setup directories in a list file (7b84dba6) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java

+115 −48

Original line number	Original line	Diff line number	Diff line
	@@ -34,6 +34,7 @@ import java.nio.file.Path;
	import java.nio.file.Paths;		import java.nio.file.Paths;
	import java.util.ArrayList;		import java.util.ArrayList;
	import java.util.Collections;		import java.util.Collections;
			import java.util.HashMap;
	import java.util.HashSet;		import java.util.HashSet;
	import java.util.List;		import java.util.List;
	import java.util.Properties;		import java.util.Properties;
	@@ -53,6 +54,8 @@ import ij.gui.GenericDialog;

	public class EyesisCorrectionParameters {		public class EyesisCorrectionParameters {
	public static class CorrectionParameters{		public static class CorrectionParameters{
			public static final String [] KEY_DIRS= {"rootDirectory",
			"sourceDirectory","linkedModels","videoDirectory","x3dDirectory","resultsDirectory"};
	public static final String AUX_PREFIX = "AUX-";		public static final String AUX_PREFIX = "AUX-";
	public boolean swapSubchannels01= true; // false; // (false: 0-1-2, true - 1-0-2)		public boolean swapSubchannels01= true; // false; // (false: 0-1-2, true - 1-0-2)
	public boolean split= true;		public boolean split= true;
	@@ -855,40 +858,40 @@ public class EyesisCorrectionParameters {
	gd.addCheckbox ("Save current settings with results", this.saveSettings);		gd.addCheckbox ("Save current settings with results", this.saveSettings);

	gd.addTab("Directories","Direcories paths");		gd.addTab("Directories","Direcories paths");
	gd.addStringField ("Source files directory", this.sourceDirectory, 60);		gd.addStringField ("Source files directory", this.sourceDirectory, 80);
	gd.addCheckbox ("Select source directory", false);		gd.addCheckbox ("Select source directory", false);
	gd.addCheckbox ("Use individual subdirectory for image set", this.use_set_dirs);		gd.addCheckbox ("Use individual subdirectory for image set", this.use_set_dirs);

	gd.addStringField ("Source sequences list file", this.sourceSequencesList, 60);		gd.addStringField ("Source sequences list file", this.sourceSequencesList, 80);
	gd.addCheckbox ("Select source sequences file", false);		gd.addCheckbox ("Select source sequences file", false);
	gd.addCheckbox ("Use source list to iterate multiple sequences", this.useSourceList);		gd.addCheckbox ("Use source list to iterate multiple sequences", this.useSourceList);

	gd.addStringField ("Sensor calibration directory", this.sensorDirectory, 60);		gd.addStringField ("Sensor calibration directory", this.sensorDirectory, 80);
	gd.addCheckbox ("Select sensor calibration directory", false);		gd.addCheckbox ("Select sensor calibration directory", false);

	gd.addStringField ("Aberration kernels (sharp) directory", this.sharpKernelDirectory, 60);		gd.addStringField ("Aberration kernels (sharp) directory", this.sharpKernelDirectory, 80);
	gd.addCheckbox ("Select aberration kernels (sharp) directory", false);		gd.addCheckbox ("Select aberration kernels (sharp) directory", false);
	gd.addStringField ("Aberration kernels (smooth) directory", this.smoothKernelDirectory, 60);		gd.addStringField ("Aberration kernels (smooth) directory", this.smoothKernelDirectory, 80);
	gd.addCheckbox ("Select aberration kernels (smooth) directory", false);		gd.addCheckbox ("Select aberration kernels (smooth) directory", false);

	gd.addStringField ("Aberration kernels for DCT directory", this.dctKernelDirectory, 60);		gd.addStringField ("Aberration kernels for DCT directory", this.dctKernelDirectory, 80);
	gd.addCheckbox ("Select aberration kernels for DCT directory", false);		gd.addCheckbox ("Select aberration kernels for DCT directory", false);

	gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 60);		gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 80);
	gd.addCheckbox ("Select aberration kernels for CLT directory", false);		gd.addCheckbox ("Select aberration kernels for CLT directory", false);

	gd.addStringField ("x3d model version", this.x3dModelVersion, 20); // 10a		gd.addStringField ("x3d model version", this.x3dModelVersion, 20); // 10a
	gd.addStringField ("JP4 source image copy model subdirectory", this.jp4SubDir, 20); // 10b		gd.addStringField ("JP4 source image copy model subdirectory", this.jp4SubDir, 20); // 10b

	gd.addStringField ("Linked reference models", this.linkedModels, 60,		gd.addStringField ("Linked reference models", this.linkedModels, 80,
	"Directory where links to reference models directories will be created.");		"Directory where links to reference models directories will be created.");
	gd.addCheckbox ("Select linked reference models directory", false);		gd.addCheckbox ("Select linked reference models directory", false);

	gd.addStringField ("Video directory", this.videoDirectory, 60,		gd.addStringField ("Video directory", this.videoDirectory, 80,
	"Directory to store combined video files.");		"Directory to store combined video files.");
	gd.addCheckbox ("Select video directory", false);		gd.addCheckbox ("Select video directory", false);

	gd.addStringField ("x3d output directory", this.x3dDirectory, 60);		gd.addStringField ("x3d output directory", this.x3dDirectory, 80);
	gd.addCheckbox ("Select x3d output directory", false);		gd.addCheckbox ("Select x3d output directory", false);

	gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs);		gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs);
	@@ -897,18 +900,18 @@ public class EyesisCorrectionParameters {
	"When using timestamp as a subdirectory, add this prefix");		"When using timestamp as a subdirectory, add this prefix");
	gd.addStringField ("x3d subdirectory suffix", this.x3dSubdirSuffix, 10,		gd.addStringField ("x3d subdirectory suffix", this.x3dSubdirSuffix, 10,
	"When using timestamp as a subdirectory, add this suffix");		"When using timestamp as a subdirectory, add this suffix");
	gd.addStringField ("ML output directory", this.mlDirectory, 60,		gd.addStringField ("ML output directory", this.mlDirectory, 80,
	"Non-empty directory with no \"/\" separator makes it a subdirectory of the model version directory");		"Non-empty directory with no \"/\" separator makes it a subdirectory of the model version directory");
	gd.addCheckbox ("Select ML output directory", false,"Erase text field or use \"/\" in it to enable absolute directory path selection");		gd.addCheckbox ("Select ML output directory", false,"Erase text field or use \"/\" in it to enable absolute directory path selection");

	gd.addStringField("Equirectangular maps directory (may be empty)", this.equirectangularDirectory, 60);		gd.addStringField("Equirectangular maps directory (may be empty)", this.equirectangularDirectory, 80);
	gd.addCheckbox("Select equirectangular maps directory", false);		gd.addCheckbox("Select equirectangular maps directory", false);
	gd.addStringField("Results directory", this.resultsDirectory, 60);		gd.addStringField("Results directory", this.resultsDirectory, 80);
	gd.addCheckbox("Select results directory", false);		gd.addCheckbox("Select results directory", false);

	gd.addTab("Prefix/suffix","Prefixes and suffixes for various file types");		gd.addTab("Prefix/suffix","Prefixes and suffixes for various file types");
	gd.addStringField("Source files prefix", this.sourcePrefix, 60);		gd.addStringField("Source files prefix", this.sourcePrefix, 80);
	gd.addStringField("Source files suffix", this.sourceSuffix, 60);		gd.addStringField("Source files suffix", this.sourceSuffix, 80);
	gd.addNumericField("First subcamera (in the source filenames)", this.firstSubCamera, 0);		gd.addNumericField("First subcamera (in the source filenames)", this.firstSubCamera, 0);
	gd.addNumericField("First subcamera (in config (clt, sensor) directories)", this.firstSubCameraConfig, 0);		gd.addNumericField("First subcamera (in config (clt, sensor) directories)", this.firstSubCameraConfig, 0);
	gd.addNumericField("Number of subcameras in this camera", this.numSubCameras, 0);		gd.addNumericField("Number of subcameras in this camera", this.numSubCameras, 0);
	@@ -1071,58 +1074,58 @@ public class EyesisCorrectionParameters {

	gd.addTab ("File paths", "Select files and directories paths (common to main and optional auxiliary)");		gd.addTab ("File paths", "Select files and directories paths (common to main and optional auxiliary)");
	gd.addMessage ("============ Common to the main and optional auxiliary camera============");		gd.addMessage ("============ Common to the main and optional auxiliary camera============");
	gd.addStringField ("GPU tile_processor_gpu project absolute path", this.tile_processor_gpu, 60,		gd.addStringField ("GPU tile_processor_gpu project absolute path", this.tile_processor_gpu, 80,
	"Keep empty to use default GPU kernels");		"Keep empty to use default GPU kernels");
	gd.addCheckbox ("Select GPU directory", false);		gd.addCheckbox ("Select GPU directory", false);

	gd.addCheckbox ("Save current settings with results", this.saveSettings); // 1		gd.addCheckbox ("Save current settings with results", this.saveSettings); // 1
	gd.addStringField ("Source files directory", this.sourceDirectory, 60); // 2		gd.addStringField ("Source files directory", this.sourceDirectory, 80); // 2
	gd.addCheckbox ("Select source directory", false); // 3		gd.addCheckbox ("Select source directory", false); // 3
	gd.addCheckbox ("Use individual subdirectory for each image set (timestamp as name)", this.use_set_dirs); //10		gd.addCheckbox ("Use individual subdirectory for each image set (timestamp as name)", this.use_set_dirs); //10

	gd.addStringField ("Source sequences list file", this.sourceSequencesList, 60); // 10x		gd.addStringField ("Source sequences list file", this.sourceSequencesList, 80); // 10x
	gd.addCheckbox ("Select source sequences file", false); // 10y		gd.addCheckbox ("Select source sequences file", false); // 10y
	gd.addCheckbox ("Use source list to iterate multiple sequences", this.useSourceList); // 10z		gd.addCheckbox ("Use source list to iterate multiple sequences", this.useSourceList); // 10z

	gd.addStringField ("x3d model version", this.x3dModelVersion, 60); // 10a		gd.addStringField ("x3d model version", this.x3dModelVersion, 80); // 10a
	gd.addStringField ("jp4 source copy subdirectory", this.jp4SubDir, 60); // 10b		gd.addStringField ("jp4 source copy subdirectory", this.jp4SubDir, 80); // 10b

	gd.addStringField ("Linked reference models", this.linkedModels, 60,		gd.addStringField ("Linked reference models", this.linkedModels, 80,
	"Directory where links to reference models directories will be created.");		"Directory where links to reference models directories will be created.");
	gd.addCheckbox ("Select linked reference models directory", false);		gd.addCheckbox ("Select linked reference models directory", false);

	gd.addStringField ("Video directory", this.videoDirectory, 60,		gd.addStringField ("Video directory", this.videoDirectory, 80,
	"Directory to store combined video files.");		"Directory to store combined video files.");
	gd.addCheckbox ("Select video directory", false);		gd.addCheckbox ("Select video directory", false);

	gd.addStringField ("x3d output directory", this.x3dDirectory, 60); // 8		gd.addStringField ("x3d output directory", this.x3dDirectory, 80); // 8
	gd.addCheckbox ("Select x3d output (top model) directory", false); // 9		gd.addCheckbox ("Select x3d output (top model) directory", false); // 9

	gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs); //10		gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs); //10

	// gd.addStringField ("Source files prefix", this.sourcePrefix, 60); // 13		// gd.addStringField ("Source files prefix", this.sourcePrefix, 80); // 13
	// gd.addStringField ("Source files suffix", this.sourceSuffix, 60); // 14		// gd.addStringField ("Source files suffix", this.sourceSuffix, 80); // 14

	gd.addStringField ("x3d subdirectory prefix", this.x3dSubdirPrefix, 10, // 14a		gd.addStringField ("x3d subdirectory prefix", this.x3dSubdirPrefix, 10, // 14a
	"When using timestamp as a subdirectory, add this prefix");		"When using timestamp as a subdirectory, add this prefix");

	gd.addStringField ("ML output directory", this.mlDirectory, 60,		gd.addStringField ("ML output directory", this.mlDirectory, 80,
	"Non-empty directory with no \"/\" separator makes it a subdirectory of the model version directory");		"Non-empty directory with no \"/\" separator makes it a subdirectory of the model version directory");
	gd.addCheckbox ("Select ML output directory", false,"Erase text field or use \"/\" in it to enable absolute directory path selection");		gd.addCheckbox ("Select ML output directory", false,"Erase text field or use \"/\" in it to enable absolute directory path selection");

	gd.addMessage ("============ Main camera============");		gd.addMessage ("============ Main camera============");

	gd.addStringField ("Sensor calibration directory", this.sensorDirectory, 60); // 4		gd.addStringField ("Sensor calibration directory", this.sensorDirectory, 80); // 4
	gd.addCheckbox ("Select sensor calibration directory", false); // 5		gd.addCheckbox ("Select sensor calibration directory", false); // 5
	gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 60); // 6		gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 80); // 6
	gd.addCheckbox ("Select aberration kernels for CLT directory", false); // 7		gd.addCheckbox ("Select aberration kernels for CLT directory", false); // 7
	gd.addStringField ("Results directory", this.resultsDirectory, 60); // 11		gd.addStringField ("Results directory", this.resultsDirectory, 80); // 11
	gd.addCheckbox ("Select results directory", false); // 12		gd.addCheckbox ("Select results directory", false); // 12
	gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0); // 15		gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0); // 15
	gd.addNumericField("First subcamera (in config (clt, sensor) directories)", this.firstSubCameraConfig, 0);		gd.addNumericField("First subcamera (in config (clt, sensor) directories)", this.firstSubCameraConfig, 0);
	gd.addNumericField("Number of subcameras in this camera ", this.numSubCameras, 0); // 16		gd.addNumericField("Number of subcameras in this camera ", this.numSubCameras, 0); // 16
	gd.addStringField ("Source files prefix", this.sourcePrefix, 60); // 13		gd.addStringField ("Source files prefix", this.sourcePrefix, 80); // 13
	gd.addStringField ("Source files suffix", this.sourceSuffix, 60); // 14		gd.addStringField ("Source files suffix", this.sourceSuffix, 80); // 14
	gd.addStringField ("Sensor files prefix", this.sensorPrefix, 40); // 17		gd.addStringField ("Sensor files prefix", this.sensorPrefix, 40); // 17
	gd.addStringField ("Sensor files suffix", this.sensorSuffix, 40); // 18		gd.addStringField ("Sensor files suffix", this.sensorSuffix, 40); // 18

	@@ -1132,17 +1135,17 @@ public class EyesisCorrectionParameters {
	"When using timestamp as a subdirectory, add this suffix");		"When using timestamp as a subdirectory, add this suffix");

	gd.addMessage ("============ Auxiliary camera============");		gd.addMessage ("============ Auxiliary camera============");
	gd.addStringField ("Aux sensor calibration directory", this.aux_camera.sensorDirectory, 60); // 4b		gd.addStringField ("Aux sensor calibration directory", this.aux_camera.sensorDirectory, 80); // 4b
	gd.addCheckbox ("Select aux sensor calibration directory", false); // 5b		gd.addCheckbox ("Select aux sensor calibration directory", false); // 5b
	gd.addStringField ("Aberration kernels for aux CLT directory", this.aux_camera.cltKernelDirectory, 60); // 6b		gd.addStringField ("Aberration kernels for aux CLT directory", this.aux_camera.cltKernelDirectory, 80); // 6b
	gd.addCheckbox ("Select aberration kernels for aux CLT directory", false); // 7b		gd.addCheckbox ("Select aberration kernels for aux CLT directory", false); // 7b
	gd.addStringField ("Aux results directory", this.aux_camera.resultsDirectory, 60); // 11b		gd.addStringField ("Aux results directory", this.aux_camera.resultsDirectory, 80); // 11b
	gd.addCheckbox ("Select aux results directory", false); // 12b		gd.addCheckbox ("Select aux results directory", false); // 12b
	gd.addNumericField("First aux subcamera (in the source filename)", this.aux_camera.firstSubCamera, 0); // 15b		gd.addNumericField("First aux subcamera (in the source filename)", this.aux_camera.firstSubCamera, 0); // 15b
	gd.addNumericField("First aux subcamera (in config (clt, sensor) directories)",this.aux_camera.firstSubCameraConfig, 0);		gd.addNumericField("First aux subcamera (in config (clt, sensor) directories)",this.aux_camera.firstSubCameraConfig, 0);
	gd.addNumericField("Number of aux subcameras in this camera ", this.aux_camera.numSubCameras, 0); // 16b		gd.addNumericField("Number of aux subcameras in this camera ", this.aux_camera.numSubCameras, 0); // 16b
	gd.addStringField ("Aux Source files prefix", this.aux_camera.sourcePrefix, 60); // 13		gd.addStringField ("Aux Source files prefix", this.aux_camera.sourcePrefix, 80); // 13
	gd.addStringField ("Aux Source files suffix", this.aux_camera.sourceSuffix, 60); // 14		gd.addStringField ("Aux Source files suffix", this.aux_camera.sourceSuffix, 80); // 14
	gd.addStringField ("Aux sensor files prefix", this.aux_camera.sensorPrefix, 40); // 17b		gd.addStringField ("Aux sensor files prefix", this.aux_camera.sensorPrefix, 40); // 17b
	gd.addStringField ("Aux sensor files suffix", this.aux_camera.sensorSuffix, 40); // 18b		gd.addStringField ("Aux sensor files suffix", this.aux_camera.sensorSuffix, 40); // 18b
	gd.addStringField ("Aux CLT kernel files prefix", this.aux_camera.cltKernelPrefix, 40); // 19b		gd.addStringField ("Aux CLT kernel files prefix", this.aux_camera.cltKernelPrefix, 40); // 19b
	@@ -1541,12 +1544,83 @@ public class EyesisCorrectionParameters {
	e.printStackTrace();		e.printStackTrace();
	return null;		return null;
	}		}
	Path basedir = seq_path.getParent();		Path base_path = seq_path.getParent();
			// first - scan all file and set sourceDirectory, x3dDirectory, linkedModels,videoDirectory,resultsDirectory
			// String [] dir_paths = new String[KEY_DIRS.length];
			HashMap<String,String> dir_map = new HashMap<String,String>();
			for (String line:lines){
			String[] tokens = line.split("#")[0].trim().split("[\\s,;=]+");
			if ((tokens.length > 2) && (tokens[0].toUpperCase().equals("SET"))) {
			parse_set:
			{
			for (String dir_name:KEY_DIRS) if (dir_name.equals(tokens[1])) {
			dir_map.put(dir_name,tokens[2]);
			System.out.println("Parsed SET: "+tokens[1]+" in line: "+line);
			break parse_set;
			}
			System.out.println("*********** Unknown SET: "+tokens[1]+" in line: "+line);
			}
			}
			}
			if (dir_map.containsKey("rootDirectory")) {
			base_path=base_path.resolve(Paths.get(dir_map.get("rootDirectory")));
			File base_dir = new File(base_path.toString());
			if (!base_dir.exists()) {
			base_dir.mkdirs();
			}
			}
			// set sourceDirectory:
			if (dir_map.containsKey("sourceDirectory")) {
			this.sourceDirectory=(base_path.resolve(Paths.get(dir_map.get("sourceDirectory")))).toString();
			}
			if ((this.sourceDirectory == null) \|\|
			(this.sourceDirectory.trim().length() == 0) \|\|
			!(new File(this.sourceDirectory).exists())) {
			System.out.println("Problem with source scenes directory ("+this.sourceDirectory+", using current: "+seq_path.getParent());
			this.sourceDirectory = seq_path.getParent().toString();
			}
			Path source_path = Paths.get(this.sourceDirectory);
			File source_dir = new File(source_path.toString());
			if (!source_dir.exists()) {
			source_dir.mkdirs();
			}
			// Set other directories (possibly relative to base_path)
			for (int i = 2; i < KEY_DIRS.length; i++) { // skip "rootDirectory" and "sourceDirectory"
			if (dir_map.containsKey(KEY_DIRS[i])) {
			Path dir_path=base_path.resolve(Paths.get(dir_map.get(KEY_DIRS[i])));
			File dir_file = new File(dir_path.toString());
			if (!dir_file.exists()) {
			dir_file.mkdirs();
			}
			switch (i) {
			case 2:
			this.linkedModels = dir_path.toString();
			System.out.println("this.linkedModels="+this.linkedModels);
			break;
			case 3:
			this.videoDirectory = dir_path.toString();
			System.out.println("this.videoDirectory="+this.videoDirectory);
			break;
			case 4:
			this.x3dDirectory = dir_path.toString();
			System.out.println("this.x3dDirectory="+this.x3dDirectory);
			break;
			case 5:
			this.resultsDirectory = dir_path.toString();
			System.out.println("this.resultsDirectory="+this.resultsDirectory);
			break;
			}
			}
			}
			// process source sequence directories
	ArrayList<PathFirstLast> path_list= new ArrayList<PathFirstLast>();		ArrayList<PathFirstLast> path_list= new ArrayList<PathFirstLast>();
	for (String line:lines){		for (String line:lines){
	String[] tokens = line.split("#")[0].trim().split("[\\s,;]+");		String[] tokens = line.split("#")[0].trim().split("[\\s,;=]+");
	if ((tokens.length > 0) && (tokens[0].length() > 0)) {		if ((tokens.length > 0) &&
	Path dir_path = basedir.resolve(Paths.get(tokens[0]));		(tokens[0].length() > 0) &&
			(!tokens[0].toUpperCase().equals("SET"))
			) {
			Path dir_path = source_path.resolve(Paths.get(tokens[0]));
	path_list.add(new PathFirstLast(		path_list.add(new PathFirstLast(
	dir_path.toString(),		dir_path.toString(),
	((tokens.length > 1)? Integer.parseInt(tokens[1]):0),		((tokens.length > 1)? Integer.parseInt(tokens[1]):0),
	@@ -1555,14 +1629,7 @@ public class EyesisCorrectionParameters {
	}		}
	return path_list.toArray(new PathFirstLast[0]);		return path_list.toArray(new PathFirstLast[0]);
	}		}
	//Path newPath = path.resolve(childPath);
	/*
	public static File [] getSeqScenes(String seq_path) {
	File seq_file = new File(seq_path);
	File [] scene_files =seq_file.listFiles();
	return scene_files; // may contain non-directories, will be filtered by filterScenes
	}
	*/

	public boolean selectSourceSets(int debugLevel) {		public boolean selectSourceSets(int debugLevel) {
	// PathFirstLast [] pfl=getSourceSets(this.sourceSequencesList);		// PathFirstLast [] pfl=getSourceSets(this.sourceSequencesList);