Testing to see if this creates then deletes T1w's

in the correct place/subject space.

Author: bendhouseart

petdeface/noanat.py

@@ -0,0 +1,299 @@
+"""Functionality for handling cases where anatomical images are not available."""
+import nibabel
+import numpy
+import shutil
+import os
+import re
+from pathlib import Path
+from typing import Union, Dict, Optional
+
+
+def get_data_path(filename: str) -> Path:
+    """Get the path to a data file included in the package.
+    
+    Parameters
+    ----------
+    filename : str
+        Name of the file to get the path for. This should be relative to the data directory.
+        For example: "sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii"
+    
+    Returns
+    -------
+    Path
+        Path to the requested data file
+        
+    Raises
+    ------
+    FileNotFoundError
+        If the requested file is not found in the package data
+    """
+    # Get the path to the data directory
+    data_dir = Path(__file__).parent.parent / "data"
+    
+    # Construct the full path
+    full_path = data_dir / filename
+    
+    # Check if the file exists
+    if not full_path.exists():
+        raise FileNotFoundError(f"Could not find data file {filename} in data directory")
+    
+    return full_path
+
+
+def get_default_anat() -> Path:
+    """Get the path to the default anatomical image.
+    
+    Returns
+    -------
+    Path
+        Path to the default T1w image that should be used when no anatomical
+        image is available for a PET scan.
+    """
+    return get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii")
+
+
+def get_default_anat_data() -> nibabel.Nifti1Image:
+    """Get the default anatomical image as a nibabel image object.
+    
+    Returns
+    -------
+    nibabel.Nifti1Image
+        The default T1w image loaded as a nibabel image object
+    """
+    return nibabel.load(get_default_anat())
+
+
+def extract_subject_id(input_str: str) -> str:
+    """Extract subject ID from various input formats.
+    
+    This function can handle:
+    - Full paths (e.g., "/path/to/sub-123/anat/file.nii")
+    - Subject IDs with prefix (e.g., "sub-123")
+    - Raw subject IDs (e.g., "123")
+    
+    Parameters
+    ----------
+    input_str : str
+        Input string containing a subject ID in any format
+        
+    Returns
+    -------
+    str
+        Extracted subject ID without the 'sub-' prefix
+        
+    Raises
+    ------
+    ValueError
+        If no valid subject ID can be extracted
+    """
+    # Pattern to match 'sub-XXXX' in various contexts
+    # The pattern captures everything after 'sub-' until it hits a non-alphanumeric character or the end of the string
+    pattern = r'sub-([a-zA-Z0-9]+)(?:_|$)'
+    
+    # Try to find a match
+    match = re.search(pattern, input_str)
+    
+    if match:
+        # Return the captured group (the subject ID without 'sub-' prefix)
+        return match.group(1)
+    else:
+        # If no 'sub-' prefix is found, check if the input is a valid subject ID
+        if re.match(r'^[a-zA-Z0-9]+$', input_str):
+            return input_str
+        else:
+            # Try a more flexible approach for paths
+            path_match = re.search(r'sub-([a-zA-Z0-9]+)', input_str)
+            if path_match:
+                return path_match.group(1)
+            else:
+                raise ValueError(f"Could not extract a valid subject ID from '{input_str}'")
+
+
+def copy_default_anat_to_subject(bids_dir: Union[str, Path], subject_id: str) -> dict:
+    """Copy the default anatomical image to a PET subject's folder in a BIDS dataset.
+    
+    This function extracts the subject ID from the provided string using regex,
+    then copies the default anatomical image and its JSON metadata to the subject's folder in the BIDS dataset.
+    
+    Parameters
+    ----------
+    bids_dir : Union[str, Path]
+        Path to the BIDS dataset
+    subject_id : str
+        Subject ID in any format:
+        - Full path (e.g., "/path/to/sub-123/anat/file.nii")
+        - Subject ID with prefix (e.g., "sub-123")
+        - Raw subject ID (e.g., "123")
+        
+    Returns
+    -------
+    dict
+        A dictionary containing information about the created files and directories:
+        {
+            'subject_dir': Path to the subject directory,
+            'anat_dir': Path to the anatomical directory,
+            'created_dirs': List of paths to newly created directories,
+            'created_files': List of paths to newly created files
+        }
+        
+    Raises
+    ------
+    FileNotFoundError
+        If the BIDS directory or subject directory does not exist
+    ValueError
+        If the subject ID is invalid or cannot be extracted
+    """
+    # Convert bids_dir to Path if it's a string
+    bids_dir = Path(bids_dir)
+    
+    # Check if the BIDS directory exists
+    if not bids_dir.exists():
+        raise FileNotFoundError(f"BIDS directory {bids_dir} does not exist")
+    
+    # Extract subject ID using regex
+    try:
+        extracted_id = extract_subject_id(subject_id)
+    except ValueError as e:
+        raise ValueError(f"Invalid subject ID: {e}")
+    
+    # Create the subject directory structure
+    subject_dir = bids_dir / f"sub-{extracted_id}"
+    
+    # Check if the subject directory exists
+    if not subject_dir.exists():
+        raise FileNotFoundError(f"Subject directory {subject_dir} does not exist")
+    
+    anat_dir = subject_dir / "anat"
+    
+    # Create the anatomical directory if it doesn't exist
+    created_dirs = []
+    if not anat_dir.exists():
+        anat_dir.mkdir(parents=True, exist_ok=True)
+        created_dirs.append(anat_dir)
+    
+    # Define the target file paths
+    target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii"
+    target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
+    
+    # Get the source file paths
+    source_nii = get_default_anat()
+    source_json = get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json")
+    
+    # Copy the files
+    created_files = []
+    shutil.copy2(source_nii, target_nii)
+    created_files.append(target_nii)
+    
+    shutil.copy2(source_json, target_json)
+    created_files.append(target_json)
+    
+    print(f"Copied default anatomical image to {target_nii}")
+    print(f"Copied default anatomical metadata to {target_json}")
+    
+    # Return information about created files and directories
+    return {
+        'subject_dir': subject_dir,
+        'anat_dir': anat_dir,
+        'created_dirs': created_dirs,
+        'created_files': created_files
+    }
+
+
+def remove_default_anat(
+    bids_dir: Union[str, Path], 
+    subject_id: Optional[str] = None, 
+    created_items: Optional[Dict] = None
+) -> None:
+    """Remove the default anatomical image and directory created for a subject.
+    
+    This function can be used in two ways:
+    1. With the bids_dir and subject_id to identify what to remove
+    2. With the bids_dir and the dictionary returned by copy_default_anat_to_subject
+    
+    Parameters
+    ----------
+    bids_dir : Union[str, Path]
+        Path to the BIDS dataset
+    subject_id : Optional[str]
+        Subject ID in any format (if created_items is not provided)
+    created_items : Optional[Dict]
+        Dictionary returned by copy_default_anat_to_subject (if subject_id is not provided)
+        
+    Returns
+    -------
+    None
+        
+    Raises
+    ------
+    ValueError
+        If neither subject_id nor created_items is provided, or if both are provided
+    FileNotFoundError
+        If the BIDS directory or subject directory does not exist
+    """
+    # Convert bids_dir to Path if it's a string
+    bids_dir = Path(bids_dir)
+    
+    # Check if the BIDS directory exists
+    if not bids_dir.exists():
+        raise FileNotFoundError(f"BIDS directory {bids_dir} does not exist")
+    
+    # Determine which approach to use
+    if subject_id is not None and created_items is not None:
+        raise ValueError("Cannot provide both subject_id and created_items")
+    elif subject_id is None and created_items is None:
+        raise ValueError("Must provide either subject_id or created_items")
+    
+    if created_items is not None:
+        # Use the dictionary returned by copy_default_anat_to_subject
+        anat_dir = created_items['anat_dir']
+        created_files = created_items['created_files']
+        created_dirs = created_items['created_dirs']
+    else:
+        # Extract subject ID using regex
+        try:
+            extracted_id = extract_subject_id(subject_id)
+        except ValueError as e:
+            raise ValueError(f"Invalid subject ID: {e}")
+        
+        # Create the subject directory structure
+        subject_dir = bids_dir / f"sub-{extracted_id}"
+        
+        # Check if the subject directory exists
+        if not subject_dir.exists():
+            raise FileNotFoundError(f"Subject directory {subject_dir} does not exist")
+        
+        anat_dir = subject_dir / "anat"
+        
+        # Define the file paths
+        target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii"
+        target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
+        
+        # Check if the files exist
+        created_files = []
+        if target_nii.exists():
+            created_files.append(target_nii)
+        if target_json.exists():
+            created_files.append(target_json)
+        
+        # Check if the directory exists and is empty
+        created_dirs = []
+        if anat_dir.exists():
+            # Only add to created_dirs if it's empty or only contains our files
+            remaining_files = set(anat_dir.iterdir()) - set(created_files)
+            if not remaining_files:
+                created_dirs.append(anat_dir)
+    
+    # Remove the files
+    for file_path in created_files:
+        if file_path.exists():
+            file_path.unlink()
+            print(f"Removed file: {file_path}")
+    
+    # Remove the directories (only if they're empty)
+    for dir_path in created_dirs:
+        if dir_path.exists() and not any(dir_path.iterdir()):
+            dir_path.rmdir()
+            print(f"Removed directory: {dir_path}")
+    
+    print("Cleanup completed successfully")
+

petdeface/utils.py

@@ -0,0 +1,42 @@
+"""Utility functions for the petdeface package."""
+from importlib import resources
+from pathlib import Path
+from typing import Union
+
+
+def get_data_path(filename: str) -> Path:
+    """Get the path to a data file included in the package.
+    
+    Parameters
+    ----------
+    filename : str
+        Name of the file to get the path for. This should be relative to the data directory.
+        For example: "sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii"
+    
+    Returns
+    -------
+    Path
+        Path to the requested data file
+        
+    Raises
+    ------
+    FileNotFoundError
+        If the requested file is not found in the package data
+    """
+    try:
+        with resources.path('petdeface.data', filename) as path:
+            return path
+    except Exception as e:
+        raise FileNotFoundError(f"Could not find data file {filename} in package data") from e
+
+
+def get_default_anat() -> Path:
+    """Get the path to the default anatomical image.
+    
+    Returns
+    -------
+    Path
+        Path to the default T1w image that should be used when no anatomical
+        image is available for a PET scan.
+    """
+    return get_data_path("sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii")