small changes to experiment set up

SVN: 28486

screening/bsa_lab/czi-metadata-dropbox.py

@@ -11,8 +11,12 @@ 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.
+Dropbox script for uploading a .czi file. Images contained in the file are displayed in openBIS and metadata is extracted from the czi file and 
+stored in a file called "samplename-metadata.txt" uploaded in the dataset. The czi file needs to be put in a directory inside the incoming folder. 
+The name of this directory should be Y-X, where Y is name of the project (already existing in openBIS) and X the name of the experiment 
+where the sample will be uploaded. If the experiment does not exist yet, it will be created.
+As many samples are created as many czi files are contained in the incoming directory. The samples are named like the czi file.
+ 
 '''
 
 
@@ -22,74 +26,166 @@ 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 tryToCreateReaderForFile(fileName):
+		for reader in ImageReader().getReaders():
+			if reader.isThisType(fileName):
+				return reader
+		return None
 
 def process(transaction):
 	
 	incoming = transaction.getIncoming()
 
 
+#read each czi file contained in the incoming directory and extract all the metadata to a metadata.txt file
+#extract also some specific metadata which will be set as properties in openBIS
 	def readCzi(incoming):
 		filename_list = {}
 		for cziFile in glob.glob(os.path.join(incoming, '*.czi')):
 			objective =''
 			scaling = None
+			z_step_size = None
+			pixel_dwell_time = None
+			channel_name_0 = ''
+			channel_name_1 = ''
+			channel_name_2 = ''
+			channel_name_3 = ''
+			channel_name_4 = ''
+			channel_name_5 = ''
+			channel_name_6 = ''
+			channel_name_7 = ''
+			detector_gain_0 = None
+			detector_gain_1 = None
+			detector_gain_2 = None
+			detector_gain_3 = None
+			detector_gain_4 = None
+			detector_gain_5 = None
+			detector_gain_6 = None
+			detector_gain_7 = 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())
-  			
+			
+			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
+				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
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock AcquisitionModeSetup ScalingX 0", item_label):
+						scaling = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Z Positions Interval Increment 0", item_label):
+						z_step_size = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock AcquisitionModeSetup PixelPeriod 0", item_label):
+						pixel_dwell_time = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 0", item_label):
+						channel_name_0 = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 1", item_label):
+						channel_name_1 = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 2", item_label):
+						channel_name_2 = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 3", item_label):
+						channel_name_3 = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 4", item_label):
+						channel_name_4 = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 5", item_label):
+						channel_name_5 = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 6", item_label):
+						channel_name_6 = item_value
+					
+					if re.search ("Metadata Experiment ExperimentBlocks AcquisitionBlock MultiTrackSetup TrackSetup Detectors Detector ImageChannelName 7", item_label):
+						channel_name_7 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 0", item_label):
+						detector_gain_0 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 1", item_label):
+						detector_gain_1 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 2", item_label):
+						detector_gain_2 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 3", item_label):
+						detector_gain_3 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 4", item_label):
+						detector_gain_4 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 5", item_label):
+						detector_gain_5 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 6", item_label):
+						detector_gain_6 = item_value
+					
+					if re.search ("Metadata Information Image Dimensions Channels Channel DetectorSettings Gain 7", item_label):
+						detector_gain_7 = None
+ 					
+ 					
  					
 			f.close()
 			reader.close();
-			filename_list[filename] = { "objective" : objective, "scaling" : scaling}
+			filename_list[filename] = { "objective" : objective, "scaling" : scaling, "z_step_size" : z_step_size, "pixel_dwell_time" : pixel_dwell_time, "channel_name_0" : channel_name_0, "channel_name_1" : channel_name_1, "channel_name_2" : channel_name_2, "channel_name_3" : channel_name_3, "channel_name_4" : channel_name_4, "channel_name_5" : channel_name_5, "channel_name_6" : channel_name_6, "channel_name_7" : channel_name_7, "detector_gain_0" : detector_gain_0, "detector_gain_1" : detector_gain_1, "detector_gain_2" : detector_gain_2, "detector_gain_3" : detector_gain_3, "detector_gain_4" : detector_gain_4, "detector_gain_5" : detector_gain_5, "detector_gain_6" : detector_gain_6, "detector_gain_7" : detector_gain_7  }
 			
 			
 		return filename_list
 			   
 	cziInfo = readCzi(incoming.getPath())
-	
-	directoryName = os.path.basename(incoming.getPath())
 
+
+	directoryName = os.path.basename(incoming.getPath())
 	names = re.split(r"[-]",directoryName)
 	projectName = names[0] + "-IMG"
 	experimentName = names[1]
-
+	experiment = "/PANTAZIS_GROUP/" + projectName + "/" + experimentName  
+	exp = transaction.getExperiment(experiment)
+	if not exp:
+		exp = transaction.createNewExperiment(experiment, 'IMAGING')
 	
 	for name in cziInfo.keys():
-		print "name", name
 		sampleIdentifier = "/PANTAZIS_GROUP/" + name
+		print "sample is", sampleIdentifier
 		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"])
+# 		sample.setPropertyValue("Z_STEP_SIZE", cziInfo[name]["z_step_size"])
+# 		sample.setPropertyValue("PIXEL_DWELL_TIME", cziInfo[name]["pixel_dwell_time"])
+# 		sample.setPropertyValue("CHANNEL_NAME_0", cziInfo[name]["channel_name_0"])
+# 		sample.setPropertyValue("CHANNEL_NAME_1", cziInfo[name]["channel_name_1"])
+# 		sample.setPropertyValue("CHANNEL_NAME_2", cziInfo[name]["channel_name_2"])
+# 		sample.setPropertyValue("CHANNEL_NAME_3", cziInfo[name]["channel_name_3"])
+# 		sample.setPropertyValue("CHANNEL_NAME_4", cziInfo[name]["channel_name_4"])
+# 		sample.setPropertyValue("CHANNEL_NAME_5", cziInfo[name]["channel_name_5"])
+# 		sample.setPropertyValue("CHANNEL_NAME_6", cziInfo[name]["channel_name_6"])
+# 		sample.setPropertyValue("CHANNEL_NAME_7", cziInfo[name]["channel_name_7"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_0", cziInfo[name]["detector_gain_0"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_1", cziInfo[name]["detector_gain_1"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_2", cziInfo[name]["detector_gain_2"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_3", cziInfo[name]["detector_gain_3"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_4", cziInfo[name]["detector_gain_4"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_5", cziInfo[name]["detector_gain_5"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_6", cziInfo[name]["detector_gain_6"])
+# 		sample.setPropertyValue("DETECTOR_GAIN_7", cziInfo[name]["detector_gain_7"])
 
 		imageDataset = SimpleImageContainerDataConfig()
 		imageDataset.setPlate("PANTAZIS_GROUP", name)
@@ -99,33 +195,14 @@ def process(transaction):
 		imageDataset.setImageLibrary("BioFormats")
 		imageDataset.setMeasuredData(True)
 		
- 		sampleNamePath = incoming.getPath() + '/' + name  + '.czi'
- 		metadataPath = incoming.getPath() + '/' + name  + '-metadata.txt'
- 		dataSet = transaction.createNewImageDataSet(imageDataset, File(sampleNamePath))
+		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())
+
  
 
 	
@@ -133,8 +210,7 @@ def process(transaction):
 	
   		
   	
-# 		
-# 	 
+