Startup
This commit is contained in:
sfop
@@ -1,6 +1,7 @@
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from startup import *
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from ijutils import *
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from mathutils import *
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import ch.psi.pshell.imaging.Filter as Filter
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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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@@ -12,6 +13,7 @@ from ch.psi.pshell.imaging.Utils import sub
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REMOVE_BACKGROUND = True
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PLOT_PROFILE = True
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"""
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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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@@ -34,44 +36,8 @@ def get_centroid(source):
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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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def arroff(a, value = "mean"):
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"""Subtract offset to all elemets in series.
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Args:
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a(list, tuple, array ...): subscriptable object containing numbers
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type(int or str, optional): value to subtract from the array, or "mean" or "min".
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Returns:
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List
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"""
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if value=="mean":
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value = mean(a)
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elif value=="min":
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value = min(a)
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return [x-value for x in a]
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def arrsubback(data, a, b):
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"""Subtract offset to all elemets in series.
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Args:
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a(list, tuple, array ...): subscriptable object containing numbers
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type(int or str, optional): value to subtract from the array, or "mean" or "min".
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Returns:
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List
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"""
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return [y-(a*y+b) for y in a]
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import ch.psi.pshell.imaging.Filter as Filter
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"""
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class SimulatedSource(Filter):
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def process(self, img, data):
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@@ -94,7 +60,13 @@ class SimulatedSource(Filter):
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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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if isinstance(source, basestring):
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self.source = get_context().getClassByName("SfCamera")(source, source)
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self.private_source = True
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self.source.initialize()
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else:
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self.private_source = False
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self.source = source
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self.com_x_samples, self.com_y_samples = [], []
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self.rms_x_samples, self.rms_y_samples = [], []
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self.background = None
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@@ -122,7 +94,7 @@ class ImageStats(DeviceBase):
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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.bg_en = False
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self.num_images = 5
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class BackgroundSubtractor(Filter):
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@@ -135,6 +107,7 @@ class ImageStats(DeviceBase):
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self.backgroundFilter = BackgroundSubtractor(self)
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self.initialize()
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self.start()
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#class SourceListener (ImageListener):
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# def __init__(self, dev):
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@@ -154,17 +127,8 @@ class ImageStats(DeviceBase):
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self.rms_x_samples, self.rms_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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#print "A"
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self.source.waitNext(5000)
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#print "B"
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#time.sleep(0.2)
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#print "Ok"
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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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x_profile_x = self.source.data.getRowSelectionX(True)
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@@ -172,7 +136,7 @@ class ImageStats(DeviceBase):
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y_profile_x = self.source.data.getColSelectionX(True)
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#Remove background
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if (self.bg_en == False) and REMOVE_BACKGROUND:
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if (self.source.backgroundEnabled == False) and REMOVE_BACKGROUND:
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(a, b, amp, com, sigma) = fit_gaussian_linear(x_profile, x_profile_x)
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x_profile = [x_profile[i]-(a*x_profile_x[i]+b) for i in range(len(x_profile))]
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(a, b, amp, com, sigma) = fit_gaussian_linear(y_profile, y_profile_x)
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@@ -187,44 +151,37 @@ class ImageStats(DeviceBase):
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p = get_plots("Profile")
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if (p is None) or (len(p)==0):
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p = plot([x_profile, y_profile], ["x_profile", "yprofile"], [x_profile_x,y_profile_x], title ="Profile")
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else:
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if p is not None:
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p[0].removeMarker(None)
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p[1].removeMarker(None)
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p[0].getSeries(0).setData(x_profile_x, x_profile)
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p[1].getSeries(0).setData(y_profile_x, y_profile)
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p[0].addMarker(com_x, None, "COM = " + str(com_x), Color.GREEN)
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p[1].addMarker(com_y, None, "COM = " + str(com_y), Color.GREEN)
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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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self.source.filter = self.backgroundFilter if self.bg_en else None
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self.source.backgroundEnabled = value
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def captureBackground(self, images):
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try:
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self.source.filter = None
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imgs = []
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for i in range(images):
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self.source.waitNext(5000)
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imgs.append(cam3.output)
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#TODO:
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self.background = cam3.output
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finally:
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self.enableBackground(self.bg_en)
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def grabBackground(self, images):
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self.source.captureBackground(images,0)
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def doClose(self):
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print "close"
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self.source.filter = None
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#self.source.removeListener(self.listener)
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if self.private_source:
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self.source.close()
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else:
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self.source.backgroundEnabled = False
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def start(self):
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pass
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if self.private_source:
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self.source.polling = 200
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self.source.waitNext(2000)
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def stop(self):
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pass
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if self.private_source:
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self.source.polling = 0
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def get_simulated_source(img):
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@@ -235,16 +192,14 @@ def get_simulated_source(img):
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show_panel(simulated_source)
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return simulated_source
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"""
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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", "SLG-LCAM-C041"), True)
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add_device(image_stats.source, True)
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#cam3.waitNext(2000)
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add_device(ImageStats("image_stats", cam3), True)
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cam3.waitNext(2000)
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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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@@ -253,9 +208,14 @@ if __name__ == "__builtin__":
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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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image_stats.captureBackground(5)
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#image_stats.enableBackground(True)
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image_stats.grabBackground(1)
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def before_sample():
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image_stats.update()
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tscan(sensors, 10, 0.1, before_read = before_sample)
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image_stats.enableBackground(False)
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try:
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tscan(sensors, 10, 0.1, before_read = before_sample)
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finally:
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image_stats.enableBackground(False)
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image_stats.stop()
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"""
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