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Merge pull request #141 from slaclab/analyzeNpyScan
Merge analyzeNpyScan into deveopment
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,226 @@ | ||
| import os | ||
| import sys | ||
|
|
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| import h5py | ||
| import numpy as np | ||
|
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| ## actually not psana, should rename | ||
| ## need this for DataSource.smalldata in analysis script | ||
| from calibrationSuite.psana2Base import * ##DataSource | ||
|
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| ##from calibrationSuite.argumentParser import ArgumentParser | ||
| ##import importlib.util | ||
| from calibrationSuite.psanaCommon import PsanaCommon | ||
|
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| ## do we actually need this? | ||
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| class PsanaBase(PsanaCommon): ## not actually psana, should rename | ||
| def __init__(self, analysisType="scan"): | ||
| super().__init__(analysisType) | ||
| commandUsed = sys.executable + " " + " ".join(sys.argv) | ||
| ##logger.info("Ran with cmd: " + commandUsed) | ||
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| self.psanaType = 0 | ||
| print("in nonPsanaBase") | ||
| ##logger.info("in nonPsanaBase") | ||
| self.myrun = None | ||
| self.setupNonPsana() | ||
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| def setupNonPsana(self): | ||
| ## temp hack ## | ||
| ##self.args = ArgumentParser().parse_args() | ||
| ## now done in PsanaCommon | ||
| defaultConfigFileName = "suiteConfig.py" | ||
| secondaryConfigFileName = defaultConfigFileName if self.args.configFile is None else self.args.configFile | ||
| # secondaryConfigFileName is returned if env var not set | ||
| configFileName = os.environ.get("SUITE_CONFIG", secondaryConfigFileName) | ||
| config = self.importConfigFile(configFileName) | ||
| if config is None: | ||
| print("\ncould not find or read config file: " + configFileName) | ||
| print("please set SUITE_CONFIG env-var or use the '-cf' cmd-line arg to specify a valid config file") | ||
| print("exiting...") | ||
| sys.exit(1) | ||
| self.experimentHash = config.experimentHash | ||
| ## temp ## | ||
| nonXtcFiles = self.args.nonXtcFiles | ||
| if nonXtcFiles is not None: | ||
| self.file = None ## nonPsanaBase only used as substitute xtc reader | ||
| print(nonXtcFiles) | ||
| self.setupNonXtcFiles(nonXtcFiles) | ||
|
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| if "run" not in dir(self) or self.run is None: | ||
| self.run = 666666 | ||
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| self.ignoreEventCodeCheck = True | ||
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| def setupNonXtcFiles(self, nonXtcFiles): | ||
| if nonXtcFiles.endswith("h5"): | ||
| self.h5File = h5py.File(nonXtcFiles) ## need concat | ||
| self.getDataFromFile() | ||
| self.getStepInfoFromFile() | ||
| self.npyFile = False | ||
| elif nonXtcFiles.endswith("npy"): | ||
| if "," in nonXtcFiles: | ||
| self.data = np.concatenate([np.load(f) for f in nonXtcFiles.split(",")]) | ||
| else: | ||
| self.data = np.load(nonXtcFiles) | ||
| fixAlexOrdering = True | ||
| if fixAlexOrdering: | ||
| self.data = np.array([np.array([self.data[:, :, i]]) for i in range(self.data.shape[2])]) | ||
|
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| self.setDataArray(self.data) | ||
| self.h5File = False | ||
| else: | ||
| raise Exception("non-psana file formats h5 and npy only") | ||
|
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| ## def importConfigFile(self, file_path): | ||
| ## if not os.path.exists(file_path): | ||
| ## print(f"The file '{file_path}' does not exist") | ||
| ## return None | ||
| ## spec = importlib.util.spec_from_file_location("config", file_path) | ||
| ## config_module = importlib.util.module_from_spec(spec) | ||
| ## spec.loader.exec_module(config_module) | ||
| ## return config_module | ||
|
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| def getDataFromFile(self): | ||
| self.data = self.h5File["frames"][()] | ||
| self.setDataArray(self.data) | ||
|
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| def getStepInfoFromFile(self): | ||
| try: | ||
| self.step_value = self.h5File["step_value"][()] | ||
| except: | ||
| print("could not find step_value in h5 file foo") | ||
| self.step_value = [None] | ||
|
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| def setDataArray(self, data): | ||
| self.data = data | ||
| print("data shape:", self.data.shape) | ||
| self.dataIter = iter(self.data) | ||
| print("have set up dataIter") | ||
| self.myrun = MyRun(self.data) | ||
|
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| def getStepGen(self): | ||
| self.stepIndex = -1 ## needed? | ||
| return self.stepGen() | ||
|
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| def setupPsana(self): ## should rename to setupBase or whatever | ||
| print("in fake setupPsana; get info from npy or h5 and fake stuff") | ||
| if False: | ||
| self.ds = DataSource(files=[nonXtcFiles]) ## to make smalldata happy | ||
| print("data source is", self.ds) | ||
| else: | ||
| self.ds = psana.DataSource(exp="rixx1005922", run=6) ##66) | ||
| ##self.ds = psana.MPIDataSource('exp=detdaq23:run=1')##66) | ||
| ## get event to make smd call happy | ||
| ##evt = next(self.ds.events()) | ||
| self.skipZeroCheck = True ## some Alex data gets entirely lost else | ||
|
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||
| if False: | ||
| self.getDataFromFile() | ||
| self.getStepInfoFromFile() | ||
|
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| def stepGen(self): | ||
| while True: | ||
| try: | ||
| self.stepIndex += 1 | ||
| step = Step(next(self.dataIter), self.stepIndex) | ||
| yield step | ||
| except: | ||
| ##raise StopIteration | ||
| return | ||
| ##print("in stepGen, stepIndex:", self.stepIndex) | ||
|
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| def getScanValue(self, step, useStringInfo=False): | ||
| if useStringInfo: | ||
| ##print("no idea how to use stringInfo, giving up") | ||
| ##sys.exit(0) | ||
| pass | ||
| ##print(self.step_value[step.nStep]) | ||
| ##print(type(self.step_value[step.nStep])) | ||
| return self.step_value[step.nStep] | ||
|
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| def getEventCodes(self, foo): | ||
| return [283] | ||
|
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| def plainGetRawData(self, evt): | ||
| return evt.astype("uint16") | ||
|
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| def getFlux(self, foo): | ||
| return 1 | ||
|
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| def get_smalldata(self, filename): ##, gather_interval=100): | ||
| try: | ||
| return self.ds.smalldata(filename=filename) ##, gather_interval=gather_interval) | ||
| except Exception: | ||
| print("can't make smalldata - is datasource defined?") | ||
| return None | ||
|
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|
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| class MyRun(object): | ||
| def __init__(self, array): | ||
| ## it would probably be smarter to have a reader (?) class instead | ||
| ## of loading everything into memory | ||
| ## could do | ||
| ## with h5py.File('TID.data') as data: | ||
| ## frames = data['frames'] | ||
| ## eventN = 0 | ||
| ## while True: | ||
| ## try: | ||
| ## event = frames[eventN++, :...] | ||
| ## yield event | ||
| ## except: | ||
| ## return | ||
| self.array = array | ||
|
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| def events(self): | ||
| ## it would be smarter to yield the next event instead of filling RAM | ||
| ##return(np.vstack(self.array)) | ||
| return self.array | ||
|
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|
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| class Step(object): | ||
| def __init__(self, array, nStep): | ||
| self.array = array | ||
| self.nStep = nStep | ||
|
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| def events(self): | ||
| return self.array | ||
|
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| if __name__ == "__main__": | ||
| npb = NonPsanaBase() | ||
|
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| print("try running over 2, 3, 2 step data with step calls") | ||
| ##npb.setDataArray(np.load("../data/testStepData.npy")) | ||
| npb.setDataArray(np.load("testStepData.npy")) | ||
| stepGen = npb.getStepGen() | ||
| ##stepGen = npb.dataIter doesn't work because we want step.events below | ||
| for nStep, step in enumerate(stepGen): | ||
| print("step %d" % (nStep)) | ||
| for nEvt, evt in enumerate(step.events()): | ||
| print("nEvt, evt:", nEvt, evt) | ||
|
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| print("end up with stepIndex:", npb.stepIndex) | ||
|
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| if True: | ||
| print("try running over 1, 3, 2 non-step data with step calls") | ||
| npb.setDataArray(np.load("../data/testNoStepData.npy")) | ||
| stepGen = npb.getStepGen() | ||
| for nStep, step in enumerate(stepGen): | ||
| print("step %d" % (nStep)) | ||
| for nEvt, evt in enumerate(step.events()): | ||
| print(nEvt, evt) | ||
|
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| print("try running over 2, 3, 2 non-step data with event call") | ||
| npb.setDataArray(np.load("../data/testStepData.npy")) | ||
| evtGen = npb.myrun.events() | ||
| for nEvt, evt in enumerate(evtGen): | ||
| print(nEvt, evt) | ||
|
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| print("try running over 1, 3, 2 non-step data with event call") | ||
| npb.setDataArray(np.load("../data/testNoStepData.npy")) | ||
| evtGen = npb.myrun.events() | ||
| for nEvt, evt in enumerate(evtGen): | ||
| print(nEvt, evt) |
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