138 lines
4.8 KiB
Python
138 lines
4.8 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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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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def doUpdate(self):
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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(3000)
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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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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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pass
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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", simulated_source), True)
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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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