Feat(tracker): add rotation calculations

IFTPipeline.jl/Project.toml

@@ -7,6 +7,8 @@ version = "0.1.0"
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 FixedPointNumbers = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 Folds = "41a02a25-b8f0-4f67-bc48-60067656b558"
@@ -20,13 +22,17 @@ Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
 
 [compat]
 ArgParse = "1.1"
+DataFrames = "1.7.0"
+Dates = "1.10.9"
 Folds = "0.2"
 HDF5 = "0.16, 0.17"
 IceFloeTracker = "0.6.4"
 LoggingExtras = "1.0"
 Pkg = "1.9"
 PyCall = "1.96"
 TOML = "1.0"
+TimeZones = "1.21.3"

IFTPipeline.jl/src/IFTPipeline.jl

@@ -49,6 +49,7 @@ include("preprocess.jl")
 include("feature-extraction.jl")
 include("tracker.jl")
 include("h5.jl")
+include("rotations.jl")
 
 export cache_vector,
     sharpen,
@@ -77,7 +78,8 @@ export cache_vector,
     mkclitrack!,
     mkfilenames,
     makeh5files,
-    getlatlon
+    getlatlon,
+    get_rotation_single
 
 export IceFloeTracker
 end

IFTPipeline.jl/src/cli.jl

@@ -4,6 +4,7 @@ using ArgParse
 using IceFloeTracker
 using IFTPipeline
 using Serialization
+using TimeZones
 
 function mkclipreprocess!(settings)
     @add_arg_table! settings["preprocess"] begin
@@ -318,7 +319,7 @@ function mkclimakeh5_single!(settings)
         "--passtime"
         help = "Satellite pass time"
         required = true
-        arg_type = DateTime
+        arg_type = ZonedDateTime
 
         "--truecolor"
         help = "Path to truecolor image"
@@ -498,7 +499,7 @@ function mkclitrack_single!(settings)
         help = "Path to object with satellite pass times"
         required = true
         nargs = '+'
-        arg_type = DateTime
+        arg_type = ZonedDateTime
 
         "--latlon"
         help = "Path to geotiff image with latitude/longitude data"
@@ -645,6 +646,19 @@ function mkclilandmask_single!(settings)
     return nothing
 end
 
+function mkcli_get_rotation_single!(settings)
+    @add_arg_table! settings["get_rotation_single"] begin
+        "--input", "-i"
+        help = "Tracked floes CSV file with a 'satellite' column"
+        required = true
+
+        "--output", "-o"
+        help = "Tracked floes CSV file with rotations calculated"
+        required = true
+    end
+    return nothing
+end
+
 function mkcli!(settings, common_args)
     d = Dict(
         "landmask" => mkclilandmask!,
@@ -658,6 +672,7 @@ function mkcli!(settings, common_args)
         "makeh5files_single" => mkclimakeh5_single!,
         "track" => mkclitrack!,
         "track_single" => mkclitrack_single!,
+        "get_rotation_single" => mkcli_get_rotation_single!,
     )
 
     for t in keys(d)
@@ -714,6 +729,10 @@ function main()
         "track_single"
         help = "Pair ice floes in day k with ice floes in day k+1"
         action = :command
+
+        "get_rotation_single"
+        help = "Get rotation of the ice floes"
+        action = :command
     end
 
     command_common_args = []

IFTPipeline.jl/src/h5.jl

@@ -139,7 +139,7 @@ function makeh5files(;
 end
 
 function makeh5files_single(;
-    passtime::DateTime,
+    passtime::ZonedDateTime,
     iftversion::Union{String,Nothing}=nothing,
     truecolor::String,
     falsecolor::String,
@@ -148,7 +148,7 @@ function makeh5files_single(;
     output::String,
 )
     latlondata = getlatlon(truecolor)
-    ptsunix = Int64(Dates.datetime2unix(passtime))
+    ptsunix = Int64(Dates.datetime2unix(DateTime(passtime)))
     labeled_ = load_labeled_img(labeled)
 
     if isnothing(iftversion)

IFTPipeline.jl/src/rotations.jl

@@ -0,0 +1,136 @@
+using DataFrames
+using TimeZones
+using Dates
+using CSV
+
+# Base.tryparse(::Type{ZonedDateTime}, str) = ZonedDateTime
+# default_format(::Type{ZonedDateTime}) = Format("yyyy-mm-dd\\THH:MM:SS.sZ")
+
+"""
+Make a CSV of pairwise rotations between floes detected on adjacent days. 
+
+Loads the floes from the `input` CSV file, and uses the columns:
+- `floe` ID
+- `satellite` name
+- `mask` – the binary mask (choose a column using argument `mask_column`)
+- `passtime` in ISO8601 format (with trailing Z or +00:00), e.g. 2022-09-11T09:21:00+00:00  (choose a column using argument `time_column`)
+- `date` of the overpass in YYYY-MM-DD format
+
+Returns a CSV with one row per floe comparison. 
+In the following, `i=1` means the earlier observation, `i=2` the later.
+
+Columns returned:
+- `ID` of the floe
+- Angle measures `theta_<deg,rad>` – angle between floe image in degrees or radians
+- Time measurements:
+  - `delta_time_sec` – number of seconds between overpass in the two measurements
+  - `omega_<deg,rad>_per_<sec,hour,day>` – mean angular velocity of rotation in degrees or radians per second hour or day.
+- Metadata 
+  - `satellite<i>` – which satellite measurement `i` was from
+  - `date<i>` – which date measurement `i` was taken
+  - `datetime<i>` – which UTC time measurement `i`'s overpass occurred
+- Original data
+  - `mask<i>` – the binary mask used for the measurement
+"""
+function get_rotation_single(;
+    input::String, output::String, mask_column=:mask, time_column=:passtime
+)
+    input_df = DataFrame(CSV.File(input))
+
+    input_df[!, mask_column] = eval.(Meta.parse.(input_df[:, mask_column]))
+    input_df[!, time_column] = ZonedDateTime.(input_df[:, time_column])
+
+    results = []
+    for row in eachrow(input_df)
+        append!( # adds the 0 – n measurements from `get_rotation_measurements` to the results array
+            results,
+            get_rotation_measurements(
+                row, input_df; mask_column=mask_column, time_column=time_column
+            ),
+        )
+    end
+    results_df = DataFrame(results)
+    @info results_df
+
+    FileIO.save(output, results_df)
+    return results_df
+end
+
+function get_rotation_measurements(
+    measurement::DataFrameRow, df::DataFrame; mask_column, time_column
+)
+    filtered_df = subset(
+        df,
+        :ID => ByRow(==(measurement[:ID])),
+        :date => ByRow(==(measurement[:date] - Dates.Day(1))),
+    )
+
+    results = [
+        get_rotation_measurements(
+            earlier_measurement, measurement; mask_column, time_column
+        ) for earlier_measurement in eachrow(filtered_df)
+    ]
+
+    return results
+end
+
+function get_rotation_measurements(
+    row1::DataFrameRow, row2::DataFrameRow; mask_column, time_column
+)
+    theta_rad = get_rotation(row1[mask_column], row2[mask_column])
+    theta_deg = rad2deg(theta_rad)
+
+    dt = row2[time_column] - row1[time_column]
+    dt_sec = dt / Dates.Second(1)
+    dt_hour = dt / Dates.Hour(1)
+    dt_day = dt / Dates.Day(1)
+
+    omega_deg_per_sec = (theta_deg) / (dt_sec)
+    omega_deg_per_hour = (theta_deg) / (dt_hour)
+    omega_deg_per_day = (theta_deg) / (dt_day)
+
+    omega_rad_per_sec = (theta_rad) / (dt_sec)
+    omega_rad_per_hour = (theta_rad) / (dt_hour)
+    omega_rad_per_day = (theta_rad) / (dt_day)
+
+    return (
+        ID=row1.ID,
+        theta_deg,
+        theta_rad,
+        delta_time_sec=dt_sec,
+        omega_deg_per_sec,
+        omega_deg_per_hour,
+        omega_deg_per_day,
+        omega_rad_per_sec,
+        omega_rad_per_hour,
+        omega_rad_per_day,
+        satellite1=row1.satellite,
+        satellite2=row2.satellite,
+        date1=row1.date,
+        date2=row2.date,
+        datetime1=row1[time_column],
+        datetime2=row2[time_column],
+        mask1=row1[mask_column],
+        mask2=row2[mask_column],
+    )
+end
+
+"""
+Get the angle in radians to rotate mask1 to mask2.
+"""
+function get_rotation(
+    mask1, mask2; mxshift::Tuple{Int64,Int64}=(100, 100), mxrot::Float64=Float64(pi)
+)
+    affine_map, _ = IceFloeTracker.Register.RegisterQD.qd_rigid(
+        IceFloeTracker.centered(mask1),
+        IceFloeTracker.centered(mask2),
+        mxshift,
+        mxrot;
+        print_interval=typemax(Int),
+    )
+    linear_map = affine_map.linear
+    cosθ = linear_map[1, 1]
+    sinθ = linear_map[2, 1]
+    θ = atan(sinθ, cosθ)
+    return θ
+end

IFTPipeline.jl/src/tracker.jl

@@ -42,7 +42,7 @@ end
     track_single(
         imgs::Array{String},
         props::Array{String},
-        passtimes::Array{DateTime},
+        passtimes::Array{ZonedDateTime},
         latlon::String,
         output::String,
         ...
@@ -65,7 +65,7 @@ Following are the default set of thresholds `condition_thresholds` used for floe
 function track_single(;
     imgs::Array{String},
     props::Array{String},
-    passtimes::Array{DateTime},
+    passtimes::Array{ZonedDateTime},
     latlon::String,
     output::String,
     dist::Array{Int}=[15, 30, 120],
@@ -139,7 +139,7 @@ function track_single(;
     adduuid!(props_)
 
     tracked_floes = long_tracker(props_, condition_thresholds, mc_thresholds)
-    FileIO.save(output, select!(tracked_floes, Not(:mask, :psi)))
+    FileIO.save(output, select!(tracked_floes, Not(:psi)))
     return tracked_floes
 end
 

IFTPipeline.jl/test/Project.toml

@@ -6,6 +6,7 @@ Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 ImageTransformations = "02fcd773-0e25-5acc-982a-7f6622650795"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

IFTPipeline.jl/test/test_inputs/rotation/floes.tracked.synthetic.csv

@@ -0,0 +1,8 @@
+ID,satellite,passtime,date,mask
+1,terra,2020-01-01T12:00:00Z,2020-01-01,Bool[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
+1,terra,2020-01-02T12:00:00Z,2020-01-02,Bool[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
+1,terra,2020-01-03T12:00:00Z,2020-01-03,Bool[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
+1,terra,2020-01-04T12:00:00Z,2020-01-04,Bool[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
+1,terra,2020-01-05T12:00:00Z,2020-01-05,Bool[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
+1,terra,2020-01-06T12:00:00Z,2020-01-06,Bool[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
+1,terra,2020-01-06T12:00:00Z,2020-01-06,Bool[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0; 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0; 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ]

PythonSetupForIFTPipeline.jl/setup.jl

@@ -1,6 +1,5 @@
 # Instantiate all the dependencies
 using Pkg
-Pkg.instantiate()
 
 # Force PyCall to use the Conda version on Linux.
 ENV["PYTHON"] = ""

csvjoin/.gitignore

@@ -0,0 +1,98 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json

csvjoin/README.md

@@ -0,0 +1,15 @@
+# csvjoin
+
+The joiner combines two csv files using a simple join.
+
+## Run the code
+
+You can run the local version of the code from this directory by calling
+```bash
+pipx run . csvjoin
+```
+
+You can run the code anywhere by calling:
+```bash
+pipx run --spec "git+https://github.com/wilhelmuslab/ice-floe-tracker-pipeline#egg=csvjoin&subdirectory=csvjoin" csvjoin
+```

csvjoin/csvjoin.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3.11
+"""Utility to join two csv files."""
+
+from enum import Enum
+from functools import partial
+import pathlib
+from typing import Annotated
+
+import pandas
+import typer
+
+app = typer.Typer()
+
+
+class HOW(str, Enum):
+    left = "left"
+    right = "right"
+    outer = "outer"
+    inner = "inner"
+    cross = "cross"
+
+
+@app.command()
+def main(
+    left: Annotated[pathlib.Path, typer.Argument(help="path to left csv file")],
+    left_on: Annotated[str, typer.Argument(help="column on which to join")],
+    right: Annotated[pathlib.Path, typer.Argument(help="path to right csv file")],
+    right_on: Annotated[str, typer.Argument(help="column on which to join")],
+    output: Annotated[pathlib.Path, typer.Argument(help="path to output csv file")],
+    how: Annotated[HOW, typer.Option(help="type of join")] = HOW.left,
+    on_is_utc: Annotated[
+        bool, typer.Option(help="`on` is a datetime which should be treated as UTC")
+    ] = False,
+):
+    """Join two csv files."""
+    left_df = read_df(path=left, index_col=left_on, on_is_utc=on_is_utc)
+    right_df = read_df(path=right, index_col=right_on, on_is_utc=on_is_utc)
+    output_df = left_df.join(right_df, how=how.value)
+    output_df.to_csv(output, date_format="%Y-%m-%dT%H:%M:%SZ")
+
+def read_df(path, index_col, on_is_utc=False):
+    read_kwargs = dict(index_col=index_col)
+    if on_is_utc:
+        read_kwargs["converters"] = {index_col: partial(pandas.to_datetime, utc=True)}
+    df = pandas.read_csv(path, **read_kwargs)
+    return df
+
+if __name__ == "__main__":
+    app()

csvjoin/pyproject.toml

@@ -0,0 +1,26 @@
+[project]
+name = "csvjoin"
+version = "0.1.0"
+description = "Utility to join two csv files."
+requires-python = ">=3.10"
+authors = [{ name = "John G. Holland", email = "john_holland1@brown.edu" }]
+
+
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3 :: Only",
+]
+
+dependencies = ["typer", "pandas"]
+
+[project.scripts]
+csvjoin = "csvjoin:app"
+
+[build-system]
+requires = ["setuptools>=43.0.0", "wheel", "hatchling"]
+build-backend = "hatchling.build"

csvjoin/test/data_with_Z.csv

@@ -0,0 +1,9 @@
+overpass time,measurement
+2022-09-14T08:12:55Z,dogs
+2022-09-14T13:02:42Z,cats
+2022-09-15T08:55:28Z,dogs
+2022-09-15T12:07:34Z,cats
+2022-09-14T08:12:55Z,moose
+2022-09-14T13:02:42Z,moose
+2022-09-15T08:55:28Z,moose
+2022-09-15T12:07:34Z,moose

csvjoin/test/data_without_Z.csv

@@ -0,0 +1,9 @@
+overpass time,measurement
+2022-09-14T08:12:55,dogs
+2022-09-14T13:02:42,cats
+2022-09-15T08:55:28,dogs
+2022-09-15T12:07:34,cats
+2022-09-14T08:12:55,moose
+2022-09-14T13:02:42,moose
+2022-09-15T08:55:28,moose
+2022-09-15T12:07:34,moose

csvjoin/test/expected-output.csv

@@ -0,0 +1,9 @@
+overpass time,measurement,date,satellite
+2022-09-14T08:12:55Z,dogs,2022-09-14,aqua
+2022-09-14T13:02:42Z,cats,2022-09-14,terra
+2022-09-15T08:55:28Z,dogs,2022-09-15,aqua
+2022-09-15T12:07:34Z,cats,2022-09-15,terra
+2022-09-14T08:12:55Z,moose,2022-09-14,aqua
+2022-09-14T13:02:42Z,moose,2022-09-14,terra
+2022-09-15T08:55:28Z,moose,2022-09-15,aqua
+2022-09-15T12:07:34Z,moose,2022-09-15,terra

csvjoin/test/times.csv

@@ -0,0 +1,5 @@
+date,satellite,overpass time
+2022-09-14,aqua,2022-09-14T08:12:55Z
+2022-09-14,terra,2022-09-14T13:02:42Z
+2022-09-15,aqua,2022-09-15T08:55:28Z
+2022-09-15,terra,2022-09-15T12:07:34Z

workflow/flow.cylc

@@ -22,7 +22,7 @@
 
             done[-P1D] => done
         """
-        R1/P0Y = done => tracking 
+        R1/P0Y = done => tracking => get_rotation
 
     [[queues]]
         [[[fetchdata]]]
@@ -50,6 +50,8 @@
             date=$(isodatetime "$CYLC_TASK_CYCLE_POINT" --print-format CCYY-MM-DD)
             date_without_dashes=${date//-/}
             all_overpass_time_file="overpass-times.csv"
+            tracked_floes_file="floes.tracked.csv"
+            rotation_tracked_floes_file="floes.tracked.rotation.csv"
 
             {% if IFT_INSTALL == "Inject" %}
                 IFT={{ IFT_COMMAND }}
@@ -85,6 +87,14 @@
                 {{ raise('COLORIZE_INSTALL not recognized.') }}
             {% endif %}
 
+            {% if CSVJOIN_INSTALL == "Inject" %}
+                CSVJOIN = {{ CSVJOIN_COMMAND }}
+            {% elif CSVJOIN_INSTALL == "Source" %}
+                CSVJOIN = "pipx run --spec git+https://github.com/wilhelmuslab/ice-floe-tracker-pipeline@{{ CSVJOIN_VERSION }}#subdirectory=csvjoin csvjoin"
+            {% else %}
+                {{ raise('CSVJOIN_INSTALL not recognized.') }}
+            {% endif %}
+
             JULIA_DEBUG={{ JULIA_DEBUG }}
 
     [[done]]
@@ -106,6 +116,11 @@
         script = """
             ${COLORIZE} --help
         """
+    [[init_csvjoin]]
+        inherit = INIT
+        script = """
+            ${CSVJOIN} --help
+        """
     [[init_iftp]]
         inherit = INIT
         script = """
@@ -293,7 +308,7 @@
         # Package intermediate and final outputs into HDF5 files
         script = """
         ${IFT} makeh5files_single \
-            --passtime "$(cat ${overpass_time_file} | tr -d 'Z\n\r')" \
+            --passtime "$(cat ${overpass_time_file} | tr -d '\n\r')" \
             --truecolor ${truecolor_file} \
             --falsecolor ${falsecolor_file} \
             --labeled ${labeled_file} \
@@ -315,8 +330,8 @@
                 --imgs ${images[@]} \
                 --props ${props[@]} \
                 --latlon ${landmasks[0]} \
-                --passtimes $(cat ${passtimes[@]} | tr 'Z\n\r' ' ') \
-                --output floes.tracked.csv \
+                --passtimes $(cat ${passtimes[@]} | tr '\n\r' ' ') \
+                --output ${tracked_floes_file} \
                 --dist {{ TRACK_DIST | join(" ") }} \
                 --dt-thresh {{ TRACK_DT_THRESH | join(" ") }} \
                 --Sminimumarea {{ TRACK_SMINIMUMAREA }} \
@@ -341,3 +356,16 @@
         """
         [[[directives]]]
             --mem = 64G
+
+    [[get_rotation]]
+        script = """
+        tracked_floes_with_satellites=${tracked_floes_file/.csv/.satellite.csv}
+        ${CSVJOIN} \
+            ${tracked_floes_file} "passtime" \
+            ${all_overpass_time_file} "overpass time" \
+            ${tracked_floes_with_satellites} \
+            --on-is-utc
+        ${IFT} get_rotation_single \
+            -i ${tracked_floes_with_satellites} \
+            -o ${rotation_tracked_floes_file}
+        """

workflow/rose-suite.conf

@@ -51,6 +51,13 @@ COLORIZE_INSTALL="Source"
 COLORIZE_VERSION="v2.0.0"
 COLORIZE_COMMAND="" 
 
+#--------------------------------------------------
+# CSV Joiner
+#--------------------------------------------------
+CSVJOIN_INSTALL="Inject"
+CSVJOIN_VERSION="v0.1.0"
+CSVJOIN_COMMAND="pipx run --spec /project/pipeline/csvjoin csvjoin"
+
 #--------------------------------------------------
 # Preprocessing Options
 #--------------------------------------------------