Perens stereotaxic mri (#370)

* add perens mri * update requirement for perens_mri * remove hardcoded path * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix formatting to pass checks * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix linting issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_stereotaxic_mri_mouse.py Co-authored-by: Adam Tyson <[email protected]> * remove sitk in favour of brainglobe utils * move download and extraction logic into a seperate function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * replace functions that could instead use bg atlas functionality * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add stereotaxic atlas to readme * Update brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_stereotaxic_mri_mouse.py Co-authored-by: Alessandro Felder <[email protected]> * Update brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_stereotaxic_mri_mouse.py Co-authored-by: Alessandro Felder <[email protected]> * update to follow new template * removed weird nested function * change template to reference for consistency * update URL to new version, gubra updated this to fix label issue in lsfm * add progress bar * add more print statements so progress is easier to observe * added correct orientation * added print statement to structure information function * Update brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_stereotaxic_mri_mouse.py Co-authored-by: Alessandro Felder <[email protected]> * add bg atlas name to readme --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <[email protected]> Co-authored-by: Alessandro Felder <[email protected]>
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diff --git a/README.md b/README.md
@@ -41,6 +41,7 @@ A number of atlases are in development, but those available currently are:
 | [BlueBrain Barrel Cortex Atlas](https://doi.org/10.1162/imag_a_00209) | 10 and 25 micron | P56 | STPT | allen_mouse_bluebrain_barrels_10um, allen_mouse_bluebrain_barrels_25um
 | [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3) | 40 micron | ~ 3 months post hatching | MRI | unam_axolotl_40um
 | [Prairie Vole Brain Atlas](https://doi.org/10.7554/eLife.87029.3.sa0) | 25 micron | Unknown | LSFM | prairie_vole_25um
+| [Gubra's stereotaxic MRI mouse brain atlas](https://doi.org/10.1007/s12021-023-09623-9) | 25 micron | 10-week-old  | MRI | perens_stereotaxic_mouse_mri_25um
 
 ## Installation
 

diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_stereotaxic_mri_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_stereotaxic_mri_mouse.py
@@ -0,0 +1,344 @@
+import multiprocessing as mp
+import os
+import time
+import urllib.request
+from pathlib import Path
+
+import numpy as np
+import py7zr
+from brainglobe_utils.IO.image import load_any
+from rich.progress import Progress, track
+
+from brainglobe_atlasapi import BrainGlobeAtlas, utils
+from brainglobe_atlasapi.atlas_generation.mesh_utils import (
+    Region,
+    create_region_mesh,
+)
+from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data
+from brainglobe_atlasapi.structure_tree_util import get_structures_tree
+
+# The Perens atlas re-uses information from the Allen atlas, so it's useful to
+# have an instance of the Allen atlas around
+allen_atlas = BrainGlobeAtlas("allen_mouse_25um")
+PARALLEL = True  # disable parallel mesh extraction for easier debugging
+
+HEADERS = {
+    "User-Agent": (
+        "Mozilla/5.0 "
+        "(Windows NT 10.0; "
+        "Win64; x64; "
+        "rv:129.0) "
+        "Gecko/20100101 "
+        "Firefox/129.0"
+    ),
+    "Accept": (
+        "text/html,"
+        "application/xhtml+xml,"
+        "application/xml;q=0.9,"
+        "image/avif,"
+        "image/webp,"
+        "image/png,"
+        "image/svg+xml,"
+        "*/*;q=0.8"
+    ),
+    "Accept-Language": "en-GB,en;q=0.5",
+    "Accept-Encoding": "gzip, deflate, br, zstd",
+    "DNT": "1",
+    "Sec-GPC": "1",
+    "Host": "www.neuropedia.dk",
+    "Connection": "keep-alive",
+    "Upgrade-Insecure-Requests": "1",
+    "Sec-Fetch-Dest": "document",
+    "Sec-Fetch-Mode": "navigate",
+    "Sec-Fetch-Site": "none",
+    "Sec-Fetch-User": "?1",
+    "TE": "trailers",
+    "Priority": "u=0, i",
+}
+
+
+# Copy-paste this script into a new file and fill in the functions to package
+# your own atlas.
+
+### Metadata ###
+
+# The minor version of the atlas in the brainglobe_atlasapi, this is internal,
+# if this is the first time this atlas has been added the value should be 0
+# (minor version is the first number after the decimal point, ie the minor
+# version of 1.2 is 2)
+__version__ = 0
+
+# The expected format is FirstAuthor_SpeciesCommonName, e.g. kleven_rat, or
+# Institution_SpeciesCommonName, e.g. allen_mouse.
+ATLAS_NAME = "perens_stereotaxic_mri_mouse"
+
+# DOI of the most relevant citable document
+CITATION = "Perens et al. 2023, https://doi.org/10.1007/s12021-023-09623-9"
+
+# The scientific name of the species, ie; Rattus norvegicus
+SPECIES = "Mus musculus"
+
+# The URL for the data files
+ATLAS_LINK = "https://www.neuropedia.dk/resource/multimodal-3d-mouse-brain-atlas-framework-with-the-skull-derived-coordinate-system/"
+ATLAS_FILE_URL = "https://www.neuropedia.dk/wp-content/uploads/Multimodal_mouse_brain_atlas_files_v2.7z"
+# The orientation of the **original** atlas data, in BrainGlobe convention:
+# https://brainglobe.info/documentation/setting-up/image-definition.html#orientation
+ORIENTATION = "lai"
+
+# The id of the highest level of the atlas. This is commonly called root or
+# brain. Include some information on what to do if your atlas is not
+# hierarchical
+ROOT_ID = 997
+
+# The resolution of your volume in microns. Details on how to format this
+# parameter for non isotropic datasets or datasets with multiple resolutions.
+RESOLUTION = 25
+
+BG_ROOT_DIR = Path.home() / "brainglobe_workingdir" / ATLAS_NAME
+
+
+def download_resources():
+    """
+    Download the necessary resources for the atlas.
+
+    If possible, please use the Pooch library to retrieve any resources.
+    """
+    download_dir_path = BG_ROOT_DIR / "downloads"
+    download_dir_path.mkdir(exist_ok=True)
+    atlas_files_dir = download_dir_path / "atlas_files"
+
+    ## Download atlas_file
+    utils.check_internet_connection()
+
+    destination_path = download_dir_path / "atlas_download.7z"
+    if not os.path.isdir(
+        atlas_files_dir / "Multimodal_mouse_brain_atlas_files"
+    ):
+        req = urllib.request.Request(ATLAS_FILE_URL, headers=HEADERS)
+        with (
+            urllib.request.urlopen(req) as response,
+            open(destination_path, "wb") as out_file,
+        ):
+            total = int(response.headers.get("content-length", 0))
+            with Progress() as progress:
+                task = progress.add_task("[cyan]Downloading...", total=total)
+                while not progress.finished:
+                    chunk = response.read(1024)
+                    if not chunk:
+                        break
+                    out_file.write(chunk)
+                    progress.update(task, advance=len(chunk))
+        with py7zr.SevenZipFile(destination_path, mode="r") as z:
+            z.extractall(path=atlas_files_dir)
+        destination_path.unlink()
+
+
+def retrieve_reference_and_annotation():
+    """
+    Retrieve the desired reference and annotation as two numpy arrays.
+
+    Returns:
+        tuple: A tuple containing two numpy arrays. The first array is the
+        reference volume, and the second array is the annotation volume.
+    """
+    print("loading reference and annotation volume")
+    download_dir_path = BG_ROOT_DIR / "downloads"
+    atlas_files_dir = download_dir_path / "atlas_files"
+
+    annotations_file = (
+        atlas_files_dir
+        / "Multimodal_mouse_brain_atlas_files"
+        / "MRI_space_oriented"
+        / "mri_ano.nii.gz"
+    )
+    reference_file = (
+        atlas_files_dir
+        / "Multimodal_mouse_brain_atlas_files"
+        / "MRI_space_oriented"
+        / "mri_temp.nii.gz"
+    )
+
+    annotated_volume = load_any(annotations_file)
+    reference_volume = load_any(reference_file)
+
+    return reference_volume, annotated_volume
+
+
+def retrieve_hemisphere_map():
+    """
+    Retrieve a hemisphere map for the atlas.
+
+    If your atlas is asymmetrical, you may want to use a hemisphere map.
+    This is an array in the same shape as your template,
+    with 0's marking the left hemisphere, and 1's marking the right.
+
+    If your atlas is symmetrical, ignore this function.
+
+    Returns:
+        numpy.array or None: A numpy array representing the hemisphere map,
+        or None if the atlas is symmetrical.
+    """
+    return None
+
+
+def retrieve_structure_information():
+    """
+    Retrieve the structures tree and meshes for the Allen mouse brain atlas.
+
+    Returns:
+        pandas.DataFrame: A DataFrame containing the atlas information.
+    """
+    # Since this atlas inherits from the allen can we not simply get the data
+    # from the bgapi?
+    print("determining structures")
+    allen_atlas = BrainGlobeAtlas("allen_mouse_25um")
+    allen_structures = allen_atlas.structures_list
+    allen_structures = [
+        {
+            "id": i["id"],
+            "name": i["name"],
+            "acronym": i["acronym"],
+            "structure_id_path": i["structure_id_path"],
+            "rgb_triplet": i["rgb_triplet"],
+        }
+        for i in allen_structures
+    ]
+    return allen_structures
+
+
+def retrieve_or_construct_meshes():
+    """
+    This function should return a dictionary of ids and corresponding paths to
+    mesh files. Some atlases are packaged with mesh files, in these cases we
+    should use these files. Then this function should download those meshes.
+    In other cases we need to construct the meshes ourselves. For this we have
+    helper functions to achieve this.
+    """
+    print("constructing meshes")
+
+    download_dir_path = BG_ROOT_DIR / "downloads"
+    meshes_dir_path = download_dir_path / "meshes"
+    meshes_dir_path.mkdir(exist_ok=True)
+
+    tree = get_structures_tree(structures)
+
+    labels = np.unique(annotated_volume).astype(np.int32)
+    for key, node in tree.nodes.items():
+        if key in labels:
+            is_label = True
+        else:
+            is_label = False
+
+        node.data = Region(is_label)
+
+    # Mesh creation
+    closing_n_iters = 2  # not used for this atlas
+    decimate_fraction = 0.2  # not used for this atlas
+
+    smooth = False
+    start = time.time()
+    if PARALLEL:
+        pool = mp.Pool(mp.cpu_count() - 2)
+
+        try:
+            pool.map(
+                create_region_mesh,
+                [
+                    (
+                        meshes_dir_path,
+                        node,
+                        tree,
+                        labels,
+                        annotated_volume,
+                        ROOT_ID,
+                        closing_n_iters,
+                        decimate_fraction,
+                        smooth,
+                    )
+                    for node in tree.nodes.values()
+                ],
+            )
+        except mp.pool.MaybeEncodingError:
+            # error with returning results from pool.map but we don't care
+            pass
+    else:
+        for node in track(
+            tree.nodes.values(),
+            total=tree.size(),
+            description="Creating meshes",
+        ):
+            create_region_mesh(
+                (
+                    meshes_dir_path,
+                    node,
+                    tree,
+                    labels,
+                    annotated_volume,
+                    ROOT_ID,
+                    closing_n_iters,
+                    decimate_fraction,
+                    smooth,
+                )
+            )
+
+    print(
+        "Finished mesh extraction in: ",
+        round((time.time() - start) / 60, 2),
+        " minutes",
+    )
+
+    # Create meshes dict
+    meshes_dict = dict()
+    structures_with_mesh = []
+    for s in structures:
+        # Check if a mesh was created
+        mesh_path = meshes_dir_path / f'{s["id"]}.obj'
+        if not mesh_path.exists():
+            print(f"No mesh file exists for: {s}, ignoring it")
+            continue
+        else:
+            # Check that the mesh actually exists (i.e. not empty)
+            if mesh_path.stat().st_size < 512:
+                print(f"obj file for {s} is too small, ignoring it.")
+                continue
+
+        structures_with_mesh.append(s)
+        meshes_dict[s["id"]] = mesh_path
+
+    print(
+        f"In the end, {len(structures_with_mesh)} "
+        "structures with mesh are kept"
+    )
+
+    return meshes_dict
+
+
+### If the code above this line has been filled correctly, nothing needs to be
+### edited below (unless variables need to be passed between the functions).
+if __name__ == "__main__":
+    BG_ROOT_DIR.mkdir(exist_ok=True)
+    download_resources()
+    reference_volume, annotated_volume = retrieve_reference_and_annotation()
+    hemispheres_stack = retrieve_hemisphere_map()
+    structures = retrieve_structure_information()
+    meshes_dict = retrieve_or_construct_meshes()
+    print("wrapping up atlas")
+    output_filename = wrapup_atlas_from_data(
+        atlas_name=ATLAS_NAME,
+        atlas_minor_version=__version__,
+        citation=CITATION,
+        atlas_link=ATLAS_LINK,
+        species=SPECIES,
+        resolution=(RESOLUTION,) * 3,
+        orientation=ORIENTATION,
+        root_id=ROOT_ID,
+        reference_stack=reference_volume,
+        annotation_stack=annotated_volume,
+        structures_list=structures,
+        meshes_dict=meshes_dict,
+        working_dir=BG_ROOT_DIR,
+        hemispheres_stack=None,
+        cleanup_files=False,
+        compress=True,
+        scale_meshes=True,
+    )
diff --git a/pyproject.toml b/pyproject.toml
@@ -56,6 +56,7 @@ allenmouse = ["allensdk"]
 allenmouse_barrels = [
     "allensdk",
     "voxcell"]
+perens_stereotaxic_mri_mouse = ["py7zr"]
 
 atlasgen = [
     "loguru",