Read scalar maps from previous qsirecon runs

qsirecon/data/pipelines/ingress_scalars_for_bundles.yaml

@@ -0,0 +1,43 @@
+name: bundle_scalar_map
+anatomical: []
+nodes:
+
+-   action: import_scalars
+    input: qsirecon
+    name: dipy_dki_ingress
+    parameters:
+        # Whatever was specified with --datasets dipydki=/x/y/z
+        dataset_name: dipydki
+        # Do you want a copy of the inputs to go in the output dataset?
+        # Metadata from the input will be included in the output no matter what
+        copy_inputs: false
+    # This is where the tsv will go
+    qsirecon_suffix: DIPYDKI
+    # Future idea: Get ALFF/REHO/something into ACPC, then resample into each dwi ACPC space
+
+-   action: autotrack
+    input: dsistudio_gqi
+    name: autotrackgqi
+    parameters:
+        tolerance: 22,26,30
+        track_id: Fasciculus,Cingulum,Aslant,Corticos,Thalamic_R,Reticular,Optic,Fornix,Corpus
+        track_voxel_ratio: 2.0
+        yield_rate: 1.0e-06
+    qsirecon_suffix: DSIStudio
+    software: DSI Studio
+
+-   action: bundle_map
+    input: autotrackgqi
+    name: bundle_means
+    scalars_from:
+    - dipy_dki_ingress
+    software: qsirecon
+
+-   action: template_map
+    input: qsirecon
+    name: template_map
+    parameters:
+        interpolation: NearestNeighbor
+    scalars_from:
+    - dipy_dki
+    software: qsirecon

qsirecon/data/recon_scalar_bids_config.json

@@ -0,0 +1,29 @@
+{
+    "name": "qsirecon",
+    "entities": [
+        {
+            "name": "cohort",
+            "pattern": "(?:^|_)cohort-([0-9]+)",
+            "dtype": "int"
+        },
+        {
+            "name": "seg",
+            "pattern": "(?:^|_)seg-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "bundles",
+            "pattern": "(?:^|_)bundles-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "param",
+            "pattern": "(?:^|_)param-([a-zA-Z0-9]+)"
+        },
+        {
+            "name": "bundle",
+            "pattern": "(?:^|_)bundle-([a-zA-Z0-9]+)"
+        }
+    ],
+    "default_path_patterns": [
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{seg}][_model-{model}][_bundles-{bundles}][_param-{param}][_bundle-{bundle}][_label-{label}][_desc-{desc}]_{suffix<dwimap|config|dwi>}.{extension<nii|nii.gz|fib|fib.gz|mif|mif.gz|pickle.gz|b|bvec|bval|txt|json>|nii.gz}"
+    ]
+}

qsirecon/workflows/recon/build_workflow.py

@@ -27,7 +27,12 @@
 from .scalar_mapping import init_scalar_to_bundle_wf, init_scalar_to_template_wf
 from .steinhardt import init_steinhardt_order_param_wf
 from .tortoise import init_tortoise_estimator_wf
-from .utils import init_conform_dwi_wf, init_discard_repeated_samples_wf, init_test_wf
+from .utils import (
+    init_conform_dwi_wf,
+    init_discard_repeated_samples_wf,
+    init_test_wf,
+    init_import_scalars_wf,
+)
 
 
 def _check_repeats(nodelist):
@@ -286,6 +291,8 @@ def workflow_from_spec(inputs_dict, node_spec):
             return init_scalar_to_template_wf(**kwargs)
         if node_spec["action"] == "test_workflow":
             return init_test_wf(**kwargs)
+        if node_spec["action"] == "import_scalars":
+            return init_import_scalars_wf(**kwargs)
 
     raise Exception("Unknown node %s" % node_spec)
 

qsirecon/workflows/recon/scalar_mapping.py

@@ -12,17 +12,20 @@
 
 import logging
 
+from bids.layout import BIDSLayout
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 
+from ... import config
 from ...interfaces.bids import DerivativesDataSink
 from ...interfaces.interchange import recon_workflow_input_fields
 from ...interfaces.recon_scalars import ReconScalarsTableSplitterDataSink
 from ...interfaces.scalar_mapping import BundleMapper, TemplateMapper
 from ...utils.bids import clean_datasinks
 from .utils import init_scalar_output_wf
 
+
 LOGGER = logging.getLogger("nipype.workflow")
 
 
@@ -199,3 +202,53 @@ def init_scalar_to_surface_wf(
 ):
     """Maps scalar data to a surface."""
     raise NotImplementedError()
+
+
+def init_import_scalars_wf(
+    inputs_dict,
+    name="import_scalars",
+    qsirecon_suffix="",
+    params={},
+):
+    """Read in scalars from an input dataset."""
+
+    from qsirecon.data import load as load_data
+
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=recon_workflow_input_fields,
+        ),
+        name="inputnode",
+    )
+    outputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=[
+                "scalar_image_info",
+                "recon_scalars",
+            ]
+        ),
+        name="outputnode",
+    )
+    workflow = Workflow(name=name)
+    dataset_name = params.get("dataset")
+    if not dataset_name:
+        raise Exception("Must specify a dataset key in the recon spec parameters")
+
+    dataset_path = config.execution.datasets.get(dataset_name)
+    if dataset_path is None:
+        raise Exception(
+            f"Dataset {dataset_name} is not available in the specified "
+            "inputs datasets. Either change the recon spec yaml file or "
+            f"include --datasets {dataset_name}=/path/to/dataset on the command line."
+        )
+    scalars_cfg = load_data("recon_scalars_bids_config.json")
+    layout = BIDSLayout(dataset_path, config=[scalars_cfg], validate=False)
+
+    # Find all dwimaps that have the same entities (-desc) as the input dwi file
+    input_dwi_file = config.execution.layout.get(inputs_dict["dwi_file"])
+    dwimaps = layout.get(suffix="dwimap", **input_dwi_file.entities)
+
+    # Send them to the scalar gatherer
+
+
+    return workflow