from os.path import realpath, exists, join
from larch import (Group, Parameter, isParameter, param_value, use_plugin_path,
isNamedClass)
use_plugin_path('io')
from xdi import read_xdi
from columnfile import write_ascii
use_plugin_path('xafs')
from feffit import feffit_dataset, feffit_transform, feffit, feffit_report
from feffdat import feffpath
use_plugin_path('wx')
from plotter import (_newplot, _plot)
import pystache
def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
if hasattr(data, 'wavenumber'):
data.k = data.wavenumber
gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
import json
import numpy as np
import glob
from .file_utils import nativepath
from .site_config import get_fileroot, LARCH_SCANDB, LARCH_INSTDB
from .utils import plain_ascii
from .scandb import InstrumentDB
from . import scandb
import epics
import larch
from larch.utils import OrderedDict
larch_site_config = larch.site_config
larch.use_plugin_path('epics')
from stepscan_utils import EpicsScanDB
class LarchScanDBWriter(object):
"""Writer for Larch Interface that writes to both Stdout
and Messages table of scandb
"""
def __init__(self, stdout=None, scandb=None, _larch=None):
if stdout is None:
stdout = sys.stdout
self.scandb = scandb
self.writer = stdout
self._larch = _larch
def write(self, text, color=None, bkg=None, **kws):
import wx.lib.agw.flatnotebook as flat_nb
import wx.lib.scrolledpanel as scrolled
import wx.lib.mixins.inspection
try:
from wx._core import PyDeadObjectError
except:
PyDeadObjectError = Exception
import epics
from epics.wx import DelayedEpicsCallback, EpicsFunction
from larch import Interpreter, use_plugin_path, isParameter
from larch.fitting import fit_report
use_plugin_path('math')
from fitpeak import fit_peak
from wxmplot import PlotFrame, PlotPanel
from ..datafile import StepScanData
from ..scandb import ScanDB
from ..file_utils import fix_filename
from .gui_utils import (SimpleText, FloatCtrl, Closure, pack, add_button,
add_menu, add_choice, add_menu, check,
CEN, RCEN, LCEN, FRAMESTYLE, Font)
CEN |= wx.ALL
FILE_WILDCARDS = "Scan Data Files(*.0*,*.dat,*.xdi)|*.0*;*.dat;*.xdi|All files (*.*)|*.*"
FNB_STYLE = flat_nb.FNB_NO_X_BUTTON|flat_nb.FNB_SMART_TABS|flat_nb.FNB_NO_NAV_BUTTONS
from os.path import realpath, exists, join
from larch import (Group, Parameter, isParameter, param_value, use_plugin_path, isNamedClass)
use_plugin_path('io')
from xdi import read_xdi
from columnfile import write_ascii
use_plugin_path('xafs')
from feffit import feffit_dataset, feffit_transform, feffit, feffit_report
from feffdat import feffpath
use_plugin_path('wx')
from plotter import (_newplot, _plot)
import pystache
def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
if hasattr(data, 'wavenumber'):
data.k = data.wavenumber
from os.path import realpath, exists, join
from larch import Group, Parameter, isParameter, param_value, use_plugin_path, isNamedClass
use_plugin_path("io")
from xdi import read_xdi
use_plugin_path("xafs")
from feffit import feffit_dataset, feffit_transform, feffit, feffit_report
from feffdat import feffpath
use_plugin_path("wx")
from plotter import _newplot, _plot
def do_fit(self, which):
if which == "testrun":
folder = self.testrun
else:
folder = self.baseline
data = read_xdi(join(self.path, "UO2.chik"), _larch=self._larch)
gds = Group(
amp=Parameter(1, vary=True, _larch=self._larch),
enot=Parameter(0.01, vary=True, _larch=self._larch),
sso=Parameter(0.003, vary=True, _larch=self._larch),
ssu=Parameter(0.003, vary=True, _larch=self._larch),
sso2=Parameter(0.003, vary=True, _larch=self._larch),
dro=Parameter(0.0001, vary=True, _larch=self._larch),
import sys
import time
import numpy as np
from collections import OrderedDict
if sys.version_info[0] > 2: # Python2 only, for now
from io import StringIO
from configparser import ConfigParser
else:
from ConfigParser import ConfigParser
from cStringIO import StringIO
from larch import use_plugin_path, Group
use_plugin_path('io')
from fileutils import get_homedir, get_timestamp
try:
from epics import PV, caget, caput, get_pv, poll
HAS_EPICS = True
except ImportError:
HAS_EPICS = False
try:
use_plugin_path('epics')
from larch_plugins.epics.larchscan import LarchStepScan
import epicsscan
from epicsscan.positioner import Positioner
from epicsscan.detectors import get_detector, Counter
import wx.dataview as dv
HAS_DV = True
except:
pass
from wxutils import (SimpleText, EditableListBox, Font, FloatCtrl, pack, Popup,
Button, get_icon, Check, MenuItem, Choice, FileOpen,
FileSave, fix_filename, HLine, GridPanel, CEN, LEFT,
RIGHT)
import larch
from larch_plugins.wx import (PeriodicTablePanel, XRFDisplayFrame,
FILE_WILDCARDS, CalibrationFrame)
ROI_WILDCARD = 'Data files (*.dat)|*.dat|ROI files (*.roi)|*.roi|All files (*.*)|*.*'
larch.use_plugin_path('epics')
try:
from larch_plugins.epics import Epics_MultiXMAP, Epics_Xspress3
from scandb import ScanDB
except:
pass
class DetectorSelectDialog(wx.Dialog):
"""Connect to an Epics MCA detector
Can be either XIA xMAP or Quantum XSPress3
"""
msg = '''Select XIA xMAP or Quantum XSPress3 MultiElement MCA detector'''
det_types = ('ME-4', 'other')
def_prefix = '13QX4:' # SDD1:'
def_nelem = 4
4/14/2011: fluo_det.py: detection dependent part in fluorescence yield.
Original fluo.py was modified to fluo_new.py.
readf1f2a.py is used instead of original readf1f2.py
fluo_new.py is being split into two.
fluo_elem.py is for elemtnal dependence: fluorescenc yield, crosssection.
fluo_det.py is for detection dependnece: detector efficiency, attenuation, sample
* for attenuation, total cross-section([4]) is used instead of photoelectric ([2]).
** for fluorescence yield, photoelectric is used.
"""
import math
import numpy
import sys
from larch import use_plugin_path
use_plugin_path('xray')
use_plugin_path('xsw')
from physical_constants import AVOGADRO, BARN
pre_edge_margin = 150. # FY calculated from 150 eV below the absorption edge.
fluo_emit_min = 500. # minimum energy for emitted fluorescence. ignore fluorescence emissions below 500eV
det_res = 100. # detector resoltuion in eV, used in sim_GaussPeaks
'''
----------------------------------------------------------------------------------------------------------
class: Material, ElemFY, SampleMatrix2
----------------------------------------------------------------------------------------------------------
'''
class Material:
# make up the Python Interface to the feffpath library. While information
# about Authorship may be retained in some files for historical reasons,
# this work is hereby placed in the Public Domain. This work is
# published from: United States.
#
# Note that the onepath and feffpath libraries themselves are NOT
# public domain, nor is the Fortran source code for Feff that it
# relies upon.
#
# Author: Bruce Ravel (bravel AT bnl DOT gov).
# Last update: 12 December, 2014
import larch
from larch import (Group, Parameter, isParameter, ValidateLarchPlugin, param_value,
use_plugin_path, isNamedClass, Interpreter)
use_plugin_path('xafs')
use_plugin_path('xray')
from xraydb_plugin import atomic_symbol
import sys
from os import name
from os.path import isfile
from numpy import array
#installdir = larch.site_config.larchdir
installdir = larch.larchlib.larchdir
dlldir = larch.larchlib.get_dlldir()
dllfile=installdir+'/dlls/'+dlldir
if not dllfile in sys.path:
4/14/2011: fluo_det.py: detection dependent part in fluorescence yield.
Original fluo.py was modified to fluo_new.py.
readf1f2a.py is used instead of original readf1f2.py
fluo_new.py is being split into two.
fluo_elem.py is for elemtnal dependence: fluorescenc yield, crosssection.
fluo_det.py is for detection dependnece: detector efficiency, attenuation, sample
* for attenuation, total cross-section([4]) is used instead of photoelectric ([2]).
** for fluorescence yield, photoelectric is used.
"""
import math
import numpy
import sys
from larch import use_plugin_path
use_plugin_path('xray')
use_plugin_path('xsw')
from physical_constants import AVOGADRO, BARN
pre_edge_margin=150. # FY calculated from 150 eV below the absorption edge.
fluo_emit_min=500. # minimum energy for emitted fluorescence. ignore fluorescence emissions below 500eV
det_res=100. # detector resoltuion in eV, used in sim_GaussPeaks
'''
----------------------------------------------------------------------------------------------------------
class: Material, ElemFY, SampleMatrix2
----------------------------------------------------------------------------------------------------------
'''
class Material:
def __init__(self, composition, density, thickness=1,_larch=None):
#!/usr/bin/env python
import os
import sys
import copy
import time
import gc
import numpy as np
from larch import Group, ValidateLarchPlugin, use_plugin_path
from larch.utils import OrderedDict
from larch_plugins.io import XDIFile, XDIFileException, iso8601_time
use_plugin_path('xrfmap')
from xsp3_hdf5 import XSPRESS3_TAUS, estimate_icr
@ValidateLarchPlugin
def read_gsexdi(fname, _larch=None, nmca=4, bad=None, **kws):
"""Read GSE XDI Scan Data to larch group,
summing ROI data for MCAs and apply deadtime corrections
"""
group = _larch.symtable.create_group()
group.__name__ ='GSE XDI Data file %s' % fname
xdi = XDIFile(str(fname))
group._xdi = xdi
group.filename = fname
group.npts = xdi.npts
group.bad_channels = bad
group.dtc_taus = XSPRESS3_TAUS
"""
Triggers, Counters, Detectors for Step Scan
"""
import time
from ordereddict import OrderedDict
from epics_interface import PV, caget, caput, poll
from epics.devices import Scaler, MCA, Struck
from larch import use_plugin_path
use_plugin_path("epics")
from xspress3 import Xspress3
from .saveable import Saveable
DET_DEFAULT_OPTS = {
"scaler": {"use_calc": True, "nchans": 8},
"areadetector": {"file_plugin": "TIFF1", "auto_increment": True},
"mca": {"nrois": 32, "use_full": False, "use_net": False},
"xspress3": {"MultiChannelScaler": "", "nmcas": 4, "nrois": 32, "nbins": 10},
"multimca": {"nrois": 32, "nmcas": 4, "use_full": False, "use_net": False},
}
AD_FILE_PLUGINS = ("TIFF1", "JPEG1", "NetCDF1", "HDF1", "Nexus1", "Magick1")
class Trigger(Saveable):
"""Detector Trigger for a scan. The interface is:
trig = Trigger(pvname, value=1)
## feff85exafs unit testing system using larch
## see HEADERS/license.h for feff's license information
import os
import nose
from os.path import isfile, isdir, join
import sys
sys.path.append(join('wrappers', 'python'))
from math import isnan
import larch
from f85ut import ut
larch.use_plugin_path('xafs')
from feffdat import feffpath
larch.use_plugin_path('io')
from columnfile import read_ascii
import re
#folders = ('Copper',)
#folders = ('ferrocene',)
#folders = ('Copper', 'NiO', 'UO2', 'Zircon', 'ferrocene', 'bromoadamantane')
folders = ('Copper', 'NiO', 'UO2', 'Zircon', 'ferrocene', 'bromoadamantane',
'LCO-para', 'LCO-perp')
tests = dict()
doscf = os.getenv('FEFF_TEST_SCF', 'False')
#!/usr/bin/env python
import os
import sys
import copy
import time
import gc
import numpy as np
from larch import Group, ValidateLarchPlugin, use_plugin_path
from larch.utils import OrderedDict
from larch_plugins.io import XDIFile, XDIFileException, iso8601_time
use_plugin_path('xrfmap')
from xsp3_hdf5 import XSPRESS3_TAUS, estimate_icr
@ValidateLarchPlugin
def read_gsexdi(fname, _larch=None, nmca=4, bad=None, **kws):
"""Read GSE XDI Scan Data to larch group,
summing ROI data for MCAs and apply deadtime corrections
"""
group = _larch.symtable.create_group()
group.__name__ = 'GSE XDI Data file %s' % fname
xdi = XDIFile(str(fname))
group._xdi = xdi
group.filename = fname
group.npts = xdi.npts
group.bad_channels = bad
#!/usr/bin/env python
import os
import sys
import copy
import time
import gc
import numpy as np
from larch import Group, ValidateLarchPlugin, use_plugin_path
from larch.utils import OrderedDict
from larch_plugins.io import XDIFile, XDIFileException, iso8601_time
use_plugin_path('xrmmap')
from xsp3_hdf5 import XSPRESS3_TAUS, estimate_icr
@ValidateLarchPlugin
def read_gsexdi(fname, _larch=None, nmca=4, bad=None, **kws):
"""Read GSE XDI Scan Data to larch group,
summing ROI data for MCAs and apply deadtime corrections
"""
group = _larch.symtable.create_group()
group.__name__ ='GSE XDI Data file %s' % fname
xdi = XDIFile(str(fname))
group._xdi = xdi
group.filename = fname
group.npts = xdi.npts
group.bad_channels = bad
group.dtc_taus = XSPRESS3_TAUS
#!/usr/bin/env python
import os
import sys
import copy
import time
import gc
import numpy as np
from larch import Group, ValidateLarchPlugin, use_plugin_path
from larch.utils import OrderedDict
from larch_plugins.io import XDIFile, XDIFileException, iso8601_time
use_plugin_path('xrmmap')
from xsp3_hdf5 import XSPRESS3_TAUS, estimate_icr
@ValidateLarchPlugin
def read_gsexdi(fname, _larch=None, nmca=4, bad=None, **kws):
"""Read GSE XDI Scan Data to larch group,
summing ROI data for MCAs and apply deadtime corrections
"""
group = _larch.symtable.create_group()
group.__name__ = 'GSE XDI Data file %s' % fname
xdi = XDIFile(str(fname))
group._xdi = xdi
group.filename = fname
group.npts = xdi.npts
group.bad_channels = bad
yet to be implemented:
-- th2th tth_start_rel tth_finish_rel intervals time
-- automatic plotting
-- save/read configuration
"""
import os
import time
import numpy as np
from ConfigParser import ConfigParser
from cStringIO import StringIO
from larch import use_plugin_path, Group
from larch.utils.ordereddict import OrderedDict
use_plugin_path('io')
from fileutils import get_homedir, get_timestamp
try:
from epics import PV, caget, caput, get_pv, poll
HAS_EPICS = True
except ImportError:
HAS_EPICS = False
try:
use_plugin_path('epics')
from larch_plugins.epics.larchscan import LarchStepScan
import epicsscan
from epicsscan.positioner import Positioner
