junifer 0.0.6.dev219__py3-none-any.whl → 0.0.6.dev248__py3-none-any.whl

junifer/data/utils.py

@@ -4,14 +4,14 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Dict, List, MutableMapping, Optional, Union
 
 import numpy as np
 
-from ..utils.logging import logger
+from ..utils import logger, raise_error
 
 
-__all__ = ["closest_resolution"]
+__all__ = ["closest_resolution", "get_native_warper"]
 
 
 def closest_resolution(
@@ -49,3 +49,67 @@ def closest_resolution(
         closest = np.min(valid_resolution)
 
     return closest
+
+
+def get_native_warper(
+    target_data: MutableMapping,
+    other_data: MutableMapping,
+    inverse: bool = False,
+) -> Dict:
+    """Get correct warping specification for native space.
+
+    Parameters
+    ----------
+    target_data : dict
+        The target data from the pipeline data object.
+    other_data : dict
+        The other data in the pipeline data object.
+    inverse : bool, optional
+        Whether to get the inverse warping specification (default False).
+
+    Returns
+    -------
+    dict
+        The correct warping specification.
+
+    Raises
+    ------
+    RuntimeError
+        If no warper or multiple possible warpers are found.
+
+    """
+    # Get possible warpers
+    possible_warpers = []
+    for entry in other_data["Warp"]:
+        if not inverse:
+            if (
+                entry["src"] == target_data["prewarp_space"]
+                and entry["dst"] == "native"
+            ):
+                possible_warpers.append(entry)
+        else:
+            if (
+                entry["dst"] == target_data["prewarp_space"]
+                and entry["src"] == "native"
+            ):
+                possible_warpers.append(entry)
+
+    # Check for no warper
+    if not possible_warpers:
+        raise_error(
+            klass=RuntimeError,
+            msg="Could not find correct warping specification",
+        )
+
+    # Check for multiple possible warpers
+    if len(possible_warpers) > 1:
+        raise_error(
+            klass=RuntimeError,
+            msg=(
+                "Cannot proceed as multiple warping specification found, "
+                "adjust either the DataGrabber or the working space: "
+                f"{possible_warpers}"
+            ),
+        )
+
+    return possible_warpers[0]

junifer/datagrabber/aomic/id1000.py

@@ -169,15 +169,28 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                             "space": "native",
                         },
                     },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
+                    "Warp": [
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "MNI152NLin2009cAsym",
+                            "dst": "native",
+                            "warper": "ants",
+                        },
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "native",
+                            "dst": "MNI152NLin2009cAsym",
+                            "warper": "ants",
+                        },
+                    ],
                 }
             )
         # Set default types

junifer/datagrabber/aomic/piop1.py

@@ -204,15 +204,28 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                             "space": "native",
                         },
                     },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
+                    "Warp": [
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "MNI152NLin2009cAsym",
+                            "dst": "native",
+                            "warper": "ants",
+                        },
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "native",
+                            "dst": "MNI152NLin2009cAsym",
+                            "warper": "ants",
+                        },
+                    ],
                 }
             )
         # Set default types

junifer/datagrabber/aomic/piop2.py

@@ -202,15 +202,28 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                             "space": "native",
                         },
                     },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
+                    "Warp": [
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "MNI152NLin2009cAsym",
+                            "dst": "native",
+                            "warper": "ants",
+                        },
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "native",
+                            "dst": "MNI152NLin2009cAsym",
+                            "warper": "ants",
+                        },
+                    ],
                 }
             )
         # Set default types

junifer/datagrabber/base.py

@@ -96,7 +96,12 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         # Update metadata
         for _, t_val in out.items():
             self.update_meta(t_val, "datagrabber")
-            t_val["meta"]["element"] = named_element
+            # Conditional for list dtype vals like Warp
+            if isinstance(t_val, list):
+                for entry in t_val:
+                    entry["meta"]["element"] = named_element
+            else:
+                t_val["meta"]["element"] = named_element
 
         return out
 

junifer/datagrabber/datalad_base.py

@@ -181,14 +181,21 @@ class DataladDataGrabber(BaseDataGrabber):
         """
         to_get = []
         for type_val in out.values():
-            # Iterate to check for nested "types" like mask
-            for k, v in type_val.items():
-                # Add base data type path
-                if k == "path":
-                    to_get.append(v)
-                # Add nested data type path
-                if isinstance(v, dict) and "path" in v:
-                    to_get.append(v["path"])
+            # Conditional for list dtype vals like Warp
+            if isinstance(type_val, list):
+                for entry in type_val:
+                    for k, v in entry.items():
+                        if k == "path":
+                            to_get.append(v)
+            else:
+                # Iterate to check for nested "types" like mask
+                for k, v in type_val.items():
+                    # Add base data type path
+                    if k == "path":
+                        to_get.append(v)
+                    # Add nested data type path
+                    if isinstance(v, dict) and "path" in v:
+                        to_get.append(v["path"])
 
         if len(to_get) > 0:
             logger.debug(f"Getting {len(to_get)} files using datalad:")

junifer/datagrabber/dmcc13_benchmark.py

@@ -150,7 +150,7 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep-1.3.2/{subject}/{session}/"
-                        "/func/{subject}_{session}_task-{task}_acq-mb4"
+                        "func/{subject}_{session}_task-{task}_acq-mb4"
                         "{phase_encoding}_run-{run}_"
                         "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
                     ),
@@ -221,15 +221,28 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                             "space": "native",
                         },
                     },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep-1.3.2/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
+                    "Warp": [
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep-1.3.2/{subject}/anat/"
+                                "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "MNI152NLin2009cAsym",
+                            "dst": "native",
+                            "warper": "ants",
+                        },
+                        {
+                            "pattern": (
+                                "derivatives/fmriprep-1.3.2/{subject}/anat/"
+                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                                "mode-image_xfm.h5"
+                            ),
+                            "src": "native",
+                            "dst": "MNI152NLin2009cAsym",
+                            "warper": "ants",
+                        },
+                    ],
                 }
             )
         # Set default types

junifer/datagrabber/hcp1200/hcp1200.py

@@ -122,13 +122,24 @@ class HCP1200(PatternDataGrabber):
                 "pattern": "{subject}/T1w/T1w_acpc_dc_restore.nii.gz",
                 "space": "native",
             },
-            "Warp": {
-                "pattern": (
-                    "{subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz"
-                ),
-                "src": "MNI152NLin6Asym",
-                "dst": "native",
-            },
+            "Warp": [
+                {
+                    "pattern": (
+                        "{subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz"
+                    ),
+                    "src": "MNI152NLin6Asym",
+                    "dst": "native",
+                    "warper": "fsl",
+                },
+                {
+                    "pattern": (
+                        "{subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz"
+                    ),
+                    "src": "native",
+                    "dst": "MNI152NLin6Asym",
+                    "warper": "fsl",
+                },
+            ],
         }
         # The replacements
         replacements = ["subject", "task", "phase_encoding"]

junifer/datagrabber/multiple.py

@@ -8,6 +8,7 @@
 from typing import Dict, List, Tuple, Union
 
 from ..api.decorators import register_datagrabber
+from ..typing import DataGrabberLike
 from ..utils import deep_update, raise_error
 from .base import BaseDataGrabber
 
@@ -37,7 +38,7 @@ class MultipleDataGrabber(BaseDataGrabber):
 
     """
 
-    def __init__(self, datagrabbers: List[BaseDataGrabber], **kwargs) -> None:
+    def __init__(self, datagrabbers: List[DataGrabberLike], **kwargs) -> None:
         # Check datagrabbers consistency
         # Check for same element keys
         first_keys = datagrabbers[0].get_element_keys()

junifer/datagrabber/pattern.py

@@ -89,7 +89,7 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
           .. code-block:: none
 
             {
-              "mandatory": ["pattern", "src", "dst"],
+              "mandatory": ["pattern", "src", "dst", "warper"],
               "optional": []
             }
 
@@ -127,11 +127,22 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
                 "pattern": "...",
                 "space": "...",
               },
-              "Warp": {
-                "pattern": "...",
-                "src": "...",
-                "dst": "...",
-              }
+          }
+
+        except ``Warp``, which needs to be a list of dictionaries as there can
+        be multiple spaces to warp (for example, with fMRIPrep):
+
+        .. code-block:: none
+
+          {
+              "Warp": [
+                {
+                  "pattern": "...",
+                  "src": "...",
+                  "dst": "...",
+                  "warper": "...",
+                },
+              ],
           }
 
         taken from :class:`.HCP1200`.
@@ -380,42 +391,61 @@ class PatternDataGrabber(BaseDataGrabber, PatternValidationMixin):
             t_pattern = self.patterns[t_type]
             # Copy data type dictionary in output
             out[t_type] = deepcopy(t_pattern)
-            # Iterate to check for nested "types" like mask
-            for k, v in t_pattern.items():
-                # Resolve pattern for base data type
-                if k == "pattern":
-                    logger.info(f"Resolving path from pattern for {t_type}")
+            # Conditional for list dtype vals like Warp
+            if isinstance(t_pattern, list):
+                for idx, entry in enumerate(t_pattern):
+                    logger.info(
+                        f"Resolving path from pattern for {t_type}.{idx}"
+                    )
                     # Resolve pattern
-                    base_data_type_pattern_path = self._get_path_from_patterns(
+                    dtype_pattern_path = self._get_path_from_patterns(
                         element=element,
-                        pattern=v,
-                        data_type=t_type,
+                        pattern=entry["pattern"],
+                        data_type=f"{t_type}.{idx}",
                     )
                     # Remove pattern key
-                    out[t_type].pop("pattern")
+                    out[t_type][idx].pop("pattern")
                     # Add path key
-                    out[t_type].update({"path": base_data_type_pattern_path})
-                # Resolve pattern for nested data type
-                if isinstance(v, dict) and "pattern" in v:
-                    # Set nested type key for easier access
-                    t_nested_type = f"{t_type}.{k}"
-                    logger.info(
-                        f"Resolving path from pattern for {t_nested_type}"
-                    )
-                    # Resolve pattern
-                    nested_data_type_pattern_path = (
-                        self._get_path_from_patterns(
+                    out[t_type][idx].update({"path": dtype_pattern_path})
+            else:
+                # Iterate to check for nested "types" like mask
+                for k, v in t_pattern.items():
+                    # Resolve pattern for base data type
+                    if k == "pattern":
+                        logger.info(
+                            f"Resolving path from pattern for {t_type}"
+                        )
+                        # Resolve pattern
+                        base_dtype_pattern_path = self._get_path_from_patterns(
                             element=element,
-                            pattern=v["pattern"],
-                            data_type=t_nested_type,
+                            pattern=v,
+                            data_type=t_type,
+                        )
+                        # Remove pattern key
+                        out[t_type].pop("pattern")
+                        # Add path key
+                        out[t_type].update({"path": base_dtype_pattern_path})
+                    # Resolve pattern for nested data type
+                    if isinstance(v, dict) and "pattern" in v:
+                        # Set nested type key for easier access
+                        t_nested_type = f"{t_type}.{k}"
+                        logger.info(
+                            f"Resolving path from pattern for {t_nested_type}"
+                        )
+                        # Resolve pattern
+                        nested_dtype_pattern_path = (
+                            self._get_path_from_patterns(
+                                element=element,
+                                pattern=v["pattern"],
+                                data_type=t_nested_type,
+                            )
+                        )
+                        # Remove pattern key
+                        out[t_type][k].pop("pattern")
+                        # Add path key
+                        out[t_type][k].update(
+                            {"path": nested_dtype_pattern_path}
                         )
-                    )
-                    # Remove pattern key
-                    out[t_type][k].pop("pattern")
-                    # Add path key
-                    out[t_type][k].update(
-                        {"path": nested_data_type_pattern_path}
-                    )
 
         return out