Improve fitting in deep sulci for ages 28-30 weeks

gifit/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.2.1'
+__version__ = '0.3.0'
 
 DISPLAY_TITLE = r"""
        _             _  __ _ _   

gifit/__main__.py

@@ -21,7 +21,7 @@
                         formatter_class=ArgumentDefaultsHelpFormatter)
 parser.add_argument('--no-fail', dest='no_fail', action='store_true',
                     help='Produce exit code 0 even if any subprocesses do not.')
-parser.add_argument('-m', '--model', dest='model', type=str, default='e',
+parser.add_argument('-m', '--model', dest='model', type=str, default='h',
                     help='Name of built-in model to use, or a path to a custom CSV model.')
 parser.add_argument('-s', '--size', dest='size', type=int, default=81920,
                     help='Output mesh size')

gifit/model.py

@@ -5,7 +5,7 @@
 from typing import NewType, Self, Iterator
 
 _MODEL_PARAM_TYPES: defaultdict[str, type] = defaultdict(lambda: str)
-_MODEL_PARAM_TYPES['approximate_age'] = int
+_MODEL_PARAM_TYPES['approximate_age'] = float
 _MODEL_PARAM_TYPES['stage'] = int
 _MODEL_PARAM_TYPES['gyrification_index'] = float
 

gifit/models/README

@@ -0,0 +1,6 @@
+f.csv is the same as e.csv, but with smaller stretch weight.
+
+g.csv implements the idea of fitting to one voxel deeper for old brains,
+before re-expanding outwards back to the boundary. This can improve fitting
+into tight sulci.
+

gifit/models/f.csv

@@ -0,0 +1,14 @@
+approximate_age,surface_area,gyrification_index,stage,iso_value,size,iter_outer,iter_inner,step_size,laplacian_weight,stretch_weight,self_weight,self_dist,oversample,taubin,comments
+25,9500,1,0,10,20480,600,100,0.2,0.000002,100,0.5,0.005,0,10,Brains 23-25 clumped together
+26,10000,1.02,0,10,20480,300,100,0.2,0.000002,40,0.5,0.005,0,10,
+26,10000,1.02,1,10,20480,300,100,0.2,0.000002,40,0.5,0.005,0,10,
+27,10000,1.05,0,10,20480,300,100,0.2,0.000002,30,0.5,0.005,0,10,
+27,10000,1.05,1,10,20480,300,100,0.2,0.000002,30,0.5,0.005,0,10,
+28,10000,1.07,0,10,20480,300,100,0.2,0.000002,20,0.5,0.005,0,10,
+28,10000,1.07,1,10,20480,300,100,0.2,0.000002,20,0.5,0.005,0,10,
+29,10000,1.12,0,10,20480,300,100,0.2,0.000002,4,0.5,0.005,0,10,
+29,10000,1.12,1,10,20480,300,100,0.2,0.000002,1,0.5,0.005,0,10,
+30,10000,1.17,0,10,20480,300,100,0.2,0.000002,4,0.5,0.005,0,10,
+30,10000,1.17,1,10,20480,300,100,0.2,0.000002,1,0.5,0.005,0,10,
+31,10000,1.2,0,10,20480,300,100,0.2,0.000002,4,0.5,0.005,0,10,
+31,10000,1.2,1,10,20480,300,100,0.2,0.000002,1,0.5,0.005,0,10,

gifit/models/g.csv

@@ -0,0 +1,16 @@
+approximate_age,surface_area,gyrification_index,stage,iso_value,size,iter_outer,iter_inner,step_size,laplacian_weight,stretch_weight,self_weight,self_dist,oversample,taubin,comments
+25,9500,1,0,10,20480,600,100,0.2,0.000002,100,0.5,0.005,0,10,Brains 23-25 clumped together
+26,10000,1.02,0,10,20480,300,100,0.2,0.000002,40,0.5,0.005,0,10,
+26,10000,1.02,1,10,20480,300,100,0.2,0.000002,40,0.5,0.005,0,10,
+27,10000,1.05,0,10,20480,300,100,0.2,0.000002,30,0.5,0.005,0,10,
+27,10000,1.05,1,10,20480,300,100,0.2,0.000002,30,0.5,0.005,0,10,
+27.5,10000,1.06,0,9,20480,600,100,0.2,0.000002,20,0.5,0.005,0,10,"older brains strategy: fit inwards one voxel deeper than boundary, then take small steps back outwards to boundary. May improve results in narrow sulci e.g. at calcarine and parieto-occipital sulcus"
+27.5,10000,1.06,1,10,20480,100,100,0.05,0.000002,20,0.5,0.005,0,1,
+28,10000,1.07,0,9,20480,600,100,0.2,0.000002,10,0.5,0.005,0,10,
+28,10000,1.07,1,10,20480,100,100,0.05,0.000002,10,0.5,0.005,0,1,
+29,10000,1.12,0,9,20480,600,100,0.2,0.000002,10,0.5,0.005,0,10,
+29,10000,1.12,1,10,20480,100,100,0.05,0.000002,5,0.5,0.005,0,1,
+30,10000,1.17,0,9,20480,600,100,0.2,0.000002,10,0.5,0.005,0,10,
+30,10000,1.17,1,10,20480,100,100,0.05,0.000002,2,0.5,0.005,0,1,
+31,10000,1.2,0,9,20480,600,100,0.2,0.000002,10,0.5,0.005,0,10,
+31,10000,1.2,1,10,20480,100,100,0.05,0.000002,1,0.5,0.005,0,1,

gifit/models/h.csv

@@ -0,0 +1,16 @@
+approximate_age,surface_area,gyrification_index,stage,iso_value,size,iter_outer,iter_inner,step_size,laplacian_weight,stretch_weight,self_weight,self_dist,oversample,taubin,comments
+25,9500,1,0,10,20480,600,100,0.2,0.000002,100,0.5,0.005,0,10,Brains 23-25 clumped together
+26,10000,1.02,0,10,20480,300,100,0.2,0.000002,40,0.5,0.005,0,10,
+26,10000,1.02,1,10,20480,300,100,0.2,0.000002,40,0.5,0.005,0,10,
+27,10000,1.05,0,10,20480,300,100,0.2,0.000002,30,0.5,0.005,0,10,
+27,10000,1.05,1,10,20480,300,100,0.2,0.000002,30,0.5,0.005,0,10,
+27.5,10000,1.06,0,9,20480,600,100,0.2,0.000002,20,0.5,0.005,0,10,"older brains strategy: fit inwards one voxel deeper than boundary, then take small steps back outwards to boundary. May improve results in narrow sulci e.g. at calcarine and parieto-occipital sulcus"
+27.5,10000,1.06,1,10,20480,100,100,0.05,0.000002,10,0.5,0.005,0,1,
+28,10000,1.07,0,9,20480,600,100,0.2,0.000002,5,0.5,0.005,0,8,
+28,10000,1.07,1,10,20480,100,100,0.05,0.000002,0.5,0.5,0.005,0,1,
+29,10000,1.12,0,9,20480,600,100,0.2,0.000002,3,0.5,0.005,0,6,
+29,10000,1.12,1,10,20480,100,100,0.05,0.000002,0.5,0.5,0.005,0,1,
+30,10000,1.17,0,9,20480,600,100,0.2,0.000002,3,0.5,0.005,0,4,
+30,10000,1.17,1,10,20480,100,100,0.05,0.000002,0.5,0.5,0.005,0,1,
+31,10000,1.2,0,9,20480,600,100,0.2,0.000002,3,0.5,0.005,0,4,
+31,10000,1.2,1,10,20480,100,100,0.05,0.000002,0.5,0.5,0.005,0,1,