LMS-2585 minimal Flex dropbox

SVN: 23440

screening/etc/example-dropbox-configuration/opera-flex/minimal-data-set-handler.py

+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import ImageMetadata, SimpleImageDataConfig, Location
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+
+from ch.systemsx.cisd.imagereaders.bioformats import FlexHelper
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.utils import DropboxUtils
+
+""" 
+The code needed to import Evotec/PerkinElmer Opera Flex files with images.
+"""
+class OperaFlexImageDataSet(SimpleImageDataConfig):
+
+    """
+    Returns meta-data for each image in the specified image container. 
+
+    Parameter imagePath: path to the flex container with many images
+    Parameter imageIdentifiers: identifiers of all images contained in the image file.
+    """
+    def extractImagesMetadata(self, imagePath, imageIdentifiers):
+        tokens = []
+        self.flexHelper = FlexHelper(incoming.getAbsolutePath() + '/' + imagePath)
+        for image in imageIdentifiers:
+            token = ImageMetadata()
+            
+            token.well = extractWellCode(imagePath)
+            imageIndex = image.getTimeSeriesIndex()
+            token.tileNumber = self.flexHelper.getTileNumber(imageIndex)
+            token.channelCode = self.flexHelper.getChannelCode(imageIndex)
+            
+            token.imageIdentifier = image
+            tokens.append(token)
+        return tokens
+
+    """ Extracts well code (e.g. C2) from the flex file path. """
+    def extractWellCode(self, imagePath):
+        basename = os.path.basename(imagePath)
+        fileName = os.path.splitext(basename)[0]
+        row = int(fileName[0:3])
+        col = int(fileName[3:6])
+        well = DropboxUtils.translateRowNumberIntoLetterCode(row) + str(col)
+        return well
+
+    """
+    Calculates the width and height of the matrix of tiles (a.k.a. fields or sides) in the well 
+    using the content of the Flex file. Passed parameters are not used.
+
+    Returns:
+        Geometry
+    """
+    def getTileGeometry(self, imageTokens, maxTileNumber):
+        tileLocations = self._getTileLocationsMap().values()
+        return DropboxUtils.figureGeometry(tileLocations)
+    
+    """
+    For a given tile number and tiles geometry returns (x,y) which describes where the tile is
+    located on the well.
+    Uses flex file to find this out.
+     
+    Parameter tileNumber: number of the tile
+    Parameter tileGeometry: the geometry of the well matrix
+    Returns:
+         Location
+    """
+    def getTileCoordinates(self, tileNumber, tileGeometry):
+        return self._getTileLocationsMap().get(tileNumber)
+    
+    def _getTileLocationsMap(self):
+        tileSpatialPoints = self.flexHelper.getTileCoordinates()
+        # a maximal distance between two points so that they are still considered to describe one point
+        precision = 1e-7
+        return DropboxUtils.tryFigureLocations(tileSpatialPoints, precision)
+    
+
+if incoming.isDirectory():
+    imageDataset = OperaFlexImageDataSet()
+    imageDataset.setRawImageDatasetType()
+    # we use BioFormat library to interpret images with .flex extension
+    imageDataset.setImageLibrary("BioFormats", "TiffDelegateReader")
+    imageDataset.setRecognizedImageExtensions(["flex"])
+    
+    # Here one can add more specific configuration code.
+    # For simplisity we just assume that the plate sample "/MY-SPACE/MY-PLATE" already exists.
+    imageDataset.setPlate("MY-SPACE", "MY-PLATE")
+    
+    # boilerplate code
+    tr = service.transaction()
+    dataSetRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
+    dataSet = tr.createNewDataSet(dataSetRegistrationDetails)
+    tr.moveFile(incoming.getAbsolutePath(), dataSet)