Merge branch '29-systematic-error'

main.py

@@ -84,15 +84,19 @@ def placefiducial():
     and intra-operative images. FLE is added to each
     marker location.
     """
-    jsonstring = json.dumps(request.json)
-    position = [json.loads(jsonstring)[0],
-                    json.loads(jsonstring)[1], 0.0]
+    x_pos = request.json.get("x_pos")
+    y_pos = request.json.get("y_pos")
+    position = [x_pos, y_pos, 0.0]
     if _is_valid_fiducial(position):
-        moving_fle = json.loads(jsonstring)[2]
-        fixed_fle = json.loads(jsonstring)[3]
-
-        fixed_fle = FLE(independent_fle = fixed_fle)
-        moving_fle = FLE(independent_fle = moving_fle)
+        moving_ind_fle = request.json.get("pre_op_ind_fle", [0., 0., 0.])
+        fixed_ind_fle = request.json.get("intra_op_ind_fle", [0., 0., 0.])
+        moving_sys_fle = request.json.get("pre_op_sys_fle", [0., 0., 0.])
+        fixed_sys_fle = request.json.get("intra_op_sys_fle", [0., 0., 0.])
+
+        fixed_fle = FLE(independent_fle = fixed_ind_fle,
+                        systematic_fle = fixed_sys_fle)
+        moving_fle = FLE(independent_fle = moving_ind_fle,
+                         systematic_fle = moving_sys_fle)
 
         fixed_fid = fixed_fle.perturb_fiducial(position)
         moving_fid = moving_fle.perturb_fiducial(position)

static/main.js

@@ -26,6 +26,10 @@ var intraOpFLEStdDev = [];
 var preOpFLEEAV = 0;
 var intraOpFLEEAV = 0;
 
+//we can have a systematic error too
+var preOpSysError = [];
+var intraOpSysError = [];
+
 //page elements for convenience
 var preOpImage = document.getElementById("pre-operative-image");
 var preOpCanvas = document.getElementById("pre-operative-canvas");
@@ -290,7 +294,13 @@ function placeFiducial(x, y) {
       headers: {
 	"Content-Type": "application/json"
       },
-      body: JSON.stringify([x, y, preOpFLEStdDev, intraOpFLEStdDev])
+	      body: JSON.stringify({
+		      "x_pos": x,
+		      "y_pos": y,
+		      "pre_op_ind_fle": preOpFLEStdDev, 
+		      "intra_op_ind_fle": intraOpFLEStdDev,
+		      "pre_op_sys_fle": preOpSysError, 
+		      "intra_op_sys_fle": intraOpSysError})
     })
     .then(resp => {
       if (resp.ok)
@@ -435,6 +445,10 @@ function init_fles() {
         intraOpFLEStdDev = data.fixed_fle_sd;
         preOpFLEEAV = data.moving_fle_eav;
         intraOpFLEEAV = data.fixed_fle_eav;
+
+        preOpSysError = [0.0, 0.0, 0.0];
+        intraOpSysError = [0.0, 0.0, 0.0];
+
 	console.log(data);
       });
     })

tests/test_main.py

@@ -2,6 +2,7 @@
 
 """Fiducial Registration Educational Demonstration tests"""
 from html.parser import HTMLParser
+import json
 import pytest
 import main as sksfmain # pylint: disable=unused-import
 
@@ -84,6 +85,39 @@ def testserve_placefiducial(client):
     parser.feed(str(fid.data))
     assert parser.title_ok
 
+    #normal usage
+    x_pos = 0.0
+    y_pos = 0.0
+    pre_op_ind_fle = [0.0, 0.0, 0.0]
+    intra_op_ind_fle = [2.0, 2.0, 2.0]
+    postdata = dict(
+             x_pos=x_pos,
+             y_pos=y_pos,
+             pre_op_ind_fle=pre_op_ind_fle,
+             intra_op_ind_fle=intra_op_ind_fle)
+    fid = client.post('/placefiducial', data = json.dumps(postdata),
+                    content_type='application/json')
+    assert json.loads(fid.data.decode()).get("valid_fid")
+
+    #we should be able to apply a systematic error
+    x_pos = 100.0
+    y_pos = 250.0
+    pre_op_sys_fle = [0.0, 0.0, 0.0]
+    intra_op_sys_fle = [2.0, 2.0, -2.0]
+    postdata = dict(
+             x_pos=x_pos,
+             y_pos=y_pos,
+             pre_op_sys_fle=pre_op_sys_fle,
+             intra_op_sys_fle=intra_op_sys_fle)
+    fid = client.post('/placefiducial', data = json.dumps(postdata),
+                    content_type='application/json')
+
+    intra_op_fid = json.loads(fid.data.decode()).get("fixed_fid")
+    pre_op_fid = json.loads(fid.data.decode()).get("moving_fid")
+    assert intra_op_fid == [102.0, 252.0, -2.0]
+    assert pre_op_fid == [100.0, 250.0, 0.0]
+
+
 def testserve_register(client):
     """Serve register"""
     #get should not be allowed