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mm_blurb_generator.py

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+#@ File(style="open") filename
+#@ OMEXMLService omeservice
+
+# Author : Thomas Pengo <[email protected]>
+# License : GPL-3
+
+TEMPLATE_GENERAL 		= "The data was acquired on a {ID} microscope, using a {magnification}x {NA} NA objective. The pixel size is {pxx_microns:.2f} microns. "
+TEMPLATE_CHANNEL		= "The excitation wavelength for channel {ch} is {ex} and the {exposureTime} is {} milliseconds. "
+TEMPLATE_3D				= "The step size is {pzz_microns:.2f} microns. "
+TEMPLATE_TIME			= "Images were acquired with a time interval of {timeInterval}. "
+
+BLURB = ""
+
+# Get a BioFormats reader
+from loci.formats import ImageReader
+ir = ImageReader()
+
+# Adapted from https://github.com/ome/bioformats/blob/develop/components/formats-gpl/utils/GetPhysicalMetadata.java
+m = omeservice.createOMEXMLMetadata()
+
+ir.setMetadataStore(m)
+ir.setId(filename.getAbsolutePath())
+
+# Some checks
+ninstruments 	= m.getInstrumentCount()
+if ninstruments > 1:
+	error("More than one instrument found. Automatic generation will not work...")
+nobjectives		= m.getObjectiveCount(0)
+if nobjectives > 1:
+	error("More than one objective found. Automatic generation will not work...")
+
+# TODO ADD MODALITY
+ID		 		= m.getMicroscopeManufacturer(0)
+if ID == None:
+	ff = str(ir.getFormat())
+	if "Zeiss" in ff:
+		ID="Zeiss"
+	elif "Nikon" in ff:
+		ID="Nikon"
+	elif "Olympus" in ff:
+		ID="Olympus"
+
+magnification 	= str(m.getObjectiveNominalMagnification(0,0))
+NA 				= str(m.getObjectiveLensNA(0,0))
+
+# Pixel size
+nimages = m.getImageCount()
+print "Found {} images".format(nimages)
+
+from ome.units import UNITS
+pxx_microns = m.getPixelsPhysicalSizeX(0).value(UNITS.MICROMETER)
+
+# Is it 3D?
+is3D = ir.getSizeZ()>1
+pzz_microns = m.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER)
+
+# TODO Is it a time series?
+
+# BLURB GENERATION
+BLURB += TEMPLATE_GENERAL.format(ID=ID, magnification=magnification, NA=NA, pxx_microns=pxx_microns)
+if is3D:
+	BLURB += TEMPLATE_3D.format(pzz_microns=pzz_microns)
+
+# TODO Extract channel information
+#for ic in ir.getSizeC():
+#	ex = m.getChannelExcitationWavelength(0,ic)
+#	et = m.getPlaneExposureTime(0,0)
+
+print "\n\n\n-----------------"
+print BLURB
+print "-----------------\n\n\n"