Update roaching engine per gen3

Convert getWindowedFlux function to gen3, which just estimate a rough flux for a windowed exposure, fiberTrace and detectorMap

import logging
import time

import numpy as np
import pandas as pd
from lsst.ip.isr import AssembleCcdTask

config = AssembleCcdTask.ConfigClass()
config.doTrim = TrueassembleTask = AssembleCcdTask(config=config)

from pfs.drp.stella.extractSpectraTask import ExtractSpectraTask

config = ExtractSpectraTask.ConfigClass()
config.doCrosstalk = Trueconfig.validate()
extractSpectra = ExtractSpectraTask(config=config)

def getWindowedFluxes(butler, dataId, fiberTrace, detectorMap, darkVariance=30, **kwargs):
"""Return an estimate of the median flux in each fibre butler: a butler pointing at the data dataId:a dict specifying the desired data fiberTraces: a dict indexed by arm containing the appropriate FiberTrace objects If None, read and construct the FiberTrace kwargs: overrides for dataId """ start = time.time()
dataId = dataId.copy()
dataId.update(kwargs)

exp = butler.get("raw", dataId)
exp = exp.convertF()

md = exp.getMetadata()
row0, row1 = md["W_CDROW0"], md["W_CDROWN"]

maskVal = exp.mask.getPlaneBitMask(["SAT", "NO_DATA"])
exp.mask.array[0:row0] = maskVal
exp.mask.array[row1 + 1:] = maskVal
exp.image.array[exp.mask.array != 0] = np.NaN # not 0; we're going to use np.nanmedian later for amp in exp.getDetector():
exp[amp.getRawBBox()].image.array -= np.nanmedian(exp[amp.getRawHorizontalOverscanBBox()].image.array)

exp = assembleTask.assembleCcd(exp)
exp.variance = exp.image
exp.variance.array += darkVariance # need a floor to the noise to reduce the b arm spectra = extractSpectra.run(exp.maskedImage, fiberTrace, detectorMap).spectra.toPfsArm(dataId)
spectra.flux[spectra.mask != 0] = np.NaN

df = pd.DataFrame(dict(flux=np.nanmedian(spectra.flux, axis=1), fiberId=spectra.fiberId))
# calculating time. totalTime = round(time.time() - start, 1)
logging.info(f'{dataId{color:#cf8e6d}} flux extracted in {totalTime{color:#cf8e6d}}s')
return df