From e0bd902121f74aeaf6f217be3cd0cb727ac8896f Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 1 Mar 2011 09:21:31 +0000
Subject: [PATCH] minor: example dropbox for importing hcs images and creating
sample and experiment on the fly
SVN: 20161
---
.../data-set-handler.py | 119 ++++++++++++++++++
.../jython-flexible-images/example-images.zip | Bin 0 -> 10429 bytes
2 files changed, 119 insertions(+)
create mode 100755 screening/etc/example-dropbox-configuration/jython-flexible-images/data-set-handler.py
create mode 100644 screening/etc/example-dropbox-configuration/jython-flexible-images/example-images.zip
diff --git a/screening/etc/example-dropbox-configuration/jython-flexible-images/data-set-handler.py b/screening/etc/example-dropbox-configuration/jython-flexible-images/data-set-handler.py
new file mode 100755
index 00000000000..dcd2d013cfb
--- /dev/null
+++ b/screening/etc/example-dropbox-configuration/jython-flexible-images/data-set-handler.py
@@ -0,0 +1,119 @@
+#! /usr/bin/env python
+# This is an example Jython dropbox for importing HCS image datasets
+
+import os
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import *
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+
+
+class ImageDataSetFlexible(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.
+
+ Example file name: bDZ01-1A_wD17_s3_z123_t321_cGFP
+ Returns:
+ ImageMetadata
+ """
+ def extractImageMetadata(self, imagePath):
+ image_tokens = ImageMetadata()
+
+ basename = os.path.splitext(imagePath)[0]
+ #
+ token_dict = {}
+ for token in basename.split("_"):
+ token_dict[token[:1]] = token[1:]
+
+ image_tokens.well = token_dict["w"]
+ fieldText = token_dict["s"]
+ try:
+ image_tokens.tileNumber = int(fieldText)
+ except ValueError:
+ raise Exception("Cannot parse field number from '" + fieldText + "' in '" + basename + "' file name.")
+
+ image_tokens.channelCode = token_dict["c"]
+ return image_tokens
+
+ """
+ Overrides the default implementation which returns (1, maxTileNumber) geometry.
+
+ 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);
+
+ """
+ Overrides the default implementation which does the same thing (to demonstrate how this can be done).
+
+ 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)
+
+""" sample type code of the plate, needed if a new sample is registered automatically """
+PLATE_TYPE_CODE = "PLATE"
+SIRNA_EXP_TYPE = "SIRNA_HCS"
+DEFAULT_SPACE = "TEST"
+""" project and experiment where new plates will be registered """
+DEFAULT_PROJECT_CODE = "TEST-PROJECT"
+DEFAULT_EXPERIMENT_CODE = "E1"
+
+PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
+PLATE_GEOMETRY = "384_WELLS_16X24"
+
+if incoming.isDirectory():
+ tokens = incoming.getName().split(".")
+ if len(tokens) < 2:
+ print "Invalid name:", incoming.getName()
+ exit
+ plateCode = tokens[0]
+ experimentCode = tokens[1]
+
+ config = ImageDataSetFlexible()
+ config.setRawImageDatasetType()
+ config.setPlate(DEFAULT_SPACE, plateCode)
+ #factory.registerImageDataset(config, incoming, service)
+ imageRegistrationDetails = factory.createImageRegistrationDetails(config, incoming)
+
+ tr = service.transaction(incoming, factory)
+
+ sampleIdentifier = "/"+DEFAULT_SPACE+"/"+plateCode
+ plate = tr.getSample(sampleIdentifier)
+ if plate == None:
+ expIdentifier = "/"+DEFAULT_SPACE+"/"+DEFAULT_PROJECT_CODE+"/"+experimentCode
+ #expIdentifier = "/"+DEFAULT_SPACE+"/"+DEFAULT_PROJECT_CODE+"/"+DEFAULT_EXPERIMENT_CODE
+ experiment = tr.getExperiment(expIdentifier)
+ if experiment == None:
+ experiment = tr.createNewExperiment(expIdentifier)
+ experiment.setType(SIRNA_EXP_TYPE)
+ experiment.setPropertyValue("MICROSCOPE", "BD_PATHWAY_855")
+ experiment.setPropertyValue("DESCRIPTION", "koko")
+
+ plate = tr.createNewSample(sampleIdentifier)
+ plate.setType(PLATE_TYPE_CODE)
+ plate.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, PLATE_GEOMETRY)
+ plate.setExperiment(experiment)
+ tr.commit()
+ tr = service.transaction(incoming, factory)
+
+ imageDataset = tr.createNewDataSet(imageRegistrationDetails)
+ imageDataset.setSample(plate)
+ imageDataSetFolder = tr.moveFile(incoming.getPath(), imageDataset)
+ imageDatasetCode = imageDataset.getDataSetCode()
+ print "Registered dataset:", imageDatasetCode
+ tr.commit()
+
diff --git a/screening/etc/example-dropbox-configuration/jython-flexible-images/example-images.zip b/screening/etc/example-dropbox-configuration/jython-flexible-images/example-images.zip
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--
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