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brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_devccf_mouse.py

@@ -1,11 +1,10 @@
 import argparse
-import json
 import time
 from pathlib import Path
-import pooch
 
 import numpy as np
 import pandas as pd
+import pooch
 from brainglobe_utils.IO.image import load_nii
 from rich.progress import track
 
@@ -15,7 +14,6 @@
     create_region_mesh,
 )
 from brainglobe_atlasapi.atlas_generation.wrapup import wrapup_atlas_from_data
-
 from brainglobe_atlasapi.config import DEFAULT_WORKDIR
 from brainglobe_atlasapi.structure_tree_util import get_structures_tree
 
@@ -29,101 +27,127 @@
 PACKAGER = "Carlo Castoldi <castoldi[at]ipmc.cnrs.fr>"
 ATLAS_FILE_URL = "https://doi.org/10.6084/m9.figshare.26377171.v1"
 
-TIMEPOINTS = (
-    "E11.5",
-    "E13.5",
-    "E15.5",
-    "E18.5",
-    "P04",
-    "P14",
-    "P56"
-)
+TIMEPOINTS = ("E11.5", "E13.5", "E15.5", "E18.5", "P04", "P14", "P56")
 MODALITIES = (
-    "LSFM",     # Light Sheet Fluorescence Microscopy
+    "LSFM",  # Light Sheet Fluorescence Microscopy
     "MRI-adc",  # MRI Apparent Diffusion Coefficient
     "MRI-dwi",  # MRI Difusion Weighted Imaging
-    "MRI-fa",   # MRI Fractional Anisotropy
+    "MRI-fa",  # MRI Fractional Anisotropy
     "MRI-MTR",  # MRI Magnetization Transfer Ratio
-    "MRI-T2"    # MRI T2-weighted
+    "MRI-T2",  # MRI T2-weighted
 )
 
+
 def pooch_init(download_dir_path: Path, timepoints: list[str]) -> pooch.Pooch:
     utils.check_internet_connection()
 
-    empty_registry = {a+".zip": None for a in [*timepoints, "DevCCFv1_OntologyStructure.xlsx"]}
+    empty_registry = {
+        a + ".zip": None
+        for a in [*timepoints, "DevCCFv1_OntologyStructure.xlsx"]
+    }
     p = pooch.create(
         path=download_dir_path,
         base_url="doi:10.6084/m9.figshare.26377171.v1/",
-        registry=empty_registry
+        registry=empty_registry,
+    )
+    p.load_registry(
+        Path(__file__).parent.parent / "hashes" / (ATLAS_NAME + ".txt")
     )
-    p.load_registry(Path(__file__).parent.parent/"hashes"/(ATLAS_NAME+".txt"))
     return p
 
+
 def fetch_animal(pooch_: pooch.Pooch, age: str, modality: str):
     assert age in TIMEPOINTS, f"Unknown age timepoint: '{age}'"
-    archive = age+".zip"
+    archive = age + ".zip"
     if modality == "LSFM":
         resolution_um = 20
     elif modality in MODALITIES:
         match age:
             case "E11.5":
                 resolution_um = 31.5
-                raise RuntimeError("Can't generate an atlas at embryonic stage with MRI reference images.")
+                raise RuntimeError(
+                    "Can't generate an atlas at embryonic stage with MRI reference images."
+                )
             case "E13.5":
                 resolution_um = 34
-                raise RuntimeError("Can't generate an atlas at embryonic stage with MRI reference images.")
+                raise RuntimeError(
+                    "Can't generate an atlas at embryonic stage with MRI reference images."
+                )
             case "E15.5":
                 resolution_um = 37.5
-                raise RuntimeError("Can't generate an atlas at embryonic stage with MRI reference images.")
+                raise RuntimeError(
+                    "Can't generate an atlas at embryonic stage with MRI reference images."
+                )
             case "E18.5":
                 resolution_um = 40
-                raise RuntimeError("Can't generate an atlas at embryonic stage with MRI reference images.")
+                raise RuntimeError(
+                    "Can't generate an atlas at embryonic stage with MRI reference images."
+                )
             case _:
                 resolution_um = 50
     else:
         raise RuntimeError(f"Unknown reference image modality: {modality}")
     members = [
         f"{age}/{age.replace('.','-')}_DevCCF_Annotations_{resolution_um}um.nii.gz",
-        f"{age}/{age.replace('.','-')}_{modality}_{resolution_um}um.nii.gz"
+        f"{age}/{age.replace('.','-')}_{modality}_{resolution_um}um.nii.gz",
     ]
-    annotations_path, reference_path = pooch_.fetch(archive,
-                        progressbar=True,
-                        processor=pooch.Unzip(extract_dir=".", members=members)
-                        )
+    annotations_path, reference_path = pooch_.fetch(
+        archive,
+        progressbar=True,
+        processor=pooch.Unzip(extract_dir=".", members=members),
+    )
     annotations = load_nii(annotations_path, as_array=True)
     reference = load_nii(reference_path, as_array=True)
     return annotations, reference, resolution_um
 
+
 def fetch_ontology(pooch_: pooch.Pooch):
-    devccfv1_path = pooch_.fetch("DevCCFv1_OntologyStructure.xlsx", progressbar=True)
+    devccfv1_path = pooch_.fetch(
+        "DevCCFv1_OntologyStructure.xlsx", progressbar=True
+    )
     xl = pd.ExcelFile(devccfv1_path)
     # xl.sheet_names # it has two excel sheets
-                     # 'DevCCFv1_Ontology', 'README'
+    # 'DevCCFv1_Ontology', 'README'
     df = xl.parse("DevCCFv1_Ontology", header=1)
     df = df[["Acronym", "ID16", "Name", "Structure ID Path16", "R", "G", "B"]]
-    df.rename(columns={
-        "Acronym": "acronym",
-        "ID16": "id",
-        "Name": "name",
-        "Structure ID Path16": "structure_id_path",
-        "R": "r",
-        "G": "g",
-        "B": "b"
-    }, inplace=True)
+    df.rename(
+        columns={
+            "Acronym": "acronym",
+            "ID16": "id",
+            "Name": "name",
+            "Structure ID Path16": "structure_id_path",
+            "R": "r",
+            "G": "g",
+            "B": "b",
+        },
+        inplace=True,
+    )
     structures = list(df.to_dict(orient="index").values())
     for structure in structures:
         if structure["acronym"] == "mouse":
             structure["acronym"] = "root"
         structure_path = structure["structure_id_path"]
-        structure["structure_id_path"] = [int(id) for id in structure_path.strip("/").split("/")]
-        structure["rgb_triplet"] = [structure["r"], structure["g"], structure["b"]]
+        structure["structure_id_path"] = [
+            int(id) for id in structure_path.strip("/").split("/")
+        ]
+        structure["rgb_triplet"] = [
+            structure["r"],
+            structure["g"],
+            structure["b"],
+        ]
         del structure["r"]
         del structure["g"]
         del structure["b"]
     return structures
 
-def create_meshes(output_path: str|Path,
-                  structures, annotation_volume, root_id, decimate_fraction):
+
+def create_meshes(
+    output_path: str | Path,
+    structures,
+    annotation_volume,
+    root_id,
+    decimate_fraction,
+):
     if not isinstance(output_path, Path):
         output_path = Path(output_path)
     output_path.mkdir(exist_ok=True)
@@ -150,7 +174,7 @@ def create_meshes(output_path: str|Path,
         # total=5,
         description="Creating meshes",
     ):
-        output_file = output_path/f"{node.identifier}.obj"
+        output_file = output_path / f"{node.identifier}.obj"
         if output_file.exists():
             # print(f"mesh already existing: {output_file.exists()} - {output_file}")
             continue
@@ -175,6 +199,7 @@ def create_meshes(output_path: str|Path,
     )
     return output_path
 
+
 def create_mesh_dict(structures, meshes_dir_path):
     meshes_dict = dict()
     structures_with_mesh = []
@@ -197,21 +222,25 @@ def create_mesh_dict(structures, meshes_dir_path):
     )
     return meshes_dict, structures_with_mesh
 
+
 class HideChoicesRawTextHelpFormatter(argparse.RawTextHelpFormatter):
     def _get_help_string(self, action):
         help_text = action.help
         if action.choices:
-            help_text = help_text.split('(choices')[0].strip()
+            help_text = help_text.split("(choices")[0].strip()
         return help_text
 
     def _format_action_invocation(self, action):
         if action.option_strings:
-            return ', '.join(action.option_strings)
+            return ", ".join(action.option_strings)
         if action.metavar:
             return action.metavar
         return super()._format_action_invocation(action)
 
-arg_parser = argparse.ArgumentParser(formatter_class=HideChoicesRawTextHelpFormatter)
+
+arg_parser = argparse.ArgumentParser(
+    formatter_class=HideChoicesRawTextHelpFormatter
+)
 timepoints_help = """the age timepoint at which the atlas will be generated.
     Options are:
         - E11.5         ⅂
@@ -221,7 +250,7 @@ def _format_action_invocation(self, action):
         - P04           ⅂
         - P14           |- Postnatal day
         - P56           ⅃
-    
+
 By default, it generates an atlas for each timepoint.
 """
 modalities_help = """the acquisition modalities with which the reference image was captured.
@@ -236,44 +265,73 @@ def _format_action_invocation(self, action):
 By default, LSFM
 """
 decimate_fraction_help = "fraction of the original number of meshes' vertices to be kept. Must be a number > 0 and <= 1.\nBy default, 0.2"
+
+
 def decimate_fraction_type(arg):
     try:
         f = float(arg)
         if 0 < f <= 1:
             return f
     except ValueError:
         pass
-    raise argparse.ArgumentTypeError(f"invalid value: '{arg}' (must be a number > 0 and <= 1)")
-arg_parser.add_argument("-t", "--timepoints", default=TIMEPOINTS, type=str, nargs="+", choices=TIMEPOINTS, help=timepoints_help)
-arg_parser.add_argument("-m", "--modality", default="LSFM", type=str, choices=MODALITIES, help=modalities_help)
-arg_parser.add_argument("-d", "--decimate-fraction", default=0.2, type=decimate_fraction_type, help=decimate_fraction_help)
+    raise argparse.ArgumentTypeError(
+        f"invalid value: '{arg}' (must be a number > 0 and <= 1)"
+    )
+
+
+arg_parser.add_argument(
+    "-t",
+    "--timepoints",
+    default=TIMEPOINTS,
+    type=str,
+    nargs="+",
+    choices=TIMEPOINTS,
+    help=timepoints_help,
+)
+arg_parser.add_argument(
+    "-m",
+    "--modality",
+    default="LSFM",
+    type=str,
+    choices=MODALITIES,
+    help=modalities_help,
+)
+arg_parser.add_argument(
+    "-d",
+    "--decimate-fraction",
+    default=0.2,
+    type=decimate_fraction_type,
+    help=decimate_fraction_help,
+)
 
 if __name__ == "__main__":
     params = vars(arg_parser.parse_args())
     timepoints = params["timepoints"]
     modality = params["modality"]
     decimate_fraction = params["decimate_fraction"]
     atlas_name = f"{ATLAS_NAME}_{modality}"
-    bg_root_dir = DEFAULT_WORKDIR/atlas_name
-    download_dir_path = bg_root_dir/"downloads"
+    bg_root_dir = DEFAULT_WORKDIR / atlas_name
+    download_dir_path = bg_root_dir / "downloads"
     download_dir_path.mkdir(exist_ok=True, parents=True)
     pooch_ = pooch_init(download_dir_path, timepoints)
     structures = fetch_ontology(pooch_)
 
     for age in timepoints:
         atlas_name = f"{atlas_name}_{age.replace('.', '-')}"
-        annotation_volume, reference_volume, resolution_um = fetch_animal(pooch_, age, modality)
-        atlas_dir = bg_root_dir/atlas_name
+        annotation_volume, reference_volume, resolution_um = fetch_animal(
+            pooch_, age, modality
+        )
+        atlas_dir = bg_root_dir / atlas_name
         atlas_dir.mkdir(exist_ok=True)
         print(f"Saving atlas data at {atlas_dir}")
         # Create meshes:
-        meshes_dir_path = atlas_dir/"meshes"
+        meshes_dir_path = atlas_dir / "meshes"
         create_meshes(
             meshes_dir_path,
             structures,
             annotation_volume,
             ROOT_ID,
-            decimate_fraction
+            decimate_fraction,
         )
         meshes_dict, structures_with_mesh = create_mesh_dict(
             structures, meshes_dir_path
@@ -286,7 +344,7 @@ def decimate_fraction_type(arg):
             citation=CITATION,
             atlas_link=ATLAS_LINK,
             species=SPECIES,
-            resolution=(resolution_um,)*3,
+            resolution=(resolution_um,) * 3,
             orientation=ORIENTATION,
             root_id=ROOT_ID,
             reference_stack=reference_volume,
@@ -295,9 +353,9 @@ def decimate_fraction_type(arg):
             meshes_dict=meshes_dict,
             working_dir=atlas_dir,
             atlas_packager=PACKAGER,
-            hemispheres_stack=None, # it is symmetric
+            hemispheres_stack=None,  # it is symmetric
             cleanup_files=False,
             compress=True,
             scale_meshes=True,
         )
-        print("Done. Atlas generated at: ", output_filename)
+        print("Done. Atlas generated at: ", output_filename)