dropbox script for extracting metadata from czi files and uploading the czi...

dropbox script for extracting metadata from czi files and uploading the czi and the metadata in a text file. For Pantazis lab.

SVN: 28484

screening/bsa_lab/czi-metadata-dropbox.py

+import os, glob, re, csv, time, shutil
+from java.io import File
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, ImageMetadata, Location
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageContainerDataConfig, ChannelColor
+from loci.formats import ImageReader
+
+
+
+from time import *
+from datetime import *
+
+'''
+Dropbox script for uploading a .lsm/ .czi file. Images contained in the file are displayed in openBIS and metadate is extracted from the lsm file and 
+stored in a file called "metadata.txt" uploaded in the dataset. The lsm or czi file needs to be put in a directory inside the incoming folder. The name of this directory is then taken as sample name for openBIS.
+'''
+
+
+print '###################################'
+tz=localtime()[3]-gmtime()[3]
+d=datetime.now()
+print d.strftime("%Y-%m-%d %H:%M:%S GMT"+"%+.2d" % tz+":00")
+
+class BioFormatsHelper(ImageReader):
+  def tryToCreateReaderForFile(fileName):
+    for reader in ImageReader().getReaders():
+      if reader.isThisType(fileName):
+        return reader
+    return None
+
+def process(transaction):
+	
+	incoming = transaction.getIncoming()
+
+
+	def readCzi(incoming):
+		filename_list = {}
+		for cziFile in glob.glob(os.path.join(incoming, '*.czi')):
+			objective =''
+			scaling = None
+			(dir, file) = os.path.split(cziFile)
+			(filename, extension) = os.path.splitext(file)
+			helper = BioFormatsHelper()
+			reader = helper.getReader(cziFile)
+			reader.setId(cziFile)
+  			
+  			globalMetadata = str(reader.getGlobalMetadata().toString())
+  			
+			list_globalMetadata = re.split(r"[,]",globalMetadata)
+			metadataFile = dir+"/" + filename + "-metadata.txt"
+			f = open(metadataFile, "a")
+			for item in list_globalMetadata:
+  				f.write(item)
+  				f.write('\n')
+  				if re.search ("=", item):
+  					item_total = re.split(r"[=]", item)
+  					item_label = item_total[0]
+  					item_value = item_total[1]
+  					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock AcquisitionModeSetup Objective 0", item_label):
+  						objective = item_value
+						
+  					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock AcquisitionModeSetup ScalingX 0", item_label):
+  						scaling = item_value
+ 					
+			f.close()
+			reader.close();
+			filename_list[filename] = { "objective" : objective, "scaling" : scaling}
+			
+			
+		return filename_list
+			   
+	cziInfo = readCzi(incoming.getPath())
+	
+	directoryName = os.path.basename(incoming.getPath())
+
+	names = re.split(r"[-]",directoryName)
+	projectName = names[0] + "-IMG"
+	experimentName = names[1]
+
+	
+	for name in cziInfo.keys():
+		print "name", name
+		sampleIdentifier = "/PANTAZIS_GROUP/" + name
+		sample = transaction.createNewSample(sampleIdentifier, "MICROSCOPY_IMG")
+		experiment = "/PANTAZIS_GROUP/" + projectName + "/" + experimentName  
+		exp = transaction.getExperiment(experiment)
+		if not exp:
+			exp = transaction.createNewExperiment(experiment, 'IMAGING')
+
+		sample.setExperiment(exp)
+		sample.setPropertyValue("OBJECTIVE", cziInfo[name]["objective"])
+		sample.setPropertyValue("SCALING", cziInfo[name]["scaling"])
+
+		imageDataset = SimpleImageContainerDataConfig()
+		imageDataset.setPlate("PANTAZIS_GROUP", name)
+		imageDataset.setMicroscopyData(True)
+		imageDataset.setDataSetType("MICROSCOPY_IMG")
+		imageDataset.setRecognizedImageExtensions(['lif', 'dv', 'tif', 'tiff','nd2', 'lsm', 'czi'])
+		imageDataset.setImageLibrary("BioFormats")
+		imageDataset.setMeasuredData(True)
+		
+ 		sampleNamePath = incoming.getPath() + '/' + name  + '.czi'
+ 		metadataPath = incoming.getPath() + '/' + name  + '-metadata.txt'
+ 		dataSet = transaction.createNewImageDataSet(imageDataset, File(sampleNamePath))
+		
+		transaction.moveFile(sampleNamePath, dataSet)
+		transaction.moveFile(metadataPath, dataSet)
+
+# 		transaction.moveFile(sampleNamePath, dataSet)
+
+
+# 	def moveFiles(incoming):
+# 		for cziFile in glob.glob(os.path.join(incoming, '*.czi')):
+# 			(incoming, file) = os.path.split(cziFile)
+# 			(filename, extension) = os.path.splitext(file)
+# 			newDir = incoming + '/' + filename
+# 			print "newdir", newDir
+# 			if not os.path.exists(newDir):
+# 				os.makedirs(newDir)
+# 			shutil.move(incoming + '/' + file, newDir)
+# 		for txtFile in glob.glob(os.path.join(incoming, '*.txt')):
+# 			print "textfile", txtFile
+# 			(incoming, file) = os.path.split(txtFile)
+# 			(filename, extension) = os.path.splitext(file)		
+# 			shutil.move(incoming + '/' + file, newDir)
+# 			
+# 				
+# 	moveFiles(incoming.getPath())
+ 
+
+	
+	
+	
+  		
+  	
+# 		
+# 	 
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