chore: update plotter settings for off-screen rendering and high-reso…

…lution output

src/mkit/physics/mtm.py

@@ -74,7 +74,7 @@ def force(self, disp: npt.ArrayLike) -> npt.NDArray[np.floating]:
 
     def stiffness_sparse_matrix(self) -> scipy.sparse.coo_array:
         builder = ti.linalg.SparseMatrixBuilder(
-            self.n_verts * 3, self.n_verts * 3, int(1e6)
+            self.n_verts * 3, self.n_verts * 3, int(1e7)
         )
         self._stiffness_matrix(builder)
         K_ti: ti.linalg.SparseMatrix = builder.build()

tasks/00-register/plot/align.py

@@ -3,29 +3,47 @@
 import pyvista as pv
 from pyvista.plotting.plotter import Plotter
 from pyvista.plotting.themes import DocumentProTheme
+from vtkmodules.vtkRenderingAnnotation import vtkLegendBoxActor
+from vtkmodules.vtkRenderingCore import vtkTextProperty
 
 DATA_DIR = pathlib.Path("/home/liblaf/Documents/data/target/120056/pre")
 TEMPLATE_DIR = pathlib.Path("/home/liblaf/Documents/data/template")
 
-pl = Plotter(window_size=(600, 800), theme=DocumentProTheme())
+pl = Plotter(
+    off_screen=True,
+    window_size=(2880, 3840),
+    theme=DocumentProTheme(),
+)
 pl.add_axes()
 
 target: pv.PolyData = pv.read(DATA_DIR / "02-face.ply")
 template: pv.PolyData = pv.read(DATA_DIR / "03-face.vtu")
-pl.add_mesh(target, label="Target Face", opacity=0.3)
-pl.add_mesh(template, label="Template Face", opacity=0.3)
+pl.add_mesh(target, label="目标面部", opacity=0.3)
+pl.add_mesh(template, label="模板面部", opacity=0.3)
 pl.view_vector([1.0, 0.0, 0.0], viewup=[0.0, 0.0, -1.0])
 pl.zoom_camera(1.6)
-pl.add_legend(size=(0.5, 0.2), loc="upper center")
+legend: vtkLegendBoxActor = pl.add_legend(size=(0.5, 0.2), loc="upper center")
+text: vtkTextProperty = legend.GetEntryTextProperty()
+text.SetFontFamily(4)
+text.SetFontFile("/usr/share/fonts/noto-cjk/NotoSansCJK-Light.ttc")
+# legend.SetEntryTextProperty(text)
+# pl.render()
 pl.save_graphic("align-face.pdf")
+pl.save_graphic("align-face.svg")
+pl.screenshot("align-face.png")
 pl.clear_actors()
 
 pl.set_color_cycler("default")
 target: pv.PolyData = pv.read(DATA_DIR / "02-skull.ply")
-pl.add_mesh(target, label="Target Skull", opacity=0.3)
+pl.add_mesh(target, label="目标颌骨", opacity=0.3)
 template: pv.PolyData = pv.read(DATA_DIR / "03-mandible.vtu")
-pl.add_mesh(template, label="Template Mandible", opacity=0.3)
+pl.add_mesh(template, label="模板下颌骨", opacity=0.3)
 template: pv.PolyData = pv.read(DATA_DIR / "03-maxilla.vtu")
-pl.add_mesh(template, label="Template Maxilla", opacity=0.3)
-pl.add_legend(size=(0.5, 0.2), loc="upper center")
+pl.add_mesh(template, label="模板上颌骨", opacity=0.3)
+legend: vtkLegendBoxActor = pl.add_legend(size=(0.5, 0.2), loc="upper center")
+text: vtkTextProperty = legend.GetEntryTextProperty()
+text.SetFontFamily(4)
+text.SetFontFile("/usr/share/fonts/noto-cjk/NotoSansCJK-Light.ttc")
 pl.save_graphic("align-skull.pdf")
+pl.save_graphic("align-skull.svg")
+pl.screenshot("align-skull.png")

tasks/00-register/plot/register.py

@@ -3,6 +3,8 @@
 import pyvista as pv
 from pyvista.plotting.plotter import Plotter
 from pyvista.plotting.themes import DocumentProTheme
+from vtkmodules.vtkRenderingAnnotation import vtkLegendBoxActor
+from vtkmodules.vtkRenderingCore import vtkTextProperty
 
 DATA_DIR = pathlib.Path("/home/liblaf/Documents/data/target/120056/pre")
 TEMPLATE_DIR = pathlib.Path("/home/liblaf/Documents/data/template")
@@ -12,20 +14,26 @@
 
 target: pv.PolyData = pv.read(DATA_DIR / "02-face.ply")
 template: pv.PolyData = pv.read(DATA_DIR / "99-face.vtu")
-pl.add_mesh(target, label="Target Face", opacity=0.3)
-pl.add_mesh(template, label="Result Face", opacity=0.3)
+pl.add_mesh(target, label="目标面部", opacity=0.3)
+pl.add_mesh(template, label="配准结果", opacity=0.3)
 pl.view_vector([1.0, 0.0, 0.0], viewup=[0.0, 0.0, -1.0])
 pl.zoom_camera(1.6)
-pl.add_legend(size=(0.5, 0.2), loc="upper center")
-pl.save_graphic("register-face.pdf")
+legend: vtkLegendBoxActor = pl.add_legend(size=(0.5, 0.2), loc="upper center")
+text: vtkTextProperty = legend.GetEntryTextProperty()
+text.SetFontFamily(4)
+text.SetFontFile("/usr/share/fonts/noto-cjk/NotoSansCJK-Light.ttc")
+pl.save_graphic("register-face.svg")
 pl.clear_actors()
 
 pl.set_color_cycler("default")
 target: pv.PolyData = pv.read(DATA_DIR / "02-skull.ply")
-pl.add_mesh(target, label="Target Skull", opacity=0.3)
+pl.add_mesh(target, label="目标颌骨", opacity=0.3)
 template: pv.PolyData = pv.read(DATA_DIR / "99-mandible.vtu")
-pl.add_mesh(template, label="Result Mandible", opacity=0.3)
+pl.add_mesh(template, label="配准结果下颌骨", opacity=0.3)
 template: pv.PolyData = pv.read(DATA_DIR / "99-maxilla.vtu")
-pl.add_mesh(template, label="Result Maxilla", opacity=0.3)
-pl.add_legend(size=(0.5, 0.2), loc="upper center")
-pl.save_graphic("register-skull.pdf")
+pl.add_mesh(template, label="配准结果上颌骨", opacity=0.3)
+legend: vtkLegendBoxActor = pl.add_legend(size=(0.5, 0.2), loc="upper center")
+text: vtkTextProperty = legend.GetEntryTextProperty()
+text.SetFontFamily(4)
+text.SetFontFile("/usr/share/fonts/noto-cjk/NotoSansCJK-Light.ttc")
+pl.save_graphic("register-skull.svg")

tasks/02-simulation/src/mtm-inspect.py

@@ -57,7 +57,7 @@ def n_free(self) -> int:
 def main(
     input_file: Annotated[pathlib.Path, typer.Argument(exists=True, dir_okay=False)],
     *,
-    poisson_ratio: Annotated[float, typer.Option()] = 0.46,
+    poisson_ratio: Annotated[float, typer.Option()] = 0.01,
 ) -> None:
     ti.init(ti.cpu, default_fp=ti.float64, debug=True)
     mesh: meshio.Mesh = mkit.io.load_meshio(input_file)
@@ -69,6 +69,7 @@ def main(
     free_mask: npt.NDArray[np.bool_] = np.repeat(model.free_mask, 3)
     stiffness = stiffness[free_mask][:, free_mask]
     ic(np.linalg.cond(stiffness))
+    print(poisson_ratio, np.linalg.cond(stiffness), sep=",")
 
 
 if __name__ == "__main__":

tasks/03-eval/Makefile

@@ -1,5 +1,5 @@
 DATA_DIR  ?= $(HOME)/Documents/data
-TARGET_ID ?= 117412
+TARGET_ID ?= 120056
 export DATA_DIR
 export TARGET_ID
 

tasks/03-eval/data/cond.csv

@@ -0,0 +1,51 @@
+nu,cond
+0.00,6.3216632112124
+0.01,6.425992097565894
+0.02,6.536583509940744
+0.03,6.653991008986903
+0.04,6.7788815904816095
+0.05,6.911926247768419
+0.06,7.054012417855549
+0.07,7.205995589659337
+0.08,7.369009434500302
+0.09,7.544270358474558
+0.10,7.733122270924384
+0.11,7.937246362846694
+0.12,8.158617156783983
+0.13,8.399324971054927
+0.14,8.662023352223873
+0.15,8.94995579255462
+0.16,9.266778190678961
+0.17,9.617087022211244
+0.18,10.006358607119566
+0.19,10.441505284968741
+0.20,10.930866313310464
+0.21,11.48520225627498
+0.22,12.118299733405518
+0.23,12.848061127468158
+0.24,13.698155536667251
+0.25,14.700664785846378
+0.26,15.900497076142639
+0.27,17.361214454432965
+0.28,19.177840088004288
+0.29,21.497719207337607
+0.30,24.56098929293268
+0.31,28.790231187652594
+0.32,35.00342622929775
+0.33,45.011194795853136
+0.34,63.78844975910162
+0.35,111.71071604776593
+0.36,486.89897529114353
+0.37,1173.055330029466
+0.38,329.11342089331515
+0.39,108.38521611031145
+0.40,66.30942337933283
+0.41,50.54704097490089
+0.42,90.6608314669174
+0.43,913.7044933275236
+0.44,238.70778498695006
+0.45,16756.052460450795
+0.46,445.0688078835202
+0.47,1173.4515413664415
+0.48,1033.0825022180727
+0.49,1180.0497537036363

tasks/03-eval/data/poisson-ratio.csv

@@ -0,0 +1,48 @@
+nu,mean,std,50%,90%,95%,99%,2mm,max,Acond
+0.00,0.6436854944406247,0.508211514275162,0.5143301651452407,1.3370014676800135,1.6562352607449118,2.3856813186703696,97.17798594847775,2.964648973890964,3.7232e+01
+0.01,0.6425192296882204,0.5072221223054793,0.5133229118201252,1.334911193899578,1.6549733531778785,2.3804235679136463,97.20140515222484,2.9647040056459804,3.8539e+01
+0.02,0.6417020508384645,0.5059991730617928,0.5131156767870105,1.3342556624245328,1.6549871776039193,2.372087496171505,97.28337236533959,2.9641486509349364,3.5464e+01
+0.03,0.6406087573245044,0.5049140049512655,0.5122620582678784,1.3335104647408678,1.6521015896447466,2.363165054665815,97.29508196721312,2.9638158734508777,3.5637e+01
+0.04,0.6400059125442199,0.503529342097124,0.5116878715512917,1.331013605441007,1.6453670090682202,2.3506383152581427,97.33021077283374,2.96255635244046,3.8166e+01
+0.05,0.6387471336104931,0.5024972014548974,0.5100829046783557,1.3292563472207706,1.6426809039725765,2.3432977318630943,97.34192037470727,2.962080732947801,3.6228e+01
+0.06,0.6380526944300415,0.5011348982695332,0.5098212544377858,1.3281777834448956,1.6417092183934994,2.3341678243065855,97.41217798594849,2.960467200945664,3.7570e+01
+0.07,0.6371055169000541,0.4998883430449226,0.5096740438966975,1.328276379387855,1.640691237805295,2.323944690095794,97.45901639344262,2.958966996475687,3.6433e+01
+0.08,0.6359396640044177,0.49873761536663225,0.5093077404339731,1.3259614492974252,1.6368394531754147,2.312227472222196,97.51756440281031,2.957523081645553,3.6907e+01
+0.09,0.6350499727154633,0.4974092046074097,0.5088457576185332,1.324452889702656,1.636861774602664,2.302326447107868,97.58782201405153,2.9552551282952533,3.7159e+01
+0.10,0.6336232975628493,0.4963388562524495,0.5078224528870998,1.32293641016397,1.6344098094319388,2.2938586371853407,97.63466042154568,2.9534863048211486,3.7897e+01
+0.11,0.6328871251379288,0.4948986936893204,0.5072726266968172,1.3220048916240252,1.6298731176883654,2.283968071884734,97.66978922716628,2.950104554809719,3.6044e+01
+0.12,0.6319417114639978,0.4935389011957286,0.5066836654756367,1.3219893540446148,1.6288930441404024,2.2765695811529425,97.75175644028104,2.946556137391195,3.9119e+01
+0.13,0.6307032721182066,0.4923146597913789,0.5059721392785546,1.3214274184069739,1.6254671022346907,2.2706564911948015,97.78688524590164,2.9429117389567825,3.4510e+01
+0.14,0.6291140606352214,0.49122182536604647,0.5045645943492305,1.316833190029764,1.6187740641482138,2.265076743193898,97.88056206088994,2.9391193958627224,3.1368e+01
+0.15,0.628029694313524,0.4898731765802,0.5032201643114704,1.3164806689994315,1.6151437418294903,2.2575759416735,97.92740046838408,2.933732162177898,3.7691e+01
+0.16,0.6269032693696117,0.4885303958618954,0.5019103812370003,1.3165186340537345,1.614251658624402,2.246413562711069,97.9625292740047,2.9274891089290453,3.6289e+01
+0.17,0.6257608850879047,0.48718374820645943,0.5015277780052758,1.3156990458908027,1.6134377670684046,2.229561375326008,97.97423887587823,2.9201973301625705,3.8606e+01
+0.18,0.6243383244961367,0.48594507899915607,0.4999516410814028,1.3145126814920296,1.6078600350945689,2.2159348996747137,98.00936768149883,2.905503419423471,3.6173e+01
+0.19,0.6229589402970617,0.48467685684759176,0.49897181839630067,1.3140136660591566,1.6035198662178007,2.211654134256098,98.02107728337238,2.8775667420624815,3.6633e+01
+0.20,0.6216216832141159,0.4834038829887474,0.49748969404613996,1.3130582352198874,1.5995976821102393,2.202273391591223,98.06791569086651,2.847149040489746,3.7089e+01
+0.21,0.6196793589377662,0.48232320587498395,0.4942325118951646,1.3112711582941745,1.59615228200651,2.1933161473636202,98.0913348946136,2.815935289211311,3.9145e+01
+0.22,0.6182801217040707,0.4811077799622207,0.49294592913412716,1.3081767549930328,1.594729292034007,2.186889874275234,98.13817330210773,2.779920105682111,3.7102e+01
+0.23,0.616395359539496,0.48002685360983693,0.49132074792056424,1.3056235841695414,1.5909562941442896,2.174188825572754,98.19672131147541,2.742095148886994,3.7875e+01
+0.24,0.6144882255747562,0.47896485670167854,0.4882527345531119,1.306683200692286,1.591722717478634,2.1617022415318115,98.23185011709603,2.74760562502443,3.8145e+01
+0.25,0.6130620293122008,0.4779134643848884,0.48608295601361645,1.3071372274618978,1.5857794306410966,2.1338233111405502,98.33723653395785,2.755221792306614,3.9462e+01
+0.26,0.6107974998994434,0.4770882988972844,0.48397926222155796,1.3058638238351536,1.5849625495206883,2.1208621526500924,98.4192037470726,2.7630602158647917,4.0864e+01
+0.27,0.6085847945206262,0.47643682181461067,0.4817113607508198,1.3040670207941512,1.5799688352199603,2.0935324145262646,98.48946135831382,2.774012469297665,4.1044e+01
+0.28,0.6056241890666662,0.4760337026037962,0.4780667280813017,1.3011754989645432,1.5734648255668975,2.075366621307315,98.53629976580797,2.7891600963862655,4.1919e+01
+0.29,0.6027459803600431,0.47592909356414886,0.4746249212070599,1.3001069628193591,1.5666741730263045,2.0628396993010965,98.53629976580797,2.810226732296211,4.2724e+01
+0.30,0.5972980517265462,0.4758877408362762,0.4680538806869471,1.2900974284439213,1.570463315582105,2.090667468720454,98.44262295081968,2.8461063530547177,4.3442e+01
+0.31,0.602624711800535,0.47984766764525205,0.4734759631477259,1.3057545066244154,1.5767821153575858,2.117025649118628,98.32552693208432,2.8932390440054623,4.4058e+01
+0.32,0.6018427786187228,0.4838653137466017,0.4712897704233062,1.3053145393916639,1.56358367566278,2.171073597077213,98.20843091334895,2.9551145825807006,4.4554e+01
+0.33,0.6042746884631574,0.4941413574976656,0.4695118866678002,1.3041074675334878,1.5754890854077703,2.2449344175330532,97.74004683840751,3.022677838790262,4.4912e+01
+0.34,0.6103855961057112,0.5153554386931599,0.4675369711211894,1.3115180217767297,1.6102797012278425,2.403126636726336,97.21311475409837,3.4889949767913238,4.5115e+01
+0.35,0.6316175275555828,0.5517676511780409,0.47172890457594263,1.360923927448038,1.6983795909758477,2.5982871790480573,96.60421545667448,4.218038393028542,4.5143e+01
+0.36,0.6485992670987134,0.5763403291228087,0.4827247220023939,1.3858452281371398,1.7205406442031776,2.7629697837291163,96.29976580796253,5.132279644038273,4.4979e+01
+0.37,0.7275060903534227,0.7192597641967652,0.5093183000847857,1.5273123128085746,2.156192457887878,3.6280452001615524,94.25058548009369,7.22054594921821,4.4603e+01
+0.38,0.8587846698629444,0.9487642275220576,0.5595124875742967,1.8328660900279894,2.811192951155063,4.73938376202156,91.10070257611243,8.85002466415335,4.3999e+01
+0.39,0.9163322496927252,1.1561986671796836,0.5331476720281825,2.078954462441546,3.276599994145661,5.850787609032701,89.47306791569088,11.095714607298383,4.3153e+01
+0.40,1.0064287722485084,1.3124994183206873,0.5827131536914274,2.297846357706188,3.570401834415907,6.659170572669691,88.37236533957847,13.647526402765415,4.3847e+01
+0.41,1.0289822677910443,1.316109946464314,0.625840331229708,2.243063930319991,3.5268398927994165,6.590908698713706,88.11475409836066,15.707958431218472,4.3869e+01
+0.42,1.090555797388937,1.443613796730073,0.6427055056165487,2.5810007266690946,3.839781909750283,7.270436553224068,86.97892271662764,16.20036833449145,4.4665e+01
+0.43,1.2183316498814967,1.5557783673886707,0.6853741531740467,3.0890556003913416,4.441663670158224,7.479709823734423,83.58313817330212,14.842204253742333,4.4656e+01
+0.44,1.2598922604062681,1.6389171591360208,0.7047160013134127,3.1895872483648398,4.619434533094917,8.014194078211913,83.24355971896956,16.625172888370745,4.4686e+01
+0.45,1.2746480395277013,1.868450471423506,0.6801870312572966,3.0574946531309695,4.56745651027739,9.308980277826091,83.77049180327869,25.44521859813193,4.5663e+01
+0.46,1.3507084026101197,1.9190740049021635,0.7506665031475351,3.278187764352422,4.830121522054622,9.367187330365441,82.0608899297424,28.484339055781746,4.6349e+01

tasks/03-eval/plot/poisson-ratio.py

@@ -0,0 +1,36 @@
+import matplotlib.pyplot as plt
+import pandas as pd
+
+
+def main() -> None:
+    df: pd.DataFrame = pd.read_csv("data/poisson-ratio.csv")
+    df = df[df["nu"] < 0.39]
+    plt.figure()
+    plt.plot(df["nu"], df["mean"])
+    plt.xlabel("Poisson's ratio")
+    plt.ylabel("Mean Error (mm)")
+    plt.savefig("img/mean.pdf")
+
+    plt.figure()
+    plt.plot(df["nu"], df["95%"])
+    plt.xlabel("Poisson's ratio")
+    plt.ylabel("95% Error (mm)")
+    plt.savefig("img/95.pdf")
+
+    plt.figure()
+    plt.plot(df["nu"], df["max"])
+    plt.xlabel("Poisson's ratio")
+    plt.ylabel("Max Error (mm)")
+    plt.savefig("img/max.pdf")
+
+    df: pd.DataFrame = pd.read_csv("data/cond.csv")
+    df = df[df["nu"] < 0.38]
+    plt.figure()
+    plt.plot(df["nu"], df["cond"])
+    plt.xlabel("Poisson's ratio")
+    plt.ylabel("cond(K11)")
+    plt.savefig("img/cond.pdf")
+
+
+if __name__ == "__main__":
+    main()