Fix tool

kostrykin · Mar 11, 2024 · e48ecdf · e48ecdf
1 parent 7c2ae17
commit e48ecdf
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Showing 2 changed files with 14 additions and 6 deletions.
diff --git a/tools/orientationpy/orientationpy-cli.py b/tools/orientationpy/orientationpy-cli.py
@@ -15,7 +15,7 @@
     parser.add_argument('--sigma', type=float, required=True)
     parser.add_argument('--min_coherency', type=float, required=True)
     parser.add_argument('--min_energy', type=float, required=True)
-    parser.add_argument('--bin_size', type=int, required=True)
+    parser.add_argument('--bin_size', type=float, required=True)
     parser.add_argument('--output_angle_tsv', type=str, default=None)
     args = parser.parse_args()
 
@@ -24,6 +24,8 @@
     im = np.squeeze(im)
     assert im.ndim == 2
 
+    assert args.bin_size > 0
+
     Gy, Gx = orientationpy.computeGradient(im, mode=args.mode)
     structureTensor = orientationpy.computeStructureTensor([Gy, Gx], sigma=args.sigma)
     orientations = orientationpy.computeOrientation(structureTensor, computeEnergy=True, computeCoherency=True)
@@ -39,7 +41,7 @@
         angles,
         range=(-90, +90),
         weights=weights,
-        bins=180 / args.bin_size,
+        bins=round(180 / args.bin_size),
     )
     hidx = np.argmax(hist)
     angle = (bin_edges[hidx] + bin_edges[hidx + 1]) / 2
@@ -48,5 +50,5 @@
     if args.output_angle_tsv:
         with open(args.output_angle_tsv, 'w') as fp:
             writer = csv.writer(fp, delimiter='\t', lineterminator='\n')
-            writer.writerow('Angle')
-            writer.writerow(angle)
+            writer.writerow(['Angle'])
+            writer.writerow([angle])
diff --git a/tools/orientationpy/orientationpy.xml b/tools/orientationpy/orientationpy.xml
@@ -23,6 +23,7 @@
     --sigma $sigma
     --min_energy $min_energy
     --min_coherency $min_coherency
+    --bin_size $bin_size
     
     ## Outputs
     
@@ -40,36 +41,41 @@
         <param argument="--sigma" type="float" label="Spatial scale (in pixels)" value="2" />
         <param argument="--min_energy" type="float" label="Minimum energy" value="0.1" min="0" max="1" />
         <param argument="--min_coherency" type="float" label="Minimum coherency" value="0.2" min="0" max="1" />
+        <param argument="--bin_size" type="float" label="Histogram bin size" value="1" min="0" max="1" help="Governs the precision of the estimation (smaller is better). Must be strictly positive." />
     </inputs>
     <outputs>
         <data format="tsv" name="output_angle_tsv" from_work_dir="output_angle.tsv" />
     </outputs>
     <tests>
+        <!-- Test negative angle -->
         <test>
             <param name="image" value="input1.tif" />
             <param name="mode" value="finite_difference" />
             <param name="sigma" value="2" />
             <param name="min_energy" value="0.1" />
             <param name="min_coherency" value="0.2" />
+            <param name="bin_size" value="2" />
             <output name="output_angle_tsv">
                 <assert_contents>
                     <has_line line="Angle" />
-                    <has_line line="45" />
+                    <has_line line="-44.95" />
                     <has_n_lines n="2" />
                     <has_n_columns n="1" />
                 </assert_contents>
             </output>
         </test>
+        <!-- Test positive angle -->
         <test>
             <param name="image" value="input2.tif" />
             <param name="mode" value="finite_difference" />
             <param name="sigma" value="2" />
             <param name="min_energy" value="0.1" />
             <param name="min_coherency" value="0.2" />
+            <param name="bin_size" value="2" />
             <output name="output_angle_tsv">
                 <assert_contents>
                     <has_line line="Angle" />
-                    <has_line line="-45" />
+                    <has_line line="45.05" />
                     <has_n_lines n="2" />
                     <has_n_columns n="1" />
                 </assert_contents>