Beispiel #1
0
def test():
    # print("Test not yet written, ending program")
    import main, itktest
    # import processing
    testfish = "/scratch/images/J29-33/rec_J29-33_33D_PTAwt_16p2_30mm_w4Dd__x218_y232_z1013_orig_10um.nhdr"
    hparts, npdata = main.unpacker(testfish, hdrstring=False)
    npdata = npdata.reshape(hparts["dsize"][::-1])
    
    #Canny Testing
    npcanny = itktest.canny_edge_detector(npdata[85], returnNP=True)
    
    #Hough Lines testing
    #output = hough_lines(npcanny, d2_iscanny=True)
    #print(output)
    
    
    #Coordinate testing
    boolean_data=npdata>18783.5193537
    print(get_coordinates(boolean_data))
Beispiel #2
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    #Make sure we have the right type for ITK
    if type(volume)==np.ndarray:
        
        itk_volume=si.GetImageFromArray(np.float32(volume))
        print(type(itk_volume))
        #returnNP=True
    else:
        itk_volume=volume
        
    #Do the edge detection
    canny_edges_volume=si.CannyEdgeDetection(itk_volume, **kwargs)
    
    if returnNP:
        return np.asanyarray(si.GetArrayFromImage(canny_edges_volume),dtype="bool8")
    
    return canny_edges_volume 

#def  Buffer<TImage>::GetArrayFromImage(TImage*) [with TImage = itk::Image<float, 2u>]

if __name__=='__main__':
    import main
    #import processing
    testfish="/scratch/images/J29-33/rec_J29-33_33D_PTAwt_16p2_30mm_w4Dd__x218_y232_z1013_orig_10um.nhdr"
    hparts,npdata=main.unpacker(testfish,hdrstring=False)
    npdata=npdata.reshape(hparts["dsize"][::-1])
    canny_edge_detector(npdata, returnNP=True)
    canny_
    
    
Beispiel #3
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#%load_ext cythonmagic
import gc
gc.enable()

from scipy import ndimage

'''
This is an experiment in the processing of the fish using some of the tools in scipy.ndimage.
For the experimental purpose, see trevor's lab notebook page 17.
'''
#Stage 1. Load Files

#filename="/scratch/joinedImages/resized/rec_J29-33_33D_PTAwt_16p2_30mm_w4Dd_x292_y292_z1047_cubic-0-5_10.0um.nrrd"
#filename="/scratch/joinedImages/uint16/rec_J29-33_33D_PTAwt_16p2_30mm_w4Dd_uint16_x586_y586_z2095_5.0um.nrrd"
filename="/scratch/joinedImages/uint16/rec_J29-33_33D_PTAwt_16p2_30mm_w4Dd_uint16_x293_y293_z1047_10.0um.nrrd"
header,npdata=main.unpacker(filename)
npdata=npdata.reshape(header["dsize"][::-1])

#Automatic thresholding of the file
thresh=processing.autothreshold(npdata)
print(npdata.shape)

mask=npdata>thresh
#threshed=np.where(mask, npdata, npdata.min)

#Do some binary morphology to get rid of excess stuff



result=processing.binaryClosing(mask,structure=None, iterations=15)
result2=processing.binaryOpening(result,kernel=None, iterations=1)