comparison stack_max_projs.groovy @ 1:9be687213bc9 draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero commit 39c8ae77d15d77ddcd8a0bb70f46d1be1531e9cc

0:a02156aa8bda

 * ********************************************* DO NOT MODIFY ****************************************************
 * ****************************************************************************************************************
 */

// Version number = date of last modif
VERSION = "20241212"

/**
 * *****************************************************************************************************************
 * **************************************** Beginning of the script ***********************************************
 * ****************************************************************************************************************

						FolderOpener.open(
							current_directory.getAbsolutePath(),
							" filter=" + fluo_pattern_list[i]
						)
					)
					if (!GraphicsEnvironment.isHeadless()){
						samplesMap.get(unique_identifier).get(
						fluo_channels_list[i]).show()
					}
				}
			}
		} else {
			// It is easy as all images are used
			println "Processing " + unique_identifier + " Greys"
			samplesMap.get(unique_identifier).put(final_color, FolderOpener.open(current_directory.getAbsolutePath()))
			if (!GraphicsEnvironment.isHeadless()){
				samplesMap.get(unique_identifier).get(
				final_color).show()
			}
		}
	}

	// Explore the HashMap and save to tiff
	for(String unique_identifier : samplesMap.keySet()){
		// get the channel map
		Map<String, ImagePlus> channelsMap = samplesMap.get(unique_identifier)
		ArrayList<String> channels = []
		ArrayList<ImagePlus> current_images = []

		for(String channel : channelsMap.keySet()){
			channels.add(channel)
			current_images.add(channelsMap.get(channel))
		}
		// Get number of time:
		int nT = current_images[0].nSlices

		// Merge all
		ImagePlus merged_imps = Concatenator.run(current_images as ImagePlus[])
		// Re-order to make a multi-channel, time-lapse image
		ImagePlus final_imp
		if (channels.size() == 1 && nT == 1) {
			final_imp = merged_imps
		} else {
			final_imp = HyperStackConverter.toHyperStack(merged_imps, channels.size() , 1, nT, "xytcz", "Color")
		}
		// set LUTs
		(0..channels.size()-1).each{
			final_imp.setC(it + 1)
			IJ.run(final_imp, channels[it], "")
			final_imp.resetDisplayRange()
		}
		// Save to tiff
		final_imp.setTitle(unique_identifier)

1:9be687213bc9

 * ********************************************* DO NOT MODIFY ****************************************************
 * ****************************************************************************************************************
 */

// Version number = date of last modif
VERSION = "20241213"

/**
 * *****************************************************************************************************************
 * **************************************** Beginning of the script ***********************************************
 * ****************************************************************************************************************

						FolderOpener.open(
							current_directory.getAbsolutePath(),
							" filter=" + fluo_pattern_list[i]
						)
					)
					// println samplesMap.get(unique_identifier).get(fluo_channels_list[i]).getDimensions()
					if (!GraphicsEnvironment.isHeadless()){
						samplesMap.get(unique_identifier).get(fluo_channels_list[i]).show()
					}
				}
			}
		} else {
			// It is easy as all images are used
			println "Processing " + unique_identifier + " Greys"
			samplesMap.get(unique_identifier).put(final_color, FolderOpener.open(current_directory.getAbsolutePath()))
			// println samplesMap.get(unique_identifier).get(final_color).getDimensions()
			if (!GraphicsEnvironment.isHeadless()){
				samplesMap.get(unique_identifier).get(final_color).show()
			}
		}
	}

	// Explore the HashMap and save to tiff
	for(String unique_identifier : samplesMap.keySet()){
		// get the channel map
		Map<String, ImagePlus> channelsMap = samplesMap.get(unique_identifier)
		ArrayList<String> channels = []
		ArrayList<ImagePlus> current_images = []
		int ref_nT = 0
		boolean all_compatibles = true

		for(String channel : channelsMap.keySet()){
			channels.add(channel)
			current_images.add(channelsMap.get(channel))
			if (ref_nT == 0) {
				ref_nT = channelsMap.get(channel).nSlices
			} else {
				if (ref_nT != channelsMap.get(channel).nSlices) {
					all_compatibles = false
				}
			}
		}
		
		if (all_compatibles) {
			// Merge all
			ImagePlus merged_imps = Concatenator.run(current_images as ImagePlus[])
			// Re-order to make a multi-channel, time-lapse image
			ImagePlus final_imp
			if (channels.size() == 1 && nT == 1) {
				final_imp = merged_imps
			} else {
				try {
					final_imp = HyperStackConverter.toHyperStack(merged_imps, channels.size() , 1, ref_nT, "xytcz", "Color")
					// set LUTs
					(0..channels.size()-1).each{
						final_imp.setC(it + 1)
						IJ.run(final_imp, channels[it], "")
						final_imp.resetDisplayRange()
					}
				} catch(Exception e) {
					println "Could not create the hyperstack for " + unique_identifier + ": " + e
					continue
				}
			}
		} else {
			println "Not all channels have the same number of slices:"
			(0..channels.size()-1).each{
				println "Channel " + channels[it] + " has " + current_images[it].getDimensions() + " whCZT."
			}
			if (channelsMap.containsKey("Greys")) {
				println "Will keep only Greys channel"
				final_imp = channelsMap.get("Greys")
			} else {
				println "Will keep only " + channels[0] + " channel"
				final_imp = current_images[0]
				IJ.run(final_imp, channels[0], "")
			}
			final_imp.resetDisplayRange()
		}
		// Save to tiff
		final_imp.setTitle(unique_identifier)