Merge branch 'main' into main

02_CODE/Dockerfile.ubuntu24.04.ifort

@@ -1,3 +1,5 @@
+# https://pythonspeed.com/articles/activate-conda-dockerfile/
+
 FROM ubuntu:24.04
 
 ENV DEBIAN_FRONTEND noninteractive
@@ -64,5 +66,3 @@ ENV PATH="/opt/cargo/bin:${PATH}"
 # conda init, source .bashrc, conda activate
 RUN conda init bash
 RUN echo "conda activate hfe-essentials" >> ~/.bashrc
-
-# https://pythonspeed.com/articles/activate-conda-dockerfile/

02_CODE/Dockerfile.ubuntu24.04.ifort.thrusections

@@ -0,0 +1,68 @@
+FROM ubuntu:24.04
+
+ENV DEBIAN_FRONTEND noninteractive
+ENV LC_ALL=en_US.UTF-8
+ENV LANG=en_US.UTF-8
+
+RUN apt-get update && apt-get install -y \
+apt-utils cargo clang clang-tidy cmake \
+fonts-cmu ftp gcc gcovr \
+git g++ gfortran libboost-dev libcgns-dev \
+libfltk1.3-dev libfreetype6-dev libgl1-mesa-dev libgl1-mesa-dri libhdf5-dev \
+libocct-data-exchange-dev libocct-foundation-dev libocct-ocaf-dev libopenblas-dev libopenmpi-dev \
+libpetsc-complex-dev libxfixes-dev libxcursor-dev libxft-dev libxi-dev \
+libxinerama-dev libxmu-dev libslepc-complex3.19-dev mesa-common-dev python3-pip \
+swig tcl-dev tk-dev valgrind vim wget \
+sudo locales \
+&& apt-get clean
+
+RUN locale-gen en_US.UTF-8
+
+# install ifort compiler
+RUN wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+RUN echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+RUN sudo apt update && sudo apt upgrade -y
+RUN sudo apt-get install -y intel-basekit intel-hpckit
+RUN /bin/bash -c "source /opt/intel/oneapi/setvars.sh"
+RUN unset PYTHONPATH
+
+# Install miniconda
+RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+bash ~/miniconda.sh -b -p /opt/miniconda && rm ~/miniconda.sh
+ENV PATH="/opt/miniconda/bin:$PATH"
+
+# Create a conda environment
+RUN conda create -n hfe-essentials python=3.12
+SHELL ["conda", "run", "-n", "hfe-essentials", "/bin/bash", "-c"]
+# Copy hfe requirements.txt and install requirements
+COPY ./requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+RUN pip install -U scikit-image
+RUN pip install imutils
+
+# Set GitHub username and personal access token
+ARG GITHUB_USERNAME
+ARG GITHUB_TOKEN
+ARG USER_UID=1000
+ARG USER_GID=1000
+
+# Install the meshing package
+RUN git clone -b ThruSections --single-branch https://${GITHUB_USERNAME}:${GITHUB_TOKEN}@github.com/artorg-unibe-ch/spline_mesher.git ./pyhexspline/spline_mesher
+WORKDIR ./pyhexspline/spline_mesher
+RUN pip install -e .
+
+# Change ownership of the conda environment to the hfe user
+RUN useradd -ms /bin/bash hfe
+RUN chown -R hfe:hfe /opt/miniconda/envs/hfe-essentials
+
+USER hfe
+WORKDIR /home/hfe
+RUN mkdir -p ~/.ssh
+RUN chmod 700 ~/.ssh
+ENV PATH="/opt/cargo/bin:${PATH}"
+
+# conda init, source .bashrc, conda activate
+RUN conda init bash
+RUN echo "conda activate hfe-essentials" >> ~/.bashrc
+
+# https://pythonspeed.com/articles/activate-conda-dockerfile/

02_CODE/cfg/hfe-tibia.yaml

@@ -9,6 +9,7 @@ hydra:
   mode: MULTIRUN
   sweeper:
     params:
+
       simulations.grayscale_filenames: C0000000
 
       # C0003093, C0003096

02_CODE/cfg/mesh.yaml

@@ -12,18 +12,18 @@ meshing_settings:
   outside_val: 1                      # threshold value for the outside of the mask
   lower_thresh: 0                     # lower threshold for the mask
   upper_thresh: 0.9                   # upper threshold for the mask
-  s: 400                               # smoothing factor of the spline
+  s: 1000                               # smoothing factor of the spline
   k: 3                                # degree of the spline
   interp_points: 350                  # number of points to interpolate the spline
   thickness_tol: 0.50                 # minimum cortical thickness tolerance: 3 * XCTII voxel size
   phases: 2                           # 1: only external contour, 2: external and internal contour
   center_square_length_factor: 0.4    # size ratio of the refinement square: 0 < l_f < 1
   mesh_order: 1                       # set order of the mesh (1: linear, 2: quadratic)
   sweep_factor: 1                     # factor for the sweep used in hydra for the sensitivity analysis
-  n_elms_longitudinal: 6
-  n_elms_transverse_trab: 12
+  n_elms_longitudinal: 60
+  n_elms_transverse_trab: 15
   n_elms_transverse_cort: 3
-  n_elms_radial: 15                   # ! Should be 10 if trab_refinement is True
+  n_elms_radial: 20                   # ! Should be 10 if trab_refinement is True
   ellipsoid_fitting: True
   show_plots: False                   # show plots during construction
   show_gmsh: False                    # show gmsh GUI

02_CODE/cfg/socket.yaml

@@ -1,19 +1,14 @@
 solver:
   site: remote # local or remote
-    # abaqus: /var/DassaultSystemes/SIMULIA/Commands/abq2021hf4                     # monterosa (Abaqus 2021)
-    # abaqus: /var/DassaultSystemes/SIMULIA/Commands/abq2021hf6                     # simone-kubuntu
-  abaqus: /storage/workspaces/artorg_msb/hpc_abaqus/Software/DassaultSystemes/SIMULIA/Commands/abq2024 # ubelix 
-socket_paths: # paths that are socket specific (you might need to change them)
-  # SIMONE-KUBUNTU
-  # workdir: /home/simoneponcioni/Documents/01_PHD/03_Methods/HFE
-  # scratchdir: /home/simoneponcioni/.SCRATCH
-  # odb2vtk: "/home/simoneponcioni/Documents/04_TOOLS/ODB2VTK/python/odb2vtk.py"
-  # MONTEROSA
-  # workdir: /home/sp20q110/HFE
-  # scratchdir: /home/sp20q110/.SCRATCH
-  # odb2vtk: "/home/sp20q110/TOOLS/ODB2VTK/python/odb2vtk.py"
-  # UBELIX
-  workdir: /storage/workspaces/artorg_msb/hpc_abaqus/poncioni/HFE
-  scratchdir: /storage/workspaces/artorg_msb/hpc_abaqus/poncioni/.SCRATCH
-  odb2vtk: /storage/workspaces/artorg_msb/hpc_abaqus/poncioni/TOOLS/ODB2VTK/python/odb2vtk.py
 
+  # abaqus: /var/DassaultSystemes/SIMULIA/Commands/abq2021hf4                     # monterosa (Abaqus 2021)
+  abaqus: /var/DassaultSystemes/SIMULIA/Commands/abq2021hf6                       # simone-kubuntu
+
+socket_paths: # paths that are socket specific (you might need to change them)
+  # workdir: /Users/msb/Documents/01_PHD/03_Methods/CLEAN-HFE-ACCURATE            # simone-macbook
+  workdir: /home/simoneponcioni/Documents/01_PHD/03_Methods/HFE                   # simone-kubuntu
+  scratchdir: /home/simoneponcioni/.SCRATCH                                       # simone-kubuntu
+  odb2vtk: "/home/simoneponcioni/Documents/04_TOOLS/ODB2VTK/python/odb2vtk.py"    # simone-kubuntu
+  # workdir: /home/sp20q110/HFE                                                   # monterosa
+  # scratchdir: /home/sp20q110/.SCRATCH                                           # monterosa
+  # odb2vtk: "/home/sp20q110/TOOLS/ODB2VTK/python/odb2vtk.py"                     # monterosa

02_CODE/src/hfe_abq/aim2fe.py

@@ -167,8 +167,11 @@ def aim2fe_psl(cfg, sample):
         bone = imutils.read_aim_mask_combined("MASK", filenames, bone)
 
     # image_list = ["BMD", "SEG", "CORTMASK", "TRABMASK"]
-    for _, item in enumerate(image_list):
-        bone = imutils.adjust_image_size(item, bone, cfg, imutils.CropType.crop)
+    if cfg.registration.registration is True:
+        for _, item in enumerate(image_list):
+            bone = imutils.adjust_image_size(item, bone, cfg, imutils.CropType.crop)
+    else:
+        pass
 
     # Save images with colorbar
     imutils.save_images_with_colorbar(cfg, sample, bone)
@@ -263,7 +266,10 @@ def aim2fe_psl(cfg, sample):
         """
 
         bone["elsets"] = []
+        if "FEelSize" not in bone or bone["FEelSize"]:
+            bone["FEelSize"] = int(round(cfg.mesher.element_size / spacing[0])) * bone["Spacing"]
         CoarseFactor = bone["FEelSize"][0] / bone["Spacing"][0]
+        bone["CoarseFactor"] = CoarseFactor
         BVTVscaled_shape = bone["BVTVscaled"].shape
         bone["MESH"] = np.ones(
             ([int(dim) for dim in np.floor(np.array(BVTVscaled_shape) / CoarseFactor)])

02_CODE/src/hfe_accurate/hfe_accurate.py

@@ -40,7 +40,7 @@
 def pipeline_hfe(cfg, folder_id, grayscale_filename):
     '''
     # TODO: reactivate this for mesh sensitivity analysis
-    n_sim = int(15)  # has to match sweep in config
+    # n_sim = int(15)  # has to match sweep in config
     # min = 5, 5, 2, 7
     # max = 20, 50, 10, 50 did not work, reducing to 20, 40, 10, 40
     n_elms_longitudinal = np.linspace(1, 20, n_sim, dtype=int)
@@ -61,7 +61,7 @@ def pipeline_hfe(cfg, folder_id, grayscale_filename):
     )
     cfg.meshing_settings.n_elms_radial = int(n_radial[sweep - 1].item())
     '''
-    
+
     # timing
     time_record = {}
     start_full = time()

02_CODE/src/hfe_accurate/postprocessing.py

@@ -318,7 +318,8 @@ def write_data_summary(
             "max_force_FZ_MAX",
             "disp_at_max_force_FZ_MAX",
             "stiffness_1D_FZ_MAX",
-            "yield_force_FZ_MAX" "yield_disp_FZ_MAX",
+            "yield_force_FZ_MAX",
+            "yield_disp_FZ_MAX",
         ]
 
     def append_list_as_row(filename: str, list_of_elem: list) -> None:

02_CODE/src/hfe_utils/imutils.py

@@ -407,6 +407,7 @@ def adjust_image_size(name, bone, cfg, croptype=CropType.crop):
     Expansions in x and y dimension,
     will probably not affect strength, but will lower stiffness.
     """
+    logger.info(f"Adjust image size for {name}")
     # get bone values
     img_array = bone[name + "_array"]
     spacing = bone["Spacing"]

02_CODE/src/pipeline_runner.py

@@ -3,12 +3,14 @@
 # this code creates a list of executables to run in parallel
 
 
+import json
 import logging
 import warnings
 import os
 from enum import Enum
 from pprint import pprint
 from time import time
+
 import json
 from pathlib import Path
 

QMSKI/convergence_study/convergence_radius.csv.bak

@@ -0,0 +1,56 @@
+Sample,DOFs,simulation_time,n_elms_longitudinal,n_elms_transverse_trab,n_elms_transverse_cort,n_elms_radial,max_force_FZ_MAX,disp_at_max_force_FZ_MAX,stiffness_1D_FZ_MAX,yield_force_FZ_MAX,yield_disp_FZ_MAX
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