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Commit 6ec06eb3 authored by Edward Andò's avatar Edward Andò
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slight improvement in readability in ldic

parent 8e3008e1
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scripts/spam-ldic
View file @ 6ec06eb3
......@@ -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))
......
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