Rhapso 0.1.92__py3-none-any.whl

Rhapso/fusion/neuroglancer_link_gen/utils/utils.py

@@ -0,0 +1,303 @@
+"""
+Utility functions
+"""
+import json
+import os
+import shutil
+import subprocess
+from pathlib import Path
+from typing import List, Optional, Union
+
+import boto3
+import pandas as pd
+
+# IO types
+PathLike = Union[str, Path]
+
+
+def create_folder(dest_dir: PathLike, verbose: Optional[bool] = False) -> None:
+    """
+    Create new folders.
+
+    Parameters
+    ------------------------
+    dest_dir: PathLike
+        Path where the folder will be created if it does not exist.
+    verbose: Optional[bool]
+        If we want to show information about the folder status. Default False.
+
+    Raises
+    ------------------------
+    OSError:
+        if the folder exists.
+
+    """
+
+    if not (os.path.exists(dest_dir)):
+        try:
+            if verbose:
+                print(f"Creating new directory: {dest_dir}")
+            os.makedirs(dest_dir)
+        except OSError as e:
+            if e.errno != os.errno.EEXIST:
+                raise
+
+
+def delete_folder(dest_dir: PathLike, verbose: Optional[bool] = False) -> None:
+    """
+    Delete a folder path.
+    Parameters
+    ------------------------
+    dest_dir: PathLike
+        Path that will be removed.
+    verbose: Optional[bool]
+        If we want to show information about the folder status. Default False.
+
+    Raises
+    ------------------------
+    shutil.Error:
+        If the folder could not be removed.
+
+    Returns
+    ------------------------
+        None
+
+    """
+    if os.path.exists(dest_dir):
+        try:
+            shutil.rmtree(dest_dir)
+            if verbose:
+                print(f"Folder {dest_dir} was removed!")
+        except shutil.Error as e:
+            print(f"Folder could not be removed! Error {e}")
+
+
+def execute_command_helper(
+    command: str,
+    print_command: bool = False,
+    stdout_log_file: Optional[PathLike] = None,
+) -> None:
+    """
+    Execute a shell command.
+
+    Parameters
+    ------------------------
+    command: str
+        Command that we want to execute.
+    print_command: bool
+        Bool that dictates if we print the command in the console.
+
+    Raises
+    ------------------------
+    CalledProcessError:
+        if the command could not be executed (Returned non-zero status).
+
+    """
+
+    if print_command:
+        print(command)
+
+    if stdout_log_file and len(str(stdout_log_file)):
+        save_string_to_txt("$ " + command, stdout_log_file, "a")
+
+    popen = subprocess.Popen(
+        command, stdout=subprocess.PIPE, universal_newlines=True, shell=True
+    )
+    for stdout_line in iter(popen.stdout.readline, ""):
+        yield str(stdout_line).strip()
+    popen.stdout.close()
+    return_code = popen.wait()
+    if return_code:
+        raise subprocess.CalledProcessError(return_code, command)
+
+
+def execute_command(config: dict) -> None:
+    """
+    Execute a shell command with a given configuration.
+
+    Parameters
+    ------------------------
+    command: str
+        Command that we want to execute.
+    print_command: bool
+        Bool that dictates if we print the command in the console.
+
+    Raises
+    ------------------------
+    CalledProcessError:
+        if the command could not be executed (Returned non-zero status).
+
+    """
+
+    for out in execute_command_helper(
+        config["command"], config["verbose"], config["stdout_log_file"]
+    ):
+        if len(out):
+            config["logger"].info(out)
+
+        if config["exists_stdout"]:
+            save_string_to_txt(out, config["stdout_log_file"], "a")
+
+
+def check_path_instance(obj: object) -> bool:
+    """
+    Checks if an objects belongs to pathlib.Path subclasses.
+
+    Parameters
+    ------------------------
+    obj: object
+        Object that wants to be validated.
+
+    Returns
+    ------------------------
+    bool:
+        True if the object is an instance of Path subclass, False otherwise.
+    """
+
+    for childclass in Path.__subclasses__():
+        if isinstance(obj, childclass):
+            return True
+
+    return False
+
+
+def save_dict_as_json(
+    filename: str, dictionary: dict, verbose: Optional[bool] = False
+) -> None:
+    """
+    Saves a dictionary as a json file.
+
+    Parameters
+    ------------------------
+    filename: str
+        Name of the json file.
+    dictionary: dict
+        Dictionary that will be saved as json.
+    verbose: Optional[bool]
+        True if you want to print the path where the file was saved.
+
+    """
+
+    if dictionary is None:
+        dictionary = {}
+
+    else:
+        for key, value in dictionary.items():
+            # Converting path to str to dump dictionary into json
+            if check_path_instance(value):
+                # TODO fix the \\ encode problem in dump
+                dictionary[key] = str(value)
+
+    with open(filename, "w") as json_file:
+        json.dump(dictionary, json_file, indent=4)
+
+    if verbose:
+        print(f"- Json file saved: {filename}")
+
+
+def read_json_as_dict(filepath: str) -> dict:
+    """
+    Reads a json as dictionary.
+
+    Parameters
+    ------------------------
+    filepath: PathLike
+        Path where the json is located.
+
+    Returns
+    ------------------------
+    dict:
+        Dictionary with the data the json has.
+
+    """
+
+    dictionary = None
+
+    if os.path.exists(filepath):
+        with open(filepath) as json_file:
+            dictionary = json.load(json_file)
+
+    return dictionary
+
+
+def save_string_to_txt(txt: str, filepath: PathLike, mode="w") -> None:
+    """
+    Saves a text in a file in the given mode.
+
+    Parameters
+    ------------------------
+    txt: str
+        String to be saved.
+
+    filepath: PathLike
+        Path where the file is located or will be saved.
+
+    mode: str
+        File open mode.
+
+    """
+
+    with open(filepath, mode) as file:
+        file.write(txt + "\n")
+
+
+def create_s3_client() -> boto3.client:
+    """
+    Create and return a boto3 S3 client.
+
+    Returns
+    -------
+    boto3.Client
+        A boto3 S3 client object.
+    """
+    return boto3.client("s3")
+
+
+def list_folders_s3(
+    s3_client: boto3.client, bucket_name: str, prefix: str
+) -> list:
+    """
+    List top-level folders in an S3 bucket with a specified prefix.
+
+    Parameters
+    ----------
+    s3_client : boto3.Client
+        The S3 client object.
+    bucket_name : str
+        The name of the S3 bucket.
+    prefix : str
+        The prefix to filter folders.
+
+    Returns
+    -------
+    list
+        A list of folder names.
+    """
+    response = s3_client.list_objects_v2(
+        Bucket=bucket_name, Prefix=prefix, Delimiter="/"
+    )
+    return [
+        content.get("Prefix").rstrip("/")
+        for content in response.get("CommonPrefixes", [])
+    ]
+
+
+def save_to_csv(data: List[dict], file_path: str) -> str:
+    """
+    Save the given data to a CSV file.
+
+    Parameters
+    ----------
+    data : List[dict]
+        The data to be saved.
+    file_path : str
+        The file path for the CSV file.
+
+    Returns
+    -------
+    str
+        The path of the saved CSV file.
+    """
+    df = pd.DataFrame(data)
+    df.to_csv(file_path, index=False)
+    return file_path

Rhapso/fusion/neuroglancer_link_gen_worker.py

@@ -0,0 +1,30 @@
+'''
+Worker script with hard-coded parameters to generate Neuroglancer link
+'''
+
+from Rhapso.fusion.neuroglancer_link_gen.main import generate_neuroglancer_link
+
+# Hard-coded parameters
+ZARR_PATH = "s3://martin-test-bucket/output7/multiscale_channel_488.zarr"
+VMIN = 90
+VMAX = 400
+JSON_UPLOAD_BUCKET = "martin-test-bucket"
+JSON_UPLOAD_PATH = "NG_out.json"
+JSON_LOCAL_OUTPUT = "results"
+DATASET_TYPE = "hcr"
+OPACITY = 0.5
+BLEND = "default"
+
+if __name__ == "__main__":
+    # Call the function with hard-coded parameters
+    generate_neuroglancer_link(
+        zarr_path=ZARR_PATH,
+        vmin=VMIN,
+        vmax=VMAX,
+        json_upload_bucket=JSON_UPLOAD_BUCKET,
+        json_upload_path=JSON_UPLOAD_PATH,
+        json_local_output=JSON_LOCAL_OUTPUT,
+        dataset_type=DATASET_TYPE,
+        opacity=OPACITY,
+        blend=BLEND
+    )