Revise the jython script for timelapse movies

script/CARE_generic.py

@@ -1,6 +1,6 @@
-# @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
+# @File(label="Input path (.tif or folder with .tifs)", required=false, value='/home/random/Development/imagej/project/CSBDeep/script', style="both") input
+# @File(label="Output path (.tif or folder)", required=false, value='/home/random/Development/imagej/project/CSBDeep/script/out', style="directory") output
+# @File(label="Model file", required=false, value='/home/random/Development/imagej/project/CSBDeep/data/Tobias Boothe/models/phago_C2_no_transform_model.zip', style="file") 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
@@ -16,14 +16,13 @@
 from java.io import File
 import sys
 from de.csbdresden.csbdeep.commands import GenericNetwork
+from ij import IJ
+from ij.plugin import Duplicator
+import os
 
-def getFileName(path):
-	fileparts = path.split("/")
-	return fileparts[len(fileparts)-1]
-
-def runNetwork(inputPath, outputPath):
+def runNetwork(outputPath, imp):
+	inputPath = imp.getOriginalFileInfo().fileName
 	print("input: " + inputPath + ", output: " + outputPath)
-	imp = io.open(inputPath)
 	mymod = (command.run(GenericNetwork, False,
 		"input", imp,
 		"nTiles", nTiles,
@@ -38,27 +37,54 @@ def runNetwork(inputPath, outputPath):
 	print(myoutput)
 	io.save(myoutput, outputPath)
 
-if input.endswith(".tif"):
-	if output.endswith(".tif"):
-		runNetwork(input, output)
+
+inputPath = input.getPath() # Extract input file path
+outputPath = output.getPath()  # Extract output file path
+
+if inputPath.endswith(".tif"): # If processing a single .tif file
+
+	impSource = IJ.openImage(inputPath) 
+
+	[width, height, nChannels, nSlices, nFrames] = impSource.getDimensions()
+	if nChannels > 1: # if more than 1 channel, exit
+		print("ERROR: please provide an image with a single channel")
+		sys.exit()	
+
+	if outputPath.endswith(".tif"):
+		if nFrames > 1: # If there is only 1 specified .tif file but multiple frames
+			print("ERROR: To process an hyperstack with multiple frames, please provide a directory as output")
+			sys.exit()
+		runNetwork(outputPath, impSource)
+
 	else:
-		if not(output.endswith("/")):
-			output += "/"
-		runNetwork(input, output + getFileName(input))
-else:
-	if output.endswith(".tif"):
+		print("Processing: " + input.getName())
+		print("Found "+str(impSource.getNFrames())+" frames to process")
+
+		for dt in xrange(nFrames): # For each frame
+			frame = dt+1 # Frames in the movie will begin at 1
+			# Duplicate the frame of interest
+			impSingleTp = Duplicator().run(impSource, 1, 1, 1, nSlices, frame, frame)
+			# Create a new output fileName
+			root, ext = os.path.splitext(input.getName())
+			outputFileName = root + "_frame" + str(frame) + ".tif"
+			# Run the network
+			print("Processing: " + outputFileName)
+			runNetwork(os.path.join(outputPath, outputFileName), impSingleTp)
+
+elif input.isDirectory():
+	if outputPath.endswith(".tif"):
 		print("ERROR: please provide a directory as output, because your input is also a directory")
 		sys.exit()
-	if not(output.endswith("/")):
-		output += "/"
-	if not(input.endswith("/")):
-		input += "/"
-	if(output == input):
+	if(outputPath == inputPath):
 		print("ERROR: please provide an output directory that is not the same as the input directory")
 		sys.exit()
-	directory = File(input);
-	listOfFilesInFolder = directory.listFiles();
 
+	listOfFilesInFolder = input.listFiles();
 	for file in listOfFilesInFolder:
-		if file.toString().endswith(".tif"):
-			runNetwork(file.toString(), output + getFileName(file.toString()))
+		if file.getName().endswith(".tif"):
+			impSource = IJ.openImage(file.toString()) 
+			runNetwork(os.path.join(outputPath, file.getName()), impSource)
+
+else: # input is not a directory but not a .tif file either
+	print("ERROR: please provide a .tif file or directory for input")
+	sys.exit()