From 69a86e0a8ef82ce3c2232b99f72717a184f4d4cf Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 12 Dec 2024 13:33:24 +0100
Subject: [PATCH] add a new tool to get max proj on omero

---
 .../.shed.yml                                 |   7 +
 ...max_projections_stack_and_upload_omero.xml | 132 ++++++++++++
 .../stack_max_projs.groovy                    | 194 ++++++++++++++++++
 .../upload_omero.sh                           |  21 ++
 4 files changed, 354 insertions(+)
 create mode 100644 tools/max_projections_stack_and_upload_omero/.shed.yml
 create mode 100644 tools/max_projections_stack_and_upload_omero/max_projections_stack_and_upload_omero.xml
 create mode 100644 tools/max_projections_stack_and_upload_omero/stack_max_projs.groovy
 create mode 100644 tools/max_projections_stack_and_upload_omero/upload_omero.sh

diff --git a/tools/max_projections_stack_and_upload_omero/.shed.yml b/tools/max_projections_stack_and_upload_omero/.shed.yml
new file mode 100644
index 0000000..26aad63
--- /dev/null
+++ b/tools/max_projections_stack_and_upload_omero/.shed.yml
@@ -0,0 +1,7 @@
+categories:
+   - Imaging
+description: Combine images from max projections to stack and upload to the omero server
+name: max_projections_stack_and_upload_omero
+owner: lldelisle
+long_description: Uses a groovy to combine images and a bash script to upload as dataset to the omero server
+remote_repository_url: https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero
diff --git a/tools/max_projections_stack_and_upload_omero/max_projections_stack_and_upload_omero.xml b/tools/max_projections_stack_and_upload_omero/max_projections_stack_and_upload_omero.xml
new file mode 100644
index 0000000..ec02398
--- /dev/null
+++ b/tools/max_projections_stack_and_upload_omero/max_projections_stack_and_upload_omero.xml
@@ -0,0 +1,132 @@
+<tool id="max_projections_stack_and_upload_omero" name="Stack MaxProj" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="BSD-3">
+    <description>And upload to omero</description>
+    <macros>
+        <token name="@TOOL_VERSION@">20241212</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="20240614">Fiji</requirement>
+        <requirement type="package" version="5.19.4">omero-py</requirement>
+        <requirement type="package" version="5.3.1">gawk</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #import os
+        ## the user wants to use a non-public OMERO instance
+        ## check if credentials are set in the user-preferences, if not warn the user and exit
+        #set $username = $__user__.extra_preferences.get('omero_account|username', "")
+        #set $password = $__user__.extra_preferences.get('omero_account|password', "")
+        #if str($upload_omero.upload_omero_select) == "yes":
+            #if ($username == "" or $password ==""):
+                echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 &&
+                exit 1 &&
+            #end if
+        #end if
+        
+        ## Prefix to directories provided by users
+        #set $prefix = "/data/mount_s3/image_storage/"
+        ## Prepare output directory
+        mkdir output &&
+        ## Use ln -s for input
+        #if not os.path.isdir($prefix + "/" + str($base_dir)):
+            echo "Base dir $base_dir does not exists" &&
+            exit 1 &&
+        #end if
+        ln -s '${prefix}/${base_dir}/' input &&
+        ## Run the groovy
+        ImageJ --ij2 --headless --console --run '$__tool_directory__/'stack_max_projs.groovy 
+            'base_dir="input/",output_dir="output/",suffix_white="$suffix_white",suffix_fluo="$suffix_fluo",pattern_green="$pattern_green",pattern_red="$pattern_red"' > output.log
+        ## Upload to omero
+        #if str($upload_omero.upload_omero_select) == "yes":
+            && bash '$__tool_directory__/'upload_omero.sh '$upload_omero.omero_host' '$credentials' '$upload_omero.cond_create.to_create' '$upload_omero.cond_create.project_name_or_id' '$upload_omero.cond_create.dataset_name_or_id' >> output.log
+        #end if
+    ]]></command>
+    <configfiles>
+        <configfile name="credentials"><![CDATA[
+    #set $username = $__user__.extra_preferences.get('omero_account|username', "")
+    #set $password = $__user__.extra_preferences.get('omero_account|password', "")
+$username
+$password
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="base_dir" type="text" value="" label="Directory on s3 with all directories" help="For example Pierre/ViventisLightSheet/20220617_104242_MixCell_50pc_20pc_72hstart/"/>
+        <param name="suffix_white" type="text" value="_BF_max" label="Suffix for white channel directory" help="Leave empty if you are not interested"/>
+        <param name="suffix_fluo" type="text" value="_Fluo_max" label="Suffix for fluo channel(s) directory" help="Leave empty if you are not interested"/>
+        <param name="pattern_green" type="text" value="_H2B-GFP" label="Pattern for green channel images" help="Leave empty if you are not interested"/>
+        <param name="pattern_red" type="text" value="_RFP670" label="Pattern for red channel images" help="Leave empty if you are not interested"/>
+        <conditional name="upload_omero">
+            <param name="upload_omero_select" type="select" label="Upload your images to omero?" >
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="omero_host" type="text" label="OMERO host URL">
+                    <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
+                    <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
+                </param>
+                <param name="plateName" type="text" value="Experiment:0" label="Name of the plate (on omero)" />
+                <conditional name="cond_create">
+                    <param name="to_create" type="select" label="Create the project/dataset on OMERO or use existing one?">
+                        <option value="both">Create a new Project and a new Dataset</option>
+                        <option value="dataset">Use an existing Project and create in a new Dataset</option>
+                        <option value="none">Use an existing Dataset</option>
+                    </param>
+                    <when value="both">
+                        <param name="project_name_or_id" type="text" value="MyNewProject" label="Name of the project (on omero)" />
+                        <param name="dataset_name_or_id" type="text" value="MyNewDataset" label="Name of the dataset (on omero)" />
+                    </when>
+                    <when value="dataset">
+                        <param name="project_name_or_id" type="integer" min="1" value="12" label="ID of the project (on omero)" />
+                        <param name="dataset_name_or_id" type="text" value="MyNewDataset" label="Name of the dataset (on omero)" />
+                    </when>
+                    <when value="none">
+                        <param name="project_name_or_id" type="integer" min="1" value="12" label="ID of the project (on omero)" />
+                        <param name="dataset_name_or_id" type="integer" min="1" value="56" label="ID of the dataset (on omero)" />
+                    </when>
+                </conditional>
+                <param name="get_stacks_in_galaxy" type="boolean" checked="false" label="Get stacks in galaxy" />
+            </when>
+            <when value="no">
+                <param name="get_stacks_in_galaxy" type="hidden" value="true"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: logfile" />
+        <collection name="list_output" type="list" label="${tool.name} on ${on_string}: Stacks">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tif" directory="output/" ext="tiff" />
+            <filter>upload_omero['get_stacks_in_galaxy']</filter>
+        </collection>
+    </outputs>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+It will use images coming from the Viventis Lightsheet which are on the s3 server to make a "T-stack" per well and upload it to omero.
+This wrapper uses ImageJ to combine images (with a groovy) and omero-py to import the images.
+
+Usage
+.....
+
+
+**Input**
+
+- One path with directory with data
+- suffix_white which allow to find the directories with the 'Grays' channel and extract the `unique identifier`
+- suffix_fluo which allow to find the directories with the fluo channels (Red and Green) and extract the `unique identifier` to be able to merge with the 'Grays'
+- pattern_green which allow to filter for green images in the fluo directory.
+- pattern_red which allow to filter for red images in the fluo directory.
+- URL of omero
+- Name/ID of the Project in omero
+- Name/ID of the Dataset in omero
+- Whether the Dataset/Projects should be created
+
+**Output**
+
+- A log file with info
+- Optionally all images as T-stack
+- On OMERO your images all channels combined and all time points combined
+    ]]></help>
+</tool>
\ No newline at end of file
diff --git a/tools/max_projections_stack_and_upload_omero/stack_max_projs.groovy b/tools/max_projections_stack_and_upload_omero/stack_max_projs.groovy
new file mode 100644
index 0000000..7ea0395
--- /dev/null
+++ b/tools/max_projections_stack_and_upload_omero/stack_max_projs.groovy
@@ -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
diff --git a/tools/max_projections_stack_and_upload_omero/upload_omero.sh b/tools/max_projections_stack_and_upload_omero/upload_omero.sh
new file mode 100644
index 0000000..9d50cae
--- /dev/null
+++ b/tools/max_projections_stack_and_upload_omero/upload_omero.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+omero_server="$1"
+omero_user="$(cat $2 | awk 'NR==2{print $0}')"
+omero_password="$(cat $2 | awk 'NR==3{print $0}')"
+to_create=$3
+project_name_or_id=$4
+dataset_name_or_id=$5
+
+if [ "$to_create" = "both" ]; then
+    # Create a project:
+    project_name_or_id=$(${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Project name="${project_name_or_id}" | awk -F ":" 'END{print $NF}')
+    echo "Just created the new project ${project_name_or_id}"
+fi
+if [ "$to_create" = "both" ] || [ "$to_create" = "dataset" ]; then
+    dataset_name_or_id=$(${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new Dataset name="${dataset_name_or_id}" | awk -F ":" 'END{print $NF}')
+    echo "Just created the new dataset ${dataset_name_or_id}"
+    ${omero_path} obj -s ${omero_server} -u ${omero_user} -w ${omero_password} new ProjectDatasetLink parent=Project:${project_name_or_id} child=Dataset:${dataset_name_or_id}
+fi
+echo "Start upload"
+omero import -s ${omero_server} -u ${omero_user} -w ${omero_password} --depth 1 -T Dataset:id:"${dataset_name_or_id}" output 2>&1
+echo "Upload finished"