| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2017-12-26 20:18:10 -0600 (Tue, 26 Dec 2017) $ |
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| 4 | # $Author: toby $ |
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| 5 | # $Revision: 3207 $ |
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| 6 | # $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2img_CBF.py $ |
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| 7 | # $Id: G2img_CBF.py 3207 2017-12-27 02:18:10Z toby $ |
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| 8 | ########### SVN repository information ################### |
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| 9 | ''' |
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| 10 | *Module G2img_SFRM: .sfrm image file* |
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| 11 | --------------------------------------- |
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| 12 | |
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| 13 | ''' |
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| 14 | |
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| 15 | from __future__ import division, print_function |
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| 16 | import time |
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| 17 | import GSASIIobj as G2obj |
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| 18 | import GSASIIpath |
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| 19 | import numpy as np |
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| 20 | GSASIIpath.SetVersionNumber("$Revision: 3207 $") |
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| 21 | class SFRM_ReaderClass(G2obj.ImportImage): |
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| 22 | '''Routine to read a Read Bruker Advance image data .sfrm file. |
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| 23 | ''' |
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| 24 | def __init__(self): |
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| 25 | super(self.__class__,self).__init__( # fancy way to self-reference |
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| 26 | extensionlist=('.sfrm',), |
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| 27 | strictExtension=True, |
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| 28 | formatName = 'SFRM image', |
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| 29 | longFormatName = 'Bruker SFRM Binary Data Format image file' |
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| 30 | ) |
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| 31 | |
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| 32 | def ContentsValidator(self, filename): |
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| 33 | '''no test used at this time |
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| 34 | ''' |
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| 35 | return True |
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| 36 | |
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| 37 | def Reader(self,filename, ParentFrame=None, **unused): |
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| 38 | '''Read using Bob's routine :func:`GetSFRMData` |
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| 39 | ''' |
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| 40 | self.Comments,self.Data,self.Npix,self.Image = GetSFRMData(self,filename) |
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| 41 | if self.Npix == 0 or not len(self.Comments): |
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| 42 | return False |
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| 43 | self.LoadImage(ParentFrame,filename) |
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| 44 | return True |
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| 45 | |
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| 46 | def GetSFRMData(self,filename): |
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| 47 | 'Read cbf compressed binarydetector data sfrm file' |
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| 48 | |
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| 49 | if GSASIIpath.GetConfigValue('debug'): |
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| 50 | print ('Read cbf compressed binary detector data sfrm file: '+filename) |
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| 51 | File = open(filename,'rb') |
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| 52 | sizexy = [0,0] |
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| 53 | pixSize = [135.3,135.3] #Pixium4700? |
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| 54 | cent = [0,0] |
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| 55 | wave = 1.54187 #default <CuKa> |
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| 56 | dist = 250. |
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| 57 | stream = File.read() |
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| 58 | if 'bytes' in str(type(stream)): |
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| 59 | stream = stream.decode('latin-1') |
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| 60 | starter = 'IMG: ' |
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| 61 | meanwaves = {'Cu':1.54051,'Ti':2.74841,'Cr':2.28962,'Fe':1.93597, |
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| 62 | 'Co':1.78892,'Mo':0.70926,'Ag':0.559363} |
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| 63 | imageBeg = stream.find(starter)+4 |
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| 64 | head = np.array(list(stream[:imageBeg].split('CFR:')[0])) |
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| 65 | head = head.reshape(-1,80) |
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| 66 | lines = [] |
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| 67 | for line in head: |
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| 68 | line = ''.join(line) |
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| 69 | lines.append(line) |
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| 70 | fields = line.split(':')[1].split() |
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| 71 | if 'TARGET' in line: |
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| 72 | wave = meanwaves[fields[0]] |
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| 73 | target = fields[0].capitalize() |
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| 74 | elif 'DISTANC' in line: |
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| 75 | dist = float(fields[1])*10. |
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| 76 | elif 'ANGLES' in line: |
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| 77 | twoth = float(fields[0]) |
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| 78 | elif 'CENTER' in line: |
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| 79 | cent = [float(fields[0]),float(fields[1])] |
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| 80 | elif 'NROWS' in line: |
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| 81 | sizexy[1] = int(fields[0]) |
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| 82 | elif 'NCOLS' in line: |
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| 83 | sizexy[0] = int(fields[0]) |
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| 84 | elif 'FORMAT' in line: |
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| 85 | frmt = int(fields[0]) |
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| 86 | elif 'HDRBLKS' in line: |
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| 87 | imageBeg = 512*int(fields[0]) |
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| 88 | elif 'NOVERFL' in line: |
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| 89 | Nunder = int(fields[0]) |
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| 90 | N2byte = 2*int(fields[1]) |
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| 91 | if N2byte%16: |
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| 92 | N2byte = (N2byte//16+1)*16 |
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| 93 | N4byte = 4*int(fields[2]) |
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| 94 | if N4byte%16: |
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| 95 | N4byte = (N4byte//16+1)*16 |
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| 96 | if frmt == 86: |
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| 97 | lines = ['FORMAT 86 Bruker files currently not readible by GSAS-II',] |
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| 98 | return lines,0,0,0 |
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| 99 | nxy = sizexy[0]*sizexy[1] |
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| 100 | cent = [cent[0]*pixSize[0]/1000.,cent[1]*pixSize[1]/1000.] |
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| 101 | cent[0] += dist*np.tan(np.pi*twoth/180.) |
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| 102 | File.seek(imageBeg) |
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| 103 | img = File.read(nxy) |
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| 104 | img2byte = File.read(N2byte) |
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| 105 | img4byte = File.read(N4byte) |
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| 106 | time0 = time.time() |
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| 107 | img = np.array(np.frombuffer(img,dtype='u1'),dtype=np.int32) |
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| 108 | img2byte = np.array(np.frombuffer(img2byte,dtype='u2'),dtype=np.int32) |
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| 109 | img4byte = np.array(np.frombuffer(img4byte,dtype='u4'),dtype=np.int32) |
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| 110 | ins2byte = np.argwhere(img==255) |
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| 111 | for j,i in enumerate(list(ins2byte)): |
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| 112 | img[i] = img2byte[j] |
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| 113 | ins4byte = np.argwhere(img==65535) |
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| 114 | for j,i in enumerate(list(ins4byte)): |
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| 115 | img[i] = img4byte[j] |
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| 116 | image = np.reshape(img,(sizexy[1],sizexy[0])) |
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| 117 | print ('import time: %.3f'%(time.time()-time0)) |
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| 118 | data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent, |
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| 119 | 'size':sizexy,'target':target,'tilt':-twoth,'rotation':90.} |
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| 120 | data['pixLimit'] = 5 |
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| 121 | data['calibdmin'] = 1.0 |
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| 122 | data['cutoff'] = .5 |
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| 123 | Npix = sizexy[0]*sizexy[1] |
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| 124 | |
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| 125 | return lines,data,Npix,image |
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| 126 | |
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