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#!/usr/bin/python
import sys
import time
import numpy as np
from configparser import ConfigParser
from epics.utils import IOENCODING
from .. import Device, get_pv, poll, caput, caget
MAX_ROIS = 32
class DXP(Device):
_attrs = ('PreampGain','MaxEnergy','ADCPercentRule','BaselineCutPercent',
'BaselineThreshold','BaselineFilterLength','BaselineCutEnable',
'InputCountRate', 'OutputCountRate',
'GapTime','PeakingTime','EnergyThreshold','MaxWidth',
'PresetMode', 'TriggerPeakingTime',
'TriggerGapTime','TriggerThreshold')
def __init__(self,prefix,mca=1):
self._prefix = "%sdxp%i" % (prefix, mca)
Device.__init__(self, self._prefix, delim=':')
poll()
class ROI(Device):
"""epics ROI device for MCA record
>>> from epics.devices.mca import ROI, MCA
>>> r = ROI('PRE:mca1', roi=1)
>>> print r.name, r.left, r.right
arguments
---------
prefix MCA record prefix
roi integer for ROI (0 through 31)
bgr_width width in bins for calculating NET counts
data_pv optional PV name to read counts from (not needed
for most MCA records, but useful for some)
attribute (read/write)
----------------------
LO, left low bin for ROI
HI, right high bin for ROI
NM, name name
properties (read only)
-----------------------
center roi center bin
width roi width (in bins)
address == prefix
total sum counts in ROI
net background-subtracted sum counts in ROI
methods
-------
clear remove ROI
"""
_nonpvs = ('_prefix', '_pvs', '_delim', 'attrs', 'width', 'center',
'bgr_width', 'address', 'net', 'total', '_dat_', '_net_')
_aliases = {'left': 'LO', 'right': 'HI', 'name': 'NM'}
def __init__(self, prefix, roi=0, bgr_width=3, data_pv=None):
self.address = self._prefix = '%s.R%i' % (prefix, roi)
self.bgr_width = bgr_width
_attrs = ('NM', 'LO', 'HI')
Device.__init__(self,self._prefix, delim='',
attrs=_attrs, aliases=self._aliases,
with_poll=False)
if data_pv is None:
data_pv = self.address
if isinstance(data_pv, basestring):
data_pv = get_pv(data_pv)
self._pvs['_dat_'] = data_pv
self._pvs['_net_'] = get_pv(self.address + 'N')
def __eq__(self, other):
"""used for comparisons"""
return (self.LO == getattr(other, 'LO', None) and
self.HI == getattr(other, 'HI', None) and
self.bgr_width == getattr(other, 'bgr_width', None) )
def __ne__(self, other): return not self.__eq__(other)
def __lt__(self, other): return self.LO < getattr(other, 'LO', None)
def __le__(self, other): return self.LO <= getattr(other, 'LO', None)
def __gt__(self, other): return self.LO > getattr(other, 'LO', None)
def __ge__(self, other): return self.LO >= getattr(other, 'LO', None)
def __repr__(self):
"string representation"
pref = self._prefix
if pref.endswith('.'):
pref = pref[:-1]
return "<ROI '%s', name='%s', range=[%s:%s]>" % (pref, self.NM,
self.LO, self.HI)
#return "<ROI '%s', name='%s', range=[%i:%i]>" % (pref, self.NM,
# self.LO, self.HI)
@property
def total(self):
return self.get_counts(net=False)
@property
def sum(self):
return self.get_counts(net=False)
@property
def net(self):
return self.get_counts(net=True)
@property
def center(self):
return int(round(self.HI + self.LO)/2.0)
@property
def width(self):
return int(round(self.HI - self.LO))
def clear(self):
self.NM = ''
self.LO = -1
self.HI = -1
def get_counts(self, data=None, net=False):
"""
calculate total and net counts for a spectra
Parameters:
-----------
* data: numpy array of spectra or None to read from PV
* net: bool to set net counts (default=False: total counts returned)
"""
# implicitly read data from a PV
if data is None and self._pvs['_dat_'] is not None:
data = self._pvs['_dat_'].get()
if net and not isinstance(data, np.ndarray):
data = self._pvs['_net_'].get()
if not isinstance(data, np.ndarray):
return data
total = data[self.LO:self.HI+1].sum()
if not net:
return total
# calculate net counts
bgr_width = int(self.bgr_width)
ilmin = max((self.LO - bgr_width), 0)
irmax = min((self.HI + bgr_width), len(data)-1) + 1
bgr_counts = np.concatenate((data[ilmin:self.LO],
data[self.HI+1:irmax])).mean()
return (total - bgr_counts*(self.HI-self.LO))
class MCA(Device):
_attrs =('CALO', 'CALS', 'CALQ', 'TTH', 'EGU',
'PRTM', 'PLTM', 'ACQG', 'NUSE', 'DWEL',
'ERTM', 'ELTM', 'IDTIM')
_nonpvs = ('_prefix', '_pvs', '_delim',
'_npts', 'rois', '_nrois', 'rois')
def __init__(self, prefix, mca=None, nrois=None, data_pv=None):
self._prefix = prefix
self._npts = None
self._nrois = nrois
if self._nrois is None:
self._nrois = MAX_ROIS
self.rois = []
if isinstance(mca, int):
self._prefix = "%smca%i" % (prefix, mca)
Device.__init__(self,self._prefix, delim='.',
attrs=self._attrs, with_poll=False)
self._pvs['VAL'] = get_pv("%sVAL" % self._prefix, auto_monitor=False)
self._pvs['_dat_'] = None
if data_pv is not None:
self._pvs['_dat_'] = get_pv(data_pv)
poll()
def get_rois(self, nrois=None):
self.rois = []
data_pv = self._pvs['_dat_']
prefix = self._prefix
if prefix.endswith('.'):
prefix = prefix[:-1]
if nrois is None:
nrois = self._nrois
for i in range(nrois):
roi = ROI(prefix=prefix, roi=i, data_pv=data_pv)
if roi.NM is None:
break
if len(roi.NM.strip()) <= 0 or roi.HI <= 0:
break
self.rois.append(roi)
poll()
return self.rois
def del_roi(self, roiname):
self.get_rois()
for roi in self.rois:
if roi.NM.strip().lower() == roiname.strip().lower():
roi.clear()
poll(0.010, 1.0)
self.set_rois(self.rois)
def add_roi(self, roiname, lo=-1, hi=-1, calib=None):
"""add an roi, given name, lo, and hi channels, and
an optional calibration other than that of this mca.
That is, specifying an ROI with all of lo, hi AND calib
will set the ROI **by energy** so that it matches the
provided calibration. To add an ROI to several MCAs
with differing calibration, use
cal_1 = mca1.get_calib()
for mca im (mca1, mca2, mca3, mca4):
mca.add_roi('Fe Ka', lo=600, hi=700, calib=cal_1)
"""
if lo < 0 or hi <0:
return
rois = self.get_rois()
try:
iroi = len(rois)
except:
iroi = 0
if iroi >= MAX_ROIS:
raise ValueError('too many ROIs - cannot add more %i/%i' % (iroi, MAX_ROIS))
data_pv = self._pvs['_dat_']
prefix = self._prefix
if prefix.endswith('.'): prefix = prefix[:-1]
roi = ROI(prefix=prefix, roi=iroi, data_pv=self._pvs['_dat_'])
roi.NM = roiname.strip()
offset, scale = 0.0, 1.0
if calib is not None:
off, slope, quad = self.get_calib()
offset = calib[0] - off
scale = calib[1] / slope
roi.LO = round(offset + scale*lo)
roi.HI = round(offset + scale*hi)
rois.append(roi)
self.set_rois(rois)
def set_rois(self, rois, calib=None):
"""set all rois, with optional calibration that those
ROIs correspond to (if they have a different energy
calibration), and ensures they are ordered and contiguous.
A whole set of ROIs can be copied by energy from one mca
to another with:
rois = mca1.get_rois()
calib = mca1.get_calib()
mca2.set_rois(rois, calib=calib)
"""
data_pv = self._pvs['_dat_']
prefix = self._prefix
if prefix.endswith('.'): prefix = prefix[:-1]
offset, scale = 0.0, 1.0
if calib is not None:
off, slope, quad = self.get_calib()
offset = calib[0] - off
scale = calib[1] / slope
# do an explicit get here to make sure all data is
# available before trying to sort it!
poll(0.0050, 1.0)
[(r.get('NM'), r.get('LO')) for r in rois]
roidat = [(r.NM, r.LO, r.HI) for r in sorted(rois)]
iroi = 0
self.rois = []
for name, lo, hi in roidat:
if len(name)<1 or lo<0 or hi<0:
continue
roi = ROI(prefix=prefix, roi=iroi, data_pv=data_pv)
roi.NM = name.strip()
roi.LO = round(offset + scale*lo)
roi.HI = round(offset + scale*hi)
self.rois.append(roi)
iroi += 1
# erase any remaning ROIs
for i in range(iroi, MAX_ROIS):
lo = caget("%s.R%iLO" % (prefix, i))
if lo < 0:
break
caput("%s.R%iLO" % (prefix, i), -1)
caput("%s.R%iHI" % (prefix, i), -1)
caput("%s.R%iNM" % (prefix, i), '')
def clear_rois(self, nrois=None):
for roi in self.get_rois(nrois=nrois):
roi.clear()
self.rois = []
def get_calib(self):
return [self.get(i) for i in ('CALO','CALS','CALQ')]
def get_energy(self):
if self._npts is None:
self._npts = len(self.get('VAL'))
en = np.arange(self._npts, dtype='f8')
cal = self.get_calib()
return cal[0] + en*(cal[1] + en*cal[2])
class MultiXMAP(Device):
"""
multi-Channel XMAP DXP device
"""
attrs = ['PresetReal','Dwell','Acquiring', 'EraseStart','StopAll',
'PresetMode', 'PixelsPerBuffer_RBV', 'NextPixel',
'PixelsPerRun', 'Apply', 'AutoApply', 'CollectMode',
'SyncCount', 'BufferSize_RBV']
pathattrs = ('FilePath', 'FileTemplate', 'FileWriteMode',
'FileName', 'FileNumber', 'FullFileName_RBV',
'Capture', 'NumCapture', 'WriteFile_RBV',
'AutoSave', 'EnableCallbacks', 'ArraySize0_RBV',
'FileTemplate_RBV', 'FileName_RBV', 'AutoIncrement')
_nonpvs = ('_prefix', '_pvs', '_delim', 'filesaver',
'pathattrs', '_nonpvs', 'nmca', 'dxps', 'mcas')
def __init__(self, prefix, filesaver='netCDF1:',nmca=4):
self.filesaver = filesaver
self._prefix = prefix
self.nmca = nmca
self.dxps = [DXP(prefix, mca=i+1) for i in range(nmca)]
self.mcas = [MCA(prefix, mca=i+1) for i in range(nmca)]
Device.__init__(self, prefix, attrs=self.attrs,
delim='', mutable=True)
for p in self.pathattrs:
pvname = '%s%s%s' % (prefix, filesaver, p)
self.add_pv(pvname, attr=p)
def get_calib(self):
return [m.get_calib() for m in self.mcas]
def get_rois(self):
return [m.get_rois() for m in self.mcas]
def roi_calib_info(self):
buff = ['[rois]']
add = buff.append
rois = self.get_rois()
for iroi in range(len(rois[0])):
name = rois[0][iroi].NM
s = [[rois[m][iroi].LO, rois[m][iroi].HI] for m in range(self.nmca)]
dat = repr(s).replace('],', '').replace('[', '').replace(']','').replace(',','')
add("ROI%2.2i = %s | %s" % (iroi, name, dat))
caldat = np.array(self.get_calib())
add('[calibration]')
add("OFFSET = %s " % (' '.join(["%.7g" % i for i in caldat[:, 0]])))
add("SLOPE = %s " % (' '.join(["%.7g" % i for i in caldat[:, 1]])))
add("QUAD = %s " % (' '.join(["%.7g" % i for i in caldat[:, 2]])))
add('[dxp]')
for a in self.dxps[0]._attrs:
vals = [str(dxp.get(a, as_string=True)).replace(' ','_') for dxp in self.dxps]
add("%s = %s" % (a, ' '.join(vals)))
return buff
def restore_rois(self, roifile):
"""restore ROI setting from ROI.dat file"""
cp = ConfigParser()
cp.read(roifile)
rois = []
self.mcas[0].clear_rois()
prefix = self.mcas[0]._prefix
if prefix.endswith('.'):
prefix = prefix[:-1]
iroi = 0
for a in cp.options('rois'):
if a.lower().startswith('roi'):
name, dat = cp.get('rois', a).split('|')
lims = [int(i) for i in dat.split()]
lo, hi = lims[0], lims[1]
roi = ROI(prefix=prefix, roi=iroi)
roi.LO = lo
roi.HI = hi
roi.NM = name.strip()
rois.append(roi)
iroi += 1
poll(0.050, 1.0)
self.mcas[0].set_rois(rois)
cal0 = self.mcas[0].get_calib()
for mca in self.mcas[1:]:
mca.set_rois(rois, calib=cal0)
def Write_CurrentConfig(self, filename=None):
buff = []
add = buff.append
add('#Multi-Element xMAP Settings saved: %s' % time.ctime())
add('[general]')
add('prefix= %s' % self._prefix)
add('nmcas = %i' % self.nmca)
add('filesaver= %s' % self.filesaver)
d.add('starting roi....')
buff.extend( self.roi_calib_info() )
d.add('wrote roi / calib / dxp')
buff = '\n'.join(buff)
if filename is not None:
fh = open(filename,'w', encoding=IOENCODING)
fh.write(buff)
fh.close()
d.add('wrote file')
# d.show()
return buff
def start(self):
"Start Struck"
self.EraseStart = 1
if self.Acquiring == 0:
poll()
self.EraseStart = 1
return self.EraseStart
def stop(self):
"Stop Struck Collection"
self.StopAll = 1
return self.StopAll
def next_pixel(self):
"Advance to Next Pixel:"
self.NextPixel = 1
return self.NextPixel
def finish_pixels(self, timeout=2):
"Advance to Next Pixel until CurrentPixel == PixelsPerRun"
pprun = self.PixelsPerRun
cur = self.dxps[0].get('CurrentPixel')
t0 = time.time()
while cur < pprun and time.time()-t0 < timeout:
time.sleep(0.1)
pprun = self.PixelsPerRun
cur = self.dxps[0].get('CurrentPixel')
ok = cur >= pprun
if not ok:
print('XMAP needs to finish pixels ', cur, ' / ' , pprun)
for i in range(pprun-cur):
self.next_pixel()
time.sleep(0.10)
self.FileCaptureOff()
return ok, pprun-cur
def readmca(self,n=1):
"Read a Struck MCA"
return self.get('mca%i' % n)
def SCAMode(self):
"put XMAP in SCA mapping mode"
self.CollectMode = 2
def SpectraMode(self):
"put XMAP in MCA spectra mode"
self.stop()
self.CollectMode = 0
self.PresetMode = 0
# wait until BufferSize is ready
buffsize = -1
t0 = time.time()
while time.time() - t0 < 5:
self.CollectMode = 0
time.sleep(0.05)
if self.BufferSize_RBV < 16384:
break
def MCAMode(self, filename=None, filenumber=None, npulses=11):
"put XMAP in MCA mapping mode"
self.AutoApply = 1
self.stop()
self.PresetMode = 0
self.setFileWriteMode(2)
if npulses < 2:
npulses = 2
self.CollectMode = 1
self.PixelsPerRun = npulses
# First, make sure ArraySize0_RBV for the netcdf plugin
# is the correct value
self.FileCaptureOff()
self.start()
f_size = -1
t0 = time.time()
while (f_size < 16384) and time.time()-t0 < 10:
for i in range(5):
time.sleep(0.1)
self.NextPixel = 1
f_size = self.fileGet('ArraySize0_RBV')
if f_size > 16384:
break
#
self.PixelsPerRun = npulses
self.SyncCount = 1
self.setFileNumber(filenumber)
if filename is not None:
self.setFileName(filename)
# wait until BufferSize is ready
self.Apply = 1
self.CollectMode = 1
self.PixelsPerRun = npulses
time.sleep(0.50)
t0 = time.time()
while time.time() - t0 < 10:
time.sleep(0.25)
if self.BufferSize_RBV > 16384:
break
# set expected number of buffers to put in a single file
ppbuff = self.PixelsPerBuffer_RBV
time.sleep(0.25)
if ppbuff is None:
ppbuff = 124
self.setFileNumCapture(1 + (npulses-1)/ppbuff)
f_buffsize = -1
t0 = time.time()
while time.time()- t0 < 5:
time.sleep(0.1)
f_buffsize = self.fileGet('ArraySize0_RBV')
if self.BufferSize_RBV == f_buffsize:
break
time.sleep(0.5)
return
def filePut(self,attr, value, **kw):
return self.put("%s%s" % (self.filesaver, attr), value, **kw)
def fileGet(self, attr, **kw):
return self.get("%s%s" % (self.filesaver, attr), **kw)
def setFilePath(self, pathname):
return self.filePut('FilePath', pathname)
def setFileTemplate(self, fmt):
return self.filePut('FileTemplate', fmt)
def setFileWriteMode(self, mode):
return self.filePut('FileWriteMode', mode)
def setFileName(self, fname):
return self.filePut('FileName', fname)
def nextFileNumber(self):
self.setFileNumber(1+self.fileGet('FileNumber'))
def setFileNumber(self, fnum=None):
if fnum is None:
self.filePut('AutoIncrement', 1)
else:
self.filePut('AutoIncrement', 0)
return self.filePut('FileNumber',fnum)
def getLastFileName(self):
return self.fileGet('FullFileName_RBV',as_string=True)
def FileCaptureOn(self):
return self.filePut('Capture', 1)
def FileCaptureOff(self):
return self.filePut('Capture', 0)
def setFileNumCapture(self,n):
return self.filePut('NumCapture', n)
def FileWriteComplete(self):
return (0==self.fileGet('WriteFile_RBV') )
def getFileTemplate(self):
return self.fileGet('FileTemplate_RBV',as_string=True)
def getFileName(self):
return self.fileGet('FileName_RBV',as_string=True)
def getFileNumber(self):
return self.fileGet('FileNumber_RBV')
def getFilePath(self):
return self.fileGet('FilePath_RBV',as_string=True)
def getFileNameByIndex(self,index):
return self.getFileTemplate() % (self.getFilePath(), self.getFileName(), index)
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