Source code for G2img_SFRM

# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2021-08-19 18:38:36 +0000 (Thu, 19 Aug 2021) $
# $Author: toby $
# $Revision: 5014 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2img_SFRM.py $
# $Id: G2img_SFRM.py 5014 2021-08-19 18:38:36Z toby $
########### SVN repository information ###################
'''
*Module G2img_SFRM: .sfrm image file*
---------------------------------------

'''

from __future__ import division, print_function
import time
import GSASIIobj as G2obj
import GSASIIpath
import numpy as np
GSASIIpath.SetVersionNumber("$Revision: 5014 $")
[docs]class SFRM_ReaderClass(G2obj.ImportImage): '''Routine to read a Read Bruker Advance image data .sfrm file. ''' def __init__(self): super(self.__class__,self).__init__( # fancy way to self-reference extensionlist=('.sfrm',), strictExtension=True, formatName = 'SFRM image', longFormatName = 'Bruker SFRM Binary Data Format image file' )
[docs] def ContentsValidator(self, filename): '''no test used at this time ''' return True
[docs] def Reader(self,filename, ParentFrame=None, **unused): '''Read using Bob's routine :func:`GetSFRMData` ''' self.Comments,self.Data,self.Npix,self.Image = GetSFRMData(self,filename) if self.Npix == 0 or not len(self.Comments): return False self.LoadImage(ParentFrame,filename) return True
[docs]def GetSFRMData(self,filename): 'Read cbf compressed binarydetector data sfrm file' if GSASIIpath.GetConfigValue('debug'): print ('Read cbf compressed binary detector data sfrm file: '+filename) File = open(filename,'rb') sizexy = [0,0] pixSize = [135.3,135.3] #Pixium4700? cent = [0,0] wave = 1.54187 #default <CuKa> dist = 250. stream = File.read() if 'bytes' in str(type(stream)): stream = stream.decode('latin-1') starter = 'IMG: ' meanwaves = {'Cu':1.54051,'Ti':2.74841,'Cr':2.28962,'Fe':1.93597, 'Co':1.78892,'Mo':0.70926,'Ag':0.559363} imageBeg = stream.find(starter)+4 head = np.array(list(stream[:imageBeg].split('CFR:')[0])) head = head.reshape(-1,80) lines = [] for line in head: line = ''.join(line) lines.append(line) fields = line.split(':')[1].split() if 'TARGET' in line: wave = meanwaves[fields[0]] target = fields[0].capitalize() elif 'DISTANC' in line: dist = float(fields[1])*10. elif 'ANGLES' in line: twoth = float(fields[0]) elif 'CENTER' in line: cent = [float(fields[0]),float(fields[1])] elif 'NROWS' in line: sizexy[1] = int(fields[0]) elif 'NCOLS' in line: sizexy[0] = int(fields[0]) elif 'FORMAT' in line: frmt = int(fields[0]) elif 'HDRBLKS' in line: imageBeg = 512*int(fields[0]) elif 'NOVERFL' in line: Nunder = int(fields[0]) N2byte = 2*int(fields[1]) if N2byte%16: N2byte = (N2byte//16+1)*16 N4byte = 4*int(fields[2]) if N4byte%16: N4byte = (N4byte//16+1)*16 if frmt == 86: lines = ['FORMAT 86 Bruker files currently not readible by GSAS-II',] return lines,0,0,0 nxy = sizexy[0]*sizexy[1] cent = [cent[0]*pixSize[0]/1000.,cent[1]*pixSize[1]/1000.] cent[0] += dist*np.tan(np.pi*twoth/180.) File.seek(imageBeg) img = File.read(nxy) img2byte = File.read(N2byte) img4byte = File.read(N4byte) time0 = time.time() img = np.array(np.frombuffer(img,dtype='u1'),dtype=np.int32) img2byte = np.array(np.frombuffer(img2byte,dtype='u2'),dtype=np.int32) img4byte = np.array(np.frombuffer(img4byte,dtype='u4'),dtype=np.int32) ins2byte = np.argwhere(img==255) for j,i in enumerate(list(ins2byte)): img[i] = img2byte[j] ins4byte = np.argwhere(img==65535) for j,i in enumerate(list(ins4byte)): img[i] = img4byte[j] image = np.reshape(img,(sizexy[1],sizexy[0])) print ('import time: %.3f'%(time.time()-time0)) data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'det2theta':0.0, 'size':sizexy,'target':target,'tilt':-twoth,'rotation':90.,'twoth':str(round(twoth,1))} data['pixLimit'] = 5 data['calibdmin'] = 1.0 data['cutoff'] = .5 Npix = sizexy[0]*sizexy[1] return lines,data,Npix,image