From 05c6fbb0e848a5860097afc731e15a55eaa1ec4b Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 16 Feb 2011 12:32:03 +0000
Subject: [PATCH] LMS-1992 jython dropbox: doc
SVN: 20012
---
.../openbis/dss/etl/dto/api/v1/Channel.java | 4 +-
.../dss/etl/dto/api/v1/ImageMetadata.java | 12 ++--
.../etl/dto/api/v1/SimpleImageDataConfig.java | 66 -------------------
3 files changed, 8 insertions(+), 74 deletions(-)
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 3107de89fdc..845f51b1449 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 f8ee61cee00..bbcf2d0ffc0 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 e37e5fcb79d..badc03e57d8 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
*/
--
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