Source code for pwem.protocols.protocol_mathematical_operator

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# * Authors:    Daniel Marchán (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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import pyworkflow.protocol.params as params
from pwem.protocols import EMProtocol
from pyworkflow.object import Integer, Float, String

[docs]class ProtMathematicalOperator(EMProtocol): """ Protocol to make mathematical operations on different inputs """ PARAM1 = 'X1' PARAM2 = 'X2' _label = 'mathematical operator' def __init__(self, **args): EMProtocol.__init__(self, **args) def _defineParams(self, form): """attr2 Defines the parameters the protocol form will show and its behaviour :param form: """ form.addSection(label='Input') # Attribute X1 form.addParam('input1', params.IntParam, label='Input %s:' % self.PARAM1, default=3, allowsPointers=True, help='Write the value you want to consider as %s or' ' if it is a input pointer select from the list of available inputs.' % self.PARAM1) # Attribute X2 form.addParam('input2', params.IntParam, label='Input %s:' % self.PARAM2, default=2, allowsPointers=True, help='Write the value you want to consider as %s or' ' if it is a input pointer select from the list of available inputs.' % self.PARAM2) # Result form.addParam('expression', params.StringParam, label="Formula: ", important=True, default = "%s + (%s*3)" % (self.PARAM1, self.PARAM2), help='Write the mathematical formula you want to calculate, e.g: (%s + %s) * %s * 0.9 \n' 'Please note that %s and %s would be replaced by the value you selected for each case.' ' It is important to use upper cases when writing the expression.' % (self.PARAM1, self.PARAM2, self.PARAM1, self.PARAM1, self.PARAM2)) form.addParam('typeResult', params.EnumParam, default=1, choices=['Int', 'Float', 'String'], label='Result type:', help='Choose the variable type you want your result to be, e.g: Integer', expertLevel=params.LEVEL_ADVANCED) def _insertAllSteps(self): self._insertFunctionStep(self.computeStep, self.getParam1(), self.getParam2() , prerequisites=[])
[docs] def computeStep(self, attr1, attr2): """ Applies the formula to each of the attributes or the numeric formula provided. Complex python code could be run separating lines with ; To use numpy you could do: import numpy; item._resolution.set(numpy.random.randint(10)) """ str1 = str(attr1) str2 = str(attr2) strInit = self.expression.get() strInit = strInit.replace(self.PARAM1, str1) self.formula = strInit.replace(self.PARAM2, str2)"FORMULA after replacement: %s" % self.formula) result = eval(self.formula)"RESULT: %s" % result ) self.createResultOutput(result)'To calculate: %s' % self.formula)'Result = %s' % result)
[docs] def createResultOutput(self, result): """ The output can be an Integer, Float or String. Other protocols can use it in those Params if it has set allowsPointer=True """ tpR = self.typeResult.get() if tpR == 0: resultNum = Integer(result) elif tpR == 1: resultNum = Float(result) elif tpR == 2: resultNum = String(result) self._defineOutputs(result=resultNum)
[docs] def formulaNeedsParam(self, param): """ return True if the formula uses the param passed""" return param in self.expression.get()
[docs] def formulaNeedsInput(self): """ Returns true if there is need for any input""" return self.formulaNeedsParam(self.PARAM1) or self.formulaNeedsParam(self.PARAM2)
def _summary(self): summary = [] summary.append('To calculate: %s' % self.expression.get()) if hasattr(self, "formula"): summary.append('To calculate: %s' % self.formula) if hasattr(self, "result"): summary.append('Result = %s' % self.result) return summary def _validate(self): errors = [] if self.formulaNeedsParam(self.PARAM1): if self.getParam1() is None: errors.append('Input %s should be provided.' % self.PARAM1) if self.formulaNeedsParam(self.PARAM2): if self.getParam2() is None: errors.append('Input %s should be provided.' % self.PARAM2) return errors
[docs] def getParam2(self): return self.input2.get()
[docs] def getParam1(self): return self.input1.get()