avni.tools.common module#

avni.tools.common.stage(file: str, overwrite: bool = False)[source]#

Stages a file in the AVNI file directories for testing

Parameters

filestr: file name to be staged
overwritebool, optional: overwite any existing symlink or file, by default False

Raises

IOError: File not found or a symlink already exists

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.parse_line(line: str, rx_dict: dict)[source]#

Function used to parse line with key word from rx_dict

Parameters

linestr: Line to search
rx_dictdict: Do a regex search against all defined regexes

Returns

key,match: Result of the first matching regex, None if not found

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.ifwithindepth(start_depths: numpy.ndarray, end_depths: numpy.ndarray, depth_in_km: numpy.ndarray)[source]#

Check if a set of depths are within a range of depths

Parameters

start_depthsnp.ndarray: Starting depth for the range
end_depthsnp.ndarray: End depth for the range
depth_in_kmnp.ndarray: Depths to check for

Returns

output: index of depth range that each depth_in_km belongs to

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.makegrid(latitude: Union[list, tuple, numpy.ndarray], longitude: Union[list, tuple, numpy.ndarray], depth_in_km: Union[None, list, tuple, numpy.ndarray] = None)[source]#

Make a 2D or 3D grid out of input locations and depths.

Parameters

latitudetp.Union[list,tuple,np.ndarray]: Latitudes of locations queried
longitudetp.Union[list,tuple,np.ndarray]: Longitudes of locations queried
depth_in_kmtp.Union[None,list,tuple,np.ndarray], optional: Depths of locations queried, by default None

Returns

nrows,latitude,longitude,[optional: depth_in_km]: A 2D or 3D grid with nrows rows found by unraveling (depth_in_km,latitude,longitude)

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.convert2nparray(value: Union[str, list, tuple, float, numpy.int64, numpy.ndarray, bool], int2float: bool = True, allowstrings: bool = True) → numpy.ndarray[source]#

Converts input value to a float numpy array. Boolean are returned as Boolean arrays.

Parameters

valuetp.Union[str,list,tuple,float,np.int64,np.ndarray,bool]: A single value or a set of values.
int2floatbool, optional: Convert integer to floats, by default True
allowstringsbool, optional: Check if value has strings, by default True

Returns

np.ndarray: Output values as a numpy array.

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.precision_and_scale(x: float, max_digits: int = 14) → Tuple[int, int][source]#

Returns precision and scale of a float

Parameters

xfloat: A floating point number
max_digitsint, optional: Maximum digits or magnitude, by default 14

Returns

tp.Tuple[int, int]: Returns precision and scale of a float

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.alphanum_key(s: str) → list[source]#

Helper tool to sort lists in ascending numerical order (natural sorting), rather than lexicographic sorting

Parameters

sstr: string to sort

Returns

list: Sorted list

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.diffdict(first_dict: dict, second_dict: dict) → dict[source]#

Helper tool to get difference in two dictionaries

Parameters

first_dictdict: First dictionary
second_dictdict: Second dictionary

Returns

dict: Difference

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.df2nparray(dataframe: pandas.core.frame.DataFrame) → numpy.ndarray[source]#

Helper tool to return the named numpy array of the pandas dataframe

Parameters

dataframepd.DataFrame: Input Pandas Dataframe

Returns

np.ndarray: Equivalent named numpy array

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.krunge(n: int, x: float, h: Union[int, float], y: Union[list, tuple, numpy.ndarray], f: Union[list, tuple, numpy.ndarray], m: int = 0, phi: numpy.ndarray = array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), savey: numpy.ndarray = array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]))[source]#

Some sort of integration or interpolation? x is incremented on second and fourth calls. Resets itself after 5’th call.

Parameters

nint: number of points
xfloat: indepent variable for points
htp.Union[int,float]: step size
ytp.Union[list,tuple,np.ndarray]: function evaluated at each point
ftp.Union[list,tuple,np.ndarray]: function evaluated at each point
mint, optional: call number, by default 0
phinp.ndarray, optional: Intermediate variable, by default np.zeros(6)
saveynp.ndarray, optional: Intermediate variable, by default np.zeros(6)

avni.tools.common.firstnonspaceindex(string: str) → Tuple[int, int][source]#

Gets the first and last non-space index of a string

Parameters

stringstr: String to search

Returns

tp.Tuple[int,int]: First and last non-space index

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.get_fullpath(path: str) → str[source]#

Provides the full path by replacing . and ~ in path

Parameters

pathstr: Input file or folder path

Returns

str: Full path after replacing . and ~ in path

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.listfolders(path: str) → list[source]#

Return a list of directories in a path

Parameters

pathstr: Input file or folder path

Returns

list: List of directories

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.get_installdir(module: str = 'avni', checkwrite: bool = True, checkenv: bool = True) → str[source]#

Get the installation directory for any module in the current machine.

Parameters

modulestr, optional: Module to search for, by default ‘avni’
checkwritebool, optional: Checks for write access to the files, by default True
checkenvbool, optional: Checks if the directory is specified as an environment variable, by default True

Returns

str: Path to installation directory

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.get_filedir(module: str = 'avni', subdirectory: Union[None, str] = None, checkwrite: bool = True, makedir: bool = True) → str[source]#

Get the local files directory for any module in the current machine.

Parameters

modulestr, optional: Module to search for, by default ‘avni’
subdirectorytp.Union[None,str], optional: A directory inside the main directory, by default None
checkwritebool, optional: Checks for write access to the files, by default True
makedirbool, optional: Make a new directory if it doesn’t exist, by default True

Returns

str: Path to local files directory

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.get_cptdir(module: str = 'avni', checkwrite: bool = True, makedir: bool = True) → str[source]#

Get the directory with color palettes for any module in the current machine.

Parameters

modulestr, optional: Module to search for, by default ‘avni’
checkwritebool, optional: Checks for write access to the files, by default True
makedirbool, optional: Make a new directory if it doesn’t exist, by default True

Returns

str: Path to local CPT color palette directory

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.get_configdir(module: str = 'avni', checkwrite: bool = True, makedir: bool = True) → str[source]#

Get the directory containing configuration files.

Parameters

modulestr, optional: Module to search for, by default ‘avni’
checkwritebool, optional: Checks for write access to the files, by default True
makedirbool, optional: Make a new directory if it doesn’t exist, by default True

Returns

str: Path to local config directory as specified in constants.configfolder()

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.get_projections(checkwrite: bool = True, makedir: bool = True, types: str = 'radial') → Tuple[str, bool][source]#

Get the file containing projection matrices.

Parameters

checkwritebool, optional: Checks for write access to the files, by default True
makedirbool, optional: Make a new directory if doesn’t exist, by default True
typesstr, optional: Type can be radial or lateral, by default ‘radial’

Returns

tp.Tuple[str,bool]: First entry is location of projection file Second end is whether this file already exists in the file system

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.writejson(nparray: numpy.ndarray, filename: str, encoding: str = 'utf-8')[source]#

Writes a json file from a numpy array

Parameters

nparraynp.ndarray: Input numpy array to write to JSON
filenamestr: Output JSON file name
encodingstr, optional: File encoding, by default ‘utf-8’
:Authors:: Raj Moulik (moulik@caa.columbia.edu)
:Last Modified:: 2023.02.16 5.00

avni.tools.common.readjson(filename: str, encoding: str = 'utf-8') → numpy.ndarray[source]#

Reading from a JSON file to a numpy array

Parameters

filenamestr: Input JSON file name
encodingstr, optional: File encoding, by default ‘utf-8’

Returns

np.ndarray: Output numpy array

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.uniquenumpyrow(a: numpy.ndarray)[source]#

Gets the unique rows from a numpy array and the indices. e.g. to get unique lat-lon values

Parameters

anp.ndarray: A numpy aray with multiple rows that needs to searched

Returns

unique_a,idx: Unique rows and their indices

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.sanitised_input(prompt: str, type_=None, min_=None, max_=None, range_=None)[source]#

Provide a user prompt with values between min-max or range of values

For specific values: user_input = sanitised_input(“Replace(r)/Ignore(i) this datum?”, str.lower, range_=(‘r’, ‘i’) For a range: age = sanitised_input(“Enter your age: “, int, range_=xrange(100))

Parameters

promptstr: Prompt to the user
type_optional: type of input needed, by default None
min_optional: Minimum value, by default None
max_optional: Maximum value, by default None
range_optional: Range of values, by default None

Returns

ui: User input

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.appendunits(ureg=None, system: str = 'mks', unitsfile: str = '/home/pm5113/Github/avni-private/avni/config/units.ini')[source]#

Append the custom units from unitsfile to ureg registry

Parameters

ureg_type_, optional: Input unit registry, by default constants.ureg
systemstr, optional: Default unit system; if not the same as ureg changes it, by default ‘mks’
unitsfilestr, optional: additional definitions to add to ureg, by default get_configdir()+’/’+constants.customunits
:Authors:: Raj Moulik (moulik@caa.columbia.edu)
:Last Modified:: 2023.02.16 5.00

avni.tools.common.convert2units(valstring: str)[source]#

Returns the value with units from a string that has units.

Parameters

valstringstr: A string to convert. Only space allowed is that between value and unit.

Returns

vals: Value with units

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00

avni.tools.common.decimals(value: Union[list, tuple, numpy.ndarray]) → numpy.ndarray[source]#

Returns the number of decimals in a set of floating point numbers.

Parameters

valuetp.Union[list,tuple,np.ndarray]: Set of floating point numbers

Returns

np.ndarray: Number of decimals in each float

Authors: Raj Moulik (moulik@caa.columbia.edu)
Last Modified: 2023.02.16 5.00