Source code for pwem.protocols.protocol_boxsize_checkpoint

# **************************************************************************
# *
# * Authors:     Daniel Marchán (da.marchan@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
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import pyworkflow.protocol.params as params
from pwem.protocols import EMProtocol
from pyworkflow.object import Integer
from pyworkflow.protocol.params import  StringParam
import numpy as np
import re
import time
import os

BOXSIZE= 'boxSize'

[docs]class ProtBoxSizeCheckpoint(EMProtocol): """ Protocol to make a validation operations on particle picking boxsize. For sanity check all the generated outputs are even numbers. """ _label = 'box size checkpoint' _possibleOutputs = {BOXSIZE: Integer} outputsToDefine = {} def __init__(self, **args): EMProtocol.__init__(self, **args) def _defineParams(self, form): """ Defines the parameters the protocol form will show and its behaviour :param form: """ form.addSection(label='Input') form.addParam('boxSize1', params.IntParam, label='Particle box size reference (px)', allowsPointers=True, important=True, help='This is the reference size of the boxed particles (in pixels).\n' 'For sanity check if it is not, it will be transform to an even number.') form.addParam('boxSize2', params.IntParam, label='Particle box size secondary reference (px)', allowsPointers=True, important=True, help='This is a secondary size of the boxed particles (in pixels).\n' 'For sanity check if it is not, it will be transform to an even number.') form.addParam('disagreeFactor', params.FloatParam, default=0.2, label='Maximum proportional difference', help='This proportion is calulated with the following formula:\n' 'Proportional diff = 1 - min(boxSize1, boxSize2)/max(boxSize1, boxSize2)') form.addParam('boolBoxSize1', params.BooleanParam, default=True, label='If disagreed stayed with the primary reference?', help='Select yes if you want to use the primary reference as output.') form.addParam('boolBoxSizeAvg', params.BooleanParam, default=False, label='Average the particle boxsize?', help='Select yes if you want to use an average of the box sizes as output.') form.addParam('boolTimer', params.BooleanParam, default=False, label='Use timer?', help='Select yes if you want to use a timer to take the decision.') form.addParam('timeout', StringParam, default="1h", condition="boolTimer==%d" % True, label='Time to wait:', help='Time in seconds that the protocol will remain ' 'running. A correct format is an integer number in ' 'seconds or the following syntax: {days}d {hours}h ' '{minutes}m {seconds}s separated by spaces ' 'e.g: 1d 2h 20m 15s, 10m 3s, 1h, 20s or 25.') def _insertAllSteps(self): self.initParams() self._checkNewInput()
[docs] def initParams(self): self.outputDone = False
[docs] def createOutput(self, modifiedSet): pass
def _stepsCheck(self): self._checkNewInput() self._checkNewOutput() def _checkNewInput(self): if self.outputDone: return None boxSize1 = self.boxSize1.get() boxSize2 = self.boxSize2.get() fDeps = self._insertNewOperationsStep(boxSize1, boxSize2) self.updateSteps() def _insertNewOperationsStep(self, boxSize1, boxSize2): deps = [] stepId = self._insertFunctionStep('applyComparisonStep', boxSize1, boxSize2, prerequisites=[]) deps.append(stepId) return deps def _checkNewOutput(self): if self.outputDone: self.createResultsOutput()
[docs] def applyComparisonStep(self, boxSize1, boxSize2): """ Applies the formula to make the comparison of the two box size. It has four cases: - Stays within the limits of the maximum proportional difference and outputs the average box size (default). - Stays within the limits of the maximum proportional difference and outputs the primary reference. - Goes out of the maximum proportional difference and outputs the primary reference (default). - Goes out of the maximum proportional difference and outputs the average box size. """ diff_p = 1 - min(boxSize1, boxSize2)/max(boxSize1, boxSize2) self.info("Calculating the difference between reference box size %d and secondary box size %d" %(boxSize1, boxSize2)) if diff_p <= self.disagreeFactor.get(): self.info("The proportional difference was within the threshold %f<%f" %(diff_p, self.disagreeFactor.get())) if self.boolBoxSizeAvg.get(): boxSize = np.mean([boxSize1, boxSize2]) self.info("Using average box size %d" %boxSize) else: boxSize = boxSize1 self.info("Using reference box size %d" %boxSize) else: self.info("The proportional difference was out of threshold %f>%f" % (diff_p, self.disagreeFactor.get())) if self.boolBoxSize1.get(): boxSize = boxSize1 self.info("Using reference box size %d" % boxSize) else: boxSize = np.mean([boxSize1, boxSize2]) self.info("Using average box size %d" % boxSize) if self.boolTimer.get(): self._insertFunctionStep(self.waitingStep) self.registerEvenBoxSize(boxSize) self.outputDone = True
[docs] def waitingStep(self): lastTimeCheck = 0 timeout = self.getTimeOutInSeconds(self.timeout.get()) finished = False while not finished: if lastTimeCheck % 300 == 0: self.info("Remaining time: %s seconds. Next check in 5 minutes" % str(timeout - lastTimeCheck)) time.sleep(10) lastTimeCheck += 10 finished = (lastTimeCheck > timeout or self.waitingHasFinished())
[docs] def getTimeOutInSeconds(self, timeOut): timeOutFormatRegexList = {r'\d+s': 1, r'\d+m': 60, r'\d+h': 3600, r'\d+d': 72000} try: return int(timeOut) except Exception: seconds = 0 for regex, secondsUnit in timeOutFormatRegexList.items(): matchingTimes = re.findall(regex, timeOut) for matchTime in matchingTimes: seconds += int(matchTime[:-1]) * secondsUnit return seconds
def _getStopWaitingFilename(self): return self._getExtraPath("APPROVE_CHECKPOINT.TXT")
[docs] def getActions(self): if self.isRunning(): return [('APPROVE CHECKPOINT', self.stopWait)] else: return []
[docs] def stopWait(self): f = open(self._getStopWaitingFilename(), 'w') f.close()
[docs] def waitingHasFinished(self): return os.path.exists(self._getStopWaitingFilename())
[docs] def registerOutput(self, outputName, value): self.outputsToDefine[outputName] = value
[docs] def registerEvenBoxSize(self, boxSize): boxSize = transform2EvenNumber(boxSize) self.registerOutput(BOXSIZE, Integer(boxSize))
[docs] def createResultsOutput(self): """ The output is an even Integer. Other protocols can use it in those Params if it has set allowsPointer=True """ self._defineOutputs(**self.outputsToDefine)
def _summary(self): summary = [] return summary def _validate(self): errors = [] if not self.boolBoxSize1.get() and not self.boolBoxSizeAvg.get(): errors.append('One of the two options should be selected as True.') if self.boolTimer.get(): timeInSec = self.getTimeOutInSeconds(self.timeout.get()) if timeInSec == 0: errors.append('Time format is wrong. A correct format is an ' 'integer number in seconds or the following syntax: ' '{days}d {hours}h {minutes}m {seconds}s separated by' ' spaces e.g: 1d 2h 20m 15s, 10m 3s, 1h, 20s or 25.') return errors
[docs]def transform2EvenNumber(var): if var % 2 != 0: var = round(var / 2) * 2 return var