driftlessmap 1.1.0__tar.gz → 1.2.0__tar.gz

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/CITATION.cff

@@ -4,7 +4,7 @@ message: >-
   HERBS paper listed under references.
 title: DriftlessMap
 type: software
-version: 1.1.0
+version: 1.2.0
 authors:
   - name: Mohebi & Associates
     website: https://www.mohebi-associates.org/

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: driftlessmap
-Version: 1.1.0
+Version: 1.2.0
 Summary: Interactive histology registration and brain-atlas mapping
 Author: Pearl Saldanha, Jacopo Paglia, Jonathan R. Whitlock, Mohebi & Associates, Ali Mohebi
 Author-email: Jingyi Guo Fuglstad <jingyi.g.fuglstad@gmail.com>
@@ -98,11 +98,19 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 - Safe, versioned project and object archives.
 - Support for custom compatible atlases.
 
-## Install
+## Install from PyPI
 
-DriftlessMap 1.1.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
+DriftlessMap 1.2.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
 3.14 in a dedicated environment is recommended for new installations.
 
+Install the latest stable release:
+
+```bash
+python -m pip install driftlessmap
+```
+
+For a dedicated Conda environment:
+
 ```bash
 conda create --name DriftlessMap python=3.14 -y
 conda activate DriftlessMap

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/README.md

@@ -43,11 +43,19 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 - Safe, versioned project and object archives.
 - Support for custom compatible atlases.
 
-## Install
+## Install from PyPI
 
-DriftlessMap 1.1.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
+DriftlessMap 1.2.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
 3.14 in a dedicated environment is recommended for new installations.
 
+Install the latest stable release:
+
+```bash
+python -m pip install driftlessmap
+```
+
+For a dedicated Conda environment:
+
 ```bash
 conda create --name DriftlessMap python=3.14 -y
 conda activate DriftlessMap

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/WhatsNew.md

@@ -3,6 +3,44 @@
 This cumulative release history is maintained as a single document. New
 releases are added at the top; earlier release notes remain below them.
 
+## DriftlessMap 1.2.0
+
+Release date: 27 July 2026
+
+This release adds a versioned probe-localization export designed for
+downstream electrophysiology and NWB workflows.
+
+### Probe-localization export schema 2
+
+The **Export probe localization files** action now creates four companion
+files:
+
+- `_contacts.csv` contains physical probe contacts, ordered deepest to
+  shallowest, with atlas coordinates and anatomical assignments.
+- `_track.csv` contains labeled samples along the fitted centerline, ordered
+  from insertion to tip and spaced no farther apart than one atlas voxel. This
+  is the appropriate input for localizing continuously estimated unit depths.
+- `_trajectory.csv` records insertion, tip, angles, fit quality, atlas and
+  coordinate-system metadata, export schema, software version, and the
+  probe-model tip-to-contact offset.
+- `_regions.csv` summarizes region IDs, names, acronyms, contact totals, and
+  reconstructed path lengths.
+
+Track samples include distance from insertion and tip, atlas-space
+coordinates, and the structure ID, acronym, and name at each point. For
+recognized Allen CCFv3 atlases, the export includes Allen voxel coordinates
+and physical coordinates alongside the existing explicitly qualified
+estimated Bregma values.
+
+### Upgrade notes
+
+Downstream tools that assign unit locations should require schema 2 and use
+the track table rather than inferring region boundaries from the contact or
+region summaries. Re-merge probes saved by older versions to generate the
+complete reconstruction and export metadata.
+
+---
+
 ## DriftlessMap 1.1.0
 
 Release date: 27 July 2026

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/driftlessmap/object_control.py

@@ -895,7 +895,7 @@ class ProbeInfoWindow(QDialog):
         # export and close buttons
         ok_btn = QDialogButtonBox(QDialogButtonBox.StandardButton.Ok)
         self.export_btn = ok_btn.addButton(
-            "Export probe CSV files",
+            "Export probe localization files",
             QDialogButtonBox.ButtonRole.ActionRole,
         )
         self.export_btn.clicked.connect(self.export_coordinates)
@@ -919,7 +919,7 @@ class ProbeInfoWindow(QDialog):
         )
         file_path, _ = QFileDialog.getSaveFileName(
             self,
-            "Choose a base name for the three probe CSV files",
+            "Choose a base name for the probe localization CSV files",
             "{}_probe_export.csv".format(safe_name or "probe"),
             "CSV files (*.csv)",
         )
@@ -938,7 +938,7 @@ class ProbeInfoWindow(QDialog):
             return
         QMessageBox.information(
             self,
-            "Probe CSV files exported",
+            "Probe localization files exported",
             "Created:\n{}".format(
                 "\n".join(str(path) for path in paths.values())
             ),

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/driftlessmap/probe_csv.py

@@ -1,4 +1,4 @@
-"""CSV exports for probe contacts, trajectory metadata, and regions."""
+"""CSV exports for probe contacts, labeled track, trajectory, and regions."""
 
 import csv
 from pathlib import Path
@@ -159,6 +159,54 @@ def iter_probe_contact_rows(probe_name, probe_data):
         yield row
 
 
+def iter_probe_track_rows(probe_name, probe_data):
+    """Yield labeled centerline samples ordered from insertion to tip."""
+    reconstruction = _reconstruction(probe_data)
+    coordinates = reconstruction["coordinates"]
+    if "track" not in coordinates:
+        raise ValueError(
+            "This probe has no labeled centerline. Re-merge the probe with the "
+            "current DriftlessMap version before exporting it."
+        )
+    track = coordinates["track"]
+    source_axes = reconstruction["atlas"]["source_axes"]
+    count = int(track["count"])
+    sample_indexes = np.asarray(track["sample_index"], dtype=int)
+    depth_from_insertion = np.asarray(
+        track["axial_depth_from_insertion_um"], dtype=float
+    )
+    distance_from_tip = np.asarray(
+        track["axial_distance_up_from_tip_um"], dtype=float
+    )
+    structure_ids = np.asarray(track["structure_id"], dtype=int)
+    structure_acronyms = np.asarray(
+        track["structure_acronym"], dtype=object
+    )
+    structure_names = np.asarray(track["structure_name"], dtype=object)
+
+    for index in range(count):
+        coordinate = _indexed_coordinate_record(track, index)
+        row = {
+            "probe_name": probe_name,
+            "track_sample_index": int(sample_indexes[index]),
+            "axial_depth_from_insertion_um": float(
+                depth_from_insertion[index]
+            ),
+            "axial_distance_up_from_tip_um": float(
+                distance_from_tip[index]
+            ),
+        }
+        row.update(_coordinate_columns(coordinate, source_axes))
+        row.update(
+            {
+                "structure_id": int(structure_ids[index]),
+                "structure_acronym": str(structure_acronyms[index]),
+                "structure_name": str(structure_names[index]),
+            }
+        )
+        yield row
+
+
 def probe_trajectory_row(probe_name, probe_data):
     """Return one complete trajectory-summary row."""
     reconstruction = _reconstruction(probe_data)
@@ -167,8 +215,14 @@ def probe_trajectory_row(probe_name, probe_data):
     coordinates = reconstruction["coordinates"]
     source_axes = atlas["source_axes"]
     settings = probe.get("settings") or {}
+    software = reconstruction.get("software") or {}
+    contacts = coordinates["contacts"]
+    track = coordinates.get("track") or {}
     row = {
         "probe_name": probe_name,
+        "reconstruction_schema_version": int(reconstruction["schema_version"]),
+        "software_name": software.get("name", "DriftlessMap"),
+        "software_version": software.get("version") or "unknown",
         "probe_type": settings.get(
             "probe_type_name", probe_data.get("probe_type_name", "unspecified")
         ),
@@ -183,7 +237,14 @@ def probe_trajectory_row(probe_name, probe_data):
         "ML_tilt_direction": probe_data.get("ml_tilt", "unspecified"),
         "insertion_to_tip_length_um": float(probe_data["probe_length"]),
         "vertical_depth_change_um": float(probe_data["dv"]),
+        "tip_to_lowest_contact_center_um": float(
+            np.min(contacts["axial_distance_up_from_tip_um"])
+        ),
     }
+    if track:
+        row["track_sampling_interval_um"] = float(
+            track["sampling_interval_um"]
+        )
     if atlas.get("source_version"):
         row["atlas_version"] = atlas["source_version"]
     if atlas.get("identifier"):
@@ -293,22 +354,36 @@ def write_probe_csv(path, probe_name, probe_data):
 def _export_paths(path):
     path = Path(path)
     base_name = path.stem if path.suffix else path.name
-    for suffix in ("_contacts", "_trajectory", "_regions"):
+    for suffix in ("_contacts", "_track", "_trajectory", "_regions"):
         if base_name.endswith(suffix):
             base_name = base_name[: -len(suffix)]
             break
     parent = path.parent
     return {
         "contacts": parent / "{}_contacts.csv".format(base_name),
+        "track": parent / "{}_track.csv".format(base_name),
         "trajectory": parent / "{}_trajectory.csv".format(base_name),
         "regions": parent / "{}_regions.csv".format(base_name),
     }
 
 
 def write_probe_csv_files(path, probe_name, probe_data):
-    """Write separate contact, trajectory, and region CSV files."""
+    """Write contacts, labeled track, trajectory, and region CSV files."""
     paths = _export_paths(path)
     write_probe_csv(paths["contacts"], probe_name, probe_data)
+    _write_rows(
+        paths["track"],
+        iter_probe_track_rows(probe_name, probe_data),
+        (
+            "probe_name",
+            "track_sample_index",
+            "axial_depth_from_insertion_um",
+            "axial_distance_up_from_tip_um",
+            "structure_id",
+            "structure_acronym",
+            "structure_name",
+        ),
+    )
     trajectory = probe_trajectory_row(probe_name, probe_data)
     _write_rows(paths["trajectory"], [trajectory], tuple(trajectory))
     _write_rows(

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/driftlessmap/probe_reconstruction.py

@@ -5,7 +5,7 @@ from pathlib import Path
 import numpy as np
 
 
-PROBE_RECONSTRUCTION_SCHEMA_VERSION = 1
+PROBE_RECONSTRUCTION_SCHEMA_VERSION = 2
 HERBS_AXES = ("LR", "AP", "DV")
 HERBS_AXIS_DIRECTIONS = ("right", "anterior", "superior")
 _OPPOSITE_DIRECTION = {
@@ -243,6 +243,10 @@ def build_probe_reconstruction(
     contact_vox_index,
     contact_structure_ids,
     contact_local_from_tip_base_um,
+    track_bregma_vox=None,
+    track_vox_index=None,
+    track_structure_ids=None,
+    track_axial_depth_from_insertion_um=None,
     probe_length_um,
     probe_settings,
     site_face,
@@ -260,6 +264,9 @@ def build_probe_reconstruction(
 
     Contacts are flattened column-major. Within a column, index zero is the
     contact nearest the geometric tip for probe geometries generated by HERBS.
+    The optional track arrays describe the fitted probe centerline in
+    insertion-to-tip order and make downstream per-unit localization possible
+    without requiring access to the original atlas annotation volume.
     """
     voxel_size_um = float(voxel_size_um)
     if not np.isfinite(voxel_size_um) or voxel_size_um <= 0:
@@ -335,6 +342,76 @@ def build_probe_reconstruction(
             allen_ccf_to_estimated_bregma_mm(contacts["allen_ccf_um"])
         )
 
+    track = None
+    supplied_track_values = (
+        track_bregma_vox,
+        track_vox_index,
+        track_structure_ids,
+        track_axial_depth_from_insertion_um,
+    )
+    if any(value is not None for value in supplied_track_values):
+        if not all(value is not None for value in supplied_track_values):
+            raise ValueError(
+                "Track coordinates, indexes, structure IDs, and axial depths "
+                "must be supplied together."
+            )
+        track_bregma_vox = np.asarray(track_bregma_vox, dtype=float)
+        track_vox_index = np.asarray(track_vox_index, dtype=int)
+        track_structure_ids = np.ravel(
+            np.asarray(track_structure_ids, dtype=int)
+        )
+        track_axial_depth_from_insertion_um = np.ravel(
+            np.asarray(track_axial_depth_from_insertion_um, dtype=float)
+        )
+        track_count = len(track_axial_depth_from_insertion_um)
+        if (
+            track_bregma_vox.shape != (track_count, 3)
+            or track_vox_index.shape != (track_count, 3)
+            or len(track_structure_ids) != track_count
+        ):
+            raise ValueError(
+                "Track coordinate arrays must contain the same number of rows."
+            )
+        if track_count < 2:
+            raise ValueError("A reconstructed track requires at least two samples.")
+        if np.any(np.diff(track_axial_depth_from_insertion_um) < 0):
+            raise ValueError(
+                "Track depths must be ordered from insertion toward the tip."
+            )
+
+        track_record = _coordinate_record(
+            track_bregma_vox,
+            bregma_herbs_vox,
+            voxel_size_um,
+            normalized_axis_info,
+            voxel_index=track_vox_index,
+            allen_ccf=allen_ccf,
+        )
+        track = {
+            "count": track_count,
+            "ordering": "insertion-to-tip",
+            "sample_index": np.arange(track_count, dtype=int),
+            "axial_depth_from_insertion_um": (
+                track_axial_depth_from_insertion_um
+            ),
+            "axial_distance_up_from_tip_um": (
+                float(probe_length_um)
+                - track_axial_depth_from_insertion_um
+            ),
+            "structure_id": track_structure_ids,
+            "structure_acronym": _structure_text(
+                track_structure_ids, label_info, "abbrev"
+            ),
+            "structure_name": _structure_text(
+                track_structure_ids, label_info, "label"
+            ),
+            **track_record,
+        }
+        if track_count > 1:
+            track["sampling_interval_um"] = float(
+                np.median(np.diff(track_axial_depth_from_insertion_um))
+            )
+
     source_name = "Allen Mouse Common Coordinate Framework"
     source_version = "CCFv3 2017"
     if not allen_ccf:
@@ -405,5 +482,6 @@ def build_probe_reconstruction(
                 allen_ccf=allen_ccf,
             ),
             "contacts": contacts,
+            **({"track": track} if track is not None else {}),
         },
     }

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/driftlessmap/probe_utiles.py

@@ -1050,6 +1050,30 @@ def calculate_probe_info(
         "trajectory_fit": trajectory_fit,
     }
 
+    # Sample the fitted centerline at no more than one atlas voxel between
+    # points. The resulting labeled track is persisted with the reconstruction
+    # so downstream tools can assign continuous unit depths to atlas regions
+    # without reopening DriftlessMap's processed annotation volume.
+    track_vector = np.asarray(pc_ep, dtype=float) - np.asarray(pc_sp, dtype=float)
+    track_length_vox = float(np.linalg.norm(track_vector))
+    if track_length_vox <= np.finfo(float).eps:
+        return None, PROBE_COORDINATES_OUTSIDE_ATLAS
+    track_direction = track_vector / track_length_vox
+    track_count = max(2, int(np.ceil(probe_length_with_tip_um / vxsize_um)) + 1)
+    track_depth_um = np.linspace(
+        0.0, float(probe_length_with_tip_um), track_count
+    )
+    track_pnt = (
+        np.asarray(pc_sp, dtype=float)
+        + (track_depth_um / vxsize_um)[:, None] * track_direction
+    )
+    track_vox = (track_pnt + np.asarray(bregma, dtype=float)).astype(int)
+    if not coordinates_in_bounds(track_vox, label_data.shape):
+        return None, PROBE_COORDINATES_OUTSIDE_ATLAS
+    track_labels = label_data[
+        track_vox[:, 0], track_vox[:, 1], track_vox[:, 2]
+    ]
+
     atlas_metadata = atlas_metadata or {}
     data_dict["reconstruction"] = build_probe_reconstruction(
         insertion_bregma_vox=pc_sp,
@@ -1060,6 +1084,10 @@ def calculate_probe_info(
         contact_vox_index=contact_vox,
         contact_structure_ids=contact_labels,
         contact_local_from_tip_base_um=sites_loc_to_base_temp,
+        track_bregma_vox=track_pnt,
+        track_vox_index=track_vox,
+        track_structure_ids=track_labels,
+        track_axial_depth_from_insertion_um=track_depth_um,
         probe_length_um=probe_length_with_tip_um,
         probe_settings=probe_settings,
         site_face=site_face,

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/driftlessmap/version.py

@@ -1,3 +1,3 @@
 """Canonical DriftlessMap version."""
 
-__version__ = "1.1.0"
+__version__ = "1.2.0"

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/driftlessmap.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: driftlessmap
-Version: 1.1.0
+Version: 1.2.0
 Summary: Interactive histology registration and brain-atlas mapping
 Author: Pearl Saldanha, Jacopo Paglia, Jonathan R. Whitlock, Mohebi & Associates, Ali Mohebi
 Author-email: Jingyi Guo Fuglstad <jingyi.g.fuglstad@gmail.com>
@@ -98,11 +98,19 @@ See [CITATION.cff](CITATION.cff) for machine-readable citation metadata.
 - Safe, versioned project and object archives.
 - Support for custom compatible atlases.
 
-## Install
+## Install from PyPI
 
-DriftlessMap 1.1.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
+DriftlessMap 1.2.0 supports Python 3.10–3.14 and Qt 6 through PyQt6. Python
 3.14 in a dedicated environment is recommended for new installations.
 
+Install the latest stable release:
+
+```bash
+python -m pip install driftlessmap
+```
+
+For a dedicated Conda environment:
+
 ```bash
 conda create --name DriftlessMap python=3.14 -y
 conda activate DriftlessMap

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/tests/test_object_control.py

@@ -133,7 +133,7 @@ class ProbeInfoWindowTests(unittest.TestCase):
 
         self.assertEqual(
             window.export_btn.text(),
-            "Export probe CSV files",
+            "Export probe localization files",
         )
         self.assertIn("AP tilt from vertical : ", labels)
         self.assertIn("Vertical depth change : ", labels)
@@ -158,6 +158,7 @@ class ProbeInfoWindowTests(unittest.TestCase):
                 "driftlessmap.object_control.write_probe_csv_files",
                 return_value={
                     "contacts": "/tmp/probe_export_contacts.csv",
+                    "track": "/tmp/probe_export_track.csv",
                     "trajectory": "/tmp/probe_export_trajectory.csv",
                     "regions": "/tmp/probe_export_regions.csv",
                 },

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/tests/test_packaging_metadata.py

@@ -113,6 +113,7 @@ class PackagingMetadataTests(unittest.TestCase):
             sorted(path.name for path in REPOSITORY_ROOT.glob("WhatsNew*.md")),
             ["WhatsNew.md"],
         )
+        self.assertIn("## DriftlessMap 1.2.0", history)
         self.assertIn("## DriftlessMap 1.1.0", history)
         for version in (
             "1.0.5",

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/tests/test_probe_csv.py

@@ -8,6 +8,7 @@ import numpy as np
 from driftlessmap.probe_csv import (
     iter_probe_contact_rows,
     iter_probe_region_rows,
+    iter_probe_track_rows,
     probe_trajectory_row,
     write_probe_csv_files,
 )
@@ -43,6 +44,14 @@ def probe_data():
             np.array([[10.0, -8.0, 12.0], [50.0, -8.0, 12.0]]),
             np.array([[30.0, 16.0, 12.0]]),
         ],
+        track_bregma_vox=np.array(
+            [[0.0, 0.0, value] for value in np.linspace(1.0, -4.0, 6)]
+        ),
+        track_vox_index=np.array(
+            [[228, 263, value] for value in range(160, 154, -1)]
+        ),
+        track_structure_ids=np.array([10, 10, 10, 11, 11, 11]),
+        track_axial_depth_from_insertion_um=np.linspace(0, 10000, 6),
         probe_length_um=10000,
         probe_settings={"probe_type_name": "test", "tip_length": 175},
         site_face="Front",
@@ -115,6 +124,9 @@ class ProbeCsvTests(unittest.TestCase):
 
         self.assertEqual(trajectory["insertion_to_tip_length_um"], 10000)
         self.assertEqual(trajectory["fit_inliers"], 3)
+        self.assertEqual(trajectory["reconstruction_schema_version"], 2)
+        self.assertEqual(trajectory["tip_to_lowest_contact_center_um"], 185)
+        self.assertEqual(trajectory["track_sampling_interval_um"], 2000)
         self.assertIn("insertion_allen_AP_vox", trajectory)
         self.assertIn("tip_allen_AP_vox", trajectory)
         self.assertNotIn("structure_id", trajectory)
@@ -129,7 +141,19 @@ class ProbeCsvTests(unittest.TestCase):
             all(value != "" for row in regions for value in row.values())
         )
 
-    def test_writer_creates_three_consistent_csv_files(self):
+    def test_track_rows_are_in_insertion_to_tip_order(self):
+        rows = list(iter_probe_track_rows("probe one", probe_data()))
+
+        self.assertEqual(len(rows), 6)
+        self.assertEqual(rows[0]["axial_depth_from_insertion_um"], 0)
+        self.assertEqual(rows[0]["axial_distance_up_from_tip_um"], 10000)
+        self.assertEqual(rows[-1]["axial_depth_from_insertion_um"], 10000)
+        self.assertEqual(rows[-1]["axial_distance_up_from_tip_um"], 0)
+        self.assertEqual(rows[0]["structure_acronym"], "R10")
+        self.assertEqual(rows[-1]["structure_acronym"], "R11")
+        self.assertIn("allen_AP_vox", rows[0])
+
+    def test_writer_creates_four_consistent_csv_files(self):
         with tempfile.TemporaryDirectory() as folder:
             selected_path = Path(folder) / "probe_export.csv"
             paths = write_probe_csv_files(
@@ -140,6 +164,7 @@ class ProbeCsvTests(unittest.TestCase):
                 paths,
                 {
                     "contacts": Path(folder) / "probe_export_contacts.csv",
+                    "track": Path(folder) / "probe_export_track.csv",
                     "trajectory": (
                         Path(folder) / "probe_export_trajectory.csv"
                     ),
@@ -152,9 +177,11 @@ class ProbeCsvTests(unittest.TestCase):
                     tables[table_name] = list(csv.DictReader(csv_file))
 
         self.assertEqual(len(tables["contacts"]), 3)
+        self.assertEqual(len(tables["track"]), 6)
         self.assertEqual(len(tables["trajectory"]), 1)
         self.assertEqual(len(tables["regions"]), 2)
         self.assertNotIn("record_type", tables["contacts"][0])
+        self.assertIn("structure_id", tables["track"][0])
         self.assertNotIn("structure_id", tables["trajectory"][0])
         self.assertNotIn("herbs_ML_vox", tables["regions"][0])
 

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/tests/test_probe_mapping.py

@@ -127,6 +127,15 @@ class ProbeMappingTests(unittest.TestCase):
             ],
             "3D fitted-line intersection with atlas brain mask",
         )
+        track = info["reconstruction"]["coordinates"]["track"]
+        self.assertGreaterEqual(track["count"], 2)
+        self.assertEqual(track["ordering"], "insertion-to-tip")
+        self.assertTrue(
+            np.all(np.diff(track["axial_depth_from_insertion_um"]) >= 0)
+        )
+        self.assertEqual(
+            track["structure_acronym"], ["TR"] * track["count"]
+        )
 
 
 if __name__ == "__main__":

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/tests/test_probe_reconstruction.py

@@ -135,6 +135,14 @@ class ProbeReconstructionTests(unittest.TestCase):
                 np.array([[10.0, -8.0, 12.0], [50.0, -8.0, 12.0]]),
                 np.array([[30.0, 16.0, 12.0]]),
             ],
+            track_bregma_vox=np.array(
+                [[0.0, 0.0, value] for value in np.linspace(1.0, -4.0, 6)]
+            ),
+            track_vox_index=np.array(
+                [[228, 263, value] for value in range(160, 154, -1)]
+            ),
+            track_structure_ids=np.array([10, 10, 10, 11, 11, 11]),
+            track_axial_depth_from_insertion_um=np.linspace(0, 10000, 6),
             probe_length_um=10000,
             probe_settings={"probe_type_name": "test", "tip_length": 175},
             site_face="Front",
@@ -165,7 +173,7 @@ class ProbeReconstructionTests(unittest.TestCase):
         atlas = payload["atlas"]
         contacts = payload["coordinates"]["contacts"]
 
-        self.assertEqual(payload["schema_version"], 1)
+        self.assertEqual(payload["schema_version"], 2)
         self.assertEqual(atlas["source_version"], "CCFv3 2017")
         self.assertEqual(atlas["source_axes"], ["AP", "DV", "LR"])
         self.assertEqual(tuple(atlas["source_shape_vox"]), (528, 320, 456))
@@ -196,6 +204,14 @@ class ProbeReconstructionTests(unittest.TestCase):
         transform = atlas["estimated_stereotaxic_transform"]
         self.assertFalse(transform["ground_truth"])
         self.assertIn("brain surface", transform["targeting_note"])
+        track = payload["coordinates"]["track"]
+        self.assertEqual(track["ordering"], "insertion-to-tip")
+        self.assertEqual(track["count"], 6)
+        np.testing.assert_allclose(
+            track["axial_distance_up_from_tip_um"],
+            [10000, 8000, 6000, 4000, 2000, 0],
+        )
+        self.assertEqual(track["structure_acronym"], ["R10"] * 3 + ["R11"] * 3)
 
     def test_payload_round_trips_inside_one_herbs_object(self):
         data = {

{driftlessmap-1.1.0 → driftlessmap-1.2.0}/tests/test_version.py

@@ -16,7 +16,7 @@ class VersionTests(unittest.TestCase):
         cls.app = QApplication.instance() or QApplication([])
 
     def test_public_package_version_uses_the_canonical_value(self):
-        self.assertEqual(__version__, "1.1.0")
+        self.assertEqual(__version__, "1.2.0")
         self.assertEqual(driftlessmap.__version__, __version__)
 
     def test_about_dialog_reports_version_and_current_repository(self):