#!/usr/bin/env python # ---------------------------------------------------------------------------------------------------- import os, math import re # ---------------------------------------------------------------------------------------------------- import traceback # ---------------------------------------------------------------------------------------------------- # SimTk modules import BaseObjectSimTk from UtilitiesSimTk import * import LogSimTk # ---------------------------------------------------------------------------------------------------- def strToNumericCmpIReverse( x, y ): return int( y ) - int( x ) def strToNumericCmpI( x, y ): return int( x ) - int( y ) # ---------------------------------------------------------------------------------------------------- class IsimGridFileSimTk( BaseObjectSimTk.BaseObjectSimTk ): # { # ------------------------------------------------------------------------------------------------- def __init__( self, isimDisplay, fileName ): # { """Constructor for IsimGridFileSimTk""" BaseObjectSimTk.BaseObjectSimTk.__init__( self ) # attributes self._isimDisplay = isimDisplay self._fileName = fileName # the file prefix will be set in derived classes self._filePrefix = None self._fileFormat = None # step index if fileName is not None: generateStepGivenFileName( fileName ) self.setFileFormatBasedOnFileName() else: self._stepIndex = 0 # } end of __init__ # ------------------------------------------------------------------------------------------------- # accessors for file name def setFileName( self, fileName ): # { """Set accessor for FileName""" if fileName is not self._fileName: self.setStepIndexGivenFileName( fileName ) self._fileName = fileName # } end of setFileName # ------------------------------------------------------------------------------------------------- def getFileName( self ): # { """Get accessor for FileName""" return self._fileName; # } end of getFileName # ------------------------------------------------------------------------------------------------- # accessors for file prefix def setFilePrefix( self, filePrefix ): # { """Set accessor for FilePrefix""" self._filePrefix = filePrefix # } end of setFilePrefix # ------------------------------------------------------------------------------------------------- def getFilePrefix( self ): # { """Get accessor for FilePrefix""" return self._filePrefix; # } end of getFilePrefix # ------------------------------------------------------------------------------------------------- # accessors for file format def setFileFormat( self, fileFormat ): # { """Set accessor for file format""" self._fileFormat = fileFormat # } end of setFileFormat # ------------------------------------------------------------------------------------------------- def getFileFormat( self ): # { """Get accessor for file format""" return self._fileFormat # } end of getFileFormat # ------------------------------------------------------------------------------------------------- # accessors for step index def setStepIndex( self, stepIndex ): # { """Set accessor for step index""" self._stepIndex = stepIndex # } end of setStepIndex def getStepIndex( self ): # { """Get accessor for step index""" return self._stepIndex # } end of getStepIndex # ------------------------------------------------------------------------------------------------- # accessors for Isim display def setIsimDisplay( self, isimDisplay ): # { """Set accessor for Isim display""" self._isimDisplay = isimDisplay # } end of setIsimDisplay # ------------------------------------------------------------------------------------------------- def getIsimDisplay( self ): # { """Get accessor for Isim display""" return self._isimDisplay # } end of getIsimDisplay # ------------------------------------------------------------------------------------------------- # generate format string used in building file names def getFullFileName( self, mcStep, fileSuffix = None, ionIndex = -1 ): # { """Get full file name""" return self._isimDisplay.buildFullFileName( self.getFilePrefix(), mcStep, fileSuffix, ionIndex ) # } end of getFullFileName # ------------------------------------------------------------------------------------------------- # get file name def getFileName( self, mcStep, fileSuffix = None, ionIndex = -1 ): # { """Get file name""" return self._isimDisplay.buildFileName( self.getFilePrefix(), mcStep, fileSuffix, ionIndex ) # } end of getFileName # ------------------------------------------------------------------------------------------------- # generate file name give MC step def generateFileNameGivenStep( self, step, fileSuffix=None, requiredDigits=None ): # { """Helper method to generate file names Step is the MC step index fileSuffix is optional -- appended to file name requiredDigits number of digits in step name (defaults to 7) file name prefix is obtained via self.getFilePrefix() """ return self._isimDisplay.buildPartialFileNameGivenStep( self.getFilePrefix(), step, fileSuffix, requiredDigits ) # } end of generateFileNameGivenStep # ------------------------------------------------------------------------------------------------- # parse MC step from file name def generateStepGivenFileName( fileName, stepIndex = -1, separator = '_' ): # { """Helper method to get MS step from file name: 'GRID_POTENTIAL_0000600.dx' would return 600 """ numberDensityMatch = re.compile( 'GRID_NUMBER_DENSITIES' ) if numberDensityMatch.match( fileName ): stepIndex = -3 else: stepIndex = -1 # (1) remove file suffix, if present # (2) split name by '_' # (3) remove initial zeros fileName = UtilitiesSimTk.removeSuffix( fileName ) sections = fileName.split( separator ) stepSection = sections[stepIndex] # print "QQQ In generateStepGivenFileName stepIndex=" + str( stepIndex ) + ' step=' + stepSection + ' file=' + fileName return stepSection.lstrip( '0' ) generateStepGivenFileName = staticmethod( generateStepGivenFileName ) # } end of generateStepGivenFileName # ------------------------------------------------------------------------------------------------- # get files of specified type (grid_potential, charge density, number density) def getAvailableFiles( workingDirectory, fileType, ionIndex = None ): # { """Get files of the specified type present in the working directory""" # get list of all files of specified type regExMatchType = re.compile( fileType ) fileList = UtilitiesSimTk.getFilesInDirectory( workingDirectory, regExMatchType, None ) # diagnostics # print "QQQ getAvailableFiles: Files in fileList type=" + fileType # print str( fileList ) # filter ion types if ionIndex was set if ionIndex is not None: regExMatchTypeId = re.compile( '_' + str( ionIndex ) + '_' ) regExMatchTypeSuffix = re.compile( '.dx$' ) newFileList = [] for file in fileList: if regExMatchTypeId.search( file ) and regExMatchTypeSuffix.search( file ): newFileList.append( file ) fileList = newFileList return fileList # designate method as a static method for class getAvailableFiles= staticmethod( getAvailableFiles ) # } end of getAvailableFiles # ------------------------------------------------------------------------------------------------- # get MC steps for files of specified type def getAvailableMcStepsForFileOfSpecifiedType( workingDirectory, fileType, ionIndex = None ): # { """Get MC steps for the specified file type present in the working directory""" fileList = IsimGridFileSimTk.getAvailableFiles( workingDirectory, fileType, ionIndex ) stepDict = {} for file in fileList: value = IsimGridFileSimTk.generateStepGivenFileName( file ) if value.isdigit(): stepDict[value] = 1 stepList = stepDict.keys() if stepList is not None: # stepList.sort( cmp=strToNumericCmpIReverse ) stepList.sort( strToNumericCmpIReverse ) return stepList getAvailableMcStepsForFileOfSpecifiedType = staticmethod( getAvailableMcStepsForFileOfSpecifiedType ) # } end of getAvailableMcStepsForFileOfSpecifiedType # ------------------------------------------------------------------------------------------------- def getInstanceGivenFilePrefix( filePrefix, isimDisplay ): # { """Factory method to get class instance given file prefix""" rePrefix = re.compile( filePrefix ) if rePrefix.match( IsimPotentialFileSimTk.getFilePrefix() ): return IsimPotentialFileSimTk( isimDisplay ) elif rePrefix.match( IsimChargeDensityFileSimTk.getFilePrefix() ): return IsimChargeDensityFileSimTk( isimDisplay ) elif rePrefix.match( IsimNumberDensityFileSimTk.getFilePrefix() ): return IsimNumberDensityFileSimTk( isimDisplay ) else: raise valueError, ('filePrefix=<' + filePrefix + '> unrecognized.') getInstanceGivenFilePrefix = staticmethod( getInstanceGivenFilePrefix ) # } end of getInstanceGivenFilePrefix # ------------------------------------------------------------------------------------------------- # } end of class IsimGridFileSimTk class IsimPotentialFileSimTk( IsimGridFileSimTk ): # { # ------------------------------------------------------------------------------------------------- def __init__( self, isimDisplay, fileName = None ): # { """Constructor for IsimPotentialFileSimTk""" IsimGridFileSimTk.__init__( self, isimDisplay, fileName ) # attributes self._filePrefix = IsimPotentialFileSimTk.getFilePrefix() # } end of __init__ # ------------------------------------------------------------------------------------------------- def getFilePrefix( ): # { """IsimPotentialFileSimTk""" return 'GRID_POTENTIAL_' getFilePrefix = staticmethod( getFilePrefix ) # } end of getFilePrefix def getAbbreviation( self ): # { """IsimPotentialFileSimTk""" return 'P' # } end of getAbbreviation # } end of class IsimPotentialFileSimTk class IsimChargeDensityFileSimTk( IsimGridFileSimTk ): # { # ------------------------------------------------------------------------------------------------- def __init__( self, isimDisplay, fileName = None ): # { """Constructor for IsimChargeDensityFileSimTk""" IsimGridFileSimTk.__init__( self, isimDisplay, fileName ) # attributes self._filePrefix = IsimChargeDensityFileSimTk.getFilePrefix() # } end of __init__ # ------------------------------------------------------------------------------------------------- def getFilePrefix( ): # { """IsimChargeDensityFileSimTk""" return 'GRID_CHARGE_DENSITY_' getFilePrefix = staticmethod( getFilePrefix ) # } end of getFilePrefix def getAbbreviation( self ): # { """Get abbreviation for file type""" return 'CD' # } end of class IsimChargeDensityFileSimTk class IsimNumberDensityFileSimTk( IsimGridFileSimTk ): # { # ------------------------------------------------------------------------------------------------- def __init__( self, isimDisplay, fileName = None ): # { """Constructor for IsimNumberDensityFileSimTk""" IsimGridFileSimTk.__init__( self, isimDisplay, fileName ) # attributes self._filePrefix = IsimNumberDensityFileSimTk.getFilePrefix() self._ionIndex = -1 self._ionName = None self._ionFileNameStepIndex = -3 self._ionFileNameIdIndex = -2 self._ionFileNameIonNameIndex = -1 self._ionAbbreviation = None # } end of __init__ # ------------------------------------------------------------------------------------------------- def getFilePrefix( ): # { """IsimNumberDensityFileSimTk""" return 'GRID_NUMBER_DENSITIES_' getFilePrefix = staticmethod( getFilePrefix ) # } end of getFilePrefix def getAbbreviation( self ): # { """Get abbreviation for file type""" return self._ionAbbreviation # ------------------------------------------------------------------------------------------------- # accessors for ion index def setIonIndex( self, ionIndex ): # { """Set accessor for ion index""" self._ionIndex = ionIndex # } end of setIonIndex def getIonIndex( self ): # { """Get accessor for ion index""" return self._ionIndex # } end of getIonIndex # ------------------------------------------------------------------------------------------------- # accessors for ion name def setIonName( self, ionName ): # { """Set accessor for ion name""" self._ionName = ionName # } end of setIonName def getIonName( self ): # { """Get accessor for ion name""" return self._ionName # } end of getIonName # ------------------------------------------------------------------------------------------------- # accessors for ion abbreviation def setIonAbbreviation( self, ionAbbreviation ): # { """Set accessor for ion abbreviation""" self._ionAbbreviation = ionAbbreviation # } end of setIonAbbreviation def getIonAbbreviation( self ): # { """Get accessor for ion abbreviation""" return self._ionAbbreviation # } end of getIonAbbreviation # ------------------------------------------------------------------------------------------------- # parse MC step from file name # overrides super class method def generateStepGivenFileName( self, fileName, stepIndex = -1, separator = '_' ): # { """Helper method to get MS step from file name: 'NUMBER_DENSITIES_0000600_1.dx' would return 600 """ # use -2 index instead of default -1 to get step field self._stepIndex = IsimGridFileSimTk.generateStepGivenFileName( self, fileName, self._ionFileNameStepIndex, separator ) return self._stepIndex # } end of generateStepGivenFileName # ------------------------------------------------------------------------------------------------- # parse ion index from file name # uses related super class method def generateIonIndexGivenFileName( self, fileName, stepIndex = -1, separator = '_' ): # { """Helper method to get ion index from file name: 'NUMBER_DENSITIES_0000600_1_CALCIUM.dx' would return 1 """ # use -1 index to get ion index field self._ionIndex = IsimGridFileSimTk.generateStepGivenFileName( self, fileName, self._ionFileNameIdIndex, separator ) return self._ionIndex # } end of generateIonIndexGivenFileName # ------------------------------------------------------------------------------------------------- # } end of class IsimNumberDensityFileSimTk