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GeezerVison is showing github.com — PRMS-Python/prms_python/data.py at master · PRMS-Python/PRMS-Python

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# -*- coding: utf-8 -*-
'''
data.py -- holds ``Data`` class for standard PRMS climate input data.
'''
import pandas as pd
from shutil import copyfile
class Data(object):
"""
Object to access or create a PRMS data file with ability to load/assign it to a
date-time indexed pandas.DataFrame for data management, analysis and visualization.
It can be used to build a new PRMS data file from user defined metadata and a
``pandas.DataFrame`` of PRMS datetime-indexed climatic forcing and observation
variables.
The class properties ``metadata`` and ``data_frame`` can be later assigned if no
``base_file`` is given on initialization, allowing for the creation of PRMS climatic
forcing file in a Python environment.
Keyword Arguments:
base_file (str, optional): path to standard PRMS data file
na_rep (int, optional): how to represent missing values default = -999
Attributes:
date_header (list): date and time header for PRMS data file
valid_input_variables (tuple): valid hydro-climate variables for PRMS data file
Note:
If using the ``Data`` class to create a new data file, it is up to the user
to ensure that the metadata and :class:`pandas.DataFrame` assigned are correct
and compatible.
"""
## data file constant attributes
date_header = ['year',
'month',
'day',
'hh',
'mm',
'sec']
valid_input_variables = ('gate_ht',
'humidity',
'lake_elev',
'pan_evap',
'precip',
'rain_day',
'runoff',
'snowdepth',
'solrad',
'tmax',
'tmin',
'wind_speed')
def __init__(self, base_file=None, na_rep=-999):
self.base_file = base_file
self.na_rep = na_rep
self._metadata = None
self._data_frame = None
@property
def metadata(self):
"""
:obj:`dict`:A property that gets and sets the header information from
a standard PRMS climate input data file held in a Python dictionary. As
a property it can be assigned directly to overwrite or create a new PRMS
data file. As such the user is in control and must supply the correct
syntax for PRMS standard data files, e.g. text lines before header should
begin with "//". Here is an example of the information gathered and held in
this attribute:
Example:
>>> data.metadata
{
'data_startline' : 6,
'data_variables' : ['runoff 1', 'runoff 2', 'tmin', 'tmax', 'ppt']
'text_before_header' : "Title of data file \\n //some comments\\nrunoff 2
\\ntmin 1\\ntmax 1\\nppt 1\\nrunoff 2\\ntmin 1
\\ntmax 1\\nppt 1\\n
########################################\\n"
}
Note:
When assigning or creating a new data file, the ``Data.write`` method will
assign the appropriate date header that follows the line of number signs "#".
Raises:
ValueError: if data in metadata is accessed before data is assigned,
e.g. if accessed to write a PRMS data file from a ``Data`` instance
that was initialized without a valid PRMS data file.
TypeError: if an object that is not a Python dictionary is assigned.
"""
# to avoid overwriting pre-assigned data, check if already exists
if isinstance(self._metadata, dict):
return self._metadata
elif not self.base_file:
raise ValueError('No data file was given on initialization')
## starting list for variable names in data file
input_data_names = []
text_before_header = str()
## open data file and read header information
with open(self.base_file, 'r') as inf:
for idx,l in enumerate(inf):
text_before_header+=l
if idx == 0: ## first line always string identifier of the file- may use later
data_head = l.rstrip()
elif l.startswith('/'): ## comment lines
continue
if l.startswith(Data.valid_input_variables):
h = l.split() ## split, first name and second number of columns
if int(h[1]) > 1: ## more than one input time series of a particular variable
for el in range(int(h[1])):
tmp = '{var_name} {var_ind}'.format(var_name = h[0], var_ind = el+1)
input_data_names.append(tmp)
elif int(h[1]) == 1:
input_data_names.append(h[0])
if l.startswith('#'): ## end of header info and begin time series input data
data_startline = idx+1 ## 0 indexed line of first data entry
break
self._metadata = dict([('data_startline',data_startline),
('data_variables',input_data_names),
('text_before_header',text_before_header)])
return self._metadata
@metadata.setter
def metadata(self, dic):
if not isinstance(dic, dict):
raise TypeError('Must assign a Python dictionary for new Data object/file metadata')
self._metadata = dic
@property
def data_frame(self):
"""
A property that gets and sets the climatic forcing data for a standard PRMS
climate input data file as a :class:`pandas.DataFrame`.
Example:
d is a Data instance, calling
>>> d.data_frame
input variables runoff 1 runoff 2 runoff 3 precip tmax tmin
date
1996-12-27 0.54 1.6 NaN 0.0 46 32.0
1996-12-28 0.65 1.6 NaN 0.0 45 24.0
1996-12-29 0.80 1.6 NaN 0.0 44 28.0
1996-12-30 0.90 1.6 NaN 0.0 51 33.0
1996-12-31 1.00 1.7 NaN 0.0 47 32.0
shows the date-indexed ``pd.DataFrame`` of the input data that is created
when a ``Data`` object is initiated if given a valid ``base_file``, i.e.
file path to a PRMS climate data file.
Raises:
ValueError: if attribute is accessed before either assigning a PRMS data
file on ``Data`` initialization or not assigning a compatabile
date-indexed ``pandas.DataFrame`` of hydro-climate variables.
TypeError: if a data type other than ``pandas.DataFrame`` is assigned.
"""
if not self._metadata:
self.metadata
elif not isinstance(self._data_frame, pd.DataFrame) and self.base_file == None:
raise ValueError('No data base_file given on initialization, '\
'therefore you must assign a DataFrame'\
+' before accessing the .data_frame attribute!')
# to avoid overwriting pre-assigned data
elif isinstance(self._data_frame, pd.DataFrame):
return self._data_frame
df = pd.read_csv(self.base_file, header = None, skiprows = self.metadata['data_startline'],
delim_whitespace = True, na_values = [self.na_rep]) ## read data file
df.columns = Data.date_header + self.metadata['data_variables']
date = pd.Series(pd.to_datetime(df.year * 10000 + df.month * 100 +\
df.day, format = '%Y%m%d'), index = df.index)
df.index = pd.to_datetime(date) ## assign datetime index
df.drop(Data.date_header, axis = 1, inplace = True) ## unneeded columns
df.columns.name = 'input variables' ; df.index.name = 'date'
self._data_frame = df
return self._data_frame
@data_frame.setter
def data_frame(self, df):
if not isinstance(df, pd.DataFrame):
raise TypeError("Must assign a Pandas.DataFrame object for PRMS data input")
self._data_frame = df
def modify(self, func, vars_to_adjust):
"""
Apply a user defined function to one or more variable(s) in the data file.
The ``modify`` method allows for inplace modification of one or more
time series inputs in the data file based on a user defined function.
Arguments:
func (function): function to apply to each variable in vars_to_adjust
vars_to_adjust (list or tuple): collection of variable names to apply func to.
Returns:
None
Example:
Here is an example of loading a data file, modifying the temperature inputs
(*tmin* and *tmax*) by adding two degrees to each element, and rewritting the
modified data to disk,
>>> d = Data('path_to_data_file')
>>> def f(x):
return x + 2
>>> d.modify(f,['tmax','tmin'])
>>> d.write('data_temp_plus_2')
"""
if not isinstance(self._data_frame, pd.DataFrame):
self.data_frame # will raise ValueError from data_frame property
for v in vars_to_adjust:
self._data_frame[v] = self._data_frame[v].apply(func)
def write(self, out_path):
"""
Writes the current state of the ``Data`` to PRMS text format
utilizing the ``Data.metadata`` and ``Data.data_frame`` instance
properties. If ``Data.data_frame`` was never accessed or assigned
new values then this method simply copies the original PRMS
data file to ``out_path``.
Arguments:
out_path (str): full path to save or copy the current PRMS data
in PRMS text format.
Returns:
None
Raises:
ValueError: if the ``write`` method is called without assigning either
an initial data (``base_file``) path or assigning correct ``metadata``
and ``data_frame`` properties.
"""
# if file data was never accessed- unchanged
if not isinstance(self._data_frame, pd.DataFrame):
if self.base_file:
copyfile(self.base_file, out_path)
else: # if data not from original file and dataframe never assigned
raise ValueError('No data base_file was given and'\
+' no data was assigned!')
## reconstruct PRMS data file format, don't overwrite date-indexed
else:
df = self._data_frame[self.metadata['data_variables']]
df['year'] = self._data_frame.index.year
df['month'] = self._data_frame.index.month
df['day'] = self._data_frame.index.day
df['hh'] = df['mm'] = df['sec'] = 0
df = df[Data.date_header + self._metadata['data_variables']]
with open(out_path,'w') as outf: # write comment header then data
outf.write(self._metadata['text_before_header'])
df.to_csv(outf, sep=' ', header=None,\
index=False, na_rep=self.na_rep, lineterminator='\n')
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