Commit 8e4a0856 authored by jlaura's avatar jlaura Committed by GitHub
Browse files

Updates Indexing Issues (#34) 

* Makes gdal an optional dependency

* Refactors all bae I/O into a single namespace.

* typos

* Fixes the gdal dependency test

* Adds tests for the JSON

* Tests fail without test data

* Updates for comments from @thareUSGS

* Adds ISIS3 V2 ControlNetwork Reader

* Adds hcube mixin object

* Updates to support tif M3, and fixes indexing issues
parent 7353260b

plio/io/hcube.py

+12 −7
Original line number Diff line number Diff line 
import numpy as np

import gdal



from ..utils.indexing import _LocIndexer, _iLocIndexer





class HCube(object):

    """

    A Mixin class for use with the io_gdal.GeoDataset class
@@ -27,7 +30,6 @@ class HCube(object): 
    

    @tolerance.setter

    def tolerance(self, val):

        wv = self.wavelengths

        if isinstance(val, int):

            self._tolerance = val

            self._reindex()
@@ -39,7 +41,8 @@ class HCube(object): 
            self._wavelengths = np.round(self._original_wavelengths, decimals=self.tolerance)



    def __getitem__(self, key):

        return _iLocIndexer(self)

        i = _iLocIndexer(self)

        return i[key]

    

    @property

    def loc(self):
@@ -54,7 +57,6 @@ class HCube(object): 


        y = key[1]

        x = key[2]

        

        if isinstance(x, slice):

            xstart = ifnone(x.start,0)

            xstop = ifnone(x.stop,self.raster_size[0])
@@ -68,7 +70,10 @@ class HCube(object): 
        else:

            raise TypeError("Loc style access elements must be slices, e.g., [:] or [10:100]")

            

        pixels = (xstart, ystart, xstop, ystop)

        pixels = (xstart, ystart, xstep, ystep)

        if isinstance(key[0], (int, np.integer)):

            return self.read_array(band=int(key[0]+1), pixels=pixels)

        else:

            arrs = []

            for b in key[0]:

                arrs.append(self.read_array(band=int(b+1), pixels=pixels))

plio/io/io_moon_minerology_mapper.py

+9 −2
Original line number Diff line number Diff line
@@ -14,6 +14,13 @@ class M3(GeoDataset, HCube): 
        if not hasattr(self, '_wavelengths'):

            try:

                info = gdal.Info(self.file_name, format='json')

                if 'Resize' in info['metadata']['']['Band_1']:

                    wavelengths = [float(j.split(' ')[-1].replace('(','').replace(')', '')) for\

                                  i,j in sorted(info['metadata'][''].items(),

                                  key=lambda x: float(x[0].split('_')[-1]))]

                    # This is a geotiff translated from the PDS IMG

                else:

                    # This is a PDS IMG

                    wavelengths = [float(j) for i, j in sorted(info['metadata'][''].items(),

                                    key=lambda x: float(x[0].split('_')[-1]))]

                self._original_wavelengths = wavelengths

plio/utils/indexing.py

+7 −4
Original line number Diff line number Diff line
@@ -44,6 +44,9 @@ class _LocIndexer(object): 
        if isinstance(sl, slice):

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

        return self.data_array._read(key)
@@ -52,7 +55,7 @@ class _LocIndexer(object): 
        vals = np.abs(self.data_array.wavelengths-value)

        minidx = np.argmin(vals)

        if vals[minidx] >= tolerance:

            warning.warn("Absolute difference between requested value and found values is {}".format(vals[minidx]))

            warnings.warn("Absolute difference between requested value and found values is {}".format(vals[minidx]))

        return minidx

    

class _iLocIndexer(object):