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--- documents:120206pyip_cooking:python_imagej_cookbook [2018/07/16 00:23] – [Particle Analysis] kota
+++ documents:120206pyip_cooking:python_imagej_cookbook [2018/12/10 23:07] – [Plugin: MiToBo h-dome transformation] kota
@@ Line 95: / Line 95: @@
 print op.getDirectory()+ op.getFileName()
 </code>
+==== Getting the directory where the curently opened image is stored ====
+<code python:1>
+from ij import IJ
+imp = IJ.getImage()
+print imp.getOriginalFileInfo().directory
+</code>
+... can also be done by ''%%IJ.getDirectory("image")%%'', but with this IJ method, one cannot specify target ImagePlus object. See also the [[https://github.com/imagej/imagej1/blob/master/ij/IJ.java#L1652-L1663|source code of IJ.getDirectory]]
+Be careful not to mix with the usage of ''%%getFileInfo%%''. This does not hold directory information.
 ==== Regular Expression to get meta information from file name ====
@@ Line 772: / Line 785: @@
 imps[0].show() # Channel 1
 imps[1].show() # Channel 2
+</code>
+==== Channel Merge ====
+[Image > Color > Merge Channels...]
+<code python linenums:1>
+from ij import ImagePlus
+from ij.plugin import RGBStackMerge, RGBStackConverter
+impc1 = ImagePlus("path/to/image.tif")
+impc2 = ImagePlus("path/to/image.tif")
+mergeimp = RGBStackMerge.mergeChannels([impc2, None, impc1, None, None, None, None], True)
+# convert the composite image to the RGB image
+RGBStackConverter.convertToRGB(mergeimp)
+mergeimp.show()
 </code>
 ==== Z projection ====
@@ Line 1522: / Line 1554: @@
 cm.setPointSize(3)
 </code>
-===== Plugin: LOCI BioFormats, Replacing OME-TIFF XML =====
+===== Plugin: LOCI BioFormats =====
+==== Importing CZI file ====
+<code python linenums:1>
+from loci.plugins import BF
+from loci.plugins.in import ImporterOptions
+filepath = "/path/to/image/my.czi"
+# Options for Bioformats plugin, includeing the image path
+options = ImporterOptions()
+options.setOpenAllSeries(True)
+options.setShowOMEXML(False)
+options.setStitchTiles(False)
+options.setId(filepath)
+fullimps = BF.openImagePlus(options)
+#fullimps now holds multiple images contained within the czi file.
+# open the first one.
+fullimps[0].show()
+</code>
+See here for more on metadata parsing and so on: [[https://gist.github.com/ctrueden/6282856|bio-formats.py]]
+==== Replacing OME-TIFF XML ====
 <code python linenums:1>
@@ Line 1841: / Line 1899: @@
     print p, resmap.get(p)
 </code>
+===== Plugin: MiToBo h-dome transformation =====
+h-dome is useful for spot detection in a noisy background. [[https://www.researchgate.net/publication/261206082_A_new_approach_for_spot_detection_in_total_internal_reflection_fluorescence_microscopy | For example, see this reference]]. The example here uses Plugin MiToBo, a huge collection of various components.
+<code python>
+from de.unihalle.informatik.MiToBo.core.datatypes.images import MTBImage
+from de.unihalle.informatik.MiToBo.morphology import HDomeTransform3D
+from ij import IJ
+imp = IJ.getImage()
+mtb = MTBImage.createMTBImage( imp.duplicate() )
+hdome = HDomeTransform3D(mtb, 10.0)
+hdome.runOp()
+mtbdone = hdome.getResultImage()
+imp2 = mtbdone.getImagePlus()
+imp2.show()
+</code>
 ===== R: Multi-Peak fitting using R =====