From 704aacd95c0793ce38416997fe280b72cd02984e Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 08:28:33 +0000 Subject: [PATCH 1/8] #162 Update devcontainer --- .devcontainer/devcontainer.json | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index fcbc0f4..6586561 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,11 +1,18 @@ { "name": "decode", "image":"python:3.11", - "onCreateCommand": "pip install poetry==1.7.1", - "postCreateCommand": "poetry install", + "features": { + "ghcr.io/devcontainers-contrib/features/poetry:2": { + "version": "1.8.3" + } + }, "containerEnv": { "POETRY_VIRTUALENVS_CREATE": "false" }, + "runArgs": [ + "--name=decode" + ], + "postCreateCommand": "poetry install", "customizations": { "vscode": { "extensions": [ From ceaef053e09f795d5c46deeaae71d148b67eff6c Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 08:36:14 +0000 Subject: [PATCH 2/8] #162 Update Poetry installation in workflows --- .github/workflows/gh-pages.yaml | 9 ++++++--- .github/workflows/pypi.yaml | 9 ++++++--- .github/workflows/tests.yaml | 9 ++++++--- 3 files changed, 18 insertions(+), 9 deletions(-) diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 58f5c77..4aa6c1c 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -12,11 +12,14 @@ jobs: env: POETRY_VIRTUALENVS_CREATE: false steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: "3.11" - - run: pip install poetry && poetry install + - uses: abatilo/actions-poetry@v3 + with: + poetry-version: "1.8.3" + - run: poetry install - run: docs/build - uses: peaceiris/actions-gh-pages@v3 with: diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml index ce39d69..c668938 100644 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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: pytest -v tests From ae8ee21efdaafd0f7cfe889490a788bd5a206e04 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 08:36:29 +0000 Subject: [PATCH 3/8] #162 Update project dependencies --- poetry.lock | 1415 +++++++++++++++++++++++++----------------------- pyproject.toml | 16 +- 2 files changed, 734 insertions(+), 697 deletions(-) diff --git a/poetry.lock b/poetry.lock index 87016af..6acc223 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,27 +2,31 @@ [[package]] name = "accessible-pygments" -version = "0.0.4" +version = "0.0.5" description = "A collection of accessible pygments styles" optional = false -python-versions = "*" +python-versions = ">=3.9" files = [ - {file = "accessible-pygments-0.0.4.tar.gz", hash = "sha256:e7b57a9b15958e9601c7e9eb07a440c813283545a20973f2574a5f453d0e953e"}, - {file = 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"2f0ba442a4891e0d15d65faa4cbf434698688198f7d19215675e3fb5539ac782" +content-hash = "055e05d92074104728fbc614387c85b4db4678c9263bd06d855b798f4c351a33" diff --git a/pyproject.toml b/pyproject.toml index a64ed40..c6b4b6a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,25 +20,25 @@ documentation = "https://deshima-dev.github.io/decode/" [tool.poetry.dependencies] python = ">=3.9, <3.13" -astropy = "^5.2" +astropy = ">=5.2, <7.0" dems = "^0.9" matplotlib = "^3.7" numpy = "^1.23" pandas = ">=1.5, <3.0" scikit-learn = "^1.2" scipy = "^1.10" -xarray = "^2023.1" +xarray = ">=2023.1, <2025.0" zarr = "^2.14" -fire = "^0.5.0" +fire = "^0.5" [tool.poetry.group.dev.dependencies] -black = "^23.11" +black = "^24.4" ipython = "^8.18" -myst-parser = "^2.0" -pydata-sphinx-theme = "^0.14" +myst-parser = "^3.0" +pydata-sphinx-theme = "^0.15" pyright = "^1.1" -pytest = "^7.4" -sphinx = "^7.2" +pytest = "^8.2" +sphinx = "^7.3" [tool.poetry.scripts] decode-qlook = "decode.qlook:main" From 65f51c52ed967c6941a40907b5cbd45afde05451 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 09:00:13 +0000 Subject: [PATCH 4/8] #162 Add qlook commands for X/Y scan --- decode/qlook.py | 221 ++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 216 insertions(+), 5 deletions(-) diff --git a/decode/qlook.py b/decode/qlook.py index 8d18a34..1d2447f 100644 --- a/decode/qlook.py +++ b/decode/qlook.py @@ -1,4 +1,13 @@ -__all__ = ["auto", "pswsc", "raster", "skydip", "still", "zscan"] +__all__ = [ + "auto", + "pswsc", + "raster", + "skydip", + "still", + "xscan", + "yscan", + "zscan", +] # standard library @@ -441,6 +450,138 @@ def still( return save_qlook(fig, file, overwrite=overwrite, **options) +def xscan( + dems: Path, + /, + *, + # options for loading + include_mkid_ids: Optional[Sequence[int]] = DEFAULT_INCL_MKID_IDS, + exclude_mkid_ids: Optional[Sequence[int]] = DEFAULT_EXCL_MKID_IDS, + data_type: Literal["auto", "brightness", "df/f"] = DEFAULT_DATA_TYPE, + # options for analysis + chan_weight: Literal["uniform", "std", "std/tx"] = "std/tx", + pwv: Literal["0.5", "1.0", "2.0", "3.0", "4.0", "5.0"] = "5.0", + # options for saving + format: str = DEFAULT_FORMAT, + outdir: Path = DEFAULT_OUTDIR, + overwrite: bool = DEFAULT_OVERWRITE, + suffix: str = "zscan", + **options: Any, +) -> Path: + """Quick-look at an observation of subref X-axis focus scan. + + Args: + dems: Input DEMS file (netCDF or Zarr). + include_mkid_ids: MKID IDs to be included in analysis. + Defaults to all MKID IDs. + exclude_mkid_ids: MKID IDs to be excluded in analysis. + Defaults to bad MKID IDs found on 2023-11-19. + data_type: Data type of the input DEMS file. + Defaults to the ``long_name`` attribute in it. + chan_weight: Weighting method along the channel axis. + uniform: Uniform weight (i.e. no channel dependence). + std: Inverse square of temporal standard deviation of sky. + std/tx: Same as std but std is divided by the atmospheric + transmission calculated by the ATM model. + pwv: PWV in units of mm. Only used for the calculation of + the atmospheric transmission when chan_weight is std/tx. + format: Output image format of quick-look result. + outdir: Output directory for the quick-look result. + suffix: Suffix that precedes the file extension. + overwrite: Whether to overwrite the output if it exists. + + Keyword Args: + options: Other options for saving the output (e.g. dpi). + + Returns: + Absolute path of the saved file. + + """ + return _scan( + dems, + "x", + # options for loading + include_mkid_ids=include_mkid_ids, + exclude_mkid_ids=exclude_mkid_ids, + data_type=data_type, + # options for analysis + chan_weight=chan_weight, + pwv=pwv, + # options for saving + format=format, + outdir=outdir, + overwrite=overwrite, + suffix=suffix, + **options, + ) + + +def yscan( + dems: Path, + /, + *, + # options for loading + include_mkid_ids: Optional[Sequence[int]] = DEFAULT_INCL_MKID_IDS, + exclude_mkid_ids: Optional[Sequence[int]] = DEFAULT_EXCL_MKID_IDS, + data_type: Literal["auto", "brightness", "df/f"] = DEFAULT_DATA_TYPE, + # options for analysis + chan_weight: Literal["uniform", "std", "std/tx"] = "std/tx", + pwv: Literal["0.5", "1.0", "2.0", "3.0", "4.0", "5.0"] = "5.0", + # options for saving + format: str = DEFAULT_FORMAT, + outdir: Path = DEFAULT_OUTDIR, + overwrite: bool = DEFAULT_OVERWRITE, + suffix: str = "zscan", + **options: Any, +) -> Path: + """Quick-look at an observation of subref Y-axis focus scan. + + Args: + dems: Input DEMS file (netCDF or Zarr). + include_mkid_ids: MKID IDs to be included in analysis. + Defaults to all MKID IDs. + exclude_mkid_ids: MKID IDs to be excluded in analysis. + Defaults to bad MKID IDs found on 2023-11-19. + data_type: Data type of the input DEMS file. + Defaults to the ``long_name`` attribute in it. + chan_weight: Weighting method along the channel axis. + uniform: Uniform weight (i.e. no channel dependence). + std: Inverse square of temporal standard deviation of sky. + std/tx: Same as std but std is divided by the atmospheric + transmission calculated by the ATM model. + pwv: PWV in units of mm. Only used for the calculation of + the atmospheric transmission when chan_weight is std/tx. + format: Output image format of quick-look result. + outdir: Output directory for the quick-look result. + suffix: Suffix that precedes the file extension. + overwrite: Whether to overwrite the output if it exists. + + Keyword Args: + options: Other options for saving the output (e.g. dpi). + + Returns: + Absolute path of the saved file. + + """ + return _scan( + dems, + "y", + # options for loading + include_mkid_ids=include_mkid_ids, + exclude_mkid_ids=exclude_mkid_ids, + data_type=data_type, + # options for analysis + chan_weight=chan_weight, + pwv=pwv, + # options for saving + format=format, + outdir=outdir, + overwrite=overwrite, + suffix=suffix, + **options, + ) + + def zscan( dems: Path, /, @@ -459,10 +600,78 @@ def zscan( suffix: str = "zscan", **options: Any, ) -> Path: - """Quick-look at an observation of subref axial focus scan. + """Quick-look at an observation of subref Z-axis focus scan. + + Args: + dems: Input DEMS file (netCDF or Zarr). + include_mkid_ids: MKID IDs to be included in analysis. + Defaults to all MKID IDs. + exclude_mkid_ids: MKID IDs to be excluded in analysis. + Defaults to bad MKID IDs found on 2023-11-19. + data_type: Data type of the input DEMS file. + Defaults to the ``long_name`` attribute in it. + chan_weight: Weighting method along the channel axis. + uniform: Uniform weight (i.e. no channel dependence). + std: Inverse square of temporal standard deviation of sky. + std/tx: Same as std but std is divided by the atmospheric + transmission calculated by the ATM model. + pwv: PWV in units of mm. Only used for the calculation of + the atmospheric transmission when chan_weight is std/tx. + format: Output image format of quick-look result. + outdir: Output directory for the quick-look result. + suffix: Suffix that precedes the file extension. + overwrite: Whether to overwrite the output if it exists. + + Keyword Args: + options: Other options for saving the output (e.g. dpi). + + Returns: + Absolute path of the saved file. + + """ + return _scan( + dems, + "z", + # options for loading + include_mkid_ids=include_mkid_ids, + exclude_mkid_ids=exclude_mkid_ids, + data_type=data_type, + # options for analysis + chan_weight=chan_weight, + pwv=pwv, + # options for saving + format=format, + outdir=outdir, + overwrite=overwrite, + suffix=suffix, + **options, + ) + + +def _scan( + dems: Path, + axis: Literal["x", "y", "z"], + /, + *, + # options for loading + include_mkid_ids: Optional[Sequence[int]] = DEFAULT_INCL_MKID_IDS, + exclude_mkid_ids: Optional[Sequence[int]] = DEFAULT_EXCL_MKID_IDS, + data_type: Literal["auto", "brightness", "df/f"] = DEFAULT_DATA_TYPE, + # options for analysis + chan_weight: Literal["uniform", "std", "std/tx"] = "std/tx", + pwv: Literal["0.5", "1.0", "2.0", "3.0", "4.0", "5.0"] = "5.0", + # options for saving + format: str = DEFAULT_FORMAT, + outdir: Path = DEFAULT_OUTDIR, + overwrite: bool = DEFAULT_OVERWRITE, + suffix: str = "_scan", + **options: Any, +) -> Path: + """Quick-look at an observation of subref axial/radial focus scan. Args: dems: Input DEMS file (netCDF or Zarr). + axis: Axis of the scan (either ``'x'``, ``'y'``, or ``'z'``). include_mkid_ids: MKID IDs to be included in analysis. Defaults to all MKID IDs. exclude_mkid_ids: MKID IDs to be excluded in analysis. @@ -503,7 +712,7 @@ def zscan( series = da_on.weighted(weight.fillna(0)).mean("chan") # save result - suffixes = f".{suffix}.{format}" + suffixes = f".{suffix.replace('_', axis)}.{format}" file = Path(outdir) / Path(dems).with_suffix(suffixes).name if format in DATA_FORMATS: @@ -512,10 +721,10 @@ def zscan( fig, axes = plt.subplots(1, 2, figsize=DEFAULT_FIGSIZE) ax = axes[0] - plot.data(series, hue="aste_subref_z", ax=ax) + plot.data(series, hue=f"aste_subref_{axis}", ax=ax) ax = axes[1] - plot.data(series, x="aste_subref_z", ax=ax) + plot.data(series, x=f"aste_subref_{axis}", ax=ax) for ax in axes: ax.set_title(Path(dems).name) @@ -745,6 +954,8 @@ def main() -> None: "raster": raster, "skydip": skydip, "still": still, + "xscan": xscan, + "yscan": yscan, "zscan": zscan, } ) From f1a9014a8539c008f5248e4ce6256f8d0f661634 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 09:01:43 +0000 Subject: [PATCH 5/8] =?UTF-8?q?#162=20Update=20package=20version=20(2.13.0?= =?UTF-8?q?=20=E2=86=92=202.14.0)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- CITATION.cff | 2 +- README.md | 2 +- decode/__init__.py | 2 +- pyproject.toml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index a617a54..be708db 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -3,7 +3,7 @@ message: "If you use this software, please cite it as below." title: "de:code" abstract: "DESHIMA code for data analysis" -version: 2.13.0 +version: 2.14.0 date-released: 2024-06-12 license: "MIT" doi: "10.5281/zenodo.3384216" diff --git a/README.md b/README.md index 764dff7..b8d9fd1 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ DESHIMA code for data analysis ## Installation ```shell -pip install decode==2.13.0 +pip install decode==2.14.0 ``` ## Quick look diff --git a/decode/__init__.py b/decode/__init__.py index f226d6d..7ffd9c6 100644 --- a/decode/__init__.py +++ b/decode/__init__.py @@ -10,7 +10,7 @@ "select", "utils", ] -__version__ = "2.13.0" +__version__ = "2.14.0" # submodules diff --git a/pyproject.toml b/pyproject.toml index c6b4b6a..43f37c3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "decode" -version = "2.13.0" +version = "2.14.0" description = "DESHIMA code for data analysis" authors = [ "Akio Taniguchi ", From 96021ca50a56737e8a45bf0233310365ccdeb1ba Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 09:02:18 +0000 Subject: [PATCH 6/8] #162 Update release date --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index be708db..9b010cc 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,7 +4,7 @@ message: "If you use this software, please cite it as below." title: "de:code" abstract: "DESHIMA code for data analysis" version: 2.14.0 -date-released: 2024-06-12 +date-released: 2024-07-06 license: "MIT" doi: "10.5281/zenodo.3384216" url: "https://github.com/deshima-dev/decode" From 23a2a6a97395cee22a4863b8437dd4485474cc06 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 09:11:03 +0000 Subject: [PATCH 7/8] #162 Ignore type checking errors on Matplotlib --- decode/qlook.py | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/decode/qlook.py b/decode/qlook.py index 1d2447f..ad94cdc 100644 --- a/decode/qlook.py +++ b/decode/qlook.py @@ -149,14 +149,14 @@ def pswsc( fig, axes = plt.subplots(1, 2, figsize=DEFAULT_FIGSIZE) - ax = axes[0] + ax = axes[0] # type: ignore plot.data(da.scan, ax=ax) - ax = axes[1] + ax = axes[1] # type: ignore plot.data(spec, x="frequency", s=5, hue=None, ax=ax) ax.set_ylim(get_robust_lim(spec)) - for ax in axes: + for ax in axes: # type: ignore ax.set_title(Path(dems).name) ax.grid(True) @@ -259,11 +259,11 @@ def raster( fig, axes = plt.subplots(1, 2, figsize=(12, 5.5)) - ax = axes[0] + ax = axes[0] # type: ignore plot.data(series, ax=ax) ax.set_title(Path(dems).name) - ax = axes[1] + ax = axes[1] # type: ignore map_lim = max(abs(cube.lon).max(), abs(cube.lat).max()) max_pix = cont.where(cont == cont.max(), drop=True) @@ -276,7 +276,7 @@ def raster( f"dEl = {float(max_pix.lat):+.1f} {cont.lat.attrs['units']}" ) - for ax in axes: + for ax in axes: # type: ignore ax.grid(True) fig.tight_layout() @@ -353,13 +353,13 @@ def skydip( fig, axes = plt.subplots(1, 2, figsize=DEFAULT_FIGSIZE) - ax = axes[0] + ax = axes[0] # type: ignore plot.data(series, hue="secz", ax=ax) - ax = axes[1] + ax = axes[1] # type: ignore plot.data(series, x="secz", ax=ax) - for ax in axes: + for ax in axes: # type: ignore ax.set_title(Path(dems).name) ax.grid(True) @@ -436,13 +436,13 @@ def still( fig, axes = plt.subplots(1, 2, figsize=DEFAULT_FIGSIZE) - ax = axes[0] + ax = axes[0] # type: ignore plot.state(da, add_colorbar=False, add_legend=False, ax=ax) - ax = axes[1] + ax = axes[1] # type: ignore plot.data(series, add_colorbar=False, ax=ax) - for ax in axes: + for ax in axes: # type: ignore ax.set_title(Path(dems).name) ax.grid(True) @@ -720,13 +720,13 @@ def _scan( fig, axes = plt.subplots(1, 2, figsize=DEFAULT_FIGSIZE) - ax = axes[0] + ax = axes[0] # type: ignore plot.data(series, hue=f"aste_subref_{axis}", ax=ax) - ax = axes[1] + ax = axes[1] # type: ignore plot.data(series, x=f"aste_subref_{axis}", ax=ax) - for ax in axes: + for ax in axes: # type: ignore ax.set_title(Path(dems).name) ax.grid(True) From 7717f21fa4f379292a969b946bc8949ba5d660b6 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Sat, 6 Jul 2024 11:22:18 +0000 Subject: [PATCH 8/8] #162 Do not use xarray >=2024.3 that raises AttributeError AttributeError: 'ScipyArrayWrapper' object has no attribute 'oindex' https://github.com/pydata/xarray/issues/8909 --- poetry.lock | 14 +++++++------- pyproject.toml | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6acc223..761b0d3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2054,24 +2054,24 @@ files = [ [[package]] name = "xarray" -version = "2024.6.0" +version = "2024.2.0" description = "N-D labeled arrays and datasets in Python" optional = false python-versions = ">=3.9" files = [ - {file = "xarray-2024.6.0-py3-none-any.whl", hash = "sha256:721a7394e8ec3d592b2d8ebe21eed074ac077dc1bb1bd777ce00e41700b4866c"}, - {file = "xarray-2024.6.0.tar.gz", hash = "sha256:0b91e0bc4dc0296947947640fe31ec6e867ce258d2f7cbc10bedf4a6d68340c7"}, + {file = "xarray-2024.2.0-py3-none-any.whl", hash = "sha256:a31a9b37e39bd5aeb098070a75d6dd4d59019eb339d735b86108b9e0cb391f94"}, + {file = "xarray-2024.2.0.tar.gz", hash = "sha256:a105f02791082c888ebe2622090beaff2e7b68571488d62fe6afdab35b4b717f"}, ] [package.dependencies] numpy = ">=1.23" -packaging = ">=23.1" -pandas = ">=2.0" +packaging = ">=22" +pandas = ">=1.5" [package.extras] accel = ["bottleneck", "flox", "numbagg", "opt-einsum", "scipy"] complete = ["xarray[accel,dev,io,parallel,viz]"] -dev = ["hypothesis", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "xarray[complete]"] +dev = ["hypothesis", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "xarray[complete]"] io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"] parallel = ["dask[complete]"] viz = ["matplotlib", "nc-time-axis", "seaborn"] @@ -2131,4 +2131,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", [metadata] lock-version = "2.0" python-versions = ">=3.9, <3.13" -content-hash = "055e05d92074104728fbc614387c85b4db4678c9263bd06d855b798f4c351a33" +content-hash = "12417f64c6e79dc1562c73d12714aff0cfd255821baee27ff3236973aad45d12" diff --git a/pyproject.toml b/pyproject.toml index 43f37c3..f6b00a8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ numpy = "^1.23" pandas = ">=1.5, <3.0" scikit-learn = "^1.2" scipy = "^1.10" -xarray = ">=2023.1, <2025.0" +xarray = ">=2023.1, <2024.3" zarr = "^2.14" fire = "^0.5"