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 SaveOutHighResData(filePath,\
fileIn="../../../CypherReader/UnitTests/LocalData/NUG2TestData.pxp"):
"""
Assuming the model corrections works, gets the Data to save out
Args:
fileIn : where the pxp is coming from
folderPath: where to save the data to (folder only)
Returns:
None
"""
allData = LoadHiResData(fileIn)
lowResTime,lowResSep,lowResForce,highResTime,sepExpected,\
highCorrForce,highResForce = GetOriginalAndCorrected(allData)
# get the *uncorrected* force ...
highResForceObj = WaveObj(DataY=highResForce.DataY,Note=highResForce.Note)
highResSepObj = WaveObj(DataY=sepExpected,Note=highResForce.Note)
# make a wave data group to save out
toSave = WaveDataGroup({"sep":lowResSep,"force":lowResForce})
toSave.HighBandwidthSetAssociatedWaves({"sep":highResSepObj,
"force":highResForceObj})
# save out the wave data as a group
actualFilePath = \
BinaryHDF5Io.SaveWaveGroupAsTimeSepForceHDF5(filePath,toSave)
return actualFilePath
def DataFromFileCache(self, FilePath):
"""
Gets the cached data from 'FileName'
Args:
FilePath: Where the file is located
Returns:
Data, formatted like a wave data group. will *always* be time,sep,
force
"""
# dont want to throw an error if the high res doesnt have a separation
return BinaryHDF5Io.ReadWaveIntoWaveGroup(FilePath, ErrorOnNoSep=False)
def GetHighResData(filePath):
"""
Given a file path, reads the data into a TimeSepForceObj, for easy reading.
Args:
filePath: where to get the data from
Returns:
A timeSepForceObj, presummabyly with high resolution data
"""
dataGroup = BinaryHDF5Io.ReadWaveIntoWaveGroup(filePath)
return TimeSepForceObj(dataGroup)
def DataToFile(self, WaveName, Data):
"""
Caches 'Data' to 'FileName', notifying it is saved
Args:
Data: see SaveAndNotify
FileName: see SaveAndNotify
Returns:
File path (actual path to the file)
"""
# get the extensions
assert WaveName not in self
# get the actual data to save out
# False: dont want to throw an error if Hi res isn't complete
return BinaryHDF5Io.SaveWaveGroupAsTimeSepForceHDF5(
self.CacheLoc, Data, False)
def __init__(self, MetaIds, WaveGroupObj, ParamVals, ParamIds):
"""
Args:
MetaIds: a dict with <table>/<ids> pairs for the The ids for all of the
tables associated with the User Meta (e.g User, TipType, etc),
as well as the experiment and model
WaveGroupObj: AssociatedWaveData we want to save out
Returns: A newly constructed traceObj
"""
self.MetaIds = MetaIds
self.WaveObj = WaveGroupObj
self.ParamVals = ParamVals
self.ParamIds = ParamIds
self.SaveName = BinaryHDF5Io.GetFileSaveName(WaveGroupObj.\
GetNoteElement())
self.idDot = ap.Namespace(**copy.deepcopy(self.MetaIds))
def PushToDatabase(ModelName, AssociatedWaveData, MetaViewParams,
ParameterDescriptions, CurrentParams, SqlObj):
"""
In a single operation, adds (or updates) a trace to the database.
If necessary (ie: if trace never added before), saves out the binary file.
Essentially a Model-friendly wrapper for SyncTraceWithDatabase
Args:
ModelName: String name of the model to use. Inserted if new.
AssociatedWaveData: See Model, WaveDataGroup. Includes the dictionary
of name:waveobj pairs to insert, Converted to Sep:Force on insert.
MetaViewParams: a dict of <table>:<ids> associated with the (user) meta
information tables
ParameterDescriptions: the meta information associated with the
parameters
CurrentParams: The current parameters (vals)associated. sorted to match
ParameterDescriptions.
SqlObj: The connection object to use
Returns:
updated id namespace object. For all tables (except parameters)
calling "NamespaceObject.<tablename>" will give the integer id used
for this insert.
"""
# check that we actualy have data to push
if (len(AssociatedWaveData) == 0):
raise ValueError("Nothing to push to database.")
# POST: something to push
# Get all of the meta data for the wave (e.g. pulling speed, etc)
# (XXX assume it is the same for all associated waves)
WaveNames = AssociatedWaveData.keys()
# convert all the view parameters to ids
toIdStr = lambda x: ("id" + x)
allIds = dict([(toIdStr(table), MetaViewParams[table][toIdStr(table)])
for table in MetaViewParams])
# if the source already exists for this model,
# then we want to *update* everything, not insert again
ModelData = InsertOrGetModelId(ModelName, SqlObj=SqlObj)
ModelId = ModelData.idModel
# tableName is a helper function that gets a table name from a
# SqlAlchemy object (e.g., that which is returned from a query)
idName = lambda SqlAlch: toIdStr(SqlAlch.__table__.name)
# add the model ID
allIds[idName(ModelData)] = ModelId
# Get the rows in the database associated with each parameter
# XXX inefficient use of SqlObj (repeated instantiation). Fix later...
paramIds = ParameterDescriptions.GetSqlParamIds(ModelRow=ModelData,
SqlObj=SqlObj)
# get the name of the file to save the data as
ElementForName = AssociatedWaveData.GetNoteElement()
SourceFile = BinaryHDF5Io.GetFileSaveName(ElementForName)
# get the ID associated with the experiment
Experiment = InsertOrGetSourceFile(SourceFile, SqlObj=SqlObj)
idExpMeta = Experiment.idExpMeta
allIds[idName(Experiment)] = idExpMeta
# Go ahead and concatenate all of the associated waves
# XXX TODO deal with high resolution waves?
# We now have everything needed to push this data to the database:
# (0) the actual data is in WaveData
# (1) all meta information needed by TraceMeta is in WaveData.Note
# (2) all Model information is in ModelData
# (3) all Parameter information is in paramIds (for meta) and just the
# parameter values we have saved
# (4) The many 'user meta' data points (e.g. tip type) are in
# We now pass all of this information to our SqlModel, which takes
# care of most of the hairy details. (e.g. linking, etc)
# XXX TODO: move most of above to the Sql model?
mObj = TraceObj(allIds, AssociatedWaveData, CurrentParams, paramIds)
idDot = SyncTraceWithDatabase(mObj, SqlObj=SqlObj)
idDot.idExpMeta = idExpMeta
idDot.idModel = ModelId
return idDot