Merge pull request #9 from whyjz/px_v1.0

Finalizing Pixel Track 1.0 Documentation
whyjz · Jun 5, 2019 · f279e65 · f279e65
2 parents acd45dd + 0bcfc0c
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diff --git a/.gitignore b/.gitignore
@@ -4,8 +4,8 @@
 **/gmt.history
 **/*.aux.xml
 **/isce.log
-pixeltrack/Landsat8_example/20160803203709_20160718203706/*
-pixeltrack/test_folder
+pixeltrack/Demo_Data/20180401-20180417*.tif
 other_process/log_getUncertaintyDEM_grdtrack_output.xyz
 dhdt/Demo_DEMs/HookerFJL_10m_dhdt*
 dhdt/Demo_DEMs/refgeo_10m_TSpickle.p
+Utilities/unused/PXData/*
diff --git a/Doc/dhdt_workflow.dia → Doc/dhdt/dhdt_workflow.dia b/Doc/dhdt_workflow.dia → Doc/dhdt/dhdt_workflow.dia
diff --git a/Doc/dhdt_workflow.eps → Doc/dhdt/dhdt_workflow.eps b/Doc/dhdt_workflow.eps → Doc/dhdt/dhdt_workflow.eps
diff --git a/Doc/pixeltrack/README.rst b/Doc/pixeltrack/README.rst
diff --git a/README.rst b/README.rst
@@ -14,7 +14,7 @@ Required Platform and Software
 
 dh/dt **[v1.0]**:
 
-- python, with the following modules installed 
+- python >= 3.0, with the following modules installed 
     - numpy 
     - scipy
     - matplotlib
@@ -26,10 +26,12 @@ dh/dt **[v1.0]**:
 pixel tracking **[v1.0]**:
 
 - ISCE >= 2.0.0 (built with your python)
-- python, with the following modules installed
+- python >= 3.0, with the following modules installed
     - numpy 
     - scipy
     - gdal
+    - geopandas
+    - shapely
 
 Folder Structure
 ----------------
@@ -42,12 +44,12 @@ Folder Structure
 - pixeltrack: Main programs for pixel tracking **[v1.0]**
     - pixeltrack.py: main program
     - defaults.ini: template configuration file
-    - Demo_Tifs: Demo input files
+    - Demo_Data: Demo input files
 
 Detailed Description
 --------------------
-- Doc/dhdt/README.rst: **[v1.0]** dh/dt documentation
-- Doc/pixeltrack/README.rst: **[v1.0]** pixel tracking documentation
+- dhdt/README.rst: **[v1.0]** dh/dt documentation
+- pixeltrack/README.rst: **[v1.0]** pixel tracking documentation
 
 Version History
 ---------------
@@ -60,8 +62,11 @@ Here's the reference to cite for dh/dt **[v1.0]**:
   on Franz Josef Land, Russian Arctic. Remote Sensing of Environment 211, 357–375. 
   http://doi.org/10.1016/j.rse.2018.04.004
 
-There's still no reference to cite for pixel tracking **[v1.0]**, but you can use our
-reference(s) for the old version for credits.
+Here's the reference to cite for pixel tracking **[v1.0]**: 
+
+- Willis, M. J., Zheng, W., Durkin, W. J., Pritchard, M. E., Ramage, J. M., 
+  Dowdeswell, J. A., … Porter, C. C. (2018). Massive destabilization of an Arctic ice cap. 
+  Earth and Planetary Science Letters, 502, 146–155. http://doi.org/10.1016/j.epsl.2018.08.049
 
 The dh/dt **[v0.2]** and the pixel tracking **[v0.2]** was developed by Whyjay Zheng,
 William J. Durkin, and Professor Matthew Pritchard, Cornell University.
@@ -72,4 +77,4 @@ Melkonian et al. Here is the reference to cite:
 - Melkonian, A. K., Willis, M. J., & Pritchard, M. E. (2014). 
   Satellite-derived volume loss rates and glacier speeds for 
   the Juneau Icefield , Alaska. Journal of Glaciology, 
-  60(222), 743–760.
+  60(222), 743–760.
diff --git a/...int_nans/demo/html/inpaint_nans_demo.html → ...int_nans/demo/html/inpaint_nans_demo.html b/...int_nans/demo/html/inpaint_nans_demo.html → ...int_nans/demo/html/inpaint_nans_demo.html
diff --git a/...aint_nans/demo/html/inpaint_nans_demo.png → ...aint_nans/demo/html/inpaint_nans_demo.png b/...aint_nans/demo/html/inpaint_nans_demo.png → ...aint_nans/demo/html/inpaint_nans_demo.png
diff --git a/...t_nans/demo/html/inpaint_nans_demo_01.png → ...t_nans/demo/html/inpaint_nans_demo_01.png b/...t_nans/demo/html/inpaint_nans_demo_01.png → ...t_nans/demo/html/inpaint_nans_demo_01.png
diff --git a/...t_nans/demo/html/inpaint_nans_demo_02.png → ...t_nans/demo/html/inpaint_nans_demo_02.png b/...t_nans/demo/html/inpaint_nans_demo_02.png → ...t_nans/demo/html/inpaint_nans_demo_02.png
diff --git a/...t_nans/demo/html/inpaint_nans_demo_03.png → ...t_nans/demo/html/inpaint_nans_demo_03.png b/...t_nans/demo/html/inpaint_nans_demo_03.png → ...t_nans/demo/html/inpaint_nans_demo_03.png
diff --git a/...t_nans/demo/html/inpaint_nans_demo_04.png → ...t_nans/demo/html/inpaint_nans_demo_04.png b/...t_nans/demo/html/inpaint_nans_demo_04.png → ...t_nans/demo/html/inpaint_nans_demo_04.png
diff --git a/...t_nans/demo/html/inpaint_nans_demo_05.png → ...t_nans/demo/html/inpaint_nans_demo_05.png b/...t_nans/demo/html/inpaint_nans_demo_05.png → ...t_nans/demo/html/inpaint_nans_demo_05.png
diff --git a/...t_nans/demo/html/inpaint_nans_demo_06.png → ...t_nans/demo/html/inpaint_nans_demo_06.png b/...t_nans/demo/html/inpaint_nans_demo_06.png → ...t_nans/demo/html/inpaint_nans_demo_06.png
diff --git a/...Inpaint_nans/demo/inpaint_nans_demo_old.m → ...Inpaint_nans/demo/inpaint_nans_demo_old.m b/...Inpaint_nans/demo/inpaint_nans_demo_old.m → ...Inpaint_nans/demo/inpaint_nans_demo_old.m
diff --git a/.../Inpaint_nans/doc/Nomination comments.rtf → .../Inpaint_nans/doc/Nomination comments.rtf b/.../Inpaint_nans/doc/Nomination comments.rtf → .../Inpaint_nans/doc/Nomination comments.rtf
diff --git a/...npaint_nans/doc/methods_of_inpaint_nans.m → ...npaint_nans/doc/methods_of_inpaint_nans.m b/...npaint_nans/doc/methods_of_inpaint_nans.m → ...npaint_nans/doc/methods_of_inpaint_nans.m
diff --git a/...le/Inpaint_nans/Inpaint_nans/garden50.jpg → ...le/Inpaint_nans/Inpaint_nans/garden50.jpg b/...le/Inpaint_nans/Inpaint_nans/garden50.jpg → ...le/Inpaint_nans/Inpaint_nans/garden50.jpg
diff --git a/.../Inpaint_nans/Inpaint_nans/inpaint_nans.m → .../Inpaint_nans/Inpaint_nans/inpaint_nans.m b/.../Inpaint_nans/Inpaint_nans/inpaint_nans.m → .../Inpaint_nans/Inpaint_nans/inpaint_nans.m
diff --git a/...paint_nans/Inpaint_nans/inpaint_nans_bc.m → ...paint_nans/Inpaint_nans/inpaint_nans_bc.m b/...paint_nans/Inpaint_nans/inpaint_nans_bc.m → ...paint_nans/Inpaint_nans/inpaint_nans_bc.m
diff --git a/...int_nans/Inpaint_nans/inpaint_nans_demo.m → ...int_nans/Inpaint_nans/inpaint_nans_demo.m b/...int_nans/Inpaint_nans/inpaint_nans_demo.m → ...int_nans/Inpaint_nans/inpaint_nans_demo.m
diff --git a/...paint_nans/Inpaint_nans/monet_adresse.jpg → ...paint_nans/Inpaint_nans/monet_adresse.jpg b/...paint_nans/Inpaint_nans/monet_adresse.jpg → ...paint_nans/Inpaint_nans/monet_adresse.jpg
diff --git a/...npaint_nans/Inpaint_nans/test/test_main.m → ...npaint_nans/Inpaint_nans/test/test_main.m b/...npaint_nans/Inpaint_nans/test/test_main.m → ...npaint_nans/Inpaint_nans/test/test_main.m
diff --git a/...rack/SVZ_example/Inpaint_nans/license.txt → ...ldPX/SVZ_example/Inpaint_nans/license.txt b/...rack/SVZ_example/Inpaint_nans/license.txt → ...ldPX/SVZ_example/Inpaint_nans/license.txt
diff --git a/pixeltrack/SVZ_example/ampoffToGrd.bash → ...unused/OldPX/SVZ_example/ampoffToGrd.bash b/pixeltrack/SVZ_example/ampoffToGrd.bash → ...unused/OldPX/SVZ_example/ampoffToGrd.bash
diff --git a/pixeltrack/SVZ_example/bedrock_offset.m → ...unused/OldPX/SVZ_example/bedrock_offset.m b/pixeltrack/SVZ_example/bedrock_offset.m → ...unused/OldPX/SVZ_example/bedrock_offset.m
diff --git a/pixeltrack/SVZ_example/findCoreg_subpix.bash → ...d/OldPX/SVZ_example/findCoreg_subpix.bash b/pixeltrack/SVZ_example/findCoreg_subpix.bash → ...d/OldPX/SVZ_example/findCoreg_subpix.bash
diff --git a/...ltrack/SVZ_example/generate_paramtxt.bash → .../OldPX/SVZ_example/generate_paramtxt.bash b/...ltrack/SVZ_example/generate_paramtxt.bash → .../OldPX/SVZ_example/generate_paramtxt.bash
diff --git a/pixeltrack/SVZ_example/getEPSG.py → ...ities/unused/OldPX/SVZ_example/getEPSG.py b/pixeltrack/SVZ_example/getEPSG.py → ...ities/unused/OldPX/SVZ_example/getEPSG.py
diff --git a/pixeltrack/SVZ_example/getGTiffMedian.py → ...nused/OldPX/SVZ_example/getGTiffMedian.py b/pixeltrack/SVZ_example/getGTiffMedian.py → ...nused/OldPX/SVZ_example/getGTiffMedian.py
diff --git a/pixeltrack/SVZ_example/image_coregistar.py → ...sed/OldPX/SVZ_example/image_coregistar.py b/pixeltrack/SVZ_example/image_coregistar.py → ...sed/OldPX/SVZ_example/image_coregistar.py
diff --git a/pixeltrack/SVZ_example/inpaint_nans.m → ...s/unused/OldPX/SVZ_example/inpaint_nans.m b/pixeltrack/SVZ_example/inpaint_nans.m → ...s/unused/OldPX/SVZ_example/inpaint_nans.m
diff --git a/pixeltrack/SVZ_example/inpaint_nans_bc.m → ...nused/OldPX/SVZ_example/inpaint_nans_bc.m b/pixeltrack/SVZ_example/inpaint_nans_bc.m → ...nused/OldPX/SVZ_example/inpaint_nans_bc.m
diff --git a/pixeltrack/SVZ_example/quick_get_error.bash → ...ed/OldPX/SVZ_example/quick_get_error.bash b/pixeltrack/SVZ_example/quick_get_error.bash → ...ed/OldPX/SVZ_example/quick_get_error.bash
diff --git a/...ck/SVZ_example/realistic_speed_error.bash → ...PX/SVZ_example/realistic_speed_error.bash b/...ck/SVZ_example/realistic_speed_error.bash → ...PX/SVZ_example/realistic_speed_error.bash
diff --git a/...ack/SVZ_example/setup_pixel_tracking.bash → ...dPX/SVZ_example/setup_pixel_tracking.bash b/...ack/SVZ_example/setup_pixel_tracking.bash → ...dPX/SVZ_example/setup_pixel_tracking.bash
diff --git a/pixeltrack/SVZ_example/smooth_step2.m → ...s/unused/OldPX/SVZ_example/smooth_step2.m b/pixeltrack/SVZ_example/smooth_step2.m → ...s/unused/OldPX/SVZ_example/smooth_step2.m
diff --git a/pixeltrack/SVZ_example/smooth_step2_forerr.m → ...d/OldPX/SVZ_example/smooth_step2_forerr.m b/pixeltrack/SVZ_example/smooth_step2_forerr.m → ...d/OldPX/SVZ_example/smooth_step2_forerr.m
diff --git a/pixeltrack/SVZ_example/smoothing.bash → ...s/unused/OldPX/SVZ_example/smoothing.bash b/pixeltrack/SVZ_example/smoothing.bash → ...s/unused/OldPX/SVZ_example/smoothing.bash
diff --git a/pixeltrack/old_defaults_px.ini → Utilities/unused/OldPX/old_defaults_px.ini b/pixeltrack/old_defaults_px.ini → Utilities/unused/OldPX/old_defaults_px.ini
diff --git a/pixeltrack/old_landsat8_2016_200_216.txt → ...nused/OldPX/old_landsat8_2016_200_216.txt b/pixeltrack/old_landsat8_2016_200_216.txt → ...nused/OldPX/old_landsat8_2016_200_216.txt
diff --git a/pixeltrack/old_nodelist.txt → Utilities/unused/OldPX/old_nodelist.txt b/pixeltrack/old_nodelist.txt → Utilities/unused/OldPX/old_nodelist.txt
diff --git a/pixeltrack/old_pixeltrack.py → Utilities/unused/OldPX/old_pixeltrack.py b/pixeltrack/old_pixeltrack.py → Utilities/unused/OldPX/old_pixeltrack.py
diff --git a/Doc/dhdt/README.rst → dhdt/README.rst b/Doc/dhdt/README.rst → dhdt/README.rst
diff --git a/pixeltrack/Demo_Data/20180401-20180417_ampoff.p b/pixeltrack/Demo_Data/20180401-20180417_ampoff.p
diff --git a/pixeltrack/Demo_Data/20180401-20180417_bedrock_vx-vs-vy.png b/pixeltrack/Demo_Data/20180401-20180417_bedrock_vx-vs-vy.png
diff --git a/pixeltrack/Demo_Data/20180401-20180417_bedrock_vx.png b/pixeltrack/Demo_Data/20180401-20180417_bedrock_vx.png
diff --git a/pixeltrack/Demo_Data/20180401-20180417_bedrock_vy.png b/pixeltrack/Demo_Data/20180401-20180417_bedrock_vy.png
diff --git a/pixeltrack/Demo_Data/20180401-20180417_velo_correction.txt b/pixeltrack/Demo_Data/20180401-20180417_velo_correction.txt
@@ -0,0 +1,15 @@
+Total points over bedrock =      463
+-------- Unit: Pixels --------
+median_x_px    = -1.188
+median_y_px    =  0.344
+std_x_px       =  0.499
+std_y_px       =  0.458
+mean_x_px      = -1.210
+mean_y_px      =  0.334
+-------- Unit: Velocity (L/T; most likely m/day) --------
+median_x       = -1.113
+median_y       =  0.322
+std_x          =  0.468
+std_y          =  0.429
+mean_x         = -1.134
+mean_y         =  0.313
diff --git a/pixeltrack/Demo_Data/LC08_L1TP_170002_20180401_20180416_01_T2_B8_cropped.TIF b/pixeltrack/Demo_Data/LC08_L1TP_170002_20180401_20180416_01_T2_B8_cropped.TIF
diff --git a/...avilov_T46XEP_20180508T071621_B08.tif.vrt → ...0180401_20180416_01_T2_B8_cropped.TIF.vrt b/...avilov_T46XEP_20180508T071621_B08.tif.vrt → ...0180401_20180416_01_T2_B8_cropped.TIF.vrt
@@ -1,14 +1,14 @@
-<VRTDataset rasterXSize="3669" rasterYSize="2395">
+<VRTDataset rasterXSize="2920" rasterYSize="2007">
   <SRS>PROJCS["WGS 84 / UTM zone 46N",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",93],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["Easting",EAST],AXIS["Northing",NORTH],AUTHORITY["EPSG","32646"]]</SRS>
-  <GeoTransform>  5.1352600000000000e+05,  1.0000817661488144e+01,  0.0000000000000000e+00,  8.8188260000000000e+06,  0.0000000000000000e+00, -1.0000000000000000e+01</GeoTransform>
-  <VRTRasterBand dataType="Float32" band="1">
+  <GeoTransform>  5.0915250000000000e+05,  1.5000000000000000e+01,  0.0000000000000000e+00,  8.8225725000000000e+06,  0.0000000000000000e+00, -1.5000000000000000e+01</GeoTransform>
+  <VRTRasterBand dataType="UInt16" band="1">
     <ColorInterp>Gray</ColorInterp>
     <SimpleSource>
-      <SourceFilename relativeToVRT="1">Vavilov_T46XEP_20180508T071621_B08.tif</SourceFilename>
+      <SourceFilename relativeToVRT="1">LC08_L1TP_170002_20180401_20180416_01_T2_B8_cropped.TIF</SourceFilename>
       <SourceBand>1</SourceBand>
-      <SourceProperties RasterXSize="3669" RasterYSize="2395" DataType="Float32" BlockXSize="3669" BlockYSize="1" />
-      <SrcRect xOff="0" yOff="0" xSize="3669" ySize="2395" />
-      <DstRect xOff="0" yOff="0" xSize="3669" ySize="2395" />
+      <SourceProperties RasterXSize="2920" RasterYSize="2007" DataType="UInt16" BlockXSize="2920" BlockYSize="1" />
+      <SrcRect xOff="0" yOff="0" xSize="2920" ySize="2007" />
+      <DstRect xOff="0" yOff="0" xSize="2920" ySize="2007" />
     </SimpleSource>
   </VRTRasterBand>
 </VRTDataset>
diff --git a/pixeltrack/Demo_Data/LC08_L1TP_170002_20180417_20180501_01_T2_B8_cropped.TIF b/pixeltrack/Demo_Data/LC08_L1TP_170002_20180417_20180501_01_T2_B8_cropped.TIF
diff --git a/...avilov_T46XEP_20180529T073609_B08.tif.vrt → ...0180417_20180501_01_T2_B8_cropped.TIF.vrt b/...avilov_T46XEP_20180529T073609_B08.tif.vrt → ...0180417_20180501_01_T2_B8_cropped.TIF.vrt
@@ -1,14 +1,14 @@
-<VRTDataset rasterXSize="3669" rasterYSize="2395">
+<VRTDataset rasterXSize="2920" rasterYSize="2007">
   <SRS>PROJCS["WGS 84 / UTM zone 46N",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Transverse_Mercator"],PARAMETER["latitude_of_origin",0],PARAMETER["central_meridian",93],PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],PARAMETER["false_northing",0],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["Easting",EAST],AXIS["Northing",NORTH],AUTHORITY["EPSG","32646"]]</SRS>
-  <GeoTransform>  5.1352600000000000e+05,  1.0000817661488144e+01,  0.0000000000000000e+00,  8.8188260000000000e+06,  0.0000000000000000e+00, -1.0000000000000000e+01</GeoTransform>
-  <VRTRasterBand dataType="Float32" band="1">
+  <GeoTransform>  5.0915250000000000e+05,  1.5000000000000000e+01,  0.0000000000000000e+00,  8.8225725000000000e+06,  0.0000000000000000e+00, -1.5000000000000000e+01</GeoTransform>
+  <VRTRasterBand dataType="UInt16" band="1">
     <ColorInterp>Gray</ColorInterp>
     <SimpleSource>
-      <SourceFilename relativeToVRT="1">Vavilov_T46XEP_20180529T073609_B08.tif</SourceFilename>
+      <SourceFilename relativeToVRT="1">LC08_L1TP_170002_20180417_20180501_01_T2_B8_cropped.TIF</SourceFilename>
       <SourceBand>1</SourceBand>
-      <SourceProperties RasterXSize="3669" RasterYSize="2395" DataType="Float32" BlockXSize="3669" BlockYSize="1" />
-      <SrcRect xOff="0" yOff="0" xSize="3669" ySize="2395" />
-      <DstRect xOff="0" yOff="0" xSize="3669" ySize="2395" />
+      <SourceProperties RasterXSize="2920" RasterYSize="2007" DataType="UInt16" BlockXSize="2920" BlockYSize="1" />
+      <SrcRect xOff="0" yOff="0" xSize="2920" ySize="2007" />
+      <DstRect xOff="0" yOff="0" xSize="2920" ySize="2007" />
     </SimpleSource>
   </VRTRasterBand>
 </VRTDataset>
diff --git a/pixeltrack/Demo_Tifs/bedrock.dbf → pixeltrack/Demo_Data/bedrock.dbf b/pixeltrack/Demo_Tifs/bedrock.dbf → pixeltrack/Demo_Data/bedrock.dbf
diff --git a/pixeltrack/Demo_Tifs/bedrock.prj → pixeltrack/Demo_Data/bedrock.prj b/pixeltrack/Demo_Tifs/bedrock.prj → pixeltrack/Demo_Data/bedrock.prj
diff --git a/pixeltrack/Demo_Tifs/bedrock.qpj → pixeltrack/Demo_Data/bedrock.qpj b/pixeltrack/Demo_Tifs/bedrock.qpj → pixeltrack/Demo_Data/bedrock.qpj
diff --git a/pixeltrack/Demo_Data/bedrock.shp b/pixeltrack/Demo_Data/bedrock.shp
diff --git a/pixeltrack/Demo_Tifs/bedrock.shx → pixeltrack/Demo_Data/bedrock.shx b/pixeltrack/Demo_Tifs/bedrock.shx → pixeltrack/Demo_Data/bedrock.shx