def imsave_al(image, im, path):

    dic = oib.image_info(im)
    if dic['time_interval'] == None:
        t = 0
    else:
        t = float(dic['time_interval'])
    sx = (1 / float(dic['xsize']))

    filename = [
        os.path.splitext(filename)[0] for filename in os.listdir(path)
        if filename.endswith(('.nd2'))
    ]
    filename
    i = 0
    for img in image:
        i += 1
        filename_save = (path + '/' + ('%s%i' % (filename[0], i)) + '.tif')
        filename_save
        if os.path.isfile(filename_save) == True:
            print 'the file already exist'
        else:
            tifffile.imsave(filename_save,
                            img.transpose(0, 1, 4, 2, 3),
                            imagej=True,
                            resolution=(sx, sx),
                            metadata={
                                'mode': 'color',
                                'finterval': t,
                                'unit': 'micron'
                            })
def align(im, warp_matrix):

    dic = oib.image_info(im)

    x = int(dic['frame_size_x'])
    y = int(dic['frame_size_y'])
    c = int(dic['channels'])
    z = int(dic['z_steps'])
    t = int(dic['time_frames'])

    with bioformats.ImageReader(im, perform_init=True) as rdr:
        image = np.empty([t, z, y, x, c], np.uint16)
        for c in range(c):
            image[:, :, :, :, c] = rdr.read(c=1, rescale=False)
            image[:, :, :, :, c] = cv2.warpAffine(
                (rdr.read(c=0, rescale=False)),
                warp_matrix, (y, x),
                flags=cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)
            for t in range(t):
                image[t, :, :, :, c] = cv2.warpAffine(
                    (rdr.read(t=t, z=0, c=0, rescale=False)),
                    warp_matrix, (y, x),
                    flags=cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)
                for z in range(z):
                    image[:, z, :, :, c] = cv2.warpAffine(
                        (rdr.read(z=z, c=0, rescale=False)),
                        warp_matrix, (y, x),
                        flags=cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)

    return image
Ejemplo n.º 3
0
def align(im, warp_matrix):


    dic = oib.image_info(im)

    x = int(dic['frame_size_x'])
    y = int(dic['frame_size_y'])
    c = int(dic['channels'])
    z = int(dic['z_steps'])
    t = int(dic['time_frames'])

    with bioformats.ImageReader(im, perform_init=True) as rdr:
        image = np.empty([t,z,y,x,c], np.uint16)
        for c in range(c):
            image[:,:,:,:,c] = rdr.read(c=1, rescale=False)
            image[:,:,:,:,c] = cv2.warpAffine((rdr.read(c=0, rescale=False)),
                                               warp_matrix, (y,x), flags=cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)
            for t in range(t):
                image[t,:,:,:,c] = cv2.warpAffine((rdr.read(t=t, z=0, c=0, rescale=False)),
                                                   warp_matrix, (y,x), flags=cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)
                for z in range(z):
                    image[:,z,:,:,c] = cv2.warpAffine((rdr.read(z=z, c=0, rescale=False)),
                                                       warp_matrix, (y,x), flags=cv2.INTER_LINEAR + cv2.WARP_INVERSE_MAP)

    return image
Ejemplo n.º 4
0
def imsave_al(image, im, path):

    dic = oib.image_info(im)
    if dic['time_interval'] == None:
        t = 0
    else:
        t = float(dic['time_interval'])
    sx = (1/float(dic['xsize']))

    filename = [os.path.splitext(filename)[0] for filename in os.listdir(path) if filename.endswith(('.nd2'))]
    filename
    i = 0
    for img in image:
        i+=1
        filename_save = (path+ '/' + ('%s%i' %(filename[0], i)) + '.tif')
        filename_save
        if os.path.isfile(filename_save) == True:
            print 'the file already exist'
        else:
            tifffile.imsave(filename_save, img.transpose(0,1,4,2,3), imagej=True, resolution = (sx,sx), metadata = {'mode' : 'color', 'finterval' : t, 'unit' : 'micron'})