Created tests for USGS Spectral Library Version 7 convert function (#146

) * splib07 * spectral 7 converter start * Splib 07 test one file * Finished Spectral Version 7 convert * Finish client changes to spectral convert function * Condensed to one script * Fix oswalk and other changes * Remove duplicate spectra * remove aster files * Remove duplicate spectra * Change to unknown * Fix spelling * Move convert function to mineral.py * Fix band num * Fix reload error travis ci * update reload to py3 * remove unused import * fix mineral import * remove sys path import * removed bad import statements * Change spectra names to v7 * Worked on testing * Allow cli to work with spectral v7 and v6 * Fix ftp url * Remove ftp calls, fix overwrite error in nosetests * Remove Spectral 7 library * Repush with gitignore updated
capstone-coal · May 8, 2018 · 2c59bac · 2c59bac
1 parent 2e9c882
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diff --git a/Dockerfile b/Dockerfile
@@ -15,7 +15,7 @@
 # Floor, Boston, MA 02110-1301, USA.
 
 # Use an official Python runtime as a base image (host debian:jessie)
-FROM python:3-slim
+FROM python:3.6-slim
 
 MAINTAINER COAL Developers <[email protected]>
 

diff --git a/examples/example07_mineral.py b/examples/example07_mineral.py
@@ -0,0 +1,164 @@
+# Copyright (C) 2017-2018 COAL Developers
+#
+# This program is free software; you can redistribute it and/or 
+# modify it under the terms of the GNU General Public License 
+# as published by the Free Software Foundation; version 2.
+#
+# This program is distributed in the hope that it will be useful, 
+# but WITHOUT ANY WARRANTY; without even the implied warranty 
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public 
+# License along with this program; if not, write to the Free 
+# Software Foundation, Inc., 51 Franklin Street, Fifth 
+# Floor, Boston, MA 02110-1301, USA.
+# encoding: utf-8
+
+'''
+example_mineral -- an example script which demonstrates COAL mineral classification
+
+example_mineral provides a CLI which demonstrates how the COAL Mineral Classification 
+API provides methods for generating visible-light and mineral classified images. 
+Mineral classification can take hours to days depending on the size of the spectral 
+library and the available computing resources, so running a script in the background 
+is recommended. More reading an this example can be seen at 
+https://capstone-coal.github.io/docs#usage
+
+@author:     COAL Developers
+
+@copyright:  Copyright (C) 2017-2018 COAL Developers
+
+@license:    GNU General Public License version 2
+
+@contact:    [email protected]
+'''
+
+import sys
+import os
+from sys import path
+from os import getcwd
+import inspect
+
+from argparse import ArgumentParser
+from argparse import RawDescriptionHelpFormatter
+
+import logging
+
+import sys
+import os
+import pycoal
+sys.path.insert(0, '../pycoal')
+import mineral
+import mining
+import environment
+
+__all__ = []
+
+DEBUG = 1
+TESTRUN = 0
+PROFILE = 0
+
+
+input_filename = 'avng.jpl.nasa.gov/AVNG_2015_data_distribution/L2/ang20150420t182050_rfl_v1e/ang20150420t182050_corr_v1e_img.hdr'
+library_filename='../pycoal/tests/s07_AV95_envi.hdr'
+
+def run_mineral(input_filename, library_filename):
+    '''
+    ...
+    '''
+    logging.info("Starting mineral classification with input file '%s' and spectral library '%s'." %(input_filename, library_filename))
+    # path to save RGB image
+    rgb_filename = "ang20150420t182050_corr_v1e_img_rgb.hdr"
+
+    # path to save mineral classified image
+    classified_filename = "ang20150420t182050_corr_v1e_img_class.hdr"
+
+    # create a new mineral classification instance
+    mineral_classification = mineral.MineralClassification(library_filename)
+
+    # generate a georeferenced visible-light image
+    mineral_classification.to_rgb(input_filename, rgb_filename)
+
+    # generate a mineral classified image
+    mineral_classification.classify_image(input_filename, classified_filename)
+
+def main(argv=None):
+    '''Command line options.'''
+    logging.basicConfig(filename='pycoal.log',level=logging.INFO, format='%(asctime)s %(message)s')
+    if argv is None:
+        argv = sys.argv
+    else:
+        sys.argv.extend(argv)
+
+    program_name = os.path.basename(sys.argv[0])
+    program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
+    program_license = '''%s
+
+  VERSION %s
+
+  Copyright (C) 2017-2018 COAL Developers
+
+  This program is free software; you can redistribute it and/or 
+  modify it under the terms of the GNU General Public License 
+  as published by the Free Software Foundation; version 2.
+
+  This program is distributed in the hope that it will be useful, 
+  but WITHOUT ANY WARRANTY; without even the implied warranty 
+  of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+  See the GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public 
+  License along with this program; if not, write to the Free 
+  Software Foundation, Inc., 51 Franklin Street, Fifth 
+  Floor, Boston, MA 02110-1301, USA.
+
+USAGE
+''' % (program_shortdesc, pycoal.version)
+
+    try:
+        # Setup argument parser
+        parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter)
+        parser.add_argument("-i", "--image", dest="image", default=input_filename, help="Input file to be processed [default: ang20150420t182050_corr_v1e_img.hdr]")
+        parser.add_argument("-s", "--slib", dest="slib", default=library_filename, help="Spectral Library filename [default: s07_AV95_envi.hdr]")
+
+        # Process arguments
+        args = parser.parse_args(['-i', input_filename, '-s', library_filename])
+        #args = parser.parse_args()
+
+        image = args.image
+        slib = args.slib
+
+        run_mineral(image, slib)
+
+    except KeyboardInterrupt:
+        ### handle keyboard interrupt ###
+        return 0
+    except Exception as e:
+        if DEBUG or TESTRUN:
+            raise e
+        indent = len(program_name) * " "
+        sys.stderr.write(program_name + ": " + repr(e) + "\n")
+        sys.stderr.write(indent + "  for help use --help")
+        return 2
+
+if __name__ == "__main__":
+    if DEBUG:
+        sys.argv.append("-h")
+        sys.argv.append("-v")
+        sys.argv.append("-r")
+    if TESTRUN:
+        import doctest
+        doctest.testmod()
+    if PROFILE:
+        import cProfile
+        import pstats
+        profile_filename = 'example_mineral_profile.txt'
+        cProfile.run('main()', profile_filename)
+        statsfile = open("profile_stats.txt", "wb")
+        p = pstats.Stats(profile_filename, stream=statsfile)
+        stats = p.strip_dirs().sort_stats('cumulative')
+        stats.print_stats()
+        statsfile.close()
+        sys.exit(0)
+    sys.exit(main())
diff --git a/examples/example_mining.py b/examples/example_mining.py
@@ -52,7 +52,7 @@
 TESTRUN = 0
 PROFILE = 0
 
-def run_mining(mineral_filename="ang20150420t182050_corr_v1e_img_class.hdr", mining_filename="ang20150420t182050_corr_v1e_img_class_mining.hdr"):
+def run_mining(mineral_filename="ang20150420t182050_corr_v1e_img_class.hdr", mining_filename="ang20150420t182050_corr_v1e_img_class_mining.hdr",spectral_version="6"):
     '''
     ...
     '''
@@ -61,12 +61,15 @@ def run_mining(mineral_filename="ang20150420t182050_corr_v1e_img_class.hdr", min
 
     # path to save mining classified image
     mining_filename = "ang20150420t182050_corr_v1e_img_class_mining.hdr"
+
+    #Spectral Library Verison Number, Change to 7 if you want to use USGS Spectral Library Version 7
+    spectral_version = "6"
 
     # create a new mining classification instance
     mining_classification = mining.MiningClassification()
 
     # generate a mining classified image
-    mining_classification.classify_image(mineral_filename, mining_filename)
+    mining_classification.classify_image(mineral_filename, mining_filename,spectral_version)
 
 def main(argv=None): # IGNORE:C0111
     '''Command line options.'''
@@ -106,15 +109,17 @@ def main(argv=None): # IGNORE:C0111
         parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter)
         parser.add_argument("-mi", "--mineral_input", dest="input", default='ang20150420t182050_corr_v1e_img_class.hdr', help="Input classified mineral file to be processed [default: ang20150420t182050_corr_v1e_img_class.hdr]")
         parser.add_argument("-mo", "--mining_output", dest="output", default='ang20150420t182050_corr_v1e_img_class_mining.hdr', help="Output mining classified image filename [default: ang20150420t182050_corr_v1e_img_class_mining.hdr]")
+        parser.add_argument("-v", "--spectral_version", dest="spectral_version", default='6', help="USGS Spectral Library Version Number")
 
         # Process arguments
-        args = parser.parse_args(['-mi', 'ang20150420t182050_corr_v1e_img_class.hdr', '-mo', 'ang20150420t182050_corr_v1e_img_class_mining.hdr'])
+        args = parser.parse_args(['-mi', 'ang20150420t182050_corr_v1e_img_class.hdr', '-mo', 'ang20150420t182050_corr_v1e_img_class_mining.hdr', '-v', '6'])
         #args = parser.parse_args()
 
         mineral_filename = args.input
         mining_filename = args.output
+        spectral_version = args.spectral_version
 
-        run_mining(mineral_filename, mining_filename)
+        run_mining(mineral_filename, mining_filename, spectral_version)
     except KeyboardInterrupt:
         ### handle keyboard interrupt ###
         return 0
@@ -145,4 +150,4 @@ def main(argv=None): # IGNORE:C0111
         stats.print_stats()
         statsfile.close()
         sys.exit(0)
-    sys.exit(main())
+    sys.exit(main())
diff --git a/examples/example_spectral07.py b/examples/example_spectral07.py
@@ -0,0 +1,46 @@
+#!/usr/bin/python
+#Copyright (C) 2017-2018 COAL Developers
+#
+# This program is free software; you can redistribute it and/or 
+# modify it under the terms of the GNU General Public License 
+# as published by the Free Software Foundation; version 2.
+#
+# This program is distributed in the hope that it will be useful, 
+# but WITHOUT ANY WARRANTY; without even the implied warranty 
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public 
+# License along with this program; if not, write to the Free 
+# Software Foundation, Inc., 51 Franklin Street, Fifth 
+# Floor, Boston, MA 02110-1301, USA.
+# encoding: utf-8
+
+'''
+example_spectral07.py -- a script which will generate envi .sli and .hdr convolved library
+files of `USGS Spectral Library Version 7 <https://speclab.cr.usgs.gov/spectral-lib.html>`_
+
+Dependencies
+`USGS Spectral Library Version 7 <https://speclab.cr.usgs.gov/spectral-lib.html>`_
+must be downloaded and unzipped to the examples directory
+
+All files generated will be located in the examples directory
+
+
+@author:     COAL Developers
+
+@copyright:  2017-2018 COAL Developers. All rights reserved.
+
+@license:    GNU General Public License version 2
+
+@contact:    [email protected]
+'''
+
+import os
+import sys
+import pycoal
+sys.path.insert(0, '../pycoal')
+import mineral
+
+usgs_convolved = mineral.FullSpectralLibrary7Convert()
+usgs_convolved.convert('usgs_splib07')
diff --git a/pycoal/cli/mining.py b/pycoal/cli/mining.py
@@ -42,18 +42,20 @@ def main(argv=None):  # IGNORE:C0111
     parser = ArgumentParser(description=program_description,formatter_class=RawDescriptionHelpFormatter)
     parser.add_argument("-mi", "--mineral_input", dest="input", help="Input classified mineral file to be processed")
     parser.add_argument("-mo", "--mining_output", dest="output", help="Output mining classified image filename")
+    parser.add_argument("-v", "--spectral_version", dest="spectral_version", help="USGS Spectral Library Version Number (6 or 7)")
 
     # Process arguments
     args = parser.parse_args()
 
     mineral_filename = args.input
     mining_filename = args.output
+    spectral_version = args.spectral_version
 
     # create a new mining classification instance
     mining_classification = MiningClassification()
 
     # generate a mining classified image
-    mining_classification.classify_image(mineral_filename, mining_filename)
+    mining_classification.classify_image(mineral_filename, mining_filename, spectral_version)
 
 
 if __name__ == '__main__':