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',
...
...
@@ -943,7 +943,7 @@ 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="Greyscale image of reference state for correlation")
parser.add_argument('lab1',
metavar='lab1',
type=argparse.FileType('r'),
help="Labelled image of reference state for correlation")
parser.add_argument('im2',
metavar='im2',
type=argparse.FileType('r'),
help="Greyscale image of deformed state for correlation")
parser.add_argument('-mar',
'--margin',
type=int,
default=5,
dest='margin',
help="Margin in pixels. Default = 5")
parser.add_argument('-rst',
'--return-status-threshold',
type=int,
default=2,
dest='RETURN_STAT_THRESHOLD',
help='Skip labels already correlated with at least this return status (requires -pf obviously). Default = 2')
parser.add_argument('-ld',
'--label-dilate',
type=int,
default=1,
dest='LABEL_DILATE',
help="Number of times to dilate labels. Default = 1")
parser.add_argument('-pf',
'-phiFile',
dest='PHIFILE',
default=None,
type=argparse.FileType('r'),
help="Path to TSV file containing initial Phi guess for each label. Default = None")
parser.add_argument('-nomask',
'--no-mask',
action="store_false",
dest='MASK',
help='Don\'t mask each label\'s image')
parser.add_argument('-od',
'--out-dir',
type=str,
default=None,
dest='OUT_DIR',
help="Output directory, default is the dirname of input file")
parser.add_argument('-pre',
'--prefix',
type=str,
default=None,
dest='PREFIX',
help="Prefix for output files (without extension). Default is basename of input file")
args=parser.parse_args()
# If we have no out dir specified, deliver on our default promise -- this can't be done inline before since parser.parse_args() has not been run at that stage.
ifargs.OUT_DIRisNone:
args.OUT_DIR=os.path.dirname(args.im1.name)
# However if we have no dir, notice this and make it the current directory.
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")