diff --git a/plio/io/hcube.py b/plio/io/hcube.py
deleted file mode 100644
index 2e45197a532dce96b7df749cbdf848d71b07531b..0000000000000000000000000000000000000000
--- a/plio/io/hcube.py
+++ /dev/null
@@ -1,208 +0,0 @@
-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):
- """
- A Mixin class for use with the io_gdal.GeoDataset class
- 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):
- if not hasattr(self, '_wavelengths'):
- try:
- info = gdal.Info(self.file_name, format='json')
- wavelengths = [float(j) for i, j in sorted(info['metadata'][''].items(),
- key=lambda x: float(x[0].split('_')[-1]))]
- self._original_wavelengths = wavelengths
- self._wavelengths = np.round(wavelengths, self.tolerance)
- except:
- 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)
-
- @tolerance.setter
- def tolerance(self, val):
- if isinstance(val, int):
- self._tolerance = val
- self._reindex()
- else:
- raise TypeError
-
- def _reindex(self):
- if self._original_wavelengths is not None:
- self._wavelengths = np.round(self._original_wavelengths, decimals=self.tolerance)
-
- def __getitem__(self, key):
- i = _iLocIndexer(self)
- return i[key]
-
- @property
- def loc(self):
- return _LocIndexer(self)
-
- @property
- 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
-
- y = key[1]
- x = key[2]
- if isinstance(x, slice):
- xstart = ifnone(x.start,0)
- xstop = ifnone(x.stop,self.raster_size[0])
- xstep = xstop - xstart
- else:
- raise TypeError("Loc style access elements must be slices, e.g., [:] or [10:100]")
- if isinstance(y, slice):
- ystart = ifnone(y.start, 0)
- ystop = ifnone(y.stop, self.raster_size[1])
- ystep = ystop - ystart
- else:
- raise TypeError("Loc style access elements must be slices, e.g., [:] or [10:100]")
-
- pixels = (xstart, ystart, xstep, ystep)
- if isinstance(key[0], (int, np.integer)):
- return self.read_array(band=int(key[0]+1), pixels=pixels)
-
- elif isinstance(key[0], slice):
- # Given some slice iterate over the bands and get the bands and pixel space requested
- 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 = []
- for b in key[0]:
- arrs.append(self.read_array(band=int(b+1), pixels=pixels))
- return np.stack(arrs)
diff --git a/plio/io/io_crism.py b/plio/io/io_crism.py
deleted file mode 100644
index fb841077a02416f400cb9e0460c65f6aa57cbbe5..0000000000000000000000000000000000000000
--- a/plio/io/io_crism.py
+++ /dev/null
@@ -1,61 +0,0 @@
-import os
-import numpy as np
-from .io_gdal import GeoDataset
-from .hcube import HCube
-
-try:
- from libpyhat.derived import crism
- from libpyhat.derived.utils import get_derived_funcs
- libpyhat_enabled = True
-except:
- print('No libpyhat module. Unable to attach derived product functions')
- libpyhat_enabled = False
-
-import gdal
-
-
-class Crism(GeoDataset, HCube):
- """
- An Crism specific reader with the spectral mixin.
- """
- def __init__(self, file_name):
-
- GeoDataset.__init__(self, file_name)
- HCube.__init__(self)
-
- self.derived_funcs = {}
-
- if libpyhat_enabled:
- self.derived_funcs = get_derived_funcs(crism)
-
- def __getattr__(self, name):
- try:
- func = self.derived_funcs[name]
-
- setattr(self, name, func.__get__(self))
- return getattr(self, name)
-
- except KeyError as keyerr:
- raise AttributeError("'Crism' object has no attribute '{}'".format(name)) from None
-
- @property
- def wavelengths(self):
- if not hasattr(self, '_wavelengths'):
- try:
- info = gdal.Info(self.file_name, format='json')
- wv = dict((k,v) for (k,v) in info['metadata'][''].items() if 'Band' in k) # Only get the 'Band_###' keys
- wavelengths = [float(j.split(" ")[0]) for i, j in sorted(wv.items(),
- key=lambda x: int(x[0].split('_')[-1]))]
- self._original_wavelengths = wavelengths
- self._wavelengths = np.round(wavelengths, self.tolerance)
- except:
- self._wavelengths = []
- return self._wavelengths
-
-def open(input_data):
- if os.path.splitext(input_data)[-1] == 'hdr':
- # GDAL wants the img, but many users aim at the .hdr
- input_data = os.path.splitext(input_data)[:-1] + '.img'
- ds = Crism(input_data)
-
- return ds
diff --git a/plio/io/io_moon_minerology_mapper.py b/plio/io/io_moon_minerology_mapper.py
deleted file mode 100644
index 3a4a7a439176f65ff95e175eedae46e10c050d17..0000000000000000000000000000000000000000
--- a/plio/io/io_moon_minerology_mapper.py
+++ /dev/null
@@ -1,67 +0,0 @@
-import os
-import numpy as np
-from .io_gdal import GeoDataset
-from .hcube import HCube
-
-try:
- from libpyhat.derived import m3
- from libpyhat.derived.utils import get_derived_funcs
- libpyhat_enabled = True
-except:
- print('No libpyhat module. Unable to attach derived product functions')
- libpyhat_enabled = False
-
-import gdal
-
-
-class M3(GeoDataset, HCube):
- """
- An M3 specific reader with the spectral mixin.
- """
- def __init__(self, file_name):
-
- GeoDataset.__init__(self, file_name)
- HCube.__init__(self)
-
- self.derived_funcs = {}
-
- if libpyhat_enabled:
- self.derived_funcs = get_derived_funcs(m3)
-
- def __getattr__(self, name):
- try:
- func = self.derived_funcs[name]
-
- setattr(self, name, func.__get__(self))
- return getattr(self, name)
-
- except KeyError as keyerr:
- raise AttributeError("'M3' object has no attribute '{}'".format(name)) from None
-
- @property
- def wavelengths(self):
- 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
- self._wavelengths = np.round(wavelengths, self.tolerance)
- except:
- self._wavelengths = []
- return self._wavelengths
-
-def open(input_data):
- if os.path.splitext(input_data)[-1] == 'hdr':
- # GDAL wants the img, but many users aim at the .hdr
- input_data = os.path.splitext(input_data)[:-1] + '.img'
- ds = M3(input_data)
-
- return ds