corrected filenames in o-o version

02_CODE/cfg/hfe-nodaratis.yaml

@@ -9,7 +9,7 @@ hydra:
   mode: MULTIRUN
   sweeper:
     params:
-      simulations.grayscale_filenames: C0003093
+      simulations.grayscale_filenames: C0003104
 
 
 mesher:
@@ -20,7 +20,7 @@ mesher:
 image_processing:
   origaim_separate: False           # For Hosseini Dataset, Image parameters are read from original aim, not from processed BMD file, as there they were deleted by medtool pre-processing
   mask_separate: True               # Standard evaluation gives two separate mask file (CORTMASK and TRABMASK), False if one maskfile with two different labels
-  imtype: BMD                       # NATIVE or BMD
+  imtype: NATIVE                    # NATIVE or BMD
   bvtv_scaling: 1                   # 0: no scaling, 1: Scaling of BVTV 61um to BVTV 11.4um [Hosseini2017]
   bvtv_slope: 0.963                 # bvtv intercept, added to each image voxel
   bvtv_intercept: 0.03814           # bvtv intercept, added to each image voxel

02_CODE/cfg/mesh.yaml

@@ -12,7 +12,7 @@ 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: 100                              # smoothing factor of the spline
   k: 3                                # degree of the spline
   interp_points: 200                  # number of points to interpolate the spline
   dp_simplification_outer: 3          # Ramer-Douglas-Peucker simplification factor for the periosteal contour
@@ -26,9 +26,9 @@ meshing_settings:
   n_elms_longitudinal: 3              
   n_elms_transverse_trab: 15          
   n_elms_transverse_cort: 3           
-  n_elms_radial: 20                   # ! Should be 10 if trab_refinement is True
+  n_elms_radial: 80                   # ! Should be 40 if trab_refinement is True
   ellipsoid_fitting: True
-  
+
   show_plots: False                   # show plots during construction
   show_gmsh: False                    # show gmsh GUI
   write_mesh: True                    # write mesh to file

02_CODE/cfg/paths-nodaratis.yaml

@@ -10,11 +10,11 @@ paths:
   odb_python_script: 02_CODE/src/hfe_abq/readODB_acc.py
 
 filenames:
-  filename_postfix_cort_mask: _V3_CORT_MASK.mha
-  filename_postfix_trab_mask: _V3_TRAB_MASK.mha
+  filename_postfix_cort_mask: _CORT_MASK_UNCOMP.mha
+  filename_postfix_trab_mask: _TRAB_MASK_UNCOMP.mha
   filename_postfix_mask: _MASK.AIM                                  # if mask separate == False, give this filename
   filename_postfix_bmd: _UNCOMP.mha
-  filename_postfix_seg: _SEG.mha
+  filename_postfix_seg: _UNCOMP_SEG.mha
   filename_postfix_common: _common_region_MASK.mhd                  # if registration is true -> file of common region
   filename_postfix_transform: _transformation.tfm                   # if registration is true -> transformation file
 

02_CODE/cfg/simulations-nodaratis.yaml

@@ -1,6 +1,8 @@
 simulations:
   grayscale_filenames:
     C0003093
+    C0003104
 
   folder_id:
-    C0003093: 442_R_75_F
+    C0003093: 442_R_75_F
+    C0003104: 438_L_71_F

02_CODE/cfg/socket.yaml

@@ -2,24 +2,24 @@ solver:
   site: remote # local or remote
 
   # * simone-kubuntu
-  # abaqus: /var/DassaultSystemes/SIMULIA/Commands/abq2021hf6
+  abaqus: /var/DassaultSystemes/SIMULIA/Commands/abq2021hf6
   # * monterosa
   # abaqus: /var/DassaultSystemes/SIMULIA/Commands/abq2021hf4
   # * Ubelix
-  abaqus: /storage/workspaces/artorg_msb/hpc_abaqus/Software/DassaultSystemes/SIMULIA/Commands/abq2024
+  # abaqus: /storage/workspaces/artorg_msb/hpc_abaqus/Software/DassaultSystemes/SIMULIA/Commands/abq2024
 
 socket_paths: # paths that are socket specific (you might need to change them)
   # * simone-macbook
   # workdir: /Users/msb/Documents/01_PHD/03_Methods/CLEAN-HFE-ACCURATE
   # * 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"
+  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
+  # 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

02_CODE/src/hfe_accurate/material_mapping.py

@@ -907,7 +907,8 @@ def material_mapping_spline(
     botnodes = bone["bnds_bot"]
     topnodes = bone["bnds_top"]
     RP_coords_s = bone["reference_point_coord"]
-    inp_filename = filenames["INPname"]
+    # inp_filename = filenames["INPname"]
+    inp_filename = filenames.inp_name
     save_dir = Path(inp_filename).parent
 
     abq = AbaqusWriter(

02_CODE/src/hfe_accurate/preprocessing.py

@@ -451,7 +451,7 @@ def msl_triangulation(cfg, SEG_array, cortmask, trabmask, spacing, tolerance):
     try:
         dimZ = (np.shape(SEG_array) * spacing)[2]
     except TypeError:
-        spacing = spacing[0]  # assuming isotropic spacing
+        spacing = np.array([spacing[0], spacing[1], spacing[2]])
         dimZ = (np.shape(SEG_array) * spacing)[2]
 
     SEG_vtk, trabmask, cortmask, spacing, tolerance, dimZ = input_sanity_check(

02_CODE/src/hfe_utils/imutils.py

@@ -279,48 +279,45 @@ def AIMreader(fileINname, spacing):
     imvtk = reader.GetOutput()
     return imvtk, spacing, scaling, slope, intercept, header
 
-def mha_reader(filename):
-    imsitk = sitk.ReadImage(filename)
-    print(type(imsitk))
-    spacing = imsitk.GetSpacing()
-    scaling = None
-    slope = None
-    intercept = None
-    header = None
-    return imsitk, spacing, scaling, slope, intercept, header
 
 def mha_header_reader(filename):
     reader = sitk.ImageFileReader()
-    reader.SetFileName(filename)
+    reader.SetFileName(str(filename.resolve()))
     reader.LoadPrivateTagsOn()
     reader.ReadImageInformation()
 
     # Extract metadata and replace _LINEBREAK_ with actual line breaks for SimpleITK compatibility
     metadata = {}
     for k in reader.GetMetaDataKeys():
-        v = reader.GetMetaData(k).replace('_LINEBREAK_', '\n')
+        v = reader.GetMetaData(k).replace("_LINEBREAK_", "\n")
         metadata[k] = v
-        print("({0}) = = \"{1}\"".format(k, v))
+        print('({0}) = = "{1}"'.format(k, v))
 
     # Extract Density: slope from the metadata
     density_slope = None
     density_intercept = None
     mu_scaling = None
     for _, value in metadata.items():
-        if 'Density: slope' in value or 'Density: intercept' in value or 'Mu_Scaling' in value:
-            lines = value.split('\n')
+        if (
+            "Density: slope" in value
+            or "Density: intercept" in value
+            or "Mu_Scaling" in value
+        ):
+            lines = value.split("\n")
             for line in lines:
-                if 'Density: slope' in line:
+                if "Density: slope" in line:
                     density_slope = float(line.split()[-1])
-                elif 'Density: intercept' in line:
+                elif "Density: intercept" in line:
                     density_intercept = float(line.split()[-1])
-                elif 'Mu_Scaling' in line:
+                elif "Mu_Scaling" in line:
                     mu_scaling = int(line.split()[-1])
 
     spacing = reader.GetSpacing()
-
+    spacing = np.array(spacing)
+
     return spacing, mu_scaling, density_slope, density_intercept
 
+
 def read_img_param(filenames: FileConfig):
     """
     Reads image parameters from the AIM image header.
@@ -340,20 +337,20 @@ def read_img_param(filenames: FileConfig):
     print("\n ... read images")
 
     raw_filename = filenames.raw_name
-    print(f'raw_filename: {raw_filename}')
-    if raw_filename.suffix == 'AIM*':
+    print(f"raw_filename: {raw_filename}")
+    if ".AIM" in raw_filename.suffix:
         try:
             _, spacing, scaling, slope, intercept, _ = AIMreader(
-                raw_filename, np.array([0.0606997, 0.0606997, 0.0606997])
+                str(raw_filename.resolve()), np.array([0.0606997, 0.0606997, 0.0606997])
             )
         except Exception as e:
             logger.exception(f"An error occurred while using AIMreader: {e}")
             raise
-    if raw_filename.suffix in ('.mha', '.mhd'):
+    if raw_filename.suffix in (".mha", ".mhd"):
         try:
             spacing, scaling, slope, intercept = mha_header_reader(raw_filename)
         except Exception as e:
-            logger.exception(f"An error occurred while using mhd_reader: {e}")
+            logger.exception(f"An error occurred while using mha_header_reader: {e}")
             raise
 
     return spacing, scaling, slope, intercept
@@ -383,38 +380,48 @@ def read_image(name, filenames, bone, lock):
     4. Updates the bone dictionary with the processed image array.
     """
 
+    if name == "BMD" or name == "NATIVE":
+        image = filenames.raw_name
+    elif name == "SEG":
+        image = filenames.seg_name
+    elif name == "TRABMASK":
+        image = filenames.trab_mask_name
+    elif name == "CORTMASK":
+        image = filenames.cort_mask_name
+
     print("\n ... read file: " + name)
 
     spacing = bone["Spacing"]
-    if name.suffix == '*AIM*':
-        IMG_vtk = AIMreader(filenames[name + "name"], spacing)[0]
+    if "AIM" in filenames.filename_postfix_bmd:
+        image = str(image.resolve())
+        IMG_vtk = AIMreader(image, spacing)[0]
         IMG_array = vtk2numpy(IMG_vtk)
         IMG_sitk = sitk.GetImageFromArray(IMG_array)
     else:
-        IMG_sitk = general_image_reader(filenames[name])
-
+        IMG_sitk = general_image_reader(image)
+        IMG_sitk = sitk.PermuteAxes(IMG_sitk, [2, 1, 0])
     # pad image to avoid having non-zero values at the boundary
     IMG_pad = pad_image(IMG_sitk, iso_pad_size=10)
     IMG_pad = sitk.Flip(IMG_pad, [True, False, False])
 
     #! ONLY FOR TIBIA VALIDATION DATASET
-    if "C0003114" in filenames[name + "name"]:
+    if "C0003114" in filenames.sample:
         print("Removing 35 slices")
         IMG_pad = IMG_pad[:-35, :, :]
         print(IMG_pad.GetSize())
-    elif "C0003111" in filenames[name + "name"]:
+    elif "C0003111" in filenames.sample:
         print("Removing 35 slices")
         IMG_pad = IMG_pad[:-35, :, :]
         print(IMG_pad.GetSize())
-    elif "C0003106" in filenames[name + "name"]:
+    elif "C0003106" in filenames.sample:
         print("Removing 35 slices")
         IMG_pad = IMG_pad[35:, :, :]
         print(IMG_pad.GetSize())
-    elif "C0003096" in filenames[name + "name"]:
+    elif "C0003096" in filenames.sample:
         print("Removing 10 slices")
         IMG_pad = IMG_pad[:-10, :, :]
         print(IMG_pad.GetSize())
-    elif "C0003094" in filenames[name + "name"]:
+    elif "C0003094" in filenames.sample:
         print("Removing 10 slices")
         IMG_pad = IMG_pad[5:-10, :, :]
         print(IMG_pad.GetSize())

02_CODE/src/hfe_utils/io_utils.py

@@ -14,8 +14,10 @@
 
 
 def ext(filename, new_ext):
-    """changes the file extension"""
-    return filename.replace("." + filename.split(".")[-1], new_ext)
+    """Changes the file extension."""
+    if isinstance(filename, Path):
+        filename = str(filename.resolve())
+    return filename.rsplit(".", 1)[0] + new_ext
 
 
 def print_mem_usage():
@@ -415,7 +417,9 @@ def log_summary(bone, config, filenames, var):
 
 
 class FileConfig:
-    def __init__(self, cfg, sample: str, pipeline: str = "fast", origaim_separate: bool = True):
+    def __init__(
+        self, cfg, sample: str, pipeline: str = "fast", origaim_separate: bool = True
+    ):
         self.cfg = cfg
         self.sample = sample
         self.pipeline = pipeline
@@ -452,7 +456,9 @@ def boundary_conditions(self) -> str:
 
     @property
     def file_mask(self) -> Path:
-        if self.pipeline == "fast" or (self.pipeline == "accurate" and not self.cfg.image_processing.mask_separate):
+        if self.pipeline == "fast" or (
+            self.pipeline == "accurate" and not self.cfg.image_processing.mask_separate
+        ):
             return Path(f"{self.sample}{self.cfg.filenames.filename_postfix_mask}")
         return None
 
@@ -524,7 +530,7 @@ def set_filenames(self):
             "INPname": str(self.inp_name),
             "VTKname": str(self.vtk_name),
             "SUMname": str(self.sum_name),
-            "VER_BPVname": str(self.ver_bpv_name)
+            "VER_BPVname": str(self.ver_bpv_name),
         }
 
         if self.pipeline == "fast":
@@ -544,10 +550,10 @@ def set_filenames(self):
                 filename["MASKname"] = str(self.mask_name)
 
         return filename
-    
+
     # Usage
     # cfg = ...  # Your configuration object
     # sample = "sample_name"
     # file_config = FileConfig(cfg, sample)
     # print(file_config.bmd_name)
-    # print(file_config.inp_name)
+    # print(file_config.inp_name)