help="Path to TSV file containing initial F guess, can be single-point registration or multiple point correlation. Default = None")
help="Path to TSV file containing initial Phi guess, can be single-point registration or multiple point correlation. Default = None")
parser.add_argument('-pfb',
'--phiFile-bin-ratio',
...
...
@@ -408,7 +408,7 @@ def ddicParser(parser):
dest='PHIFILE',
default=None,
type=argparse.FileType('r'),
help="Path to TSV file containing initial F guess, can be single-point registration or multiple point correlation. Default = None")
help="Path to TSV file containing initial Phi guess, can be single-point registration or multiple point correlation. Default = None")
parser.add_argument('-pfb',
'--phiFile-bin-ratio',
...
...
@@ -837,7 +837,7 @@ def gdicParser(parser):
dest='PHIFILE',
default=None,
type=argparse.FileType('r'),
help="Path to TSV file containing initial F guess, can be single-point registration or multiple point correlation. Default = None")
help="Path to TSV file containing initial Phi guess, can be single-point registration or multiple point correlation. Default = None")
parser.add_argument('-pfb',
'--phiFile-bin-ratio',
...
...
@@ -1840,9 +1840,9 @@ def register(parser):
'-mar',
'--margin',
type=float,
default=0.1,
default=None,
dest='MARGIN',
help='Interpolation margin in proportions of image size. Default = 0.1, which means 0.1 * image size from both sides in all directions')
help='Interpolation margin in pixels. Default is the default for spam.DIC.registerMultiscale')
parser.add_argument('-m3',
'-mar3',
...
...
@@ -1851,7 +1851,7 @@ def register(parser):
type=int,
default=None,
dest='MARGIN',
help="Interpolation margin in pixels. Default = 0.1 * image size from both sides in all directions")
help='ZYX interpolation margin in pixels. Default is the default for spam.DIC.registerMultiscale')
parser.add_argument('-ug',
'--update-gradient',
...
...
@@ -1933,7 +1933,6 @@ def register(parser):
else:
args.PREFIX+="-registration"
returnargs
...
...
@@ -2498,7 +2497,7 @@ def passPhiField(parser):
dest='PHIFILE',
default=None,
type=argparse.FileType('r'),
help="Path to TSV file containing initial F guess, can be single-point registration or multiple point correlation. Default = None")
help="Path to TSV file containing initial Phi guess, can be single-point registration or multiple point correlation. Default = None")
parser.add_argument('-pfb',
'--phiFile-bin-ratio',
...
...
@@ -2524,7 +2523,8 @@ def passPhiField(parser):
parser.add_argument('-lab1',
'--labelledFile1',
dest='LAB1',
default=None,
nargs='+',
default=[],
type=argparse.FileType('r'),
help="Path to tiff file containing a labelled image 1 that defines zones to correlate. Disactivates -hws and -ns options")
...
...
@@ -2560,6 +2560,28 @@ def passPhiField(parser):
dest='im1shape',
help="Size of im1 in pixels Z Y X")
parser.add_argument('-pf2',
'-phiFile2',
dest='PHIFILE2',
nargs='+',
default=[],
type=argparse.FileType('r'),
help="Path to second spam-ddic TSV file(s). Default = None")
parser.add_argument('-pf2b',
'--phiFile2-bin-ratio',
type=int,
default=1,
dest='PHIFILE2_BIN_RATIO',
help="Ratio of binning level between second 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")