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?]")
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?]")
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)
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]
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
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
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
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
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."
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."