def SetSource(self, source_name=None, source_obj=None):
"""
Sets a new source for data retrieving, an specfile.
If the file exists, self.Source will be the Specfile
object associated to this file.
Parameters:
source_name: name of the specfile
"""
if source_name == self.SourceName: return 1
if source_name is not None:
if source_obj is not None:
self.Source = source_obj
else:
try:
self.Source = specfile.Specfile(source_name)
except:
self.Source = None
else:
self.Source = None
self.SourceInfo = None
if self.Source is None:
self.SourceName = None
return 0
else:
self.SourceName = source_name
return 1
def loadTransmissionTable(self, filename):
# read with our wrapper
sf = specfile.Specfile(filename)
scan = sf[0]
data = scan.data()
labels = scan.alllabels()
scan = None
sf = None
nLabels = len(labels)
if nLabels not in [2, 3]:
txt = "Expected a two column file got %d columns" % nLabels
raise IOError(txt)
if nLabels == 3 and labels[0].lower().startswith("point"):
energyIdx = 1
transmissionIdx = 2
else:
energyIdx = 0
transmissionIdx = 1
# sort energies in ascending order
energy = data[energyIdx, :]
transmission = data[transmissionIdx, :]
idx = numpy.argsort(energy)
energy = numpy.take(energy, idx)
transmission = numpy.take(transmission, idx)
ddict = {}
ddict["use"] = 1
ddict["energy"] = energy
ddict["transmission"] = transmission
ddict["name"] = os.path.basename(filename)
ddict["comment"] = ""
self.setTransmissionTable(ddict, updating=True)
def __init__(self, fname=None, cntx=1, cnty=None, csig=None, cmon=None, csec=None, norm=None):
"""reads the given specfile"""
if (fname == 'DUMMY!'):
return
if (HAS_SPECFILE is False):
print("WARNING: 'specfile' is missing -> check requirements!")
return
if (fname is None):
raise NameError("Provide a SPEC data file to load with full path")
elif not os.path.isfile(fname):
raise OSError("File not found: '%s'" % fname)
else:
self.fname = fname
if hasattr(self, 'sf'):
pass
else:
self.sf = specfile.Specfile(fname) #sf = specfile file
print("Loaded SPEC file: {0}".format(fname))
# print("The total number of scans is: {0}".format(self.sf.scanno())
#if HAS_SIMPLEMATH: self.sm = SimpleMath.SimpleMath()
#set common attributes
self.cntx = cntx
self.cnty = cnty
self.csig = csig
self.cmon = cmon
self.csec = csec
self.norm = norm
def compute(self):
fileName = xoppy_calc_xxcom(NAME=self.NAME,
SUBSTANCE=self.SUBSTANCE,
DESCRIPTION=self.DESCRIPTION,
FRACTION=self.FRACTION,
GRID=self.GRID,
GRIDINPUT=self.GRIDINPUT,
GRIDDATA=self.GRIDDATA,
ELEMENTOUTPUT=self.ELEMENTOUTPUT)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def compute(self):
fileName = xoppy_calc_xtubes(ITUBE=self.ITUBE, VOLTAGE=self.VOLTAGE)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def generateXRFData(nRows=5, nColumns=10, nDet=1, nTimes=3, presetTime=1, same=True):
"""
:param int nRows:
:param int nColumns:
:param int nDet:
:param int nTimes: number of different live times
:param int presetTime: exposure time for each spectrum
:param bool same: same spectrum in all pixels (add pixel index as constant background otherwise)
:returns: data(nRows, nColumns, nChannels), liveTime(nRows*nColumns)
"""
from PyMca5.PyMcaDataDir import PYMCA_DATA_DIR as dataDir
from PyMca5.PyMcaIO import specfilewrapper as specfile
spe = os.path.join(dataDir, "Steel.spe")
sf = specfile.Specfile(spe)
counts = sf[0].mca(1).astype(numpy.int32)
#counts = numpy.arange(counts.size, dtype=int) # for testing
data = numpy.zeros((nDet, nRows, nColumns, counts.size), dtype=counts.dtype)
liveTime = numpy.zeros((nDet, nRows, nColumns), dtype=numpy.float64)
nTimes *= nDet
initialTime = presetTime
mcaIndex = 0
for i in range(nRows):
for j in range(nColumns):
for k in range(nDet):
if same:
data[k, i, j] = counts
else:
data[k, i, j] = counts + mcaIndex*nDet + k
liveTime[k, i, j] = initialTime * (1 + mcaIndex % nTimes)/float(nTimes)
mcaIndex += 1
return data, liveTime
def compute(self):
fileName = xoppy_calc_xraylib_widget(FUNCTION=self.FUNCTION,ELEMENT=self.ELEMENT,ELEMENTORCOMPOUND=self.ELEMENTORCOMPOUND,COMPOUND=self.COMPOUND,TRANSITION_IUPAC_OR_SIEGBAHN=self.TRANSITION_IUPAC_OR_SIEGBAHN,TRANSITION_IUPAC_TO=self.TRANSITION_IUPAC_TO,TRANSITION_IUPAC_FROM=self.TRANSITION_IUPAC_FROM,TRANSITION_SIEGBAHN=self.TRANSITION_SIEGBAHN,SHELL=self.SHELL,ENERGY=self.ENERGY)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile",fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ",fileName)
out = np.loadtxt(fileName)
print("data shape: ",out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [ line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ","").split(" ")
print("data labels: ",labels)
#
# build and send orange table
#
domain = Domain([ ContinuousVariable(i) for i in labels ])
table = Table.from_numpy(domain, out)
self.send("xoppy_table",table)
else:
print("File %s contains %d scans. Cannot send it as xoppy_table"%(fileName,sf.scanno()))
def compute(self):
fileName = xoppy_calc_xbfield(PERIOD=self.PERIOD,
NPER=self.NPER,
NPTS=self.NPTS,
IMAGNET=self.IMAGNET,
ITYPE=self.ITYPE,
K=self.K,
GAP=self.GAP,
GAPTAP=self.GAPTAP,
FILE=self.FILE)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def testSimpleSpecfileVersusPyMca(self):
import glob
import PyMca5
from PyMca5 import PyMcaDataDir
from PyMca5.PyMcaIO import specfilewrapper as Specfile
fileList = glob.glob(
os.path.join(PyMcaDataDir.PYMCA_DATA_DIR, '*.dat'))
self.testSimpleSpecfileImport()
for filename in fileList:
self._sf = self.specfileClass(filename)
a = self._sf
nScans = a.getNumberOfScans()
sf = Specfile.Specfile(filename)
for i in range(nScans):
scan = sf[i]
if PyMca5.version() > "5.1.1":
# previous versions of PyMca5 could segfault here
labels0 = a.getScanLabels(i)
labels1 = scan.alllabels()
for j in range(len(labels0)):
self.assertEqual(labels0[j], labels1[j],
"Read <%s> instead of <%s>" %\
(labels0[j], labels1[j]))
data0 = a.getScanData(i)
data1 = scan.data().T
M = abs(data0 - data1).max()
if M > 1.0e-8:
raise ValueError("Error reading data")
def testSimpleSpecfileVersusPyMca(self):
import glob
try:
from PyMca5 import PyMcaDataDir
from PyMca5.PyMcaIO import specfilewrapper as Specfile
except ImportError:
print("\n ****** Skipping: PyMca not installed ******* \n")
return
fileList = glob.glob(os.path.join(PyMcaDataDir.PYMCA_DATA_DIR, '*.dat'))
self.testSimpleSpecfileImport()
for filename in fileList:
self._sf = self.specfileClass(filename)
a = self._sf
nScans = a.getNumberOfScans()
sf = Specfile.Specfile(filename)
for i in range(nScans):
scan = sf[i]
labels0 = a.getScanLabels(i)
labels1 = scan.alllabels()
for j in range(len(labels0)):
self.assertEqual(labels0[j], labels1[j],
"Read <%s> instead of <%s>" %\
(labels0[j], labels1[j]))
data0 = a.getScanData(i)
data1 = scan.data().T
M = abs(data0 - data1).max()
if M > 1.0e-8:
raise ValueError("Error reading data")
def _loadFromFile(self):
stack = self.getStackDataObject()
if stack is None:
return
mcaIndex = stack.info.get('McaIndex')
if not (mcaIndex in [0, -1, 2]):
raise IndexError("1D index must be 0, 2, or -1")
# test io dependencies
if h5py is None:
filefilter = []
else:
filefilter = ['HDF5 (*.h5 *.nxs *.hdf *.hdf5)']
filefilter.append('CSV (*.csv *.txt)')
if silx_open is not None:
filefilter.append('Any (*)')
filename, ffilter = PyMcaFileDialogs.\
getFileList(parent=None,
filetypelist=filefilter,
message='Load',
mode='OPEN',
single=True,
getfilter=True,
currentfilter=filefilter[0])
if len(filename):
if DEBUG:
print("file name = %s file filter = %s" % (filename, ffilter))
else:
if DEBUG:
print("nothing selected")
return
filename = filename[0]
positioners = {}
if not ffilter.startswith('CSV'):
h5GroupName = getGroupNameDialog(filename)
if h5GroupName is None:
return
with h5open(filename) as h5f:
h5Group = h5f[h5GroupName]
positioners = {}
for dsname in h5Group:
# links and subgroups just ignored for the time being
if not is_dataset(h5Group[dsname]):
continue
positioners[dsname] = h5Group[dsname][()]
else:
sf = specfilewrapper.Specfile(filename)
scan = sf[0]
labels = scan.alllabels()
data = scan.data()
scan = None
sf = None
for i, label in enumerate(labels):
positioners[label] = data[i, :]
self._stackWindow.setPositioners(positioners)
def compute(self):
fileName = xoppy_calc_xurgent(TITLE=self.TITLE,
ENERGY=self.ENERGY,
CUR=self.CUR,
SIGX=self.SIGX,
SIGY=self.SIGY,
SIGX1=self.SIGX1,
SIGY1=self.SIGY1,
ITYPE=self.ITYPE,
PERIOD=self.PERIOD,
N=self.N,
KX=self.KX,
KY=self.KY,
PHASE=self.PHASE,
EMIN=self.EMIN,
EMAX=self.EMAX,
NENERGY=self.NENERGY,
D=self.D,
XPC=self.XPC,
YPC=self.YPC,
XPS=self.XPS,
YPS=self.YPS,
NXP=self.NXP,
NYP=self.NYP,
MODE=self.MODE,
ICALC=self.ICALC,
IHARM=self.IHARM,
NPHI=self.NPHI,
NSIG=self.NSIG,
NALPHA=self.NALPHA,
DALPHA=self.DALPHA,
NOMEGA=self.NOMEGA,
DOMEGA=self.DOMEGA)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def refresh(self):
self._sourceObjectList=[]
self.__fileHeaderList = []
for name in self.__sourceNameList:
if not os.path.exists(name):
raise ValueError("File %s does not exists" % name)
for name in self.__sourceNameList:
self._sourceObjectList.append(specfile.Specfile(name))
self.__fileHeaderList.append(False)
self.__lastKeyInfo = {}
def __init__(self, spec_file='/home/qiu/data/ma4171/sixcvertical.spec'):
self.spec_file = spec_file
self.scan_selector = specfilewrapper.Specfile(spec_file)
self.motor_angles = {}
self.trans = 1
self.mon = 1
self.potential = None
self.current = None
self.scan_no = None
self.frame_no = None
def compute(self):
fileName = xoppy_calc_xtc(TITLE=self.TITLE,
ENERGY=self.ENERGY,
CUR=self.CUR,
SIGE=self.SIGE,
TEXT_MACHINE=self.TEXT_MACHINE,
SIGX=self.SIGX,
SIGY=self.SIGY,
SIGX1=self.SIGX1,
SIGY1=self.SIGY1,
TEXT_BEAM=self.TEXT_BEAM,
PERIOD=self.PERIOD,
NP=self.NP,
TEXT_UNDULATOR=self.TEXT_UNDULATOR,
EMIN=self.EMIN,
EMAX=self.EMAX,
N=self.N,
TEXT_ENERGY=self.TEXT_ENERGY,
IHMIN=self.IHMIN,
IHMAX=self.IHMAX,
IHSTEP=self.IHSTEP,
TEXT_HARM=self.TEXT_HARM,
IHEL=self.IHEL,
METHOD=self.METHOD,
IK=self.IK,
NEKS=self.NEKS,
TEXT_PARM=self.TEXT_PARM,
RUN_MODE_NAME=self.RUN_MODE_NAME)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def set_params(self,
E_keV=0.0,
cen=(0, 0),
pixelsize=(0, 0),
sdd=0.0,
spec_filename="",
edf_path=""):
self.E_keV = E_keV
self.wavelength = 12.39854 * self.E_keV
self.k0 = 2. * np.pi / self.wavelength
self.cen = cen
self.pixelsize = pixelsize
self.sdd = sdd
self.spec = specfilewrapper.Specfile(spec_filename)
self.img_loader = edf_image.edf_image_loader(spec_filename, edf_path)
def testStackFastFit(self):
# TODO: this is done in PyMcaBatchTest on multiple input formats
# so not needed here
return
from PyMca5.PyMcaIO import specfilewrapper as specfile
from PyMca5.PyMcaIO import ConfigDict
from PyMca5.PyMcaCore import DataObject
spe = os.path.join(self.dataDir, "Steel.spe")
cfg = os.path.join(self.dataDir, "Steel.cfg")
sf = specfile.Specfile(spe)
self.assertTrue(len(sf) == 1, "File %s cannot be read" % spe)
self.assertTrue(sf[0].nbmca() == 1, "Spe file should contain MCA data")
counts = sf[0].mca(1)
channels = numpy.arange(counts.size)
sf = None
configuration = ConfigDict.ConfigDict()
configuration.read(cfg)
calibration = configuration["detector"]["zero"], \
configuration["detector"]["gain"], 0.0
initialTime = configuration["concentrations"]["time"]
# Fit MCA data with different dimensions: vector, image, stack
for ndim in [1, 2, 3]:
# create the data
imgShape = tuple(range(3, 3 + ndim))
data = numpy.tile(counts, imgShape + (1, ))
nTimes = 3
live_time = numpy.arange(numpy.prod(imgShape), dtype=int)
live_time = initialTime + (live_time % nTimes) * initialTime
# create the stack data object
stack = DataObject.DataObject()
stack.data = data
stack.info = {}
stack.info["McaCalib"] = calibration
stack.info["McaLiveTime"] = live_time
stack.x = [channels]
# Test the fast XRF
# we need to make sure we use fundamental parameters and
# the time read from the file
configuration["concentrations"]["usematrix"] = 0
configuration["concentrations"]["useautotime"] = 1
# make sure we use the SNIP background
configuration['fit']['stripalgorithm'] = 1
self._verifyFastFit(stack, configuration, live_time, nTimes)
def compute(self):
fileName = xoppy_calc_xfilter(EMPTY1=self.EMPTY1,
EMPTY2=self.EMPTY2,
NELEMENTS=self.NELEMENTS,
SOURCE=self.SOURCE,
ENER_MIN=self.ENER_MIN,
ENER_MAX=self.ENER_MAX,
ENER_N=self.ENER_N,
SOURCE_FILE=self.SOURCE_FILE,
EL1_SYM=self.EL1_SYM,
EL1_THI=self.EL1_THI,
EL2_SYM=self.EL2_SYM,
EL2_THI=self.EL2_THI,
EL3_SYM=self.EL3_SYM,
EL3_THI=self.EL3_THI,
EL4_SYM=self.EL4_SYM,
EL4_THI=self.EL4_THI,
EL5_SYM=self.EL5_SYM,
EL5_THI=self.EL5_THI)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def compute(self):
fileName = xoppy_calc_ws(TITLE=self.TITLE,
ENERGY=self.ENERGY,
CUR=self.CUR,
PERIOD=self.PERIOD,
N=self.N,
KX=self.KX,
KY=self.KY,
EMIN=self.EMIN,
EMAX=self.EMAX,
NEE=self.NEE,
D=self.D,
XPC=self.XPC,
YPC=self.YPC,
XPS=self.XPS,
YPS=self.YPS,
NXP=self.NXP,
NYP=self.NYP)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def compute(self):
fileName = xoppy_calc_bm(TYPE_CALC=self.TYPE_CALC,
MACHINE_NAME=self.MACHINE_NAME,
RB_CHOICE=self.RB_CHOICE,
MACHINE_R_M=self.MACHINE_R_M,
BFIELD_T=self.BFIELD_T,
BEAM_ENERGY_GEV=self.BEAM_ENERGY_GEV,
CURRENT_A=self.CURRENT_A,
HOR_DIV_MRAD=self.HOR_DIV_MRAD,
VER_DIV=self.VER_DIV,
PHOT_ENERGY_MIN=self.PHOT_ENERGY_MIN,
PHOT_ENERGY_MAX=self.PHOT_ENERGY_MAX,
NPOINTS=self.NPOINTS,
LOG_CHOICE=self.LOG_CHOICE,
PSI_MRAD_PLOT=self.PSI_MRAD_PLOT,
PSI_MIN=self.PSI_MIN,
PSI_MAX=self.PSI_MAX,
PSI_NPOINTS=self.PSI_NPOINTS)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def compute(self):
fileName = xoppy_calc_xf1f2(DATASETS=self.DATASETS,
MAT_FLAG=self.MAT_FLAG,
MAT_LIST=self.MAT_LIST,
DESCRIPTOR=self.DESCRIPTOR,
DENSITY=self.DENSITY,
CALCULATE=self.CALCULATE,
GRID=self.GRID,
GRIDSTART=self.GRIDSTART,
GRIDEND=self.GRIDEND,
GRIDN=self.GRIDN,
THETAGRID=self.THETAGRID,
ROUGH=self.ROUGH,
THETA1=self.THETA1,
THETA2=self.THETA2,
THETAN=self.THETAN)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def compute(self):
fileName = xoppy_calc_mlayer(MODE=self.MODE,
SCAN=self.SCAN,
F12_FLAG=self.F12_FLAG,
SUBSTRATE=self.SUBSTRATE,
ODD_MATERIAL=self.ODD_MATERIAL,
EVEN_MATERIAL=self.EVEN_MATERIAL,
ENERGY=self.ENERGY,
THETA=self.THETA,
SCAN_STEP=self.SCAN_STEP,
NPOINTS=self.NPOINTS,
ODD_THICKNESS=self.ODD_THICKNESS,
EVEN_THICKNESS=self.EVEN_THICKNESS,
NLAYERS=self.NLAYERS,
FILE=self.FILE)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def compute(self):
fileName = xoppy_calc_xcrystal(FILEF0=self.FILEF0,FILEF1F2=self.FILEF1F2,FILECROSSSEC=self.FILECROSSSEC,CRYSTAL_MATERIAL=self.CRYSTAL_MATERIAL,MILLER_INDEX_H=self.MILLER_INDEX_H,MILLER_INDEX_K=self.MILLER_INDEX_K,MILLER_INDEX_L=self.MILLER_INDEX_L,I_ABSORP=self.I_ABSORP,TEMPER=self.TEMPER,MOSAIC=self.MOSAIC,GEOMETRY=self.GEOMETRY,SCAN=self.SCAN,UNIT=self.UNIT,SCANFROM=self.SCANFROM,SCANTO=self.SCANTO,SCANPOINTS=self.SCANPOINTS,ENERGY=self.ENERGY,ASYMMETRY_ANGLE=self.ASYMMETRY_ANGLE,THICKNESS=self.THICKNESS,MOSAIC_FWHM=self.MOSAIC_FWHM,RSAG=self.RSAG,RMER=self.RMER,ANISOTROPY=self.ANISOTROPY,POISSON=self.POISSON,CUT=self.CUT,FILECOMPLIANCE=self.FILECOMPLIANCE)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile",fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ",fileName)
out = np.loadtxt(fileName)
print("data shape: ",out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [ line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ","").split(" ")
print("data labels: ",labels)
self.send("xoppy_data",out)
else:
print("File %s contains %d scans. Cannot send it as xoppy_table"%(fileName,sf.scanno()))
def compute(self):
fileName = xoppy_calc_nsources(TEMPERATURE=self.TEMPERATURE,ZONE=self.ZONE,MAXFLUX_F=self.MAXFLUX_F,MAXFLUX_EPI=self.MAXFLUX_EPI,MAXFLUX_TH=self.MAXFLUX_TH,NPOINTS=self.NPOINTS)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile",fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ",fileName)
out = np.loadtxt(fileName)
print("data shape: ",out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [ line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ","").split(" ")
print("data labels: ",labels)
self.send("xoppy_data",out)
else:
print("File %s contains %d scans. Cannot send it as xoppy_table"%(fileName,sf.scanno()))
def compute(self):
fileName = xoppy_calc_xfh(FILEF0=self.FILEF0,FILEF1F2=self.FILEF1F2,FILECROSSSEC=self.FILECROSSSEC,ILATTICE=self.ILATTICE,HMILLER=self.HMILLER,KMILLER=self.KMILLER,LMILLER=self.LMILLER,I_ABSORP=self.I_ABSORP,TEMPER=self.TEMPER,ENERGY=self.ENERGY,ENERGY_END=self.ENERGY_END,NPOINTS=self.NPOINTS)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile",fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ",fileName)
out = np.loadtxt(fileName)
print("data shape: ",out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [ line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ","").split(" ")
print("data labels: ",labels)
self.send("xoppy_data",out)
else:
print("File %s contains %d scans. Cannot send it as xoppy_table"%(fileName,sf.scanno()))
def compute(self):
fileName = xoppy_calc_xinpro(CRYSTAL_MATERIAL=self.CRYSTAL_MATERIAL,
MODE=self.MODE,
ENERGY=self.ENERGY,
MILLER_INDEX_H=self.MILLER_INDEX_H,
MILLER_INDEX_K=self.MILLER_INDEX_K,
MILLER_INDEX_L=self.MILLER_INDEX_L,
ASYMMETRY_ANGLE=self.ASYMMETRY_ANGLE,
THICKNESS=self.THICKNESS,
TEMPERATURE=self.TEMPERATURE,
NPOINTS=self.NPOINTS,
SCALE=self.SCALE,
XFROM=self.XFROM,
XTO=self.XTO)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def compute(self):
fileName = xoppy_calc_mare(CRYSTAL=self.CRYSTAL,
H=self.H,
K=self.K,
L=self.L,
HMAX=self.HMAX,
KMAX=self.KMAX,
LMAX=self.LMAX,
FHEDGE=self.FHEDGE,
DISPLAY=self.DISPLAY,
LAMBDA=self.LAMBDA,
DELTALAMBDA=self.DELTALAMBDA,
PHI=self.PHI,
DELTAPHI=self.DELTAPHI)
#send specfile
if fileName == None:
print("Nothing to send")
else:
self.send("xoppy_specfile", fileName)
sf = specfile.Specfile(fileName)
if sf.scanno() == 1:
#load spec file with one scan, # is comment
print("Loading file: ", fileName)
out = np.loadtxt(fileName)
print("data shape: ", out.shape)
#get labels
txt = open(fileName).readlines()
tmp = [line.find("#L") for line in txt]
itmp = np.where(np.array(tmp) != (-1))
labels = txt[itmp[0]].replace("#L ", "").split(" ")
print("data labels: ", labels)
self.send("xoppy_data", out)
else:
print(
"File %s contains %d scans. Cannot send it as xoppy_table"
% (fileName, sf.scanno()))
def _parseDatResults(self, filename):
"""
:param str filename:
:returns tuple: list(nparams), ndarray(nparams, nrows, ncolumns)
"""
from PyMca5.PyMcaIO import specfilewrapper as specfile
self.assertTrue(os.path.isfile(filename),
"Batch fit result file <%s> not present" % filename)
sf = specfile.Specfile(filename)
labels = sf[0].alllabels()
scanData = sf[0].data()
sf = None
nParams, nPoints = scanData.shape
idxRow = labels.index('row')
idxColumn = labels.index('column')
nRows = int(numpy.round(max(scanData[idxRow, :]))) + 1
nColumns = int(numpy.round(max(scanData[idxColumn, :]))) + 1
colfast = scanData[idxRow, 0] == scanData[idxRow, 1]
if colfast:
order = 'C'
else:
order = 'F'
scanData = scanData.reshape((nParams, nRows, nColumns), order=order)
return labels, scanData
def __init__(self, filename):
DataObject.DataObject.__init__(self)
sf = specfile.Specfile(filename)
scan = sf[1]
data = scan.data()
nMca, nchannels = data.shape
nMca = nMca - 1
xValues = data[0, :] * 1
xValues.shape = -1
if 0:
self.data = numpy.zeros((nMca, nchannels), numpy.float32)
self.data[:, :] = data[1:, :]
self.data.shape = 1, nMca, nchannels
else:
self.data = data[1:, :]
self.data.shape = 1, nMca, nchannels
data = None
#perform a least squares adjustment to a line
x = numpy.arange(nchannels).astype(numpy.float32)
Sxy = numpy.dot(x, xValues.T)
Sxx = numpy.dot(x, x.T)
Sx = x.sum()
Sy = xValues.sum()
d = nchannels * Sxx - Sx * Sx
zero = (Sxx * Sy - Sx * Sxy) / d
gain = (nchannels * Sxy - Sx * Sy) / d
#and fill the requested information to be identified as a stack
self.info['SourceName'] = [filename]
self.info["SourceType"] = "SpecFileStack"
self.info["Size"] = 1, nMca, nchannels
self.info["NumberOfFiles"] = 1
self.info["FileIndex"] = 0
self.info["McaCalib"] = [zero, gain, 0.0]
self.info["Channel0"] = 0.0
def _workOnBackend(self, backend):
from PyMca5.PyMcaGui.physics.xrf import McaAdvancedFit
from PyMca5.PyMcaGraph.Plot import Plot
Plot.defaultBackend = backend
widget = McaAdvancedFit.McaAdvancedFit()
widget.show()
self.qapp.processEvents()
# read the data
from PyMca5 import PyMcaDataDir
dataDir = PyMcaDataDir.PYMCA_DATA_DIR
from PyMca5.PyMcaIO import specfilewrapper as specfile
from PyMca5.PyMcaPhysics.xrf import ClassMcaTheory
from PyMca5.PyMcaPhysics.xrf import ConcentrationsTool
from PyMca5.PyMcaIO import ConfigDict
dataFile = os.path.join(dataDir, "Steel.spe")
self.assertTrue(os.path.isfile(dataFile),
"File %s is not an actual file" % dataFile)
sf = specfile.Specfile(dataFile)
self.assertTrue(len(sf) == 1, "File %s cannot be read" % dataFile)
self.assertTrue(sf[0].nbmca() == 1, "Spe file should contain MCA data")
y = counts = sf[0].mca(1)
x = channels = numpy.arange(y.size).astype(numpy.float)
sf = None
widget.setData(x, y)
self.qapp.processEvents()
# read the fit configuration
configFile = os.path.join(dataDir, "Steel.cfg")
self.assertTrue(os.path.isfile(configFile),
"File %s is not an actual file" % configFile)
configuration = ConfigDict.ConfigDict()
configuration.read(configFile)
widget.configure(configuration)
self.qapp.processEvents()
time.sleep(1)
# switch log axis
# widget.graphWindow.yLogButton clicked
isLogy0 = widget.graphWindow.isYAxisLogarithmic()
self.mouseClick(widget.graphWindow.yLogButton, qt.Qt.LeftButton)
self.qapp.processEvents()
isLogy1 = widget.graphWindow.isYAxisLogarithmic()
self.assertTrue(isLogy0 != isLogy1, "Y scale not toggled!")
time.sleep(1)
# reset zoom
widget.graphWindow.resetZoom()
# swith energy axis:
# widget.graphWindow._energyIconSignal
# widget.graphWindow.energyButton clicked
label0 = widget.graphWindow.getGraphXLabel()
self.mouseClick(widget.graphWindow.energyButton, qt.Qt.LeftButton)
self.qapp.processEvents()
label1 = widget.graphWindow.getGraphXLabel()
self.assertTrue(label0 != label1, "Energy scale not toggled!")
self.assertTrue(label0.lower() in ["channel", "energy"],
"Unexpected plot X label <%s>" % label0)
self.assertTrue(label1.lower() in ["channel", "energy"],
"Unexpected plot X label <%s>" % label0)
# reset zoom
widget.graphWindow.resetZoom()
# fit:
# callback widget.fit
# widget.graphWindow.fitButton clicked
# widget.graphWindow._fitIconSignal
self.assertTrue(not widget._fitdone(),
"Bad fit widget state. Fit should not be finished")
self.mouseClick(widget.graphWindow.fitButton, qt.Qt.LeftButton)
self.qapp.processEvents()
self.assertTrue(widget._fitdone(),
"Bad fit widget state. Fit should be finished")
# toggle matrix spectrum
curveList0 = widget.graphWindow.getAllCurves(just_legend=True)
self.mouseClick(widget.matrixSpectrumButton, qt.Qt.LeftButton)
self.qapp.processEvents()
curveList1 = widget.graphWindow.getAllCurves(just_legend=True)
self.assertTrue(
abs(len(curveList0) - len(curveList1)) == 1,
"Matrix spectrum not working!!")
# toggle peaks
curveList0 = widget.graphWindow.getAllCurves(just_legend=True)
for curve in ["Data", "Fit", "Continuum", "Pile-up"]:
self.assertTrue(curve in curveList0,
"Curve <%s> expected but not found" % curve)
self.mouseClick(widget.peaksSpectrumButton, qt.Qt.LeftButton)
self.qapp.processEvents()
curveList1 = widget.graphWindow.getAllCurves(just_legend=True)
self.assertTrue(
len(curveList0) != len(curveList1), "Peaks spectrum not working!!")
time.sleep(1)
from PyMca5.PyMcaGui.plotting import PyMcaPrintPreview
PyMcaPrintPreview.resetSingletonPrintPreview()
