From d194c91ba52010269bb502215080e36ac28ac222 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 28 Sep 2011 08:34:04 +0000
Subject: [PATCH] LMS-2526 Sanofi: dropbox
SVN: 23118
---
.../dropbox-all-in-one-with-library.py | 3 +-
.../dist/etc/sanofi-dropbox/registration.py | 52 +++++++++++++++----
2 files changed, 44 insertions(+), 11 deletions(-)
diff --git a/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py b/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
index 9c218110e16..de152e71a34 100644
--- a/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
+++ b/sanofi/dist/etc/sanofi-dropbox/dropbox-all-in-one-with-library.py
@@ -5,6 +5,7 @@ Each directory should contain:
- raw images on the main level
- optionally: segmentation images in the directory containin "_ROITiff"
- optionally: analysis results in the xml file
+- optionally: xdce file with image metadata (used to fix colors of the channels determined by the wavelength)
If all kinds of data are provided, 3 datasets will be registered for each incoming directory.
Segmentation and analysis dataset will be linked to the raw images dataset.
"""
@@ -20,7 +21,7 @@ from ch.systemsx.cisd.openbis.generic.shared.basic.dto.api import ValidationExce
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClause, MatchClauseAttribute
-reload(utils)
+#reload(utils)
reload(config)
# Can be switched on manually only after the module's code has been changed on the fly:
#reload(plateinitializer)
diff --git a/sanofi/dist/etc/sanofi-dropbox/registration.py b/sanofi/dist/etc/sanofi-dropbox/registration.py
index dffa5dae31f..b681268d4c3 100755
--- a/sanofi/dist/etc/sanofi-dropbox/registration.py
+++ b/sanofi/dist/etc/sanofi-dropbox/registration.py
@@ -16,6 +16,7 @@ from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, I
from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import Channel
from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import ChannelColorRGB
+from ch.systemsx.cisd.openbis.dss.etl.custom.incell import IncellImageMetadataParser
from ch.systemsx.cisd.openbis.dss.etl.custom.geexplorer import GEExplorerImageAnalysisResultParser
from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
@@ -97,27 +98,58 @@ class MyImageDataSetConfig(SimpleImageDataConfig):
# can be made available.
# It is usually useful to add "-depth 12" parameter additionally
# if the original image has color depth > 8 bits.
- buffer.appendImageMagicConvert("-edge 1 -depth 12", "Edge detection")
+ # buffer.appendImageMagicConvert("-edge 1 -depth 12", "Edge detection")
return buffer.getTransformations()
-
+
+ # sets the basic colors
def createChannel(self, channelCode):
- channelCode = channelCode.upper()
channel = Channel(channelCode, channelCode)
+ channelCode = channelCode.upper()
if (channelCode == "DAPI"):
- #channel.setWavelengthAndColor(455)
- channel.setChannelColorRGB(ChannelColorRGB(0,0,255))
+ channel.setChannelColorRGB(ChannelColorRGB(0, 77, 255))
elif (channelCode == "FITC"):
- #channel.setWavelengthAndColor(525)
- channel.setChannelColorRGB(ChannelColorRGB(0,255,0))
+ channel.setChannelColorRGB(ChannelColorRGB(56, 255, 0))
elif (channelCode == "CY5"):
- #channel.setWavelengthAndColor(705)
- channel.setChannelColorRGB(ChannelColorRGB(255,0,0))
+ channel.setChannelColorRGB(ChannelColorRGB(244, 0, 0))
+
+ channel.setAvailableTransformations(self.getAvailableChannelTransformations(channelCode))
+ # color of other channels will be set automatically
return channel
+class RawImageDataSetConfig(MyImageDataSetConfig):
+ _codeToWavelengthMap = None
+
+ def __init__(self, incomingDir):
+ MyImageDataSetConfig.__init__(self, incomingDir)
+ self._codeToWavelengthMap = self._tryReadCodeToWavelengthMap(incomingDir)
+ def _tryReadCodeToWavelengthMap(self, incomingDir):
+ imageMetadataFile = utils.findFileByExt(incomingDir, "xdce")
+ if imageMetadataFile is not None:
+ parser = IncellImageMetadataParser(imageMetadataFile.getPath())
+ channelCodes = parser.getChannelCodes()
+ channelWavelengths = parser.getChannelWavelengths()
+ codeToWavelengthMap = {}
+ for i in range(0, len(channelCodes)):
+ codeToWavelengthMap[channelCodes[i].upper()] = channelWavelengths[i]
+ return codeToWavelengthMap
+ return None
+
+ # overrides the basic colors by using the wavelengths found in the xdce file
+ def createChannel(self, channelCode):
+ channel = MyImageDataSetConfig.createChannel(self, channelCode)
+ channelCode = channelCode.upper()
+ if self._codeToWavelengthMap is not None:
+ if channelCode in self._codeToWavelengthMap:
+ wavelength = self._codeToWavelengthMap[channelCode]
+ # This will override the color from the superclass and set it
+ # using Bruton's algorithm.
+ channel.setWavelengthAndColor(wavelength)
+ return channel
+
def createRawImagesDataset(incoming, plate, batchName, transaction, factory):
- imageDatasetConfig = MyImageDataSetConfig(incoming)
+ imageDatasetConfig = RawImageDataSetConfig(incoming)
imageDatasetConfig.setRawImageDatasetType()
imageDatasetConfig.setFileFormatType(config.IMAGE_DATASET_FILE_FORMAT)
imageDatasetConfig.setUseImageMagicToGenerateThumbnails(config.USE_IMAGE_MAGIC_CONVERT_TOOL)
--
GitLab