205 lines
6.9 KiB
Python
205 lines
6.9 KiB
Python
from startup import *
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from ijutils import *
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from ch.psi.pshell.imaging.Overlays import *
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import ch.psi.pshell.imaging.Pen as Pen
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import java.awt.Color as Color
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import random
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import ch.psi.pshell.imaging.ImageListener as ImageListener
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from operator import add, mul, sub, truediv
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def arrmul(a, b):
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"""Multiply 2 series of the same size.
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Args:
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a(list, tuple, array ...): subscriptable object containing numbers
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b(list, tuple, array ...): subscriptable object containing numbers
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Returns:
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List
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"""
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return map(mul, a, b)
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def center_of_mass(data, x = None):
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"""Calculate the center of mass of a series, and its rms.
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Args:
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data(list, tuple, array ...): subscriptable object containing numbers
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x(list, tuple, array ..., optional): x coordinates
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Returns:
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Tuple (com, rms)
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"""
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if x is None:
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x = Arr.indexesDouble(len(data))
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data_sum = sum(data)
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if (data_sum==0):
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return float('nan')
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xmd = arrmul( x, data)
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com = sum(xmd) / data_sum
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xmd2 = arrmul( x, xmd)
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com2 = sum(xmd2) / data_sum
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rms = math.sqrt(abs(com2 - com * com))
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return (com, rms)
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def get_centroid(source):
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bi = source.getImage()
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if bi is None:
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return None
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op = show_panel(bi, "Original")
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ip = load_image(bi)
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plot(get_histogram(ip), title = "Histogram")
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grayscale(ip)
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invert(ip)
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gaussian_blur(ip)
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auto_threshold(ip)
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#binary_erode(ip)
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show_panel(ip.getBufferedImage(), "Image")
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(results,output_img)=analyse_particles(ip, 2000,20000, exclude_edges=False, print_table=True)
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op.clearOverlays()
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show_panel(output_img.getBufferedImage(), "Outlines")
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if results.size()>0:
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centroid = (results.getValue("XM",0), results.getValue("YM",0))
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ov = Crosshairs(Pen(Color.ORANGE), java.awt.Point(int(centroid[0]),int(centroid[1])), java.awt.Dimension(15,15))
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op.addOverlay(ov)
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return centroid
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import ch.psi.pshell.imaging.Filter as Filter
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class SimulatedSource(Filter):
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def process(self, img, data):
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self.img=img
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if img is None:
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return None
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ip = load_image(img)
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pad_h = int((random.random()-0.5) * 500)
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pad_v = int((random.random()-0.5) * 500)
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#print "Pad = " , (pad_h, pad_v)
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ip = pad_image(ip, -pad_h, pad_h, pad_v, -pad_v, fill_color = Color.BLACK)
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return ip.getBufferedImage()
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#return img
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def waitNext(self, timeout):
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self.pushImage(self.process(self.img, None))
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class ImageStats(DeviceBase):
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def __init__(self, name, source):
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DeviceBase.__init__(self, name)
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self.source = source
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self.com_x_samples, self.com_y_samples = [], []
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class ComX(Readable):
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def read(self):
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if len(self.image_stats.com_x_samples)==0: return None
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return mean(self.image_stats.com_x_samples)
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self.com_x_mean = ComX(); self.com_x_mean.image_stats = self
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class ComY(Readable):
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def read(self):
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if len(self.image_stats.com_y_samples)==0: return None
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return mean(self.image_stats.com_y_samples)
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self.com_y_mean = ComY(); self.com_y_mean.image_stats = self
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class ComXVar(Readable):
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def read(self):
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if len(self.image_stats.com_x_samples)==0: return None
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return stdev(self.image_stats.com_x_samples)
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self.com_x_stdev = ComXVar(); self.com_x_stdev.image_stats = self
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class ComXVar(Readable):
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def read(self):
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if len(self.image_stats.com_y_samples)==0: return None
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return stdev(self.image_stats.com_y_samples)
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self.com_y_stdev = ComXVar(); self.com_y_stdev.image_stats = self
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set_device_alias(self.com_x_mean, name + " com x mean")
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set_device_alias(self.com_y_mean, name + " com y mean")
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set_device_alias(self.com_x_stdev, name + " com x stdev")
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set_device_alias(self.com_y_stdev, name + " com y stdev")
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self.bg_en = False
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self.num_images = 1
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self.initialize()
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class SourceListener (ImageListener):
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def __init__(self, dev):
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self.dev=dev
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def onImage(self, origin, image, data):
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print "On image"
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self.dev.doUpdate()
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def onError(self, origin, ex):
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self.dev.com_x_samples, self.dev.com_y_samples = [], []
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self.listener = SourceListener(self)
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self.source.addListener(self.listener)
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def doUpdate(self):
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print "Update"
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self.com_x_samples, self.com_y_samples = [], []
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for i in range(self.num_images):
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#if type(self.source) is not ch.psi.pshell.imaging.FileSource:
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# self.source.waitNext(5000)
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#centroid = get_centroid(self.source)
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#print "cent ", centroid
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#if centroid is not None:
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# self.com_x_samples.append(centroid[0])
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# self.com_y_samples.append(centroid[1])
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x_profile = self.source.data.integrateVertically(True)
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y_profile = self.source.data.integrateHorizontally(True)
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com_x,rms_x = center_of_mass(x_profile)
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com_y,rms_y = center_of_mass(y_profile)
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self.com_x_samples.append(com_x)
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self.com_y_samples.append(com_y)
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def setNumberOfImages(self, value):
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self.num_images = value
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def enableBackground(self, value):
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self.bg_en = value
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def captureBackground(self, images):
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self.doInitialize()
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def doClose(self):
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print "close"
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self.source.removeListener(self.listener)
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def start(self):
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pass
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def stop(self):
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pass
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def get_simulated_source(img):
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simulated_source = SimulatedSource()
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simulated_source.img=None
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simulated_source.initialize()
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img.addListener(simulated_source)
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show_panel(simulated_source)
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return simulated_source
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if __name__ == "__builtin__":
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#simulated_source = get_simulated_source(image)
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#print get_centroid(simulated_source)
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add_device(ImageStats("image_stats", cam2), True)
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cam2.waitNext(5000)
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image_stats.enableBackground(False)
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#for i in range (10):
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# image_stats.update()
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# print image_stats.take(), image_stats.com_x_mean.read(), image_stats.com_y_mean.read()
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# time.sleep(1)
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image_stats.setNumberOfImages(3)
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sensors = [image_stats.com_x_mean, image_stats.com_y_mean, image_stats.com_x_stdev, image_stats.com_y_stdev]
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try:
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tscan(sensors, 10, 0.1)
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finally:
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image_stats.close()
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