Adding test for KrausPfeifer1998, fixing .classify for same. Closes

#62
brycefrank · Oct 12, 2019 · b6b6ef0 · b6b6ef0
1 parent 4963445
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Showing 10 changed files with 188 additions and 22 deletions.
diff --git a/.gitignore b/.gitignore
@@ -20,20 +20,9 @@ changelog_0.2.1.md
 pyfortest/temp.*
 /.idea
 /.vs
-/docs/api/setup.rst
-/docs/api/pyfortest.test_pyfor.rst
-/docs/api/pyfortest.test_collection.rst
-/docs/api/pyfortest.rst
-/docs/html/.doctrees/advanced
-/docs/html/.doctrees/api
-/docs/html/.doctrees/topics
-/docs/html/.doctrees
-/docs/html/api/pyfortest.html
-/docs/html/api/pyfortest.test_collection.html
-/docs/html/api/pyfortest.test_pyfor.html
-/docs/html/api/setup.html
-/docs/html/_sources
-/docs/html/_static
-/pyfortest/__pycache__
-/__pycache__
+/environment.yml~
+/CHANGELOG.md~
+/README.md~
+/.environment.yml.un~
+/.CHANGELOG.md.un~
 /temp_tif.tif
diff --git a/README.md b/README.md
@@ -16,11 +16,11 @@ memory optimized API for managing large collections of tiles.
 
 ## Release Status
 
-Current Release: 0.3.5
+Current Release: 0.3.6
 
-Release Date: September 9, 2019
+Release Date: []
 
-Release Status: 0.3.5 is an adolescent LiDAR data processing package adequate for single tile processing and large acqusitions.
+Release Status: 0.3.6 is an adolescent LiDAR data processing package adequate for single tile processing and large acqusitions.
 
 ## What Does pyfor Do?
 

diff --git a/pyfor.pyproj b/pyfor.pyproj
@@ -0,0 +1,128 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003" DefaultTargets="Build">
+  <PropertyGroup>
+    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+    <SchemaVersion>2.0</SchemaVersion>
+    <ProjectGuid>{aa3e2147-3c18-4aa6-9a18-4dd5b1504264}</ProjectGuid>
+    <ProjectHome />
+    <StartupFile>setup.py</StartupFile>
+    <SearchPath />
+    <WorkingDirectory>.</WorkingDirectory>
+    <OutputPath>.</OutputPath>
+    <ProjectTypeGuids>{888888a0-9f3d-457c-b088-3a5042f75d52}</ProjectTypeGuids>
+    <LaunchProvider>Standard Python launcher</LaunchProvider>
+    <InterpreterId>CondaEnv|CondaEnv|pyfor_env</InterpreterId>
+    <TestFramework>unittest</TestFramework>
+    <UnitTestPattern>test_*.py</UnitTestPattern>
+    <UnitTestRootDirectory>pyfortest</UnitTestRootDirectory>
+  </PropertyGroup>
+  <PropertyGroup Condition="'$(Configuration)' == 'Debug'" />
+  <PropertyGroup Condition="'$(Configuration)' == 'Release'" />
+  <PropertyGroup>
+    <VisualStudioVersion Condition=" '$(VisualStudioVersion)' == '' ">10.0</VisualStudioVersion>
+  </PropertyGroup>
+  <ItemGroup>
+    <Content Include="docs\html\advanced\groundfilter.html" />
+    <Content Include="docs\html\advanced\handlinglargeacquisitions.html" />
+    <Content Include="docs\html\advanced\index.html" />
+    <Content Include="docs\html\advanced\understandingcomponents.html" />
+    <Content Include="docs\html\api\index.html" />
+    <Content Include="docs\html\api\modules.html" />
+    <Content Include="docs\html\api\pyfor.clip.html" />
+    <Content Include="docs\html\api\pyfor.cloud.html" />
+    <Content Include="docs\html\api\pyfor.collection.html" />
+    <Content Include="docs\html\api\pyfor.gisexport.html" />
+    <Content Include="docs\html\api\pyfor.ground_filter.html" />
+    <Content Include="docs\html\api\pyfor.html" />
+    <Content Include="docs\html\api\pyfor.metrics.html" />
+    <Content Include="docs\html\api\pyfor.rasterizer.html" />
+    <Content Include="docs\html\api\pyfor.voxelizer.html" />
+    <Content Include="docs\html\genindex.html" />
+    <Content Include="docs\html\gettingstarted.html" />
+    <Content Include="docs\html\index.html" />
+    <Content Include="docs\html\installation.html" />
+    <Content Include="docs\html\introduction.html" />
+    <Content Include="docs\html\py-modindex.html" />
+    <Content Include="docs\html\search.html" />
+    <Content Include="docs\html\searchindex.js" />
+    <Content Include="docs\html\structure.html" />
+    <Content Include="docs\html\topics\canopyheightmodel.html" />
+    <Content Include="docs\html\topics\clipping.html" />
+    <Content Include="docs\html\topics\index.html" />
+    <Content Include="docs\html\topics\normalization.html" />
+    <Content Include="docs\html\_images\chm_final.png" />
+    <Content Include="docs\html\_images\simple_plot.png" />
+    <Content Include="docs\html\_sources\index.rst.txt" />
+    <Content Include="docs\html\_static\ajax-loader.gif" />
+    <Content Include="docs\html\_static\basic.css" />
+    <Content Include="docs\html\_static\comment-bright.png" />
+    <Content Include="docs\html\_static\comment-close.png" />
+    <Content Include="docs\html\_static\comment.png" />
+    <Content Include="docs\html\_static\css\badge_only.css" />
+    <Content Include="docs\html\_static\css\theme.css" />
+    <Content Include="docs\html\_static\doctools.js" />
+    <Content Include="docs\html\_static\documentation_options.js" />
+    <Content Include="docs\html\_static\down-pressed.png" />
+    <Content Include="docs\html\_static\down.png" />
+    <Content Include="docs\html\_static\file.png" />
+    <Content Include="docs\html\_static\fonts\fontawesome-webfont.svg" />
+    <Content Include="docs\html\_static\jquery-3.2.1.js" />
+    <Content Include="docs\html\_static\jquery.js" />
+    <Content Include="docs\html\_static\js\modernizr.min.js" />
+    <Content Include="docs\html\_static\js\theme.js" />
+    <Content Include="docs\html\_static\minus.png" />
+    <Content Include="docs\html\_static\plus.png" />
+    <Content Include="docs\html\_static\pygments.css" />
+    <Content Include="docs\html\_static\searchtools.js" />
+    <Content Include="docs\html\_static\underscore-1.3.1.js" />
+    <Content Include="docs\html\_static\underscore.js" />
+    <Content Include="docs\html\_static\up-pressed.png" />
+    <Content Include="docs\html\_static\up.png" />
+    <Content Include="docs\html\_static\websupport.js" />
+    <Content Include="docs\img\chm_final.png" />
+    <Content Include="docs\img\clipped.png" />
+    <Content Include="docs\img\simple_plot.png" />
+    <Content Include="docs\img\unclipped.png" />
+    <Content Include="docs\index.html" />
+    <Content Include="docs\logo.png" />
+    <Content Include="docs\norm_sample.png" />
+    <Content Include="docs\tile.png" />
+    <Content Include="License.txt" />
+  </ItemGroup>
+  <ItemGroup>
+    <Compile Include="docs\conf.py" />
+    <Compile Include="pyfortest\test_collection.py" />
+    <Compile Include="pyfortest\test_pyfor.py" />
+    <Compile Include="pyfortest\__init__.py" />
+    <Compile Include="pyfor\clip.py" />
+    <Compile Include="pyfor\cloud.py" />
+    <Compile Include="pyfor\collection.py" />
+    <Compile Include="pyfor\gisexport.py" />
+    <Compile Include="pyfor\ground_filter.py" />
+    <Compile Include="pyfor\metrics.py" />
+    <Compile Include="pyfor\rasterizer.py" />
+    <Compile Include="pyfor\voxelizer.py" />
+    <Compile Include="pyfor\__init__.py" />
+    <Compile Include="setup.py" />
+  </ItemGroup>
+  <ItemGroup>
+    <Folder Include="docs" />
+    <Folder Include="docs\html" />
+    <Folder Include="docs\html\advanced" />
+    <Folder Include="docs\html\api" />
+    <Folder Include="docs\html\topics" />
+    <Folder Include="docs\html\_images" />
+    <Folder Include="docs\html\_sources" />
+    <Folder Include="docs\html\_static" />
+    <Folder Include="docs\html\_static\css" />
+    <Folder Include="docs\html\_static\fonts" />
+    <Folder Include="docs\html\_static\js" />
+    <Folder Include="docs\img" />
+    <Folder Include="pyfor" />
+    <Folder Include="pyfortest" />
+  </ItemGroup>
+  <ItemGroup>
+    <InterpreterReference Include="CondaEnv|CondaEnv|pyfor_env" />
+  </ItemGroup>
+  <Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v$(VisualStudioVersion)\Python Tools\Microsoft.PythonTools.targets" />
+</Project>
diff --git a/pyfor/cloud.py b/pyfor/cloud.py
@@ -115,6 +115,19 @@ def __init__(self, path):
         self.normalized = None
         self.crs = None
 
+    @classmethod
+    def from_pdal(cls, ins):
+        """
+        Converts a PDAL `ins` argument from a PDAL `filters.python` into a `Cloud` object.
+
+        :param ins: The `ins` argument from PDAL.
+        """
+
+        df = pd.DataFrame(ins)
+        df = df.rename(columns={"X": "x", "Y": "y", "Z":"z", "ReturnNumber": "return_num"})
+        cloud_data = pyfor.cloud.CloudData(df, header=None)
+        return cls(cloud_data)
+
     def _get_las_points(self, las):
         """
         Reads points into pandas dataframe.

diff --git a/pyfor/ground_filter.py b/pyfor/ground_filter.py
@@ -200,6 +200,9 @@ def _filter(self, grid):
         """
         Runs the actual ground filter. Generally used as an internal function that is called by user functions
         (.bem, .classify, .ground_points).
+
+        :param grid: A `pyfor.rasterizer.Grid` object.
+        :return: A `pandas.DataFrame` of filtered points.
         """
         np.seterr(divide='ignore', invalid='ignore')
 
@@ -256,7 +259,9 @@ def bem(self, cloud, cell_size):
     def classify(self, cloud, ground_int=2):
         """
         Sets the classification of the original input cloud points to ground (default 2 as per las specification). This
-        performs the adjustment of the input `Cloud` object **in place**. Only implemented for `.las` files.
+        performs the adjustment of the input `Cloud` object **in place**. Only implemented for `.las` files. Additionally,
+        the original ground classification is preserved if it exists, so this will only add additional ground points for
+        already classified point clouds.
 
         :param cloud: A cloud object.
         :param ground_int: The integer to set classified points to, the default is 2 in the las specification for ground
@@ -265,8 +270,8 @@ def classify(self, cloud, ground_int=2):
 
         if cloud.extension == '.las':
             grid = cloud.grid(self.cell_size)
-            self._filter(grid)
-            grid.cloud.data.points["classification"][grid.cloud.data.points['v_i'] <= self.g + self.w] = ground_int
+            filtered_point_ids = self._filter(grid).index
+            grid.cloud.data.points["classification"][filtered_point_ids] = ground_int
         else:
             print("This is only implemented for .las files.")
 

diff --git a/pyfortest/__pycache__/__init__.cpython-36.pyc b/pyfortest/__pycache__/__init__.cpython-36.pyc
diff --git a/pyfortest/__pycache__/test_collection.cpython-36.pyc b/pyfortest/__pycache__/test_collection.cpython-36.pyc
diff --git a/pyfortest/__pycache__/test_pyfor.cpython-36.pyc b/pyfortest/__pycache__/test_pyfor.cpython-36.pyc
diff --git a/pyfortest/test_pyfor.py b/pyfortest/test_pyfor.py
@@ -384,6 +384,10 @@ def setUp(self):
     def test_filter(self):
         self.test_kp_filter._filter(self.test_cloud.grid(self.test_kp_filter.cell_size))
 
+    def test_classify(self):
+        self.test_kp_filter.classify(self.test_cloud)
+        self.assertEqual(133410, np.sum(self.test_cloud.data.points["classification"] == 2))
+
 class Zhang2003TestCase(unittest.TestCase):
     def setUp(self):
         self.test_cloud = cloud.Cloud(test_las)

diff --git a/test_environment.yml b/test_environment.yml
@@ -0,0 +1,27 @@
+name: pyfor_env
+
+dependencies:
+  - python=3.7
+  - gdal
+  - rasterio
+  - conda-forge::pyproj
+  - numpy
+  - pandas
+  - scipy
+  - scikit-image
+  - scikit-learn
+  - pyqtgraph
+  - matplotlib
+  - pyopengl
+  - numba
+  - libkml
+  - geopandas
+  - joblib
+  - poppler
+  - conda-forge::lastools
+  - pip:
+      - laspy
+      - laxpy
+      - sphinx_rtd_theme
+      - python-coveralls
+      - plyfile