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--- documents:120206pyip_cooking:python_imagej_cookbook [2021/10/19 17:55] – added scijava scripting in a script kota
+++ documents:120206pyip_cooking:python_imagej_cookbook [2021/11/17 07:34] – [Shell Command] kota
@@ Line 1364: / Line 1364: @@
 For more explanation about this processing, see [[http://rsbweb.nih.gov/ij/developer/api/ij/plugin/filter/GaussianBlur.html|the explanation in javadoc]].
+==== Background Subtraction (Rolling Ball) ====
+Menu item [Process > Subtract Background]
+<code python>
+from ij import IJ
+from ij.plugin.filter import BackgroundSubtracter
+imp = IJ.getImage()
+ip = imp.getProcessor()
+radius = 50.0
+createBackground = False
+lightBackground = False
+useParaboloid = False
+doPresmooth = False
+correctCorners = False
+bs = BackgroundSubtracter()
+bs.rollingBallBackground(ip, radius, createBackground, lightBackground, useParaboloid, doPresmooth, correctCorners)
+imp.updateAndDraw()
+</code>
+If the image is in RGB, then use a different method (rollingBallBrightnessBackground).
+For more explanation about this processing, see [[https://imagej.nih.gov/ij/developer/api/ij/ij/plugin/filter/BackgroundSubtracter.html|the explanation in javadoc]].
 ==== ImageCalculator ====
@@ Line 2330: / Line 2357: @@
 See explanation in [[http://www.prasannatech.net/2008/09/implementing-java-interfaces-in-jython.html|here]].
+==== Shell Command ====
+To run Shell command in OSX, here is an example.
+<code python>
+from java.lang import Runtime
+from java.util import Scanner
+def runShellCommand( cmd ):
+	proc = Runtime.getRuntime().exec(cmd)
+	istream = proc.getInputStream()
+	scan = Scanner(istream).useDelimiter("\\n")
+	for ss in scan:
+		print ss
+runShellCommand( "pwd" )
+runShellCommand( "ls -la" )
+</code>
+==== Is dockr daemon running? ====
+Check if the docker daemon is running ():
+<code python>
+from java.lang import Runtime
+from java.util import Scanner
+def checkDockerRunning( cmd ):
+	proc = Runtime.getRuntime().exec(cmd)
+	inputst = proc.getInputStream()
+	s = Scanner(inputst).useDelimiter("\\n")
+	if not s.hasNext():
+		print "Please start docker desktop!"
+		return False
+	for ss in s:
+		print ss
+		if ss.startswith("CONTAINER ID"):
+			return True
+		else:
+			print "Please start docker desktop!"
+			return False
+# below is for OSX. WIth win, just "docker ps"
+cmd = "/usr/local/bin/docker ps"
+if checkDockerRunning( cmd ):
+	print "Docker running"
+else:
+	print "Docker not running"
+</code>
 ===== JAVADOCS =====