TF: smooth subband, Doc update

AlanLoh · Jul 23, 2024 · db5a10d · db5a10d
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diff --git a/docs/source/_autosummary/nenupy.astro.jones_mueller.JonesMatrix.rst b/docs/source/_autosummary/nenupy.astro.jones_mueller.JonesMatrix.rst
@@ -44,18 +44,15 @@
       ~JonesMatrix.getfield
       ~JonesMatrix.half_waveplate_retarder
       ~JonesMatrix.item
-      ~JonesMatrix.itemset
       ~JonesMatrix.left_circular
       ~JonesMatrix.linear
       ~JonesMatrix.linear_retarder
       ~JonesMatrix.max
       ~JonesMatrix.mean
       ~JonesMatrix.min
-      ~JonesMatrix.newbyteorder
       ~JonesMatrix.nonzero
       ~JonesMatrix.partition
       ~JonesMatrix.prod
-      ~JonesMatrix.ptp
       ~JonesMatrix.put
       ~JonesMatrix.quarter_waveplate_retarder
       ~JonesMatrix.ravel
@@ -73,6 +70,7 @@
       ~JonesMatrix.sum
       ~JonesMatrix.swapaxes
       ~JonesMatrix.take
+      ~JonesMatrix.to_device
       ~JonesMatrix.to_mueller
       ~JonesMatrix.tobytes
       ~JonesMatrix.tofile
@@ -95,13 +93,18 @@
       ~JonesMatrix.base
       ~JonesMatrix.ctypes
       ~JonesMatrix.data
+      ~JonesMatrix.device
       ~JonesMatrix.dtype
       ~JonesMatrix.flags
       ~JonesMatrix.flat
       ~JonesMatrix.imag
+      ~JonesMatrix.itemset
       ~JonesMatrix.itemsize
+      ~JonesMatrix.mT
       ~JonesMatrix.nbytes
       ~JonesMatrix.ndim
+      ~JonesMatrix.newbyteorder
+      ~JonesMatrix.ptp
       ~JonesMatrix.real
       ~JonesMatrix.shape
       ~JonesMatrix.size

diff --git a/docs/source/_autosummary/nenupy.astro.jones_mueller.JonesVector.rst b/docs/source/_autosummary/nenupy.astro.jones_mueller.JonesVector.rst
@@ -45,17 +45,14 @@
       ~JonesVector.getfield
       ~JonesVector.horizontal
       ~JonesVector.item
-      ~JonesVector.itemset
       ~JonesVector.left_circular
       ~JonesVector.linear
       ~JonesVector.max
       ~JonesVector.mean
       ~JonesVector.min
-      ~JonesVector.newbyteorder
       ~JonesVector.nonzero
       ~JonesVector.partition
       ~JonesVector.prod
-      ~JonesVector.ptp
       ~JonesVector.put
       ~JonesVector.ravel
       ~JonesVector.repeat
@@ -72,6 +69,7 @@
       ~JonesVector.sum
       ~JonesVector.swapaxes
       ~JonesVector.take
+      ~JonesVector.to_device
       ~JonesVector.to_stokes
       ~JonesVector.tobytes
       ~JonesVector.tofile
@@ -95,13 +93,18 @@
       ~JonesVector.base
       ~JonesVector.ctypes
       ~JonesVector.data
+      ~JonesVector.device
       ~JonesVector.dtype
       ~JonesVector.flags
       ~JonesVector.flat
       ~JonesVector.imag
+      ~JonesVector.itemset
       ~JonesVector.itemsize
+      ~JonesVector.mT
       ~JonesVector.nbytes
       ~JonesVector.ndim
+      ~JonesVector.newbyteorder
+      ~JonesVector.ptp
       ~JonesVector.real
       ~JonesVector.shape
       ~JonesVector.size

diff --git a/docs/source/_autosummary/nenupy.astro.jones_mueller.MuellerMatrix.rst b/docs/source/_autosummary/nenupy.astro.jones_mueller.MuellerMatrix.rst
@@ -44,18 +44,15 @@
       ~MuellerMatrix.getfield
       ~MuellerMatrix.half_waveplate_retarder
       ~MuellerMatrix.item
-      ~MuellerMatrix.itemset
       ~MuellerMatrix.left_circular
       ~MuellerMatrix.linear
       ~MuellerMatrix.linear_retarder
       ~MuellerMatrix.max
       ~MuellerMatrix.mean
       ~MuellerMatrix.min
-      ~MuellerMatrix.newbyteorder
       ~MuellerMatrix.nonzero
       ~MuellerMatrix.partition
       ~MuellerMatrix.prod
-      ~MuellerMatrix.ptp
       ~MuellerMatrix.put
       ~MuellerMatrix.quarter_waveplate_retarder
       ~MuellerMatrix.ravel
@@ -73,6 +70,7 @@
       ~MuellerMatrix.sum
       ~MuellerMatrix.swapaxes
       ~MuellerMatrix.take
+      ~MuellerMatrix.to_device
       ~MuellerMatrix.to_hermitian
       ~MuellerMatrix.to_jones
       ~MuellerMatrix.tobytes
@@ -96,13 +94,18 @@
       ~MuellerMatrix.base
       ~MuellerMatrix.ctypes
       ~MuellerMatrix.data
+      ~MuellerMatrix.device
       ~MuellerMatrix.dtype
       ~MuellerMatrix.flags
       ~MuellerMatrix.flat
       ~MuellerMatrix.imag
+      ~MuellerMatrix.itemset
       ~MuellerMatrix.itemsize
+      ~MuellerMatrix.mT
       ~MuellerMatrix.nbytes
       ~MuellerMatrix.ndim
+      ~MuellerMatrix.newbyteorder
+      ~MuellerMatrix.ptp
       ~MuellerMatrix.real
       ~MuellerMatrix.shape
       ~MuellerMatrix.size

diff --git a/docs/source/_autosummary/nenupy.astro.jones_mueller.PolarVector.rst b/docs/source/_autosummary/nenupy.astro.jones_mueller.PolarVector.rst
@@ -45,17 +45,14 @@
       ~PolarVector.getfield
       ~PolarVector.horizontal
       ~PolarVector.item
-      ~PolarVector.itemset
       ~PolarVector.left_circular
       ~PolarVector.linear
       ~PolarVector.max
       ~PolarVector.mean
       ~PolarVector.min
-      ~PolarVector.newbyteorder
       ~PolarVector.nonzero
       ~PolarVector.partition
       ~PolarVector.prod
-      ~PolarVector.ptp
       ~PolarVector.put
       ~PolarVector.ravel
       ~PolarVector.repeat
@@ -72,6 +69,7 @@
       ~PolarVector.sum
       ~PolarVector.swapaxes
       ~PolarVector.take
+      ~PolarVector.to_device
       ~PolarVector.tobytes
       ~PolarVector.tofile
       ~PolarVector.tolist
@@ -94,13 +92,18 @@
       ~PolarVector.base
       ~PolarVector.ctypes
       ~PolarVector.data
+      ~PolarVector.device
       ~PolarVector.dtype
       ~PolarVector.flags
       ~PolarVector.flat
       ~PolarVector.imag
+      ~PolarVector.itemset
       ~PolarVector.itemsize
+      ~PolarVector.mT
       ~PolarVector.nbytes
       ~PolarVector.ndim
+      ~PolarVector.newbyteorder
+      ~PolarVector.ptp
       ~PolarVector.real
       ~PolarVector.shape
       ~PolarVector.size

diff --git a/docs/source/_autosummary/nenupy.astro.jones_mueller.PolarizerMatrix.rst b/docs/source/_autosummary/nenupy.astro.jones_mueller.PolarizerMatrix.rst
@@ -44,18 +44,15 @@
       ~PolarizerMatrix.getfield
       ~PolarizerMatrix.half_waveplate_retarder
       ~PolarizerMatrix.item
-      ~PolarizerMatrix.itemset
       ~PolarizerMatrix.left_circular
       ~PolarizerMatrix.linear
       ~PolarizerMatrix.linear_retarder
       ~PolarizerMatrix.max
       ~PolarizerMatrix.mean
       ~PolarizerMatrix.min
-      ~PolarizerMatrix.newbyteorder
       ~PolarizerMatrix.nonzero
       ~PolarizerMatrix.partition
       ~PolarizerMatrix.prod
-      ~PolarizerMatrix.ptp
       ~PolarizerMatrix.put
       ~PolarizerMatrix.quarter_waveplate_retarder
       ~PolarizerMatrix.ravel
@@ -73,6 +70,7 @@
       ~PolarizerMatrix.sum
       ~PolarizerMatrix.swapaxes
       ~PolarizerMatrix.take
+      ~PolarizerMatrix.to_device
       ~PolarizerMatrix.tobytes
       ~PolarizerMatrix.tofile
       ~PolarizerMatrix.tolist
@@ -94,13 +92,18 @@
       ~PolarizerMatrix.base
       ~PolarizerMatrix.ctypes
       ~PolarizerMatrix.data
+      ~PolarizerMatrix.device
       ~PolarizerMatrix.dtype
       ~PolarizerMatrix.flags
       ~PolarizerMatrix.flat
       ~PolarizerMatrix.imag
+      ~PolarizerMatrix.itemset
       ~PolarizerMatrix.itemsize
+      ~PolarizerMatrix.mT
       ~PolarizerMatrix.nbytes
       ~PolarizerMatrix.ndim
+      ~PolarizerMatrix.newbyteorder
+      ~PolarizerMatrix.ptp
       ~PolarizerMatrix.real
       ~PolarizerMatrix.shape
       ~PolarizerMatrix.size

diff --git a/docs/source/_autosummary/nenupy.astro.jones_mueller.StokesVector.rst b/docs/source/_autosummary/nenupy.astro.jones_mueller.StokesVector.rst
@@ -46,17 +46,14 @@
       ~StokesVector.getfield
       ~StokesVector.horizontal
       ~StokesVector.item
-      ~StokesVector.itemset
       ~StokesVector.left_circular
       ~StokesVector.linear
       ~StokesVector.max
       ~StokesVector.mean
       ~StokesVector.min
-      ~StokesVector.newbyteorder
       ~StokesVector.nonzero
       ~StokesVector.partition
       ~StokesVector.prod
-      ~StokesVector.ptp
       ~StokesVector.put
       ~StokesVector.ravel
       ~StokesVector.repeat
@@ -73,6 +70,7 @@
       ~StokesVector.sum
       ~StokesVector.swapaxes
       ~StokesVector.take
+      ~StokesVector.to_device
       ~StokesVector.to_jones
       ~StokesVector.tobytes
       ~StokesVector.tofile
@@ -96,13 +94,18 @@
       ~StokesVector.base
       ~StokesVector.ctypes
       ~StokesVector.data
+      ~StokesVector.device
       ~StokesVector.dtype
       ~StokesVector.flags
       ~StokesVector.flat
       ~StokesVector.imag
+      ~StokesVector.itemset
       ~StokesVector.itemsize
+      ~StokesVector.mT
       ~StokesVector.nbytes
       ~StokesVector.ndim
+      ~StokesVector.newbyteorder
+      ~StokesVector.ptp
       ~StokesVector.real
       ~StokesVector.shape
       ~StokesVector.size

diff --git a/docs/source/_images/io_images/plot_dynamic_spectrum.png b/docs/source/_images/io_images/plot_dynamic_spectrum.png
diff --git a/nenupy/__init__.py b/nenupy/__init__.py
@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2023, nenupy"
 __credits__ = ["Alan Loh"]
 __license__ = "MIT"
-__version__ = "2.7.6"
+__version__ = "2.7.7"
 __maintainer__ = "Alan Loh"
 __email__ = "alan.loh@obspm.fr"
 

diff --git a/nenupy/astro/jones_mueller.py b/nenupy/astro/jones_mueller.py
@@ -146,7 +146,7 @@ def __new__(cls, input_array: np.ndarray):
 
     @classmethod
     def elliptical(cls, theta: float, delta: float):
-        r"""Ideal elliptical, producing elliptically polarized light with azimuth :math:`\psi` and ellipticity :math:`\omega` such that :math`\tan(2\psi)=\tan(2\theta)\cos(\delta)` and :math:`\sin(2\omega)=\sin(2\theta)\sin(\delta).
+        r"""Ideal elliptical, producing elliptically polarized light with azimuth :math:`\psi` and ellipticity :math:`\omega` such that :math:`\tan(2\psi)=\tan(2\theta)\cos(\delta)` and :math:`\sin(2\omega)=\sin(2\theta)\sin(\delta)`.
 
         :param theta: in degrees.
         :type theta: `float`
@@ -264,7 +264,7 @@ def __new__(cls, input_array: np.ndarray):
 
     @classmethod
     def elliptical(cls, theta: float, delta: float):
-        r"""Ideal elliptical, producing elliptically polarized light with azimuth :math:`\psi` and ellipticity :math:`\omega` such that :math`\tan(2\psi)=\tan(2\theta)\cos(\delta)` and :math:`\sin(2\omega)=\sin(2\theta)\sin(\delta).
+        r"""Ideal elliptical, producing elliptically polarized light with azimuth :math:`\psi` and ellipticity :math:`\omega` such that :math:`\tan(2\psi)=\tan(2\theta)\cos(\delta)` and :math:`\sin(2\omega)=\sin(2\theta)\sin(\delta)`.
 
         :param theta: in degrees.
         :type theta: `float`
@@ -315,7 +315,7 @@ def linear_retarder(cls, theta: float, delta: float):
     def to_hermitian(self) -> np.ndarray:
         r"""
         .. math::
-            \mathbf{H} = \frac{1}{4} \sum_{i,j=0}^{3} M_{ij}( \mathbf{sigma_i} \kron \mathbf{\sigma}_j^{\star})
+            \mathbf{H} = \frac{1}{4} \sum_{i,j=0}^{3} M_{ij}( \mathbf{\sigma_i} \otimes \mathbf{\sigma}_j^{\star})
 
         ref : https://arxiv.org/pdf/1906.11198.pdf eq. 6
         """

diff --git a/nenupy/io/tf.py b/nenupy/io/tf.py
@@ -263,10 +263,10 @@ def flatten_subband(cls):
 
         """
 
-        def wrapper_task(data, channels):
-            return utils.flatten_subband(data=data, channels=channels)
+        def wrapper_task(data, channels, smooth_frequency_profile):
+            return utils.flatten_subband(data=data, channels=channels, smooth_frequency_profile=smooth_frequency_profile)
 
-        return cls("Flatten subband", wrapper_task, ["channels"], repeatable=False)
+        return cls("Flatten subband", wrapper_task, ["channels", "smooth_frequency_profile"], repeatable=False)
 
     @classmethod
     def remove_channels(cls):
@@ -977,15 +977,15 @@ class Spectra:
 
     """
 
-    def __init__(self, filename: str, check_missing_data: bool = True):
+    def __init__(self, filename: str, check_missing_data: bool = False):
         """Generate an instance of :class:`~nenupy.io.tf.Spectra`.
 
         Parameters
         ----------
         filename : `str`
             Path to the *UnDySPuTeD* file to read.
         check_missing_data : `bool`, optional
-            Check for missing data, not checking may speed up the reading time, by default `True`
+            Check for missing data, not checking may speed up the reading time, by default `False`
 
         Raises
         ------
@@ -1009,6 +1009,7 @@ def __init__(self, filename: str, check_missing_data: bool = True):
         )
 
         # Compute the main data block descriptors (time / frequency / beam)
+        log.info("Computing time-freequency axes...")
         subband_width_hz = SUBBAND_WIDTH.to_value(u.Hz)
         self._block_start_unix = (
             data["TIMESTAMP"][~bad_block_mask]
@@ -1194,6 +1195,8 @@ def get(self, file_name: str = None, **pipeline_kwargs) -> SData:
             Desired rebinning time resolution, can either be given as a :class:`~astropy.units.Quantity` object or a float (assumed to be in sec in that case). Note that the :meth:`~nenupy.io.tf.TFTask.time_rebin` task should be present in the planned pipeline (:attr:`~nenupy.io.tf.Spectra.pipeline`).
         rebin_df : `float` or :class:`~astropy.units.Quantity`, default: ``None``
             Desired rebinning frequency resolution, can either be given as a :class:`~astropy.units.Quantity` object or float (assumed to be in kHz in that case). Note that the :meth:`~nenupy.io.tf.TFTask.frequency_rebin` task should be present in the planned pipeline (:attr:`~nenupy.io.tf.Spectra.pipeline`).
+        smooth_frequency_profile : `bool`, default `False`
+            Keyword used if :meth:`~nenupy.io.tf.TFTask.flatten_subband` is in the pipeline: smooth the frequency profile, this option mau result in unexpected behavior if the subbands are not contiguous or the selected beamlets do not belong to the same digital beam. 
         remove_channels : `list` or :class:`~numpy.ndarray`, default: ``None``
             List of subband channels to remove, e.g. `remove_channels=[0,1,-1]` would remove the first, second (low-freq) and last channels from each subband. Note that the :meth:`~nenupy.io.tf.TFTask.remove_channels` task should be present in the planned pipeline (:attr:`~nenupy.io.tf.Spectra.pipeline`).
         dreambeam_skycoord : :class:`~astropy.coordinates.SkyCoord`, default: ``None``