P<octvalue>[0-7]+)"
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")|(?P<hex>"
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"(?P<hexsign>[+-]?)"
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r"\s*0x"
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"(?P<hexvalue>[0-9a-fA-F]+)"
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")|(?P<bin>"
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"(?P<binsign>[+-]?)"
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r"\s*0b"
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"(?P<binvalue>[01]+)"
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")|(?P<dec>"
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"(?P<rsign>[+-]?)"
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r"\s*"
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r"(?P<rvalue>(?:\d+\.\d+|\d+\.|\.\d+|\d+))"
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"(?:"
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"[Ee]"
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r"(?P<rexpoent>[+-]?\d+)"
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")?"
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"(?:"
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r"\s*"
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r"(?P<sep>(?(rvalue)\+|))?"
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r"\s*"
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"(?P<isign>(?(rvalue)(?(sep)[+-]?|[+-])|[+-]?)?)"
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r"\s*"
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r"(?P<ivalue>(?:\d+\.\d+|\d+\.|\.\d+|\d+))"
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"(?:"
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"[Ee]"
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r"(?P<iexpoent>[+-]?\d+)"
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")?"
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"[ij]"
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")?"
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")"
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")")
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nmatch = re.compile(r"\s*([a-zA-Z_][a-zA-Z0-9_]*)")
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gsmatch = re.compile(r'\s*(\()')
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gematch = re.compile(r'\s*(\))')
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def recalculateFMatch(self):
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fks = sorted(self.functions.keys(), key=len, reverse=True)
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oks = sorted(self.ops.keys(), key=len, reverse=True)
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uks = sorted(self.unary_ops.keys(), key=len, reverse=True)
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self.fmatch = re.compile(r'\s*(' + '|'.join(map(re.escape,fks)) + ')')
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self.omatch = re.compile(r'\s*(' + '|'.join(map(re.escape,oks)) + ')')
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self.umatch = re.compile(r'\s*(' + '|'.join(map(re.escape,uks)) + ')')
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def addFn(self,id,str,latex,args,func):
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self.functions[id] = {
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'str': str,
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'latex': latex,
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'args': args,
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'func': func}
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def addOp(self,id,str,latex,single,prec,func):
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if single:
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raise RuntimeError("Single Ops Not Yet Supported")
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self.ops[id] = {
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'str': str,
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'latex': latex,
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'args': 2,
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'prec': prec,
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'func': func}
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def addUnaryOp(self,id,str,latex,func):
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self.unary_ops[id] = {
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'str': str,
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'latex': latex,
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'args': 1,
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'prec': 0,
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'func': func}
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def addConst(self,name,value):
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self.constants[name] = value
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@@ -0,0 +1,2 @@
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from . import equation_base as equation_base
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from .ExpressionCore import ExpressionValue, ExpressionFunction, ExpressionVariable, Core
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@@ -0,0 +1,106 @@
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try:
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import numpy as np
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has_numpy = True
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except ImportError:
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import math
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has_numpy = False
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try:
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import scipy.constants
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has_scipy = True
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except ImportError:
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has_scipy = False
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import operator as op
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from .similar import sim, nsim, gsim, lsim
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def equation_extend(core):
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def product(*args):
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if len(args) == 1 and has_numpy:
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return np.prod(args[0])
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else:
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return reduce(op.mul,args,1)
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def sumargs(*args):
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if len(args) == 1:
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return sum(args[0])
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else:
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return sum(args)
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core.addOp('+',"({0:s} + {1:s})","\\left({0:s} + {1:s}\\right)",False,3,op.add)
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core.addOp('-',"({0:s} - {1:s})","\\left({0:s} - {1:s}\\right)",False,3,op.sub)
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core.addOp('*',"({0:s} * {1:s})","\\left({0:s} \\times {1:s}\\right)",False,2,op.mul)
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core.addOp('/',"({0:s} / {1:s})","\\frac{{{0:s}}}{{{1:s}}}",False,2,op.truediv)
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core.addOp('%',"({0:s} % {1:s})","\\left({0:s} \\bmod {1:s}\\right)",False,2,op.mod)
|
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core.addOp('^',"({0:s} ^ {1:s})","{0:s}^{{{1:s}}}",False,1,op.pow)
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core.addOp('**',"({0:s} ^ {1:s})","{0:s}^{{{1:s}}}",False,1,op.pow)
|
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core.addOp('&',"({0:s} & {1:s})","\\left({0:s} \\land {1:s}\\right)",False,4,op.and_)
|
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core.addOp('|',"({0:s} | {1:s})","\\left({0:s} \\lor {1:s}\\right)",False,4,op.or_)
|
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core.addOp('</>',"({0:s} </> {1:s})","\\left({0:s} \\oplus {1:s}\\right)",False,4,op.xor)
|
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core.addOp('&|',"({0:s} </> {1:s})","\\left({0:s} \\oplus {1:s}\\right)",False,4,op.xor)
|
||||
core.addOp('|&',"({0:s} </> {1:s})","\\left({0:s} \\oplus {1:s}\\right)",False,4,op.xor)
|
||||
core.addOp('==',"({0:s} == {1:s})","\\left({0:s} = {1:s}\\right)",False,5,op.eq)
|
||||
core.addOp('=',"({0:s} == {1:s})","\\left({0:s} = {1:s}\\right)",False,5,op.eq)
|
||||
core.addOp('~',"({0:s} ~ {1:s})","\\left({0:s} \\approx {1:s}\\right)",False,5,sim)
|
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core.addOp('!~',"({0:s} !~ {1:s})","\\left({0:s} \\not\\approx {1:s}\\right)",False,5,nsim)
|
||||
core.addOp('!=',"({0:s} != {1:s})","\\left({0:s} \\neg {1:s}\\right)",False,5,op.ne)
|
||||
core.addOp('<>',"({0:s} != {1:s})","\\left({0:s} \\neg {1:s}\\right)",False,5,op.ne)
|
||||
core.addOp('><',"({0:s} != {1:s})","\\left({0:s} \\neg {1:s}\\right)",False,5,op.ne)
|
||||
core.addOp('<',"({0:s} < {1:s})","\\left({0:s} < {1:s}\\right)",False,5,op.lt)
|
||||
core.addOp('>',"({0:s} > {1:s})","\\left({0:s} > {1:s}\\right)",False,5,op.gt)
|
||||
core.addOp('<=',"({0:s} <= {1:s})","\\left({0:s} \\leq {1:s}\\right)",False,5,op.le)
|
||||
core.addOp('>=',"({0:s} >= {1:s})","\\left({0:s} \\geq {1:s}\\right)",False,5,op.ge)
|
||||
core.addOp('=<',"({0:s} <= {1:s})","\\left({0:s} \\leq {1:s}\\right)",False,5,op.le)
|
||||
core.addOp('=>',"({0:s} >= {1:s})","\\left({0:s} \\geq {1:s}\\right)",False,5,op.ge)
|
||||
core.addOp('<~',"({0:s} <~ {1:s})","\\left({0:s} \lessapprox {1:s}\\right)",False,5,lsim)
|
||||
core.addOp('>~',"({0:s} >~ {1:s})","\\left({0:s} \\gtrapprox {1:s}\\right)",False,5,gsim)
|
||||
core.addOp('~<',"({0:s} <~ {1:s})","\\left({0:s} \lessapprox {1:s}\\right)",False,5,lsim)
|
||||
core.addOp('~>',"({0:s} >~ {1:s})","\\left({0:s} \\gtrapprox {1:s}\\right)",False,5,gsim)
|
||||
core.addUnaryOp('!',"(!{0:s})","\\neg{0:s}",op.not_)
|
||||
core.addUnaryOp('-',"-{0:s}","-{0:s}",op.neg)
|
||||
core.addFn('abs',"abs({0:s})","\\left|{0:s}\\right|",1,op.abs)
|
||||
core.addFn('sum',"sum({0:s})","\\sum\\left({0:s}\\right)",'+',sumargs)
|
||||
core.addFn('prod',"prod({0:s})","\\prod\\left({0:s}\\right)",'+',product)
|
||||
if has_numpy:
|
||||
core.addFn('floor',"floor({0:s})","\\lfloor {0:s} \\rfloor",1,np.floor)
|
||||
core.addFn('ceil',"ceil({0:s})","\\lceil {0:s} \\rceil",1,np.ceil)
|
||||
core.addFn('round',"round({0:s})","\\lfloor {0:s} \\rceil",1,np.round)
|
||||
core.addFn('sin',"sin({0:s})","\\sin\\left({0:s}\\right)",1,np.sin)
|
||||
core.addFn('cos',"cos({0:s})","\\cos\\left({0:s}\\right)",1,np.cos)
|
||||
core.addFn('tan',"tan({0:s})","\\tan\\left({0:s}\\right)",1,np.tan)
|
||||
core.addFn('re',"re({0:s})","\\Re\\left({0:s}\\right)",1,np.real)
|
||||
core.addFn('im',"re({0:s})","\\Im\\left({0:s}\\right)",1,np.imag)
|
||||
core.addFn('sqrt',"sqrt({0:s})","\\sqrt{{{0:s}}}",1,np.sqrt)
|
||||
core.addConst("pi",np.pi)
|
||||
core.addConst("e",np.e)
|
||||
core.addConst("Inf",np.Inf)
|
||||
core.addConst("NaN",np.NaN)
|
||||
else:
|
||||
core.addFn('floor',"floor({0:s})","\\lfloor {0:s} \\rfloor",1,math.floor)
|
||||
core.addFn('ceil',"ceil({0:s})","\\lceil {0:s} \\rceil",1,math.ceil)
|
||||
core.addFn('round',"round({0:s})","\\lfloor {0:s} \\rceil",1,round)
|
||||
core.addFn('sin',"sin({0:s})","\\sin\\left({0:s}\\right)",1,math.sin)
|
||||
core.addFn('cos',"cos({0:s})","\\cos\\left({0:s}\\right)",1,math.cos)
|
||||
core.addFn('tan',"tan({0:s})","\\tan\\left({0:s}\\right)",1,math.tan)
|
||||
core.addFn('re',"re({0:s})","\\Re\\left({0:s}\\right)",1,complex.real)
|
||||
core.addFn('im',"re({0:s})","\\Im\\left({0:s}\\right)",1,complex.imag)
|
||||
core.addFn('sqrt',"sqrt({0:s})","\\sqrt{{{0:s}}}",1,math.sqrt)
|
||||
core.addConst("pi",math.pi)
|
||||
core.addConst("e",math.e)
|
||||
core.addConst("Inf",float("Inf"))
|
||||
core.addConst("NaN",float("NaN"))
|
||||
if has_scipy:
|
||||
core.addConst("h",scipy.constants.h)
|
||||
core.addConst("hbar",scipy.constants.hbar)
|
||||
core.addConst("m_e",scipy.constants.m_e)
|
||||
core.addConst("m_p",scipy.constants.m_p)
|
||||
core.addConst("m_n",scipy.constants.m_n)
|
||||
core.addConst("c",scipy.constants.c)
|
||||
core.addConst("N_A",scipy.constants.N_A)
|
||||
core.addConst("mu_0",scipy.constants.mu_0)
|
||||
core.addConst("eps_0",scipy.constants.epsilon_0)
|
||||
core.addConst("k",scipy.constants.k)
|
||||
core.addConst("G",scipy.constants.G)
|
||||
core.addConst("g",scipy.constants.g)
|
||||
core.addConst("q",scipy.constants.e)
|
||||
core.addConst("R",scipy.constants.R)
|
||||
core.addConst("sigma",scipy.constants.e)
|
||||
core.addConst("Rb",scipy.constants.Rydberg)
|
||||
@@ -0,0 +1,49 @@
|
||||
_tol = 1e-5
|
||||
|
||||
def sim(a,b):
|
||||
if (a==b):
|
||||
return True
|
||||
elif a == 0 or b == 0:
|
||||
return False
|
||||
if (a<b):
|
||||
return (1-a/b)<=_tol
|
||||
else:
|
||||
return (1-b/a)<=_tol
|
||||
|
||||
def nsim(a,b):
|
||||
if (a==b):
|
||||
return False
|
||||
elif a == 0 or b == 0:
|
||||
return True
|
||||
if (a<b):
|
||||
return (1-a/b)>_tol
|
||||
else:
|
||||
return (1-b/a)>_tol
|
||||
|
||||
def gsim(a,b):
|
||||
if a >= b:
|
||||
return True
|
||||
return (1-a/b)<=_tol
|
||||
|
||||
def lsim(a,b):
|
||||
if a <= b:
|
||||
return True
|
||||
return (1-b/a)<=_tol
|
||||
|
||||
def set_tol(value=1e-5):
|
||||
r"""Set Error Tolerance
|
||||
|
||||
Set the tolerance for detriming if two numbers are simliar, i.e
|
||||
:math:`\left|\frac{a}{b}\right| = 1 \pm tolerance`
|
||||
|
||||
Parameters
|
||||
----------
|
||||
value: float
|
||||
The Value to set the tolerance to show be very small as it respresents the
|
||||
percentage of acceptable error in detriming if two values are the same.
|
||||
"""
|
||||
global _tol
|
||||
if isinstance(value,float):
|
||||
_tol = value
|
||||
else:
|
||||
raise TypeError(type(value))
|
||||
Reference in New Issue
Block a user