inital checking

stitch_a_day_macos.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
+	doneFileName=input+File.separator+replace(file, suffix, "")+".macrodone";
+	if ( File.exists(doneFileName) )
+	{
+		print("Skipping: "+doneFileName);
+		return;
+	}
+
+	print("Processing: " + input + File.separator + file);
+
+	pathElements = split(input,File.separator);
+	date = split(pathElements[2], " ");
+	date=date[0];
+	specimen = pathElements[3];
+
+	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
+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+"]");
+
+	xmlfile = input+filename_without_suffix+".xml";
+
+	run("Calculate pairwise shifts ...", "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] process_tile=[All tiles] process_timepoint=[All Timepoints] "+
+	"select=["+xmlfile+"] ");
+	
+	run("Filter pairwise shifts ...", "filter_by_link_quality min_r=0.7 max_r=1 max_shift_in_x=0 max_shift_in_y=0 max_shift_in_z=0 max_displacement=0 "+ 
+	"select=["+xmlfile+"] ");
+
+	run("Optimize globally and apply shifts ...", "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] process_tile=[All tiles] process_timepoint=[All Timepoints] relative=2.500 absolute=3.500 global_optimization_strategy=[Two-Round using Metadata to align unconnected Tiles] fix_group_0-0 " +
+	"select=["+xmlfile+"]" );
+
+	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+"] ");
+
+	donefile = File.open(doneFileName);
+	File.close(donefile)
+}

stitch_a_day_windows.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
+	doneFileName=input+File.separator+replace(file, suffix, "")+".macrodone";
+	if ( File.exists(doneFileName) )
+	{
+		print("Skipping: "+doneFileName);
+		return;
+	}
+	print("Processing: " + input + File.separator + file);
+
+	pathElements = split(input,File.separator);
+	date = split(pathElements[1], " ");
+	date=date[0];
+	specimen = pathElements[2];
+
+	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
+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+"]");
+
+	xmlfile = input+filename_without_suffix+".xml";
+
+	run("Calculate pairwise shifts ...", "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] process_tile=[All tiles] process_timepoint=[All Timepoints] "+
+	"select=["+xmlfile+"] ");
+	
+	run("Filter pairwise shifts ...", "filter_by_link_quality min_r=0.7 max_r=1 max_shift_in_x=0 max_shift_in_y=0 max_shift_in_z=0 max_displacement=0 "+ 
+	"select=["+xmlfile+"] ");
+
+	run("Optimize globally and apply shifts ...", "process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations] process_tile=[All tiles] process_timepoint=[All Timepoints] relative=2.500 absolute=3.500 global_optimization_strategy=[Two-Round using Metadata to align unconnected Tiles] fix_group_0-0 " +
+	"select=["+xmlfile+"]" );
+
+	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=2 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)
+
+}
+