documents:120206pyip_cooking:python_imagej_cookbook
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documents:120206pyip_cooking:python_imagej_cookbook [2016/12/09 08:23] – [Union of multiple ROIs] a bit of additions kota | documents:120206pyip_cooking:python_imagej_cookbook [2017/12/03 13:03] – [Automatic Brightness/Contrast Button] updated github repo link kota | ||
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Here is an example, using re package. To construct pattern, several web services are available such as: | Here is an example, using re package. To construct pattern, several web services are available such as: | ||
- | http:// | + | http:// |
+ | or\\ | ||
+ | https:// | ||
<code python linenums: | <code python linenums: | ||
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This is an expaple of using regular expression to match file names, and to collect images as a ImagePlus array then convert it to a Hyperstack. | This is an expaple of using regular expression to match file names, and to collect images as a ImagePlus array then convert it to a Hyperstack. | ||
- | https:// | + | https:// |
<code python linenums: | <code python linenums: | ||
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- if the count is larger than " | - if the count is larger than " | ||
- | The jython | + | The Jython |
<code python linenums: | <code python linenums: | ||
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* [[http:// | * [[http:// | ||
* [[http:// | * [[http:// | ||
+ | |||
+ | ===== Plugin: Shape Smoothing ===== | ||
+ | |||
+ | Shape smoothing by reducing the number of Fourier descriptors. | ||
+ | The plugin page is [[http:// | ||
+ | The github page is [[https:// | ||
+ | |||
+ | <code python> | ||
+ | from ij import IJ | ||
+ | from de.biomedical_imaging.ij.shapeSmoothing import ShapeSmoothingUtil | ||
+ | |||
+ | # https:// | ||
+ | |||
+ | imp = IJ.getImage() | ||
+ | ss = ShapeSmoothingUtil() | ||
+ | ss.setBlackBackground(True) | ||
+ | # Relative proportion FDs (%) | ||
+ | thresholdValue = 2 | ||
+ | # FD in % or absolute number | ||
+ | thresholdIsPercentual = True | ||
+ | # If True, a table, containing all FDs, will be shown after processing | ||
+ | doOutputDescriptors = False | ||
+ | |||
+ | ss.fourierFilter(imp.getProcessor(), | ||
+ | </ | ||
===== Plugin: Auto Threshold ===== | ===== Plugin: Auto Threshold ===== | ||
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Clone the project below, compile and install it as a plugin. | Clone the project below, compile and install it as a plugin. | ||
- | https:// | + | https:// |
<code python linenums: | <code python linenums: |
documents/120206pyip_cooking/python_imagej_cookbook.txt · Last modified: 2022/10/16 07:12 by kota