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Created: 2012-01-03 11:57:05 Last updated: 2012-01-03 11:58:43

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A KUP domain image segmentation workflow that identifies ans annotates important regions on microscopic Kidney biopsy images (vessels and glomerulus)

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Workflow Components

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Inputs (1)

Name	Description
imageFile

Processors (22)

Name	Type	Description
uploadImage	wsdl	Wsdl http://localhost:8080/axis2/services/ImageService?wsdl Wsdl Operation uploadImage
uploadImage_input	xmlsplitter
uploadImage_output	xmlsplitter
transformImage	wsdl	Wsdl http://localhost:8080/axis2/services/ImageService?wsdl Wsdl Operation transformImage
transformImage_input	xmlsplitter
ConvertTo8Bit	stringconstant	Value ConvertTo8Bit
transformImage_output	xmlsplitter
transformImage_2	wsdl	Wsdl http://localhost:8080/axis2/services/ImageService?wsdl Wsdl Operation transformImage
transformImage_2_input	xmlsplitter
AutoThresholdImage	stringconstant	Value AutoThresholdImage
transformImage_2_output	xmlsplitter
extractFeatures	wsdl	Wsdl http://localhost:8080/axis2/services/ImageService?wsdl Wsdl Operation extractFeatures
extractFeatures_input	xmlsplitter
KUP_Enhance	stringconstant	Value KUP_Enhance
extractFeatures_2	wsdl	Wsdl http://localhost:8080/axis2/services/ImageService?wsdl Wsdl Operation extractFeatures
extractFeatures_2_input	xmlsplitter
KUP_ObjectDetection	stringconstant	Value KUP_ObjectDetection
ShowSegmentedImage	beanshell	Script URL inputURL = null; inputURL = new URL(url); byte[] contents; if (inputURL.openConnection().getContentLength() == -1) { // Content size unknown, must read first... byte[] buffer = new byte[1024]; int bytesRead = 0; int totalBytesRead = 0; InputStream is = inputURL.openStream(); while (bytesRead != -1) { totalBytesRead += bytesRead; bytesRead = is.read(buffer, 0, 1024); } contents = new byte[totalBytesRead]; } else { contents = new byte[inputURL.openConnection().getContentLength()]; } int bytesRead = 0; int totalBytesRead = 0; InputStream is = inputURL.openStream(); while (bytesRead != -1) { bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead); totalBytesRead += bytesRead; if (contents.length==totalBytesRead) break; } image = contents;
getImageURL	wsdl	Wsdl http://localhost:8080/axis2/services/ImageService?wsdl Wsdl Operation getImageURL
getImageURL_input	xmlsplitter
getImageURL_output	xmlsplitter
Encode_Byte_Array_to_Base_64	localworker	Script import org.apache.commons.codec.binary.Base64; base64 = new String(Base64.encodeBase64(bytes));

Beanshells (1)

Name	Description	Inputs	Outputs
ShowSegmentedImage		url	image

Outputs (1)

Name	Description
image

Datalinks (23)

Source	Sink
uploadImage_input:output	uploadImage:parameters
Encode_Byte_Array_to_Base_64:base64	uploadImage_input:image
uploadImage:parameters	uploadImage_output:input
transformImage_input:output	transformImage:parameters
ConvertTo8Bit:value	transformImage_input:transformationMethodName
uploadImage_output:return	transformImage_input:imageReference
transformImage:parameters	transformImage_output:input
transformImage_2_input:output	transformImage_2:parameters
AutoThresholdImage:value	transformImage_2_input:transformationMethodName
transformImage_output:return	transformImage_2_input:imageReference
transformImage_2:parameters	transformImage_2_output:input
extractFeatures_input:output	extractFeatures:parameters
KUP_Enhance:value	extractFeatures_input:extractionMethodName
transformImage_2_output:return	extractFeatures_input:imageReference
extractFeatures_2_input:output	extractFeatures_2:parameters
KUP_ObjectDetection:value	extractFeatures_2_input:extractionMethodName
extractFeatures:parameters	extractFeatures_2_input:imageReference
getImageURL_output:return	ShowSegmentedImage:url
getImageURL_input:output	getImageURL:parameters
extractFeatures_2:parameters	getImageURL_input:imageReference
getImageURL:parameters	getImageURL_output:input
imageFile	Encode_Byte_Array_to_Base_64:bytes
ShowSegmentedImage:image	image