Merge pull request #112 from kostrykin/2d_auto_threshold/dev

Fix bug in "Threshold image" tool

tools/2d_auto_threshold/auto_threshold.py

@@ -43,7 +43,7 @@ def do_thresholding(in_fn, out_fn, th_method, block_size=5, threshold=0, invert_
     parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method')
     parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold')
     parser.add_argument('threshold', type=float, default=0, help='Manual thresholding value')
-    parser.add_argument('invert_output', default=False, type=bool, help='Values below/above the threshold are labeled with 0/255 if False, and with 255/0 otherwise')
+    parser.add_argument('--invert_output', default=False, action='store_true', help='Values below/above the threshold are labeled with 0/255 by default, and with 255/0 if this argument is used')
     args = parser.parse_args()
 
     do_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.threshold, args.invert_output)

tools/2d_auto_threshold/auto_threshold.xml

@@ -2,7 +2,7 @@
     <description>with scikit-image</description>
     <macros>
         <token name="@TOOL_VERSION@">0.18.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -23,7 +23,7 @@
     '$th_method.method_id'
     '$th_method.block_size'
     '$th_method.threshold'
-    '$invert_output'
+    $invert_output
     ]]>
     </command>
     <inputs>
@@ -72,7 +72,7 @@
                 <param name="block_size" type="integer" value="5" label="Odd size of pixel neighborhood for determining the threshold" />
             </when>
         </conditional>
-        <param name="invert_output" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
+        <param name="invert_output" type="boolean" checked="false" truevalue="--invert_output" falsevalue="" label="Invert output labels" help="Pixels are usually assigned the label 0 if the pixel value is below (or equal to) the threshold, and 255 if it is above the threshold. If this option is activated, pixels are assigned the label 255 if the pixel value is below (or equal to) the threshold, and 0 if it is above the threshold." />
     </inputs>
     <outputs>
        <data format="tiff" name="output" from_work_dir="out.tif" />