feat: implement nqm2ms2

.github/workflows/CI.yml

@@ -9,10 +9,71 @@ on:
   workflow_dispatch:
 
 jobs:
-  validation:
-    uses: microsoft/action-python/.github/workflows/validation.yml@0.7.3
-    with:
-      workdir: '.'
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Black
+        uses: microsoft/action-python@0.7.0
+        with:
+          black: true
+          python_version: 3.12
+          workdir: '.'
+
+      - name: Bandit
+        uses: microsoft/action-python@0.7.0
+        with:
+          bandit: true
+          python_version: 3.12
+          workdir: '.'
+
+      - name: Pylint
+        uses: microsoft/action-python@0.7.0
+        with:
+          pylint: true
+          python_version: 3.12
+          workdir: '.'
+
+    #   - name: Pyright
+    #     uses: microsoft/action-python@0.7.0
+    #     with:
+    #       pyright: true
+
+      - name: Flake8
+        uses: microsoft/action-python@0.7.0
+        with:
+          flake8: true
+          python_version: 3.12
+          workdir: '.'
+
+  testing:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Initialize CASA data directory
+        run: mkdir -p ~/.casa/data
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          architecture: 'x64'
+
+      - name: install nro45data
+        run: pip install -e .[casa6,test]
+
+      - name: Pytest
+        run: pytest -v
+
+#   validation:
+#     needs: init_casadata
+#     uses: microsoft/action-python/.github/workflows/validation.yml@0.7.3
+#     with:
+#       workdir: '.'
 
 #   publish:
 #     uses: microsoft/action-python/.github/workflows/publish.yml@0.6.4

README.md

@@ -7,7 +7,7 @@ IO utility module to read Position-Switch (PSW) data of Nobeyama 45m telescope.
 ```
 git clone https://github.com/tnakazato/nro45data.git
 cd nro45data
-pip install .
+pip install .[casa6]
 ```
 
 ## Usage
@@ -18,3 +18,10 @@ pip install .
 import nro45data.psw as psw
 psw.nqm2fits('mydata.nqm', 'mydata.fits')
 ```
+
+`nqm2ms2` converts NRO 45m PSW data (.nqm) to MS2.
+
+```python
+import nro45data.psw as psw
+psw.nqm2ms2('mydata.nqm', 'mydata.ms')
+```

docs/source/conf.py

@@ -20,7 +20,6 @@
 exclude_patterns = []
 
 
-
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 

pyproject.toml

@@ -26,6 +26,12 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+casa6 = [
+    "casatools"
+]
+casacore = [
+    "python-casacore"
+]
 spark = [
     "pyspark>=3.0.0"
 ]
@@ -178,6 +184,7 @@ limit-inference-results=100
 persistent="yes"
 suggestion-mode="yes"
 unsafe-load-any-extension="no"
+disable="W,C,R"
 
 [tool.pylint.'MESSAGES CONTROL']
 enable="c-extension-no-member"

src/nro45data/psw/__init__.py

@@ -1,9 +1,19 @@
+import logging
+
 from .io import _read_psw
 from .io import _to_fits
 from .ms2 import _to_ms2
 from .ms4 import _to_ms4
 
 
+logging.basicConfig(
+    format="%(asctime)s\t%(levelname)s\t%(funcName)s\t%(message)s",
+    # format='%(levelname)s %(message)s',
+    datefmt="%Y/%m/%d %H:%M:%S",
+    level=logging.INFO,
+)
+
+
 def nqm2fits(nqmfile: str, fitsfile: str, overwrite: bool = False) -> bool:
     """Convert NRO45m PSW data (.nqm) to FITS.
 

src/nro45data/psw/io/__init__.py

@@ -1,2 +1,4 @@
 from .reader import _read_psw
-from .fits import _to_fits
+from .fits import _to_fits
+
+__all__ = ["_read_psw", "_to_fits"]

src/nro45data/psw/io/fits.py

@@ -1,12 +1,12 @@
-from typing import List, Tuple, TYPE_CHECKING
+from typing import TYPE_CHECKING
 
 import astropy.io.fits as fits
 
 if TYPE_CHECKING:
     from astropy.io.fits.hdu.hdulist import HDUList
 
 
-def _to_fits(hdulist: 'HDUList', fitsfile: str, overwrite: bool = False) -> bool:
+def _to_fits(hdulist: "HDUList", fitsfile: str, overwrite: bool = False) -> bool:
     """Export HDUList to FITS.
 
     Args:
@@ -24,13 +24,9 @@ def _to_fits(hdulist: 'HDUList', fitsfile: str, overwrite: bool = False) -> bool
     output_hdulist = fits.HDUList([primary_hdu, hdulist[0]])
 
     try:
-        output_hdulist.writeto(
-            fitsfile,
-            output_verify='fix+warn',
-            overwrite=overwrite
-        )
+        output_hdulist.writeto(fitsfile, output_verify="fix+warn", overwrite=overwrite)
     except Exception as e:
         print(e)
         status = False
 
-    return status
+    return status

src/nro45data/psw/io/reader.py

@@ -1,8 +1,7 @@
 import collections
 import os
 import re
-import tempfile
-from typing import List, Tuple, TYPE_CHECKING
+from typing import List, Tuple
 
 from astropy.io.fits.hdu.hdulist import HDUList
 
@@ -21,7 +20,7 @@ def _is_nro_psw(filename: str) -> bool:
         True if the file is in NRO 45m PSW format, otherwise False.
     """
     expected = "XTENSION='BINTABLE'"
-    with open(filename, 'rb') as f:
+    with open(filename, "rb") as f:
         first_record = f.read(FITS_RECORD_SIZE).decode()
 
     return first_record.startswith(expected)
@@ -36,7 +35,7 @@ def _read_header_and_data(filename: str) -> Tuple[List[str], bytes]:
     Returns:
         List of header records and binary data
     """
-    with open(filename, 'rb+') as f:
+    with open(filename, "rb+") as f:
         # header
         header = []
         is_end_of_header = False
@@ -50,7 +49,7 @@ def _read_header_and_data(filename: str) -> Tuple[List[str], bytes]:
                 num_records += 1
                 record = record_bytes.decode()
                 header.append(record)
-                is_end_of_header = record.strip() == 'END'
+                is_end_of_header = record.strip() == "END"
                 if is_end_of_header:
                     break
 
@@ -74,20 +73,19 @@ def _follow_fits_standard(records: List[str]) -> List[str]:
     Returns:
         List of tweaked header records
     """
+
     def __insert_space_before_value(record: str) -> str:
-        if record.startswith('END'):
+        if record.startswith("END"):
             return record
 
-        fixed_record = re.sub('=', '= ', record, count=1)
-        if ' /' in fixed_record:
-            fixed_record = fixed_record.replace(' /', '/')
-        elif fixed_record.endswith(' '):
+        fixed_record = re.sub("=", "= ", record, count=1)
+        if " /" in fixed_record:
+            fixed_record = fixed_record.replace(" /", "/")
+        elif fixed_record.endswith(" "):
             fixed_record = fixed_record[:-1]
         return fixed_record
 
-    return list(map(
-        __insert_space_before_value, records
-    ))
+    return list(map(__insert_space_before_value, records))
 
 
 def _rename_duplicate_types(records: List[str]) -> List[str]:
@@ -101,7 +99,7 @@ def _rename_duplicate_types(records: List[str]) -> List[str]:
     """
     duplicate_rows = collections.defaultdict(list)
     for i, r in enumerate(records):
-        if r.startswith('TTYPE'):
+        if r.startswith("TTYPE"):
             k = re.match(r".*= '([^']+)'.*", r)[1]
             duplicate_rows[k].append(i)
     fixed_records = records[::]
@@ -124,10 +122,7 @@ def _read_psw(filename: str) -> HDUList:
         mode: Observation mode. Either 'psw' or 'otf'.
     """
     if not _is_nro_psw(filename):
-        raise RuntimeError(
-            'Incompatible data: '
-            f'"{filename}" is not in NRO 45m PSW format.'
-        )
+        raise RuntimeError("Incompatible data: " f'"{filename}" is not in NRO 45m PSW format.')
 
     record_list, binary_data = _read_header_and_data(filename)
 
@@ -138,12 +133,8 @@ def _read_psw(filename: str) -> HDUList:
     # for r in record_list:
     #     print(r)
 
-    header = ''.join(record_list).encode()
+    header = "".join(record_list).encode()
 
-    hdulist = HDUList.fromstring(
-        header + binary_data,
-        ignore_missing_simple=True,
-        lazy_load_hdus=False
-    )
+    hdulist = HDUList.fromstring(header + binary_data, ignore_missing_simple=True, lazy_load_hdus=False)
 
     return hdulist

src/nro45data/psw/ms2/__init__.py

@@ -1,14 +1,18 @@
+import logging
+import os
+import shutil
 from typing import TYPE_CHECKING
 
+from nro45data.psw.ms2.builder import build_ms2
+from nro45data.psw.ms2.filler import fill_ms2
+
 if TYPE_CHECKING:
     from astropy.io.fits.hdu.hdulist import HDUList
 
+LOG = logging.getLogger(__name__)
+
 
-def _to_ms2(
-        hdulist: 'HDUList',
-        msfile: str,
-        overwrite: bool = False
-) -> bool:
+def _to_ms2(hdulist: "HDUList", msfile: str, overwrite: bool = False) -> bool:
     """Export HDUList to MeasurementSet v2.
 
     Not implemented yet.
@@ -22,4 +26,14 @@ def _to_ms2(
     Returns:
         Export status. True is successful.
     """
-    return False
+    if os.path.exists(msfile) and not overwrite:
+        raise FileExistsError(f"Abort since {msfile} exists and overwrite is False")
+
+    if os.path.exists(msfile):
+        LOG.info(f'Overwrite existing {msfile}...')
+        shutil.rmtree(msfile)
+
+    build_ms2(msfile)
+    fill_ms2(msfile, hdulist[0])
+
+    return True

src/nro45data/psw/ms2/_casa/__init__.py

@@ -0,0 +1,31 @@
+from ._casa6 import _is_casa6_available
+from ._casacore import _is_casacore_available
+
+if _is_casa6_available:
+    from ._casa6 import build_table
+    from ._casa6 import open_table
+    from ._casa6 import _table
+    from ._casa6 import convert_str_angle_to_rad
+    from ._casa6 import put_table_keyword
+    from ._casa6 import datestr2mjd
+    from ._casa6 import mjd2datetime
+elif _is_casacore_available:
+    from ._casacore import build_table
+    from ._casacore import open_table
+    from ._casacore import _table
+    from ._casacore import convert_str_angle_to_rad
+    from ._casacore import put_table_keyword
+    from ._casacore import datestr2mjd
+    from ._casacore import mjd2datetime
+else:
+    raise ModuleNotFoundError("Neither casatools or python-casacore is available")
+
+__all__ = [
+    "build_table",
+    "open_table",
+    "_table",
+    "convert_str_angle_to_rad",
+    "put_table_keyword",
+    "datestr2mjd",
+    "mjd2datetime"
+]