def synchro_on_scanning(self,sfscanning,timehistory,meashistory,sfscanrange=None):
"""
Calculate the average of tensmon or humidity informations on each x-ray scans performed. A trick to improve rapidity of calculation have been set.
@param sfscanning : specfile of the scanning history
@param timehistory,meashistory : time and values of measurements performed on tensmon of hummon.
@param sfscanrange : list of scannumber to synchronize
"""
scannumbers = SpecTools.get_NumberOfScans(sfscanning)
averageshistory = []
idx = 0
if sfscanrange == None:
scanrange = range(1,scannumbers+1)
else:
scanrange = sfscanrange
for scan in scanrange:
scan_starttime = SpecTools.get_ScanStartingTime(self.scanning,scan)
idx_ini,val_ini = NumpyTools.find_nearest(scan_starttime,timehistory)
idx = idx_ini
scan_endtime = SpecTools.get_ScanEndingTime(self.scanning,scan)
idx_end,val_end = NumpyTools.find_nearest(scan_endtime,timehistory)
idx = idx_end
avghistory = numpy.mean(meashistory[idx_ini:idx_end])
averageshistory.append(avghistory)
print scan, scan_starttime, scan_endtime, idx_ini, idx_end, avghistory
self.scanning_scannumbers = range(1,scannumbers+1)
self.scanning_measurements = numpy.array(averageshistory)
def CreateScanDataFileList(wdname,sf,scannumber):
"""
Create the list of localized file from specfile scan number specified
@param wdname: main working path directory containing DATA/, PROCESS/ and REPORT/ folders afterward
@type wdname: string
@param sf: specfile informations
@type sf: specfile object
@param scannumber: number of the scan data to find out
@type scannumber: string
"""
# Original ESRF directory name of files
odname = SpecTools.get_ScanValueInSpecHeaderComment(sf,scannumber,'#C qq.adet.dname')
# Equivalent directory name in the path
edname = odname.split('/')
# Set the last directory specified in wdname as the key to set the equivalency
keydname = wdname.split('/')[-2]
# Position of experiment directory name (edname) in the original directory name (odname) field :
try:
poskey = int([pos for pos in range(len(odname.split('/'))) if odname.split('/')[pos] == keydname][0])
except IndexError:# Case of keydname is not identical between original directory and actual directory
poskey = int([pos for pos in range(len(odname.split('/'))) if odname.split('/')[pos] == 'DATA'][0]) - 1
fdname = wdname + '/'.join(odname.split('/')[poskey+1::]) + '/'#Directory of the files
nbmeas = sf.select(str(scannumber)).data().shape[1]#Number of measurements recorded (can be different from expected in the command if user stop the scan)
fprefix = SpecTools.get_ScanValueInSpecHeaderComment(sf,scannumber,'#C qq.adet.prefix')
filelist = [fdname + fprefix + str(val).zfill(4) + '.edf' for val in range(0,nbmeas)]
return filelist
def CreateScanDataFileList(wdname, sf, scannumber):
"""
Create the list of localized file from specfile scan number specified
@param wdname: main working path directory containing DATA/, PROCESS/ and REPORT/ folders afterward
@type wdname: string
@param sf: specfile informations
@type sf: specfile object
@param scannumber: number of the scan data to find out
@type scannumber: string
"""
# Original ESRF directory name of files
odname = SpecTools.get_ScanValueInSpecHeaderComment(
sf, scannumber, '#C qq.adet.dname')
# Equivalent directory name in the path
edname = odname.split('/')
# Set the last directory specified in wdname as the key to set the equivalency
keydname = wdname.split('/')[-2]
# Position of edname in the odname field
poskey = int([
pos for pos in range(len(odname.split('/')))
if odname.split('/')[pos] == keydname
][0])
fdname = wdname + '/'.join(
odname.split('/')[poskey + 1::]) + '/' #Directory of the files
nbmeas = sf.select(str(scannumber)).data().shape[
1] #Number of measurements recorded (can be different from expected in the command if user stop the scan)
fprefix = SpecTools.get_ScanValueInSpecHeaderComment(
sf, scannumber, '#C qq.adet.prefix')
filelist = [
fdname + fprefix + str(val).zfill(4) + '.edf'
for val in range(0, nbmeas)
]
return filelist
def set_hummon_specfile(self,sfpath):
"""
Set the humidity monitor specfile and retrieve the data
@param sfpath : specfile path
@type sfpath : string
@return : measurements of temperature, humidity, and set-point along time onto numpy arrays.
"""
self.hummon = SpecTools.specfile.Specfile(sfpath)
self.Hum_Time,self.Hum_Temp = SpecTools.get_ScanMeasurementsAlongTime(self.hummon,'*','hum_t')
self.Hum_Time,self.Hum_RH = SpecTools.get_ScanMeasurementsAlongTime(self.hummon,'*','hum_h')
self.Hum_Time,self.Hum_SP = SpecTools.get_ScanMeasurementsAlongTime(self.hummon,'*','hum_rsp')
def set_scanning_specfile(self,sfpath):
"""
Set the X-ray scanning specfile and retrieve the data
@param sfpath : specfile path
@type sfpath : string
@return :
"""
self.scanning = SpecTools.specfile.Specfile(sfpath)
self.numberofscans_scanning = SpecTools.get_NumberOfScans(self.scanning)
instant_measurements = []
for scannumber in range(0,self.numberofscans_scanning):
instant_measurements.append(SpecTools.get_ScanStartingTime(self.scanning,scannumber+1))
self.instant_measurements = numpy.array(instant_measurements)
def set_tensmon_specfile(self,sfpath):
"""
Set the tensile monitor specfile and retrieve the data
@param sfpath : specfile path
@type sfpath : string
"""
self.tensmon = SpecTools.specfile.Specfile(sfpath)
self.Stretch_Time,self.Stretch_Volt = SpecTools.get_ScanMeasurementsAlongTime(self.tensmon,'*','strechVolt')
self.Stretch_Time,self.Stretch_N = SpecTools.get_ScanMeasurementsAlongTime(self.tensmon,'*','strechN')
self.Stretch_Time,self.Stretch_MM = SpecTools.get_ScanMeasurementsAlongTime(self.tensmon,'*','strechMM')
self.Stretch_Time_inHr = []
for i in self.Stretch_Time:
self.Stretch_Time_inHr.append((i-self.Stretch_Time[0]).days*24.+(i-self.Stretch_Time[0]).seconds/3600.)
def set_specfile(self,sfpath):
"""
Set the specfile and retrieve the data
@param sfpath : specfile path
@type sfpath : string
"""
self.specfile = SpecTools.specfile.Specfile(sfpath)
self.Stretch_Time,self.Hum_T = SpecTools.get_ScanMeasurementsAlongTime(self.specfile,'*','hum_t')
self.Stretch_Time,self.Hum_H = SpecTools.get_ScanMeasurementsAlongTime(self.specfile,'*','hum_h')
self.Stretch_Time,self.Hum_Sp = SpecTools.get_ScanMeasurementsAlongTime(self.specfile,'*','hum_rsp')
self.Stretch_Time_inHr = []
for i in self.Stretch_Time:
self.Stretch_Time_inHr.append((i-self.Stretch_Time[0]).days*24.+(i-self.Stretch_Time[0]).seconds/3600.)
def __init__(self,sfpath):
"""
Set the specfile and retrieve the date and time history of the data measurement
@param sfpath : specfile path
@type sfpath : string
"""
self.specfile = SpecTools.specfile.Specfile(sfpath)
self.numberofscans = SpecTools.get_NumberOfScans(self.specfile)
instant_measurements = []
print 'Number of scans :',self.numberofscans
for scannumber in range(0,self.numberofscans):
instant_measurements.append(SpecTools.get_ScanStartingTime(self.specfile,scannumber+1))
self.instant_measurements = numpy.array(instant_measurements)
def CreateCompositeFromScan(wdname,sf,scannumber,background=None,roi=((0,0),(512,512))): """ Create a composite image of a large 2D nparray obtained during a mesh or a scan @param wdname: working directory name @type wdname: string @param sf: specfile object @type sf: specfile object @param scannumber: number of the scan to use @type scannumber: string or integer @param background: set a background image compatible with the images size of the scan @type background: numpy 2D array @param roi: tuple of region of interest in the image @type roi: tuple of 2 tuple of integer """ # TODO : display a statut bar on file number to display or else # TODO : arrange to get the binning value in the roi # TODO : arrange this to fill in the composite according to positions # TODO : create an optional parameter roic (region of interest centered) with 3 parameters Xc, Yc, Radius pixels print 'Calculating composite of scan ',scannumber, '...' # Create the list of the specified scan : filelist = CreateScanDataFileList(wdname,sf,scannumber) #print filelist[0] #print filelist[-1] # Retrieve the size of the image : ImShape = fabio.open(filelist[0]).data.shape print ' . Image complete size =', ImShape # Handle background image : if background == None: print " . No background specified !" background = numpy.zeros(ImShape) ImSize = ImShape #Necessary for ROI implementation # TODO create the definition of ROI print ' . Image localized size =',ImSize # Definition of the composite : scan_command_field = SpecTools.get_ScanCommandField(sf,scannumber) scan_command_type = scan_command_field.split()[2] if scan_command_type == 'mesh': # Define the composite shape according to the scan command : CompositeShape = (int(scan_command_field.split()[6])+1,int(scan_command_field.split()[10])+1) elif scan_command_type == 'ascan': # Detect if it is a verticel or horizontal scan to define correctly the mesh : Motor = scan_command_field.split()[3] if Motor == 'nny' or 'stry':# Case of horizontal scan CompositeShape = (1,int(scan_command_field.split()[6])+1) elif Motor == 'nnz' or 'strz':# Case of vetical scan CompositeShape = (int(scan_command_field.split()[6])+1,1) print ' . Composite shape =', CompositeShape # Initialization of the composite image : CompositeArray = numpy.empty((CompositeShape[0]*ImSize[0],CompositeShape[1]*ImSize[1])) CompositeArray.fill(numpy.nan) print ' . Composite size =',CompositeArray.shape # Fill in the composite image : if scan_command_type == 'mesh': # Get the positions of each image along Motor1 and Motor2 # TODO : chek the orientation of mesh. Actually Motor1 is supposed to be horizontal (nny) and Motor2 vertical Motor1 = scan_command_field.split()[3] Motor2 = scan_command_field.split()[7] print ' . Motor used =',(Motor1,Motor2) SpecimenPosition1 = SpecTools.get_ScanMeasurement(sf,scannumber,Motor1) SpecimenPosition2 = SpecTools.get_ScanMeasurement(sf,scannumber,Motor2) SpecimenPosition = [SpecimenPosition1,SpecimenPosition2] Min1 = min(SpecimenPosition1) Max1 = max(SpecimenPosition1) Min2 = min(SpecimenPosition2) Max2 = max(SpecimenPosition2) Delta1 = round((Max1-Min1)/(CompositeShape[0]-1),3)# [nm] Delta2 = round((Max2-Min2)/(CompositeShape[1]-1),3)# [nm] print ' . Step between images [um] =',(Delta1*1e3,Delta2*1e3) idx = 0# Number of the file in the list for impath in filelist[0::]: #TODO verify this definitions is SpecimenPosition are in positive values Deltax1 = round(SpecimenPosition1[idx] - min(SpecimenPosition1),3) Deltax2 = round(SpecimenPosition2[idx] - min(SpecimenPosition2),3) idx1 = int(Deltax1 / Delta1) idx2 = int(Deltax2 / Delta2) imdata = fabio.open(impath).data #TODO : verify this definition (+1 strange !) #TODO : backgournd have to be roi selected to correspond to imdata size CompositeArray[0+idx1*ImSize[0]:(ImSize[0]-1)+idx1*ImSize[0]+1,0+idx2*ImSize[1]:(ImSize[1]-1)+idx2*ImSize[1]+1] = imdata - background idx = idx+1 elif scan_command_type == 'ascan': if Motor == 'nny' or 'stry':#Case of horizontal scan SpecimenPosition = SpecTools.get_ScanMeasurement(sf,scannumber,Motor) idx = 0 if SpecimenPosition[1] - SpecimenPosition[0] > 0:# Specimen moving from left to right from beam point of view for impath in filelist: imdata = fabio.open(impath).data CompositeArray[0:ImSize[0],idx*ImSize[1]:ImSize[1]+idx*ImSize[1]] = imdata idx = idx+1 """ elif SpecimenPosition[1] - SpecimenPosition[0] < 0: CompositeArray = fabio.open(filelist[0]).data #for impath in filelist[0::]: # imdata = fabio.open(impath).data # CompositeArray = numpy.hstack([imdata,CompositeArray]) if Motor == 'nnz' or 'strz': # Case of vertical scan : SpecimenPosition = SpecTools.get_ScanMeasurement(sf,scannumber,Motor) if SpecimenPosition[1] - SpecimenPosition[0] > 0: CompositeArray = fabio.open(filelist[0]).data for impath in filelist[0::]: imdata = fabio.open(impath).data CompositeArray = numpy.vstack([CompositeArray,imdata]) elif SpecimenPosition[1] - SpecimenPosition[0] < 0: CompositeArray = fabio.open(filelist[0]).data for impath in filelist[0::]: imdata = fabio.open(impath).data CompositeArray = numpy.vstack([imdata,CompositeArray]) """ print 'Calculation of composite finished !' return SpecimenPosition,CompositeArray
def CreateCompositeFromScan(wdname,
sf,
scannumber,
background=None,
roi=((0, 0), (512, 512))):
"""
Create a composite image of a large 2D nparray obtained during a mesh or a scan
@param wdname: working directory name
@type wdname: string
@param sf: specfile object
@type sf: specfile object
@param scannumber: number of the scan to use
@type scannumber: string or integer
@param background: set a background image compatible with the images size of the scan
@type background: numpy 2D array
@param roi: tuple of region of interest in the image
@type roi: tuple of 2 tuple of integer
"""
# TODO : display a statut bar on file number to display or else
# TODO : arrange to get the binning value in the roi
# TODO : arrange this to fill in the composite according to positions
# TODO : create an optional parameter roic (region of interest centered) with 3 parameters Xc, Yc, Radius pixels
print 'Calculating composite of scan ', scannumber, '...'
# Create the list of the specified scan :
filelist = CreateScanDataFileList(wdname, sf, scannumber)
#print filelist[0]
#print filelist[-1]
# Retrieve the size of the image :
ImShape = fabio.open(filelist[0]).data.shape
print ' . Image complete size =', ImShape
# Handle background image :
if background == None:
print " . No background specified !"
background = numpy.zeros(ImShape)
ImSize = ImShape #Necessary for ROI implementation
# TODO create the definition of ROI
print ' . Image localized size =', ImSize
# Definition of the composite :
scan_command_field = SpecTools.get_ScanCommandField(sf, scannumber)
scan_command_type = scan_command_field.split()[2]
if scan_command_type == 'mesh':
# Define the composite shape according to the scan command :
CompositeShape = (int(scan_command_field.split()[6]) + 1,
int(scan_command_field.split()[10]) + 1)
elif scan_command_type == 'ascan':
# Detect if it is a verticel or horizontal scan to define correctly the mesh :
Motor = scan_command_field.split()[3]
if Motor == 'nny' or 'stry': # Case of horizontal scan
CompositeShape = (1, int(scan_command_field.split()[6]) + 1)
elif Motor == 'nnz' or 'strz': # Case of vetical scan
CompositeShape = (int(scan_command_field.split()[6]) + 1, 1)
print ' . Composite shape =', CompositeShape
# Initialization of the composite image :
CompositeArray = numpy.empty(
(CompositeShape[0] * ImSize[0], CompositeShape[1] * ImSize[1]))
CompositeArray.fill(numpy.nan)
print ' . Composite size =', CompositeArray.shape
# Fill in the composite image :
if scan_command_type == 'mesh':
# Get the positions of each image along Motor1 and Motor2
# TODO : chek the orientation of mesh. Actually Motor1 is supposed to be horizontal (nny) and Motor2 vertical
Motor1 = scan_command_field.split()[3]
Motor2 = scan_command_field.split()[7]
print ' . Motor used =', (Motor1, Motor2)
SpecimenPosition1 = SpecTools.get_ScanMeasurement(
sf, scannumber, Motor1)
SpecimenPosition2 = SpecTools.get_ScanMeasurement(
sf, scannumber, Motor2)
SpecimenPosition = [SpecimenPosition1, SpecimenPosition2]
Min1 = min(SpecimenPosition1)
Max1 = max(SpecimenPosition1)
Min2 = min(SpecimenPosition2)
Max2 = max(SpecimenPosition2)
Delta1 = round((Max1 - Min1) / (CompositeShape[0] - 1), 3) # [nm]
Delta2 = round((Max2 - Min2) / (CompositeShape[1] - 1), 3) # [nm]
print ' . Step between images [um] =', (Delta1 * 1e3, Delta2 * 1e3)
idx = 0 # Number of the file in the list
for impath in filelist[0::]:
#TODO verify this definitions is SpecimenPosition are in positive values
Deltax1 = round(SpecimenPosition1[idx] - min(SpecimenPosition1), 3)
Deltax2 = round(SpecimenPosition2[idx] - min(SpecimenPosition2), 3)
idx1 = int(Deltax1 / Delta1)
idx2 = int(Deltax2 / Delta2)
imdata = fabio.open(impath).data
#TODO : verify this definition (+1 strange !)
#TODO : backgournd have to be roi selected to correspond to imdata size
CompositeArray[0 + idx1 * ImSize[0]:(ImSize[0] - 1) +
idx1 * ImSize[0] + 1,
0 + idx2 * ImSize[1]:(ImSize[1] - 1) +
idx2 * ImSize[1] + 1] = imdata - background
idx = idx + 1
elif scan_command_type == 'ascan':
if Motor == 'nny' or 'stry': #Case of horizontal scan
SpecimenPosition = SpecTools.get_ScanMeasurement(
sf, scannumber, Motor)
idx = 0
if SpecimenPosition[1] - SpecimenPosition[
0] > 0: # Specimen moving from left to right from beam point of view
for impath in filelist:
imdata = fabio.open(impath).data
CompositeArray[0:ImSize[0], idx * ImSize[1]:ImSize[1] +
idx * ImSize[1]] = imdata
idx = idx + 1
"""
elif SpecimenPosition[1] - SpecimenPosition[0] < 0:
CompositeArray = fabio.open(filelist[0]).data
#for impath in filelist[0::]:
# imdata = fabio.open(impath).data
# CompositeArray = numpy.hstack([imdata,CompositeArray])
if Motor == 'nnz' or 'strz':
# Case of vertical scan :
SpecimenPosition = SpecTools.get_ScanMeasurement(sf,scannumber,Motor)
if SpecimenPosition[1] - SpecimenPosition[0] > 0:
CompositeArray = fabio.open(filelist[0]).data
for impath in filelist[0::]:
imdata = fabio.open(impath).data
CompositeArray = numpy.vstack([CompositeArray,imdata])
elif SpecimenPosition[1] - SpecimenPosition[0] < 0:
CompositeArray = fabio.open(filelist[0]).data
for impath in filelist[0::]:
imdata = fabio.open(impath).data
CompositeArray = numpy.vstack([imdata,CompositeArray])
"""
print 'Calculation of composite finished !'
return SpecimenPosition, CompositeArray