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
importtifffile
...
...
@@ -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")
# 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")
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")
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")