Changeset 1997


Ignore:
Timestamp:
Oct 10, 2015 11:58:12 AM (8 years ago)
Author:
toby
Message:

Add API for direct image read (G2IO.ExportPowderList?) and powder exports w/o GUI (G2IO.ExportPowderList?); redo export to add new method (Writer)

Location:
trunk
Files:
1 added
5 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASII.py

    r1985 r1997  
    180180            help='',id=wx.ID_ANY,
    181181            kind=wx.ITEM_NORMAL,
    182             text='Add phase')
     182            text='Add new phase')
    183183        self.Bind(wx.EVT_MENU, self.OnAddPhase, id=item.GetId())
    184184        item = parent.Append(
    … …  
    19021902                filelist.append(filename)   
    19031903        filelist = sorted(list(set(filelist))) # remove duplicates
    1904         exporterlist = []
     1904        self.exporterlist = []
    19051905        # go through the routines and import them, saving objects that
    19061906        # have export routines (method Exporter)
    … …  
    19211921                        else:
    19221922                            exporter = clss[1](self) # create an export instance
    1923                             exporterlist.append(exporter)
     1923                            self.exporterlist.append(exporter)
    19241924            except AttributeError:
    19251925                print 'Import_'+errprefix+': Attribute Error'+str(filename)
    … …  
    19301930            if fp: fp.close()
    19311931        # Add submenu item(s) for each Exporter by its self-declared type (can be more than one)
    1932         for obj in exporterlist:
     1932        for obj in self.exporterlist:
    19331933            #print 'exporter',obj
    19341934            for typ in obj.exporttype:
    … …  
    23752375                imagefiles.sort()
    23762376                for imagefile in imagefiles:
    2377                     # if a zip file, open and extract
    2378                     if os.path.splitext(imagefile)[1].lower() == '.zip':
    2379                         extractedfile = G2IO.ExtractFileFromZip(imagefile,parent=self)
    2380                         if extractedfile is not None and extractedfile != imagefile:
    2381                             imagefile = extractedfile
    2382                     Comments,Data,Npix,Image = G2IO.GetImageData(self,imagefile)
    2383                     if Comments:
    2384                         Id = self.PatternTree.AppendItem(parent=self.root,text='IMG '+os.path.basename(imagefile))
    2385                         self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Comments'),Comments)
    2386                         Imax = np.amax(Image)
    2387                         Imin = max(0.0,np.amin(Image))          #force positive
    2388                         if self.imageDefault:
    2389                             Data = copy.copy(self.imageDefault)
    2390                             Data['showLines'] = True
    2391                             Data['ring'] = []
    2392                             Data['rings'] = []
    2393                             Data['cutoff'] = 10
    2394                             Data['pixLimit'] = 20
    2395                             Data['edgemin'] = 100000000
    2396                             Data['calibdmin'] = 0.5
    2397                             Data['calibskip'] = 0
    2398                             Data['ellipses'] = []
    2399                             Data['calibrant'] = ''
    2400                             Data['GonioAngles'] = [0.,0.,0.]
    2401                             Data['DetDepthRef'] = False
    2402                         else:
    2403                             Data['type'] = 'PWDR'
    2404                             Data['color'] = 'Paired'
    2405                             Data['tilt'] = 0.0
    2406                             Data['rotation'] = 0.0
    2407                             Data['showLines'] = False
    2408                             Data['ring'] = []
    2409                             Data['rings'] = []
    2410                             Data['cutoff'] = 10
    2411                             Data['pixLimit'] = 20
    2412                             Data['calibdmin'] = 0.5
    2413                             Data['calibskip'] = 0
    2414                             Data['edgemin'] = 100000000
    2415                             Data['ellipses'] = []
    2416                             Data['GonioAngles'] = [0.,0.,0.]
    2417                             Data['DetDepth'] = 0.
    2418                             Data['DetDepthRef'] = False
    2419                             Data['calibrant'] = ''
    2420                             Data['IOtth'] = [2.0,5.0]
    2421                             Data['LRazimuth'] = [135,225]
    2422                             Data['azmthOff'] = 0.0
    2423                             Data['outChannels'] = 2500
    2424                             Data['outAzimuths'] = 1
    2425                             Data['centerAzm'] = False
    2426                             Data['fullIntegrate'] = False
    2427                             Data['setRings'] = False
    2428                             Data['background image'] = ['',-1.0]                           
    2429                             Data['dark image'] = ['',-1.0]
    2430                             Data['Flat Bkg'] = 0.0
    2431                         Data['setDefault'] = False
    2432                         Data['range'] = [(Imin,Imax),[Imin,Imax]]
    2433                         self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Image Controls'),Data)
    2434                         Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
    2435                         self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Masks'),Masks)
    2436                         self.PatternTree.SetItemPyData(self.PatternTree.AppendItem(Id,text='Stress/Strain'),
    2437                             {'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
    2438                         self.PatternTree.SetItemPyData(Id,[Npix,imagefile])
    2439                         self.PickId = Id
    2440                         self.PickIdText = self.GetTreeItemsList(self.PickId)
    2441                         self.Image = Id
    2442                 os.chdir(dlg.GetDirectory())           # to get Mac/Linux to change directory!               
    2443                 self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,Id,'Image Controls'))             #show last one
     2377                    G2IO.ReadLoadImage(imagefile,self)
     2378                os.chdir(dlg.GetDirectory())           # to get Mac/Linux to change directory!
     2379                self.PatternTree.SelectItem(G2gd.GetPatternTreeItemId(self,self.Image,'Image Controls'))             #show last image to be read
    24442380        finally:
    24452381            path = dlg.GetDirectory()           # to get Mac/Linux to change directory!

  • trunk/GSASIIIO.py

    r1962 r1997  
    3333import GSASIIgrid as G2gd
    3434import GSASIIspc as G2spc
     35import GSASIIobj as G2obj
    3536import GSASIIlattice as G2lat
    3637import GSASIIpwdGUI as G2pdG
    … …  
    265266    dlg.CenterOnParent()
    266267    dlg.ShowModal()
    267 
     268   
     269def ReadLoadImage(imagefile,G2frame):
     270    '''Read a GSAS-II image file and load it into the data tree
     271    '''
     272    # get a list of existing Image entries
     273    ImgNames = []
     274    if G2frame.PatternTree.GetCount():
     275        item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
     276        while item:
     277            name = G2frame.PatternTree.GetItemText(item)
     278            if name.startswith('IMG'): ImgNames.append(name)       
     279            item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
     280    # if a zip file, open and extract
     281    if os.path.splitext(imagefile)[1].lower() == '.zip':
     282        extractedfile = ExtractFileFromZip(imagefile,parent=G2frame)
     283        if extractedfile is not None and extractedfile != imagefile:
     284            imagefile = extractedfile
     285    Comments,Data,Npix,Image = GetImageData(G2frame,imagefile)
     286    if Comments:
     287        TreeName = G2obj.MakeUniqueLabel('IMG '+os.path.basename(imagefile),ImgNames)
     288        print 'b=','IMG '+os.path.basename(imagefile)
     289        print 'a=',TreeName
     290        Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
     291        G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
     292        Imax = np.amax(Image)
     293        Imin = max(0.0,np.amin(Image))          #force positive
     294        if G2frame.imageDefault:
     295            Data = copy.copy(G2frame.imageDefault)
     296            Data['showLines'] = True
     297            Data['ring'] = []
     298            Data['rings'] = []
     299            Data['cutoff'] = 10
     300            Data['pixLimit'] = 20
     301            Data['edgemin'] = 100000000
     302            Data['calibdmin'] = 0.5
     303            Data['calibskip'] = 0
     304            Data['ellipses'] = []
     305            Data['calibrant'] = ''
     306            Data['GonioAngles'] = [0.,0.,0.]
     307            Data['DetDepthRef'] = False
     308        else:
     309            Data['type'] = 'PWDR'
     310            Data['color'] = 'Paired'
     311            Data['tilt'] = 0.0
     312            Data['rotation'] = 0.0
     313            Data['showLines'] = False
     314            Data['ring'] = []
     315            Data['rings'] = []
     316            Data['cutoff'] = 10
     317            Data['pixLimit'] = 20
     318            Data['calibdmin'] = 0.5
     319            Data['calibskip'] = 0
     320            Data['edgemin'] = 100000000
     321            Data['ellipses'] = []
     322            Data['GonioAngles'] = [0.,0.,0.]
     323            Data['DetDepth'] = 0.
     324            Data['DetDepthRef'] = False
     325            Data['calibrant'] = ''
     326            Data['IOtth'] = [2.0,5.0]
     327            Data['LRazimuth'] = [135,225]
     328            Data['azmthOff'] = 0.0
     329            Data['outChannels'] = 2500
     330            Data['outAzimuths'] = 1
     331            Data['centerAzm'] = False
     332            Data['fullIntegrate'] = False
     333            Data['setRings'] = False
     334            Data['background image'] = ['',-1.0]                           
     335            Data['dark image'] = ['',-1.0]
     336            Data['Flat Bkg'] = 0.0
     337        Data['setDefault'] = False
     338        Data['range'] = [(Imin,Imax),[Imin,Imax]]
     339        G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
     340        Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
     341        G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
     342        G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
     343            {'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
     344        G2frame.PatternTree.SetItemPyData(Id,[Npix,imagefile])
     345        G2frame.PickId = Id
     346        G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
     347        G2frame.Image = Id
     348   
    268349def GetImageData(G2frame,imagefile,imageOnly=False):
    269350    '''Read an image with the file reader keyed by the
    … …  
    18791960    appropriate menu items for each one and the .Exporter method is called
    18801961    directly from the menu item.
    1881    
     1962
     1963    Routines may also define a .Writer method, which is used to write a single
     1964    file without invoking any GUI objects.
    18821965    '''
    18831966    def __init__(self,
    … …  
    23682451                self.filename += self.extension
    23692452            fil = os.path.join(self.dirname,self.filename)
    2370         self.fullpath = fil
     2453        self.fullpath = os.path.abspath(fil)
    23712454        self.fp = open(fil,mode)
    23722455        return self.fp
    … …  
    24632546        return atomslist
    24642547######################################################################
     2548def ExportPowderList(G2frame):
     2549    '''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
     2550   
     2551    :param wx.Frame G2frame: the GSAS-II main data tree window
     2552    '''
     2553    extList = []
     2554    for obj in G2frame.exporterlist:
     2555        if 'powder' in obj.exporttype:
     2556            try:
     2557                obj.Writer
     2558                extList.append(obj.extension)
     2559            except AttributeError:
     2560                pass
     2561    return extList
     2562
     2563def ExportPowder(G2frame,TreeName,fileroot,extension):
     2564    '''Writes a single powder histogram using the Export routines
     2565
     2566    :param wx.Frame G2frame: the GSAS-II main data tree window
     2567    :param str TreeName: the name of the histogram (PWDR ...) in the data tree
     2568    :param str fileroot: name for file to be written, extension ignored
     2569    :param str extension: extension for file to be written (start with '.'). Must
     2570      match a powder export routine that has a Writer object.
     2571    '''
     2572    filename = os.path.abspath(os.path.splitext(fileroot)[1]+extension)
     2573    for obj in G2frame.exporterlist:
     2574        if obj.extension == extension and 'powder' in obj.exporttype:
     2575            obj.currentExportType = 'powder'
     2576            obj.InitExport(None)
     2577            obj.loadTree() # load all histograms in tree into dicts
     2578            if TreeName not in obj.Histograms:
     2579                raise Exception('Histogram not found: '+hst)
     2580            try:
     2581                obj.Writer(TreeName,filename)
     2582                return
     2583            except AttributeError:
     2584                print('Export Routine for '+extension+' does not have a .Writer method')
     2585    else:
     2586        print('No Export routine supports extension '+extension)
    24652587
    24662588def ReadCIF(URLorFile):

  • trunk/exports/G2export_csv.py

    r1836 r1997  
    126126        self.multiple = True
    127127
     128    def Writer(self,TreeName,filename=None):
     129        self.OpenFile(filename)
     130        histblk = self.Histograms[TreeName]
     131        WriteList(self,("x","y_obs","weight","y_calc","y_bkg"))
     132        digitList = 2*((13,3),) + ((13,5),) + 2*((13,3),)
     133        for vallist in zip(histblk['Data'][0],
     134                       histblk['Data'][1],
     135                       histblk['Data'][2],
     136                       histblk['Data'][3],
     137                       histblk['Data'][4],
     138                       #histblk['Data'][5],
     139                       ):
     140            line = ""
     141            for val,digits in zip(vallist,digitList):
     142                if line: line += ','
     143                line += G2py3.FormatValue(val,digits)
     144            self.Write(line)
     145        self.CloseFile()
     146       
    128147    def Exporter(self,event=None):
    129148        '''Export a set of powder data as a csv file
    … …  
    138157        filenamelist = []
    139158        for hist in self.histnam:
    140             if len(self.histnam) > 1:
    141                 # multiple files: create a unique name from the histogram
    142                 fileroot = G2obj.MakeUniqueLabel(self.MakePWDRfilename(hist),filenamelist)
    143                 # create an instrument parameter file
    144                 self.filename = os.path.join(self.dirname,fileroot + self.extension)
    145             self.OpenFile()
    146             histblk = self.Histograms[hist]
    147             WriteList(self,("x","y_obs","weight","y_calc","y_bkg"))
    148             digitList = 2*((13,3),) + ((13,5),) + 2*((13,3),)
    149             for vallist in zip(histblk['Data'][0],
    150                            histblk['Data'][1],
    151                            histblk['Data'][2],
    152                            histblk['Data'][3],
    153                            histblk['Data'][4],
    154                            #histblk['Data'][5],
    155                            ):
    156                 line = ""
    157                 for val,digits in zip(vallist,digitList):
    158                     if line: line += ','
    159                     line += G2py3.FormatValue(val,digits)
    160                 self.Write(line)
    161             self.CloseFile()
     159            #if len(self.histnam) > 1:
     160            #    # multiple files: create a unique name from the histogram
     161            #    fileroot = G2obj.MakeUniqueLabel(self.MakePWDRfilename(hist),filenamelist)
     162            #    # create an instrument parameter file
     163            #    self.filename = os.path.join(self.dirname,fileroot + self.extension)
     164            self.Writer(hist)
    162165            print('Histogram '+str(hist)+' written to file '+str(self.fullpath))
    163166

  • trunk/exports/G2export_examples.py

    r1902 r1997  
    132132        self.multiple = False # only allow one histogram to be selected
    133133
    134     def Exporter(self,event=None):
    135         '''Export a set of powder data as a text file
    136         '''
    137         # the export process starts here
    138         self.InitExport(event)
    139         # load all of the tree into a set of dicts
    140         self.loadTree()
    141         if self.ExportSelect( # set export parameters
    142             AskFile='default' # base name on the GPX file name
    143             ): return
    144         self.OpenFile()
    145         hist = self.histnam[0] # there should only be one histogram, in any case take the 1st
    146         histblk = self.Histograms[hist]
     134    def Writer(self,TreeName,filename=None):
     135        self.OpenFile(filename)
     136        histblk = self.Histograms[TreeName]
    147137        hfmt = 5*"{:12s} "
    148138        digitList = 2*((13,3),) + ((13,5),) + 2*((13,3),)
    … …  
    161151            self.Write(strg)
    162152        self.CloseFile()
     153       
     154    def Exporter(self,event=None):
     155        '''Export a set of powder data as a text file
     156        '''
     157        # the export process starts here
     158        self.InitExport(event)
     159        # load all of the tree into a set of dicts
     160        self.loadTree()
     161        if self.ExportSelect( # set export parameters
     162            AskFile='default' # base name on the GPX file name
     163            ): return
     164        hist = self.histnam[0] # there should only be one histogram, in any case take the 1st
     165        self.Writer(hist)
    163166        print(str(hist)+' written to file '+str(self.fullpath))
    164167       

  • trunk/exports/G2export_pwdr.py

    r1675 r1997  
    6262        return prmname
    6363
     64    def Writer(self,TreeName,filename=None,prmname=''):
     65        '''Write a single PWDR entry to a FXYE file
     66        '''
     67        histblk = self.Histograms[TreeName]
     68        self.OpenFile(filename) # ***rethink
     69        self.Write(TreeName[5:])
     70        if prmname: self.Write('Instrument parameter file:'+os.path.split(prmname)[1])
     71        x = 100*np.array(histblk['Data'][0])
     72        # convert weights to sigmas; use largest weight as minimum esd
     73        s = np.sqrt(np.maximum(0.,np.array(histblk['Data'][2])))
     74        s[s==0] = np.max(s)
     75        s = 1./s
     76        self.Write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE' % (
     77            len(x),len(x),x[0],(x[1]-x[0])
     78            ))
     79#            for X,Y,S in zip(x,histblk['Data'][1],s):
     80#                self.Write("{:15.6g} {:15.6g} {:15.6g}".format(X,Y,S))
     81        for XYS in zip(x,histblk['Data'][1],s):
     82            line = ''
     83            for val in XYS:
     84                line += G2py3.FormatPadValue(val,(15,6))
     85            self.Write(line)
     86        self.CloseFile()
     87       
    6488    def Exporter(self,event=None):
    6589        '''Export one or more sets of powder data as FXYE file(s)
    … …  
    6791        # the export process starts here
    6892        self.InitExport(event)
    69         # load all of the tree into a set of dicts
    70         self.loadTree()
     93        self.loadTree() # load all of the tree into a set of dicts
    7194        if self.ExportSelect( # set export parameters
    7295            AskFile='single' # get a file name/directory to save in
    … …  
    82105                # use the supplied name, but force the extension
    83106                self.filename= os.path.splitext(self.filename)[0] + self.extension
    84                
    85             histblk = self.Histograms[hist]
    86             prmname = self.WriteInstFile(hist,histblk['Instrument Parameters'][0])
    87            
    88             self.OpenFile()
    89             self.Write(hist[5:])
    90             self.Write('Instrument parameter file:'+os.path.split(prmname)[1])
    91             x = 100*np.array(histblk['Data'][0])
    92             # convert weights to sigmas; use largest weight as minimum esd
    93             s = np.sqrt(np.maximum(0.,np.array(histblk['Data'][2])))
    94             s[s==0] = np.max(s)
    95             s = 1./s
    96             self.Write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE' % (
    97                 len(x),len(x),x[0],(x[1]-x[0])
    98                 ))
    99 #            for X,Y,S in zip(x,histblk['Data'][1],s):
    100 #                self.Write("{:15.6g} {:15.6g} {:15.6g}".format(X,Y,S))
    101             for XYS in zip(x,histblk['Data'][1],s):
    102                 line = ''
    103                 for val in XYS:
    104                     line += G2py3.FormatPadValue(val,(15,6))
    105                 self.Write(line)
    106             self.CloseFile()
     107
     108            prmname = self.WriteInstFile(TreeName,histblk['Instrument Parameters'][0])
     109            self.Writer(hist,prmname=prmname)
    107110            print('Histogram '+str(hist)+' written to file '+str(self.fullpath))
    108111
    … …  
    122125        self.exporttype = ['powder']
    123126        self.multiple = True
     127       
     128    def Writer(self,TreeName,filename=None):
     129        GSASIIpath.IPyBreak()
     130
     131        self.OpenFile()
     132        histblk = self.Histograms[TreeName]
     133        self.Write('/*')    #The ugly c comment delimiter used in topas!
     134        self.Write('# '+TreeName[5:])  #evidently this by itself fails in topas
     135        self.Write('*/')
     136        x = np.array(histblk['Data'][0])
     137        # convert weights to sigmas; use largest weight as minimum esd
     138        s = np.sqrt(np.maximum(0.,np.array(histblk['Data'][2])))
     139        s[s==0] = np.max(s)
     140        s = 1./s
     141        for XYS in zip(x,histblk['Data'][1],s):
     142            line = ''
     143            for val in XYS:
     144                line += G2py3.FormatPadValue(val,(15,6))
     145            self.Write(line)
     146        self.CloseFile()
    124147
    125148    def Exporter(self,event=None):
    … …  
    144167                self.filename= os.path.splitext(self.filename)[0] + self.extension
    145168
    146             self.OpenFile()
    147             histblk = self.Histograms[hist]
    148             self.Write('/*')    #The ugly c comment delimiter used in topas!
    149             self.Write('# '+hist[5:])  #evidently this by itself fails in topas
    150             self.Write('*/')
    151             x = np.array(histblk['Data'][0])
    152             # convert weights to sigmas; use largest weight as minimum esd
    153             s = np.sqrt(np.maximum(0.,np.array(histblk['Data'][2])))
    154             s[s==0] = np.max(s)
    155             s = 1./s
    156             for XYS in zip(x,histblk['Data'][1],s):
    157                 line = ''
    158                 for val in XYS:
    159                     line += G2py3.FormatPadValue(val,(15,6))
    160                 self.Write(line)
    161             self.CloseFile()
     169            self.Writer(hist)
    162170            print('Histogram '+str(hist)+' written to file '+str(self.fullpath))
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