slight improvement in readability in ldic

scripts/spam-ldic

@@ -177,10 +177,10 @@ for im2number in range(1, len(args.inFiles)):
     if args.MASK1:
         assert(im1.shape == im1mask.shape), "\nim1 and im1mask must have the same size! Exiting."
 
-    REG               = False
-    nodePositionsFile = None
-    PhiField          = None
-
+    # Three cases to handle:
+    #   1. phi file is reg   -> define nodes and apply reg
+    #   2. phi file is field -> take everything and check NS if passed
+    #   3. no phi file       -> define nodes
     if args.PHIFILE is not None:
         PhiFromFile = spam.helpers.readCorrelationTSV(args.PHIFILE.name, fieldBinRatio=args.PHIFILE_BIN_RATIO)
         if PhiFromFile is None:
@@ -201,60 +201,60 @@ for im2number in range(1, len(args.inFiles)):
             print("\t\t", decomposedPhiInit['z'])
             del decomposedPhiInit
 
-            REG = True
+            # Create nodes
+            if args.NS is None:
+                print(f"spam-ldic: You passed a registration file {args.PHIFILE.name}, I need -ns to be defined")
+                exit()
+            nodePositions, nodesDim = spam.DIC.makeGrid(im1.shape, args.NS)
+            numberOfNodes = nodePositions.shape[0]
 
             # We have a registration to apply to all points.
             # This is done in 2 steps:
             #   1. by copying the registration's little F to the Fs of all points
             #   2. by calling the decomposePhi function to compute the translation of each point
+            # Now that we know how many points we want to correlate, initalise PhiField
+            PhiField = numpy.zeros((numberOfNodes, 4, 4))
+            for node in range(numberOfNodes):
+                if args.APPLY_F == "all":
+                    PhiField[node] = PhiInit.copy()
+                elif args.APPLY_F == "rigid":
+                    PhiField[node] = spam.deformation.computeRigidPhi(PhiInit.copy())
+                else:
+                    PhiField[node] = numpy.eye(4)
+                # trasnlation application
+                PhiField[node][0:3, -1] = spam.deformation.decomposePhi(PhiInit.copy(), PhiCentre=PhiFromFile["fieldCoords"][0], PhiPoint=nodePositions[node])["t"]
+
+        else: # we have a Phi field and not a registration
+            nodePositions   = PhiFromFile["fieldCoords"]
+            numberOfNodes   = nodePositions.shape[0]
+            nodeSpacingFile = numpy.array([numpy.unique(nodePositions[:, i])[1] - numpy.unique(nodePositions[:, i])[0] if len(numpy.unique(nodePositions[:, i])) > 1 else numpy.unique(nodePositions[:, i])[0] for i in range(3)])
+            PhiField        = PhiFromFile["PhiField"]
+
+            # In case NS is also defined, complain, but if it's the same as the loaded data, continue
+            if args.NS is not None:
+                # compare them
+                if not numpy.allclose(numpy.array(args.NS), nodeSpacingFile, atol=0.0):
+                    print(f"spam-ldic: you passed a -ns={args.NS} which contradicts the node spacing in your Phi Field TSV of {nodeSpacingFile}")
+                    print(f"\thint 1: if you pass a Phi Field TSV you don't need to also define the node spacing")
+                    print(f"\thint 2: if you want to use your Phi Field TSV {args.PHIFILE.name} on a finer node spacing, pass it with spam-passPhiField")
+                    exit()
+                else:
+                    print(f"spam-ldic: passing -ns with a Phi Field TSV is not needed")
+
+            # If it's compatible, update args.NS
+            args.NS = nodeSpacingFile
 
-        # If the read Phi-file contains multiple lines it's an F field!
-        else:
-            #print("spam-pixelSearch: Assuming loaded PhiFile is coherent with the current run.")
-            nodePositionsFile = PhiFromFile["fieldCoords"]
-            PhiField          = PhiFromFile["PhiField"]
-
-    if nodePositionsFile is None:
+    else: # No Phi file at all
         if args.NS is None:
-            print("spam-pixelSearch: You're in regular grid mode, but no -ns is set and no Phi Field TSV has been passed, exiting.")
+            print("spam-ldic: I don't have a phi file or -ns defined, so don't know how to define grid...")
             exit()
         nodePositions, nodesDim = spam.DIC.makeGrid(im1.shape, args.NS)
+        numberOfNodes = nodePositions.shape[0]
 
-    else: # nodePositionsFile is defined -- i.e., we read a regular PhiField TSV
-        nodeSpacingFile = numpy.array([numpy.unique(nodePositionsFile[:, i])[1] - numpy.unique(nodePositionsFile[:, i])[0] if len(numpy.unique(nodePositionsFile[:, i])) > 1 else numpy.unique(nodePositionsFile[:, i])[0] for i in range(3)])
-        nodePositions = nodePositionsFile
-
-        if args.NS is not None:
-            # compare them
-            if not numpy.allclose(numpy.array(args.NS), nodeSpacingFile, atol=0.0):
-                print(f"spam-pixelSearch: you passed a -ns={args.NS} which contradicts the node spacing in your Phi Field TSV of {nodeSpacingFile}")
-                print(f"\thint 1: if you pass a Phi Field TSV you don't need to also define the node spacing")
-                print(f"\thint 2: if you want to use your Phi Field TSV {args.PHIFILE.name} on a finer node spacing, pass it with spam-passPhiField")
-                exit()
-            else:
-                print(f"spam-pixelSearch: passing -ns with a Phi Field TSV is not needed")
-        else:
-            args.NS = nodeSpacingFile
-
-    ###############################################################
-
-    numberOfNodes = nodePositions.shape[0]
-
-    if PhiField is None: # Either REG mode, or not TSV at all
-        # Now that we know how many points we want to correlate, initalise PhiField
         PhiField = numpy.zeros((numberOfNodes, 4, 4))
         for node in range(numberOfNodes):
             PhiField[node] = numpy.eye(4)
 
-    if REG:
-        # If we were passed a registration Phi TSV, apply it to each point
-        for node in range(numberOfNodes):
-            if args.APPLY_F == "all":
-                PhiField[node] = PhiInit.copy()
-            elif args.APPLY_F == "rigid":
-                PhiField[node] = spam.deformation.computeRigidPhi(PhiInit.copy())
-            PhiField[node][0:3, -1] = spam.deformation.decomposePhi(PhiInit.copy(), PhiCentre=PhiFromFile["fieldCoords"][0], PhiPoint=nodePositions[node])["t"]
-
     finishedNodes = 0
 
     error = numpy.zeros((numberOfNodes))