diff stack_max_projs.groovy @ 0:a02156aa8bda draft

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero commit 69a86e0a8ef82ce3c2232b99f72717a184f4d4cf

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stack_max_projs.groovy	Thu Dec 12 12:42:20 2024 +0000
@@ -0,0 +1,194 @@
+/**
+ *
+ * The purpose of this script is to combine a series of time-lapse images into
+ * one file per image with possibly multiple channels and multiple time points
+ *
+ * To make the script run
+ *  1. Create a parent folder (base_dir) and a output folder (output_dir)
+ *  2. The struction of the base_dir must be: one directory per final image and per channel. All the directories should be: `unique_identifier` `suffix specific to channel`.
+ *  3. The image names will be sorted before being merged.
+ *  4. The images must be regular tif.
+ *
+ * The expected outputs are:
+ *  1. In the output_dir one tiff per `unique_identifier` (potentially multi-T and potentially multi-C)
+ */
+
+#@ File(style="directory", label="Directory with one directory per final image and per channel") base_dir
+#@ File(style="directory", label="Output directory (must exist)") output_dir
+#@ String(label="Suffix for white channel directory", value="_BF_max", help="Leave empty if you are not interested") suffix_white
+#@ String(label="Suffix for fluo channel(s) directory", value="_Fluo_max", help="Leave empty if you are not interested") suffix_fluo
+#@ String(label="Pattern for green channel images", value="_H2B-GFP", help="Leave empty if you are not interested") pattern_green
+#@ String(label="Pattern for red channel images", value="_RFP670", help="Leave empty if you are not interested") pattern_red
+
+
+/**
+ * *****************************************************************************************************************
+ * ********************************************* Final Variables **************************************************
+ * ********************************************* DO NOT MODIFY ****************************************************
+ * ****************************************************************************************************************
+ */
+
+// Version number = date of last modif
+VERSION = "20241212"
+
+/**
+ * *****************************************************************************************************************
+ * **************************************** Beginning of the script ***********************************************
+ * ****************************************************************************************************************
+ */
+
+try {
+
+	println "Beginning of the script"
+
+	IJ.run("Close All", "")
+
+	// Find all directories
+	File[] dir_list = base_dir.listFiles()
+
+	// The images are stored in a TreeMap where
+	// keys are unique_identifier
+	// values are a TreeMap that we call channelMap where:
+	// keys are colors (Green, Grays, Red)
+	// values are an ImagePlus (T-stack)
+	Map<Integer, Map<String, ImagePlus>> samplesMap = new TreeMap<>()
+	List<String> dir_suffix_list = [suffix_white, suffix_fluo]
+	List<String> dir_channels_list = ["Grays", "Fluo"]
+
+	List<String> fluo_pattern_list = [pattern_green, pattern_red]
+	List<String> fluo_channels_list = ["Green", "Red"]
+
+	// Loop over directories:
+	for (File current_directory : dir_list) {
+		// Ignore if it is not a directory
+		if (! current_directory.isDirectory()) {
+			continue
+		}
+		String current_directory_name = current_directory.getName()
+		// Check if it matches one of the suffix
+		String final_color = ""
+		// And find the unique identifier:
+		String unique_identifier = ""
+		for(int i = 0; i < dir_suffix_list.size(); i++){
+			if (dir_suffix_list[i] != "" && current_directory_name.endsWith(dir_suffix_list[i])) {
+				final_color = dir_channels_list[i]
+				unique_identifier = current_directory_name.replace(dir_suffix_list[i], "")
+				continue
+			}
+		}
+		if (final_color == "") {
+			println current_directory_name + " do not match any suffix."
+			continue
+		}
+		if (! samplesMap.containsKey(unique_identifier) ) {
+			// Initiate the Map
+			samplesMap.put(unique_identifier, new TreeMap<>())
+		}
+		// Generate the ImagePlus
+		if (final_color == "Fluo") {
+			for(int i = 0; i < fluo_pattern_list.size(); i++){
+				// Use pattern for each color
+				if (fluo_pattern_list[i] != "") {
+					println "Processing " + unique_identifier + " " + fluo_pattern_list[i]
+					samplesMap.get(unique_identifier).put(
+						fluo_channels_list[i],
+						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)
+
+		if (!GraphicsEnvironment.isHeadless()){
+			final_imp.show()
+		}
+
+		def fs = new FileSaver(final_imp)
+		File output_path = new File (output_dir ,final_imp.getTitle()+"_merge.tif" )
+		fs.saveAsTiff(output_path.toString() )
+
+	}
+	println "End of the script"
+
+} catch (Throwable e) {
+	println("Something went wrong: " + e)
+	e.printStackTrace()
+	throw e
+
+	if (GraphicsEnvironment.isHeadless()){
+		// Force to give exit signal of error
+		System.exit(1)
+	}
+
+}
+
+return
+
+/**
+ * ****************************************************************************************************************
+ * ******************************************* End of the script **************************************************
+ *
+ * ****************************************************************************************************************
+ *
+ * *********************************** Helpers and processing methods *********************************************
+ * ***************************************************************************************************************
+ */
+
+import ij.IJ
+import ij.ImagePlus
+import ij.io.FileSaver
+import ij.io.Opener
+import ij.plugin.Concatenator
+import ij.plugin.FolderOpener
+import ij.plugin.HyperStackConverter
+import ij.process.LUT
+
+import java.awt.GraphicsEnvironment
+import java.io.File