test_large.py

import numpy as np
from pyqtgraph.Qt import QtGui, QtCore
import pyqtgraph as pg
import pyqtgraph.opengl as gl
import orthos
import h5py

from orthos.widgets import *
from orthos.layers import *
from orthos.data_source import *

pg.setConfigOptions(antialias=False,useOpenGL=True,useWeave=True)

app = QtGui.QApplication([])
mw = MainWindow()
mw.setWindowTitle('Orthos')
mw.show()
mw.resize(800, 600)



if False:
    print "read"
    data = vigra.impex.readHDF5("/home/tbeier/Desktop/input/superpixels_10000.h5",'data')
    f = h5py.File("/home/tbeier/Desktop/input/superpixels_10000c.h5")
    print "write"
    f.create_dataset('data',shape=data.shape,data=data,chunks=(64,64,64))
    f.close()


with vigra.Timer("create raw layer"):
    f = "/home/tbeier/Desktop/input/raw.h5"
    #f = "/media/tbeier/data/datasets/hhess/2x2x2nm_chunked/data.h5"
    rawSource = VigraChunkedArrayHdf5(file_name=f,dataset_name='data')
    rawLayer = GrayscaleLayer(name='raw',levels=[0,255],dataSource=rawSource,useLut=True)



if True:
    with vigra.Timer("create pmap layer"):
        # pmap layer
        f = "/home/tbeier/Desktop/input/pmap_c1.h5"
        pmapSource = VigraChunkedArrayHdf5(file_name=f,dataset_name='data')
        pmapLayer = GrayscaleLayer(name='pmap',levels='auto',dataSource=pmapSource,useLut=True)


    with vigra.Timer("create sv layer"):
        ## supervoxel layer
        f = "/home/tbeier/Desktop/input/superpixels_10000c.h5"
        superVoxelSource = VigraChunkedArrayHdf5(file_name=f,dataset_name='data')
        superVoxelLayer = SupervoxelLayer(name='sv',dataSource=superVoxelSource)
        objectLayer = ObjectLayer(name='obj',dataSource=superVoxelSource)


    with vigra.Timer("create paint layer"):
        # paint layer
        f = "/home/tbeier/Desktop/input/labels_out.h5"
        labelsSource = VigraChunkedArrayHdf5(file_name=f,dataset_name='data',shape=rawSource.shape,
                                             mode=vigra.HDF5Mode.ReadWrite, compression=vigra.Compression.ZLIB_FAST,
                                             chunk_shape=[64,64,64],dtype='uint8')
        paintLayer = PaintLayer(name="paint",dataSource=labelsSource)

        #paintLayer = SplinePaintLayer(name="paint",dataSource=labelsSource)







spatialShape = rawSource.shape




opt = LayerViewerOptions()
opt.spatialDimensions = 3
opt.hasTimeAxis = False

with vigra.Timer("create viewer"):
    viewerWidget = LayerViewerWidget(spatialShape=spatialShape, options=opt)
    mw.setCentralWidget(viewerWidget)

with vigra.Timer("add raw layer"):
    viewerWidget.addLayer(rawLayer)
if True:
    with vigra.Timer("add pmap layer"):
        viewerWidget.addLayer(pmapLayer)
    with vigra.Timer("add sv layer"):
        viewerWidget.addLayer(superVoxelLayer)
    with vigra.Timer("add obj layer"):
        viewerWidget.addLayer(objectLayer)
    with vigra.Timer("add paint layer"):
        viewerWidget.addLayer(paintLayer)

#data = numpy.random.ones(*spatialShape)*255
#data = data.astype('uint8')
#ds = NumpyArrayDataSource(data)
#for x in range(20):
#    pmapLayer = GrayscaleLayer(name='pmap%d'%x,levels='auto',dataSource=ds,useLut=True)
#    viewerWidget.addLayer(pmapLayer)

with vigra.Timer("range changed"):
    viewerWidget.rangeChanged()

def closeCallback():
    labelsSource.flushToDisk()
mw.closeCallback = closeCallback



## Start Qt event loop unless running in interactive mode.
if __name__ == '__main__':
    import sys
    if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
        QtGui.QApplication.instance().exec_()