fusion only script and fix filename script

fix_filenames_and_create_quickview.ijm

+/*
+ * Macro template to process multiple images in a folder
+ */
+
+#@ File (label = "Input directory", style = "directory") input
+#@ String (label = "File suffix", value = ".zip") suffix
+
+
+setBatchMode(true);
+processFolder(input);
+print("Macro Done");
+setBatchMode(false);
+return;
+
+// function to scan folders/subfolders/files to find files with correct suffix
+function processFolder(input) {
+	
+	fixFileNames(input);
+	list = getFileList(input);
+	list = Array.sort(list);
+	for (i = 0; i < list.length; i++) {
+		if(File.isDirectory(input + File.separator + list[i]))
+			processFolder(input + File.separator + list[i]);
+		if(endsWith(list[i], suffix))
+			processFile(input,  list[i]);
+	}
+}
+
+/*
+ * fixes file names
+ */
+function fixFileNames(input)
+{
+	print("Fixing file names in: "+input);
+	//get prefix
+	imageSetArr = split(input, File.separator);
+	imageSetName = imageSetArr[ lengthOf(imageSetArr)-1 ];
+	//stupid windows bug needs removal of forward slashed
+	imageSetName = replace(imageSetName, "/", "");
+	//print(imageSetName);
+	list2 = getFileList(input);
+	list2 = Array.sort(list2);
+	for (i = 0; i < list2.length; i++) {
+		//print(list2[i]);
+		//only handle files with correct sufix starting with fused_
+		if(endsWith(list2[i], suffix) && startsWith(list2[i], "fused_") )
+			{
+				newName = input+File.separator+imageSetName+"_"+list2[i];
+				
+				File.rename(input+File.separator+list2[i], newName);
+				print("renaming: "+list2[i]+" to "+ imageSetName+"_"+list2[i]);
+				//now set metadata
+				open(newName);
+				setMetadata("Label", ""+imageSetName+"_"+list2[i]);
+				//print("Label: "+ getMetadata("Label") );
+				save(newName);
+				close(imageSetName+"_"+list2[i]);
+				
+			}
+
+	}
+}
+
+/*
+ * has 2 functions
+ * - create a max Z projection per File
+ * - if there are 2 channels present, creates max projects of the channel composite
+ */
+function processFile(input, file) {
+	if ( endsWith(file, "ch_1.tif.zip") )
+	{
+		imageSetArr = split(input, File.separator);
+		imageSetName = imageSetArr[ lengthOf(imageSetArr)-1 ];
+		imageSetName = replace(imageSetName, "/", "");
+
+		compositeMaxFileName = ""+input+File.separator+imageSetName+"_MAX_Composite.jpg";
+		if ( !File.exists(compositeMaxFileName))
+		{
+			open(input + File.separator + replace(file, "_ch_1", "_ch_0"));
+			open(input + File.separator + file);
+
+			imageTitles = getList("image.titles");
+			
+			run("Merge Channels...", "c4="+imageTitles[1]+" c5="+imageTitles[0]);
+			resetMinAndMax();
+			run("Z Project...", "projection=[Max Intensity]");
+			resetMinAndMax();
+			saveAs("Jpeg", compositeMaxFileName);
+			close();
+			close();
+		}
+		}
+
+	targetFileName = ""+input + File.separator + file+".jpg";
+	if ( File.exists(targetFileName))
+		return;
+	
+	print("Processing: " + input + File.separator + file);	
+	open(input + File.separator + file);
+	run("Z Project...", "projection=[Max Intensity]");
+	saveAs("Jpeg",targetFileName );
+	close();
+	close();
+}

generate_quickview_max_jpg.ijm

-/*
- * Macro template to process multiple images in a folder
- */
-
-#@ File (label = "Input directory", style = "directory") input
-#@ String (label = "File suffix", value = ".tif") suffix
-
-// See also Process_Folder.py for a version of this code
-// in the Python scripting language.
-
-print("\\Clear");
-processFolder(input);
-print("Macro Done");
-return;
-
-// function to scan folders/subfolders/files to find files with correct suffix
-function processFolder(input) {
-	list = getFileList(input);
-	list = Array.sort(list);
-	for (i = 0; i < list.length; i++) {
-		if(File.isDirectory(input + File.separator + list[i]))
-			processFolder(input + File.separator + list[i]);
-		if(endsWith(list[i], suffix))
-			processFile(input,  list[i]);
-	}
-}
-
-function processFile(input, file) {
-	targetFileName = ""+input + File.separator + file+".jpg";
-	if ( File.exists(targetFileName))
-		return;
-	
-	print("Processing: " + input + File.separator + file);
-
-open(input + File.separator + file);
-run("Z Project...", "projection=[Max Intensity]");
-saveAs("Jpeg",targetFileName );
-close();
-close();
-}

stitch_a_day_macos.ijm

@@ -69,7 +69,7 @@ function processFile(input, output, file) {
 	//print(date);
 
 	//create dataset
-run("Define dataset ...", "define_dataset=[Automatic Loader (Bioformats based)] exclude=10 bioformats_series_are?=Tiles bioformats_channels_are?=Channels move_tiles_to_grid_(per_angle)?=[Do not move Tiles to Grid (use Metadata if available)] how_to_load_images=[Load raw data virtually (with caching)] check_stack_sizes " +
+    run("Define dataset ...", "define_dataset=[Automatic Loader (Bioformats based)] exclude=10 bioformats_series_are?=Tiles bioformats_channels_are?=Channels move_tiles_to_grid_(per_angle)?=[Do not move Tiles to Grid (use Metadata if available)] how_to_load_images=[Load raw data virtually (with caching)] check_stack_sizes " +
 	"project_filename="+filename_without_suffix+".xml " +
 	"path=["+input+file+"] "+
 	"dataset_save_path=["+input+"]");
@@ -90,10 +90,11 @@ run("Define dataset ...", "define_dataset=[Automatic Loader (Bioformats based)]
 	File.makeDirectory(output+File.separator+specimen+File.separator+date);
 	File.makeDirectory(output+File.separator+specimen+File.separator+date+File.separator+filename_without_suffix);
 	print("created: "+outputPath);
+	//that might take a long time
 	run("Fuse dataset ...", "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] process_tile=[All tiles] process_timepoint=[All Timepoints] bounding_box=[Currently Selected Views] downsampling=1 pixel_type=[16-bit unsigned integer] interpolation=[Linear Interpolation] image=[Precompute Image] blend preserve_original produce=[Each timepoint & channel] fused_image=[Save as (compressed) TIFF stacks] lossless "+ 
 	"select=["+xmlfile+"] "+
 	"output_file_directory=["+outputPath+"] ");
 
 	donefile = File.open(doneFileName);
-	File.close(donefile)
+	File.close(donefile);
 }

stitch_a_day_windows.ijm

@@ -93,7 +93,7 @@ run("Define dataset ...", "define_dataset=[Automatic Loader (Bioformats based)]
 	"output_file_directory=["+outputPath+"] ");
 
 	donefile = File.open(doneFileName);
-	File.close(donefile)
+	File.close(donefile);
 
 }
 

stitch_a_day_windows_fusion_only1x.ijm

+/*
+ * Author: Stephan Janosch, janosch@mpi-cbg.de, ORCID
+ * 
+ */
+
+#@ File (label = "Input directory", style = "directory") input
+#@ File (label = "Output directory", style = "directory") output
+#@ String (label = "File suffix", value = ".tif") suffix
+#@ String (label = "File stiching indicator", value = "_stitch_") filenameStitchCondition
+
+
+// See also Process_Folder.py for a version of this code
+// in the Python scripting language.
+print("\\Clear");
+processFolder(input);
+print("Macro done");
+return;
+// function to scan folders/subfolders/files to find files with correct suffix
+function processFolder(input) {
+	//skip folder Notes
+	if ( endsWith(input, "Notes/") )
+		return;
+
+	list = getFileList(input);
+	list = Array.sort(list);
+
+	
+	print("Processing Folder: " + input);
+	for (i = 0; i < list.length; i++) {
+		if(File.isDirectory(input + File.separator + list[i]))
+		{
+			
+			processFolder(input + File.separator + list[i]);
+		}
+		if(endsWith(list[i], suffix))
+			processFile(input, output, list[i]);
+	}
+}
+
+function processFile(input, output, file) {
+	//don't process files not intended for stitching
+	if (! matches(file, ".*"+filenameStitchCondition+".*"))
+	{
+		//print("Ignoring: " + input + File.separator + file);
+		return;
+	}
+	//be nice, don't redo Files already stitched
+	print("Processing: " + input + File.separator + file);
+
+	pathElements = split(input,File.separator);
+	date = split(pathElements[1], " ");
+	date=date[0];
+	specimen = pathElements[2];
+	doneFileName=input+File.separator+replace(file, suffix, "")+".macrodone";
+
+	filename_without_suffix = replace(file, suffix, "");
+	filename_without_suffix = replace(filename_without_suffix, filenameStitchCondition, "");
+
+	//print(input);
+	//print(filename_without_suffix);
+	//print(specimen);
+	//print(date);
+
+	//create dataset
+
+	xmlfile = input+filename_without_suffix+".xml";
+
+
+	outputPath = output+File.separator+specimen+File.separator+date+File.separator+filename_without_suffix+File.separator;
+	File.makeDirectory(output+File.separator+specimen);
+	File.makeDirectory(output+File.separator+specimen+File.separator+date);
+	File.makeDirectory(output+File.separator+specimen+File.separator+date+File.separator+filename_without_suffix);
+	print("created: "+outputPath);
+	run("Fuse dataset ...", "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] process_tile=[All tiles] process_timepoint=[All Timepoints] bounding_box=[Currently Selected Views] downsampling=1 pixel_type=[16-bit unsigned integer] interpolation=[Linear Interpolation] image=[Precompute Image] blend preserve_original produce=[Each timepoint & channel] fused_image=[Save as (compressed) TIFF stacks] lossless "+ 
+	"select=["+xmlfile+"] "+
+	"output_file_directory=["+outputPath+"] ");
+
+	if (  !File.exists(doneFileName))
+	{
+	donefile = File.open(doneFileName);
+	File.close(donefile);
+	}
+
+}
+