Merge pull request #358 from WilhelmusLab/fixing_reflectance_name_con…

…vention

Fixing reflectance name convention

src/cloudmask.jl

@@ -1,10 +1,10 @@
 """
-    create_cloudmask(reflectance_image; prelim_threshold, band_7_threshold, band_2_threshold, ratio_lower, ratio_upper)
+    create_cloudmask(falsecolor_image; prelim_threshold, band_7_threshold, band_2_threshold, ratio_lower, ratio_upper)
 
 Convert a 3-channel false color reflectance image to a 1-channel binary matrix; clouds = 0, else = 1. Default thresholds are defined in the published Ice Floe Tracker article: Remote Sensing of the Environment 234 (2019) 111406.
 
 # Arguments
-- `reflectance_image`: corrected reflectance false color image - bands [7,2,1]
+- `falsecolor_image`: corrected reflectance false color image - bands [7,2,1]
 - `prelim_threshold`: threshold value used to identify clouds in band 7, N0f8(RGB intensity/255)
 - `band_7_threshold`: threshold value used to identify cloud-ice in band 7, N0f8(RGB intensity/255)
 - `band_2_threshold`: threshold value used to identify cloud-ice in band 2, N0f8(RGB intensity/255)
@@ -41,12 +41,12 @@ function create_cloudmask(
 end
 
 """
-    apply_cloudmask(reflectance_image, cloudmask)
+    apply_cloudmask(ref_image, cloudmask)
 
 Zero out pixels containing clouds where clouds and ice are not discernable. Arguments should be of the same size.
 
 # Arguments
-- `reference_image`: corrected reflectance false color image - bands [7,2,1] or grayscale
+- `ref_image`: reference image, e.g. corrected reflectance false color image bands [7,2,1] or grayscale
 - `cloudmask`: binary cloudmask with clouds = 0, else = 1
 
 """

src/find_ice_labels.jl

@@ -29,12 +29,12 @@ function find_reflectance_peaks(
 end
 
 """
-    find_ice_labels(reflectance_image, landmask; band_7_threshold, band_2_threshold, band_1_threshold, band_7_relaxed_threshold, band_1_relaxed_threshold, possible_ice_threshold)
+    find_ice_labels(falsecolor_image, landmask; band_7_threshold, band_2_threshold, band_1_threshold, band_7_relaxed_threshold, band_1_relaxed_threshold, possible_ice_threshold)
 
-Locate the pixels of obvious ice from false color reflectance image. Returns a binary mask with ice floes contrasted from background. Default thresholds are defined in the published Ice Floe Tracker article: Remote Sensing of the Environment 234 (2019) 111406.
+Locate the pixels of likely ice from false color reflectance image. Returns a binary mask with ice floes contrasted from background. Default thresholds are defined in the published Ice Floe Tracker article: Remote Sensing of the Environment 234 (2019) 111406.
 
 # Arguments
-- `reflectance_image`: corrected reflectance false color image - bands [7,2,1]
+- `falsecolor_image`: corrected reflectance false color image - bands [7,2,1]
 - `landmask`: bitmatrix landmask for region of interest
 - `band_7_threshold`: threshold value used to identify ice in band 7, N0f8(RGB intensity/255)
 - `band_2_threshold`: threshold value used to identify ice in band 2, N0f8(RGB intensity/255)
@@ -44,7 +44,7 @@ Locate the pixels of obvious ice from false color reflectance image. Returns a b
 
 """
 function find_ice_labels(
-    reflectance_image::Matrix{RGB{Float64}},
+    falsecolor_image::Matrix{RGB{Float64}},
     landmask::BitMatrix;
     band_7_threshold::Float64=Float64(5 / 255),
     band_2_threshold::Float64=Float64(230 / 255),
@@ -55,7 +55,7 @@ function find_ice_labels(
 )::Vector{Int64}
 
     ## Make ice masks
-    cv = channelview(reflectance_image)
+    cv = channelview(falsecolor_image)
 
     mask_ice_band_7 = @view(cv[1, :, :]) .< band_7_threshold #5 / 255
     mask_ice_band_2 = @view(cv[2, :, :]) .> band_2_threshold #230 / 255
@@ -64,7 +64,7 @@ function find_ice_labels(
     ice_labels = remove_landmask(landmask, ice)
     # @info "Done with masks" # to uncomment when logger is added
 
-    ## Find obvious ice floes
+    ## Find likely ice floes
     if sum(abs.(ice_labels)) == 0
         mask_ice_band_7 = @view(cv[1, :, :]) .< band_7_threshold_relaxed #10 / 255
         mask_ice_band_1 = @view(cv[3, :, :]) .> band_1_threshold_relaxed #190 / 255

src/ice-water-discrimination.jl

@@ -1,6 +1,6 @@
 """
     discriminate_ice_water(
-    reflectance_image::Matrix{RGB{Float64}},
+    falsecolor_image::Matrix{RGB{Float64}},
     normalized_image::Matrix{Gray{Float64}},
     landmask_bitmatrix::T,
     cloudmask_bitmatrix::T,
@@ -19,16 +19,16 @@
 
 
 
-Generates an image with ice floes apparent after filtering and combining previously processed versions of reflectance and truecolor images from the same region of interest. Returns an image ready for segmentation to isolate floes.
+Generates an image with ice floes apparent after filtering and combining previously processed versions of falsecolor and truecolor images from the same region of interest. Returns an image ready for segmentation to isolate floes.
 
-Note: This function mutates the landmask object to avoid unnecessary memory allocation. If you need the original landmask, make a copy before passing it to this function. Example: `discriminate_ice_water(reflectance_image, normalized_image, copy(landmask_bitmatrix), cloudmask_bitmatrix)`
+Note: This function mutates the landmask object to avoid unnecessary memory allocation. If you need the original landmask, make a copy before passing it to this function. Example: `discriminate_ice_water(falsecolor_image, normalized_image, copy(landmask_bitmatrix), cloudmask_bitmatrix)`
 
 # Arguments
-- `reflectance_image`: input image in false color reflectance
+- `falsecolor_image`: input image in false color reflectance
 - `normalized_image`: normalized version of true color image
 - `landmask_bitmatrix`: landmask for region of interest
 - `cloudmask_bitmatrix`: cloudmask for region of interest
-- `floes_threshold`: heuristic applied to original reflectance image
+- `floes_threshold`: heuristic applied to original false color image
 - `mask_clouds_lower`: lower heuristic applied to mask out clouds
 - `mask_clouds_upper`: upper heuristic applied to mask out clouds
 - `kurt_thresh_lower`: lower heuristic used to set pixel value threshold based on kurtosis in histogram
@@ -42,7 +42,7 @@ Note: This function mutates the landmask object to avoid unnecessary memory allo
 
 """
 function discriminate_ice_water(
-    reflectance_image::Matrix{RGB{Float64}},
+    falsecolor_image::Matrix{RGB{Float64}},
     normalized_image::Matrix{Gray{Float64}},
     landmask_bitmatrix::T,
     cloudmask_bitmatrix::T,
@@ -59,16 +59,16 @@ function discriminate_ice_water(
     nbins::Real=155,
 )::AbstractMatrix where {T<:AbstractArray{Bool}}
     clouds_channel = IceFloeTracker.create_clouds_channel(
-        cloudmask_bitmatrix, reflectance_image
+        cloudmask_bitmatrix, falsecolor_image
     )
-    reflectance_image_band7 = @view(channelview(reflectance_image)[1, :, :])
+    falsecolor_image_band7 = @view(channelview(falsecolor_image)[1, :, :])
 
     # first define all of the image variations
     image_clouds = IceFloeTracker.apply_landmask(clouds_channel, landmask_bitmatrix) # output during cloudmask apply, landmasked 
     image_cloudless = IceFloeTracker.apply_landmask(
-        reflectance_image_band7, landmask_bitmatrix
-    ) # channel 1 (band 7) from source reflectance image, landmasked
-    image_floes = IceFloeTracker.apply_landmask(reflectance_image, landmask_bitmatrix) # source reflectance, landmasked
+        falsecolor_image_band7, landmask_bitmatrix
+    ) # channel 1 (band 7) from source falsecolor image, landmasked
+    image_floes = IceFloeTracker.apply_landmask(falsecolor_image, landmask_bitmatrix) # source false color reflectance, landmasked
     image_floes_view = channelview(image_floes)
 
     floes_band_2 = @view(image_floes_view[2, :, :])

test/config.jl

@@ -4,8 +4,8 @@
 test_data_dir = "./test_inputs"
 test_output_dir = "./test_outputs"
 truecolor_test_image_file = "$(test_data_dir)/NE_Greenland_truecolor.2020162.aqua.250m.tiff"
-reflectance_test_image_file = "$(test_data_dir)/NE_Greenland_reflectance.2020162.aqua.250m.tiff"
-reflectance_b7_test_file = "$(test_data_dir)/ref_image_b7.png"
+falsecolor_test_image_file = "$(test_data_dir)/NE_Greenland_reflectance.2020162.aqua.250m.tiff"
+falsecolor_b7_test_file = "$(test_data_dir)/ref_image_b7.png"
 landmask_file = "$(test_data_dir)/landmask.tiff"
 landmask_no_dilate_file = "$(test_data_dir)/landmask_no_dilate.png"
 current_landmask_file = "$(test_data_dir)/current_landmask.png"

test/test-create-cloudmask.jl

@@ -5,7 +5,7 @@
     # define constants, maybe move to test config file
     matlab_cloudmask_file = "$(test_data_dir)/matlab_cloudmask.tiff"
     println("--------- Create and apply cloudmask --------")
-    ref_image = float64.(load(reflectance_test_image_file)[test_region...])
+    ref_image = float64.(load(falsecolor_test_image_file)[test_region...])
 
     matlab_cloudmask = float64.(load(matlab_cloudmask_file))
     @time cloudmask = IceFloeTracker.create_cloudmask(ref_image)

test/test-discrim-ice-water.jl

@@ -2,10 +2,10 @@
     println("------------------------------------------------")
     println("------------ Create Ice-Water Discrimination Test --------------")
     input_image = float64.(load(truecolor_test_image_file)[test_region...])
-    reflectance_image = float64.(load(reflectance_test_image_file)[test_region...])
+    falsecolor_image = float64.(load(falsecolor_test_image_file)[test_region...])
     landmask = convert(BitMatrix, load(current_landmask_file))
     landmask_no_dilate = convert(BitMatrix, float64.(load(landmask_no_dilate_file)))
-    cloudmask = IceFloeTracker.create_cloudmask(reflectance_image)
+    cloudmask = IceFloeTracker.create_cloudmask(falsecolor_image)
     matlab_ice_water_discrim =
         float64.(load("$(test_data_dir)/matlab_ice_water_discrim.png"))
 
@@ -15,7 +15,7 @@
         image_sharpened, image_sharpened_gray, landmask
     )
     ice_water_discrim = IceFloeTracker.discriminate_ice_water(
-        reflectance_image, normalized_image, landmask, cloudmask
+        falsecolor_image, normalized_image, landmask, cloudmask
     )
     @test (@test_approx_eq_sigma_eps ice_water_discrim matlab_ice_water_discrim [0, 0] 0.065) ==
         nothing

test/test-find-ice-labels.jl

@@ -2,21 +2,21 @@
     println("------------------------------------------------")
     println("------------ Create Ice Labels Test --------------")
 
-    reflectance_image = float64.(load(reflectance_test_image_file)[test_region...])
+    falsecolor_image = float64.(load(falsecolor_test_image_file)[test_region...])
     landmask = convert(BitMatrix, load(current_landmask_file))
     ice_labels_matlab = DelimitedFiles.readdlm(
         "$(test_data_dir)/ice_labels_matlab.csv", ','
     )
     ice_labels_matlab = vec(ice_labels_matlab)
 
-    @time ice_labels_julia = IceFloeTracker.find_ice_labels(reflectance_image, landmask)
+    @time ice_labels_julia = IceFloeTracker.find_ice_labels(falsecolor_image, landmask)
 
     DelimitedFiles.writedlm("ice_labels_julia.csv", ice_labels_julia, ',')
 
     @test ice_labels_matlab == ice_labels_julia
 
     @time ice_labels_ice_floe_region = IceFloeTracker.find_ice_labels(
-        reflectance_image[ice_floe_test_region...], landmask[ice_floe_test_region...]
+        falsecolor_image[ice_floe_test_region...], landmask[ice_floe_test_region...]
     )
 
     DelimitedFiles.writedlm("ice_labels_floe_region.csv", ice_labels_ice_floe_region, ',')