updates from upstream (USF-IMARS/wv2-proc)

.gitignore

@@ -1,6 +1,9 @@
 # test data
 test_data/
 
+# emacs backups
+*~
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "imagery_utils"]
+	path = imagery_utils
+	url = https://github.com/PolarGeospatialCenter/imagery_utils.git

.travis.yml

@@ -0,0 +1,23 @@
+language: python
+services:
+  - docker
+python:
+  - "2.7"
+  - "3.4"
+  - "3.5"
+  - "3.6"
+  - "3.7"
+  - "3.8"
+  - "nightly"
+before_install:
+  - DOCKER_IMAGE=7yl4r/wv_img_proc_docker:0.0.1
+  - docker pull $DOCKER_IMAGE
+  - docker run -d $DOCKER_IMAGE
+  - docker ps -a
+  - docker run $DOCKER_IMAGE -v requirements.txt:/requirements.txt -v requirements_tests.txt:/requirements_tests.txt
+install:
+  - docker exec $DOCKER_IMAGE pip install -r /requirements.txt
+before_script:
+  - docker exec $DOCKER_IMAGE pip install -r /requirements_tests.txt
+script:
+  - docker exec $DOCKER_IMAGE pytest -v -m "not testdata_required"

3d_wetlands/DT_Filter.m

@@ -0,0 +1,51 @@
+%% DT_Filter.M
+%% Written by Matt McCarthy 8/29/2016
+
+function dt_filt = DT_Filter(file,x,sz2,sz3,dev,FW,FU,UG,WA);
+filt = x;
+sz_sm(1) = sz2; % Size of unwarped(smaller) file
+sz_sm(2) = sz3;
+
+fwfilt = 75
+wafilt = 50
+sz1 = size(file);
+dt_filt =zeros(sz1(1),sz1(2),'uint8');
+
+    for a = filt+1:sz_sm(1)-filt-1; % Mode filter or median filter: 3x3 or 5x5
+        for b = filt+1:sz_sm(2)-filt-1;
+	    if file(a,b) == dev;
+		dt_filt(a,b) = dev;
+	    elseif file(a,b) == FW && a > fwfilt && b > fwfilt && a < sz_sm(1)-100 && b < sz_sm(2)-100; % For FW, use larger window to eliminate erroneous urban misclassifications
+		C = file(a-fwfilt:a+fwfilt,b-fwfilt:b+fwfilt);
+		idx = find(C == 0); % If any pixels in C are shadows, they are not included in the mode function
+		C(idx) = [];
+		mod = mode(mode(C)); % Mode of window (by definition, lower value is selected if more than one mode value)
+		if isnan(mod) == 1;
+			dt_filt(a,b) = 0; % If NaN, assign zero because Arc won't load DT tiffs w/ NaNs
+		elseif mod == FW; % Check if mode FW is actually urban tree shadow
+			idxfor = find(C == dev | C == FU); % Find upland forest, grass, and developed nearby
+			if size(idxfor,1)>0.10*size(C,1)*size(C,2); % > 10% is upland, grass, or developed
+				dt_filt(a,b) = FU; % Assumed to be non-wetland forest
+			else dt_filt(a,b) = FW;
+			end
+		else dt_filt(a,b) = FU;
+		end
+            elseif isnan(file(a,b)) == 0;
+		C = file(a-filt:a+filt,b-filt:b+filt);
+                idx = find(C == 0); % If any pixels in C are shadows, they are not included in the mode function
+                C(idx) = [];
+                    mod = mode(mode(C)); % Identify most common value (if more than one value, lower value is selected automatically)
+                    if isnan(mod) == 1; % Check if mode of box is NaN (redundancy)
+                        dt_filt(a,b) = 0; % If NaN, assign zero (Arc won't load DT tiffs w/ NaNs)
+		    elseif mod == FW;
+			D = dt_filt(a-filt:a,b-filt:b);
+			modD = mode(mode(D));
+			dt_filt(a,b) = modD;
+                    else dt_filt(a,b) = mod; % If mod is upland, marsh, water or bare/developed, assign it as such
+                    end
+            else
+                dt_filt(a,b) = 0;
+            end
+        end
+    end
+end