| 1 | # This program is public domain |
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| 2 | |
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| 3 | # Author: Paul Kienzle |
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| 4 | |
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| 5 | """ |
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| 6 | NeXus tests converted to python. |
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| 7 | """ |
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| 8 | |
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| 9 | import nxs,os,numpy,sys |
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| 10 | |
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| 11 | def memfootprint(): |
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| 12 | import gc |
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| 13 | objs = gc.get_objects() |
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| 14 | classes = set( c.__class__ for c in gc.get_objects() if hasattr(c,'__class__') ) |
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| 15 | # print "\n".join([c.__name__ for c in classes]) |
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| 16 | print "#objects=",len(objs) |
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| 17 | print "#classes=",len(classes) |
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| 18 | |
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| 19 | def leak_test1(n = 1000, mode='w5'): |
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| 20 | # import gc |
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| 21 | # gc.enable() |
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| 22 | # gc.set_debug(gc.DEBUG_LEAK) |
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| 23 | filename = "leak_test1.nxs" |
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| 24 | try: os.unlink(filename) |
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| 25 | except OSError: pass |
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| 26 | file = nxs.open(filename,mode) |
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| 27 | file.close() |
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| 28 | print "File should exist now" |
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| 29 | for i in range(n): |
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| 30 | if i%100 == 0: |
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| 31 | print "loop count %d"%i |
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| 32 | memfootprint() |
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| 33 | file.open() |
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| 34 | file.close() |
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| 35 | # gc.collect() |
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| 36 | os.unlink(filename) |
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| 37 | |
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| 38 | def _show(file, indent=0): |
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| 39 | prefix = ' '*indent |
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| 40 | link = file.link() |
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| 41 | if link: |
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| 42 | print "%(prefix)s-> %(link)s" % locals() |
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| 43 | return |
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| 44 | for attr,value in file.attrs(): |
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| 45 | print "%(prefix)s@%(attr)s: %(value)s" % locals() |
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| 46 | for name,nxclass in file.entries(): |
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| 47 | if nxclass == "SDS": |
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| 48 | shape,dtype = file.getinfo() |
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| 49 | dims = "x".join([str(x) for x in shape]) |
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| 50 | print "%(prefix)s%(name)s %(dtype)s %(dims)s" % locals() |
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| 51 | link = file.link() |
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| 52 | if link: |
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| 53 | print " %(prefix)s-> %(link)s" % locals() |
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| 54 | else: |
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| 55 | for attr,value in file.attrs(): |
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| 56 | print " %(prefix)s@%(attr)s: %(value)s" % locals() |
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| 57 | if numpy.prod(shape) < 8: |
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| 58 | value = file.getdata() |
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| 59 | print " %s%s"%(prefix,str(value)) |
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| 60 | else: |
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| 61 | print "%(prefix)s%(name)s %(nxclass)s" % locals() |
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| 62 | _show(file, indent+2) |
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| 63 | |
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| 64 | def show_structure(filename): |
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| 65 | file = nxs.open(filename) |
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| 66 | print "=== File",file.inquirefile() |
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| 67 | _show(file) |
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| 68 | |
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| 69 | |
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| 70 | def populate(filename,mode): |
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| 71 | i1 = numpy.arange(4,dtype='uint8') |
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| 72 | i2 = numpy.arange(4,dtype='int16')*1000 |
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| 73 | i4 = numpy.arange(4,dtype='int32')*1000000 |
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| 74 | i8 = numpy.arange(4,dtype='int64')*1000000000000 |
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| 75 | r4 = numpy.arange(20,dtype='float32').reshape((5,4)) |
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| 76 | r8 = numpy.arange(20,dtype='float64').reshape((5,4)) |
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| 77 | comp_array=numpy.ones((100,20),dtype='int32') |
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| 78 | for i in range(100): comp_array[i,:] *= i |
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| 79 | |
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| 80 | file = nxs.open(filename,mode) |
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| 81 | file.setnumberformat('float32','%9.3g') |
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| 82 | file.makegroup("entry","NXentry") |
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| 83 | file.opengroup("entry","NXentry") |
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| 84 | file.putattr("hugo","namenlos") |
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| 85 | file.putattr("cucumber","passion") |
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| 86 | #file.putattr("embedded_null","embedded\000null") |
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| 87 | |
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| 88 | # Write character data |
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| 89 | file.makedata("ch_data",'char',[10]) |
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| 90 | file.opendata("ch_data") |
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| 91 | file.putdata("NeXus data") |
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| 92 | file.closedata() |
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| 93 | |
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| 94 | # Write numeric data |
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| 95 | for var in ['i1','i2','i4','i8','r4']: |
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| 96 | if mode == 'w4' and var == 'i8': continue |
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| 97 | name = var+'_data' |
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| 98 | val = locals()[var] |
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| 99 | file.makedata(name,val.dtype,val.shape) |
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| 100 | file.opendata(name) |
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| 101 | file.putdata(val) |
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| 102 | file.closedata() |
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| 103 | |
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| 104 | # Write r8_data |
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| 105 | file.makedata('r8_data','float64',[5,4]) |
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| 106 | file.opendata('r8_data') |
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| 107 | file.putslab(r8[4,:],[4,0],[1,4]) |
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| 108 | file.putslab(r8[0:4,:],[0,0],[4,4]) |
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| 109 | file.putattr("ch_attribute","NeXus") |
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| 110 | file.putattr("i4_attribute",42,dtype='int32') |
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| 111 | file.putattr("r4_attribute",3.14159265,dtype='float32') |
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| 112 | ## Oops... NAPI doesn't support array attributes |
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| 113 | #file.putattr("i4_array",[3,2],dtype='int32') |
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| 114 | #file.putattr("r4_array",[3.14159265,2.718281828],dtype='float32') |
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| 115 | dataID = file.getdataID() |
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| 116 | file.closedata() |
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| 117 | |
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| 118 | # Create the NXdata group |
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| 119 | file.makegroup("data","NXdata") |
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| 120 | file.opengroup("data","NXdata") |
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| 121 | |
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| 122 | # .. demonstrate linking |
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| 123 | file.makelink(dataID) |
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| 124 | |
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| 125 | # .. demonstrate compressed data |
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| 126 | file.compmakedata("comp_data",'int32',[100,20],'lzw',[20,20]) |
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| 127 | file.opendata('comp_data') |
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| 128 | file.putdata(comp_array) |
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| 129 | file.closedata() |
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| 130 | file.flush() |
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| 131 | |
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| 132 | # .. demonstrate extensible data |
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| 133 | file.makedata('flush_data','int32',[nxs.UNLIMITED]) |
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| 134 | file.opendata('flush_data') |
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| 135 | for i in range(7): |
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| 136 | file.putslab(i,[i],[1]) |
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| 137 | file.closedata() |
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| 138 | file.flush() |
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| 139 | file.closegroup() |
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| 140 | |
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| 141 | # Create NXsample group |
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| 142 | file.makegroup('sample','NXsample') |
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| 143 | file.opengroup('sample','NXsample') |
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| 144 | file.makedata('ch_data','char',[20]) |
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| 145 | file.opendata('ch_data') |
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| 146 | file.putdata('NeXus sample') |
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| 147 | file.closedata() |
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| 148 | sampleID = file.getgroupID() |
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| 149 | file.closegroup() |
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| 150 | file.closegroup() |
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| 151 | |
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| 152 | # Demonstrate named links |
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| 153 | file.makegroup('link','NXentry') |
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| 154 | file.opengroup('link','NXentry') |
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| 155 | file.makelink(sampleID) |
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| 156 | file.makenamedlink('renLinkGroup',sampleID) |
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| 157 | file.makenamedlink('renLinkData',dataID) |
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| 158 | file.closegroup() |
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| 159 | |
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| 160 | file.close() |
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| 161 | return filename |
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| 162 | |
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| 163 | failures = 0 |
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| 164 | def fail(msg): |
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| 165 | global failures |
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| 166 | print "FAIL:",msg |
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| 167 | failures += 1 |
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| 168 | |
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| 169 | def dicteq(a,b): |
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| 170 | """ |
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| 171 | Compare two dictionaries printing how they differ. |
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| 172 | """ |
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| 173 | for k,v in a.iteritems(): |
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| 174 | if k not in b: |
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| 175 | print k,"not in",b |
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| 176 | return False |
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| 177 | if v != b[k]: |
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| 178 | print v,"not equal",b[k] |
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| 179 | return False |
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| 180 | for k,v in b.iteritems(): |
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| 181 | if k not in a: |
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| 182 | print k,"not in",a |
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| 183 | return False |
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| 184 | return True |
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| 185 | |
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| 186 | def check(filename, mode): |
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| 187 | global failures |
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| 188 | failures = 0 |
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| 189 | file = nxs.open(filename,'rw') |
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| 190 | if filename != file.inquirefile(): fail("Files don't match") |
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| 191 | |
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| 192 | # check headers |
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| 193 | num_attrs = file.getattrinfo() |
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| 194 | wxattrs = ['xmlns','xmlns:xsi','xsi:schemaLocation', 'XML_version'] |
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| 195 | w4attrs = ['HDF_version'] |
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| 196 | w5attrs = ['HDF5_Version'] |
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| 197 | extras = dict(wx=wxattrs,w4=w4attrs,w5=w5attrs) |
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| 198 | expected_attrs = ['NeXus_version','file_name','file_time']+extras[mode] |
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| 199 | for i in range(num_attrs): |
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| 200 | name,dims,type = file.getnextattr() |
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| 201 | if name not in expected_attrs: |
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| 202 | fail("attribute %s unexpected"%(name)) |
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| 203 | if num_attrs != len(expected_attrs): |
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| 204 | fail("Expected %d root attributes but got %d" |
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| 205 | % (len(expected_attrs),num_attrs)) |
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| 206 | |
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| 207 | file.opengroup('entry','NXentry') |
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| 208 | |
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| 209 | expect = dict(hugo='namenlos',cucumber='passion') |
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| 210 | #expect['embedded_null'] = "embedded\000null" |
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| 211 | get = dict((k,v) for k,v in file.attrs()) |
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| 212 | same = dicteq(get,expect) |
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| 213 | if not same: fail("/entry attributes are %s"%(get)) |
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| 214 | |
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| 215 | # Check that the numbers are written correctly |
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| 216 | for name,dtype,shape,scale in \ |
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| 217 | [('i1','int8',(4),1), |
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| 218 | ('i2','int16',(4),1000), |
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| 219 | ('i4','int32',(4),1000000), |
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| 220 | ('i8','int64',(4),1000000000000), |
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| 221 | ('r4','float32',(5,4),1), |
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| 222 | ('r8','float64',(5,4),1) |
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| 223 | ]: |
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| 224 | if mode == 'w4' and name == 'i8': continue |
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| 225 | n = numpy.prod(shape) |
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| 226 | expected = numpy.arange(n,dtype=dtype).reshape(shape)*scale |
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| 227 | file.opendata(name+'_data') |
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| 228 | get = file.getdata() |
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| 229 | file.closedata() |
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| 230 | if not (get == expected).all(): |
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| 231 | fail("%s retrieved %s"%(dtype,get)) |
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| 232 | |
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| 233 | |
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| 234 | # Check attribute types |
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| 235 | file.opendata('r8_data') |
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| 236 | get = file.getattr("ch_attribute",5,'char') |
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| 237 | if not get == "NeXus": fail("ch_attribute retrieved %s"%(get)) |
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| 238 | get = file.getattr("i4_attribute",1,'int32') |
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| 239 | if not get == numpy.int32(42): fail("i4_attribute retrieved %s"%(get)) |
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| 240 | get = file.getattr("r4_attribute",1,'float32') |
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| 241 | if ((mode=='wx' and not abs(get-3.14159265) < 1e-6) or |
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| 242 | (mode!='wx' and not get == numpy.float32(3.14159265))): |
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| 243 | fail("r4_attribute retrieved %s"%(get)) |
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| 244 | ## Oops... NAPI doesn't support array attributes |
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| 245 | #expect = numpy.array([3,2],dtype='int32') |
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| 246 | #get = file.getattr("i4_array",2,'int32') |
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| 247 | #if not (get==expect).all(): fail('i4_array retrieved %s'%(get)) |
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| 248 | #expect = numpy.array([3.14159265,2.718281828],dtype='float32') |
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| 249 | #get = file.getattr("r4_array",2,dtype='float32') |
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| 250 | #if not (get==expect).all(): fail("r4_array retrieved %s"%(get)) |
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| 251 | file.closedata() |
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| 252 | |
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| 253 | |
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| 254 | # Check reading from compressed datasets |
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| 255 | comp_array=numpy.ones((100,20),dtype='int32') |
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| 256 | for i in range(100): comp_array[i,:] *= i |
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| 257 | expected = comp_array |
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| 258 | file.opengroup('data','NXdata') #/entry/data |
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| 259 | file.opendata('comp_data') #/entry/data/comp_data |
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| 260 | get = file.getdata() |
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| 261 | file.closedata() #/entry/data/comp_data |
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| 262 | file.closegroup() #/entry/data |
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| 263 | if not (get == expected).all(): |
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| 264 | fail("compressed data differs") |
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| 265 | print get |
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| 266 | |
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| 267 | # Check strings |
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| 268 | file.opengroup('sample','NXsample') #/entry/sample |
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| 269 | file.opendata('ch_data') #/entry/sample/ch_data |
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| 270 | rawshape,rawdtype = file.getrawinfo() |
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| 271 | shape,dtype = file.getinfo() |
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| 272 | get = file.getdata() |
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| 273 | file.closedata() #/entry/sample/ch_data |
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| 274 | file.closegroup() #/entry/sample |
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| 275 | if not (shape[0]==12 and dtype=='char'): |
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| 276 | fail("returned string info is incorrect") |
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| 277 | print shape,dtype |
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| 278 | if not (rawshape[0]==20 and rawdtype=='char'): |
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| 279 | fail("returned string storage info is incorrect") |
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| 280 | print shape,dtype |
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| 281 | if not (get == "NeXus sample"): |
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| 282 | fail("returned string is incorrect") |
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| 283 | print shape,dtype |
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| 284 | |
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| 285 | |
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| 286 | file.closegroup() #/entry |
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| 287 | |
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| 288 | # Check read slab (e.g., from extensible) |
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| 289 | |
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| 290 | # Check links |
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| 291 | file.opengroup('entry','NXentry') |
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| 292 | file.opengroup('sample','NXsample') |
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| 293 | sampleid = file.getgroupID() |
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| 294 | file.closegroup() #/entry/sample |
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| 295 | file.opengroup('data','NXdata') #/entry/data |
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| 296 | file.opendata('r8_data') #/entry/data/r8_data |
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| 297 | dataid = file.getdataID() |
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| 298 | file.closedata() #/entry/data/r8_data |
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| 299 | file.closegroup() #/entry/data |
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| 300 | file.opendata('r8_data') |
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| 301 | data2id = file.getdataID() |
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| 302 | file.closedata() |
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| 303 | file.closegroup() #/entry |
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| 304 | if not (file.sameID(dataid,data2id)): |
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| 305 | fail("/entry/data/r8_data not linked to /entry/r8_data") |
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| 306 | |
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| 307 | # Check openpath and getslab |
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| 308 | file.openpath('/entry/data/comp_data') |
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| 309 | get = file.getslab([4,4],[5,3]) |
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| 310 | expected = comp_array[4:(4+5),4:(4+3)] |
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| 311 | if not (get == expected).all(): |
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| 312 | fail("retrieved compressed slabs differ") |
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| 313 | print get |
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| 314 | file.openpath('/entry/data/comp_data') |
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| 315 | get = file.getslab([4,4],[5,3]) |
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| 316 | expected = comp_array[4:(4+5),4:(4+3)] |
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| 317 | if not (get == expected).all(): |
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| 318 | fail("after reopen: retrieved compressed slabs differ") |
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| 319 | print get |
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| 320 | file.openpath('../r8_data') |
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| 321 | for k,v in file.attrs(): |
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| 322 | if k == 'target' and v != '/entry/r8_data': |
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| 323 | fail("relative openpath was not successful") |
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| 324 | |
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| 325 | return failures == 0 |
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| 326 | |
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| 327 | def populate_external(filename,mode): |
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| 328 | ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode] |
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| 329 | file = nxs.open(filename,mode) |
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| 330 | file.makegroup('entry1','NXentry') |
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| 331 | file.linkexternal('entry1','NXentry','nxfile://data/dmc01'+ext) |
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| 332 | file.makegroup('entry2','NXentry') |
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| 333 | file.linkexternal('entry2','NXentry','nxfile://data/dmc02'+ext) |
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| 334 | file.makegroup('entry3','NXentry') |
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| 335 | file.close() |
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| 336 | |
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| 337 | def check_external(filename,mode): |
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| 338 | ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode] |
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| 339 | file = nxs.open(filename,'rw') |
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| 340 | |
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| 341 | file.openpath('/entry1/start_time') |
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| 342 | time = file.getdata() |
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| 343 | |
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| 344 | get = file.inquirefile() |
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| 345 | expected = 'nxfile://data/dmc01'+ext |
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| 346 | if expected != get: fail("first external file returned %s"%(get)) |
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| 347 | |
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| 348 | file.openpath('/entry2/sample/sample_name') |
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| 349 | sample = file.getdata() |
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| 350 | |
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| 351 | get = file.inquirefile() |
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| 352 | expected = 'nxfile://data/dmc02'+ext |
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| 353 | if expected != get: fail("second external file returned %s"%(get)) |
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| 354 | |
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| 355 | file.openpath('/') |
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| 356 | remote = file.isexternalgroup('entry1','NXentry') |
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| 357 | if remote is None: |
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| 358 | fail("failed to identify /entry1 as external") |
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| 359 | remote = file.isexternalgroup('entry3','NXentry') |
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| 360 | if remote is not None: |
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| 361 | fail('incorrectly identified /entry3 as external') |
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| 362 | |
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| 363 | file.close() |
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| 364 | |
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| 365 | def test_external(mode,quiet=True): |
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| 366 | ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode] |
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| 367 | filename = 'nxext'+ext |
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| 368 | populate_external(external,mode) |
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| 369 | if not quiet: |
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| 370 | show_structure(external) |
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| 371 | failures = check_external(filename,mode) |
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| 372 | return failures |
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| 373 | |
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| 374 | def test_mode(mode,quiet=True,external=False): |
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| 375 | ext = dict(w5='.h5',w4='.hdf',wx='.xml')[mode] |
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| 376 | filename = 'NXtest'+ext |
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| 377 | populate(filename,mode=mode) |
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| 378 | if not quiet and 'NX_LOAD_PATH' in os.environ: |
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| 379 | show_structure('dmc01'+ext) |
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| 380 | if not quiet: |
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| 381 | show_structure(filename) |
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| 382 | failures = check(filename,mode) |
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| 383 | if external: failures += test_external(mode,quiet) |
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| 384 | return failures |
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| 385 | |
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| 386 | def test(): |
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| 387 | tests = 0 |
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| 388 | if '-q' in sys.argv: |
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| 389 | quiet = True |
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| 390 | else: |
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| 391 | quiet = False |
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| 392 | if '-x' in sys.argv: |
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| 393 | external = True |
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| 394 | |
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| 395 | else: |
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| 396 | external = False |
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| 397 | if 'hdf4' in sys.argv: |
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| 398 | test_mode('w4',quiet,external) |
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| 399 | tests += 1 |
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| 400 | if 'xml' in sys.argv: |
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| 401 | test_mode('wx',quiet,external) |
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| 402 | tests += 1 |
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| 403 | if 'hdf5' in sys.argv: |
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| 404 | test_mode('w5',quiet,external) |
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| 405 | tests += 1 |
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| 406 | if tests == 0: test_mode('w5',quiet,external) |
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| 407 | |
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| 408 | if __name__ == "__main__": |
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| 409 | test() |
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| 410 | #leak_test1(n=10000) |
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| 411 | |
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