-rst implemented on spam-moveLabels and spam.labels.moveLabels

scripts/spam-moveLabels

@@ -46,7 +46,7 @@ args = spam.helpers.optionsParser.moveLabelsParser(parser)
 
 
 print("+-----------------------------+")
-print("|    SPAM - Labelled mover    |")
+print("|    SPAM - Label mover       |")
 print("+-----------------------------+")
 
 print("\nCurrent Settings:")
@@ -56,9 +56,10 @@ for key in sorted(argsDict):
 
 if args.RETURN_STATUS_THRESHOLD is None:
     DVC = spam.helpers.readCorrelationTSV(args.TSVFile.name, readConvergence=False)
+    RS = None
 else:
     DVC = spam.helpers.readCorrelationTSV(args.TSVFile.name, readConvergence=True)
-
+    RS = DVC['returnStatus']
 
 # Read labelled image
 lab = tifffile.imread( args.LabFile.name )
@@ -73,6 +74,7 @@ lab = tifffile.imread( args.LabFile.name )
 
 labOut = spam.label.moveLabels(lab,
                                DVC['PhiField'],
+                               returnStatus=RS,
                                margin=args.MARGIN,
                                PhiCOM=args.PHICOM,
                                threshold=args.THRESH,

tests/test_scripts.py

@@ -519,7 +519,8 @@ class testAll(unittest.TestCase):
         #######################################################
         exitCode = subprocess.call(["spam-moveLabels",
                                     testFolder + "Lab0.tif",
-                                    testFolder + "Step0-Step1-discreteDVC.tsv"])
+                                    testFolder + "Step0-Step1-discreteDVC.tsv",
+                                    "-rst", "2"])
         self.assertEqual(exitCode, 0)
 
         # Load displaced labelled image

tools/label/label.py

@@ -1622,7 +1622,7 @@ def convexVolume(lab, boundingBoxes=None, centresOfMass=None, volumes=None, numb
 
     return convexVolume
 
-def moveLabels(lab, PhiField, boundingBoxes=None, centresOfMass=None, margin=3, PhiCOM=True, threshold=0.5, labelDilate=0, numberOfThreads=1):
+def moveLabels(lab, PhiField, returnStatus = None, boundingBoxes=None, centresOfMass=None, margin=3, PhiCOM=True, threshold=0.5, labelDilate=0, numberOfThreads=1):
     """
     This function applies a discrete Phi field (from DDIC?) over a labelled image.
 
@@ -1634,6 +1634,11 @@ def moveLabels(lab, PhiField, boundingBoxes=None, centresOfMass=None, margin=3,
         PhiField : (multidimensional x 4 x 4 numpy array of floats)
             Spatial field of Phis
             
+        returnStatus : lab.max()x1 array of ints, optional
+            Array with the return status for each label (usually returned by ``spam-ddic``)
+            If not defined (Default = None), all the labels will be moved
+            If returnStatus[i] == 2, the label will be moved, otherwise is omitted and erased from the final image
+            
         boundingBoxes : lab.max()x6 array of ints, optional
             Bounding boxes in format returned by ``boundingBoxes``.
             If not defined (Default = None), it is recomputed by running ``boundingBoxes``
@@ -1764,10 +1769,16 @@ def moveLabels(lab, PhiField, boundingBoxes=None, centresOfMass=None, margin=3,
     # Setting up queues
     q_jobs    = multiprocessing.Queue()
     q_results = multiprocessing.Queue()
+    numberOfLabelsToMove = 0
     # Adding jobs to queues
     for label in range(1, numberOfLabels+1):
-        q_jobs.put(label)
-
+        # Skip the particles if the returnStatus == 2 and returnStatus != None
+        if type(returnStatus) == numpy.ndarray and returnStatus[label] != 2:
+            pass
+        else: # Add the particles
+            q_jobs.put(label)
+            numberOfLabelsToMove += 1
+            
     for i in range(numberOfThreads):  q_jobs.put("STOP")
     # Launching workers
     for i in range(numberOfThreads):
@@ -1778,7 +1789,7 @@ def moveLabels(lab, PhiField, boundingBoxes=None, centresOfMass=None, margin=3,
     nodes_processed   = 0
     # Waiting for results
     widgets = [progressbar.FormatLabel(''), ' ', progressbar.Bar(), ' ', progressbar.AdaptiveETA()]
-    pbar = progressbar.ProgressBar(widgets=widgets, maxval=numberOfLabels)
+    pbar = progressbar.ProgressBar(widgets=widgets, maxval=numberOfLabelsToMove)
     pbar.start()
 
     while finished_threads < numberOfThreads:
@@ -1791,7 +1802,7 @@ def moveLabels(lab, PhiField, boundingBoxes=None, centresOfMass=None, margin=3,
             if result[3] > 0:
                 labOut[result[1]][result[2]] = result[3]
             nodes_processed += 1
-            widgets[0] = progressbar.FormatLabel("{}/{} ".format(nodes_processed, numberOfLabels))
+            widgets[0] = progressbar.FormatLabel("{}/{} ".format(nodes_processed, numberOfLabelsToMove))
             pbar.update(nodes_processed)
     return labOut
 

tools/tests/test_label.py

@@ -709,6 +709,19 @@ class TestFunctionLabel(unittest.TestCase):
         imLab2 = spam.label.moveLabels(imLab, PhiField, boundingBoxes = boundingBoxes, centresOfMass = centresOfMass)
         self.assertIsNotNone(imLab2)
         
+        # Test 7A -> Check that it works if the return status is equal to 2
+        transformation = {'t': [5, 5, 5]}
+        PhiField[1] = spam.deformation.computePhi(transformation)
+        imLab2 = spam.label.moveLabels(imLab, PhiField, returnStatus = numpy.array([0, 2]),boundingBoxes = boundingBoxes, centresOfMass = centresOfMass)
+        # Compute Volume and COM
+        newVol = spam.label.volumes(imLab2)[-1]
+        newCOM = spam.label.centresOfMass(imLab2)[-1]
+        self.assertEqual(0, numpy.sum(iniVol - newVol))
+        self.assertTrue(((newCOM - iniCOM) == 5).all())
+        # Test 7B -> Check that it works if the return status is different to 2
+        imLab2 = spam.label.moveLabels(imLab, PhiField, returnStatus = numpy.array([0, 0]),boundingBoxes = boundingBoxes, centresOfMass = centresOfMass)
+        self.assertEqual(1, len(numpy.unique(imLab2)))
+        
     def test_erodeLabels(self):
         # Create the sphere
         imLab = skimage.morphology.ball(20)