BioBB MORPH Command Line Help
Generic usage:
biobb_morph [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>
Morph
Morphing a morph IVD mesh to a target, creating a patient-personalized model.
Get help
Command:
biobb_morph -h
usage: morph [-h] --fileIn FILEIN [OPTIONS]
Program that morphs a morph IVD mesh to a target, producing a patient-personalized model.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_file_path1 INPUT_FILE_PATH1
Path to the input file containing source and target information (required).
--input_file_path2 INPUT_FILE_PATH2
Description for the sources paths.
--output_file_path OUTPUT_FILE_PATH
Description for the outputs path.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
-m Non-Rigid registration mode. Options:
1: AF
2: NP
3: NoBEP
4: CEPmorph
5: All
0: NONE
Default: 5.
-i Create the .inp file for specific components. Options:
1: AF
2: NP
3: NoBEP
4: All
0: NONE
Default: 4.
-a Command to call ABAQUS or Gmsh. Default: "abaqus".
-b Command to call BCPD++. Default: "bcpd".
-e Check failed elements in the resulting .inp file:
1: YES
2: Iterate value of lambda
0: NO
Default: 2.
-r Perform rigid registration initially:
1: YES
0: NO
Default: 1.
-w Perform morphing with CEP:
1: YES
0: NO
Default: 0.
-y Use interpolated files:
1: YES
0: NO
Default: 1.
-f Fuse AF and NP for the final morph:
1: YES
0: NO
Default: 1.
-c Morph external surfaces of AF and NP (including CEP):
1: YES
0: NO
Default: 1.
-d Check Hausdorff distance between 3D grids:
1: YES
0: NO
Default: 1.
--CEP Perform non-rigid registration of CEP:
1: YES
0: NO
Default: 0.
--lambdaBeta File with alpha and beta values for non-rigid registration. Default: "lambdaBeta.csv".
--TZ Create a Transition Zone:
1: YES
0: NO
Default: None.
-v List of floats for desired movement. Default: [0, 0, 0.05].
-n Distance between two nodes of the mesh. Default: 0.3.
-t Translation of AF and NP. Default: [0.0, 24.1397991, 2.94929004].
-p Plane to orthogonally project NP nodes for spline line of perimeter. Default: [1, 1, 0].
-s Parameter to reduce NP contour size. Default: 0.8.
I / O Arguments
Syntax:
input_argument (datatype): Definition
Arguments:
fileIn (string):
Path to the input file containing source and target model information.
File type: txt.sources_path (string):
Path to the morph mesh IVD.
File type: path.results_path (string):
Path to the resulting morph meshes for IVD.
File type: output.
Config Parameters
Syntax:
parameter (datatype) - (default_value): Definition
Parameters:
-morph (int): Non-Rigid registration mode. Options:
1: AF
2: NP
3: NoBEP
4: CEPmorph
5: All
0: NONE
Default: 5.
-toINP (int): Create the .inp file for specific components. Options:
1: AF
2: NP
3: NoBEP
4: All
0: NONE
Default: 4.
-abaqusCommand (str): Command used to call ABAQUS. If “-a gmsh”, the Gmsh tool is used. Default: “abaqus”.
-bcpdCommand (str): Command used to call BCPD++. Default: “bcpd”.
-checkFElem (int): Check failed elements of the resulting .inp file (Abaqus required). Options:
1: YES
2: Iterate value of lambda
0: NO
Default: 2.
-rigid (int): Perform rigid registration at the beginning of the process. Options:
1: YES
0: NO
Default: 1.
-WCEP (int): Perform morphing with CEP. Options:
1: YES
0: NO
Default: 0.
-interpo (int): Use interpolated files. Options:
1: YES
0: NO
Default: 1.
-fusion (int): Fuse the AF and NP for the final morph. Options:
1: YES
0: NO
Default: 1.
-surfRegCEP (int): Morph external surfaces of AF and NP (including CEP). Options:
1: YES
0: NO
Default: 1.
-checkHaus (int): Check Hausdorff distance between 3D grids (Euclidean distance). Options:
1: YES
0: NO
Default: 1.
–CEP (int): Perform non-rigid registration of the CEP. Options:
1: YES
0: NO
Default: 0.
–lambdaBeta (str): Text file with the alpha and beta values for non-rigid registration. Default: “lambdaBeta.csv”.
–TZ (int): Create a Transition Zone. Options:
1: YES
0: NO
Default: None.
-movement (list of float): Enter a list of floats separated by spaces to represent desired movement.
Positive: Positive direction
Negative: Negative direction
0: No movement
Default: [0, 0, 0.05].
-nodeDistance (float): Distance between two nodes of the mesh. Default: 0.3.
-moveTo (list of float): Translation of the AF and NP. Default: [0.0, 24.1397991, 2.94929004].
-plane (list of int): Plane to orthogonally project nodes of the NP to create the spline line of the perimeter. Default: [1, 1, 0].
-reduce_param (float): Parameter to reduce the size of the contour of the NP. Default: 0.8.
YAML
Common config file
properties:
morph: 5
toINP: 4
abaqusCommand: 'abaqus'
bcpdCommand: 'bcpd'
checkFElem: 2
rigid: 1
WCEP: 0
interpo: 1
fusion: 1
surfRegCEP: 1
checkHaus: 1
CEP: 0
lambdaBeta: 'lambdaBeta.csv'
TZ: 1
movement: [0, 0, 0.04]
nodeDistance: 0.4
moveTo: [0.0, 24.1397991, 2.94929004]
plane: [1, 1, 0]
reduce_param: 0.8
Command line
morph --fileIn models/IVD_L1L2_NC0031.txt -morph 5 -toINP 4 -a abaqus -b bcpd --CEP 0 -d 1 --lambdaBeta lambdaBeta.csv --TZ 1 -movement 0 0 0.04 -nodeDistance 0.4 -moveTo 0.0 24.1397991 2.94929004 -plane 1 1 0 -reduce_param 0.8