# Move to Stage 3, where we get the residence time distribution Utilities.globalIO.setStep("Step3::GetModel") # no longer in any particular file, so save in 'top level' Utilities.globalIO.setFile("") params,stdev,RSQ = GetModel.GetModelMain(fileData,modelsToUse) else: # stage 3 files exist. Just need to load the files to be able # to compare... params = [] stdev = [] RSQ = [] for num in modelsToUse: thisModelFiles = [Utilities.getModelFile(f,num) for f in fileNamesStage3] paramsTmp, stdevTmp,RSQTmp = \ Utilities.loadAll(stage3Folder, thisModelFiles) params.append(paramsTmp) stdev.append(stdevTmp) RSQ.append(RSQTmp) Utilities.ReportMessage("Skipping Stage3 since [" + cacheFileS3 + "] already exists, plotting comparison.") # for each trial, for now just look at a single Model # XXX fix this!... modelToCheck = 0 fitStdRsq = [params[modelToCheck][:],stdev[modelToCheck][:], RSQ[modelToCheck]] stats = np.concatenate(fitStdRsq) trialStats[tNum,:] = stats # POST: all trials completed. Utilities.globalIO.reset() outputDir = Utilities.globalIO.getOutputDir([],"")
# 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 Utilities.globalIO.setStep("Step2::GetPhysics") unfoldingTimes, diffusionCoeffs = \ GetPhysics.GetPhysicsMain(trackedTimes ,trackedFRET,trackedDiffusion) exit(1)