angioflow_fix_batch2: USFD_0051_cut1

.gitattributes

@@ -384,3 +384,11 @@ angioflow_fix_batch2/USFD_0026_cut1/merged_reconstruction.ply filter=lfs diff=lf
 angioflow_fix_batch2/USFD_0026_cut1/mesh.msh filter=lfs diff=lfs merge=lfs -text
 angioflow_fix_batch2/USFD_0026_cut1/mesh.vtu filter=lfs diff=lfs merge=lfs -text
 angioflow_fix_batch2/USFD_0026_cut1/reconstruction.ply filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/clipped_reconstruction.ply filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/clipped_reconstruction_fallback.ply filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/dome.ply filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/dome_sac.ply filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/geomagic_processed.obj filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/merged_reconstruction.ply filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/mesh.msh filter=lfs diff=lfs merge=lfs -text
+angioflow_fix_batch2/USFD_0051_cut1/reconstruction.ply filter=lfs diff=lfs merge=lfs -text

angioflow_fix_batch2/USFD_0051_cut1/branch_ranking.npy

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angioflow_fix_batch2/USFD_0051_cut1/done.txt

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angioflow_fix_batch2/USFD_0051_cut1/endpoints_manual.npy

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angioflow_fix_batch2/USFD_0051_cut1/forward_fusion_info.npz

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angioflow_fix_batch2/USFD_0051_cut1/geomagic_processed.obj

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angioflow_fix_batch2/USFD_0051_cut1/jnl_transient

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+/file/read-case mesh.msh
+/mesh/scale 0.001 0.001 0.001
+/define/models/unsteady-2nd-order? yes
+/define/models/viscous/laminar yes
+/define/materials/change-create air blood yes constant 1050 no no yes carreau shear-rate-dependent 3.313 0.3568 0.056 0.00345 no no no yes
+/define/boundary-conditions/zone-type 4 velocity-inlet
+/define/boundary-conditions/zone-type 5 pressure-outlet
+/define/user-defined/use-built-in-compiler? yes
+/define/user-defined/compiled-functions compile libudf yes parabolic_vinlet_udf_full.c "" ""
+/define/user-defined/compiled-functions load libudf
+/define/boundary-conditions/set/velocity-inlet surface4 () vmag yes yes udf inlet_x_velocity_transient::libudf quit
+/solve/set/p-v-coupling 24
+/solve/set/p-v-controls 2000000 0.5 0.5
+/solve/monitors/residual/convergence-criteria 0.0001 0.0001 0.0001 0.0001
+/solve/initialize/compute-defaults velocity-inlet surface4
+/solve/initialize/initialize-flow
+/file/transient-export/ensight-gold-transient ensight_files () * () absolute-pressure dynamic-pressure x-velocity y-velocity z-velocity wall-shear x-wall-shear y-wall-shear z-wall-shear dx-velocity-dx dy-velocity-dy dz-velocity-dz dx-velocity-dy dy-velocity-dx dx-velocity-dz dz-velocity-dx dy-velocity-dz dz-velocity-dy dp-dx dp-dy dp-dz dp-dt viscosity-lam x-coordinate y-coordinate z-coordinate quit no yes export-1 time-step 10 yes
+/file/autosave/data-frequency 10
+/solve/set/time-step 0.001
+/solve/dual-time-iterate 1600 100
+/file/write-case mesh_new.cas yes
+/file/write-data mesh_new.dat yes
+exit
+yes

angioflow_fix_batch2/USFD_0051_cut1/merged_centerline.npy

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angioflow_fix_batch2/USFD_0051_cut1/parabolic_vinlet_udf_full.c

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+/*
+vprofile_transient_parabolic.c
+UDF for specifying steady-state velocity profile boundary condition
+
+AUTHOR	Wenhao Ding
+DATE	22.03.2024
+
+Instruction:
+define VINREF, the maximum velocity at the center
+define FIXED_TIME_STEP and make sure MAX_PCD_SIZE is larger than int(total_time/FIXED_TIME_STEP)
+define filename (txt for the waveform, this txt file must be in the same directory as this script)
+*/
+
+#include "udf.h"
+#include <math.h>
+#include <stdio.h>
+
+#define PI 3.14159265358979323846
+#define VINREF	1.3158	/* ref inlet v  */
+#define VIN	0	/* ref inlet v  */
+#define MAX_PCD_SIZE 400001  /* Least PCD number the waveform file has cannot exceed point number in txt 574578 41160*/
+#define MAX_LOG_SIZE 600
+#define FIXED_TIME_STEP 0.00001  /* Fixed time step during transient simulation*/
+#define MAX_POINTS 6000 /* Maximum point number on the inlet*/
+#define ND_ND 3
+/* static double* Q_array[MAX_PCD_SIZE]; */
+
+
+typedef struct {
+    double x;
+    double y;
+    double z;
+} Vector3D;
+
+double dot_product(Vector3D v1, Vector3D v2) {
+    return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z;
+}
+
+Vector3D cross_product(Vector3D v1, Vector3D v2) {
+    Vector3D cross_v;
+
+    cross_v.x = v1.y * v2.z - v1.z * v2.y;
+    cross_v.y = v1.z * v2.x - v1.x * v2.z;
+    cross_v.z = v1.x * v2.y - v1.y * v2.x;
+
+    return cross_v;
+}
+
+double get_norm(Vector3D result) {
+    return sqrt(pow(result.x, 2) + pow(result.y, 2) + pow(result.z, 2));
+}
+
+double getDegAngle(Vector3D v1, Vector3D v2) {
+    Vector3D v_cross = cross_product(v1, v2);
+    double radian_angle = atan2(get_norm(v_cross), dot_product(v1, v2));
+    if (v_cross.z < 0) {
+        radian_angle = 2 * PI - radian_angle;
+    }
+    return radian_angle;
+}
+
+
+
+DEFINE_PROFILE(inlet_x_velocity_transient, thread, position)
+{   
+    /*Domain* d;*/
+    /*d = Get_Domain(1);*/
+    /*Thread* tr = Lookup_Thread(d, 5);*/
+    real x[ND_ND]; /* ND_ND=3 for 3D */
+    real curr_x, curr_y, curr_z;
+    face_t f;
+    /* real current_time;  */
+    FILE* rfile; /* declare a FILE pointer */
+    rfile = fopen("udf_waveform_5cycles.txt", "r+");
+    double Q_array[MAX_PCD_SIZE];
+    int i = 0;
+    for (i = 0; i < MAX_PCD_SIZE; i++) {
+        fscanf(rfile, "%lf", &Q_array[i]); /* that supposes one value per line */
+    }fclose(rfile);
+    /* load from csv file */
+    double centroids[MAX_POINTS][ND_ND];
+    int num_points_inlet = 0;
+    FILE* file;
+    char line[256];
+    file = fopen("inlet_centroids.csv", "r");
+    if (file == NULL)
+    {
+        Message("Error: Cannot open file %s\n", "inlet_centroids.csv");
+        return;
+    }
+    fgets(line, sizeof(line), file);
+    num_points_inlet = 0;
+    while (fgets(line, sizeof(line), file) && num_points_inlet < MAX_POINTS)
+    {
+        sscanf(line, "%lf,%lf,%lf", &centroids[num_points_inlet][0], &centroids[num_points_inlet][1], &centroids[num_points_inlet][2]);
+        num_points_inlet++;
+    }
+    fclose(file);
+    /* record average coordinates on the inlet (center) */
+    double center_x = 0.0, center_y = 0.0, center_z = 0.0;
+    for (i = 0; i < num_points_inlet; i++)
+    {
+        center_x += centroids[i][0];
+        center_y += centroids[i][1];
+        center_z += centroids[i][2];
+    }
+
+    if (num_points_inlet > 0)
+    {
+        center_x /= num_points_inlet;
+        center_y /= num_points_inlet;
+        center_z /= num_points_inlet;
+    }
+    /*Message("Average centroid coordinates: x=%lf, y=%lf, z=%lf\n", center_x, center_y, center_z);*/
+    /* get 12 clock tick */
+    double tick_x = 0.0, tick_y = 0.0, tick_z = 0.0;
+    double tick_radius = 0.0;
+    double tick_radius_record = 0.0;
+    for (i = 0; i < num_points_inlet; i++)
+    {
+        tick_radius = sqrt(pow((centroids[i][0] - center_x), 2) + pow((centroids[i][1] - center_y), 2) + pow((centroids[i][2] - center_z), 2));
+        if (tick_radius > tick_radius_record) {
+            tick_x = x[0];
+            tick_y = x[1];
+            tick_z = x[2];
+        }
+        tick_radius_record = tick_radius;
+    }
+
+    /* start spinning and record maximum radius for every sector */
+    int num_sector = 30;
+    double angle = 0.0;
+    int id_sector = 0;
+    double current_radius = 0.0;
+    /* tick & tock vector for cross and dot production */
+    Vector3D v_tick;
+    v_tick.x = tick_x - center_x;
+    v_tick.y = tick_y - center_y;
+    v_tick.z = tick_z - center_z;
+    Vector3D v_tock;
+    double radius_list[num_sector];
+    for (i = 0; i < num_sector; ++i) {
+        radius_list[i] = 0.0;
+    }
+    /* loop and fill radius_list */
+    for (i = 0; i < num_points_inlet; i++)
+    {
+        v_tock.x = centroids[i][0] - center_x;
+        v_tock.y = centroids[i][1] - center_y;
+        v_tock.z = centroids[i][2] - center_z;
+        angle = getDegAngle(v_tick, v_tock);
+        id_sector = floor((angle + PI) / (2 * PI / num_sector));
+        if (id_sector < 0) {
+            id_sector = 0;
+        }
+        if (id_sector >= num_sector) {
+            id_sector = num_sector - 1;
+        }
+        current_radius = sqrt(pow(v_tock.x, 2) + pow(v_tock.y, 2) + pow(v_tock.z, 2));
+        if (current_radius > radius_list[id_sector]) {
+            radius_list[id_sector] = current_radius;
+        }
+    }
+
+        /* clean radius list and check (sometimes there are no nodes in the sector) */
+        for (i = 0; i < num_sector; ++i) {
+            if (radius_list[i] == 0.0) {
+                radius_list[i] = tick_radius_record;
+            }
+        }
+
+    /* assign parabolic profile */
+    begin_f_loop(f, thread)
+    {
+        F_CENTROID(x, f, thread);
+        /* current_time = CURRENT_TIME */
+        int current_time_id = (int)floor(CURRENT_TIME / FIXED_TIME_STEP);
+        double current_Q_ratio = Q_array[current_time_id];
+        curr_x = x[0]; /* x[0] is x coordinate */
+        curr_y = x[1]; /* x[1] is y coordinate */
+        curr_z = x[2]; /* x[2] is z coordinate */
+
+        v_tock.x = x[0] - center_x;
+        v_tock.y = x[1] - center_y;
+        v_tock.z = x[2] - center_z;
+        angle = getDegAngle(v_tick, v_tock);
+        id_sector = floor((angle + PI) / (2 * PI / num_sector));
+        if (id_sector < 0) {
+            id_sector = 0;
+        }
+        if (id_sector >= num_sector) {
+            id_sector = num_sector - 1;
+        }
+        current_radius = radius_list[id_sector];
+
+        /* write inlet velocity profile - need to centre the x,y,z coords and divide by Rref^2 */
+        F_PROFILE(f, thread, position) = current_Q_ratio * VINREF * (1 + VIN) * (1 - (pow((curr_x - center_x), 2) + pow((curr_y - center_y), 2) + pow((curr_z - center_z), 2)) / (current_radius * current_radius));
+    }
+    end_f_loop(f, thread)
+}

angioflow_fix_batch2/USFD_0051_cut1/preprocess_log.txt

@@ -0,0 +1,97 @@
+
+============================================================
+  Session started: 2026-04-22 15:11:40
+============================================================
+
+════════════════════════════════════════════════════════════
+  Processing: USFD_0051_cut1
+════════════════════════════════════════════════════════════
+
+── Step 1: Centerline extraction ──
+Reading PLY surface file.
+Cleaning surface.
+Triangulating surface.
+Computing centerlines.
+Computing centerlines...
+Centerlines [accept / redo / skip] (default=accept): 
+── Step 2: Vessel clipping ──
+
+Current cut distances (how far from aneurysm to cut each branch):
+  Branch 0 (downstream): 4.0 mm  (branch total: 45.0 mm)
+  Branch 1 (downstream): 4.0 mm  (branch total: 20.7 mm)
+Accept these cut distances? (Y/n):   Branch 0 (downstream) distance [4.0]:   Branch 1 (downstream) distance [4.0]: 
+Current cut distances (how far from aneurysm to cut each branch):
+  Branch 0 (downstream): 11.0 mm  (branch total: 45.0 mm)
+  Branch 1 (downstream): 4.0 mm  (branch total: 20.7 mm)
+Accept these cut distances? (Y/n):   Branch 0 (downstream) distance [11.0]:   Branch 1 (downstream) distance [4.0]: 
+Current cut distances (how far from aneurysm to cut each branch):
+  Branch 0 (downstream): 12.0 mm  (branch total: 45.0 mm)
+  Branch 1 (downstream): 4.0 mm  (branch total: 20.7 mm)
+Accept these cut distances? (Y/n):   Dome protection: dome_sac.ply, 4804 vertices protected (dist < 0.50 mm)
+  Clipping: 63275 vertices removed, 4804 dome-protected
+
+  ────────────────────────────────────────────────────────
+  Cut cross-section equivalent diameters (2 openings):
+  ────────────────────────────────────────────────────────
+    Opening 0: D_eq = 5.021 mm  ←  inlet  (branch 0)
+    Opening 1: D_eq = 3.070 mm  ←  outlet (branch 1)
+  ────────────────────────────────────────────────────────
+  Suggested extension length: ~4× diameter for single outlet.
+  ────────────────────────────────────────────────────────
+
+Accept clipping? (Y/n): 
+── Step 3: Vessel extension ──
+
+  Extension modes:
+    centerline           = use original centerline only
+    straight             = straight extension from opening
+    centerline+straight  = original centerline a mm + straight b mm
+
+  Branch 0 (upstream, CL=32.9mm) mode [centerline]:     centerline part a [2.0mm]:     straight part b [2.0mm]:   Branch 1 (downstream, CL=16.6mm) mode [centerline]:     centerline part a [2.0mm]:     straight part b [2.0mm]:   Branch 0: centerline+straight, centerline=3.88 mm, straight=4.00 mm
+  Branch 1: centerline+straight, centerline=3.88 mm, straight=6.00 mm
+Accept vessel extension? (Y/n): 
+  Extension rejected.
+  Choose next action:
+    1 = re-try Step 3 with different extension settings
+    2 = go back to Step 2 and re-select clipping lengths
+  Action [1/2, default=2]: 
+  Tuning:
+    min_boundary_verts: minimum boundary vertices for a real opening.
+    init_step: choose centerline starting point.
+      Increase if extension overlaps with dome.
+  min_boundary_verts [5]:   init_step [1]:   default extension length [2.0]: 
+  Extension modes:
+    centerline           = use original centerline only
+    straight             = straight extension from opening
+    centerline+straight  = original centerline a mm + straight b mm
+
+  Branch 0 (upstream, CL=32.9mm) mode [centerline]:     centerline part a [2.0mm]:     straight part b [2.0mm]:   Branch 1 (downstream, CL=16.6mm) mode [centerline]:     centerline part a [2.0mm]:     straight part b [2.0mm]:   Branch 0: centerline+straight, centerline=3.88 mm, straight=4.00 mm
+  Branch 1: centerline+straight, centerline=3.88 mm, straight=6.00 mm
+Accept vessel extension? (Y/n):   Saved: F:\NUS\labwork\paper3\aneux\PostTr\AneuX\USFD_0051_cut1\merged_reconstruction.ply
+  Saved: branch_ranking.npy → [0, 1]
+
+── Step 4: Fallback clipping (side-wall sac isolation) ──
+  Clipping the ORIGINAL reconstruction mesh at the parent vessel.
+
+  Parent centerline: upstream branch 0 → neck → downstream branch 1
+  Upstream arc (neck → inlet): 45.0 mm
+  Downstream arc (neck → outlet): 20.7 mm
+
+  Keep upstream (toward inlet) [6.0 mm]:   Keep downstream (toward outlet) [6.0 mm]:   Single centerline: 662 pts, neck at index 452, upstream=0, downstream=1
+  Upstream cut: index 411, arc from neck = 4.1 mm
+  Downstream cut: index 493, arc from neck = 4.0 mm
+  Dome protection: dome_sac.ply, 4804 vertices protected (dist < 0.50 mm)
+  After scalar clip: 24045 vertices
+  Kept component 0 (closest to centroid), removed 3 disconnected parts
+  Saved fallback-clipped mesh → F:\NUS\labwork\paper3\aneux\PostTr\AneuX\USFD_0051_cut1\clipped_reconstruction_fallback.ply
+Accept fallback clipping? (Y/n):   Fallback clipping accepted → clipped_reconstruction_fallback.ply
+  Saved: forward_fusion_info_fallback.npz (2 branches)
+  Saved: branch_ranking_fallback.npy → [0, 1]
+
+── Step 5: Final review ──
+Accept final mesh? (Y/n): Accept final mesh? (Y/n): 
+  Branch ordering (2 branches):
+    Branch 0 = inlet (upstream)
+    Branch 1 = outlet
+  (Inlet = endpoint 0 from registration, auto-detected as upstream)
+  ✓ USFD_0051_cut1 complete.

angioflow_fix_batch2/USFD_0051_cut1/reconstruction.ply

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angioflow_fix_batch2/USFD_0051_cut1/reg_mesh_regularization.json

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+{
+  "input": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/angioflow_fix/USFD_0051_cut1/merged_reconstruction_remeshed.obj",
+  "tolerance": 0.25,
+  "mode": "millimetre",
+  "dome_sac_mm": null,
+  "stopping": null,
+  "snap_levels": null,
+  "assessment": {
+    "needs_regularization": true,
+    "worst_target_excess_sd": 1.5700413722057898,
+    "tolerance_sd": 0.25,
+    "signed_excess_sd": {
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+      "1.2": -0.46164327338154665,
+      "1.6": -0.8949544765344578
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+    "verdict": "rougher_than_reference",
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+    "guard_below_band": 1.111509986156445,
+    "target_scales": [
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+      0.5,
+      0.8,
+      1.0,
+      1.2
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+    "edge_after_measurement_remesh": 0.1100259841031317,
+    "remesher": "auto",
+    "n_seeds": 4000,
+    "elapsed_s": 165.0
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+  "surface_used": "/media/yaplab2/wd8tb/wenhao/angioflow/cfd/angioflow_fix/USFD_0051_cut1/reg_mesh.vtp",
+  "reason": "roughness above reference (worst target excess +1.57 SD); regularizer status converged"
+}

angioflow_fix_batch2/USFD_0051_cut1/remesh_info.json

@@ -0,0 +1,12 @@
+{
+ "source": "merged_reconstruction.ply",
+ "method": "mesh_regularizer.remesh(backend='pymeshlab', calibrate=True)",
+ "target_edge_mm": 0.132,
+ "edge_median_mm": 0.12943143189593684,
+ "edge_max_mm": 0.24497287489666048,
+ "area_before": 502.49616418832613,
+ "area_after": 501.88900737667535,
+ "openings": 2,
+ "opening_centroid_shift_mm": 0.11736375314813426,
+ "made_by": "angioflow/debugging/remesh_aneux_merged.py"
+}