Remove dependency on scipy, numexpr

There were some hidden dependencies on scipy.ndimage and numexpr which
were not recorded in the documentation. This update removes those
dependencies, and replaces the calculation of the slope and aspect with
only numpy functions, based on numpy version 1.6 (which is the standard
packaged with ArcGIS 10.2).

Because of the way that the scipy.ndimage functions calculated the slope
(giving a slightly smoothed result), it was necessary to update the test
data sets. We chose this route to avoid the requirement of essentially
duplicating the scipy.ndimage.convolve2d code, using only Numpy.

Modifications were also made to the way the slope is calculated for cells
adjacent to nodata values. The updated approach gives a better
representation of the slope in these areas that is of a similar scale to
the neighbouring values.

Author: wcarthur

docs/install.rst

@@ -22,8 +22,11 @@ For detailed instructions on installation of these dependencies, please see the
 
 * `Python <https://www.python.org/>`_ - v2.7 preferred
 * `Numpy <http://www.numpy.org/>`_ - v1.6.2 preferred
+* `Nose <http://nose.readthedocs.io/en/latest/index.html>`_
 * `Arcpy in ArcGIS 10.2 <http://resources.arcgis.com/en/help/main/10.2/index.html#//000v000000v7000000/>`_
 
+.. note:: ArcGIS 10.2 is packaged with a modified version of `Numpy`. In our experience, attempting to update the `Numpy` package will cause the `arcpy` library to fail catastrophically, and usually without reporting any error message. We recommend not trying to upgrade the version of `Numpy` linked to your `ArcGIS` installation.
+
 Setting the environment 
 ----------------------- 
 To enable BAL toolbox to run flawlessly, you may need to change some environment settings. The important variable to set is the ``PYTHONPATH`` variable. This should be set to the path where you have extracted the contents of the zip file. A complete discussion on environment variables in Python is given in the `Python documentation <https://docs.python.org/2/using/cmdline.html#environment-variables>`_. 
@@ -35,7 +38,7 @@ The Python documentation contains some simple instructions for setting environme
 Testing the installation
 ------------------------
 
-The code includes a suite of unit tests that ensure elements of the code base work as expected. The code should be tested before running the toolbox.
+The code includes a suite of unit tests that ensure elements of the code base work as expected. The code should be tested before running the toolbox. Users will need to install the `Nose <http://nose.readthedocs.io/en/latest/index.html>`_ package to run these tests.
 
 The test suite can be run from the main directory. On Windows, run the ``run_test_all.cmd`` script from the main BAL directory. 
 

examples/input/info/arc.dir

@@ -11,17 +11,17 @@
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+      <MDI key="STATISTICS_COVARIANCES">451.439340329464</MDI>
       <MDI key="STATISTICS_MINIMUM">12.5</MDI>
       <MDI key="STATISTICS_MAXIMUM">100</MDI>
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+      <MDI key="STATISTICS_MEAN">30.065875998121</MDI>
       <MDI key="STATISTICS_MEDIAN">0</MDI>
       <MDI key="STATISTICS_MODE">0</MDI>
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+      <MDI key="STATISTICS_STDDEV">21.24710192778</MDI>
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       <MDI key="STATISTICS_SKIPFACTORY">1</MDI>
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examples/output/bal_e.img

@@ -1,2 +1,2 @@
 <?xml version="1.0" encoding="UTF-8"?>
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+<metadata xml:lang="en"><Esri><CreaDate>20170508</CreaDate><CreaTime>14473700</CreaTime><ArcGISFormat>1.0</ArcGISFormat><ArcGISstyle>ANZLIC</ArcGISstyle><SyncOnce>TRUE</SyncOnce><DataProperties><lineage><Process ToolSource="c:\program files (x86)\arcgis\desktop10.2\ArcToolbox\Toolboxes\Data Management Tools.tbx\DefineProjection" Date="20170508" Time="144737">DefineProjection bal_e.img PROJCS['GDA_1994_MGA_Zone_50',GEOGCS['GCS_GDA_1994',DATUM['D_GDA_1994',SPHEROID['GRS_1980',6378137.0,298.257222101]],PRIMEM['Greenwich',0.0],UNIT['Degree',0.0174532925199433]],PROJECTION['Transverse_Mercator'],PARAMETER['False_Easting',500000.0],PARAMETER['False_Northing',10000000.0],PARAMETER['Central_Meridian',117.0],PARAMETER['Scale_Factor',0.9996],PARAMETER['Latitude_Of_Origin',0.0],UNIT['Meter',1.0]]</Process></lineage></DataProperties></Esri></metadata>

examples/output/bal_e.img.aux.xml

@@ -11,17 +11,17 @@
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         <IncludeOutOfRange>1</IncludeOutOfRange>
         <Approximate>0</Approximate>
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examples/output/bal_e.img.xml

@@ -1,2 +1,2 @@
 <?xml version="1.0" encoding="UTF-8"?>
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+<metadata xml:lang="en"><Esri><CreaDate>20170508</CreaDate><CreaTime>14474200</CreaTime><ArcGISFormat>1.0</ArcGISFormat><ArcGISstyle>ANZLIC</ArcGISstyle><SyncOnce>TRUE</SyncOnce><DataProperties><lineage><Process ToolSource="c:\program files (x86)\arcgis\desktop10.2\ArcToolbox\Toolboxes\Data Management Tools.tbx\DefineProjection" Date="20170508" Time="144742">DefineProjection bal_max.img PROJCS['GDA_1994_MGA_Zone_50',GEOGCS['GCS_GDA_1994',DATUM['D_GDA_1994',SPHEROID['GRS_1980',6378137.0,298.257222101]],PRIMEM['Greenwich',0.0],UNIT['Degree',0.0174532925199433]],PROJECTION['Transverse_Mercator'],PARAMETER['False_Easting',500000.0],PARAMETER['False_Northing',10000000.0],PARAMETER['Central_Meridian',117.0],PARAMETER['Scale_Factor',0.9996],PARAMETER['Latitude_Of_Origin',0.0],UNIT['Meter',1.0]]</Process></lineage></DataProperties></Esri></metadata>