Module Import alias TryExcept body Import alias handlers ExceptHandler body Print Str Import alias FunctionDef arguments args NameParam defaults NameLoad body Expr Str Assign NameStore Call AttributeLoad NameLoad attr If CompareNotEq SubscriptLoad NameLoad Slice Num Str body Assign NameStore BinOpAdd Call AttributeLoad NameLoad attr Str orelse Assign NameStore BinOpAdd Call AttributeLoad NameLoad attr Str TryExcept body If UnaryOpNot Call AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr BinOpAdd Str NameLoad handlers ExceptHandler body Print Str If CompareIs NameLoad NameLoad body Print Str Return Assign NameStore Call Call AttributeLoad NameLoad attr Str Assign NameStore Call Call AttributeLoad NameLoad attr Str NameLoad Print NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore ListLoad Assign NameStore Call AttributeLoad NameLoad attr Print Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Str attr NameLoad Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Str attr NameLoad Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Str attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num BinOpMult NameLoad Num Print BinOpAdd BinOpAdd Str Call NameLoad BinOpMult NameLoad Num Str Assign NameStore Call AttributeLoad NameLoad attr If NameLoad body Print Str Return For NameStore Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr If CompareEq NameLoad Num body Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad AttributeLoad NameLoad attr orelse If CompareEq NameLoad Num body Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad AttributeLoad NameLoad attr orelse If CompareEq NameLoad Num body Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad AttributeLoad NameLoad attr orelse If CompareEq NameLoad Num body Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad AttributeLoad NameLoad attr orelse Print Str Return Print Str NameLoad NameLoad NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr For NameStore Call NameLoad NameLoad body Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr NameLoad Index Num Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr NameLoad Index Num Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr NameLoad Index Num Print Str NameLoad Str NameLoad Str NameLoad Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr Str attr NameLoad NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Slice Num Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad Assign SubscriptStore NameLoad ExtSlice Index NameLoad Slice Slice Index NameLoad Index NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Return NameLoad decorator_list If CompareEq NameLoad Str body Assign NameStore Call NameLoad Str
N/A N/A numpy N/A N/A N/A jpype N/A N/A N/A N/A Please install jpype if you want to read microscopy formats images like LIF. N/A os reader N/A N/A fileName N/A None N/A N/A  Function to read LIF (Leica Image Format) files. The function expects a filenames a returns a list of 5D data objects
        on item for each series contained in the LIF file. The function expects to find a running Java Virtual Machine. This Machine
        should only be started ones, so make sure it is started outside this function before you call it.
		
		This function requires jpype to be installed.
	 N/A pathtoLOCI N/A N/A os getcwd N/A N/A N/A pathtoLOCI N/A -7 ilastik N/A N/A pathtoLOCI N/A N/A N/A os getcwd /ilastik/core/loci_tools.jar N/A N/A pathtoLOCI N/A N/A N/A os getcwd /core/loci_tools.jar N/A N/A N/A N/A N/A N/A jpype isJVMStarted N/A N/A N/A N/A jpype startJVM N/A N/A jpype getDefaultJVMPath N/A -Djava.class.path= pathtoLOCI N/A N/A N/A N/A JVM Start failed, propably it has been started already... N/A N/A fileName None N/A N/A No file name given N/A N/A r N/A N/A N/A jpype JClass loci.formats.ChannelFiller N/A r N/A N/A N/A jpype JClass loci.formats.ChannelSeparator r N/A fileName N/A N/A N/A r setId fileName N/A seriesData N/A N/A numSeries N/A N/A r getSeriesCount N/A Series: numSeries N/A pixelType N/A N/A r getPixelType N/A bpp N/A N/A N/A N/A jpype JClass loci.formats.FormatTools getBytesPerPixel pixelType N/A fp N/A N/A N/A N/A jpype JClass loci.formats.FormatTools isFloatingPoint pixelType N/A sgn N/A N/A N/A N/A jpype JClass loci.formats.FormatTools isSigned pixelType N/A bppMax N/A N/A numpy power 2 N/A bpp 8 N/A N/A N/A Data  N/A str N/A bpp 8  bit detected N/A little N/A N/A r isLittleEndian N/A sgn N/A N/A ERROR: cannont interpret signed data N/A N/A s N/A range numSeries N/A N/A N/A N/A r setSeries s N/A t N/A N/A r getSizeT N/A w N/A N/A r getSizeX N/A h N/A N/A r getSizeY N/A d N/A N/A r getSizeZ N/A c N/A N/A r getSizeC N/A N/A bpp 1 N/A N/A res N/A N/A numpy zeros N/A t h w d c N/A numpy uint8 N/A N/A N/A bpp 2 N/A N/A res N/A N/A numpy zeros N/A t h w d c N/A numpy uint16 N/A N/A N/A bpp 4 N/A N/A res N/A N/A numpy zeros N/A t h w d c N/A numpy uint32 N/A N/A N/A bpp 8 N/A N/A res N/A N/A numpy zeros N/A t h w d c N/A numpy uint64 N/A N/A ERROR: unrecognized bit format type N/A N/A Time, Width, Height, Depth, Channels t w h d c N/A numImages N/A N/A r getImageCount N/A i N/A range numImages N/A N/A zPos N/A N/A N/A r getZCTCoords i N/A 0 N/A cPos N/A N/A N/A r getZCTCoords i N/A 1 N/A tPos N/A N/A N/A r getZCTCoords i N/A 2 N/A Images i at channel cPos and z-slice zPos and time-point tPos N/A img N/A N/A r openBytes i N/A arr N/A N/A N/A N/A jpype JClass loci.common.DataTools makeDataArray img bpp fp little N/A data N/A N/A numpy array N/A arr N/A 0 N/A len arr N/A data N/A N/A data reshape N/A h w N/A N/A res N/A N/A tPos N/A N/A N/A zPos N/A cPos data N/A N/A N/A seriesData append res N/A N/A N/A r close N/A N/A N/A jpype shutdownJVM N/A seriesData N/A N/A N/A __name__ __main__ N/A N/A data N/A reader ERT2Dkk1_5181_SVZ_Schnitt_1.lif