Add support for USGS spectral library (#109)

Add support for USGS spectral library

Author: kormang

.gitignore

@@ -7,3 +7,4 @@ build/
 TAGS
 .project
 .pydevproject
+spectral_test_files/

setup.py

@@ -32,9 +32,10 @@
       packages=['spectral', 'spectral.algorithms', 'spectral.database',
                 'spectral.graphics', 'spectral.io', 'spectral.tests',
                 'spectral.tests.data', 'spectral.tests.data.ecostress',
-                'spectral.utilities'],
+                'spectral.tests.data.usgs', 'spectral.utilities'],
       package_data={'spectral.tests.data': ['*.spc'],
-                    'spectral.tests.data.ecostress': ['*.txt']},
+                    'spectral.tests.data.ecostress': ['*.txt'],
+                    'spectral.tests.data.usgs': ['*.txt']},
       platforms=['Platform-Independent'],
       install_requires=['numpy'],
       classifiers=['Development Status :: 4 - Beta',

spectral/database/__init__.py

@@ -2,3 +2,4 @@
 
 from .aster import AsterDatabase
 from .ecostress import EcostressDatabase
+from .usgs import USGSDatabase

spectral/database/aster.py

@@ -6,6 +6,8 @@
 
 from spectral.utilities.python23 import IS_PYTHON3, tobytes, frombytes
 
+from .spectral_database import SpectralDatabase
+
 if IS_PYTHON3:
     readline = lambda fin: fin.readline()
     open_file = lambda filename: open(filename, encoding='iso-8859-1')
@@ -132,7 +134,7 @@ def read_aster_file(filename):
     return s
 
 
-class AsterDatabase:
+class AsterDatabase(SpectralDatabase):
     '''A relational database to manage ASTER spectral library data.'''
     schemas = table_schemas
 
@@ -307,12 +309,6 @@ class Sig:
 
         return sigs
 
-    def _connect(self, sqlite_filename):
-        '''Establishes a connection to the Specbase sqlite database.'''
-        import sqlite3
-        self.db = sqlite3.connect(sqlite_filename)
-        self.cursor = self.db.cursor()
-
     def get_spectrum(self, spectrumID):
         '''Returns a spectrum from the database.
 
@@ -406,76 +402,6 @@ def get_signature(self, spectrumID):
         sig.y = list(y)
         return sig
 
-    def query(self, sql, args=None):
-        '''Returns the result of an arbitrary SQL statement.
-
-        Arguments:
-
-            `sql` (str):
-
-                An SQL statement to be passed to the database. Use "?" for
-                variables passed into the statement.
-
-            `args` (tuple):
-
-                Optional arguments which will replace the "?" placeholders in
-                the `sql` argument.
-
-        Returns:
-
-            An :class:`sqlite3.Cursor` object with the query results.
-
-        Example::
-
-            >>> sql = r'SELECT SpectrumID, Name FROM Samples, Spectra ' +
-            ...        'WHERE Spectra.SampleID = Samples.SampleID ' +
-            ...        'AND Name LIKE "%grass%" AND MinWavelength < ?'
-            >>> args = (0.5,)
-            >>> cur = db.query(sql, args)
-            >>> for row in cur:
-            ...     print row
-            ...
-            (356, u'dry grass')
-            (357, u'grass')
-        '''
-        if args:
-            return self.cursor.execute(sql, args)
-        else:
-            return self.cursor.execute(sql)
-
-    def print_query(self, sql, args=None):
-        '''Prints the text result of an arbitrary SQL statement.
-
-        Arguments:
-
-            `sql` (str):
-
-                An SQL statement to be passed to the database. Use "?" for
-                variables passed into the statement.
-
-            `args` (tuple):
-
-                Optional arguments which will replace the "?" placeholders in
-                the `sql` argument.
-
-        This function performs the same query function as
-        :meth:`spectral.database.Asterdatabase.query` except query results are
-        printed to **stdout** instead of returning a cursor object.
-
-        Example:
-
-            >>> sql = r'SELECT SpectrumID, Name FROM Samples, Spectra ' +
-            ...        'WHERE Spectra.SampleID = Samples.SampleID ' +
-            ...        'AND Name LIKE "%grass%" AND MinWavelength < ?'
-            >>> args = (0.5,)
-            >>> db.print_query(sql, args)
-            356|dry grass
-            357|grass
-        '''
-        ret = self.query(sql, args)
-        for row in ret:
-            print("|".join([str(x) for x in row]))
-
     def create_envi_spectral_library(self, spectrumIDs, bandInfo):
         '''Creates an ENVI-formatted spectral library for a list of spectra.
 

spectral/database/spectral_database.py

@@ -0,0 +1,79 @@
+
+
+class SpectralDatabase:
+    def _connect(self, sqlite_filename):
+        '''Establishes a connection to the Specbase sqlite database.'''
+        import sqlite3
+        self.db = sqlite3.connect(sqlite_filename)
+        self.cursor = self.db.cursor()
+
+    def query(self, sql, args=None):
+        '''Returns the result of an arbitrary SQL statement.
+
+        Arguments:
+
+            `sql` (str):
+
+                An SQL statement to be passed to the database. Use "?" for
+                variables passed into the statement.
+
+            `args` (tuple):
+
+                Optional arguments which will replace the "?" placeholders in
+                the `sql` argument.
+
+        Returns:
+
+            An :class:`sqlite3.Cursor` object with the query results.
+
+        Example::
+
+            >>> sql = r'SELECT SpectrumID, Name FROM Samples, Spectra ' +
+            ...        'WHERE Spectra.SampleID = Samples.SampleID ' +
+            ...        'AND Name LIKE "%grass%" AND MinWavelength < ?'
+            >>> args = (0.5,)
+            >>> cur = db.query(sql, args)
+            >>> for row in cur:
+            ...     print row
+            ...
+            (356, u'dry grass')
+            (357, u'grass')
+        '''
+        if args:
+            return self.cursor.execute(sql, args)
+        else:
+            return self.cursor.execute(sql)
+
+    def print_query(self, sql, args=None):
+        '''Prints the text result of an arbitrary SQL statement.
+
+        Arguments:
+
+            `sql` (str):
+
+                An SQL statement to be passed to the database. Use "?" for
+                variables passed into the statement.
+
+            `args` (tuple):
+
+                Optional arguments which will replace the "?" placeholders in
+                the `sql` argument.
+
+        This function performs the same query function as
+        :meth:`spectral.database.SpectralDatabase.query` except query results are
+        printed to **stdout** instead of returning a cursor object.
+
+        Example:
+
+            >>> sql = r'SELECT SpectrumID, Name FROM Samples, Spectra ' +
+            ...        'WHERE Spectra.SampleID = Samples.SampleID ' +
+            ...        'AND Name LIKE "%grass%" AND MinWavelength < ?'
+            >>> args = (0.5,)
+            >>> db.print_query(sql, args)
+            356|dry grass
+            357|grass
+        '''
+        ret = self.query(sql, args)
+        for row in ret:
+            print("|".join([str(x) for x in row]))
+