def correctMask(self):
"""
Apply spline and tilt correction to the mask if provided in fit2d format.
"""
self.DEBUG("EDPluginSPDCakev1_5.correctMask")
EDPluginSPDCakev1_5.__semaphore.acquire()
t0 = time.time()
# self.screen("%s: preCalc Mask file is in %s" % (self.getId(), self.dictGeometry["MaskFile"]))
if (self.dictGeometry["MaskFile"] not in EDPluginSPDCakev1_5.__dictMask):
strUnCorrectedEdfMask = self.dictGeometry["MaskFile"]
unCorrectedMask = fabio.open(strUnCorrectedEdfMask)
basename = os.path.join(self.getSPDCommonDirectory(), os.path.splitext(os.path.basename(strUnCorrectedEdfMask))[0])
if self.bCorrectTiltMask:
if not isinstance(unCorrectedMask, fabio.edfimage.edfimage):
strUnCorrectedEdfMask = os.path.join(self.getSPDCommonDirectory(),
os.path.splitext(os.path.basename(self.dictGeometry["MaskFile"]))[0] + ".edf")
unCorrectedEdfMask = fabio.edfimage.edfimage(header={}, data=unCorrectedMask.data.astype("float32"))
unCorrectedEdfMask.write(strUnCorrectedEdfMask)
imgConfig = self.getSPDConfig()
mskConfig = " ".join([i for i in imgConfig.split() \
if not (i.startswith("mask_file=") or i.startswith("azim_")\
or i.startswith("flood_file=") or i.startswith("dark_file="))] + ["do_dark=0", "dummy=1"])
worker = SPDworker()
worker.setExecutable(self.getExecutable())
worker.setLogFilename(os.path.join(self.getSPDCommonDirectory(), "worker-mask.log"))
worker.initialize(mskConfig)
worker.setTimeOut(self.getTimeOut())
dictLog = worker.process("outdir=%s/ %s" % (self.getSPDCommonDirectory(), strUnCorrectedEdfMask))
for oneLog in dictLog:
self.DEBUG("EDPluginSPDCakev1_5.correctMask %s: %s" % (oneLog, dictLog[oneLog]))
worker.kill(gentle=True)
worker = None
npaCorrected = -(fabio.open(basename + ".cor").data + 0.5).astype("int8")
else:
npaCorrected = -(unCorrectedMask.data).astype("int8")
strCorrectedMask = basename + ".msk"
fabio.edfimage.edfimage(data=npaCorrected, header={"Dummy":"-1"}).write(strCorrectedMask)
EDPluginSPDCakev1_5.__dictMask[self.dictGeometry["MaskFile"]] = strCorrectedMask
EDPluginSPDCakev1_5.__semaphore.release()
newConfig = []
for key in self.getSPDConfig().split():
if key.startswith("mask_file="):
newConfig.append('mask_file=%s' % os.path.abspath(EDPluginSPDCakev1_5.__dictMask[self.dictGeometry["MaskFile"]]))
else:
newConfig.append(key)
self.setSPDConfig(" ".join(newConfig))
# self.worker.setConfig(self.getSPDConfig())
self.DEBUG("%s updating mask %s took %.3fs " % (self.getId(), self.dictGeometry["MaskFile"], time.time() - t0))
def correctMask(self):
"""
Apply spline and tilt correction to the mask if provided in fit2d format.
"""
self.DEBUG("EDPluginSPDCakev1_5.correctMask")
EDPluginSPDCakev1_5.__semaphore.acquire()
t0 = time.time()
# self.screen("%s: preCalc Mask file is in %s" % (self.getId(), self.dictGeometry["MaskFile"]))
if (self.dictGeometry["MaskFile"]
not in EDPluginSPDCakev1_5.__dictMask):
strUnCorrectedEdfMask = self.dictGeometry["MaskFile"]
unCorrectedMask = fabio.open(strUnCorrectedEdfMask)
basename = os.path.join(
self.getSPDCommonDirectory(),
os.path.splitext(os.path.basename(strUnCorrectedEdfMask))[0])
if self.bCorrectTiltMask:
if not isinstance(unCorrectedMask, fabio.edfimage.edfimage):
strUnCorrectedEdfMask = os.path.join(
self.getSPDCommonDirectory(),
os.path.splitext(
os.path.basename(self.dictGeometry["MaskFile"]))[0]
+ ".edf")
unCorrectedEdfMask = fabio.edfimage.edfimage(
header={}, data=unCorrectedMask.data.astype("float32"))
unCorrectedEdfMask.write(strUnCorrectedEdfMask)
imgConfig = self.getSPDConfig()
mskConfig = " ".join([i for i in imgConfig.split() \
if not (i.startswith("mask_file=") or i.startswith("azim_")\
or i.startswith("flood_file=") or i.startswith("dark_file="))] + ["do_dark=0", "dummy=1"])
worker = SPDworker()
worker.setExecutable(self.getExecutable())
worker.setLogFilename(
os.path.join(self.getSPDCommonDirectory(),
"worker-mask.log"))
worker.initialize(mskConfig)
worker.setTimeOut(self.getTimeOut())
dictLog = worker.process(
"outdir=%s/ %s" %
(self.getSPDCommonDirectory(), strUnCorrectedEdfMask))
for oneLog in dictLog:
self.DEBUG("EDPluginSPDCakev1_5.correctMask %s: %s" %
(oneLog, dictLog[oneLog]))
worker.kill(gentle=True)
worker = None
npaCorrected = -(fabio.open(basename + ".cor").data +
0.5).astype("int8")
else:
npaCorrected = -(unCorrectedMask.data).astype("int8")
strCorrectedMask = basename + ".msk"
fabio.edfimage.edfimage(data=npaCorrected, header={
"Dummy": "-1"
}).write(strCorrectedMask)
EDPluginSPDCakev1_5.__dictMask[
self.dictGeometry["MaskFile"]] = strCorrectedMask
EDPluginSPDCakev1_5.__semaphore.release()
newConfig = []
for key in self.getSPDConfig().split():
if key.startswith("mask_file="):
newConfig.append(
'mask_file=%s' %
os.path.abspath(EDPluginSPDCakev1_5.__dictMask[
self.dictGeometry["MaskFile"]]))
else:
newConfig.append(key)
self.setSPDConfig(" ".join(newConfig))
# self.worker.setConfig(self.getSPDConfig())
self.DEBUG(
"%s updating mask %s took %.3fs " %
(self.getId(), self.dictGeometry["MaskFile"], time.time() - t0))
