68 lines
2.3 KiB
Python
68 lines
2.3 KiB
Python
import ij
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from ij.io import Opener
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from ijutils import *
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from ch.psi.pshell.imaging.Overlays import *
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from ch.psi.pshell.imaging.Utils import *
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import ch.psi.pshell.imaging.Pen as Pen
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import java.awt.Rectangle as Rectangle
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import ch.psi.pshell.imaging.Data as Data
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def integrate(ips, as_float=True):
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aux = None
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for i in range(len(ips)):
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if i==0:
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img_type = "float" if as_float else "short"
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aux = new_image(ips[i].width, ips[i].height, image_type=img_type, title = "sum", fill_color = None)
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op_image(aux, ips[i], "add", float_result=as_float, in_place=True)
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return aux
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def average (ips, roi=None, as_float=True):
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aux = integrate(ips, as_float)
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op_const(aux, "divide", float(len(ips)), in_place=True)
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return aux
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def get_image(source, roi=None, wait_next=False):
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if wait_next:
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source.waitNext(-1)
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ret = load_image(Utils.grayscale(source.output, Rectangle(roi[0], roi[1], roi[2], roi[3]) if (roi is not None) else None))
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return ret
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def grab_frames(source, samples, roi=None, wait_next=False, sleep=0):
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frames = []
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for i in range(samples):
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if sleep>0:
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time.sleep(sleep)
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aux = get_image(source, roi, wait_next)
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frames.append(aux)
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return frames
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def average_frames(source, samples=1, roi=None, wait_next=False, sleep=0, as_float=True):
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return average(grab_frames(source, samples, roi, wait_next, sleep), as_float)
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def integrate_frames(source, samples=1, roi=None, wait_next=False, sleep=0, as_float=True):
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return integrate(grab_frames(source, samples, roi, wait_next, sleep), as_float)
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def get_image_array(ip):
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if type(ip.getProcessor()) == ij.process.FloatProcessor:
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return ip.getProcessor().getFloatArray()
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else:
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return ip.getProcessor().getIntArray()
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def open_image(file_name):
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file_name = get_context().setup.expandPath(file_name)
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return Opener().openTiff(file_name, 1)
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ret = grab_frames(image, 10, sleep=0.1)
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av = average(ret, None, True)
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print type(av.getProcessor())
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#db=av.getBufferedImage().getData().getDataBuffer()
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data = get_image_array(av)
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plot(data)
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save_image(av, "{images}/float.tif","tiff")
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av = average(ret, None, False)
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save_image(av, "{images}/int.tif","tiff")
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