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ADD2/2: CreateNewDatasetFromImage
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‎src/main/java/cz/it4i/fiji/legacy/CreateNewDatasetFromImage.java‎

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package cz.it4i.fiji.legacy;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.concurrent.ExecutionException;
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import java.util.concurrent.Future;
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import cz.it4i.fiji.legacy.util.Imglib2Types;
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import net.imagej.Dataset;
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import net.imagej.ImgPlus;
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import net.imglib2.type.numeric.RealType;
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import org.scijava.ItemIO;
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import org.scijava.ItemVisibility;
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import org.scijava.command.Command;
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import org.scijava.command.CommandInfo;
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import org.scijava.command.CommandModule;
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import org.scijava.command.CommandService;
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import org.scijava.log.LogLevel;
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import org.scijava.log.LogService;
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import org.scijava.log.Logger;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import cz.it4i.fiji.legacy.util.GuiResolutionLevelParams;
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import cz.it4i.fiji.rest.util.DatasetInfo;
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@Plugin(type = Command.class, headless = true, menuPath = "Plugins>HPC DataStore>Create>Create new dataset from current image")
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public class CreateNewDatasetFromImage implements Command {
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@Parameter(label = "URL of a DatasetsRegisterService:", persistKey = "datasetserverurl")
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public String url = "someHostname:9080";
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@Parameter(label="Dataset label:")
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public String label = "provide some nickname of this dataset";
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@Parameter(label="Voxel type:", visibility = ItemVisibility.MESSAGE, required = false, persist = false)
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String voxelType;
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int fullResSizeX;
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int fullResSizeY;
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int fullResSizeZ;
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void readParams() {
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voxelType = Imglib2Types.getTypeHandler(refDatasetImg.getType()).httpType;
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fullResSizeX = (int)refDatasetImg.dimension(0);
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fullResSizeY = (int)refDatasetImg.dimension(1);
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fullResSizeZ = refDatasetImg.numDimensions() > 2 ? (int)refDatasetImg.dimension(2) : 1;
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final ImgPlus<?> ip = refDatasetImg.getImgPlus();
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res_unit = ip.axis(0).unit();
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res_x = ip.axis(0).calibratedValue(1);
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res_y = ip.axis(1).calibratedValue(1);
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if (refDatasetImg.numDimensions() > 2)
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res_z = ip.axis(2).calibratedValue(1);
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}
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@Parameter(label = "Total number of time points:", min = "1")
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public int timepoints = 1;
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@Parameter(label = "Total number of channels:", min = "1")
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public int channels = 1;
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@Parameter(label = "Total number of view angles:", min = "1")
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public int angles = 1;
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@Parameter(label = "Physical dimension of one voxel in x:", min = "0", initializer = "readParams")
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public double res_x;
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@Parameter(label = "Physical dimension of one voxel in y:", min = "0")
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public double res_y;
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@Parameter(label = "Physical dimension of one voxel in z:", min = "0")
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public double res_z;
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@Parameter(label = "Physical unit of the voxel dimension:", description = "microns")
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public String res_unit;
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@Parameter(label = "Time period between successive time points:", min = "0")
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public double time_res = 1.0;
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@Parameter(label = "Unit of the time period:", description = "seconds")
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public String time_unit = "seconds";
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@Parameter(label = "Resolution among the channels:")
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public double channel_res = 1.0;
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@Parameter(label = "Unit of channels' resolution:", description = "channel")
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public String channel_unit = "channel";
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@Parameter(label = "Resolution among the angles:")
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public double angle_res = 1.0;
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@Parameter(label = "Unit of angles' resolution:", description = "deg")
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public String angle_unit = "deg";
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@Parameter(label = "Number of resolution levels:", min = "1",
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description = "There will always be the full-resolution level [1,1,1] plus additional lower-resolution ones.")
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public int numberOfAllResLevels = 1;
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@Parameter(label = "Compression of the stored data:", choices = { "none", "gzip" })
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public String compression = "gzip";
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@Parameter
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public Dataset refDatasetImg;
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@Parameter
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public CommandService cs;
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@Parameter
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public LogService mainLogger;
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protected Logger myLogger;
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@Parameter(label = "Report corresponding macro command:", required = false)
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public boolean showRunCmd = false;
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@Parameter(type = ItemIO.OUTPUT, label="UUID of the created dataset:")
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public String newDatasetUUID;
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@Parameter(type = ItemIO.OUTPUT, label="Label of the created dataset:")
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public String newDatasetLabel;
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@Override
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public void run() {
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//logging facility
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myLogger = mainLogger.subLogger("HPC CreateDataset", LogLevel.INFO);
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DatasetInfo di = new DatasetInfo();
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di.voxelType = this.voxelType;
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di.dimensions = Arrays.asList(fullResSizeX,fullResSizeY,fullResSizeZ);
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di.timepoints = this.timepoints;
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di.channels = this.channels;
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di.angles = this.angles;
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di.voxelUnit = res_unit;
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di.voxelResolution = Arrays.asList(res_x,res_y,res_z);
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di.timepointResolution = new DatasetInfo.ResolutionWithOwnUnit(time_res, time_unit);
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di.channelResolution = new DatasetInfo.ResolutionWithOwnUnit(channel_res, channel_unit);
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di.angleResolution = new DatasetInfo.ResolutionWithOwnUnit(angle_res, angle_unit);
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di.compression = this.compression.equals("none") ? "raw" : this.compression;
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di.versions = Collections.emptyList();
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di.resolutionLevels = new ArrayList<>(numberOfAllResLevels);
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di.label = label;
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final CommandInfo rldlg_ci = new CommandInfo(GuiResolutionLevelParams.class);
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final Map<String,Object> rldlg_presets = new HashMap<>(4);
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try {
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for (int levelCnt = 1; levelCnt <= numberOfAllResLevels; ++levelCnt) {
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rldlg_presets.put("resLevelNumber", levelCnt);
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if (levelCnt == 1) {
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rldlg_presets.put("down_x", 1);
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rldlg_presets.put("down_y", 1);
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rldlg_presets.put("down_z", 1);
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}
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final Future<CommandModule> rldlg_result = cs.run(rldlg_ci, true, rldlg_presets);
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final GuiResolutionLevelParams rldlg_obj = (GuiResolutionLevelParams)rldlg_result.get().getCommand();
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if (!rldlg_obj.userClickedOK) return; //stops the whole thing!
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di.resolutionLevels.add(new DatasetInfo.ResolutionLevel(
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rldlg_obj.down_x,rldlg_obj.down_y,rldlg_obj.down_z,
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rldlg_obj.block_x,rldlg_obj.block_y,rldlg_obj.block_z ));
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if (levelCnt == 1) {
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rldlg_presets.remove("down_x");
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rldlg_presets.remove("down_y");
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rldlg_presets.remove("down_z");
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}
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}
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//finish it up with the resolutions...
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for (DatasetInfo.ResolutionLevel l : di.resolutionLevels)
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l.setDimensions(di.dimensions);
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myLogger.info("============ collected this params: ===============");
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myLogger.info(di);
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final String json = new ObjectMapper().writeValueAsString(di);
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myLogger.info("CREATED JSON:\n"+json);
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final Future<CommandModule> subcall = cs.run(CreateNewDatasetFromJSON.class, true,
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"url",url, "json",json, "showRunCmd",showRunCmd);
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newDatasetUUID = (String)subcall.get().getOutput("newDatasetUUID");
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newDatasetLabel = di.getLabel();
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} catch (ExecutionException e) {
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e.printStackTrace();
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} catch (InterruptedException e) {
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//dialog interrupted, do nothing special...
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} catch (JsonProcessingException e) {
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myLogger.error("Error converting dataset description into JSON:"+e.getMessage());
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}
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}
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}

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