function updates

Author: tdivoll

src/segmentation_f.jl

@@ -43,14 +43,14 @@ function segmentation_F(
         ice_mask_watershed_applied; min_area=lower_min_area_opening, connectivity=2
     )
     #leads
-    ice_leads = ifelse.(.!ice_mask_watershed_opened .== 0, 0.0, 1)
+    ice_leads = .!ice_mask_watershed_opened
     #Iobrd2
     not_ice_dilated = IceFloeTracker.MorphSE.dilate(
         segmentation_B_not_ice_mask; dims=IceFloeTracker.MorphSE.strel_diamond((5, 5))
     )
     #Iobrcbr2
-    not_ice_reconstructed = MorphSE.opening(
-        complement.(not_ice_dilated); dims=complement.(segmentation_B_not_ice_mask)
+    not_ice_reconstructed = IceFloeTracker.MorphSE.mreconstruct(IceFloeTracker.MorphSE.dilate,
+        complement.(not_ice_dilated), complement.(segmentation_B_not_ice_mask)
     )
     #Z(he)
     reconstructed_leads = float64.(not_ice_reconstructed .* ice_leads) .+ (60 / 255)
@@ -85,13 +85,13 @@ function segmentation_F(
     leads_bothat_opened = IceFloeTracker.prune(leads_bothat_opened)
     #BW2
     leads_bothat_filled = .!ImageMorphology.imfill(.!leads_bothat_opened, 0:160)
-    #leads_bothat_filled = .!IceFloeTracker.bwareamaxfilt(.!leads_bothat_opened)
+    leads_bothat_filled = .!IceFloeTracker.bwareamaxfilt(.!leads_bothat_opened)
     #BW2
     leads_bothat_masked = leads_bothat_filled .* cloudmask
     leads_bothat_masked = IceFloeTracker.prune(leads_bothat_masked)
     #BW3
     leads_cloudmasked_filled = .!ImageMorphology.imfill(.!leads_bothat_masked, 0:300)
-    #leads_cloudmasked_filled = .!IceFloeTracker.bwareamaxfilt(.!leads_bothat_masked)
+    leads_cloudmasked_filled = .!IceFloeTracker.bwareamaxfilt(.!leads_bothat_masked)
     #BW4
     leads_masked_branched = IceFloeTracker.branch(leads_cloudmasked_filled)
     #BW5

test/runtests.jl

@@ -17,7 +17,7 @@ testnames = [n[6:(end - 3)] for n in alltests]
 
 ## Put the filenames to test below
 
-to_test = alltests # uncomment this line to run all tests or add individual files below 
+to_test = #alltests # uncomment this line to run all tests or add individual files below 
 [
     # "test-create-landmask.jl",
     # "test-create-cloudmask.jl",
@@ -30,6 +30,7 @@ to_test = alltests # uncomment this line to run all tests or add individual file
     # "test-segmentation-b.jl",
     # "test-segmentation-c.jl",
     # "test-segmentation-d-e.jl",
+     "test-segmentation-f.jl",
     # "test-bwtraceboundary.jl",
     # "test-resample-boundary.jl",
     # "test-regionprops.jl",

test/test-segmentation-a.jl

@@ -14,35 +14,21 @@
     matlab_segmented_ice = convert(
         BitMatrix, float64.(load("$(test_data_dir)/matlab_segmented_ice.png"))
     )
-    matlab_segmented_ice_cloudmasked = (
-        load("$(test_data_dir)/matlab_segmented_ice_cloudmasked.png") .> 0.5
-    )
+    matlab_segmented_ice_cloudmasked = load("$(test_data_dir)/matlab_segmented_ice_cloudmasked.png") .>= 0.5
 
     println("---------- Segment Image - Direct Method ------------")
     @time segmented_ice_cloudmasked = IceFloeTracker.segmented_ice_cloudmasking(
         ice_water_discriminated_image, cloudmask, ice_labels
     )
-    segmented_ice_cloudmasked_filename =
-        "$(test_output_dir)/segmented_a_ice_cloudmasked_" *
-        Dates.format(Dates.now(), "yyyy-mm-dd-HHMMSS") *
-        ".png"
-    IceFloeTracker.@persist segmented_ice_cloudmasked segmented_ice_cloudmasked_filename
+    IceFloeTracker.@persist segmented_ice_cloudmasked  "./test/test_outputs/segmented_a_ice_cloudmasked.png" true
 
     @time segmented_A = IceFloeTracker.segmentation_A(segmented_ice_cloudmasked)
-    segmented_a_filename =
-        "$(test_output_dir)/segmented_a_" *
-        Dates.format(Dates.now(), "yyyy-mm-dd-HHMMSS") *
-        ".png"
-    IceFloeTracker.@persist segmented_A segmented_a_filename
+    IceFloeTracker.@persist segmented_A "./test/test_outputs/segmented_a.png" true
 
     @time segmented_ice = IceFloeTracker.kmeans_segmentation(
         ice_water_discriminated_image, ice_labels
     )
-    segmented_ice_filename =
-        "$(test_output_dir)/segmented_ice_" *
-        Dates.format(Dates.now(), "yyyy-mm-dd-HHMMSS") *
-        ".png"
-    IceFloeTracker.@persist segmented_ice segmented_ice_filename
+    IceFloeTracker.@persist segmented_ice "./test/test_outputs/segmented_a_ice.png" true
 
     @test typeof(segmented_A) == typeof(matlab_segmented_A_bitmatrix)
     @test test_similarity(matlab_segmented_A_bitmatrix, segmented_A, 0.032)

test/test-segmentation-f.jl

@@ -4,16 +4,16 @@
 
     ## Load inputs for comparison
     segmentation_B_not_ice_mask = float64.(load("$(test_data_dir)/matlab_not_ice_mask.png"))
-    segmentation_C_ice_mask = load(segmented_c_test_file) .> 0.5
+    segmentation_C_ice_mask = load(segmented_c_test_file) .>= 0.5
     cloudmask = convert(BitMatrix, load(cloudmask_test_file))
     landmask = convert(BitMatrix, load(current_landmask_file))
-    watershed_intersect = load(watershed_test_file) .> 0.5
+    watershed_intersect = load(watershed_test_file) .>= 0.5
     ice_labels =
         Int64.(
             vec(DelimitedFiles.readdlm("$(test_data_dir)/ice_labels_floe_region.csv", ','))
         )
     matlab_isolated_floes =
-        float64.(load("$(test_data_dir)/matlab_isolated_floes.png")) .> 0.5
+        float64.(load("$(test_data_dir)/matlab_isolated_floes.png")) .>= 0.5
 
     ## Run function with Matlab inputs