diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java index 3107de89fdcb7382463b3cc8c35583db7b80f40a..845f51b144947cf3754b2426896f42835f9bfb0d 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java @@ -49,13 +49,13 @@ public final class Channel extends AbstractHashable return label; } - /** Optional. Sets the description of the channel. */ + /** Sets the description of the channel.Optional. */ public void setDescription(String description) { this.description = description; } - /** Optional. Sets the wavelength of the channel. */ + /** Sets the wavelength of the channel.Optional. */ public void setWavelength(Integer wavelength) { this.wavelength = wavelength; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java index f8ee61cee007185049ec374f33583a24f41599d3..bbcf2d0ffc0db31775ce48c116bf7557deef0812 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageMetadata.java @@ -3,8 +3,8 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1; import org.apache.commons.lang.StringUtils; /** - * Store well, channel and tile number to which an image belongs. - * Optionally stores timepoint/depth-scan/image series number. + * Store well, channel and tile number to which an image belongs. Optionally stores + * timepoint/depth-scan/image series number. * * @author Tomasz Pylak */ @@ -49,26 +49,26 @@ public class ImageMetadata return well; } - /** Sets well code, e.g. A1 */ + /** Sets well code (example: "A1") */ public void setWell(String well) { this.well = well; } - /** Optional. Sets the timepoint of the image. */ + /** Sets the timepoint of the image. Optional. */ public void setTimepoint(Float value) { this.timepointOrNull = value; } - /** Optional. Sets the depth at which the image has been scanned. */ + /** Sets the depth at which the image has been scanned. Optional. */ public void setDepth(Float value) { this.depthOrNull = value; } /** - * Optional. Sets the integer series number of the image. Used to order images when there are no + * Sets the integer series number of the image. Optional. Used to order images when there are no * time or depth dimentions but there is a series of images for one well, channel and tile. Can * be also used together with time and depth dimention. */ diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java index e37e5fcb79dbb4ffa95b0c4a23975dd851bb40fc..badc03e57d896508f1f11eceba8ce39f4761a1f2 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java @@ -23,72 +23,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst /** * Allows to configure extraction of images for a plate or microscopy sample. - * <p> - * It can be used to configure the jython dropbox for image datasets easily: - * - * <pre> - * ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import * - * - * class MyImageDataSetConfig(SimpleImageDataConfig): - * """ - * Extracts tile number, channel code and well code for a given relative path to an image. - * Will be called for each file found in the incoming directory which has the allowed image extension. - * - * Returns: - * ImageMetadata - * """ - * def extractImageMetadata(self, imagePath): - * image = ImageMetadata() - * image.well = ... extract from imagePath ... - * image.channelCode = ... extract from imagePath ... - * image.tileNumber = ... extract from imagePath ... - * return image - * - * imageDataset = ImageDataSetFlexible() - * imageDataset.setRawImageDatasetType() - * space = "TEST" - * plate = incoming.getName() - * imageDataset.setPlate(space, plate) - * factory.registerImageDataset(imageDataset, incoming, service) - * </pre> - * - * Additionally one can define the tiles layout in the well by defining 'getTileGeometry' and - * 'getTileCoordinates' methods, e.g.: - * - * <pre> - * from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry - * - * ... - * - * class MyImageDataSetConfig(SimpleImageDataConfig): - * ... - * - * """ - * Calculates the width and height of the matrix of tiles (a.k.a. fields or sides) in the well. - * - * Parameter imageMetadataList: a list of metadata for each encountered image - * Parameter maxTileNumber: the biggest tile number among all encountered images - * Returns: - * Geometry - * """ - * def getTileGeometry(self, imageTokens, maxTileNumber): - * return Geometry.createFromRowColDimensions(maxTileNumber / 3, 3); - * - * """ - * For a given tile number and tiles geometry returns (x,y) which describes where the tile is - * located on the well. - * - * Parameter tileNumber: number of the tile - * Parameter tileGeometry: the geometry of the well matrix - * Returns: - * Location - * """ - * def getTileCoordinates(self, tileNumber, tileGeometry): - * columns = tileGeometry.getWidth() - * row = ((tileNumber - 1) / columns) + 1 - * col = ((tileNumber - 1) % columns) + 1 - * return Location(row, col) - * </pre> * * @author Tomasz Pylak */