feat(tracker): add long tracker support

IFTPipeline.jl/src/IFTPipeline.jl

@@ -8,7 +8,7 @@ using ArgParse
 using LoggingExtras
 using IceFloeTracker
 using IceFloeTracker: DataFrames, Dates, @dateformat_str, DataFrame, nrow, rename!, Not, select!, Date, Time, DateTime
-using IceFloeTracker: RGB, Gray, load, float64, imsharpen, getlatlon, pairfloes
+using IceFloeTracker: RGB, Gray, load, float64, imsharpen, getlatlon, pairfloes, add_passtimes!, addfloemasks!, addψs!, adduuid!, long_tracker
 using Folds
 using HDF5
 using TOML: parsefile

IFTPipeline.jl/src/tracker.jl

@@ -89,7 +89,7 @@ function track_single(;
 
     # Load the files – can we drop the memory requirements by doing two at once?
     @info "Loading $imgs"
-    imgs_ = [load_labeled_img(img) for img in imgs]
+    imgs_::Vector{Matrix{<:Integer}} = [load_labeled_img(img) for img in imgs]
 
     @info "Loading $props"
     props_ = [DataFrame(CSV.File(prop)) for prop in props]
@@ -140,8 +140,13 @@ function track_single(;
         ),
     )
 
-    labeled_floes = IceFloeTracker.pairfloes(imgs_, props_, passtimes, latlon, condition_thresholds, mc_thresholds)
-    FileIO.save(output, labeled_floes)
+    add_passtimes!(props_, passtimes)
+    addfloemasks!(props_, imgs_)
+    addψs!(props_)
+    adduuid!(props_)
+
+    tracked_floes = long_tracker(props_, condition_thresholds, mc_thresholds)
+    FileIO.save(output, tracked_floes)
     return nothing
 end
 

test/test-IFTPipeline.jl-cli.sh

@@ -29,8 +29,7 @@ initialize_test_directory () {
     : "${DATA_SOURCE:=./input_data}"
     echo "DATA_SOURCE=${DATA_SOURCE}"
 
-    TEMPDIR=$(mktemp -d -p .)
-    : "${DATA_TARGET:=$TEMPDIR}"
+    : "${DATA_TARGET:=$(mktemp -d -p .)}"
     echo "DATA_TARGET=${DATA_TARGET}"
 
     mkdir -p ${DATA_TARGET}/
@@ -121,25 +120,25 @@ track () {
 
     DATA_SOURCES=$@
 
-    TEMPDIR=$(mktemp -d -p .)
-    : "${_DATA_TARGET:=$TEMPDIR}"
-    echo "_DATA_TARGET=${_DATA_TARGET}"
+    local DATA_ROOT
+    : "${DATA_ROOT:=$(mktemp -d -p .)}"
+    echo "DATA_ROOT=${DATA_ROOT}"
 
-    _DATA_TARGET_SUBDIRS=()
+    DATA_ROOT_SUBDIRS=()
 
     for source in ${DATA_SOURCES[@]}
     do
-        _THIS_SUBDIR=${_DATA_TARGET}/$(basename $source)/
-        _DATA_TARGET_SUBDIRS+=(${_THIS_SUBDIR})
+        _THIS_SUBDIR=${DATA_ROOT}/$(basename $source)/
+        DATA_ROOT_SUBDIRS+=(${_THIS_SUBDIR})
         ${PREPROCESS} ${source} ${_THIS_SUBDIR}
     done
 
     ${IFT} track_single \
-        --imgs "${_DATA_TARGET_SUBDIRS[@]/%/labeled.tiff}" \
-        --props "${_DATA_TARGET_SUBDIRS[@]/%/labeled.props.csv}" \
-        --latlon "${_DATA_TARGET_SUBDIRS[1]/%/truecolor.tiff}" \
-        --passtimes $(cat ${_DATA_TARGET_SUBDIRS[@]/%/overpass.txt} | tr '\n' ' ') \
-        --output ${_DATA_TARGET}/paired.csv
+        --imgs "${DATA_ROOT_SUBDIRS[@]/%/labeled.tiff}" \
+        --props "${DATA_ROOT_SUBDIRS[@]/%/labeled.props.csv}" \
+        --latlon "${DATA_ROOT_SUBDIRS[1]/%/truecolor.tiff}" \
+        --passtimes $(cat ${DATA_ROOT_SUBDIRS[@]/%/overpass.txt} | tr '\n' ' ') \
+        --output ${DATA_ROOT}/paired.csv
 }
 
 

workflow/flow.cylc

@@ -248,8 +248,6 @@
     [[tracking]]
         execution retry delays = PT10M
         execution time limit = PT120M
-        [[[directives]]]
-            --mem = 64G
         # Pair and track identified floes across days
         script = """
             images=(*/labeled.tiff)
@@ -261,6 +259,8 @@
                 --imgs ${images[@]} \
                 --props ${props[@]} \
                 --latlon ${landmasks[0]} \
-                --passtimes $(cat ${passtimes[@]} | tr '\n' ' ') \
+                --passtimes $(cat ${passtimes[@]} | tr 'Z\n\r' ' ') \
                 --output floes.tracked.csv
-        """
+        """
+        [[[directives]]]
+            --mem = 64G

workflow/rose-suite.conf

@@ -21,11 +21,11 @@ PREPROCESSING="Lopez"  # "Lopez" or "Buckley"
 
 # Lopez Ice Floe Tracker settings
 # "Apptainer" or "Docker" or "Inject"
-IFT_INSTALL="Inject"
-# Version of the container image
-IFT_VERSION="v2.0-beta.2"
+IFT_INSTALL="Docker"
+# Version of the container image for "Apptainer" or "Docker" install mode
+IFT_VERSION="v2.0.0"
 # Command to run the IFT CLI if using "Inject" install mode
-IFT_COMMAND="julia --project=/workspaces/ice-floe-tracker-workspace/ice-floe-tracker-pipeline/IFTPipeline.jl /workspaces/ice-floe-tracker-workspace/ice-floe-tracker-pipeline/IFTPipeline.jl/src/cli.jl"
+IFT_COMMAND="julia --project=/path/to/IFTPipeline.jl / /path/to/IFTPipeline.jl/src/cli.jl"
 
 # Buckley Floe Size Distribution preprocessing settings
  # "Source" or "Inject"