minor updates

Author: anna-grim

src/aind_exaspim_image_compression/utils/img_util.py

@@ -165,7 +165,7 @@ def get_start_end(voxel, shape, from_center=True):
         Shape of the image patch to be read.
     from_center : bool, optional
         Indication of whether the provided coordinates represent the center of
-        the patch or the front-top-left corner. The default is True.
+        the patch or the front-top-left corner. Default is True.
 
     Return
     ------
@@ -383,15 +383,14 @@ def convert_tiff_ome_zarr(
     out_path : str
         Path to write the N5.
     chunks : Tuple[int], optional
-        Chunk shape of the N5 dataset. The default is (1, 1, 64, 128, 128).
+        Chunk shape of the N5 dataset. Default is (1, 1, 64, 128, 128).
     compressor : Blosc, optional
-        Numcodecs compressor instance for the N5 dataset. The default is
+        Numcodecs compressor instance for the N5 dataset. Default is
         Blosc(cname="zstd", clevel=5, shuffle=Blosc.SHUFFLE).
     voxel_size : Tuple[float], optional
-        Voxel spacing of the image, in nanometers. The default is
-        (748, 748, 1000).
+        Voxel spacing of the image. Default is (748, 748, 1000).
     n_levels : int, optional
-        Number of levels in the multiscale pyramid. The default is 3.
+        Number of levels in the multiscale pyramid. Default is 3.
 
     Returns
     -------
@@ -448,8 +447,8 @@ def compute_cratio(img, codec, chunk_shape=(64, 64, 64)):
         Image to compute compression ratio of.
     codec : blosc.Blosc
         Blosc codec used to compress each chunk.
-    chunk_shape : tuple of ints
-        Shape of chunks Zarr would use.
+    chunk_shape : Tuple[int]
+        Shape of chunks Zarr would use. Default is (64, 64, 64).
 
     Returns
     -------
@@ -488,10 +487,10 @@ def compute_ssim3D(img1, img2, data_range=None, window_size=16):
     img2 : numpy.ndarray
         3D Image.
     data_range : float, optional
-        Value range of input images. If None, computed from "img1". The
-        default is None.
+        Value range of input images. If None, computed from "img1". Default
+        is None.
     window_size : int, optional
-        Size of the 3D filter window. The default is 16.
+        Size of the 3D filter window. Default is 16.
 
     Returns
     -------

src/aind_exaspim_image_compression/utils/swc_util.py

@@ -52,10 +52,10 @@ def __init__(self, anisotropy=(1.0, 1.0, 1.0), min_size=0):
         ----------
         anisotropy : Tuple[float], optional
             Image to physical coordinates scaling factors to account for the
-            anisotropy of the microscope. The default is [1.0, 1.0, 1.0].
+            anisotropy of the microscope. Default is [1.0, 1.0, 1.0].
         min_size : int, optional
             Threshold on the number nodes in SWC files that are parsed and
-            returned. The default is 0.
+            returned. Default is 0.
 
         Returns
         -------
@@ -140,7 +140,7 @@ def read_from_paths(self, swc_paths):
 
         Returns
         -------
-        Dequeue[dict]
+        swc_dicts : Dequeue[dict]
             List of dictionaries whose keys and values are the attribute
             names and values from an SWC file.
 
@@ -170,7 +170,7 @@ def read_from_path(self, path):
 
         Returns
         -------
-        dict
+        result : dict
             Dictionaries whose keys and values are the attribute names and
             values from an SWC file.
 
@@ -193,7 +193,7 @@ def read_from_zips(self, zip_dir):
 
         Returns
         -------
-        Deque[dict]
+        swc_dicts : Deque[dict]
             Dictionaries whose keys and values are the attribute names and
             values from an SWC file.
 
@@ -223,7 +223,7 @@ def read_from_zip(self, zip_path):
 
         Returns
         -------
-        Dequeue[dict]
+        swc_dicts : Dequeue[dict]
             List of dictionaries whose keys and values are the attribute
             names and values from an SWC file.
 
@@ -250,7 +250,7 @@ def read_from_zipped_file(self, zip_file, path):
 
         Returns
         -------
-        dict
+        result : dict
             Dictionaries whose keys and values are the attribute names and
             values from an SWC file.
 
@@ -274,7 +274,7 @@ def read_from_gcs_swcs(self, gcs_dict):
 
         Returns
         -------
-        Dequeue[dict]
+        swc_dicts : Dequeue[dict]
             List of dictionaries whose keys and values are the attribute
             names and values from an SWC file.
 
@@ -337,7 +337,7 @@ def parse(self, content):
 
         Returns
         -------
-        dict
+        swc_dict : dict
             Dictionaries whose keys and values are the attribute names
             and values from an SWC file.
 
@@ -380,10 +380,10 @@ def process_content(self, content):
 
         Returns
         -------
-        List[str]
+        content : List[str]
             A list of strings representing the lines of text starting from the
             line immediately after the last commented line.
-        List[float]
+        offset : List[float]
             Offset used to shift coordinates.
 
         """
@@ -403,12 +403,12 @@ def read_xyz(self, xyz_str, offset=[0.0, 0.0, 0.0]):
         xyz_str : str
             Coordinate stored as a str.
         offset : List[float], optional
-            Offset used to shift coordinates if provided in the SWC file. The
-            default is [0.0, 0.0, 0.0].
+            Offset used to shift coordinates if provided in the SWC file.
+            Default is [0.0, 0.0, 0.0].
 
         Returns
         -------
-        numpy.ndarray
+        xyz : numpy.ndarray
             Coordinate of a node from an SWC file.
 
         """

src/aind_exaspim_image_compression/utils/util.py

@@ -28,7 +28,7 @@ def mkdir(path, delete=False):
         Path of directory to be created.
     delete : bool, optional
         Indication of whether to delete directory at path if it already
-        exists. The default is False.
+        exists. Default is False.
 
     Returns
     -------
@@ -69,7 +69,7 @@ def list_dir(directory, extension=None):
     directory : str
         Path to directory to be searched.
     extension : str, optional
-       Extension of filenames to be returned. The default is None.
+       Extension of filenames to be returned. Default is None.
 
     Returns
     -------
@@ -94,7 +94,7 @@ def list_subdirectory_names(directory_path):
 
     Returns
     -------
-    List[str]
+    subdir_names : List[str]
         List of the names of subdirectories.
 
     """
@@ -115,12 +115,12 @@ def list_paths(directory, extension=""):
     directory : str
         Directory to be searched.
     extension : str, optional
-        If provided, only paths of files with the extension are returned. The
-        default is an empty string.
+        If provided, only paths of files with the extension are returned.
+        Default is an empty string.
 
     Returns
     -------
-    list[str]
+    List[str]
         List of all paths within "directory".
 
     """
@@ -321,20 +321,20 @@ def list_block_paths(brain_id):
 
 def list_gcs_filenames(gcs_dict, extension):
     """
-    Lists all files in a GCS bucket with the given extension.
+    Lists filenames in a GCS bucket path filtered by file extension.
 
     Parameters
     ----------
     gcs_dict : dict
-        ...
+        Dictionary with keys "bucket_name" and "path" specifying the GCS
+        location.
     extension : str
-        File extension of filenames to be listed.
+        File extension to filter by (e.g., '.tif').
 
     Returns
     -------
-    list
-        Filenames stored at "cloud" path with the given extension.
-
+    List[str]
+        List of blob names containing the specified extension.
     """
     bucket = storage.Client().bucket(gcs_dict["bucket_name"])
     blobs = bucket.list_blobs(prefix=gcs_dict["path"])
@@ -354,7 +354,7 @@ def list_gcs_subprefixes(bucket_name, prefix):
 
     Returns
     -------
-    list[str]
+    subdirs : List[str]
          List of direct subdirectories.
 
     """
@@ -476,11 +476,11 @@ def list_s3_bucket_prefixes(bucket_name, keyword=None):
     bucket_name : str
         Name of the S3 bucket to search.
     keyword : str, optional
-        Keyword used to filter the prefixes.
+        Keyword used to filter the prefixes. Default is None.
 
     Returns
     --------
-    List[str]
+    prefixes : List[str]
         A list of top-level prefixes (directories) in the S3 bucket. If a
         keyword is provided, only the matching prefixes are returned.
 
@@ -566,7 +566,7 @@ def write_to_s3(local_path, bucket_name, prefix):
 # --- Miscellaneous ---
 def sample_once(my_container):
     """
-    Samples a single element from "my_container".
+    Samples a single element from the given container.
 
     Parameters
     ----------
@@ -575,7 +575,8 @@ def sample_once(my_container):
 
     Returns
     -------
-    sample
+    object
+        Element sampled from the given container
 
     """
     return sample(my_container, 1)[0]
@@ -590,13 +591,13 @@ def time_writer(t, unit="seconds"):
     t : float
         Runtime.
     unit : str, optional
-        Unit of time that "t" is expressed in.
+        Unit of time that "t" is expressed in. Default is "seconds".
 
     Returns
     -------
-    float
+    t : float
         Runtime
-    str
+    unit : str
         Unit of time.
 
     """