Add macro examples from OME 2020 NGFF workshop #69
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jburel
requested changes
Apr 9, 2024
| import ij.ImagePlus | ||
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| // configuration | ||
| String file = "/path/to/inputFile.tiff" |
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Propose to let the user select the file to open
file = IJ.getFilePath("Choose a Tiff File")
if (file == null) {
println "cancel"
return
}
path = file.take(file.lastIndexOf('.'))
outFile = path + ".ome.tiff"
| options.setId(outFile) | ||
| options.setSeriesOn(2, true) | ||
| ImagePlus[] imps = BF.openImagePlus(options) | ||
| imps[0].show() |
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Suggested change
| imps[0].show() | |
| imps[0].show() | |
| options.setSeriesOn(2, True); | ||
| imps = BF.openImagePlus(options) | ||
| for imp in imps: | ||
| imp.show() |
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Suggested change
| imp.show() | |
| imp.show() | |
| import math | ||
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| # configuration | ||
| file = "/path/to/inputFile.tiff" |
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file = IJ.getFilePath("Choose a Tiff File")
if file is None:
print("cancel")
sys.exit(2)
path = ('.').join(file.split('.')[:-1])
outFile = path + ".ome.tiff"
| from ome.xml.model.primitives import PositiveInteger | ||
| from java.lang import Math | ||
| from ij import IJ | ||
| import math |
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Suggested change
| import math | |
| import math | |
| import sys |
| from ome.xml.model.primitives import PositiveInteger | ||
| from ome.units import UNITS | ||
| from java.lang import Math | ||
| from ij import IJ |
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Suggested change
| from ij import IJ | |
| from ij import IJ | |
| import sys |
| writer.saveBytes(0, downsample) | ||
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| writer.close() | ||
| reader.close() |
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Suggested change
| reader.close() | |
| reader.close() | |
| IJ.log("Done") | |
| from ome.xml.model.primitives import PositiveInteger | ||
| from java.lang import Math | ||
| from ij import IJ | ||
| import math |
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Suggested change
| import math | |
| import math | |
| import sys |
| import math | ||
|
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| # configuation | ||
| file = "/path/to/inputFile.tiff" |
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file = IJ.getFilePath("Choose a Tiff File")
if file is None:
print("cancel")
sys.exit(2)
path = ('.').join(file.split('.')[:-1])
outFile = path + ".ome.tiff"
| # close reader and writer | ||
| writer.close() | ||
| reader.close() | ||
| IJ.log("Done") |
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Suggested change
| IJ.log("Done") | |
| IJ.log("Done") | |
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Adding 3 new python macro examples and a groovy example.
This have been created for the OME 2020 workshop on next gen file formats. The goal of them is to show how to use tiled and pyramidal conversions to allow large plane (>2GB) images to be opened within the ImageJ environment.
The ImageJ Macro and plugins examples have typically lived in the
bio-formats_plugins/utilsfolder. It would be good to start building a larger range of macro scripting examples in theThe one major outstanding issue with creating examples here is the ongoing testing implications for these macros.