Rename everything to brainmapper and explicitly support old cellfinde…

…r directories (#61)

* Rename everything to brainmapper and explicitly support old cellfinder directories

* Remove unnecessary test data

brainglobe_napari_io/workflows/wholebrain_cell_reader_dir.py → brainglobe_napari_io/brainmapper/brainmapper_reader_dir.py

@@ -1,7 +1,7 @@
 import json
 import os
 from pathlib import Path
-from typing import Callable, List, Optional, Tuple, Union
+from typing import Callable, Dict, List, Optional, Tuple, Union
 
 import bg_space as bgs
 from napari.types import LayerDataTuple
@@ -14,22 +14,25 @@
 PathOrPaths = Union[List[os.PathLike], os.PathLike]
 
 
-def is_wholebrain_cell_dir(path: os.PathLike) -> bool:
+def is_brainmapper_dir(path: os.PathLike) -> bool:
     """
-    Determines whether a path is to a BrainGlobe workflows whole brain
+    Determines whether a path is to a BrainGlobe brainmapper whole brain
     cell detection (previously cellfinder) output directory.
     """
     path = os.path.abspath(path)
     if os.path.isdir(path):
         filelist = os.listdir(path)
     else:
         return False
-    if "cellfinder.json" in filelist:
+    if "brainmapper.json" in filelist:
+        return True
+    # for backwards compatibility
+    elif "cellfinder.json" in filelist:
         return True
     return False
 
 
-def wholebrain_cell_read_dir(path: PathOrPaths) -> Optional[Callable]:
+def brainmapper_read_dir(path: PathOrPaths) -> Optional[Callable]:
     """A basic implementation of the napari_get_reader hook specification.
 
     Parameters
@@ -43,12 +46,23 @@ def wholebrain_cell_read_dir(path: PathOrPaths) -> Optional[Callable]:
         If the path is a recognized format, return a function that accepts the
         same path or list of paths, and returns a list of layer data tuples.
     """
-    if isinstance(path, str) and is_wholebrain_cell_dir(path):
+    if isinstance(path, str) and is_brainmapper_dir(path):
         return reader_function
     else:
         return None
 
 
+def get_metadata(directory: Path) -> Dict:
+    try:
+        with open(directory / "brainmapper.json") as json_file:
+            metadata = json.load(json_file)
+    # for backwards compatibility
+    except FileNotFoundError:
+        with open(directory / "cellfinder.json") as json_file:
+            metadata = json.load(json_file)
+    return metadata
+
+
 def reader_function(
     path: os.PathLike,
     point_size: int = 15,
@@ -78,10 +92,9 @@ def reader_function(
         layer_type=="image" if not provided
     """
 
-    print("Loading whole brain cell detection directory")
+    print("Loading brainmapper directory")
     path = Path(os.path.abspath(path))
-    with open(path / "cellfinder.json") as json_file:
-        metadata = json.load(json_file)
+    metadata = get_metadata(path)
 
     layers: List[LayerDataTuple] = []
 

brainglobe_napari_io/napari.yaml

@@ -10,9 +10,9 @@ contributions:
     title: Brainreg Read Directory Atlas Space
     python_name: brainglobe_napari_io.brainreg.reader_dir_atlas_space:brainreg_read_dir_atlas_space
 
-  - id: brainglobe-napari-io.workflows_wholebrain_cell_read_dir
-    title: Workflows Whole Brain Cell Detection Read Directory
-    python_name: brainglobe_napari_io.workflows.wholebrain_cell_reader_dir:wholebrain_cell_read_dir
+  - id: brainglobe-napari-io.brainmapper_read_dir
+    title: Brainmapper Read Directory
+    python_name: brainglobe_napari_io.brainmapper.brainmapper_reader_dir:brainmapper_read_dir
 
   - id: brainglobe-napari-io.cellfinder_read_xml
     title: Cellfinder Read XML
@@ -34,7 +34,7 @@ contributions:
       - '*.tiff'
     accepts_directories: true
 
-  - command: brainglobe-napari-io.workflows_wholebrain_cell_read_dir
+  - command: brainglobe-napari-io.brainmapper_read_dir
     filename_patterns:
     - '*.tif'
     accepts_directories: true

tests/data/brainmapper_output/brainmapper.json

@@ -0,0 +1 @@
+{"signal_planes_paths": ["2"], "background_planes_path": ["4"], "output_dir": "output", "signal_ch_ids": null, "background_ch_id": null, "registration_config": "cellfinder.conf.custom", "voxel_sizes": ["5", "2.31", "2.31"], "network_voxel_sizes": [5, 1, 1], "no_detection": false, "no_classification": false, "no_register": false, "no_analyse": false, "no_figures": false, "start_plane": 0, "end_plane": -1, "save_planes": false, "outlier_keep": false, "artifact_keep": false, "max_cluster_size": 100000, "soma_diameter": 16, "ball_xy_size": 6, "ball_z_size": 15, "ball_overlap_fraction": 0.6, "log_sigma_size": 0.2, "n_sds_above_mean_thresh": 10, "soma_spread_factor": 1.4, "trained_model": "model.h5", "model_weights": null, "network_depth": "50", "batch_size": 64, "cube_width": 50, "cube_height": 50, "cube_depth": 20, "save_empty_cubes": false, "n_free_cpus": 8, "max_ram": null, "save_csv": false, "debug": false, "sort_input_file": false, "no_models": false, "model": "resnet50_tv", "heatmap_smooth": 100, "mask_figures": true, "install_path": ".cellfinder", "download_path": "tmp", "no_amend_config": false, "atlas": "allen_mouse_100um", "orientation": "prs", "backend": "niftyreg", "affine_n_steps": 6, "affine_use_n_steps": 5, "freeform_n_steps": 6, "freeform_use_n_steps": 4, "bending_energy_weight": 0.95, "grid_spacing": -10, "smoothing_sigma_reference": -1.0, "smoothing_sigma_floating": -1.0, "histogram_n_bins_floating": 128, "histogram_n_bins_reference": 128, "paths": {"output_dir": "output_dir", "registration_output_folder": "output_dir/brainreg_output", "metadata_path": "output/brainmapper.json", "registration_metadata_path": "output_dir/brainreg_output/brainreg.json"}}

tests/tests/test_integration/test_brainmapper_reader.py

@@ -0,0 +1,90 @@
+import json
+import pathlib
+
+import pytest
+
+from brainglobe_napari_io.brainmapper import brainmapper_reader_dir
+
+brainmapper_dir = (
+    pathlib.Path(__file__).parent.parent.parent / "data" / "brainmapper_output"
+)
+registration_dir = brainmapper_dir / "registration"
+
+cellfinder_dir = (
+    pathlib.Path(__file__).parent.parent.parent / "data" / "cellfinder_output"
+)
+DOWNSAMPLED_IMAGE_SIZE = (135, 108, 77)
+
+
+@pytest.fixture
+def metadata():
+    with open(brainmapper_dir / "brainmapper.json") as json_file:
+        metadata = json.load(json_file)
+    return metadata
+
+
+def test_is_brainmapper_dir():
+    assert brainmapper_reader_dir.is_brainmapper_dir(brainmapper_dir)
+    assert not brainmapper_reader_dir.is_brainmapper_dir(
+        brainmapper_dir.parent
+    )
+    assert not brainmapper_reader_dir.is_brainmapper_dir(__file__)
+
+
+def test_is_cellfinder_dir():
+    assert brainmapper_reader_dir.is_brainmapper_dir(cellfinder_dir)
+
+
+def test_brainmapper_read_dir():
+    assert (
+        brainmapper_reader_dir.brainmapper_read_dir(str(brainmapper_dir))
+        == brainmapper_reader_dir.reader_function
+    )
+    assert brainmapper_reader_dir.brainmapper_read_dir(brainmapper_dir) is None
+    assert (
+        brainmapper_reader_dir.brainmapper_read_dir(
+            str(brainmapper_dir.parent)
+        )
+        is None
+    )
+
+
+def check_metadata(metadata):
+    assert metadata["atlas"] == "allen_mouse_100um"
+    assert metadata["orientation"] == "prs"
+    assert metadata["soma_diameter"] == 16
+
+
+def test_get_metadata():
+    check_metadata(brainmapper_reader_dir.get_metadata(brainmapper_dir))
+    check_metadata(brainmapper_reader_dir.get_metadata(cellfinder_dir))
+
+
+def test_load_brainmapper_dir():
+    layers = brainmapper_reader_dir.reader_function(brainmapper_dir)
+    assert len(layers) == 4
+
+    layer_names = ["allen_mouse_100um", "Boundaries", "Non cells", "Cells"]
+    layer_types = ["labels", "image", "points", "points"]
+    layer_shapes = [
+        DOWNSAMPLED_IMAGE_SIZE,
+        DOWNSAMPLED_IMAGE_SIZE,
+        (22, 3),
+        (103, 3),
+    ]
+    for idx, layer in enumerate(layers):
+        assert layer[1]["name"] == layer_names[idx]
+        assert layer[2] == layer_types[idx]
+        assert layer[0].shape == layer_shapes[idx]
+
+
+def test_load_registration(metadata):
+    layers = brainmapper_reader_dir.load_registration(
+        [], registration_dir, metadata
+    )
+    assert len(layers) == 2
+    assert layers[0][0].shape == DOWNSAMPLED_IMAGE_SIZE
+    assert layers[1][0].shape == DOWNSAMPLED_IMAGE_SIZE
+
+    assert layers[0][1]["name"] == "allen_mouse_100um"
+    assert layers[1][1]["name"] == "Boundaries"

tests/tests/test_integration/test_brainreg_reader.py

@@ -5,7 +5,7 @@
 brainreg_dir = (
     pathlib.Path(__file__).parent.parent.parent
     / "data"
-    / "wholebrain_cell_output"
+    / "brainmapper_output"
     / "registration"
 )
 

tests/tests/test_integration/test_brainreg_reader_atlas_space.py

@@ -5,7 +5,7 @@
 brainreg_dir = (
     pathlib.Path(__file__).parent.parent.parent
     / "data"
-    / "wholebrain_cell_output"
+    / "brainmapper_output"
     / "registration"
 )
 

tests/tests/test_unit/test_brainreg_utils.py

@@ -5,7 +5,7 @@
 brainreg_dir = (
     pathlib.Path(__file__).parent.parent.parent
     / "data"
-    / "wholebrain_cell_output"
+    / "brainmapper_output"
     / "registration"
 )