Patch 12

install_elastix_R.sh

@@ -8,9 +8,9 @@ sudo apt install python3-pip
 sudo apt install r-base
 
 #  Install elastix
-wget https://github.com/SuperElastix/elastix/releases/download/4.9.0/elastix-4.9.0-linux.tar.bz2
+wget https://github.com/SuperElastix/elastix/releases/download/5.0.0/elastix-5.0.0-linux.tar.bz2
 mkdir ~/elastix
-tar xjf elastix-4.9.0-linux.tar.bz2 -C ~/elastix
+tar xjf elastix-5.0.0-linux.tar.bz2 -C ~/elastix
 
 home=~/
 echo -e "\n# paths added by my LAMA installation" >> ~/.bashrc

lama/__init__.py

@@ -5,4 +5,4 @@
 warnings.filterwarnings("ignore")
 
 
-matplotlib.use('Agg')
+#matplotlib.use('Agg')

lama/common.py

@@ -42,6 +42,7 @@
 
 ORGAN_VOLUME_CSV_FILE = 'organ_volumes.csv'
 STAGING_INFO_FILENAME = 'staging_info_volume.csv'
+FOLDING_FILE_NAME = 'folding_report.csv'
 
 lama_root_dir = Path(lama.__file__).parent
 
@@ -116,7 +117,7 @@ def excepthook_overide(exctype, value, traceback):
 
 
 def command_line_agrs():
-    return ', '.join(sys.argv)
+    return ' '.join(sys.argv)
 
 
 def touch(file_: Path):
@@ -238,7 +239,7 @@ def write_array(array: np.ndarray, path: Union[str, Path], compressed=True, ras=
     img = sitk.GetImageFromArray(array)
     if ras:
         img.SetDirection((-1, 0, 0, 0, -1, 0, 0, 0, 1))
-    sitk.WriteImage(sitk.GetImageFromArray(array), path, compressed)
+    sitk.WriteImage(img, path, compressed)
 
 
 def read_array( path: Union[str, Path]):
@@ -373,7 +374,7 @@ def mkdir_if_not_exists(dir_: Union[str, Path]):
 
 
 def get_file_paths(folder: Union[str, Path], extension_tuple=('.nrrd', '.tiff', '.tif', '.nii', '.bmp', 'jpg', 'mnc', 'vtk', 'bin', 'npy'),
-                   pattern: str = None, ignore_folder: str = "") -> Union[List[str], List[Path]]:
+                   pattern: str = None, ignore_folders: Union[List, str] = []) -> Union[List[str], List[Path]]:
     """
     Given a directory return all image paths within all sibdirectories.
 
@@ -385,8 +386,8 @@ def get_file_paths(folder: Union[str, Path], extension_tuple=('.nrrd', '.tiff',
         Select only images with these extensions
     pattern
         Do a simple `pattern in filename` filter on filenames
-    ignore_folder
-        do not look in folder with this name
+    ignore_folders
+        do not look in folder with these names
 
     Notes
     -----
@@ -395,32 +396,33 @@ def get_file_paths(folder: Union[str, Path], extension_tuple=('.nrrd', '.tiff',
 
     Do not include hidden filenames
     """
+    paths = []
 
-    if not os.path.isdir(folder):
-        return False
-    else:
-        paths = []
+    if isinstance(ignore_folders, str):
+        ignore_folders = [ignore_folders]
 
-        for root, subfolders, files in os.walk(folder):
 
-            if ignore_folder in subfolders:
-                subfolders.remove(ignore_folder)
+    for root, subfolders, files in os.walk(folder):
 
-            for filename in files:
+        for f in ignore_folders:
+            if f in subfolders:
+                subfolders.remove(f)
 
-                if filename.lower().endswith(extension_tuple) and not filename.startswith('.'):
+        for filename in files:
 
-                    if pattern:
+            if filename.lower().endswith(extension_tuple) and not filename.startswith('.'):
 
-                        if pattern and pattern not in filename:
-                            continue
+                if pattern:
 
-                    paths.append(os.path.abspath(os.path.join(root, filename)))
+                    if pattern and pattern not in filename:
+                        continue
 
-        if isinstance(folder, str):
-            return paths
-        else:
-            return [Path(x) for x in paths]
+                paths.append(os.path.abspath(os.path.join(root, filename)))
+
+    if isinstance(folder, str):
+        return paths
+    else:
+        return [Path(x) for x in paths]
 
 
 def check_config_entry_path(dict_, key):
@@ -466,6 +468,14 @@ def getfile_endswith(dir_: Path, suffix: str):
         raise FileNotFoundError(f'cannot find path file ending with {suffix} in {dir_}') from e
 
 
+def getfile_startswith_endswith(dir_: Path, prefix: str, suffix: str):
+    try:
+        return [x for x in dir_.iterdir() if x.name.endswith(suffix) and x.name.startswith(prefix)][0]
+    except IndexError as e:
+        raise FileNotFoundError(f'cannot find path starting with {prefix} and ending with {suffix} in {dir_}') from e
+
+
+
 def get_inputs_from_file_list(file_list_path, config_dir):
     """
     Gte the input files
@@ -956,3 +966,21 @@ def cfg_load(cfg) -> Dict:
 
     else:
         raise ValueError('Config file should end in .toml or .yaml')
+
+
+def bytesToGb(numberOfBytes, precision = 3):
+    return round(numberOfBytes / (1024 ** 3), precision)
+
+def logMemoryUsageInfo():
+    proc = psutil.Process(os.getpid())
+
+    procMemInfo = proc.memory_info()
+    globalMemInfo = psutil.virtual_memory()
+
+    totalMem = bytesToGb(globalMemInfo.total, 5)
+    totalMemAvailable = bytesToGb(globalMemInfo.available, 5)
+    procMemRSS = bytesToGb(procMemInfo.rss, 5)
+    procMemVMS = bytesToGb(procMemInfo.vms, 5)
+    procMemData = bytesToGb(procMemInfo.data, 5)
+
+    logging.info(f"Memory: Process Resident: {procMemRSS}, Process Virtual: {procMemVMS}, Process data: {procMemData}.  Total Available: {totalMemAvailable}")

lama/elastix/__init__.py

@@ -13,5 +13,6 @@
 VOLUME_CALCULATIONS_FILENAME = "organvolumes.csv"
 INVERT_CONFIG = 'invert.yaml'
 REG_DIR_ORDER = 'reg_order.txt'
-IGNORE_FOLDER = 'resolution_images'  # When reading images from dir and subdirs, ignore images in this folder
+RESOLUTION_IMGS_DIR = 'resolution_images'  # When reading images from dir and subdirs, ignore images in this folder
 TRANSFORMIX_OUT = 'result.nrrd'  # This will not be correct if filetype is not nrrd
+IMG_PYRAMID_DIR = 'pyramid_images'

lama/elastix/deformations.py

@@ -22,18 +22,40 @@
 TRANSFORMIX_LOG = 'transformix.log'
 
 
-def make_deformations_at_different_scales(config: Union[LamaConfig, dict]):
+def make_deformations_at_different_scales(config: Union[LamaConfig, dict]) -> Union[None, np.array]:
     """
-    Generate jacobian determinants ans optionaly defromation vectors
+    Generate jacobian determinants and optionaly defromation vectors
 
     Parameters
     ----------
     config:
         LamaConfig object if running from other lama module
         Path to config file if running this module independently
+
+    Notes
+    -----
+    How to generate the hacobian determinants is defined by the config['generate_deformation_fields'] entry.
+
+    toml representation from the LAMA config:
+
+    [generate_deformation_fields]
+    192_to_10 = [ "deformable_192_to_10",]
+
+    This will create a set of jacobian determinants and optional deformation fields called 192_to_10 and using the
+    the named regisrtation stages in the list.
+
+    Multiple sets of key/value pairs are allowed so that diffrent jacobians determinatnts might be made. For eaxmple
+    you may want to include the affine transformation in the jacobians, which would look like so:
+
+    affine_192_to_10 = [ "affine", "deformable_192_to_10"]
+
+    Returns
+    -------
+    jacobian array if there are any negative values
     """
-    if isinstance(config, Path):
-        config = LamaConfig(config)
+
+    if isinstance(config, (str, Path)):
+        config = LamaConfig(Path(config))
 
     if not config['generate_deformation_fields']:
         return
@@ -76,8 +98,9 @@ def make_deformations_at_different_scales(config: Union[LamaConfig, dict]):
         log_jacobians_scale_dir = log_jacobians_dir / deformation_id
         log_jacobians_scale_dir.mkdir()
 
-        generate_deformation_fields(reg_stage_dirs, resolutions, deformation_scale_dir, jacobians_scale_dir,
+        neg_jac_arr = generate_deformation_fields(reg_stage_dirs, resolutions, deformation_scale_dir, jacobians_scale_dir,
                                     log_jacobians_scale_dir, make_vectors, threads=config['threads'], filetype=config['filetype'])
+        return neg_jac_arr
 
 
 def generate_deformation_fields(registration_dirs: List,
@@ -150,8 +173,9 @@ def generate_deformation_fields(registration_dirs: List,
         # Copy the tp files into the temp directory and then modify to add initail transform
 
         # pass in the last tp file [-1] as the other tp files are intyernally referenced
-        get_deformations(transform_params[-1], deformation_dir, jacobian_dir, log_jacobians_dir, filetype, specimen_id,
+        neg_jac_array = get_deformations(transform_params[-1], deformation_dir, jacobian_dir, log_jacobians_dir, filetype, specimen_id,
                          threads, jacmat, get_vectors)
+        return neg_jac_array
 
 
 def _modfy_tforms(tforms: List):
@@ -166,7 +190,7 @@ def _modfy_tforms(tforms: List):
     for i, tp in enumerate(tforms[1:]):
         initial_tp = tforms[i]
 
-        with open(tp, 'rb') as fh:
+        with open(tp, 'r') as fh:
             lines = []
             for line in fh:
                 if line.startswith('(InitialTransformParametersFileName'):
@@ -175,7 +199,7 @@ def _modfy_tforms(tforms: List):
 
         previous_tp_str = '(InitialTransformParametersFileName "{}")'.format(initial_tp)
         lines.insert(0, previous_tp_str + '\n')
-        with open(tp, 'wb') as wh:
+        with open(tp, 'w') as wh:
             for line in lines:
                 wh.write(line)
 
@@ -188,9 +212,13 @@ def get_deformations(tform: Path,
                      specimen_id: str,
                      threads: int,
                      make_jacmat: bool,
-                     get_vectors: bool = False):
+                     get_vectors: bool = False) -> Union[None, np.array]:
     """
     Generate spatial jacobians and optionally deformation files.
+
+    Returns
+    -------
+    the jacobian array if there are any values < 0
     """
 
     cmd = ['transformix',
@@ -265,5 +293,8 @@ def get_deformations(tform: Path,
 
     logging.info('Finished generating deformation fields')
 
+    if jac_min <=0:
+        return jac_arr
+