Commit 77941eb7 authored by Edward Andò's avatar Edward Andò
Browse files

Resolves #168 and #169

parent f4e61384
Pipeline #46138 passed with stages
in 31 minutes and 10 seconds
......@@ -566,7 +566,7 @@ if mpiRank == boss or not mpi:
VTKglyphDict = {'displacements': PhiField[:, 0:3, -1],
'mag(displacements)': magDisp,
'RS': returnStatus}
'returnStatus': returnStatus}
# if regsub add a line to VTK output and also save separate TSV file
if args.REGSUB:
......
......@@ -746,6 +746,11 @@ def mergeRegularGridAndDiscrete(regularGrid=None, discrete=None, labelledImage=N
Labelled volume used for discrete computation
Default = None
binningLabelled : int
Are the labelled images and their PhiField at a different bin level than
the regular field?
Default = 1
alwaysLabel : bool
If regularGrid point falls inside the label, should we use the
label displacement automatically?
......
......@@ -1754,7 +1754,7 @@ def deformImageFromFieldParser(parser):
parser.add_argument('-cgs',
action="store_true",
dest='CORRECT_GREY_FOR_STRAIN',
help='Only for field mode: Apply a correction to the greyvalues according to strain in tetrahedon? For a dray sample, greyvalues of vacuum should be =0 (Stavropoulou et al. 2020 Frontiers Eq. 12 with mu_w=0). Default = False')
help='Only for field mode: Apply a correction to the greyvalues according to strain in tetrahedon? For a dry sample, greyvalues of vacuum should be =0 (Stavropoulou et al. 2020 Frontiers Eq. 12 with mu_w=0). Default = False')
args = parser.parse_args()
......
......@@ -146,6 +146,8 @@ def detectAndFixOversegmentation(lab, nVoxThreshold=25):
same (lowest) label.
This is recursive, so a label that is merged is re-treated as a larger
grain, which is checked again.
If any labels have merged, the labels will be discontinuous integers,
running spam.label.toolkit.makeLabelsSequential is recommended.
Parameters
----------
......@@ -160,8 +162,6 @@ def detectAndFixOversegmentation(lab, nVoxThreshold=25):
--------
lab : 3D numpy array of ints ( of type spam.label.toolkit.labelType)
An array of labels with 0 as the background.
If any labels have merged, the labels will be discontinuous integers,
running spam.label.toolkit.makeLabelsSequential is recommended.
"""
lab = lab.astype(spam.label.labelType)
bb = spam.label.boundingBoxes(lab)
......
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