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Commit 384f67ff authored by Edward Andò's avatar Edward Andò
Browse files

Clarifying spam-moveGrains options

parent c5c32d88
Pipeline #49319 passed with stages
in 23 minutes and 49 seconds
......@@ -69,7 +69,7 @@ def work_on_one_job(worker_number, q_jobs, q_results):
getLabelReturn = ltk.getLabel(lab,
label,
labelDilate=0,
margin=args.DISPLACEMENT_MARGIN,
margin=args.LABEL_MARGIN,
boundingBoxes=boundingBoxes,
centresOfMass=centresOfMass)
......@@ -77,7 +77,7 @@ def work_on_one_job(worker_number, q_jobs, q_results):
subVolSize = numpy.array(getLabelReturn['subvol'].shape)
Phi = DVC['PhiField'][label].copy()
Phi[0:3,-1] *= float(args.MULTIPLY_DISPLACEMENTS)
Phi[0:3,-1] *= float(args.PHIFILE_BIN_RATIO)
# Phi will be split into a local part and a part of floored displacements
disp = numpy.floor(Phi[0:3,-1])
......
......@@ -71,7 +71,7 @@ def ldicParser(parser):
type=int,
default=1,
dest='PHIFILE_BIN_RATIO',
help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
parser.add_argument('-glt',
'--grey-low-threshold',
......@@ -312,7 +312,7 @@ def ldicParser(parser):
# 2018-03-24 check for 2D without loading images
# try:
# except BaseException:
# print("DICregularGrid: Input TIFF files need to be writeable in order to guess their dimensionality")
# print("DICregularGrid: Input TIFPhi files need to be writeable in order to guess their dimensionality")
# exit()
# 2019-03-21 EA: better check for dimensions, doesn't depend on writability of files
import tifffile
......@@ -532,7 +532,7 @@ def ddicParser(parser):
type=int,
default=1,
dest='PHIFILE_BIN_RATIO',
help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
parser.add_argument('-pfd',
......@@ -824,7 +824,7 @@ def multiModalRegistrationParser(parser):
# type=int,
# default=1,
# dest='PHIFILE_BIN_RATIO',
# help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
# help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
# parser.add_argument('-tra',
# '--translation',
......@@ -931,7 +931,7 @@ def gdicParser(parser):
type=int,
default=1,
dest='PHIFILE_BIN_RATIO',
help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
# parser.add_argument('-glt',
# '--grey-low-threshold',
......@@ -1391,7 +1391,7 @@ def moveGrainsParser(parser):
type=str,
default=None,
dest='PREFIX',
help='Prefix for output TIFF file (without extension). Default is basename of input file')
help='Prefix for output TIFPhi file (without extension). Default is basename of input file')
parser.add_argument('-com',
'--apply-phi-centre-of-mass',
......@@ -1406,13 +1406,6 @@ def moveGrainsParser(parser):
dest='THRESH',
help='Greyscale threshold to keep interpolated voxels. Default = 0.5')
parser.add_argument('-ld',
'--label-dilate',
type=int,
default=0,
dest='LABEL_DILATE',
help="Number of times to dilate labels. Default = 0")
parser.add_argument('-rst',
'--return-status-threshold',
type=int,
......@@ -1427,33 +1420,34 @@ def moveGrainsParser(parser):
dest='GREY_FILE',
help='Input greylevel tiff file corresponding to the input labelled file. This option requires a threshold to be set with -thr')
#parser.add_argument('-gt',
#'--grey-threshold',
#type=float,
#default=None,
#dest='GREY_THRESHOLD',
#help='Threshold for input greylevel file')
parser.add_argument('-om',
'--overall-margin',
type=int,
default=10,
dest='OVERALL_MARGIN',
help="Overall image margin for particle movement, this is how much the labelled image is increased before calculating. Default = 10")
help="Overall image padding for label movement near edges, this is how much the labelled image is increased before starting to place label. Default = 10")
parser.add_argument('-dm',
'--displacement-margin',
parser.add_argument('-lm',
'--label-margin',
type=int,
default=3,
dest='DISPLACEMENT_MARGIN',
help="Displacement margin for particle movement, this the padding around the extraction of each objet and show allow for rotation. Default = 3")
dest='LABEL_MARGIN',
help="Bounding box margin for each label to allow for rotation/strain of the label. Default = 3")
parser.add_argument('-ld',
'--label-dilate',
type=int,
default=0,
dest='LABEL_DILATE',
help="Number of times to dilate labels. Default = 0")
parser.add_argument('-md',
'--multipy-displacements',
parser.add_argument('-pfb',
'--phiFile-bin-ratio',
type=float,
default=1.0,
dest='MULTIPLY_DISPLACEMENTS',
help="Displacement margin for particle movement, this must be AT LEAST equal to the mazimum displacement. Default = 1.0")
default=1,
dest='PHIFILE_BIN_RATIO',
help="Ratio of binning level between loaded Phi file and labelled image. If the input Phi file has been obtained on a 500x500x500 image and the labelled image is 1000x1000x1000, this should be 2. Default = 1")
parser.add_argument('-np',
'--number-parallel-process',
......@@ -1497,7 +1491,7 @@ def ITKwatershedParser(parser):
parser.add_argument('inFile',
metavar='inFile',
type=argparse.FileType('r'),
help='Path to binary TIFF file to be watershedded')
help='Path to binary TIFPhi file to be watershedded')
parser.add_argument('-ld',
'--label-dilate',
......@@ -1511,7 +1505,7 @@ def ITKwatershedParser(parser):
type=str,
default=None,
dest='MARKER_FILE',
help='Path to labelled TIFF file to use as markers')
help='Path to labelled TIFPhi file to use as markers')
parser.add_argument('-pre',
'--prefix',
......@@ -1708,7 +1702,7 @@ def deformImageFromFieldParser(parser):
parser.add_argument('inFile',
metavar='inFile',
type=argparse.FileType('r'),
help='Path to TIFF file containing the image to deform')
help='Path to TIFPhi file containing the image to deform')
parser.add_argument('-a',
'-triangulation-alpha-value',
......@@ -1736,7 +1730,7 @@ def deformImageFromFieldParser(parser):
type=int,
default=1,
dest='PHIFILE_BIN_RATIO',
help="Ratio of binning level between loaded F file and current calculation. If the input F file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
help="Ratio of binning level between loaded Phi file and current calculation. If the input Phi file has been obtained on a 500x500x500 image and now the calculation is on 1000x1000x1000, this should be 2. Default = 1")
parser.add_argument('-od',
'--out-dir',
......
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