adds groovy version of CARE_generic script

script/CARE_generic.groovy

@@ -0,0 +1,51 @@
+# @String(label="Input path (.tif or folder with .tifs)", required=false, value='/home/random/Development/imagej/project/CSBDeep/script') input
+# @String(label="Output path (.tif or folder)", required=false, value='/home/random/Development/imagej/project/CSBDeep/script/out') output
+# @String(label="Model file", required=false, value='/home/random/Development/imagej/project/CSBDeep/data/Tobias Boothe/models/phago_C2_no_transform_model.zip') modelFile
+# @String(label="Model file", required=false, value='phago_C2_no_transform_model') _modelName
+# @Integer(label="Number of tiles", required=false, value=8) nTiles
+# @Integer(label="Tile overlap", required=false, value=32) overlap
+# @Boolean(label="Normalize input", required=false, value=true) normalizeInput
+# @Float(label="Bottom percentile", required=false, value=3.0, stepSize=0.1) percentileBottom
+# @Float(label="Top percentile", required=false, value=99.8, stepSize=0.1) percentileTop
+# @Boolean(label="Clip", required=false, value=false) clip
+# @Boolean(label="Show progress dialog", required=false, value=true) showProgressDialog
+# @DatasetIOService io
+# @CommandService command
+# @ModuleService module
+
+// modified from python https://github.com/CSBDeep/CSBDeep_fiji/blob/master/script/CARE_generic.py
+// to groovy 
+import de.csbdresden.csbdeep.commands.GenericNetwork
+
+def runNetwork(inputPath, outputPath){
+	print("\ninput: " + inputPath + ", output: " + outputPath)
+	def imp = io.open(inputPath)
+	def mymod = (command.run(GenericNetwork, false,
+		"input", imp,
+		"nTiles", nTiles,
+		"overlap", overlap,
+		"normalizeInput", normalizeInput,
+		"percentileBottom", percentileBottom,
+		"percentileTop", percentileTop,
+		"clip", clip,
+		"showProgressDialog", showProgressDialog,
+		"modelFile", modelFile)).get()
+	def myoutput = mymod.getOutput("output")
+	print("\noutput: " +myoutput)
+	io.save(myoutput, outputPath)
+}
+// Check that input and ouput are different (to avoid overwriting files)
+if((output == input)) return print("ERROR: please provide an output file/directory that is not the same as the input file/directory")
+
+// convert in/output strings to File
+def input_File = new File(input)
+def output_File = new File(output)
+
+// input & output are files	
+if ( (input_File.isFile()) && (output_File.isFile()) ) 	runNetwork(input_File.getAbsolutePath(), output_File.getAbsolutePath())
+// or folders ? 	
+else if ( (input_File.isDirectory()) && (output_File.isDirectory()) ) { 
+	input_File.listFiles().each{ file ->
+		if (file.name.endsWith(".tif"))	runNetwork(file.getAbsolutePath(), new File(output_File, file.name).getAbsolutePath() )	
+	}	
+}