diff --git a/screening/bsa_lab/czi-metadata-dropbox.py b/screening/bsa_lab/czi-metadata-dropbox.py
index 0b5f7f77b06a17f8d93b94afec64a1020367f3c6..9a4920371036e0593e2492cd8b2357281220b1c1 100644
--- a/screening/bsa_lab/czi-metadata-dropbox.py
+++ b/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):
-#
-#
+