Module ImportFrom alias Import alias ImportFrom alias Import alias ImportFrom alias ImportFrom alias ImportFrom alias alias Import alias Import alias FunctionDef arguments args defaults body If UnaryOpNot AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr body Assign AttributeStore AttributeLoad AttributeLoad NameLoad attr attr attr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr decorator_list FunctionDef arguments args defaults body Expr Call AttributeLoad AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr attr Delete AttributeDel AttributeLoad AttributeLoad NameLoad attr attr attr Assign AttributeStore AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad decorator_list ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults Num body Assign NameStore Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Num decorator_list FunctionDef arguments args NameParam defaults body If UnaryOpNot Call AttributeLoad AttributeLoad NameLoad attr attr body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str Expr Str decorator_list decorator_list ClassDef bases body FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Num body Assign NameStore NameLoad For NameStore Call NameLoad Call NameLoad NameLoad body Assign NameStore SubscriptLoad AttributeLoad SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad AttributeLoad NameLoad attr attr attr Index SubscriptLoad NameLoad Index NameLoad Assign NameStore Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad NameLoad Index NameLoad NameLoad Assign NameStore SubscriptLoad AttributeLoad SubscriptLoad AttributeLoad NameLoad attr Index AttributeLoad AttributeLoad NameLoad attr attr attr Index BinOpAdd NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore BinOpBitAnd NameLoad Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad Print Str Call NameLoad Call NameLoad NameLoad Str NameLoad Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults Num body If Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Assign NameStore AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr orelse If Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Assign NameStore SubscriptLoad AttributeLoad AttributeLoad NameLoad attr attr Slice orelse Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr If Call AttributeLoad NameLoad attr CompareLtE Call AttributeLoad NameLoad attr BinOpSub NameLoad NameLoad NameLoad body Return NameLoad orelse Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Assert CompareEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assert CompareEq AttributeLoad NameLoad attr AttributeLoad NameLoad attr If UnaryOpNot Call AttributeLoad NameLoad attr NameLoad NameLoad body Assert CompareEq Call NameLoad AttributeLoad NameLoad attr Num For NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num body For NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num body For NameStore Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num body If CompareNotEq SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad NameLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad NameLoad body Print NameLoad NameLoad NameLoad Str SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad NameLoad Str SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad NameLoad Return NameLoad Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Print Str NameLoad NameLoad Assign NameStore BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Print NameLoad Expr Str TryExcept body Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr If CompareGt AttributeLoad NameLoad attr Num body Print NameLoad Print NameLoad Return NameLoad orelse Return NameLoad handlers ExceptHandler type NameLoad name NameStore body Print NameLoad Return NameLoad Return NameLoad decorator_list NameLoad decorator_list
N/A PyQt4 QtCore N/A numpy ilastik.core dataImpex N/A shlex ilastik.core.listOfNDArraysAsNDArray ListOfNDArraysAsNDArray ilastik.core.overlays.selectionOverlay SelectionAccessor subprocess Popen PIPE N/A h5py N/A ilastik.core.jobMachine setUp N/A N/A N/A N/A N/A N/A N/A N/A N/A ilastik core jobMachine GLOBAL_WM N/A N/A N/A N/A N/A ilastik core jobMachine GLOBAL_WM N/A N/A N/A N/A ilastik core jobMachine WorkerManager N/A tearDown N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A ilastik core jobMachine GLOBAL_WM stopWorkers N/A N/A N/A N/A ilastik core jobMachine GLOBAL_WM N/A N/A N/A N/A ilastik core jobMachine GLOBAL_WM None N/A TestThread N/A N/A QtCore QObject N/A __init__ N/A N/A self baseMgr listOfResultOverlays listOfFilenames tolerance N/A 0 N/A N/A __pyqtSignals__ done() N/A N/A N/A N/A QtCore QObject __init__ self N/A N/A self baseMgr baseMgr N/A N/A self listOfResultOverlays listOfResultOverlays N/A N/A self listOfFilenames listOfFilenames N/A N/A self tolerance tolerance N/A N/A self passedTest False N/A start N/A N/A self input N/A N/A N/A N/A self timer N/A N/A QtCore QTimer N/A N/A N/A N/A QtCore QObject connect N/A self timer N/A N/A QtCore SIGNAL timeout() N/A self updateProgress N/A N/A self myTestThread N/A N/A N/A self baseMgr computeResults input N/A N/A N/A N/A self timer start 200 N/A updateProgress N/A N/A self N/A N/A N/A N/A N/A N/A N/A self myTestThread isRunning N/A N/A N/A N/A N/A self timer stop N/A N/A N/A N/A self myTestThread wait N/A N/A N/A self finalize N/A finalize N/A N/A self N/A N/A N/A N/A N/A N/A self baseMgr finalizeResults N/A N/A self passedTest N/A N/A TestHelperFunctions compareResultsWithFile N/A self baseMgr N/A self listOfResultOverlays N/A self listOfFilenames N/A self tolerance N/A N/A N/A self emit N/A N/A QtCore SIGNAL done() N/A 
        # in case you want to create ground truth overlays, use the following code instead of the above
        for i in range(len(self.listOfResultOverlays)):
            obtained = self.baseMgr.dataMgr[self.baseMgr.dataMgr._activeImageNumber].overlayMgr["Unsupervised/pLSA component %d" % (i+1)]
            dataImpex.DataImpex.exportOverlay(self.listOfFilenames[i], "h5", obtained)
         N/A N/A TestHelperFunctions N/A N/A compareResultsWithFile N/A N/A baseMgr listOfResultOverlays listOfFilenames tolerance N/A 0 N/A N/A equalOverlays True N/A i N/A range N/A len listOfResultOverlays N/A N/A obtained N/A N/A N/A N/A baseMgr dataMgr N/A N/A N/A baseMgr dataMgr _activeImageNumber overlayMgr N/A N/A listOfResultOverlays N/A i N/A prefix Ground_Truth/ N/A N/A N/A N/A dataImpex DataImpex importOverlay N/A N/A baseMgr dataMgr N/A N/A N/A baseMgr dataMgr _activeImageNumber N/A listOfFilenames N/A i prefix N/A groundTruth N/A N/A N/A N/A baseMgr dataMgr N/A N/A N/A baseMgr dataMgr _activeImageNumber overlayMgr N/A N/A prefix N/A listOfResultOverlays N/A i N/A equalOverlays N/A equalOverlays N/A N/A TestHelperFunctions compareOverlayData obtained groundTruth tolerance N/A all  N/A str N/A len listOfResultOverlays  compared overlays are equal:  equalOverlays N/A equalOverlays N/A staticmethod compareOverlayData N/A N/A overlay1 overlay2 tolerance N/A 0 N/A N/A N/A isinstance N/A N/A overlay1 _data _data ListOfNDArraysAsNDArray N/A N/A datatemp1 N/A N/A N/A overlay1 _data _data ndarrays N/A N/A N/A isinstance N/A N/A overlay1 _data _data SelectionAccessor N/A N/A datatemp1 N/A N/A N/A overlay1 _data _data N/A N/A N/A datatemp1 N/A N/A overlay1 _data _data N/A datatemp2 N/A N/A overlay2 _data _data N/A N/A N/A numpy all N/A N/A N/A numpy abs N/A datatemp1 datatemp2 tolerance N/A N/A True N/A N/A False N/A staticmethod arrayEqual N/A N/A a b N/A N/A N/A N/A N/A a shape N/A b shape N/A N/A N/A a dtype N/A b dtype N/A N/A N/A N/A numpy array_equal a b N/A N/A N/A N/A len N/A a shape 3 N/A x N/A range N/A N/A a shape N/A 0 N/A N/A y N/A range N/A N/A a shape N/A 1 N/A N/A z N/A range N/A N/A a shape N/A 2 N/A N/A N/A N/A a N/A N/A x y z N/A b N/A N/A x y z N/A N/A x y z a= N/A a N/A N/A x y z b= N/A b N/A N/A x y z N/A False N/A True N/A staticmethod compareH5Files N/A N/A file1 file2 N/A N/A N/A files to compare:  file1 file2 N/A cl N/A N/A N/A N/A h5diff -cv ' file1 ' ' file2 ' N/A args N/A N/A shlex split cl N/A args N/A 
        cl_header1 = "h5dump --header " + file1
        args_header1 = shlex.split(cl_header1)
        cl_header2 = "h5dump --header " + file2
        args_header2 = shlex.split(cl_header2)
        try:
            p1 = Popen(args_header1, stdout=PIPE, stderr=PIPE)
            out1, err1 = p1.communicate()
            p2 = Popen(args_header2, stdout=PIPE, stderr=PIPE)
            out2, err2 = p2.communicate()
            if out1 != out2:
                print "different header dumps"
                print out1
                print ""
                print out2
        except Exception, e:
            print e
            return False
        #print args
         N/A N/A N/A p N/A Popen args stdout PIPE stderr PIPE N/A N/A stdout stderr N/A N/A p communicate N/A N/A N/A p returncode 0 N/A N/A stdout N/A stderr N/A False N/A N/A True N/A N/A N/A Exception N/A e N/A N/A e N/A False N/A True N/A staticmethod N/A