Package pyucrio

The PyUCRio package provides data access and analysis support for working with UCalgary Riometer instruments, such as NORSTAR Riometers, and SWAN Hyper Spectral Riometers.

For an overview of usage and examples, visit the UCalgary Space Remote Sensing Open Data Platform, view the crib sheets, or explore the examples contained in the Github repository.

Installation:

$ pip install pyucrio

Basic usage:

> import pyucrio
> rio = pyucrio.PyUCRio()

Sub-modules

pyucrio.data

Instrument data downloading and reading module. This module presently has support for data provided by the University of Calgary, such as NORSTAR …

pyucrio.exceptions

Unique exception classes utilized by PyUCRio. These exceptions can be used to help trap specific errors raised by this library …

pyucrio.tools

Data analysis toolkit for working with riometer data available from UCalgary Space Remote Sensing …

Classes

class PyUCRio (download_output_root_path: str | None = None,
api_base_url: str | None = None,
api_timeout: int | None = None,
progress_bar_backend: Literal['auto', 'standard', 'notebook'] = 'auto')

Expand source code

class PyUCRio:
    """
    The `PyUCRio` class is the primary entry point for utilizing
    this library. It is used to initialize a session, capturing details
    about API connectivity, environment, and more. All submodules are 
    encapsulated within this class, so any usage of the library starts 
    with creating this object.

    ```python
    import pyucrio
    rio = pyucrio.PyUCRio()
    ```

    When working with this object, you can set configuration parameters, such 
    as the destination directory for downloaded data, or API special settings 
    (e.g., timeout, HTTP headers, API key). These parameters can be set when 
    instantiating the object, or after instantiating using the self-contained 
    accessible variables.
    """

    __DEFAULT_API_BASE_URL = "https://api.phys.ucalgary.ca"
    __DEFAULT_API_TIMEOUT = 10
    __DEFAULT_API_HEADERS = {
        "content-type": "application/json",
        "user-agent": "python-pyucrio/%s" % (__version__),
    }  # NOTE: these MUST be lowercase so that the decorator logic cannot be overridden

    def __init__(self,
                 download_output_root_path: Optional[str] = None,
                 api_base_url: Optional[str] = None,
                 api_timeout: Optional[int] = None,
                 progress_bar_backend: Literal["auto", "standard", "notebook"] = "auto"):
        """
        Attributes:
            download_output_root_path (str): 
                Destination directory for downloaded data. The default for this path is a 
                subfolder in the user's home directory, such  as `/home/user/pyucrio_data` 
                in Linux. In Windows and Mac, it is similar.

            api_base_url (str): 
                URL prefix to use when interacting with the UCalgary Space Remote Sensing API. By
                default this is set to `https://api.phys.ucalgary.ca`. This parameter is primarily
                used by the development team to test and build new functions using the private staging
                API.

            api_timeout (int): 
                The timeout used when communicating with the UCalgary SRS API. This value is represented in 
                seconds, and by default is `10 seconds`.
                    
            progress_bar_backend (str): 
                The progress bar backend to use. Valid choices are 'auto', 'standard', or 'notebook'. 
                Default is 'auto'. This parameter is optional.

            srs_obj (pyucalgarysrs.PyUCalgarySRS): 
                A [PyUCalgarySRS](https://docs-pyucalgarysrs.phys.ucalgary.ca/#pyucalgarysrs.PyUCalgarySRS) object. 
                If not supplied, it will create the object with some settings carried over from the PyUCRio 
                object. Note that specifying this is for advanced users and only necessary a few special use-cases.

        Raises:
            pyucrio.exceptions.PyUCRioInitializationError: an error was encountered during initialization 
                of the paths
        """
        # initialize path parameters
        self.__download_output_root_path = download_output_root_path

        # initialize api parameters
        self.__api_base_url = api_base_url
        if (api_base_url is None):
            self.__api_base_url = self.__DEFAULT_API_BASE_URL
        self.__api_timeout = api_timeout
        if (api_timeout is None):
            self.__api_timeout = self.__DEFAULT_API_TIMEOUT
        self.__api_headers = self.__DEFAULT_API_HEADERS

        # initialize progress bar parameters
        self.__progress_bar_backend = progress_bar_backend
        self._tqdm = None

        # initialize paths
        self.__initialize_paths()

        # initialize PyUCalgarySRS object
        self.__srs_obj = pyucalgarysrs.PyUCalgarySRS(
            api_headers=self.__api_headers,
            api_timeout=self.__api_timeout,
            download_output_root_path=self.download_output_root_path,
        )

        # initialize progress bar tqdm object (by pulling it from srs_obj)
        self._tqdm = self.__srs_obj._tqdm

        # initialize sub-modules
        self.__data = DataManager(self)
        self.__tools = ToolsManager()

    # ------------------------------------------
    # properties for submodule managers
    # ------------------------------------------
    @property
    def data(self):
        """
        Access to the `data` submodule from within a PyUCRio object.
        """
        return self.__data

    @property
    def tools(self):
        """
        Access to the `tools` submodule from within a PyUCRio object.
        """
        return self.__tools

    # ------------------------------------------
    # properties for configuration parameters
    # ------------------------------------------
    @property
    def api_base_url(self):
        """
        Property for the API base URL. See above for details.
        """
        return self.__api_base_url

    @api_base_url.setter
    def api_base_url(self, value: Optional[str] = None):
        if (value is None):
            self.__api_base_url = self.__DEFAULT_API_BASE_URL
        else:
            # check if http:// or https:// is in the URL
            value = value.lower()
            if (len(value) <= 8 or ("https://" not in value and "http://" not in value)):
                raise PyUCRioInitializationError("API base URL is an invalid URL")

            # remove trailing slash if there is one
            if (value[-1] == '/'):
                value = value[0:-1]
            self.__api_base_url = value
            self.__srs_obj.api_base_url = value

    @property
    def api_headers(self):
        """
        Property for the API headers. See above for details.
        """
        return self.__api_headers

    @property
    def api_timeout(self):
        """
        Property for the API timeout. See above for details.
        """
        return self.__api_timeout

    @api_timeout.setter
    def api_timeout(self, value: int):
        new_timeout = self.__DEFAULT_API_TIMEOUT
        if (value is not None):
            new_timeout = value
        self.__api_timeout = new_timeout
        self.__srs_obj.api_timeout = new_timeout

    @property
    def download_output_root_path(self):
        """
        Property for the download output root path. See above for details.
        """
        return str(self.__download_output_root_path)

    @download_output_root_path.setter
    def download_output_root_path(self, value: str):
        self.__download_output_root_path = value
        self.__initialize_paths()
        self.__srs_obj.download_output_root_path = self.__download_output_root_path

    @property
    def progress_bar_backend(self):
        """
        Property for the progress bar backend. See above for details.
        """
        return self.__progress_bar_backend

    @progress_bar_backend.setter
    def progress_bar_backend(self, value: Optional[Literal["auto", "standard", "notebook"]] = None):
        if (value is None):
            value = "auto"
        else:
            value = value.lower()  # type: ignore
        if (value != "auto" and value != "standard" and value != "notebook"):
            raise PyUCRioInitializationError("Invalid progress bar backend. Allowed values are 'auto', 'standard' or 'notebook'.")
        self.__progress_bar_backend = value
        self.__srs_obj.progress_bar_backend = value
        self._tqdm = self.__srs_obj._tqdm

    @property
    def srs_obj(self):
        """
        Property for the PyUCalgarySRS object. See above for details.
        """
        return self.__srs_obj

    # -----------------------------
    # special methods
    # -----------------------------
    def __str__(self) -> str:
        return self.__repr__()

    def __repr__(self) -> str:
        return ("PyUCRio(download_output_root_path='%s', api_base_url='%s', api_timeout=%s, progress_bar_backend='%s', " +
                "srs_obj=PyUCalgarySRS(...))") % (
                    self.__download_output_root_path,
                    self.api_base_url,
                    self.api_timeout,
                    self.progress_bar_backend,
                )

    def pretty_print(self):
        """
        A special print output for this class.
        """
        # set special strings

        # print
        print("PyUCRio:")
        print("  %-27s: %s" % ("download_output_root_path", self.download_output_root_path))
        print("  %-27s: %s" % ("api_base_url", self.api_base_url))
        print("  %-27s: %s" % ("api_timeout", self.api_timeout))
        print("  %-27s: %s" % ("progress_bar_backend", self.progress_bar_backend))
        print("  %-27s: %s" % ("srs_obj", "PyUCalgarySRS(...)"))

    # -----------------------------
    # private methods
    # -----------------------------
    def __initialize_paths(self):
        """
        Initialize the `download_output_root_path` directory.

        Raises:
            pyucrio.exceptions.PyUCRioInitializationError: an error was encountered during
                initialization of the paths
        """
        if (self.__download_output_root_path is None):
            self.__download_output_root_path = Path("%s/pyucrio_data" % (str(Path.home())))
        try:
            os.makedirs(self.download_output_root_path, exist_ok=True)
        except IOError as e:  # pragma: nocover-ok
            raise PyUCRioInitializationError("Error during output path creation: %s" % str(e)) from e

    # -----------------------------
    # public methods
    # -----------------------------
    def purge_download_output_root_path(self):
        """
        Delete all files in the `download_output_root_path` directory. Since the
        library downloads data to this directory, over time it can grow too large
        and the user can risk running out of space. This method is here to assist
        with easily clearing out this directory.

        Note that it also deletes all files in the PyUCalgarySRS object's 
        download_output_root_path path as well. Normally, these two paths are the 
        same, but it can be different if the user specifically changes it. 

        Raises:
            pyucrio.exceptions.PyUCRioPurgeError: an error was encountered during the purge operation
        """
        try:
            # purge pyucrio path
            for item in os.listdir(self.download_output_root_path):
                item = Path(self.download_output_root_path) / item
                if (os.path.isdir(item) is True and self.srs_obj.read_tar_temp_path not in str(item)):
                    shutil.rmtree(item)
                elif (os.path.isfile(item) is True):
                    os.remove(item)

            # purge pyucalgarysrs path
            self.__srs_obj.purge_download_output_root_path()
        except Exception as e:  # pragma: nocover-ok
            raise PyUCRioPurgeError("Error while purging download output root path: %s" % (str(e))) from e

    def show_data_usage(self, order: Literal["name", "size"] = "size", return_dict: bool = False) -> Any:
        """
        Print the volume of data existing in the download_output_root_path, broken down
        by dataset. Alternatively return the information in a dictionary.
        
        This can be a helpful tool for managing your disk space.

        Args:
            order (bool): 
                Order results by either `size` or `name`. Default is `size`.

            return_dict (bool): 
                Instead of printing the data usage information, return the information as a dictionary.

        Returns:
            Printed output. If `return_dict` is True, then it will instead return a dictionary with the
            disk usage information.
        
        Notes:
            Note that size on disk may differ slightly from the values determined by this 
            routine. For example, the results here will be slightly different than the output
            of a 'du' command on *nix systems.
        """
        # init
        total_size = 0
        download_pathlib_path = Path(self.download_output_root_path)

        # get list of dataset paths
        dataset_paths = []
        for f in os.listdir(download_pathlib_path):
            path_f = download_pathlib_path / f
            if (os.path.isdir(path_f) is True and str(path_f) != self.srs_obj.read_tar_temp_path):
                dataset_paths.append(path_f)

        # get size of each dataset path
        dataset_dict = {}
        longest_path_len = 0
        for dataset_path in dataset_paths:
            # get size
            dataset_size = 0
            for dirpath, _, filenames in os.walk(dataset_path):
                for filename in filenames:
                    filepath = os.path.join(dirpath, filename)
                    if (os.path.isfile(filepath) is True):
                        dataset_size += os.path.getsize(filepath)

            # check if this is the longest path name
            path_basename = os.path.basename(dataset_path)
            if (longest_path_len == 0):
                longest_path_len = len(path_basename)
            elif (len(path_basename) > longest_path_len):
                longest_path_len = len(path_basename)

            # set dict
            dataset_dict[path_basename] = {
                "path_obj": dataset_path,
                "size_bytes": dataset_size,
                "size_str": humanize.naturalsize(dataset_size),
            }

            # add to total
            total_size += dataset_size

        # return dictionary
        if (return_dict is True):
            return dataset_dict

        # print table
        #
        # order into list
        order_key = "size_bytes" if order == "size" else order
        ordered_list = []
        for path, p_dict in dataset_dict.items():
            this_dict = p_dict
            this_dict["name"] = path
            ordered_list.append(this_dict)
        if (order == "size"):
            ordered_list = reversed(sorted(ordered_list, key=lambda x: x[order_key]))
        else:
            ordered_list = sorted(ordered_list, key=lambda x: x[order_key])

        # set column data
        table_names = []
        table_sizes = []
        for item in ordered_list:
            table_names.append(item["name"])
            table_sizes.append(item["size_str"])

        # set header values
        table_headers = ["Dataset name", "Size"]

        # print as table
        table = Texttable()
        table.set_deco(Texttable.HEADER)
        table.set_cols_dtype(["t"] * len(table_headers))
        table.set_header_align(["l"] * len(table_headers))
        table.set_cols_align(["l"] * len(table_headers))
        table.header(table_headers)
        for i in range(0, len(table_names)):
            table.add_row([table_names[i], table_sizes[i]])
        print(table.draw())

        print("\nTotal size: %s" % (humanize.naturalsize(total_size)))

The PyUCRio class is the primary entry point for utilizing this library. It is used to initialize a session, capturing details about API connectivity, environment, and more. All submodules are encapsulated within this class, so any usage of the library starts with creating this object.

import pyucrio
rio = pyucrio.PyUCRio()

When working with this object, you can set configuration parameters, such as the destination directory for downloaded data, or API special settings (e.g., timeout, HTTP headers, API key). These parameters can be set when instantiating the object, or after instantiating using the self-contained accessible variables.

Attributes

download_output_root_path : str

Destination directory for downloaded data. The default for this path is a subfolder in the user's home directory, such as /home/user/pyucrio_data in Linux. In Windows and Mac, it is similar.

api_base_url : str

URL prefix to use when interacting with the UCalgary Space Remote Sensing API. By default this is set to https://api.phys.ucalgary.ca. This parameter is primarily used by the development team to test and build new functions using the private staging API.

api_timeout : int

The timeout used when communicating with the UCalgary SRS API. This value is represented in seconds, and by default is 10 seconds.

progress_bar_backend : str

The progress bar backend to use. Valid choices are 'auto', 'standard', or 'notebook'. Default is 'auto'. This parameter is optional.

srs_obj : pyucalgarysrs.PyUCalgarySRS

A PyUCalgarySRS object. If not supplied, it will create the object with some settings carried over from the PyUCRio object. Note that specifying this is for advanced users and only necessary a few special use-cases.

Raises

PyUCRioInitializationError

an error was encountered during initialization of the paths

Instance variables

prop api_base_url

Expand source code

@property
def api_base_url(self):
    """
    Property for the API base URL. See above for details.
    """
    return self.__api_base_url

Property for the API base URL. See above for details.

prop api_headers

Expand source code

@property
def api_headers(self):
    """
    Property for the API headers. See above for details.
    """
    return self.__api_headers

Property for the API headers. See above for details.

prop api_timeout

Expand source code

@property
def api_timeout(self):
    """
    Property for the API timeout. See above for details.
    """
    return self.__api_timeout

Property for the API timeout. See above for details.

prop data

Expand source code

@property
def data(self):
    """
    Access to the `data` submodule from within a PyUCRio object.
    """
    return self.__data

Access to the pyucrio.data submodule from within a PyUCRio object.

prop download_output_root_path

Expand source code

@property
def download_output_root_path(self):
    """
    Property for the download output root path. See above for details.
    """
    return str(self.__download_output_root_path)

Property for the download output root path. See above for details.

prop progress_bar_backend

Expand source code

@property
def progress_bar_backend(self):
    """
    Property for the progress bar backend. See above for details.
    """
    return self.__progress_bar_backend

Property for the progress bar backend. See above for details.

prop srs_obj

Expand source code

@property
def srs_obj(self):
    """
    Property for the PyUCalgarySRS object. See above for details.
    """
    return self.__srs_obj

Property for the PyUCalgarySRS object. See above for details.

prop tools

Expand source code

@property
def tools(self):
    """
    Access to the `tools` submodule from within a PyUCRio object.
    """
    return self.__tools

Access to the pyucrio.tools submodule from within a PyUCRio object.

Methods

def pretty_print(self)

Expand source code

def pretty_print(self):
    """
    A special print output for this class.
    """
    # set special strings

    # print
    print("PyUCRio:")
    print("  %-27s: %s" % ("download_output_root_path", self.download_output_root_path))
    print("  %-27s: %s" % ("api_base_url", self.api_base_url))
    print("  %-27s: %s" % ("api_timeout", self.api_timeout))
    print("  %-27s: %s" % ("progress_bar_backend", self.progress_bar_backend))
    print("  %-27s: %s" % ("srs_obj", "PyUCalgarySRS(...)"))

A special print output for this class.

def purge_download_output_root_path(self)

Expand source code

def purge_download_output_root_path(self):
    """
    Delete all files in the `download_output_root_path` directory. Since the
    library downloads data to this directory, over time it can grow too large
    and the user can risk running out of space. This method is here to assist
    with easily clearing out this directory.

    Note that it also deletes all files in the PyUCalgarySRS object's 
    download_output_root_path path as well. Normally, these two paths are the 
    same, but it can be different if the user specifically changes it. 

    Raises:
        pyucrio.exceptions.PyUCRioPurgeError: an error was encountered during the purge operation
    """
    try:
        # purge pyucrio path
        for item in os.listdir(self.download_output_root_path):
            item = Path(self.download_output_root_path) / item
            if (os.path.isdir(item) is True and self.srs_obj.read_tar_temp_path not in str(item)):
                shutil.rmtree(item)
            elif (os.path.isfile(item) is True):
                os.remove(item)

        # purge pyucalgarysrs path
        self.__srs_obj.purge_download_output_root_path()
    except Exception as e:  # pragma: nocover-ok
        raise PyUCRioPurgeError("Error while purging download output root path: %s" % (str(e))) from e

Delete all files in the download_output_root_path directory. Since the library downloads data to this directory, over time it can grow too large and the user can risk running out of space. This method is here to assist with easily clearing out this directory.

Note that it also deletes all files in the PyUCalgarySRS object's download_output_root_path path as well. Normally, these two paths are the same, but it can be different if the user specifically changes it.

Raises

PyUCRioPurgeError

an error was encountered during the purge operation

def show_data_usage(self, order: Literal['name', 'size'] = 'size', return_dict: bool = False) ‑> Any

Expand source code

def show_data_usage(self, order: Literal["name", "size"] = "size", return_dict: bool = False) -> Any:
    """
    Print the volume of data existing in the download_output_root_path, broken down
    by dataset. Alternatively return the information in a dictionary.
    
    This can be a helpful tool for managing your disk space.

    Args:
        order (bool): 
            Order results by either `size` or `name`. Default is `size`.

        return_dict (bool): 
            Instead of printing the data usage information, return the information as a dictionary.

    Returns:
        Printed output. If `return_dict` is True, then it will instead return a dictionary with the
        disk usage information.
    
    Notes:
        Note that size on disk may differ slightly from the values determined by this 
        routine. For example, the results here will be slightly different than the output
        of a 'du' command on *nix systems.
    """
    # init
    total_size = 0
    download_pathlib_path = Path(self.download_output_root_path)

    # get list of dataset paths
    dataset_paths = []
    for f in os.listdir(download_pathlib_path):
        path_f = download_pathlib_path / f
        if (os.path.isdir(path_f) is True and str(path_f) != self.srs_obj.read_tar_temp_path):
            dataset_paths.append(path_f)

    # get size of each dataset path
    dataset_dict = {}
    longest_path_len = 0
    for dataset_path in dataset_paths:
        # get size
        dataset_size = 0
        for dirpath, _, filenames in os.walk(dataset_path):
            for filename in filenames:
                filepath = os.path.join(dirpath, filename)
                if (os.path.isfile(filepath) is True):
                    dataset_size += os.path.getsize(filepath)

        # check if this is the longest path name
        path_basename = os.path.basename(dataset_path)
        if (longest_path_len == 0):
            longest_path_len = len(path_basename)
        elif (len(path_basename) > longest_path_len):
            longest_path_len = len(path_basename)

        # set dict
        dataset_dict[path_basename] = {
            "path_obj": dataset_path,
            "size_bytes": dataset_size,
            "size_str": humanize.naturalsize(dataset_size),
        }

        # add to total
        total_size += dataset_size

    # return dictionary
    if (return_dict is True):
        return dataset_dict

    # print table
    #
    # order into list
    order_key = "size_bytes" if order == "size" else order
    ordered_list = []
    for path, p_dict in dataset_dict.items():
        this_dict = p_dict
        this_dict["name"] = path
        ordered_list.append(this_dict)
    if (order == "size"):
        ordered_list = reversed(sorted(ordered_list, key=lambda x: x[order_key]))
    else:
        ordered_list = sorted(ordered_list, key=lambda x: x[order_key])

    # set column data
    table_names = []
    table_sizes = []
    for item in ordered_list:
        table_names.append(item["name"])
        table_sizes.append(item["size_str"])

    # set header values
    table_headers = ["Dataset name", "Size"]

    # print as table
    table = Texttable()
    table.set_deco(Texttable.HEADER)
    table.set_cols_dtype(["t"] * len(table_headers))
    table.set_header_align(["l"] * len(table_headers))
    table.set_cols_align(["l"] * len(table_headers))
    table.header(table_headers)
    for i in range(0, len(table_names)):
        table.add_row([table_names[i], table_sizes[i]])
    print(table.draw())

    print("\nTotal size: %s" % (humanize.naturalsize(total_size)))

Print the volume of data existing in the download_output_root_path, broken down by dataset. Alternatively return the information in a dictionary.

This can be a helpful tool for managing your disk space.

Args

order : bool

Order results by either size or name. Default is size.

return_dict : bool

Instead of printing the data usage information, return the information as a dictionary.

Returns

Printed output. If return_dict is True, then it will instead return a dictionary with the disk usage information.

Notes

Note that size on disk may differ slightly from the values determined by this routine. For example, the results here will be slightly different than the output of a 'du' command on *nix systems.