diff imagej2_math_jython_script.py @ 0:bb84f130a4e1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_math_jython_script.py	Tue Sep 17 17:04:59 2019 -0400
@@ -0,0 +1,78 @@
+import jython_utils
+import sys
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+error_log = sys.argv[ -8 ]
+input = sys.argv[ -7 ]
+operation = sys.argv[ -6 ]
+expression = sys.argv[ -5 ]
+if sys.argv[ -4 ] in [ None, 'None' ]:
+    bin_constant = None
+else:
+    bin_constant = int( sys.argv[ -4 ] )
+if sys.argv[ -3 ] in [ None, 'None' ]:
+    float_constant = None
+else:
+    float_constant = float( sys.argv[ -3 ] )
+tmp_output_path = sys.argv[ -2 ]
+output_datatype = sys.argv[ -1 ]
+
+# Open the input image file.
+input_image_plus = IJ.openImage( input )
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.duplicate()
+image_processor_copy = input_image_plus_copy.getProcessor()
+bit_depth = image_processor_copy.getBitDepth()
+
+try:
+    if operation.find( '_' ) > 0:
+        # Square_Root.
+        new_operation = operation.replace( '_', ' ' )
+    elif operation in [ 'Square', 'Log', 'Exp', 'Abs', 'Reciprocal' ]:
+        # Unfortunately some ImageJ commands require a "..." ending
+        # while others do not.  There seems to be no pattern.
+        new_operation = '%s' % operation
+    else:
+        new_operation = '%s...' % operation
+
+    if operation == 'Macro':
+        # Apply the macro code to the image via a call to it's
+        # ImageProcessor since this option does not work using
+        # the IJ.run() method.
+        new_expression = expression.lstrip( '"' ).rstrip( '"' )
+        options = 'code=%s' % new_expression
+        image_processor_copy.applyMacro( new_expression )
+    elif operation == 'Min':
+        # Min does not work without using the ImageProcessor.
+        image_processor_copy.min( float_constant )
+    elif operation == 'Max':
+        # Max does not work without using the ImageProcessor.
+        image_processor_copy.max( float_constant )
+    elif operation == 'Abs':
+        if bit_depth not in [ 16, 32 ]:
+            # Convert the image to 32-bit.
+            IJ.run( input_image_plus_copy, "32-bit", "" )
+            IJ.run( input_image_plus_copy, new_operation, "" )
+    elif operation == 'Reciprocal':
+        if bit_depth != 32:
+            # Convert the image to 32 bit.
+            IJ.run( input_image_plus_copy, "32-bit", "" )
+            IJ.run( input_image_plus_copy, new_operation, "" )
+    else:
+        if operation in [ 'AND', 'OR', 'XOR' ]:
+            # Value is a binary number.
+            options = 'value=%d' % bin_constant
+        elif operation in [ 'Log', 'Exp', 'Square', 'Square_Root' ]:
+            # No constant value.
+            options = ''
+        else:
+            # Value is a floating point number.
+            options = 'value=%.3f' % float_constant
+        IJ.run( input_image_plus_copy, "%s" % new_operation, "%s" % options )
+    # Save the ImagePlus object as a new image.
+    IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
+except Exception, e:
+    jython_utils.handle_error( error_log, str( e ) )