Replaced gippy with rasterio

Dockerfile

@@ -74,7 +74,6 @@ RUN pip install -U \
   scipy \
   shapely \
   xmltodict \
-  https://github.com/OpenDroneMap/gippy/archive/numpyfix.zip \
   rasterio \
   attrs==19.1.0
 

configure.sh

@@ -91,7 +91,7 @@ install() {
                          libboost-log-dev
 
     echo "Installing split-merge Dependencies"
-    pip install -U scipy numpy==1.15.4 shapely pyproj https://github.com/OpenDroneMap/gippy/archive/numpyfix.zip psutil
+    pip install -U scipy numpy==1.15.4 shapely pyproj psutil
 
     echo "Compiling SuperBuild"
     cd ${RUNPATH}/SuperBuild

opendm/dem/commands.py

@@ -1,6 +1,6 @@
 import os
 import sys
-import gippy
+import rasterio
 import numpy
 import math
 import time
@@ -236,9 +236,10 @@ def post_process(geotiff_path, output_path, smoothing_iterations=1):
 
     log.ODM_INFO('Starting post processing (smoothing)...')
 
-    img = gippy.GeoImage(geotiff_path)
-    nodata = img[0].nodata()
-    arr = img[0].read()
+    with rasterio.open(geotiff_path) as img:
+        nodata = img.nodatavals[0]
+        dtype = img.dtypes[0]
+        arr = img.read()[0]
 
         # Median filter (careful, changing the value 5 might require tweaking)
         # the lines below. There's another numpy function that takes care of 
@@ -259,11 +260,8 @@ def post_process(geotiff_path, output_path, smoothing_iterations=1):
         arr[locs] = nodata
 
         # write output
-    imgout = gippy.GeoImage.create_from(img, output_path)
-    imgout.set_nodata(nodata)
-    imgout[0].write(arr)
-    output_path = imgout.filename()
-    imgout = None
+        with rasterio.open(output_path, 'w', **img.profile) as imgout:
+            imgout.write(arr.astype(dtype), 1)
     
     log.ODM_INFO('Completed post processing to create %s in %s' % (os.path.relpath(output_path), datetime.now() - start))
 

opendm/dem/merge.py

@@ -41,10 +41,7 @@ def euclidean_merge_dems(input_dems, output_dem, creation_options={}):
         logging.disable(logging.DEBUG)
 
     with rasterio.open(existing_dems[0]) as first:
-        src_nodata = 0
-        nodatavals = first.get_nodatavals()
-        if len(nodatavals) > 0:
-            src_nodata = nodatavals[0]
+        src_nodata = first.nodatavals[0]
         res = first.res
         dtype = first.dtypes[0]
         profile = first.profile
@@ -148,10 +145,7 @@ def euclidean_merge_dems(input_dems, output_dem, creation_options={}):
                 # With rio merge this just adds an extra row, but when the
                 # imprecision occurs at each block, you get artifacts
 
-                nodata = 0
-                nodatavals = src_d.get_nodatavals()
-                if len(nodatavals) > 0:
-                    nodata = nodatavals[0]
+                nodata = src_d.nodatavals[0]
 
                 # Alternative, custom get_window using rounding
                 src_window = tuple(zip(rowcol(

opendm/mesh.py

@@ -1,6 +1,5 @@
 from __future__ import absolute_import
 import os, shutil, sys, struct, random, math
-from gippy import GeoImage
 from opendm.dem import commands
 from opendm import system
 from opendm import log

portable.Dockerfile

@@ -74,7 +74,6 @@ RUN pip install -U \
   scipy \
   shapely \
   xmltodict \
-  https://github.com/OpenDroneMap/gippy/archive/numpyfix.zip \
   rasterio \
   attrs==19.1.0