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--- documents:120206pyip_cooking:python_imagej_cookbook [2022/03/02 07:15] – [Plugin 3D ImageJ Suite] kota
+++ documents:120206pyip_cooking:python_imagej_cookbook [2022/10/16 07:12] (current) – [Using Java8 Stream] kota
@@ Line 787: / Line 787: @@
 zip command creates a list of tuples from elements of arrays a and b.
+==== Using Java8 Stream ====
+Stream-related syntax introduced from Java8 is useful for writing clear codes, but cannot be directly used in Jython. Below is a way to use StreamAPI, by introducing Jython classes implementing the Consumer interface. I took this idea from [[https://stackoverflow.com/questions/45417732/jython-function-to-java-consumer|here]]. For the Java Stream API, this page is useful: [[https://www.baeldung.com/java-8-streams|The Java 8 Stream API Tutorial]]
+<code python>
+from java.util.Arrays import asList
+from java.util.function import Predicate, Consumer, Function
+from java.util.stream import Collectors
+from java.util import Arrays
+class jc(Consumer):
+    def __init__(self, fn):
+        self.accept=fn
+class jf(Function):
+    def __init__(self, fn):
+        self.apply = fn
+class jp(Predicate):
+    def __init__(self, fn):
+        self.test = fn
+def jprint(x):
+	print x
+tt = ["a", "b", "c"]
+c = Arrays.stream(tt).count()
+print c
+print "forEach printing"
+Arrays.stream(tt).forEach(jc(lambda x: jprint("="+x)))
+print "forEach printing parallelly"
+Arrays.stream(tt).parallel().forEach(jc(lambda x: jprint("="+x)))
+print "has b?", Arrays.stream(tt).anyMatch(jp(lambda x: x=="b"))
+print "has z?", Arrays.stream(tt).anyMatch(jp(lambda x: x=="z"))
+# convert to Java List<>
+jtt = Arrays.asList(tt)
+jtt.stream().forEach(jc(lambda x: jprint("+"+x)))
+</code>
 ===== Event Listener =====
@@ Line 839: / Line 883: @@
 </code>
+===== GUI: wait for user =====
+To pause the script processing and wait for the user input (e.g. creating amanual ROI), use WaitForUserDialog class.
+<code python>
+from ij.gui import WaitForUserDialog
+print("start")
+wud = WaitForUserDialog("test: wait for user", "Click OK if you are done with your manual work")
+print("waiting...")
+wud.show()
+print("done")
+</code>
 ===== HashMap =====
@@ Line 1023: / Line 1080: @@
 maskimp.show()
 </code>
+=== Stack to Mask by a threshold value ===
+Here is an example script to create a mask from an 8-bit stack using intensity thresholding.
+The threshold value is derived by the Otsu algorithm using the full stack histogram.
+<code>
+from ij import IJ, ImagePlus, ImageStack
+from ij.plugin import ChannelSplitter
+from ij.process import StackStatistics
+from fiji.threshold import Auto_Threshold
+#imp = IJ.openImage("http://imagej.nih.gov/ij/images/confocal-series.zip")
+imp = IJ.getImage()
+imps = ChannelSplitter.split( imp )
+imp1 = imps[0]
+imp1bin = imp1.duplicate()
+# get auto threshold value
+stats = StackStatistics(imp1bin)
+histdouble = stats.histogram()
+# need this conversion from double to int
+histint = map(lambda x:int(x), histdouble)
+th = Auto_Threshold.Otsu(histint)
+for i in range(imp1bin.getStackSize()):
+	ip = imp1bin.getStack().getProcessor( i + 1)
+	ip.threshold(th)
+IJ.run(imp1bin, "Grays", "");
+imp1bin.show()
+</code>
+To do this by accessing the pixel array of the stack, here is the way. It takes a longer time than above, so this is just to show the technique to process by pixel values using float processor pixel array object.
+<code python>
+from ij import IJ, ImagePlus, ImageStack
+from ij.plugin import ChannelSplitter
+from ij.process import StackStatistics
+from ij.process import FloatProcessor
+from fiji.threshold import Auto_Threshold
+import jarray
+imp = IJ.openImage("http://imagej.nih.gov/ij/images/confocal-series.zip")
+#imp = IJ.getImage()
+imps = ChannelSplitter.split( imp )
+imp1 = imps[0]
+ww = imp1.getWidth()
+hh = imp1.getHeight()
+binstack = ImageStack( ww, hh)
+# get auto threshold value
+stats = StackStatistics(imp1)
+histdouble = stats.histogram()
+histint = map(lambda x:int(x), histdouble)
+th = Auto_Threshold.Otsu(histint)
+for i in range(imp1.getStackSize()):
+	slicepixA = imp1.getStack().duplicate().convertToFloat().getPixels(i + 1)
+#	pixmin = reduce(min, slicepixA)
+#	pixmax = reduce(max, slicepixA)
+#	print "pixvalue range:", pixmin, " - " ,pixmax
+	slicepixA = map(lambda x: 0.0 if x<th else 255.0, slicepixA)
+	fp = FloatProcessor( ww, hh, slicepixA, None)
+	bp = fp.convertToByteProcessor()
+	binstack.addSlice(str(i+1), bp)
+binimp = ImagePlus("bin", binstack)
+binimp.show()
+</code>
 ==== ROI manager ====
@@ Line 1819: / Line 1949: @@
 fullimps[0].show()
 </code>
+If you do not want to open all images (called sereies) in multi-image CZI files, replace
+<code>
+open.setOpenAllSeries(True)
+</code>
+with
+<code>
+options.setSeriesOn(seriesIndex, True)
+</code>
+with "sereiesIndex" being the seriesID e.g. 1 or 2 or 3 ...
 See here for more on metadata parsing and so on: [[https://gist.github.com/ctrueden/6282856|bio-formats.py]]
@@ Line 2241: / Line 2381: @@
 ===== Plugin: MorphoLibJ =====
+Javadoc: [[http://ijpb.github.io/MorphoLibJ/javadoc/]]
 ==== Distance Transform Watershed 3D ====
@@ Line 2504: / Line 2645: @@
 ===== JAVADOCS =====
-  * 3D ImageJ Suite [[http://wiki.cmci.info/javaapi/mcib-javadoc/|JAVADOC]] (2019 version)
+  * 3D ImageJ Suite
+    * [[http://wiki.cmci.info/javaapi/mcib-javadoc/|JAVADOC]] (2019 version, deprecated)
+    * [[https://wiki.cmci.info/mcib-javadoc/| MCIB3D Javadoc]] (2022 version)
     * [[https://github.com/mcib3d/mcib3d-core|Core Source (old)]]
     * [[https://framagit.org/mcib3d/mcib3d-core|Core Source (2021-)]]