Add methods for handling JSON

afids_utils/afids.py

@@ -178,8 +178,12 @@ def load(cls, afids_fpath: PathLike[str] | str) -> AfidSet:
                 afids_fpath
             )
         # Loading json
-        # if afids_fpath_ext = ".json":
-        #   load_json(afids_path)
+        elif afids_fpath_ext == ".json":
+            from afids_utils.ext.json import load_json
+
+            slicer_version, coord_system, afids_positions = load_json(
+                afids_fpath
+            )
         else:
             raise ValueError("Unsupported file extension")
 
@@ -229,8 +233,10 @@ def save(self, out_fpath: PathLike[str] | str) -> None:
 
             save_fcsv(self, out_fpath)
         # Saving json
-        # if out_fpath_ext = ".json":
-        #   save_json(afids_coords, out_fpath)
+        elif out_fpath_ext == ".json":
+            from afids_utils.ext.json import save_json
+
+            save_json(self, out_fpath)
         else:
             raise ValueError("Unsupported file extension")
 

afids_utils/ext/fcsv.py

@@ -29,8 +29,7 @@
 
 
 def _get_metadata(in_fcsv: list[str]) -> tuple[str, str]:
-    """
-    Internal function to extract metadata from header of fcsv files
+    """Internal function to extract metadata from header of fcsv files
 
     Parameters
     ----------
@@ -73,8 +72,7 @@ def _get_metadata(in_fcsv: list[str]) -> tuple[str, str]:
 
 
 def _get_afids(in_fcsv: list[str]) -> list[AfidPosition]:
-    """
-    Internal function for converting .fcsv file to a pl.DataFrame
+    """Internal function for grabbing AFID positions from .fcsv file
 
     Parameters
     ----------
@@ -109,8 +107,7 @@ def _get_afids(in_fcsv: list[str]) -> list[AfidPosition]:
 def load_fcsv(
     fcsv_path: PathLike[str] | str,
 ) -> tuple[str, str, list[AfidPosition]]:
-    """
-    Read in fcsv to an AfidSet
+    """Read in fcsv and extract relevant information for an AfidSet
 
     Parameters
     ----------
@@ -143,8 +140,7 @@ def save_fcsv(
     afid_set: AfidSet,
     out_fcsv: PathLike[str] | str,
 ) -> None:
-    """
-    Save fiducials to output fcsv file
+    """Save fiducials to output fcsv file
 
     Parameters
     ----------
@@ -153,11 +149,6 @@ def save_fcsv(
 
     out_fcsv
         Path of fcsv file to save AFIDs to
-
-    Raises
-    ------
-    TypeError
-        If number of fiducials to write does not match expected number
     """
     # Read in fcsv template
     with resources.open_text(

afids_utils/ext/json.py

@@ -0,0 +1,163 @@
+"""Methods for handling .json files associated with AFIDS"""
+from __future__ import annotations
+
+import json
+from importlib import resources
+from os import PathLike
+
+from typing_extensions import TypedDict
+
+from afids_utils.afids import AfidPosition, AfidSet
+from afids_utils.exceptions import InvalidFileError
+
+
+class ControlPoint(TypedDict):
+    id: str
+    label: str
+    description: str
+    associatedNodeID: str
+    position: list[float]
+    orientation: list[float]
+    selected: bool
+    locked: bool
+    visibility: bool
+    positionStatus: str
+
+
+def _get_metadata(coord_system: str) -> tuple[str, str]:
+    """Internal function to extract metadata from json files
+
+    Note: Slicer version is not currently included in the json file
+
+    Parameters:
+    -----------
+    coord_system
+        Coordinate system parsed from json_file
+
+    Returns
+    -------
+    parsed_version
+        Slicer version associated with fiducial file
+
+    parsed_coord
+        Coordinate system of fiducials
+
+    Raises
+    ------
+    InvalidFileError
+        If header is invalid from .json file
+    """
+
+    # Update if future json versions include Slicer version
+    parsed_version = "Unknown"
+    parsed_coord = coord_system
+
+    # Transform coordinate system so human-understandable
+    if parsed_coord == "0":
+        parsed_coord = "RAS"
+    elif parsed_coord == "1":
+        parsed_coord = "LPS"
+
+    if parsed_coord not in ["RAS", "LPS"]:
+        raise InvalidFileError("Invalid coordinate system")
+
+    return parsed_version, parsed_coord
+
+
+def _get_afids(control_points: list[ControlPoint]) -> list[AfidPosition]:
+    """Internal function to parse fiducial information from json file
+
+    Parameters
+    ----------
+    ctrl_points
+        List of dicts containing fiducial information from parsed json file
+
+    Returns
+    -------
+    afid_positions
+        List containing spatial position of afids
+    """
+    afids_positions = [
+        AfidPosition(
+            label=int(afid["label"]),
+            x=float(afid["position"][0]),
+            y=float(afid["position"][1]),
+            z=float(afid["position"][2]),
+            desc=afid["description"],
+        )
+        for afid in control_points
+    ]
+
+    return afids_positions
+
+
+def load_json(
+    json_path: PathLike[str] | str,
+) -> tuple[str, str, list[AfidPosition]]:
+    """Read in json and extract relevant information for an AfidSet
+
+    Parameters
+    ----------
+    json_path
+        Path to .json file containing AFIDs coordinates
+
+    Returns
+    -------
+    slicer_version
+        Slicer version associated with fiducial file
+
+    coord_system
+        Coordinate system of fiducials
+
+    afids_positions
+        List containing spatial position of afids
+    """
+    with open(json_path) as json_file:
+        afids_json = json.load(json_file)
+
+    # Grab metadata
+    slicer_version, coord_system = _get_metadata(
+        afids_json["markups"][0]["coordinateSystem"]
+    )
+    # Grab afids
+    afids_positions = _get_afids(afids_json["markups"][0]["controlPoints"])
+
+    return slicer_version, coord_system, afids_positions
+
+
+def save_json(
+    afid_set: AfidSet,
+    out_json: PathLike[str] | str,
+) -> None:
+    """Save fiducials to output json file
+
+    Parameters
+    ----------
+    afid_set
+        A complete AfidSet containing metadata and positions of AFIDs
+
+    out_json
+        Path of json file to save AFIDs to
+    """
+    # Read in json template
+    with resources.open_text(
+        "afids_utils.resources", "template.json"
+    ) as template_json_file:
+        template_content = json.load(template_json_file)
+
+        # Update header
+        template_content["markups"][0][
+            "coordinateSystem"
+        ] = afid_set.coord_system
+
+    # Loop and update with fiducial coordinates
+    for idx in range(len(template_content["markups"][0]["controlPoints"])):
+        template_content["markups"][0]["controlPoints"][idx]["position"] = [
+            afid_set.afids[idx].x,
+            afid_set.afids[idx].y,
+            afid_set.afids[idx].z,
+        ]
+
+    # Write output json
+    with open(out_json, "w") as out_json_file:
+        json.dump(template_content, out_json_file, indent=4)