Detect compressed TIFF files and remove the compression

None

/default:fits/default:metadata/default:image/default:compressionScheme
BufferedReader getReader (String fileUrl, String encoding) throws IOException {
		InputStreamReader reader;
		try {
			if (encoding == null) {
				reader = new FileReader(fileUrl);
			} else {
				reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); 
			}
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			if (encoding == null) {
				reader = new InputStreamReader (url.openStream());
			} else {
				reader = new InputStreamReader (url.openStream(), encoding);
			}
		}
		return new BufferedReader(reader);
	}


StringBuffer sb = new StringBuffer(4000);

if (encoding == void) {
	encoding = null;
}

BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);
List tiff_images_out_list = new ArrayList();
for( int i = 0; i < tiff_images_in_list.size(); i++) {
	String item = tiff_images_in_list.get(i);
	String charres = charactres_in_list.get(i);
	if(charres.matches(csresult_regex))
		tiff_images_out_list.add(item);
}


if ((url == void) || (url == null)) {
	throw new RuntimeException("The url must be specified");
}

URL inputURL = null;
if (base != void) {
	inputURL = new URL(new URL(base), url);
} else {
	inputURL = new URL(url);
}

int bytesRead = 0;
int totalBytesRead = 0;
InputStream is = inputURL.openStream();
ByteArrayOutputStream os = new ByteArrayOutputStream();
byte[] buffer = new byte[2048];
while (true) {
	bytesRead = is.read(buffer);
	if (bytesRead == -1) {
		break;	
	}

	os.write(buffer, 0, bytesRead);
}

image = os.toByteArray();
is.close();
os.close();

BufferedReader getReader (String fileUrl, String encoding) throws IOException {
		InputStreamReader reader;
		try {
			if (encoding == null) {
				reader = new FileReader(fileUrl);
			} else {
				reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); 
			}
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			if (encoding == null) {
				reader = new InputStreamReader (url.openStream());
			} else {
				reader = new InputStreamReader (url.openStream(), encoding);
			}
		}
		return new BufferedReader(reader);
	}


StringBuffer sb = new StringBuffer(4000);

if (encoding == void) {
	encoding = null;
}

BufferedReader in = getReader(fileurl, encoding);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();

Name	Description
url_to_textfile_with_image_urls	URL of a textfile that contains a list of urls serving as the input of this workflow. It contains compressed and uncompressed images.
convert_compression	Compression that should be applied to the result images list - usually 0 means: remove compression. Value range: integer from 1-6. Meaning of values := None (0), LZW (1), PACKBITS(2), DEFLATE (3), JPEG (4), CCITT G3 Fax (5), CCITT G4 Fax (6))
convert_numcolors	Number of colors (2-256)
csresult_regex	Regular expression for the compression scheme value

Name	Type	Description
Get_list_of_images	workflow
XPath_Service	xpath	Xpath Expression /default:fits/default:metadata/default:image/default:compressionScheme
Read_Text_File	localworker	Script BufferedReader getReader (String fileUrl, String encoding) throws IOException { InputStreamReader reader; try { if (encoding == null) { reader = new FileReader(fileUrl); } else { reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); } } catch (FileNotFoundException e) { // try a real URL instead URL url = new URL(fileUrl); if (encoding == null) { reader = new InputStreamReader (url.openStream()); } else { reader = new InputStreamReader (url.openStream(), encoding); } } return new BufferedReader(reader); } StringBuffer sb = new StringBuffer(4000); if (encoding == void) { encoding = null; } BufferedReader in = getReader(fileurl, encoding); String str; String lineEnding = System.getProperty("line.separator"); while ((str = in.readLine()) != null) { sb.append(str); sb.append(lineEnding); } in.close(); filecontents = sb.toString();
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Beanshell	beanshell	Script List tiff_images_out_list = new ArrayList(); for( int i = 0; i < tiff_images_in_list.size(); i++) { String item = tiff_images_in_list.get(i); String charres = charactres_in_list.get(i); if(charres.matches(csresult_regex)) tiff_images_out_list.add(item); }
convertTIFFtoTIFFByUrl	wsdl	Wsdl https://fue.onb.ac.at/axis2-l/services/IMPACTGimpImageConversionService?wsdl Wsdl Operation convertTIFFtoTIFFByUrl
convertTIFFtoTIFFByUrl_part1	xmlsplitter
convertTIFFtoTIFFByUrl_part1_2	xmlsplitter
Get_Image_From_URL	localworker	Script if ((url == void) \|\| (url == null)) { throw new RuntimeException("The url must be specified"); } URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } int bytesRead = 0; int totalBytesRead = 0; InputStream is = inputURL.openStream(); ByteArrayOutputStream os = new ByteArrayOutputStream(); byte[] buffer = new byte[2048]; while (true) { bytesRead = is.read(buffer); if (bytesRead == -1) { break; } os.write(buffer, 0, bytesRead); } image = os.toByteArray(); is.close(); os.close();
Read_Text_File_2	localworker	Script BufferedReader getReader (String fileUrl, String encoding) throws IOException { InputStreamReader reader; try { if (encoding == null) { reader = new FileReader(fileUrl); } else { reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); } } catch (FileNotFoundException e) { // try a real URL instead URL url = new URL(fileUrl); if (encoding == null) { reader = new InputStreamReader (url.openStream()); } else { reader = new InputStreamReader (url.openStream(), encoding); } } return new BufferedReader(reader); } StringBuffer sb = new StringBuffer(4000); if (encoding == void) { encoding = null; } BufferedReader in = getReader(fileurl, encoding); String str; String lineEnding = System.getProperty("line.separator"); while ((str = in.readLine()) != null) { sb.append(str); sb.append(lineEnding); } in.close(); filecontents = sb.toString();
characteriseFile_3	wsdl	Wsdl http://fue.onb.ac.at/scape-fits050-service/Fits050.wsdl Wsdl Operation characteriseFile
characteriseFile_3_characteriseFileRequest	xmlsplitter
characteriseFile_3_characteriseFileResponse	xmlsplitter
characteriseFileResponse_return	xmlsplitter
return_result	xmlsplitter
characteriseFile	wsdl	Wsdl http://fue.onb.ac.at/scape-fits050-service/Fits050.wsdl Wsdl Operation characteriseFile
characteriseFileRequest	xmlsplitter
characteriseFileResponse	xmlsplitter
characteriseFileResponse_return_2	xmlsplitter
2_result	xmlsplitter

Name	Description
2_group_4_fax_compressed_images
1_characterisation_result	Characterisation result
3_uncompressed_result_image
4_gimp_processing_log
5_uncompressed_characterisation

Source	Sink
url_to_textfile_with_image_urls	Get_list_of_images:inputUrl
Read_Text_File:filecontents	XPath_Service:xml_text
return_result:output	Read_Text_File:fileurl
XPath_Service:nodelist	Flatten_List:inputlist
Get_list_of_images:list	Beanshell:tiff_images_in_list
Flatten_List:outputlist	Beanshell:charactres_in_list
csresult_regex	Beanshell:csresult_regex
convertTIFFtoTIFFByUrl_part1:output	convertTIFFtoTIFFByUrl:part1
convert_compression	convertTIFFtoTIFFByUrl_part1:compression
convert_numcolors	convertTIFFtoTIFFByUrl_part1:numColors
Beanshell:tiff_images_out_list	convertTIFFtoTIFFByUrl_part1:inputUrl
convertTIFFtoTIFFByUrl:part1	convertTIFFtoTIFFByUrl_part1_2:input
convertTIFFtoTIFFByUrl_part1_2:outputUrl	Get_Image_From_URL:url
2_result:output	Read_Text_File_2:fileurl
characteriseFile_3_characteriseFileRequest:output	characteriseFile_3:characteriseFileRequest
Get_list_of_images:list	characteriseFile_3_characteriseFileRequest:input
characteriseFile_3:characteriseFileResponse	characteriseFile_3_characteriseFileResponse:input
characteriseFile_3_characteriseFileResponse:return	characteriseFileResponse_return:input
characteriseFileResponse_return:result	return_result:input
characteriseFileRequest:output	characteriseFile:characteriseFileRequest
convertTIFFtoTIFFByUrl_part1_2:outputUrl	characteriseFileRequest:input
characteriseFile:characteriseFileResponse	characteriseFileResponse:input
characteriseFileResponse:return	characteriseFileResponse_return_2:input
characteriseFileResponse_return_2:result	2_result:input
Beanshell:tiff_images_out_list	2_group_4_fax_compressed_images
Flatten_List:outputlist	1_characterisation_result
Get_Image_From_URL:image	3_uncompressed_result_image
convertTIFFtoTIFFByUrl_part1_2:processingLog	4_gimp_processing_log
Read_Text_File_2:filecontents	5_uncompressed_characterisation

Detect compressed TIFF files and remove the compression

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Xpath Expression

Script

Script

Script

Wsdl

Wsdl Operation

Script

Script

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Reviews (0)

Comments (0)

Other workflows that use similar services (0)