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ENH: move basicSuiteScript stuff to commonPsanaBase, basicSuite not n…
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@nstelter-slac
nstelter-slac committed Apr 4, 2024
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304 changes: 0 additions & 304 deletions calibrationSuite/basicSuiteScript.py
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## may be copied, modified, propagated, or distributed except according to
## the terms contained in the LICENSE.txt file.
##############################################################################
import argparse
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator
import sys
import h5py
from scipy.optimize import curve_fit ## here?
from calibrationSuite.fitFunctions import *
from calibrationSuite.ancillaryMethods import *
from calibrationSuite.argumentParser import ArgumentParser
from calibrationSuite.detectorInfo import DetectorInfo
import os

if os.getenv("foo") == "1":
print("psana1")
from calibrationSuite.psana1Base import *
else:
print("psana2")
from calibrationSuite.psana2Base import *


def sortArrayByList(a, data):
return [x for _, x in sorted(zip(a, data), key=lambda pair: pair[0])]


class BasicSuiteScript(PsanaBase):
def __init__(self, analysisType="scan"):
super().__init__()
print("in BasicSuiteScript, inheriting from PsanaBase, type is psana%d" %(self.psanaType))
logger.info("in BasicSuiteScript, inheriting from PsanaBase, type is psana%d" %(self.psanaType))

##mymodule = importlib.import_module(full_module_name)

self.camera = 0
##self.outputDir = '/sdf/data/lcls/ds/rix/rixx1003721/results/%s/' %(analysisType)
self.outputDir = "../%s/" % (analysisType)
logging.info("output dir: " + self.outputDir)
##self.outputDir = '/tmp'

self.detectorInfo = DetectorInfo(self.experimentHash['detectorType'])

self.className = self.__class__.__name__

try:
self.location = self.experimentHash["location"]
except:
pass
try:
self.exp = self.experimentHash["exp"]
except:
pass
try:
##if True:
self.ROIfileNames = self.experimentHash["ROIs"]
self.ROIs = []
for f in self.ROIfileNames:
self.ROIs.append(np.load(f + ".npy"))
try: ## dumb code for compatibility or expectation
self.ROI = self.ROIs[0]
except:
pass
##if False:
except:
print("had trouble finding", self.ROIfileNames)
for currName in self.ROIfileNames:
logger.exception("had trouble finding" + currName)
self.ROI = None
self.ROIs = None
try:
self.singlePixels = self.experimentHash["singlePixels"]
except:
self.singlePixels = None
try:
self.regionSlice = self.experimentHash["regionSlice"]
except:
self.regionSlice = None
if self.regionSlice is not None:
self.sliceCoordinates = [
[self.regionSlice[0].start, self.regionSlice[0].stop],
[self.regionSlice[1].start, self.regionSlice[1].stop],
]
sc = self.sliceCoordinates
self.sliceEdges = [sc[0][1] - sc[0][0], sc[1][1] - sc[1][0]]

try:
self.fluxSource = self.experimentHash["fluxSource"]
try:
self.fluxChannels = self.experimentHash["fluxChannels"]
except:
self.fluxChannels = range(8, 16) ## wave8
try:
self.fluxSign = self.experimentHash["fluxSign"]
except:
self.fluxSign = 1
except:
self.fluxSource = None

## for non-120 Hz running
self.nRunCodeEvents = 0
self.nDaqCodeEvents = 0
self.nBeamCodeEvents = 0
self.runCode = 280
self.daqCode = 281
self.beamCode = 283 ## per Matt
##self.beamCode = 281 ## don't see 283...
self.fakeBeamCode = False

##mymodule = importlib.import_module(full_module_name)

## for standalone analysis
self.file = None
if self.args.files is not None:
self.file = self.args.files
self.label = ""
if self.args.label is not None:
self.label = self.args.label

## analyzing xtcs
if self.args.run is not None:
self.run = self.args.run
if self.args.camera is not None:
self.camera = self.args.camera
if self.args.exp is not None:
self.exp = self.args.exp
if self.args.location is not None:
self.location = self.args.location
if self.args.maxNevents is not None:
self.maxNevents = self.args.maxNevents
if self.args.skipNevents is not None:
self.skipNevents = self.args.skipNevents
if self.args.path is not None:
self.outputDir = self.args.path
# if set, output folders will be relative to OUTPUT_ROOT
# if not, they will be relative to the current script file
self.outputDir = os.getenv("OUTPUT_ROOT", "") + self.outputDir
# check if outputDir exists, if does not create it and tell user
if not os.path.exists(self.outputDir):
print("could not find output dir: " + self.outputDir)
logger.info("could not find output dir: " + self.outputDir)
print("please create this dir, exiting...")
logger.info("please create this dir, exiting...")
exit(1)
# the following doesnt work with mpi parallelism (other thread could make dir b4 curr thread)
#print("so creating dir: " + self.outputDir)
#logger.info("creating dir: " + self.outputDir)
#os.makedirs(self.outputDir)
# give dir read, write, execute permissions
#os.chmod(self.outputDir, 0o777)
self.detObj = self.args.detObj
if self.args.threshold is not None:
self.threshold = eval(self.args.threshold)
else:
self.threshold = None
if self.args.fluxCut is not None:
self.fluxCut = self.args.fluxCut
try:
self.runRange = eval(self.args.runRange) ## in case needed
except:
self.runRange = None

self.fivePedestalRun = self.args.fivePedestalRun ## in case needed
self.fakePedestal = self.args.fakePedestal ## in case needed
if self.fakePedestal is not None:
self.fakePedestalFrame = np.load(self.fakePedestal) ##cast to uint32???

self.g0PedFile = self.args.g0PedFile
if self.g0PedFile is not None:
##self.g0Ped = np.load(self.g0PedFile)
self.g0Ped = np.array([np.load(self.g0PedFile)])##temp hack
print(self.g0Ped.shape)

self.g1PedFile = self.args.g0PedFile
if self.g1PedFile is not None:
##self.g1Ped = np.load(self.g1PedFile)
self.g1Ped = np.array([np.load(self.g1PedFile)])##temp hack

self.g0GainFile = self.args.g0GainFile
if self.g0GainFile is not None:
self.g0Gain = np.load(self.g0GainFile)

self.g1GainFile = self.args.g1GainFile
if self.g1GainFile is not None:
self.g1Gain = np.load(self.g1GainFile)

self.offsetFile = self.args.offsetFile
if self.offsetFile is not None:
self.offset = np.load(self.offsetFile)

if self.args.detType == "":
## assume epix10k for now
if self.args.nModules is not None:
self.detectorInfo.setNModules(self.args.nModules)
self.detType = self.detectorInfo.getCameraType()
else:
self.detType = self.args.detType

self.special = self.args.special
## done with configuration

self.ds = None
self.det = None ## do we need multiple dets in an array? or self.secondDet?

##self.setupPsana()
##do this later or skip for -file

def setROI(self, roiFile=None, roi=None):
"""Call with both file name and roi to save roi to file and use,
just name to load,
just roi to set for current job"""
if roiFile is not None:
if roi is None:
self.ROIfile = roiFile
self.ROI = np.load(roiFile)
return
else:
np.save(roiFile, roi)
self.ROI = roi

def sliceToDetector(self, sliceRow, sliceCol):## cp from AnalyzeH5: import?
return sliceRow + self.sliceCoordinates[0][0], sliceCol + self.sliceCoordinates[1][0]

def noCommonModeCorrection(self, frame):
return frame

def regionCommonModeCorrection(self, frame, region, arbitraryCut=1000):
## this takes a 2d frame
## cut keeps photons in common mode - e.g. set to <<1 photon

regionCM = np.median(frame[region][frame[region] < arbitraryCut])
return frame - regionCM

def rowCommonModeCorrection(self, frame, arbitraryCut=1000):
## this takes a 2d frame
## cut keeps photons in common mode - e.g. set to <<1 photon

##rand = np.random.random()
for r in range(self.detectorInfo.nRows):
colOffset = 0
##for b in range(0, self.detNbanks):
for b in range(0, 2):
try:
rowCM = np.median(
frame[r, colOffset : colOffset + self.detColsPerBank][
frame[r, colOffset : colOffset + self.detColsPerBank] < arbitraryCut
]
)
##if r == 280 and rand > 0.999:
##print(b, frame[r, colOffset:colOffset + self.detColsPerBank], rowCM, rowCM<arbitraryCut-1, rowCM*(rowCM<arbitraryCut-1))
##frame[r, colOffset:colOffset + self.detColsPerBank] -= rowCM*(rowCM<arbitraryCut-1)
frame[r, colOffset : colOffset + self.detColsPerBank] -= rowCM
##if r == 280 and rand > 0.999:
##print(frame[r, colOffset:colOffset + self.detColsPerBank], np.median(frame[r, colOffset:colOffset + self.detColsPerBank]))
except:
rowCM = -666
print("rowCM problem")
logger.error("rowCM problem")
print(frame[r, colOffset : colOffset + self.detColsPerBank])
colOffset += self.detColsPerBank
return frame

def colCommonModeCorrection(self, frame, arbitraryCut=1000):
## this takes a 2d frame
## cut keeps photons in common mode - e.g. set to <<1 photon

##rand = np.random.random()
for c in range(self.detCols):
rowOffset = 0
for b in range(0, self.detNbanksCol):
##for b in range(0, 2):
try:
colCM = np.median(
frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank, c][
frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank, c] < arbitraryCut
]
)
##if r == 280 and rand > 0.999:
##print(b, frame[r, colOffset:colOffset + self.detColsPerBank], rowCM, rowCM<arbitraryCut-1, rowCM*(rowCM<arbitraryCut-1))
##frame[r, colOffset:colOffset + self.detColsPerBank] -= rowCM*(rowCM<arbitraryCut-1)
frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank, c] -= colCM
##if r == 280 and rand > 0.999:
##print(frame[r, colOffset:colOffset + self.detColsPerBank], np.median(frame[r, colOffset:colOffset + self.detColsPerBank]))
except:
colCM = -666
print("colCM problem")
logger.error("colCM problem")
print(frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank], c)
rowOffset += self.detectorInfo.nRowsPerBank
return frame

def isBeamEvent(self, evt):
ec = self.getEventCodes(evt)
##print(ec[280], ec[281], ec[282], ec[283], ec[284], ec[285] )
if ec[self.runCode]:
self.nRunCodeEvents += 1
if ec[self.daqCode]:
self.nDaqCodeEvents += 1
if self.fakeBeamCode:
return True
if ec[self.beamCode]:
self.nBeamCodeEvents += 1
return True
return False

def dumpEventCodeStatistics(self):
print(
"have counted %d run triggers, %d DAQ triggers, %d beam events"
% (self.nRunCodeEvents, self.nDaqCodeEvents, self.nBeamCodeEvents)
)
logger.info(
"have counted %d run triggers, %d DAQ triggers, %d beam events"
% (self.nRunCodeEvents, self.nDaqCodeEvents, self.nBeamCodeEvents)
)


if __name__ == "__main__":
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