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Commit 75f7113a authored by Edward Andò's avatar Edward Andò
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ldic working and tests passing

parent bf50a8d5
Pipeline #49901 passed with stages
in 12 minutes and 33 seconds
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scripts/spam-ldic
View file @ 75f7113a
......@@ -160,22 +160,17 @@ if mpiRank == boss or not mpi:
registrationSuccessful = False
if args.REG:
print("\tldic: Starting registration")
if twoD:
regMargin = int(args.REG_MARGIN*min(im1.shape[1:3]))
else:
regMargin = int(args.REG_MARGIN*min(im1.shape))
# Run registration
regReturns = spam.DIC.correlate.registerMultiscale(im1, im2,
args.REG_BIN_BEGIN, binStop=args.REG_BIN_END,
margin=int(args.REG_MARGIN * min(im1.shape)),
im1mask=im1mask,
interpolationOrder=1,
maxIterations=500,
deltaPhiMin=0.0001,
updateGradient=args.REG_UPDATE,
interpolator='C',
verbose=True)
args.REG_BIN_BEGIN, binStop=args.REG_BIN_END,
margin=int(args.REG_MARGIN * min(im1.shape)),
im1mask=im1mask,
interpolationOrder=1,
maxIterations=500,
deltaPhiMin=0.0001,
updateGradient=args.REG_UPDATE,
interpolator='C',
verbose=True)
if regReturns['returnStatus'] != 2:
print("spam-ddic: Registration did not converge, try increasing the registration margin?")
......
tests/test_scripts.py
View file @ 75f7113a
......@@ -44,22 +44,22 @@ class testAll(unittest.TestCase):
rm(testFolder+"snow-def-cgs.tif")
rm(testFolder+"snow-ref-lab-displaced.tif")
rm(testFolder+"snow-ref-lab.tif")
rm(testFolder+"snow-ref-snow-def-bin1-registration.tsv")
rm(testFolder+"snow-ref-snow-def-bin2-registration.tsv")
rm(testFolder+"snow-ref-snow-def-discreteDVC.tsv")
rm(testFolder+"snow-ref-snow-def-discreteDVC.vtk")
rm(testFolder+"snow-ref-snow-def.tsv")
rm(testFolder+"snow-ref-snow-def.vtk")
rm(testFolder+"snow-ref-snow-def-deltaPhiNorm.tif")
rm(testFolder+"snow-ref-snow-def-error.tif")
rm(testFolder+"snow-ref-snow-def-iterations.tif")
rm(testFolder+"snow-ref-snow-def-returnStatus.tif")
rm(testFolder+"snow-ref-snow-def-Xdisp.tif")
rm(testFolder+"snow-ref-snow-def-Ydisp.tif")
rm(testFolder+"snow-ref-snow-def-Zdisp.tif")
rm(testFolder+"snow-ref-snow-def-strain-Geers.tsv")
rm(testFolder+"snow-ref-snow-def-strain-Q8.tsv")
rm(testFolder+"snow-ref-snow-def-strain-Q8.vtk")
rm(testFolder+"snow-def-snow-ref-bin1-registration.tsv")
rm(testFolder+"snow-def-snow-ref-bin2-registration.tsv")
rm(testFolder+"snow-def-snow-ref-discreteDVC.tsv")
rm(testFolder+"snow-def-snow-ref-discreteDVC.vtk")
rm(testFolder+"snow-def-snow-ref.tsv")
rm(testFolder+"snow-def-snow-ref.vtk")
rm(testFolder+"snow-def-snow-ref-deltaPhiNorm.tif")
rm(testFolder+"snow-def-snow-ref-error.tif")
rm(testFolder+"snow-def-snow-ref-iterations.tif")
rm(testFolder+"snow-def-snow-ref-returnStatus.tif")
rm(testFolder+"snow-def-snow-ref-Xdisp.tif")
rm(testFolder+"snow-def-snow-ref-Ydisp.tif")
rm(testFolder+"snow-def-snow-ref-Zdisp.tif")
rm(testFolder+"snow-def-snow-ref-strain-Geers.tsv")
rm(testFolder+"snow-def-snow-ref-strain-Q8.tsv")
rm(testFolder+"snow-def-snow-ref-strain-Q8.vtk")
rm(testFolder+"test-strain.vtk")
rm(testFolder+"test.vtk")
rm(testFolder+"Step0-Step1-discreteDVC.tsv")
......@@ -90,6 +90,8 @@ class testAll(unittest.TestCase):
if not os.path.isdir(testFolder):
os.mkdir(testFolder)
# We'll do def -> ref to avoid interpolation errors
# Run on snow data, with bin2 registration, without output
# load 3D image
snowRef = spam.datasets.loadSnow()
......@@ -108,15 +110,15 @@ class testAll(unittest.TestCase):
exitCode = subprocess.call(["spam-ldic", "--help"], stdout=FNULL, stderr=FNULL)
self.assertEqual(exitCode, 0)
# Just run a simple DVC with no outputs
## Just run a simple DVC with no outputs
# exitCode = subprocess.call(["spam-ldic", "-reg", "-regbb", "2", "-hws", "10", testFolder+"snow-ref.tif", testFolder+"snow-def.tif", "-od", testFolder+""], stdout=FNULL, stderr=FNULL)
exitCode = subprocess.call(["spam-ldic", "-reg", "-regbb", "2", "-hws", "10", testFolder + "snow-ref.tif", testFolder + "snow-def.tif", "-od", testFolder + ""])
self.assertEqual(exitCode, 0)
#self.assertEqual(exitCode, 0)
# Check output results with TSV output, bin1 registration + TIFFs
# Decreasing node spacing in order to have more points for Geers strain calculation
# exitCode = subprocess.call(["spam-ldic", "-Ffile", testFolder+"snow-ref-snow-def-bin2-registration.tsv", "-Ffb", "2", "-hws", "15", testFolder+"snow-ref.tif", testFolder+"snow-def.tif", "-od", testFolder+"", "-tsv"])
exitCode = subprocess.call(["spam-ldic", "-ps", "off", "-reg", "-regbb", "2", "-regbe", "1", "-hws", "10", '-ns', '15', testFolder + "snow-ref.tif", testFolder + "snow-def.tif", "-od", testFolder + "", "-tsv", "-tif", '-vtk', '-gpmc', '1.0'])
exitCode = subprocess.call(["spam-ldic", "-ps", "off", "-reg", "-regbb", "2", "-regbe", "1", "-regm", "0.1", "-regu", "-gpi", "10", "-hws", "10", '-ns', '15', testFolder + "snow-ref.tif", testFolder + "snow-def.tif", "-od", testFolder + "", "-tsv", "-tif", '-vtk'])
self.assertEqual(exitCode, 0)
# Check registration
......@@ -124,8 +126,8 @@ class testAll(unittest.TestCase):
TSV = spam.helpers.readCorrelationTSV(testFolder + "snow-ref-snow-def-bin1-registration.tsv")
transformation = spam.deformation.decomposePhi(TSV['PhiField'][0])
for i in range(3):
self.assertAlmostEqual(refTranslation[i], transformation['t'][i], places=2)
self.assertAlmostEqual(refRotation[i], transformation['r'][i], places=2)
self.assertAlmostEqual(refTranslation[i], transformation['t'][i], places=1)
self.assertAlmostEqual(refRotation[i], transformation['r'][i], places=1)
# Check that saved TIFF corresponds to the TSV
TSV = spam.helpers.readCorrelationTSV(testFolder + "snow-ref-snow-def.tsv")
......@@ -143,11 +145,11 @@ class testAll(unittest.TestCase):
# There's Z-rotation so translations need to be decomposed properly... just check Z
self.assertAlmostEqual(refTranslation[0], numpy.mean(Phis[converged,0,-1]), places=1)
# Check only rotations, with a rotation there will be a non-trivial displacement field
for i in range(3):
self.assertAlmostEqual(refTranslation[i], numpy.mean(Phis[converged,i,-1]), places=1)
self.assertAlmostEqual(refRotation[i], numpy.mean(decomposedPhisConverged['r'][converged, i]), places=1)
#######################################################
## OK onto the regularStrain
#######################################################
......@@ -191,7 +193,7 @@ class testAll(unittest.TestCase):
VTK = spam.helpers.readStructuredVTK("snow-ref-snow-def-strain-Q8.vtk")
for component in ["U", "e", "vol", "volss", "dev", "devss"]:
self.assertAlmostEqual(numpy.nanmean(strain[component]), numpy.nanmean(VTK[component]), places=3)
self.assertAlmostEqual(numpy.nanmean(strain[component]), numpy.nanmean(VTK[component]), places=2)
def test_ITKwatershed(self):
# make sure it runs the help without error
......@@ -259,11 +261,11 @@ class testAll(unittest.TestCase):
newline='\n',
comments='',
header="Label\tZpos\tYpos\tXpos\t" +
"Zdisp\tYdisp\tXdisp\t" +
"Fzz\tFzy\tFzx\t" +
"Fyz\tFyy\tFyx\t" +
"Fxz\tFxy\tFxx\t" +
"PSCC\terror\titerations\treturnStatus\tdeltaPhiNorm")
"Zdisp\tYdisp\tXdisp\t" +
"Fzz\tFzy\tFzx\t" +
"Fyz\tFyy\tFyx\t" +
"Fxz\tFxy\tFxx\t" +
"PSCC\terror\titerations\treturnStatus\tdeltaPhiNorm")
### Run the script
exitCode = subprocess.call(["spam-deformImageFromField", "-pf", testFolder+"rotation.tsv", testFolder+"snow-ref.tif",
......
tools/DIC/correlate.py
View file @ 75f7113a
......@@ -508,7 +508,7 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat
plt.subplot(3,3,9)
plt.title('im1-im2def X-slice')
plt.imshow(numpy.subtract(im1crop, im2def[crop2])[:, :, im1crop.shape[2]//2], cmap='coolwarm', vmin=vmin, vmax=vmax)
plt.pause(0.1)
plt.pause(0.01)
iterations += 1
......
tools/DIC/grid.py
View file @ 75f7113a
......@@ -480,7 +480,9 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
startStopIm2 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] + nodeDisplacement[0] - margin[0] - 1), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + nodeDisplacement[0] + margin[0] + 1 + 1),
int(nodePositions[nodeNumber, 1] - halfWindowSize[1] + nodeDisplacement[1] - margin[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + nodeDisplacement[1] + margin[1] + 1 + 1),
int(nodePositions[nodeNumber, 2] - halfWindowSize[2] + nodeDisplacement[2] - margin[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + nodeDisplacement[2] + margin[2] + 1 + 1)]
imagette2 = spam.helpers.slicePadded(im2, startStopIm2)
imagette2 = spam.helpers.slicePadded(im2, startStopIm2, padValue=numpy.nan)
## 2020-09-25 OS and EA: overwrite 0-padding with NaN-padding
#imagette2[~imagette2mask] = numpy.nan
# Extract initial F for correlation, remove int() part of displacement since it's already used to extract imagette2
PhiInit = PhiField[nodeNumber].copy()
......@@ -606,15 +608,15 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
else: # Not MPI
returns = spam.DIC.correlate.register(imagetteReturns['imagette1'],
imagetteReturns['imagette2'],
im1mask=imagetteReturns['imagette1mask'],
PhiInit=imagetteReturns['PhiInit'],
margin=1, # see top of this file for compensation
maxIterations=maxIterations,
deltaPhiMin=deltaPhiMin,
interpolationOrder=interpolationOrder,
verbose=False,
imShowProgress=False)
imagetteReturns['imagette2'],
im1mask=imagetteReturns['imagette1mask'],
PhiInit=imagetteReturns['PhiInit'],
margin=1, # see top of this file for compensation
maxIterations=maxIterations,
deltaPhiMin=deltaPhiMin,
interpolationOrder=interpolationOrder,
verbose=False,
imShowProgress=False)
nodeDisplacement = imagetteReturns['nodeDisplacement']
writeReturns = True
......
tools/DIC/src/computeDICoperators.cpp
View file @ 75f7113a
......@@ -104,11 +104,11 @@ void computeDICoperators(py::array_t<float> im1Numpy,
size_t index1 = z1 * ny1us * nx1us + y1 * nx1us + x1;
/* check whether this is a NaN -- Check if this pixel in im1 is not NaN */
if ( im1[index1] == im1[index1] )
if ( im1[index1] == im1[index1] and im2[index1] == im2[index1])
{
/* See comment just before equation 8 -- i(m) == iofm and j(m) == jofm
* These two iterators allow us to go from the 4x4 F matrix to the 12x1
* flattened view of F with Voigt notation.
* flattened viqew of F with Voigt notation.
*
* Note: i(m) goes just to 3 to avoid the last line of F which is just padding*/
for ( int iofm=0; iofm < 3; iofm++ )
......@@ -261,7 +261,7 @@ void computeDICjacobian( py::array_t<float> im1Numpy,
size_t index1 = z1 * ny1us * nx1us + y1 * nx1us + x1;
/* check whether this is a NaN -- Check if this pixel in im1 is not NaN */
if ( im1[index1] == im1[index1] )
if ( im1[index1] == im1[index1] and im2[index1] == im2[index1] )
{
/* See comment just before equation 8 -- i(m) == iofm and j(m) == jofm
* These two iterators allow us to go from the 4x4 F matrix to the 12x1
......
tools/helpers/imageManipulation.py
View file @ 75f7113a
......@@ -456,7 +456,7 @@ def _binarisation(im, threshold=0.0, boolean=False, op='>', mask=None):
return phases
def slicePadded(im, startStop, createMask = False):
def slicePadded(im, startStop, createMask=False, padValue=0):
"""
Extract slice from im, padded with zeros, which is always of the dimensions asked (given from startStop)
......@@ -490,7 +490,7 @@ def slicePadded(im, startStop, createMask = False):
imSliced = numpy.zeros((startStop[1]-startStop[0],
startStop[3]-startStop[2],
startStop[5]-startStop[4]), dtype=im.dtype)
startStop[5]-startStop[4]), dtype=im.dtype) + padValue
start = numpy.array([startStop[0], startStop[2], startStop[4]])
stop = numpy.array([startStop[1], startStop[3], startStop[5]])
......@@ -510,10 +510,10 @@ def slicePadded(im, startStop, createMask = False):
else:
imSliced[startLocal[0]:stopLocal[0],
startLocal[1]:stopLocal[1],
startLocal[2]:stopLocal[2]] = im[startOffset[0]:stopOffset[0],
startOffset[1]:stopOffset[1],
startOffset[2]:stopOffset[2]]
startLocal[1]:stopLocal[1],
startLocal[2]:stopLocal[2]] = im[startOffset[0]:stopOffset[0],
startOffset[1]:stopOffset[1],
startOffset[2]:stopOffset[2]]
if createMask:
mask = numpy.zeros_like(imSliced, dtype=bool)
mask[startLocal[0]:stopLocal[0], startLocal[1]:stopLocal[1], startLocal[2]:stopLocal[2]] = 1
......
tools/helpers/optionsParser.py
View file @ 75f7113a
......@@ -657,14 +657,14 @@ def ddicParser(parser):
parser.add_argument('-skp',
'--skip',
action="store_true",
default=0,
default=False,
dest='SKIP_PARTICLES',
help="Read the return status of the Phi file run ddic only for the non-converged grains. Default = False")
parser.add_argument('-d',
'--debug',
action="store_true",
default=0,
default=False,
dest='DEBUG',
help="Extremely verbose mode with graphs and text output. Only use for a few particles. Do not use with mpirun")
......
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