<filename>seismicpro/src/seismic_dataset.py
"""File contains seismic dataset."""
import numpy as np
from scipy.optimize import minimize
from tdigest import TDigest

from ..batchflow import Dataset
from .seismic_index import FieldIndex
from .seismic_batch import SeismicBatch


class SeismicDataset(Dataset):
    """Dataset for seismic data."""

    def __init__(self, index, batch_class=SeismicBatch, preloaded=None, *args, **kwargs):
        super().__init__(index, batch_class=batch_class, preloaded=preloaded, *args, **kwargs)

    def find_sdc_params(self, component, speed, loss, indices=None, time=None, initial_point=None,
                        method='Powell', bounds=None, tslice=None, **kwargs):
        """ Finding an optimal parameters for correction of spherical divergence.

        Parameters
        ----------
        component : str
            Component with shot gathers.
        speed : array
            Wave propagation speed depending on the depth.
            Speed is measured in milliseconds.
        loss : callable
            Function to minimize.
        indices : array-like, optonal
            Which items from dataset to use in parameter estimation.
            If `None`, defaults to first element of dataset.
        time : array, optional
           Trace time values. If `None` defaults to self.meta[src]['samples'].
           Time measured in either in samples or in milliseconds.
        initial_point : array of 2
            Started values for $v_{pow}$ and $t_{pow}$.
            If None defaults to $v_{pow}=2$ and $t_{pow}=1$.
        method : str, optional, default ```Powell```
            Minimization method, see ```scipy.optimize.minimize```.
        bounds : sequence, optional
            Sequence of (min, max) optimization bounds for each parameter.
            If `None` defaults to ((0, 5), (0, 5)).
        tslice : slice, optional
            Lenght of loaded traces.

        Returns
        -------
            : array
            Coefficients for speed and time.

        Raises
        ------
        ValueError : If Index is not FieldIndex.

        Note
        ----
        To save parameters as SeismicDataset attribute use ```save_to=D('attr_name')``` (works only
        in pipeline).
        If you want to save parameters to pipeline variable use save_to argument with following
        syntax: ```save_to=V('variable_name')```.
        """
        if not isinstance(self.index, FieldIndex):
            raise ValueError("Index must be FieldIndex, not {}".format(type(self.index)))

        if indices is None:
            indices = self.indices[:1]

        batch = self.create_batch(indices).load(components=component, fmt='segy', tslice=tslice)
        field = getattr(batch, component)[0]
        samples = batch.meta[component]['samples']

        bounds = ((0, 5), (0, 5)) if bounds is None else bounds
        initial_point = (2, 1) if initial_point is None else initial_point

        time = samples if time is None else np.array(time, dtype=int)
        step = np.diff(time[:2])[0].astype(int)
        speed = np.array(speed, dtype=int)[::step]
        args = field, time, speed

        func = minimize(loss, initial_point, args=args, method=method, bounds=bounds, **kwargs)
        return func.x

    def find_equalization_params(self, batch, component, survey_id_col, sample_size=10000,
                                 container_name='equal_params', **kwargs):
        """ Estimates 95th percentile of absolute values for each seismic survey
        in dataset for equalization.

        This method utilizes t-digest structure for batch-wise estimation of rank-based statistics,
        namely 95th percentile.

        Parameters
        ----------
        batch : SeismicBatch or B() named expression.
            Current batch from pipeline.
        component : str
            Component with shot gathers.
        survey_id_col : str
            Column in index that indicate names of seismic
            surveys from different seasons.
        sample_size: int, optional
            Number of elements to draw from each shot gather to update
            estimates if TDigest. Time for each update grows linearly
            with `sample_size`. Default is 10000.
        container_name: str, optional
            Name of the `SeismicDataset` attribute to store a dict
            with estimated percentile. Also contains `survey_id_col`
            key and corresponding value.
        kwargs: misc
            Parameters for TDigest objects.

        Raises
        ------
        ValueError : If index is not FieldIndex.
        ValueError : If shot gather with same id is contained in more
                     than one survey.

        Note
        ----
        Dictoinary with estimated percentile can be obtained from pipeline using `D(container_name)`.
        """
        if not isinstance(self.index, FieldIndex):
            raise ValueError("Index must be FieldIndex, not {}".format(type(self.index)))

        private_name = '_' + container_name
        params = getattr(self, private_name, None)
        if params is None:
            surveys = np.unique(self.index.get_df()[survey_id_col])
            delta, k = kwargs.pop('delta', 0.01), kwargs.pop('K', 25)
            params = dict(zip(surveys, [TDigest(delta, k) for _ in surveys]))
            setattr(self, private_name, params)

        for idx in batch.indices:
            surveys_by_fieldrecord = np.unique(batch.index.get_df(index=idx)[survey_id_col])
            if len(surveys_by_fieldrecord) != 1:
                raise ValueError('Field {} represents data from more than one survey!'.format(idx))
            survey = surveys_by_fieldrecord[0]

            pos = batch.index.get_pos(idx)
            sample = np.random.choice(getattr(batch, component)[pos].reshape(-1), size=sample_size)

            params[survey].batch_update(np.absolute(sample))

        statistics = dict([survey, digest.percentile(95)]
                          for survey, digest in params.items() if digest.n > 0)
        statistics['survey_id_col'] = survey_id_col
        setattr(self, container_name, statistics)

<filename>seismicpro/src/seismic_dataset.py
"""File contains seismic dataset."""
import numpy as np
from scipy.optimize import minimize
from tdigest import TDigest

from ..batchflow import Dataset
from .seismic_index import FieldIndex
from .seismic_batch import SeismicBatch


class SeismicDataset(Dataset):
    """Dataset for seismic data."""

    def __init__(self, index, batch_class=SeismicBatch, preloaded=None, *args, **kwargs):
        super().__init__(index, batch_class=batch_class, preloaded=preloaded, *args, **kwargs)

    def find_sdc_params(self, component, speed, loss, indices=None, time=None, initial_point=None,
                        method='Powell', bounds=None, tslice=None, **kwargs):
        """ Finding an optimal parameters for correction of spherical divergence.

        Parameters
        ----------
        component : str
            Component with shot gathers.
        speed : array
            Wave propagation speed depending on the depth.
            Speed is measured in milliseconds.
        loss : callable
            Function to minimize.
        indices : array-like, optonal
            Which items from dataset to use in parameter estimation.
            If `None`, defaults to first element of dataset.
        time : array, optional
           Trace time values. If `None` defaults to self.meta[src]['samples'].
           Time measured in either in samples or in milliseconds.
        initial_point : array of 2
            Started values for $v_{pow}$ and $t_{pow}$.
            If None defaults to $v_{pow}=2$ and $t_{pow}=1$.
        method : str, optional, default ```Powell```
            Minimization method, see ```scipy.optimize.minimize```.
        bounds : sequence, optional
            Sequence of (min, max) optimization bounds for each parameter.
            If `None` defaults to ((0, 5), (0, 5)).
        tslice : slice, optional
            Lenght of loaded traces.

        Returns
        -------
            : array
            Coefficients for speed and time.

        Raises
        ------
        ValueError : If Index is not FieldIndex.

        Note
        ----
        To save parameters as SeismicDataset attribute use ```save_to=D('attr_name')``` (works only
        in pipeline).
        If you want to save parameters to pipeline variable use save_to argument with following
        syntax: ```save_to=V('variable_name')```.
        """
        if not isinstance(self.index, FieldIndex):
            raise ValueError("Index must be FieldIndex, not {}".format(type(self.index)))

        if indices is None:
            indices = self.indices[:1]

        batch = self.create_batch(indices).load(components=component, fmt='segy', tslice=tslice)
        field = getattr(batch, component)[0]
        samples = batch.meta[component]['samples']

        bounds = ((0, 5), (0, 5)) if bounds is None else bounds
        initial_point = (2, 1) if initial_point is None else initial_point

        time = samples if time is None else np.array(time, dtype=int)
        step = np.diff(time[:2])[0].astype(int)
        speed = np.array(speed, dtype=int)[::step]
        args = field, time, speed

        func = minimize(loss, initial_point, args=args, method=method, bounds=bounds, **kwargs)
        return func.x

    def find_equalization_params(self, batch, component, survey_id_col, sample_size=10000,
                                 container_name='equal_params', **kwargs):
        """ Estimates 95th percentile of absolute values for each seismic survey
        in dataset for equalization.

        This method utilizes t-digest structure for batch-wise estimation of rank-based statistics,
        namely 95th percentile.

        Parameters
        ----------
        batch : SeismicBatch or B() named expression.
            Current batch from pipeline.
        component : str
            Component with shot gathers.
        survey_id_col : str
            Column in index that indicate names of seismic
            surveys from different seasons.
        sample_size: int, optional
            Number of elements to draw from each shot gather to update
            estimates if TDigest. Time for each update grows linearly
            with `sample_size`. Default is 10000.
        container_name: str, optional
            Name of the `SeismicDataset` attribute to store a dict
            with estimated percentile. Also contains `survey_id_col`
            key and corresponding value.
        kwargs: misc
            Parameters for TDigest objects.

        Raises
        ------
        ValueError : If index is not FieldIndex.
        ValueError : If shot gather with same id is contained in more
                     than one survey.

        Note
        ----
        Dictoinary with estimated percentile can be obtained from pipeline using `D(container_name)`.
        """
        if not isinstance(self.index, FieldIndex):
            raise ValueError("Index must be FieldIndex, not {}".format(type(self.index)))

        private_name = '_' + container_name
        params = getattr(self, private_name, None)
        if params is None:
            surveys = np.unique(self.index.get_df()[survey_id_col])
            delta, k = kwargs.pop('delta', 0.01), kwargs.pop('K', 25)
            params = dict(zip(surveys, [TDigest(delta, k) for _ in surveys]))
            setattr(self, private_name, params)

        for idx in batch.indices:
            surveys_by_fieldrecord = np.unique(batch.index.get_df(index=idx)[survey_id_col])
            if len(surveys_by_fieldrecord) != 1:
                raise ValueError('Field {} represents data from more than one survey!'.format(idx))
            survey = surveys_by_fieldrecord[0]

            pos = batch.index.get_pos(idx)
            sample = np.random.choice(getattr(batch, component)[pos].reshape(-1), size=sample_size)

            params[survey].batch_update(np.absolute(sample))

        statistics = dict([survey, digest.percentile(95)]
                          for survey, digest in params.items() if digest.n > 0)
        statistics['survey_id_col'] = survey_id_col
        setattr(self, container_name, statistics)

File contains seismic dataset. Dataset for seismic data. Finding an optimal parameters for correction of spherical divergence.          Parameters         ----------         component : str             Component with shot gathers.         speed : array             Wave propagation speed depending on the depth.             Speed is measured in milliseconds.         loss : callable             Function to minimize.         indices : array-like, optonal             Which items from dataset to use in parameter estimation.             If `None`, defaults to first element of dataset.         time : array, optional            Trace time values. If `None` defaults to self.meta[src]['samples'].            Time measured in either in samples or in milliseconds.         initial_point : array of 2             Started values for $v_{pow}$ and $t_{pow}$.             If None defaults to $v_{pow}=2$ and $t_{pow}=1$.         method : str, optional, default ```Powell```             Minimization method, see ```scipy.optimize.minimize```.         bounds : sequence, optional             Sequence of (min, max) optimization bounds for each parameter.             If `None` defaults to ((0, 5), (0, 5)).         tslice : slice, optional             Lenght of loaded traces.          Returns         -------             : array             Coefficients for speed and time.          Raises         ------         ValueError : If Index is not FieldIndex.          Note         ----         To save parameters as SeismicDataset attribute use ```save_to=D('attr_name')``` (works only         in pipeline).         If you want to save parameters to pipeline variable use save_to argument with following         syntax: ```save_to=V('variable_name')```. Estimates 95th percentile of absolute values for each seismic survey         in dataset for equalization.          This method utilizes t-digest structure for batch-wise estimation of rank-based statistics,         namely 95th percentile.          Parameters         ----------         batch : SeismicBatch or B() named expression.             Current batch from pipeline.         component : str             Component with shot gathers.         survey_id_col : str             Column in index that indicate names of seismic             surveys from different seasons.         sample_size: int, optional             Number of elements to draw from each shot gather to update             estimates if TDigest. Time for each update grows linearly             with `sample_size`. Default is 10000.         container_name: str, optional             Name of the `SeismicDataset` attribute to store a dict             with estimated percentile. Also contains `survey_id_col`             key and corresponding value.         kwargs: misc             Parameters for TDigest objects.          Raises         ------         ValueError : If index is not FieldIndex.         ValueError : If shot gather with same id is contained in more                      than one survey.          Note         ----         Dictoinary with estimated percentile can be obtained from pipeline using `D(container_name)`.