uk.ac.sussex.gdsc.smlm.data.config.ResultsProtosHelper Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of gdsc-smlm Show documentation
Genome Damage and Stability Centre SMLM Package Software for single molecule localisation microscopy (SMLM)
The newest version!
/*-
 * #%L
 * Genome Damage and Stability Centre SMLM Package
 *
 * Software for single molecule localisation microscopy (SMLM)
 * %%
 * Copyright (C) 2011 - 2023 Alex Herbert
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public
 * License along with this program.  If not, see
 * .
 * #L%
 */

package uk.ac.sussex.gdsc.smlm.data.config;

import uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsFileFormat;
import uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsImageSizeMode;
import uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsImageType;
import uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsSettings;
import uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsTableFormat;

/**
 * Contains helper functions for the ResultsProtos class.
 */
public final class ResultsProtosHelper {
  /** The default ResultsSettings. */
  public static class DefaultResultsSettings {
    /** Default settings instance. */
    public static final ResultsSettings INSTANCE;

    static {
      final ResultsSettings.Builder builder = ResultsSettings.newBuilder();
      // @formatter:off
      builder.getResultsImageSettingsBuilder()
        .setWeighted(true)
        .setEqualised(true)
        .setAveragePrecision(30)
        .setImageSizeMode(ResultsImageSizeMode.SCALED)
        .setScale(1)
        .setImageSize(2048)
        .setPixelSize(10)
        .setLutName("Fire");
      // @formatter:on
      builder.getResultsTableSettingsBuilder().setRoundingPrecision(4);
      builder.getResultsInMemorySettingsBuilder().setInMemory(true);
      INSTANCE = builder.build();
    }
  }

  /** No public constructor. */
  private ResultsProtosHelper() {}

  /**
   * Gets the name.
   *
   * @param value the results file format
   * @return the name
   */
  public static String getName(ResultsFileFormat value) {
    switch (value) {
      case BINARY:
        return "Binary";
      case FILE_NONE:
        return "None";
      case MALK:
        return "MALK (Molecular Accuracy Localisation Keep)";
      case TEXT:
        return "Text";
      case TSF:
        return "TSF (Tagged Spot File)";
      case UNRECOGNIZED:
        return ProtosHelperUtils.UNKNOWN;
      default:
        throw new IllegalArgumentException(ProtosHelperUtils.unknownNameMessage(value));
    }
  }

  /**
   * Gets the name.
   *
   * @param value the results image
   * @return the name
   */
  public static String getName(ResultsImageType value) {
    switch (value) {
      case DRAW_FITTED_PSF:
        return "Fitted PSF";
      case DRAW_FIT_ERROR:
        return "Fit Error";
      case DRAW_FRAME_NUMBER:
        return "Frame number";
      case DRAW_INTENSITY:
        return "Intensity";
      case DRAW_INTENSITY_AVERAGE_PRECISION:
        return "Intensity (width=av.precision)";
      case DRAW_INTENSITY_PRECISION:
        return "Intensity (width=precision)";
      case DRAW_LOCALISATIONS:
        return "Localisations";
      case DRAW_LOCALISATIONS_AVERAGE_PRECISION:
        return "Localisations (width=av.precision)";
      case DRAW_LOCALISATIONS_PRECISION:
        return "Localisations (width=precision)";
      case DRAW_NONE:
        return "None";
      case DRAW_Z_POSITION:
        return "Z position";
      case DRAW_ID:
        return "ID";
      case UNRECOGNIZED:
        return ProtosHelperUtils.UNKNOWN;
      default:
        throw new IllegalArgumentException(ProtosHelperUtils.unknownNameMessage(value));
    }
  }

  /**
   * Gets the name.
   *
   * @param value the results image
   * @return the name
   */
  public static String getName(ResultsImageSizeMode value) {
    switch (value) {
      case SCALED:
        return "Scaled";
      case IMAGE_SIZE:
        return "Image size";
      case PIXEL_SIZE:
        return "Pixel size";
      case UNRECOGNIZED:
        return ProtosHelperUtils.UNKNOWN;
      default:
        throw new IllegalArgumentException(ProtosHelperUtils.unknownNameMessage(value));
    }
  }

  /**
   * Gets the name.
   *
   * @param value the results table format
   * @return the name
   */
  public static String getName(ResultsTableFormat value) {
    switch (value) {
      case IMAGEJ:
        return "ImageJ";
      case INTERACTIVE:
        return "Interactive";
      case TABLE_NONE:
        return "None";
      case UNRECOGNIZED:
        return ProtosHelperUtils.UNKNOWN;
      default:
        throw new IllegalArgumentException(ProtosHelperUtils.unknownNameMessage(value));
    }
  }

  /**
   * Gets the extension.
   *
   * @param value the results file format
   * @return the extension
   */
  public static String getExtension(ResultsFileFormat value) {
    switch (value) {
      case BINARY:
        return "bin";
      case FILE_NONE:
        return "";
      case MALK:
        return "txt";
      case TEXT:
        return "xls";
      case TSF:
        return "tsf";
      case UNRECOGNIZED:
      default:
        return "";
    }
  }

  /**
   * Checks if the format is a GDSC file format.
   *
   * @param value the results file format
   * @return true, if a GDSC file format
   */
  public static boolean isGdsc(ResultsFileFormat value) {
    switch (value) {
      case BINARY:
      case TEXT:
        return true;
      default:
        return false;
    }
  }
}