From 0318a0fe141aaca3090e6e3b8c5c1895746a8c01 Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Tue, 17 Jun 2025 11:05:10 +0000
Subject: [PATCH 1/3] #236 Update devcontainer

---
 .devcontainer/devcontainer.json |   24 +-
 poetry.lock                     | 2268 ----------------------------
 pyproject.toml                  |  100 +-
 uv.lock                         | 2497 +++++++++++++++++++++++++++++++
 4 files changed, 2566 insertions(+), 2323 deletions(-)
 delete mode 100644 poetry.lock
 create mode 100644 uv.lock

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 6586561..ed3c162 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,23 +1,16 @@
 {
     "name": "decode",
-    "image":"python:3.11",
-    "features": {
-        "ghcr.io/devcontainers-contrib/features/poetry:2": {
-            "version": "1.8.3"
-        }
-    },
-    "containerEnv": {
-        "POETRY_VIRTUALENVS_CREATE": "false"
-    },
+    "image": "ghcr.io/astral-sh/uv:python3.12-bookworm",
     "runArgs": [
         "--name=decode"
     ],
-    "postCreateCommand": "poetry install",
+    "containerEnv": {
+        "UV_PROJECT_ENVIRONMENT": "/usr/local"
+    },
+    "postCreateCommand": "uv sync --frozen",
     "customizations": {
         "vscode": {
             "extensions": [
-                "github.vscode-pull-request-github",
-                "mhutchie.git-graph",
                 "ms-python.black-formatter",
                 "ms-python.python",
                 "streetsidesoftware.code-spell-checker",
@@ -26,12 +19,11 @@
             "settings": {
                 "files.insertFinalNewline": true,
                 "files.trimTrailingWhitespace": true,
+                "python.analysis.autoImportCompletions": true,
+                "python.languageServer": "Pylance",
                 "[python]": {
                     "editor.defaultFormatter": "ms-python.black-formatter",
-                    "editor.formatOnSave": true,
-                    "editor.insertSpaces": true,
-                    "editor.tabSize": 4,
-                    "python.languageServer": "Pylance"
+                    "editor.formatOnSave": true
                 }
             }
         }
diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index cc49c21..0000000
--- a/poetry.lock
+++ /dev/null
@@ -1,2268 +0,0 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
-
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-version = "0.0.5"
-description = "A collection of accessible pygments styles"
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-    {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"},
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-
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-pygments = ">=1.5"
-
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-tests = ["hypothesis", "pytest"]
-
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-optional = false
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-    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
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-viz = ["matplotlib", "nc-time-axis", "seaborn"]
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-
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-cover = ["pytest-cov"]
-doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-enabler = ["pytest-enabler (>=2.2)"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
-type = ["pytest-mypy"]
-
-[metadata]
-lock-version = "2.0"
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diff --git a/pyproject.toml b/pyproject.toml
index 520a324..a249aa4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,8 @@
-[tool.poetry]
+[project]
 name = "decode"
 version = "2025.4.2"
 description = "DESHIMA code for data analysis"
-authors = [
-    "Akio Taniguchi <taniguchi.akio@gmail.com>",
-    "Juri Yamanaka <j.yamanaka@a.phys.nagoya-u.ac.jp>",
-    "Shinji Fujita <s-fujita@ism.ac.jp>",
-]
+readme = "README.md"
 keywords = [
     "astronomy",
     "data-analysis",
@@ -14,40 +10,66 @@ keywords = [
     "spectroscopy",
     "submillimeter",
 ]
-license = "MIT"
-readme = "README.md"
-homepage = "https://github.com/deshima-dev/decode/"
-documentation = "https://deshima-dev.github.io/decode/"
-
-[tool.poetry.dependencies]
-python = ">=3.9, <3.13"
-astropy = ">=6.0, <8.0"
-dems = "^2024.7"
-fire = ">=0.5, <1.0"
-matplotlib = "^3"
-numpy = ">=1.23, <3.0"
-pandas = "^2"
-scikit-learn = "^1"
-scipy = "^1"
-tomli_w = "^1"
-xarray = ">=2024.0, <2026.0"
-zarr = "^2"
-
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-black = "^25"
-ipython = ">=8.0, <10.0"
-myst-parser = ">=3.0, <5.0"
-pydata-sphinx-theme = ">=0.15, <1.0"
-pyright = "^1"
-pytest = "^8"
-sphinx = ">=7.0, <9.0"
-
-[tool.poetry.scripts]
+requires-python = ">=3.9,<3.13"
+dependencies = [
+    "astropy>=6,<8",
+    "dems>=2025.6,<2026.0",
+    "fire>=0.5,<1.0",
+    "matplotlib>=3,<4",
+    "numpy>=1.23,<3.0",
+    "pandas>=2,<3",
+    "pandas-stubs>=2,<3",
+    "scikit-learn>=1,<2",
+    "scipy>=1,<2",
+    "tomli_w>=1,<2",
+    "xarray>=2024,<2026",
+    "zarr>=2,<3",
+]
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+[[project.authors]]
+name = "Akio Taniguchi"
+email = "taniguchi.akio@gmail.com"
+
+[[project.authors]]
+name = "Juri Yamanaka"
+email = "j.yamanaka@a.phys.nagoya-u.ac.jp"
+
+[[project.authors]]
+name = "Shinji Fujita"
+email = "s-fujita@ism.ac.jp"
+
+[project.license]
+file = "LICENSE"
+
+[project.scripts]
 decode-qlook = "decode.qlook:main"
 
-[tool.pyright]
-typeCheckingMode = "basic"
+[project.urls]
+homepage = "https://deshima-dev.github.io/decode"
+repository = "https://github.com/deshima-dev/decode"
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[dependency-groups]
+dev = [
+    "black>=25,<26",
+    "ipython>=8,<10",
+    "myst-parser>=3,<5",
+    "pydata-sphinx-theme>=0.15,<1.0",
+    "pyright>=1,<2",
+    "pytest>=8,<9",
+    "sphinx>=7,<9",
+]
+
+[tool.pyright]
+typeCheckingMode = "basic"
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..bba91df
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@@ -0,0 +1,2497 @@
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+sdist = { url = "https://files.pythonhosted.org/packages/23/c4/187a21ce7cf7c8f00c060dd0e04c2a81139bb7b1ab178bba83f2e1134ce2/zarr-2.18.3.tar.gz", hash = "sha256:2580d8cb6dd84621771a10d31c4d777dca8a27706a1a89b29f42d2d37e2df5ce", size = 3603224, upload-time = "2024-09-04T23:20:16.595Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ed/c9/142095e654c2b97133ff71df60979422717b29738b08bc8a1709a5d5e0d0/zarr-2.18.3-py3-none-any.whl", hash = "sha256:b1f7dfd2496f436745cdd4c7bcf8d3b4bc1dceef5fdd0d589c87130d842496dd", size = 210723, upload-time = "2024-09-04T23:20:14.491Z" },
+]
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+[[package]]
+name = "zarr"
+version = "2.18.7"
+source = { registry = "https://pypi.org/simple" }
+resolution-markers = [
+    "python_full_version >= '3.12'",
+    "python_full_version == '3.11.*'",
+]
+dependencies = [
+    { name = "asciitree", marker = "python_full_version >= '3.11'" },
+    { name = "fasteners", marker = "python_full_version >= '3.11' and sys_platform != 'emscripten'" },
+    { name = "numcodecs", version = "0.15.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "numpy", version = "2.3.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/da/1d/01cf9e3ab2d85190278efc3fca9f68563de35ae30ee59e7640e3af98abe3/zarr-2.18.7.tar.gz", hash = "sha256:b2b8f66f14dac4af66b180d2338819981b981f70e196c9a66e6bfaa9e59572f5", size = 3604558, upload-time = "2025-04-09T07:59:28.482Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/5e/d8/9ffd8c237b3559945bb52103cf0eed64ea098f7b7f573f8d2962ef27b4b2/zarr-2.18.7-py3-none-any.whl", hash = "sha256:ac3dc4033e9ae4e9d7b5e27c97ea3eaf1003cc0a07f010bd83d5134bf8c4b223", size = 211273, upload-time = "2025-04-09T07:59:27.039Z" },
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+[[package]]
+name = "zipp"
+version = "3.23.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/e3/02/0f2892c661036d50ede074e376733dca2ae7c6eb617489437771209d4180/zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166", size = 25547, upload-time = "2025-06-08T17:06:39.4Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e", size = 10276, upload-time = "2025-06-08T17:06:38.034Z" },
+]

From 037aed62b05da968d9bc32eb620eca9da1c81fbc Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Tue, 17 Jun 2025 11:05:31 +0000
Subject: [PATCH 2/3] #236 Update workflows

---
 .../workflows/{gh-pages.yaml => docs.yaml}    | 15 +++++------
 .github/workflows/pypi.yaml                   | 13 +++++-----
 .github/workflows/tests.yaml                  | 26 +++++++++----------
 3 files changed, 24 insertions(+), 30 deletions(-)
 rename .github/workflows/{gh-pages.yaml => docs.yaml} (53%)

diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/docs.yaml
similarity index 53%
rename from .github/workflows/gh-pages.yaml
rename to .github/workflows/docs.yaml
index 4aa6c1c..2c32c4d 100644
--- a/.github/workflows/gh-pages.yaml
+++ b/.github/workflows/docs.yaml
@@ -1,4 +1,4 @@
-name: GitHub Pages
+name: Docs
 
 on:
   release:
@@ -9,19 +9,16 @@ jobs:
   job:
     name: GitHub Pages
     runs-on: ubuntu-latest
+    container: ghcr.io/astral-sh/uv:python3.12-bookworm
     env:
-      POETRY_VIRTUALENVS_CREATE: false
+      UV_PROJECT_ENVIRONMENT: /usr/local
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
-      - uses: abatilo/actions-poetry@v3
-        with:
-          poetry-version: "1.8.3"
-      - run: poetry install
+          submodules: true
+      - run: uv sync --frozen
       - run: docs/build
-      - uses: peaceiris/actions-gh-pages@v3
+      - uses: peaceiris/actions-gh-pages@v4
         with:
           force_orphan: true
           github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
index c668938..2670c52 100644
--- a/.github/workflows/pypi.yaml
+++ b/.github/workflows/pypi.yaml
@@ -9,14 +9,13 @@ jobs:
   job:
     name: PyPI
     runs-on: ubuntu-latest
+    container: ghcr.io/astral-sh/uv:python3.12-bookworm
     env:
-      POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
+      UV_PROJECT_ENVIRONMENT: /usr/local
+    permissions:
+      id-token: write
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
-      - uses: abatilo/actions-poetry@v3
-        with:
-          poetry-version: "1.8.3"
-      - run: poetry publish --build
+          submodules: true
+      - run: uv build && uv publish
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index a80e524..b1c4e39 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -4,34 +4,32 @@ on:
   push:
     branches:
       - main
-      - deshima2.0
   pull_request:
     branches:
       - main
-      - deshima2.0
 
 jobs:
   job:
-    name: Test (Python ${{ matrix.python }})
+    name: Test (${{ matrix.env }})
     runs-on: ubuntu-latest
+    container: ghcr.io/astral-sh/uv:${{ matrix.env }}
     env:
-      POETRY_VIRTUALENVS_CREATE: false
+      PYTHON_DIRS: decode docs tests
+      UV_PROJECT_ENVIRONMENT: /usr/local
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.9", "3.10", "3.11", "3.12"]
+        env:
+          - python3.9-bookworm
+          - python3.10-bookworm
+          - python3.11-bookworm
+          - python3.12-bookworm
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: true
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python }}
-      - uses: abatilo/actions-poetry@v3
-        with:
-          poetry-version: "1.8.3"
-      - run: poetry install
-      - run: black --check decode docs tests
-      - run: pyright decode docs tests
+      - run: uv sync --frozen
+      - run: black --check ${PYTHON_DIRS}
+      - run: pyright ${PYTHON_DIRS}
       - run: pytest -v tests
       - run: docs/build

From fc56dc6a141dbab5da8f40a75b109d415355d2fd Mon Sep 17 00:00:00 2001
From: Akio Taniguchi <13254278+astropenguin@users.noreply.github.com>
Date: Tue, 17 Jun 2025 15:59:44 +0000
Subject: [PATCH 3/3] #236 Add df/f-to-brightness conversion (and vice versa)

---
 decode/convert.py | 102 +++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 101 insertions(+), 1 deletion(-)

diff --git a/decode/convert.py b/decode/convert.py
index f5693d1..98a0c15 100644
--- a/decode/convert.py
+++ b/decode/convert.py
@@ -1,7 +1,8 @@
-__all__ = ["coord_units", "frame", "units"]
+__all__ = ["coord_units", "frame", "to_brightness", "to_dfof", "units"]
 
 
 # standard library
+from logging import getLogger
 from typing import Optional, Sequence, TypeVar, Union
 
 
@@ -11,6 +12,10 @@
 from astropy.units import Equivalency, Quantity, Unit
 
 
+# constants
+LOGGER = getLogger(__name__)
+
+
 # type hints
 T = TypeVar("T")
 Multiple = Union[Sequence[T], T]
@@ -84,6 +89,101 @@ def frame(da: xr.DataArray, new_frame: str, /) -> xr.DataArray:
     return da.assign_coords(frame=new_frame)
 
 
+def to_brightness(
+    dems: xr.DataArray,
+    /,
+    *,
+    T_amb: float = 273.0,
+    T_room: float = 293.0,
+) -> xr.DataArray:
+    """Convert DEMS on the df/f scale to the brightness temperature scale.
+
+    Args:
+        dems: Input DEMS DataArray on the df/f scale.
+        T_amb: Default ambient temperature value to be used
+            when all ``dems.temperature`` values are NaN.
+        T_room: Default room temperature value to be used
+            when all ``dems.aste_cabin_temperature`` values are NaN.
+
+    Returns:
+        DEMS DataArray on the brightness temperature scale.
+
+    """
+    if dems.long_name == "Brightness" or dems.units == "K":
+        LOGGER.warning("DEMS may already be on the brightness temperature scale.")
+
+    if all(np.isnan(T_room_ := dems.aste_cabin_temperature)):
+        T_room_ = T_room
+
+    if all(np.isnan(T_amb_ := dems.temperature)):
+        T_amb_ = T_amb
+
+    fwd = dems.d2_resp_fwd.data
+    p0 = dems.d2_resp_p0.data
+    T0 = dems.d2_resp_t0.data
+
+    return (
+        dems.copy(
+            deep=True,
+            data=(
+                (dems.data + p0 * (T_room_ + T0) ** 0.5) ** 2 / (p0**2 * fwd)
+                - (T0 + (1 - fwd) * T_amb_) / fwd
+            ),
+        )
+        .astype(dems.dtype)
+        .assign_attrs(long_name="Brightness", units="K")
+    )
+
+
+def to_dfof(
+    dems: xr.DataArray,
+    /,
+    *,
+    T_amb: float = 273.0,
+    T_room: float = 293.0,
+) -> xr.DataArray:
+    """Convert DEMS on the brightness temperature scale to the df/f scale.
+
+    Args:
+        dems: Input DEMS DataArray on the brightness temperature scale.
+        T_amb: Default ambient temperature value to be used
+            when all ``dems.temperature`` values are NaN.
+        T_room: Default room temperature value to be used
+            when all ``dems.aste_cabin_temperature`` values are NaN.
+
+    Returns:
+        DEMS DataArray on the df/f scale.
+
+    """
+    if dems.long_name == "df/f" or dems.units == "dimensionless":
+        LOGGER.warning("DEMS may already be on the df/f scale.")
+
+    if all(np.isnan(T_room_ := dems.aste_cabin_temperature)):
+        T_room_ = T_room
+
+    if all(np.isnan(T_amb_ := dems.temperature)):
+        T_amb_ = T_amb
+
+    fwd = dems.d2_resp_fwd.data
+    p0 = dems.d2_resp_p0.data
+    T0 = dems.d2_resp_t0.data
+
+    return (
+        dems.copy(
+            deep=True,
+            data=(
+                p0
+                * (
+                    (fwd * dems.data + (1 - fwd) * T_amb_ + T0) ** 0.5
+                    - (T_room_ + T0) ** 0.5
+                )
+            ),
+        )
+        .astype(dems.dtype)
+        .assign_attrs(long_name="df/f", units="dimensionless")
+    )
+
+
 def units(
     da: xr.DataArray,
     new_units: UnitLike,