Refine NED2Subregion
-flow
-messages
-DRY and readability
Changed NED2Subregion to accept zipped NED tiles

When not doing this in a huge batch, NED tiles usually stored compressed because they take up a lot of space.
If you want to do just a few subregions, this tool will unzip only the ones you need.
If you're doing them all at once, you'll unzip everything and leave the box unchecked but that should be in the documentation.
Done testing NED2Subregion with and without missing NED tiles
Added tool parameter descriptions and time trial results
Major overhaul of PreHPCC.py to improve speed, reliability, modularity. Added test wrapper, test_tools.py.

Major problems were
*write time bottleneck due to repeated large file writing to disk
*inclusion of entire HU4 in HU8 clip processing (poor filter)
*processing of HU8s not within the selected subregion producing sliver files that were 99% NoData and sucked up disk space
*unpredictable crashing at a few points
*considerable user time spent re-running tool through entirety even if one long operation was complete (mosaic) or trying to manage stages of failure

Some solutions and refactoring:
-Added parameters to allow user input of subregion mosaic, burned mosaic to reduce re-processing time in case of failure. really, this should probably be 3 tools, not one, but these changes mitigate the problem.
-Refactored code for readability
-Reduced unnecessary calls to tools for clip, project, copy feature by relying on environment settings to handle these during other calls (e.g. env.outputCoordinateSystem, env.resample, env.extent)
-Added cleanup function to cisutils that safely deletes a list of intermediate objects
-Added pyramid creation to make checking outputs easier as invalid output is easily visually detected and major impedence later
-Moved raster calculator operations into single line, in memory, to avoid writing GBs of data repeatedly for intermediates
-Compressed intermediate rasters for faster writing--those sent to TauDEM left uncompressed

Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
-Added parameters to PreHPCC toolbox along with item descriptions

Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
Corrections to burning formula in PreHPCC, added test results
Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
-Changed WallsHU8 to select *this* HU8 based on its id code, rather than spatial overlap with certain water features inside
-tool testing continues up through TauDEM to ESRI flow direction

Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
Merge branch 'master' of https://github.com/stopyaks/CSI.git into compressed_changes

Conflicts:
	CSI_Limnology_Toolbox/CSI Limnology Tools.tbx
Updated Generate Seeds
-made selection clause more clear/less verbose using IN
-changed projection management to use environment settings rather than explicit projection tools
-readability/DRY (declare filename variables, then use variable rather than name string twice)
WallsHU8 fixed so this run doesn't inherit previous extent
names fixed (off by one char) in TauDEM to ESRI Flow Dir script
Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
Added 3 new utility tools
Added suffix to % Ha in poly, Added ZS for many ...
Changed handling of zipped file checkbox to deal with boolean correctly
Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
Added support for overlapping polygons in multiple tools
--Added "Subset Overlapping Polygons" tool that uses graph coloring algorithm to break up a feature class with overlapping polygons into mutiple feature classes, each of which has no overlaps
--Changed tool for regular zonal stats and tab area (features with no overlaps to begin with)
--Added tool to run zonal stats/tab area on the results of "Subset Overlapping Polygons", these two tools together will produce one output table
--Removed Scott's zonal stats and tab area from tools in box for time being

Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
Modified line density tool and added "Line Density for Non Overlapping Subsets"

--Drafted tools but they are untested
Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
-Repaired Line Density for Non Overlapping Subsets

Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
-Fixed output table error, tool should complete now, test is still running
Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
-Refactored line density tool to produce ONLY output table as result, intermediates in memory
-Updated multi_line_density to work with new line density tool

Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>
-Added input spatial reference check to line density

Signed-off-by: nicolejeansmith <nicole.j.smith@gmail.com>