def loadIMAGE(self, event=None):
wildcards = 'XRD image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self,
message='Choose XRD calibration file',
defaultDir=os.getcwd(),
wildcard=wildcards,
style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
# self.raw_img = plt.imread(path)
self.raw_img = tifffile.imread(path)
#self.raw_img = fabio.open(path).data
except:
print('Image not properly opened.')
pass
self.plot2Dimg.display(self.raw_img)
self.plot2Dimg.redraw()
self.AutoContrast()
self.entr_calimg.Clear()
self.entr_calimg.SetValue(path) #os.path.split(path)[-1]
def openMask(self,event=None):
wildcards = 'pyFAI mask file (*.edf)|*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose pyFAI mask file',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
try:
raw_mask = np.array(tifffile.imread(path))
except:
import fabio
raw_mask = fabio.open(path).data
self.msk_img = np.ones(raw_mask.shape)-raw_mask
self.checkIMAGE()
print('Reading mask:\n\t%s' % path)
except:
print('\nCannot read as mask file: %s\n' % path)
return
self.ch_msk.SetValue(True)
self.applyMask(event=True)
def loadIMAGE(self,event=None):
wildcards = '2DXRD image files (*.*)|*.*|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose 2D XRD image',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
path, read = '', False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
print('\nReading XRD image file: %s' % path)
image,xrmfile = None,None
try:
xrmfile = h5py.File(path, 'r')
except IOError:
try:
from larch_plugins.xrmmap import read_xrd_netcdf #,GSEXRM_MapFile
image = read_xrd_netcdf(path)
except TypeError:
try:
image = tifffile.imread(path)
except ValueError:
print('Could not read file.')
return
iname = os.path.split(path)[-1]
self.plot2Dxrd(iname, image, path=path, h5file=xrmfile)
def loadIMAGE(self,event=None):
wildcards = 'XRD image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
if os.path.exists(self.entr_calimg.GetValue()):
dfltDIR = self.entr_calimg.GetValue()
else:
dfltDIR = os.getcwd()
dlg = wx.FileDialog(self, message='Choose XRD calibration file',
defaultDir=dfltDIR,
wildcard=wildcards, style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
# self.raw_img = plt.imread(path)
self.raw_img = tifffile.imread(path)
#self.raw_img = fabio.open(path).data
except:
print('Image not properly opened.')
pass
self.plot2Dimg.display(self.raw_img)
self.plot2Dimg.redraw()
self.AutoContrast()
self.entr_calimg.Clear()
self.entr_calimg.SetValue(path) #os.path.split(path)[-1]
def openMask(self, event=None):
wildcards = 'pyFAI mask file (*.edf)|*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self,
message='Choose pyFAI mask file',
defaultDir=os.getcwd(),
wildcard=wildcards,
style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
try:
raw_mask = np.array(tifffile.imread(path))
except:
import fabio
raw_mask = fabio.open(path).data
self.msk_img = np.ones(raw_mask.shape) - raw_mask
self.checkIMAGE()
print('Reading mask: %s' % path)
except:
print('Cannot read as mask file: %s' % path)
return
self.ch_msk.SetValue(True)
self.applyMask(event=True)
def loadIMAGE(self, event=None):
wildcards = 'XRD image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self,
message='Choose XRD image',
defaultDir=os.getcwd(),
wildcard=wildcards,
style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
# self.raw_img = plt.imread(path)
self.raw_img = tifffile.imread(path)
#self.raw_img = fabio.open(path).data
except:
print('Image not properly opened.')
self.raw_img = np.zeros((1024, 1024))
else:
print('No image selected.')
self.raw_img = np.zeros((1024, 1024))
def integrate_xrd_row(rowxrd2d,
calfile,
unit='q',
steps=10001,
wedge_limits=None,
mask=None,
dark=None,
flip=True):
'''
Uses pyFAI (poni) calibration file to produce 1D XRD data from a row of 2D XRD images
Must provide pyFAI calibration file
rowxrd2d : 2D diffraction images for integration
calfile : poni calibration file
unit : unit for integration data ('2th'/'q'); default is 'q'
steps : number of steps in integration data; default is 10000
wedge_limits : azimuthal slice limits
mask : mask array for image
dark : dark image array
flip : vertically flips image to correspond with Dioptas poni file calibration
'''
if HAS_pyFAI:
try:
ai = pyFAI.load(calfile)
except:
print('Provided calibration file could not be loaded.')
return
if type(dark) is str:
try:
dark = np.array(tifffile.imread(xrd2dbkgd))
except:
dark = None
dir = -1 if flip else 1
attrs = {'mask': mask, 'dark': dark}
if unit.startswith('2th'):
attrs.update({'unit': '2th_deg'})
else:
attrs.update({'unit': 'q_A^-1'})
if wedge_limits is not None:
attrs.update({'azimuth_range': wedge_limits})
q, xrd1d = [], []
for i, xrd2d in enumerate(rowxrd2d):
row_q, row_xrd1d = calcXRD1d(xrd2d[::dir, :], ai, steps, attrs)
q += [row_q]
xrd1d += [row_xrd1d]
return np.array(q), np.array(xrd1d)
else:
print('pyFAI not imported. Cannot calculate 1D integration.')
def integrate_xrd_row(rowxrd2d, calfile, unit='q', steps=2048,
wedge_limits=None, mask=None, dark=None,
flip=True):
'''
Uses pyFAI (poni) calibration file to produce 1D XRD data from a row of 2D XRD images
Must provide pyFAI calibration file
rowxrd2d : 2D diffraction images for integration
calfile : poni calibration file
unit : unit for integration data ('2th'/'q'); default is 'q'
steps : number of steps in integration data; default is 10000
wedge_limits : azimuthal slice limits
mask : mask array for image
dark : dark image array
flip : vertically flips image to correspond with Dioptas poni file calibration
'''
if not HAS_pyFAI:
print('pyFAI not imported. Cannot calculate 1D integration.')
return
try:
ai = pyFAI.load(calfile)
except:
print('calibration file "%s" could not be loaded.' % calfile)
return
if type(dark) is str:
try:
dark = np.array(tifffile.imread(xrd2dbkgd))
except:
dark = None
dir = -1 if flip else 1
attrs = dict(mask=mask, dark=dark, method='csr',
polarization_factor=0.999, correctSolidAngle=True)
if unit.startswith('2th'):
attrs.update({'unit':'2th_deg'})
else:
attrs.update({'unit':'q_A^-1'})
if wedge_limits is not None:
attrs.update({'azimuth_range':wedge_limits})
# print("Calc XRD 1D for row", ai, steps, attrs)
q, xrd1d = [], []
for i, xrd2d in enumerate(rowxrd2d):
row_q,row_xrd1d = calcXRD1d(xrd2d[::dir,:], ai, steps, attrs)
q += [row_q]
xrd1d += [row_xrd1d]
return np.array(q), np.array(xrd1d)
def read_xrd_data(filepath):
if not os.path.exists(filepath):
return
try:
data = np.array(tifffile.imread(filepath))
except: # TypeError:
try:
from larch_plugins.xrmmap import read_xrd_netcdf
data = np.array(read_xrd_netcdf(filepath))
except:
try:
data = xrd1d(file=filepath).I
except:
return
return data
def openBkgd(self, event=None):
wildcards = 'XRD background image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self,
message='Choose XRD background image',
defaultDir=os.getcwd(),
wildcard=wildcards,
style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
self.bkgd = tifffile.imread(path)
self.checkIMAGE()
def loadIMAGE(self, event=None):
wildcards = 'XRD image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self,
message='Choose 2D XRD image',
defaultDir=os.getcwd(),
wildcard=wildcards,
style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
print('Reading file: %s' % path)
newimg = tifffile.imread(path)
self.plot2Dxrd(newimg, os.path.split(path)[-1])
def openBkgd(self,event=None):
wildcards = 'XRD background image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose XRD background image',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
self.bkgd_img = np.array(tifffile.imread(path))
self.checkIMAGE()
print('Reading background:\n\t%s' % path)
except:
print('\nCannot read as an image file: %s\n' % path)
return
def loadIMAGE(self,event=None):
wildcards = 'XRD image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self, message='Choose XRD image',
defaultDir=os.getcwd(),
wildcard=wildcards, style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
# self.raw_img = plt.imread(path)
self.raw_img = tifffile.imread(path)
#self.raw_img = fabio.open(path).data
except:
print('Image not properly opened.')
self.raw_img = np.zeros((1024,1024))
else:
print('No image selected.')
self.raw_img = np.zeros((1024,1024))
def openBkgd(self, event=None):
wildcards = 'XRD background image (*.edf,*.tif,*.tiff)|*.tif;*.tiff;*.edf|All files (*.*)|*.*'
dlg = wx.FileDialog(self,
message='Choose XRD background image',
defaultDir=os.getcwd(),
wildcard=wildcards,
style=wx.FD_OPEN)
path, read = None, False
if dlg.ShowModal() == wx.ID_OK:
read = True
path = dlg.GetPath().replace('\\', '/')
dlg.Destroy()
if read:
try:
self.bkgd_img = np.array(tifffile.imread(path))
self.checkIMAGE()
print('Reading background: %s' % path)
except:
print('Cannot read as an image file: %s' % path)
return
def read_tiff(fname, _larch=None, *args, **kws):
"""read image data from a TIFF file as an array"""
return imread(fname, *args, **kws)
def read_tiff(fname, _larch=None, *args, **kws):
"""read image data from a TIFF file as an array"""
return imread(fname, *args, **kws)
