Added channel parameter

descriptor.json

@@ -5,7 +5,7 @@
     "image": "neubiaswg5/w_nucleisegmentation-cellpose",
     "type": "singularity"
   },
-  "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE DIAMETER PROB_THRESHOLD",
+  "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE DIAMETER PROB_THRESHOLD NUC_CHANNEL",
   "inputs": [
     {
       "id": "cytomine_host",
@@ -73,6 +73,17 @@
       "set-by-server": false,
       "optional": true,
       "type": "Number"
+    },
+    {
+      "id": "nuc_channel",
+      "value-key": "@ID",
+      "command-line-flag": "--@id",
+      "name": "Nuclei channel",
+	"description": "Use default 0 for grayscale and RGB that should be converted to grayscale based on luminance. Use 1, 2 or 3 to select a specific RGB channel",
+      "default-value": 0,
+      "set-by-server": false,
+      "optional": true,
+      "type": "Number"
     }
   ],
 

wrapper.py

@@ -22,13 +22,15 @@ def main(argv):
 
         # Make sure all images have at least 224x224 dimensions
         # and that minshape / maxshape * minshape >= 224
-        nuc_channel = 0 # 0 = Grayscale, 1,2,3 = rgb channel
+        # 0 = Grayscale (if input RGB, convert to grayscale)
+        # 1,2,3 = rgb channel
+        nuc_channel = bj.parameters.nuc_channel
         resized = {}
         for bfimg in in_imgs:
             fn = os.path.join(in_path, bfimg.filename)
             img = imageio.imread(fn)
-            if len(img.shape) > 2:
-                nuc_channel = 3
+            if len(img.shape) > 2 and nuc_channel == 0:
+                img = skimage.color.rgb2gray(img)
             minshape = min(img.shape[:2])
             maxshape = max(img.shape[:2])
             if minshape != maxshape or minshape < 224:
@@ -49,7 +51,7 @@ def main(argv):
 
         # Add here the code for running the analysis script
         #"--chan", "{:d}".format(nuc_channel)
-        cmd = ["python", "-m", "cellpose", "--dir", tmp_path, "--pretrained_model", "nuclei", "--save_tif", "--no_npy", "--all_channels", "--diameter", "{:f}".format(bj.parameters.diameter), "--cellprob_threshold", "{:f}".format(bj.parameters.prob_threshold)]
+        cmd = ["python", "-m", "cellpose", "--dir", tmp_path, "--pretrained_model", "nuclei", "--save_tif", "--no_npy", "--chan", "{:d}".format(nuc_channel), "--diameter", "{:f}".format(bj.parameters.diameter), "--cellprob_threshold", "{:f}".format(bj.parameters.prob_threshold)]
         status = subprocess.run(cmd)
 
         if status.returncode != 0: