Esempio n. 1
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def PushSourceIfNeeded(ToSave, force=False):
    """
    Pushes a single wave object as a binary file if it doesn't already exist
    (and if force is False). Saves the full note, as well as 'DataY'. 
    
    Args:

         ToSave: Wave object (See ProcessSingleWave) to save out. Most likely,
         this will be a concatenation; columns of (e.g.) time, distance, force

         force: if true, force creates the file

    Returns:
        None  
    """
    # check if the file already exists
    FileName = BinaryHDF5Io.GetFileSaveName(ToSave.GetNoteElement())
    # get the pull path (to the actual database...)
    FullPath = IgorUtil.getDatabaseFile(FileName)
    if (pGenUtil.isfile(FullPath) and not force):
        # don't do anything
        return
    else:
        # save the file out, using a blank string for the file name
        # (ie: just the folder)
        DatabasePath = IgorUtil.getDatabaseFolder()
        # XXX TODO: check that path exists to file?
        try:
            BinaryHDF5Io.\
                SaveWaveGroupAsTimeSepForceHDF5(FolderPath=DatabasePath,
                                                WaveGroup=ToSave)
        except:
            print("XXX file saving disabled [off campus?]")
Esempio n. 2
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def PushSourceIfNeeded(ToSave,force=False):
    """
    Pushes a single wave object as a binary file if it doesn't already exist
    (and if force is False). Saves the full note, as well as 'DataY'. 
    
    Args:

         ToSave: Wave object (See ProcessSingleWave) to save out. Most likely,
         this will be a concatenation; columns of (e.g.) time, distance, force

         force: if true, force creates the file

    Returns:
        None  
    """
    # check if the file already exists
    FileName = BinaryHDF5Io.GetFileSaveName(ToSave.GetNoteElement())
    # get the pull path (to the actual database...)
    FullPath = IgorUtil.getDatabaseFile(FileName)
    if (pGenUtil.isfile(FullPath) and not force):
        # don't do anything
        return
    else:
        # save the file out, using a blank string for the file name
        # (ie: just the folder)
        DatabasePath = IgorUtil.getDatabaseFolder()
        # XXX TODO: check that path exists to file?
        try:
            BinaryHDF5Io.\
                SaveWaveGroupAsTimeSepForceHDF5(FolderPath=DatabasePath,
                                                WaveGroup=ToSave)
        except:
            print("XXX file saving disabled [off campus?]")
Esempio n. 3
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    def __init__(self, CacheLoc=None):
        """
        Args:
            WaveData: The raw data to save to the cache. Formatted as XXX
            AddMethod : Method to call when data is available. If no cache,
            this is all the data immediately. If we use a cache, this is 
            after we save the data

            CacheLoc: Where to save the cache. If 'None', then we don't use a 
            cache, we just save the rawdata
        """
        self.CacheLoc = CacheLoc
        self.UseCache = CacheLoc is not None
        if (self.UseCache):
            pGenUtil.ensureDirExists(CacheLoc)
        # "extensions" is used to keep track of what extensions belong to which
        # data...
        self.WaveNameMap = dict()
        self.pool = Pool(NThreads)
    def __init__(self,CacheLoc=None):
        """
        Args:
            WaveData: The raw data to save to the cache. Formatted as XXX
            AddMethod : Method to call when data is available. If no cache,
            this is all the data immediately. If we use a cache, this is 
            after we save the data

            CacheLoc: Where to save the cache. If 'None', then we don't use a 
            cache, we just save the rawdata
        """
        self.CacheLoc = CacheLoc
        self.UseCache = CacheLoc is not None
        if (self.UseCache):
            pGenUtil.ensureDirExists(CacheLoc)
        # "extensions" is used to keep track of what extensions belong to which
        # data...
        self.WaveNameMap = dict()
        self.pool = Pool(NThreads) 
Esempio n. 5
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def LoadPxpFilesFromDirectory(directory):
    """
    Given a directory, load all the pxp files into a wave

    Args:
        directory: loads all directories 
    Returns:
        see LoadAllWavesFromPxp
    """
    allFiles = pGenUtil.getAllFiles(directory,ext=".pxp")
    d = []
    for f in allFiles:
        d.extend(LoadAllWavesFromPxp(f))
    return d
    def SourceFilename(self):
        """
        Returns the source file for this wave
        
        Returns:
            Source filename, without extension or path
        """

        SrcPath = self.Note["SourceFile"]
        # convert the path to just a simple file (without extension)
        # remove everything except the file name (including the extension)
        fileWithExt = pGenUtil.getFileFromPath(SrcPath)
        # return everything before the extension
        return os.path.splitext(fileWithExt)[0]
    def SourceFilename(self):
        """
        Returns the source file for this wave
        
        Returns:
            Source filename, without extension or path
        """           

        SrcPath = self.Note["SourceFile"]
        # convert the path to just a simple file (without extension)
        # remove everything except the file name (including the extension)
        fileWithExt = pGenUtil.getFileFromPath(SrcPath)
        # return everything before the extension
        return os.path.splitext(fileWithExt)[0]
Esempio n. 8
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def GetTimeSepForce(binaryFilePath):
    """
    Given a path to a binary file, reads in (the assumed generic/default)
    dataset, and gets the columns for time, separatio, and force
    
    Returns:
        tuple of (time,sep,force) arrays
    Raises:
        IoError
    """
    # make sure we have the right extensions
    # XXX throw error otherwise?
    mFile = pGenUtil.ensureEnds(binaryFilePath, DEFAULT_HDF5_EXTENSION)
    time = ReadHDF5FileDataSet(mFile)[:, COLUMN_TIME]
    sep = ReadHDF5FileDataSet(mFile)[:, COLUMN_SEP]
    force = ReadHDF5FileDataSet(mFile)[:, COLUMN_FORCE]
    return time, sep, force
Esempio n. 9
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def GetTimeSepForce(binaryFilePath):
    """
    Given a path to a binary file, reads in (the assumed generic/default)
    dataset, and gets the columns for time, separatio, and force
    
    Returns:
        tuple of (time,sep,force) arrays
    Raises:
        IoError
    """
    # make sure we have the right extensions
    # XXX throw error otherwise?
    mFile = pGenUtil.ensureEnds(binaryFilePath, DEFAULT_HDF5_EXTENSION)
    time = ReadHDF5FileDataSet(mFile)[:, COLUMN_TIME]
    sep = ReadHDF5FileDataSet(mFile)[:, COLUMN_SEP]
    force = ReadHDF5FileDataSet(mFile)[:, COLUMN_FORCE]
    return time, sep, force
Esempio n. 10
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def ReadHDF5File(inFile):
    """
    Reads in an HDF5, does *not* do any maintenane on the file (cleaning,etc)

    Args:
        inFile: path to the file
    Returns:
        Nothing
    Raises:
        IoError
    """
    if (not pGenUtil.isfile(inFile)):
        mErr = ("ReadHDF5File : File {:s} not found.".format(inFile) +
                "Do you need to connect to a netwrok drive to find your data?")
        raise IOError(mErr)
    # POST: the file at least exists
    mFile = h5py.File(inFile, READ_MODE)
    return mFile
Esempio n. 11
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def ReadHDF5File(inFile):
    """
    Reads in an HDF5, does *not* do any maintenane on the file (cleaning,etc)

    Args:
        inFile: path to the file
    Returns:
        Nothing
    Raises:
        IoError
    """
    if (not pGenUtil.isfile(inFile)):
        mErr = ("ReadHDF5File : File {:s} not found.".format(inFile) +
                "Do you need to connect to a netwrok drive to find your data?")
        raise IOError(mErr)
    # POST: the file at least exists
    mFile = h5py.File(inFile, READ_MODE)
    return mFile
Esempio n. 12
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def AssertDataSavedCorrectly(AssociatedWaveData):
    """
    Tests the binary file is saved properly. Doesn't check for notes (assumes
    that is OK), but *does* check for data matching.

    Args:
        AssociatedWaveData: a WaveDataGroup object (see Model)

    Returns:
        None
    """
    # make a copy of the wave, to use as meta data...
    mEle = AssociatedWaveData.GetNoteElement()
    SavedFilePath = BinaryHDF5Io.GetFileSaveName(mEle)
    DataFilePath = IgorUtil.getDatabaseFile(SavedFilePath)
    assert pGenUtil.isfile(DataFilePath) , "File {:s} wasn't saved.".\
        format(DataFilePath)
    # POST: file exists. Hooray! Is it correct?
    readObj = BinaryHDF5Io.LoadHdfFileIntoWaveObj(DataFilePath)
    correctObj = AssociatedWaveData.CreateTimeSepForceWaveObject()
    # note we overload "==" to check that notes *and* data match
    assert (readObj == correctObj) , "File read back in doesn't match."
Esempio n. 13
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def AssertDataSavedCorrectly(AssociatedWaveData):
    """
    Tests the binary file is saved properly. Doesn't check for notes (assumes
    that is OK), but *does* check for data matching.

    Args:
        AssociatedWaveData: a WaveDataGroup object (see Model)

    Returns:
        None
    """
    # make a copy of the wave, to use as meta data...
    mEle = AssociatedWaveData.GetNoteElement()
    SavedFilePath = BinaryHDF5Io.GetFileSaveName(mEle)
    DataFilePath = IgorUtil.getDatabaseFile(SavedFilePath)
    assert pGenUtil.isfile(DataFilePath) , "File {:s} wasn't saved.".\
        format(DataFilePath)
    # POST: file exists. Hooray! Is it correct?
    readObj = BinaryHDF5Io.LoadHdfFileIntoWaveObj(DataFilePath)
    correctObj = AssociatedWaveData.CreateTimeSepForceWaveObject()
    # note we overload "==" to check that notes *and* data match
    assert (readObj == correctObj), "File read back in doesn't match."