Utilities.ReportError(True,msg,"Main.py")
for tNum,t in enumerate(trials):
# get the matching files for this trial
trialFiles = [ fileN for fileN in filesFound if t in fileN]
trialTimes = []
trialDiff = []
Utilities.globalIO.setTrial(t)
stage3Folder = (Utilities.globalIO.getOutputDir([],"") +
"Post_Stage3_Analysis/").\
replace("//","/")
# stage 3 recquires knowing which model we will use...
# XXX fix this to allow for different models? Pass as a param to model.
cacheFileS3 = stage3Folder + "ModelParams4.npy"
# if we have stage3, then just skip to the final ....
if (not Utilities.dirExists(cacheFileS3)
or forceStage3):
fileData = []
for f in trialFiles:
fileNameExt = os.path.basename(f)
fileName = os.path.splitext(fileNameExt)[0]
Utilities.globalIO.setFile(fileName)
Utilities.globalIO.setStep("Step1::GetTraces")
# get the output dir with no prior / after path
outputDir = Utilities.globalIO.getOutputDir([],"")
checkPointDir = outputDir + Utilities.CheckpointDir
checkPointFilePath = checkPointDir + 'Stage_'
# ensure the saving directory exists
Utilities.ensureDirExists(checkPointDir)
stageCount = 1
for t in trials:
filesFound=[ testDir+f for f in filesFound if str(f).endswith(testDataType)]
if (len(filesFound) < 1):
msg = "Couldn't find any file like [{}] in [{}]".format(testDataType,
testDir)
Utilities.ReportError(True,msg,"Main.py")
# just use a single file for this testing bit.
filesFound = [filesFound[0]]
fileNameExt = os.path.basename(filesFound[0])
fileName = os.path.splitext(fileNameExt)[0]
Utilities.globalIO.setTrial(t)
Utilities.globalIO.setFile(fileName)
Utilities.globalIO.setStep("Step1::GetTraces")
outputDir = Utilities.globalIO.getOutputDir([],"")
stage1Folder = outputDir + "Post_Stage1_Analysis/"
if (not Utilities.dirExists(stage1Folder)):
# get the X,Y velocity, times, and ratio on a per protein basis
# each of these is a list. Each element in a list corresponds to data
# for a single protein
trackedTimes,trackedFRET,trackedDiffusion = \
GetTraces.GetTracesMain(filesFound)
# get the output dir for the previous path.
else:
# the output directory exists; no sense in re-running the analysis.
# just use the text output.
Utilities.ReportMessage("Skipping Stage1 since [" + stage1Folder +
"] already exists")
trackedTimes, trackedDiffusion,trackedFRET = \
Utilities.loadAll(stage1Folder,fileNames)
# POST: now have valid, trackable diffusion, times, and FRET
# Move to stage 2. where we get the unfolding times
