examples Package¶

simple_viewer Module¶

Simple viewer for OpenMSI data

class omsi.examples.simple_viewer.MyViewer(data, mzdata)¶

Create a simple viewer with image of the data and a cruve plot for a spectrum.

Parameters:	data – Reference to the hdf5 dataset of the image mzdata – mz values of the instrument to be displayed as axis in the curve plot. may be None in case the mz data is unknown

omsi.examples.simple_viewer.main(argv=None)¶

Then main function

testHDF5Optimization Module¶

Simple test script used to test the performance of different HDF5 optimizations (using chunking) to improve the performance of hyperslap selections

omsi.examples.testHDF5Optimization.generateTestFile(omsiOutFile, xdim, ydim, zdim, xchunk, ychunk, zchunk)¶

omsi.examples.testHDF5Optimization.main(argv=None)¶

Then main function

omsi.examples.testHDF5Optimization.printHelp()¶

Print the help explaining the usage of testHDF5Optimiation

testHDF5Optimization_alignedWrite Module¶

omsi.examples.testHDF5Optimization_alignedWrite.generateTestFile(omsiOutFile, xdim, ydim, zdim, xchunk, ychunk, zchunk)¶

omsi.examples.testHDF5Optimization_alignedWrite.main(argv=None)¶

Then main function

omsi.examples.testHDF5Optimization_alignedWrite.printHelp()¶

Print the help explaining the usage of testHDF5Optimiation

test_multiprocess_slice Module¶

omsi.examples.test_multiprocess_slice.create_process(argv)¶

omsi.examples.test_multiprocess_slice.generateBaseTestFile(omsiOutFile, xdim, ydim, zdim)¶

omsi.examples.test_multiprocess_slice.generateChunkedTestFile(omsiOutFile, xdim, ydim, zdim, xchunk, ychunk, zchunk, compress=False, donorFile='/project/projectdirs/openmsi/omsi_data/old/TEST.h5')¶

omsi.examples.test_multiprocess_slice.main(argv=None)¶

Then main function

omsi.examples.test_multiprocess_slice.sliceSelect(args)¶

omsi.examples.test_multiprocess_slice.spectraSelect(args)¶

test_par Module¶

omsi.examples.test_par.create_process(argv)¶

omsi.examples.test_par.generateBaseTestFile(omsiOutFile, xdim, ydim, zdim)¶

omsi.examples.test_par.generateChunkedTestFile(omsiOutFile, xdim, ydim, zdim, xchunk, ychunk, zchunk, compress=False, donorFile='/project/projectdirs/openmsi/omsi_data/old/TEST.h5')¶

omsi.examples.test_par.main(argv=None)¶

Then main function

omsi.examples.test_par.sliceSelect(args)¶

omsi.examples.test_par.spectraSelect(args)¶

test_peakcube Module¶

omsi.examples.test_peakcube.main(argv=None)¶

Then main function

omsi.examples.test_peakcube.printHelp()¶

testhdf5_file_read Module¶

Simple test script used to test the performance of different HDF5 optimizations (using chunking) to improve the performance of hyperslap selections

omsi.examples.testhdf5_file_read.main(argv=None)¶

Then main function

omsi.examples.testhdf5_file_read.printHelp()¶

Print the help explaining the usage of testHDF5Optimiation