doc auto try8

.gitignore

@@ -4,6 +4,8 @@ test/*
 
 tmpdata/*
 
+builddoc/*
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

docs/beam.rst

 ====================
-Beam Beam Beam 
+Interferometry Beam 
 ====================
 
 

docs/cli.rst

@@ -6,20 +6,34 @@ GUI
 
 :code:`lofarBFcube` : GUI tool to load fits cube data for LOFAR beamformed observations
 
-command line
+Command line tools
 ------------
 
-.. program-output:: python -V
+Dynamic Spectrum
+~~~~~~~~~~~~~~~~
 
-.. autoprogram:: lofarSun.cli.pyms_utils:pyms_cook_wsclean_cmd_main
-   :prog: pymsCookWscleanCMD
+* :code:`h5toFitsDS`
+  
+  .. program-output:: h5toFitsDS -h
 
-:code:`h5toFitsDS` : convert a LOFAR hdf5 file to small fits files, including averaging and flagging processings
 
-:code:`pymsOverview` : msoverview implemented with casacore
+measurement set 
+~~~~~~~~~~~~~~~~
 
-:code:`pymsCookWscleanCMD` : recommended wsclean command line for LOFAR solar interferometry
 
-:code:`pymsDatetime2Index` : convert datatime to index in a LOFAR MS file
+* :code:`pymsOverview`
+  
+   .. program-output:: pymsOverview -h
+
+* :code:`pymsCookWscleanCMD`
+  
+  .. program-output:: pymsCookWscleanCMD -h
+
+* :code:`pymsDatetime2Index`
+  
+  .. program-output:: pymsDatetime2Index -h
+
+* :code:`pymsIndex2Datetime`
+  
+  .. program-output:: pymsIndex2Datetime -h
 
-:code:`pymsIndex2Datetime` : convert index to datatime in a LOFAR MS file
\ No newline at end of file

docs/conf.py

@@ -39,12 +39,17 @@ release = '0.1.0'
 extensions = ['sphinx.ext.autodoc', 
               'sphinx.ext.coverage', 
               'sphinx.ext.napoleon',
-              'sphinxcontrib-programoutput',
-              'sphinxcontrib-autoprogram']
+              'sphinxcontrib.programoutput',
+              'sphinx.ext.autosummary']
 html_favicon = 'img/image.ico'
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
+
+extensions.append('autoapi.extension')
+autoapi_type = 'python'
+autoapi_dirs = ['../lofarSun']
+
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.

docs/index.rst

@@ -86,6 +86,7 @@ The common data formats for solar and space weather studys:
 
 
 
+.. autosummary::
 
 Cite as
 -------

docs/interferometry.rst

@@ -336,7 +336,6 @@ directory '/HDD/path/to/data/' to '/lofardata'
 
 .. autofunction:: lofarSun.IM.get_peak_beam_from_psf
 
-.. autofunction:: lofarSun.cli.get_obs_info_from_ms
 
 .. rubric:: Footnotes
 

docs/requirements.txt

@@ -3,5 +3,4 @@ lofarSun
 sphinx
 sphinx_rtd_theme
 readthedocs-sphinx-search
-sphinxcontrib-programoutput
-sphinxcontrib-autoprogram
\ No newline at end of file
+sphinxcontrib-programoutput
\ No newline at end of file

lofarSun/BF/bftools.py

@@ -15,11 +15,15 @@ device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
 
 
 def h5_fetch_meta(f, SAP="000"):
-    """ get metadata from h5 file
+    """get info from the h5 file
 
     Args:
-        f (_type_): _description_
-    """
+        f (h5 file): target h5 file
+        SAP (str, optional): Sub-Array-Pointing. Defaults to "000".
+
+    Returns:
+        list: metadata of the h5 file
+    """    
 
     root_group = f["/"]
 
@@ -62,6 +66,27 @@ def h5_fetch_meta(f, SAP="000"):
 def downsample_h5_seg_by_time_ratio(data_array_uri, t_all, t_ratio_start, t_ratio_end, t_idx_count,  
                     t_c_ratio, f_c_ratio, averaging=True, flagging=False, t_idx_cut=256,
                     agg_factor=[1.66, 1.66, 0.45, 0.45], subband_edge=False, subband_ch=16, device=device):
+    """ Downsample the h5 file by time ratio
+
+    Args:
+        data_array_uri (array): dynamic spectrum
+        t_all (1d array): all time stamps
+        t_ratio_start (float): start time ratio (0-1)
+        t_ratio_end (float): end time ratio (0-1)
+        t_idx_count (int): number of total time stamps
+        t_c_ratio (int): time compression ratio
+        f_c_ratio (int): frequency compression ratio
+        averaging (bool, optional): averaging or direct sample. Defaults to True.
+        flagging (bool, optional): flagging or not. Defaults to False.
+        t_idx_cut (int, optional): factor to contour segment length for processing, to make use of the memory. Defaults to 256.
+        agg_factor (list, optional): factor for flagging. Defaults to [1.66, 1.66, 0.45, 0.45].
+        subband_edge (bool, optional): remove one channel every [subband num] channels. Defaults to False.
+        subband_ch (int, optional): number of subbands per channel. Defaults to 16.
+        device (device, optional): GPU or CPU, should be something like torch.device("cuda:0") . Defaults to device.
+
+    Returns:
+        list: [averaged dynamic spectrum, time stamps]
+    """    
 
     idx_start = int(t_ratio_start * (t_idx_count - 1))
     idx_end = int(t_ratio_end * (t_idx_count - 1))

lofarSun/cli/pyms_utils.py

 # -*- coding: utf-8 -*-
 """
-python version msoverview
+command line tools to process the lofar solar data
 
-Usage:
-
-python -m pymsoverview -f xxxxx.MS [-v]
-
-Written by Peijin Zhang
+by Peijin Zhang
 version 0.1 2022-5-23 00:24:52: Initial version
 """