Commit d6087ee4 authored by acpaquette's avatar acpaquette Committed by jlaura
Browse files

PyHAT Updates (#87) 

* Small updates to get the scripts working.

* Fixed pradius calculations, and made some small changes.

* Removed coord transforms and made body_fix func more generic.

* Updated reproj doc string.

* General refactor to socet scripts and clean up. Simplfied input for both scripts.

* Updated conf to use conda prefix

* Fixed up __getattr__ func

* Corrected attribute error text

* Uploaded notebooks for remote access

* Updated notebooks with complete footprint function

* More or less final notebook

* Forgot to tab this in under the first except block

* Updated version.

* Removed unnecessary notebooks

* Removed previously removed module

* Removed old import

* Fixes issue indexing on the hcube

* Updated hcube

* Updated io_m3 and io_crism pyhat dependency

* hcube and indexing update to handle clipping and other operations
parent d4f55f50

plio/io/hcube.py

+124 −1
Original line number Diff line number Diff line
@@ -2,6 +2,8 @@ import numpy as np 
import gdal



from ..utils.indexing import _LocIndexer, _iLocIndexer

from libpyhat.transform.continuum import continuum_correction

from libpyhat.transform.continuum import polynomial, linear, regression





class HCube(object):
@@ -10,6 +12,11 @@ class HCube(object): 
    to optionally add support for spectral labels, label

    based indexing, and lazy loading for reads.

    """

    def __init__(self, data = [], wavelengths = []):

        if len(data) != 0:

            self._data = data

        if len(wavelengths) != 0:

            self._wavelengths = wavelengths



    @property

    def wavelengths(self):
@@ -24,6 +31,21 @@ class HCube(object): 
                self._wavelengths = []

        return self._wavelengths



    @property

    def data(self):

        if not hasattr(self, '_data'):

            try:

                key = (slice(None, None, None),

                       slice(None, None, None),

                       slice(None, None, None))

                data = self._read(key)

            except Exception as e:

                print(e)

                data = []

            self._data = data



        return self._data



    @property

    def tolerance(self):

        return getattr(self, '_tolerance', 2)
@@ -52,6 +74,104 @@ class HCube(object): 
    def iloc(self):

        return _iLocIndexer(self)



    def reduce(self, how = np.mean, axis = (1, 2)):

        """

        Parameters

        ----------

        how : function

              Function to apply across along axises of the hcube



        axis : tuple

               List of axis to apply a given function along



        Returns

        -------

        new_hcube : Object

                    A new hcube object with the reduced data set

        """

        res = how(self.data, axis = axis)



        new_hcube = HCube(res, self.wavelengths)

        return new_hcube



    def continuum_correct(self, nodes, correction_nodes = np.array([]), correction = linear,

                          axis=0, adaptive=False, window=3, **kwargs):

        """

        Parameters

        ----------



        nodes : list

                A list of wavelengths for the continuum to be corrected along



        correction_nodes : list

                           A list of nodes to limit the correction between



        correction : function

                     Function specifying the type of correction to perform

                     along the continuum



        axis : int

               Axis to apply the continuum correction on



        adaptive : boolean

                   ?



        window : int

                 ?



        Returns

        -------



        new_hcube : Object

                    A new hcube object with the corrected dataset

        """



        continuum_data = continuum_correction(self.data, self.wavelengths, nodes = nodes,

                                              correction_nodes = correction_nodes, correction = correction,

                                              axis = axis, adaptive = adaptive,

                                              window = window, **kwargs)



        new_hcube = HCube(continuum_data[0], self.wavelengths)

        return new_hcube





    def clip_roi(self, x, y, band, tolerance=2):

        """

        Parameters

        ----------



        x : tuple

            Lower and upper bound along the x axis for clipping



        y : tuple

            Lower and upper bound along the y axis for clipping



        band : tuple

               Lower and upper band along the z axis for clipping



        tolerance : int

                    Tolerance given for trying to find wavelengths

                    between the upper and lower bound



        Returns

        -------



        new_hcube : Object

                    A new hcube object with the clipped dataset

        """

        wavelength_clip = []

        for wavelength in self.wavelengths:

            wavelength_upper = wavelength + tolerance

            wavelength_lower = wavelength - tolerance

            if wavelength_upper > band[0] and wavelength_lower < band[1]:

                wavelength_clip.append(wavelength)



        key = (wavelength_clip, slice(*x), slice(*y))

        data_clip = _LocIndexer(self)[key]



        new_hcube = HCube(np.copy(data_clip), np.array(wavelength_clip))

        return new_hcube



    def _read(self, key):

        ifnone = lambda a, b: b if a is None else a
@@ -76,7 +196,10 @@ class HCube(object): 


        elif isinstance(key[0], slice):

            # Given some slice iterate over the bands and get the bands and pixel space requested

            return [self.read_array(i, pixels = pixels) for i in list(range(1, self.nbands + 1))[key[0]]]

            arrs = []

            for band in list(list(range(1, self.nbands + 1))[key[0]]):

                arrs.append(self.read_array(band, pixels = pixels))

            return np.stack(arrs)



        else:

            arrs = []

plio/io/io_crism.py

+6 −6
Original line number Diff line number Diff line
@@ -4,12 +4,12 @@ from .io_gdal import GeoDataset 
from .hcube import HCube



try:

    from libpysat.derived import crism

    from libpysat.derived.utils import get_derived_funcs

    libpysat_enabled = True

    from libpyhat.derived import crism

    from libpyhat.derived.utils import get_derived_funcs

    libpyhat_enabled = True

except:

    print('No libpysat module. Unable to attach derived product functions')

    libpysat_enabled = False

    print('No libpyhat module. Unable to attach derived product functions')

    libpyhat_enabled = False



import gdal
@@ -25,7 +25,7 @@ class Crism(GeoDataset, HCube): 


        self.derived_funcs = {}



        if libpysat_enabled:

        if libpyhat_enabled:

            self.derived_funcs = get_derived_funcs(crism)



    def __getattr__(self, name):

plio/io/io_moon_minerology_mapper.py

+6 −6
Original line number Diff line number Diff line
@@ -4,12 +4,12 @@ from .io_gdal import GeoDataset 
from .hcube import HCube



try:

    from libpysat.derived import m3

    from libpysat.derived.utils import get_derived_funcs

    libpysat_enabled = True

    from libpyhat.derived import m3

    from libpyhat.derived.utils import get_derived_funcs

    libpyhat_enabled = True

except:

    print('No libpysat module. Unable to attach derived product functions')

    libpysat_enabled = False

    print('No libpyhat module. Unable to attach derived product functions')

    libpyhat_enabled = False



import gdal
@@ -25,7 +25,7 @@ class M3(GeoDataset, HCube): 


        self.derived_funcs = {}



        if libpysat_enabled:

        if libpyhat_enabled:

            self.derived_funcs = get_derived_funcs(m3)



    def __getattr__(self, name):

plio/utils/indexing.py

+19 −9
Original line number Diff line number Diff line
@@ -42,13 +42,19 @@ class _LocIndexer(object): 
        sl = key[0]

        ifnone = lambda a, b: b if a is None else a

        if isinstance(sl, slice):

            sl = list(range(ifnone(sl.start, 0), self.data_array.nbands, ifnone(sl.step, 1)))

            sl = list(range(ifnone(sl.start, 0),

                            ifnone(sl.stop, len(self.data_array.wavelengths)),

                            ifnone(sl.step, 1)))



        if isinstance(sl, (int, float)):

            idx = self._get_idx(sl)

        else:

            idx = [self._get_idx(s) for s in sl]

        key = (idx, key[1], key[2])



        if len(self.data_array.data) != 0:

            return self.data_array.data[key]



        return self.data_array._read(key)



    def _get_idx(self, value, tolerance=2):
@@ -69,8 +75,12 @@ class _iLocIndexer(object): 
        ifnone = lambda a, b: b if a is None else a

        if isinstance(sl, slice):

            sl = list(range(ifnone(sl.start, 0),

                            ifnone(sl.stop, self.data_array.nbands),

                            ifnone(sl.stop, len(self.data_array.wavelengths)),

                            ifnone(sl.step, 1)))



        key = (key[0], key[1], key[2])



        if len(self.data_array.data) != 0:

            return self.data_array.data[key]



        return self.data_array._read(key)