| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2014-12-27 11:14:59 -0600 (Sat, 27 Dec 2014) $ |
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| 4 | # $Author: $ |
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| 5 | # $Revision: $ |
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| 6 | # $URL: $ |
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| 7 | # $Id: $ |
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| 8 | ########### SVN repository information ################### |
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| 9 | ''' |
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| 10 | *Module G2img_HDF5: summed HDF5 image file* |
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| 11 | --------------------------------------- |
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| 12 | |
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| 13 | This shows an example of an importer that will handle files with |
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| 14 | more than a single image. |
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| 15 | |
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| 16 | ''' |
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| 17 | |
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| 18 | import h5py |
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| 19 | import GSASIIIO as G2IO |
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| 20 | import GSASIIpath |
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| 21 | GSASIIpath.SetVersionNumber("$Revision: $") |
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| 22 | |
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| 23 | class Hdf5_Reader(G2IO.ImportImage): |
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| 24 | '''Routine to read a HD5 image, typically from APS Sector 6. |
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| 25 | B. Frosik/SDM. Initial version. |
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| 26 | Refactored. |
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| 27 | ''' |
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| 28 | dsetlist = [] |
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| 29 | buffer = {} |
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| 30 | init = False |
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| 31 | |
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| 32 | def __init__(self): |
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| 33 | print 'start' |
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| 34 | super(self.__class__,self).__init__( # fancy way to self-reference |
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| 35 | extensionlist=('.hdf5','.hd5','.h5','.hdf'), |
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| 36 | strictExtension=True, |
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| 37 | formatName = 'HDF5 image', |
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| 38 | longFormatName = 'HDF5 image file' |
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| 39 | ) |
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| 40 | |
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| 41 | def ContentsValidator(self, filepointer): |
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| 42 | '''no test at this time |
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| 43 | ''' |
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| 44 | try: |
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| 45 | # the following does not work, filepointer is not a filename |
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| 46 | f = h5py.File(filepointer.name, 'r') |
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| 47 | f.close() |
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| 48 | return True |
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| 49 | except IOError: |
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| 50 | return False |
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| 51 | |
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| 52 | def Reader(self,filename,filepointer, ParentFrame=None, **kwarg): |
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| 53 | '''Read using HDF5 file reader, :func:`ReadData` |
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| 54 | ''' |
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| 55 | imagenum = kwarg.get('blocknum') |
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| 56 | #self.buffer = kwarg.get('buffer') |
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| 57 | |
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| 58 | if self.init is False: |
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| 59 | self.init = True |
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| 60 | self.readDataset(filename) |
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| 61 | |
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| 62 | len = self.buffer['len'] |
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| 63 | if len is 1: |
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| 64 | image = self.buffer['image'] |
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| 65 | else: |
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| 66 | images = self.buffer['image'] |
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| 67 | image = images[imagenum-1] |
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| 68 | |
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| 69 | self.Comments,self.Data,self.Npix,self.Image = self.read_set(image,imagenum=imagenum) |
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| 70 | if self.Npix == 0 or not self.Comments: |
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| 71 | return False |
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| 72 | self.LoadImage(ParentFrame,filename,imagenum) |
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| 73 | self.repeatcount = imagenum |
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| 74 | self.repeat = imagenum < len |
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| 75 | #print('Read image #'+str(imagenum)+' from file '+filename) |
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| 76 | return True |
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| 77 | |
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| 78 | def readDataset(self,filename): |
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| 79 | imagenum = 1 |
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| 80 | try: |
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| 81 | f = h5py.File(filename, 'r') |
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| 82 | self.visit(f, imagenum) |
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| 83 | except IOError: |
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| 84 | print 'cannot open file ', filename |
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| 85 | return False |
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| 86 | finally: |
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| 87 | if f is not None: |
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| 88 | f.close() |
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| 89 | |
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| 90 | |
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| 91 | def visit(self, f, imagenum): |
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| 92 | #GSASIIpath.IPyBreak() |
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| 93 | print 'visiting' |
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| 94 | def func(name, dset): |
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| 95 | datakeyword = 'data' |
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| 96 | if isinstance(dset, h5py.Dataset): |
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| 97 | self.dsetlist.append(dset.name) |
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| 98 | lastindex = dset.name.rfind(datakeyword) |
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| 99 | if lastindex is not -1: |
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| 100 | index = len(dset.name)-len(datakeyword) |
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| 101 | if index == lastindex: |
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| 102 | if self.buffer is not None: |
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| 103 | if len(dset.shape) > 2: |
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| 104 | image = dset[0,...] |
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| 105 | self.buffer['image'] = dset[0,...] |
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| 106 | self.buffer['len'] = image.shape[0] |
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| 107 | else: |
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| 108 | self.buffer['image'] = dset[()] |
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| 109 | self.buffer['len'] = 1 |
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| 110 | self.buffer['name'] = dset.name |
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| 111 | #GSASIIpath.IPyBreak() |
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| 112 | f.visititems(func) |
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| 113 | |
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| 114 | def read_set(self,image,imagenum=1): |
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| 115 | #more = False |
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| 116 | head = ['raw data'] |
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| 117 | x_dim = image.shape[0] |
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| 118 | y_dim = image.shape[1] |
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| 119 | sizexy = [x_dim,y_dim] |
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| 120 | Npix = sizexy[0]*sizexy[1] |
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| 121 | data = {'pixelSize':[200,200],'wavelength':0.15,'distance':250.0,'center':[204.8,204.8],'size':sizexy} |
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| 122 | return head,data,Npix,image |
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