Angiogenesis Feature Extraction workflow

Created: 2010-03-23 13:19:35 Last updated: 2012-01-10 08:47:41

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This is a sample Workflow based on an Image Mining Web Service developed in the context of e-LICO project (www.e-lico.eu). It demonstrates the main functionality of the Web Service, involving the application of several basic image operators on angiogenic images and then performing useful feature (e.g., image texture, vessel length, branch count, etc.) extraction.

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Inputs (1)

Name	Description
imageFile	Click 'Add File Location' to select an image file to perform image analysis on.

Processors (32)

Name	Type	Description
transformImage_2	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation transformImage
transformImage_input	xmlsplitter
transformImage_output	xmlsplitter
AdaptiveThreshold	stringconstant	Value AdaptiveThreshold
transformImage	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation transformImage
transformImage_2_input	xmlsplitter
transformImage_2_output	xmlsplitter
ConvertTo8Bit	stringconstant	Value ConvertTo8Bit
transformImage_4	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation transformImage
transformImage_4_input	xmlsplitter
transformImage_4_output	xmlsplitter
Convert2Binary	stringconstant	Value Convert2Binary
transformImage_5	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation transformImage
transformImage_5_input	xmlsplitter
transformImage_5_output	xmlsplitter
skeletonizeImage	stringconstant	Value skeletonizeImage
getImageURL	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation getImageURL
getImageURL_input	xmlsplitter
getImageURL_output	xmlsplitter
Show_final_Image	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;
extractFeatures	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation extractFeatures
Angiogenesis_Extraction	stringconstant	Value Angiogenesis_Extraction
extractFeatures_input	xmlsplitter
extractFeatures_output	xmlsplitter
Show_initial_Image	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_2	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation getImageURL
getImageURL_2_input	xmlsplitter
getImageURL_2_output	xmlsplitter
uploadImage	wsdl	Wsdl http://195.251.6.234:8080/axis2/services/ImageServiceWS?wsdl Wsdl Operation uploadImage
uploadImage_input	xmlsplitter
Encode_Byte_Array_to_Base_64	localworker	Script import org.apache.commons.codec.binary.Base64; base64 = new String(Base64.encodeBase64(bytes));
uploadImage_output	xmlsplitter

Beanshells (2)

Name	Description	Inputs	Outputs
Show_final_Image		url	image
Show_initial_Image		url	image

Outputs (3)

Name	Description
Skeletonized_Image
Image_Features
Initial_Image

Datalinks (35)

Source	Sink
transformImage_input:output	transformImage_2:parameters
ConvertTo8Bit:value	transformImage_input:transformationMethodName
uploadImage_output:return	transformImage_input:imageReference
transformImage_2:parameters	transformImage_output:input
transformImage_2_input:output	transformImage:parameters
AdaptiveThreshold:value	transformImage_2_input:transformationMethodName
transformImage_output:return	transformImage_2_input:imageReference
transformImage:parameters	transformImage_2_output:input
transformImage_4_input:output	transformImage_4:parameters
Convert2Binary:value	transformImage_4_input:transformationMethodName
transformImage_2_output:return	transformImage_4_input:imageReference
transformImage_4:parameters	transformImage_4_output:input
transformImage_5_input:output	transformImage_5:parameters
skeletonizeImage:value	transformImage_5_input:transformationMethodName
transformImage_4_output:return	transformImage_5_input:imageReference
transformImage_5:parameters	transformImage_5_output:input
getImageURL_input:output	getImageURL:parameters
transformImage_5_output:return	getImageURL_input:imageReference
getImageURL:parameters	getImageURL_output:input
getImageURL_output:return	Show_final_Image:url
extractFeatures_input:output	extractFeatures:parameters
Angiogenesis_Extraction:value	extractFeatures_input:extractionMethodName
transformImage_5_output:return	extractFeatures_input:imageReference
extractFeatures:parameters	extractFeatures_output:input
getImageURL_2_output:return	Show_initial_Image:url
getImageURL_2_input:output	getImageURL_2:parameters
uploadImage_output:return	getImageURL_2_input:imageReference
getImageURL_2:parameters	getImageURL_2_output:input
uploadImage_input:output	uploadImage:parameters
Encode_Byte_Array_to_Base_64:base64	uploadImage_input:image
imageFile	Encode_Byte_Array_to_Base_64:bytes
uploadImage:parameters	uploadImage_output:input
Show_final_Image:image	Skeletonized_Image
extractFeatures_output:return	Image_Features
Show_initial_Image:image	Initial_Image

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Information Workflow Type

Taverna 2

Information Uploader

Charala...

Information License

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Information Version 2 (of 3)

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Charalampos

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Information Statistics

3474 viewings

1683 downloads

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Version History

In chronological order:

Angiogenesis Feature Extraction workflow

Created by Charalampos on Monday 22 March 2010 14:40:41 (UTC)

Last edited by Charalampos on Tuesday 23 March 2010 11:13:41 (UTC)
Angiogenesis Feature Extraction workflow

Created by Charalampos on Tuesday 23 March 2010 13:19:35 (UTC)

Last edited by Charalampos on Tuesday 23 March 2010 13:20:43 (UTC)

Revision comment:

This version of the workflow accepts any angiogenic image (in JPG format) from users as input. Credits on myGrid team for helping with the file upload feature.
Angiogenesis Feature Extraction workflow

Created by Charalampos on Tuesday 03 January 2012 10:04:35 (UTC)

Last edited by Charalampos on Tuesday 10 January 2012 08:47:40 (UTC)

Revision comment:

Updated Server Endpoint

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Angiogenesis Feature Extraction workflow

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