cubevis 0.5.2__py3-none-any.whl

cubevis/bokeh/utils/_svg_icon.py

@@ -0,0 +1,136 @@
+########################################################################
+#
+# Copyright (C) 2023
+# Associated Universities, Inc. Washington DC, USA.
+#
+# This script is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Library General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or (at your
+# option) any later version.
+#
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Library General Public
+# License for more details.
+#
+# You should have received a copy of the GNU Library General Public License
+# along with this library; if not, write to the Free Software Foundation,
+# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
+#
+# Correspondence concerning AIPS++ should be adressed as follows:
+#        Internet email: casa-feedback@nrao.edu.
+#        Postal address: AIPS++ Project Office
+#                        National Radio Astronomy Observatory
+#                        520 Edgemont Road
+#                        Charlottesville, VA 22903-2475 USA
+#
+########################################################################
+from os import listdir
+from os.path import dirname, join, isfile, getsize
+from bokeh.core import properties
+from bokeh.models.ui.icons import SVGIcon
+from ...utils import static_vars
+
+@static_vars( values = { 'calendar': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path d="M11,3 C11.6,3 12,2.5 12,2 L12,1 C12,0.4 11.6,0 11,0 C10.4,0 10,0.4 10,1 L10,2 C10,2.5 10.4,3 11,3 Z M14,1 L13,1 L13,2 C13,3.1 12.1,4 11,4 C9.9,4 9,3.1 9,2 L9,1 L6,1 L6,2 C6,3.1 5.1,4 4,4 C2.9,4 2,3.1 2,2 L2,1 L1,1 C0.4,1 0,1.5 0,2 L0,14 C0,14.6 0.4,15 1,15 L14,15 C14.6,15 15,14.6 15,14 L15,2 C15,1.4 14.5,1 14,1 Z M5,13 L2,13 L2,10 L5,10 L5,13 Z M5,9 L2,9 L2,6 L5,6 L5,9 Z M9,13 L6,13 L6,10 L9,10 L9,13 Z M9,9 L6,9 L6,6 L9,6 L9,9 Z M13,13 L10,13 L10,10 L13,10 L13,13 Z M13,9 L10,9 L10,6 L13,6 L13,9 Z M4,3 C4.6,3 5,2.5 5,2 L5,1 C5,0.4 4.6,0 4,0 C3.4,0 3,0.4 3,1 L3,2 C3,2.5 3.4,3 4,3 Z" id="Shape" fill="#000000" fill-rule="nonzero"></path></svg>',
+                      'play': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path fill-rule="evenodd" clip-rule="evenodd" d="M12,8c0-0.35-0.19-0.64-0.46-0.82l0.01-0.02l-6-4L5.54,3.18C5.39,3.08,5.21,3,5,3C4.45,3,4,3.45,4,4v8c0,0.55,0.45,1,1,1c0.21,0,0.39-0.08,0.54-0.18l0.01,0.02l6-4l-0.01-0.02C11.81,8.64,12,8.35,12,8z"/></svg>',
+                      'pause': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path fill-rule="evenodd" clip-rule="evenodd" d="M6,3H4C3.45,3,3,3.45,3,4v8c0,0.55,0.45,1,1,1h2c0.55,0,1-0.45,1-1V4C7,3.45,6.55,3,6,3z M12,3h-2C9.45,3,9,3.45,9,4v8c0,0.55,0.45,1,1,1h2c0.55,0,1-0.45,1-1V4C13,3.45,12.55,3,12,3z"/></svg>',
+                      'stop': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path fill-rule="evenodd" clip-rule="evenodd" d="M12,3H4C3.45,3,3,3.45,3,4v8c0,0.55,0.45,1,1,1h8c0.55,0,1-0.45,1-1V4C13,3.45,12.55,3,12,3z"/></svg>',
+                      'step-forward': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path fill-rule="evenodd" clip-rule="evenodd" d="M12,3h-1c-0.55,0-1,0.45-1,1v2.72l-4.38-3.5L5.62,3.23C5.44,3.09,5.24,3,5,3C4.45,3,4,3.45,4,4v8c0,0.55,0.45,1,1,1c0.24,0,0.44-0.09,0.62-0.23l0.01,0.01L10,9.28V12c0,0.55,0.45,1,1,1h1c0.55,0,1-0.45,1-1V4C13,3.45,12.55,3,12,3z"/></svg>',
+                      'step-backward': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path fill-rule="evenodd" clip-rule="evenodd" d="M12,3c-0.24,0-0.44,0.09-0.62,0.23l-0.01-0.01L7,6.72V4c0-0.55-0.45-1-1-1H5C4.45,3,4,3.45,4,4v8c0,0.55,0.45,1,1,1h1c0.55,0,1-0.45,1-1V9.28l4.38,3.5l0.01-0.01C11.56,12.91,11.76,13,12,13c0.55,0,1-0.45,1-1V4C13,3.45,12.55,3,12,3z"/></svg>',
+                      'cube-add': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path d="M14,2 L15,2 C15.5522847,2 16,2.44771525 16,3 C16,3.55228475 15.5522847,4 15,4 L14,4 L14,5 C14,5.55228475 13.5522847,6 13,6 C12.4477153,6 12,5.55228475 12,5 L12,4 L11,4 C10.4477153,4 10,3.55228475 10,3 C10,2.44771525 10.4477153,2 11,2 L12,2 L12,1 C12,0.44771525 12.4477153,1.01453063e-16 13,0 C13.5522847,-1.01453063e-16 14,0.44771525 14,1 L14,2 Z M9.13604922,0.649170982 C8.44387329,1.19872806 8,2.04752795 8,3 C8,4.3537679 8.89669129,5.49810232 10.1285353,5.8714647 C10.1461766,5.92966908 10.1655391,5.98712523 10.1865637,6.0437739 L8,7.41037618 L1.80625275,3.53928415 L7.50386106,0.283507965 C7.81129373,0.107832154 8.18870627,0.107832154 8.49613894,0.283507965 L9.13604922,0.649170982 Z M15,7.23610651 L15,11.4196775 C15,11.7785343 14.8077139,12.1098778 14.4961389,12.2879206 L8.5,15.7142857 L8.5,8.27712382 L10.68679,6.91038005 C11.2370488,7.57591314 12.068999,8 13,8 C13.7683544,8 14.4692435,7.71114643 15,7.23610651 Z M1.05620201,4.24975008 L7.5,8.27712382 L7.5,15.7142857 L1.50386106,12.2879206 C1.19228606,12.1098778 1,11.7785343 1,11.4196775 L1,4.58032254 C1,4.46598225 1.01952108,4.35443515 1.05620201,4.24975008 Z" id="Combined-Shape" fill="#000000" fill-rule="nonzero"></path></svg>',
+                      'cube-remove': '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 19 20"><path d="M10.3645067,5.93255949 L8,7.41037618 L1.80625275,3.53928415 L7.50386106,0.283507965 C7.81129373,0.107832154 8.18870627,0.107832154 8.49613894,0.283507965 L9.13604922,0.649170982 C8.44387329,1.19872806 8,2.04752795 8,3 C8,4.43880783 9.01288495,5.64104371 10.3645067,5.93255949 Z M15,6 L15,11.4196775 C15,11.7785343 14.8077139,12.1098778 14.4961389,12.2879206 L8.5,15.7142857 L8.5,8.27712382 L12.1433981,6 L15,6 Z M1.05620201,4.24975008 L7.5,8.27712382 L7.5,15.7142857 L1.50386106,12.2879206 C1.19228606,12.1098778 1,11.7785343 1,11.4196775 L1,4.58032254 C1,4.46598225 1.01952108,4.35443515 1.05620201,4.24975008 Z M11,2 L15,2 C15.5522847,2 16,2.44771525 16,3 C16,3.55228475 15.5522847,4 15,4 L11,4 C10.4477153,4 10,3.55228475 10,3 C10,2.44771525 10.4477153,2 11,2 Z" id="Combined-Shape" fill="#000000" fill-rule="nonzero"></path></svg>',
+                      'iclean-continue': '''<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+         viewBox="0 0 20 20" enable-background="new 0 0 20 20" xml:space="preserve"><g id="repeat">
+        <g>
+                <path fill-rule="evenodd" clip-rule="evenodd" d="M14,6c0,0.55,0.45,1,1,1h4c0.55,0,1-0.45,1-1V2c0-0.55-0.45-1-1-1s-1,0.45-1,1
+                        v2.05C16.18,1.6,13.29,0,10,0C4.48,0,0,4.48,0,10c0,5.52,4.48,10,10,10s10-4.48,10-10c0-0.55-0.45-1-1-1s-1,0.45-1,1
+                        c0,4.42-3.58,8-8,8s-8-3.58-8-8s3.58-8,8-8c2.53,0,4.77,1.17,6.24,3H15C14.45,5,14,5.45,14,6z"/>
+        </g>
+</g>
+</svg>''',
+                      'iclean-finish': '''<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+         viewBox="0 0 20 20" enable-background="new 0 0 20 20" xml:space="preserve">
+<g id="refresh_1_">
+        <g>
+                <path fill-rule="evenodd" clip-rule="evenodd" d="M19,1c-0.55,0-1,0.45-1,1v2.06C16.18,1.61,13.29,0,10,0C4.48,0,0,4.48,0,10
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+                        c5.52,0,10-4.48,10-10C20,9.45,19.55,9,19,9z"/>
+        </g>
+</g>
+</svg>''',
+                      'iclean-stop': '''<svg version="1.1" fill="white" id="Capa_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 width="454.354px" height="454.354px" viewBox="0 0 454.354 454.354" style="enable-background:new 0 0 454.354 454.354;"
+	 xml:space="preserve">
+<g>
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+</g>
+</svg>''',
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+                         ### bp = https://blueprintjs.com/docs/#icons/icons-list
+                         'bp-application-lg': '''<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 viewBox="0 0 20 20" enable-background="new 0 0 20 20" xml:space="preserve">
+<g id="application">
+	<g>
+		<path fill-rule="evenodd" clip-rule="evenodd" d="M3.5,9h9C12.78,9,13,8.78,13,8.5C13,8.22,12.78,8,12.5,8h-9C3.22,8,3,8.22,3,8.5
+			C3,8.78,3.22,9,3.5,9z M3.5,11h5C8.78,11,9,10.78,9,10.5C9,10.22,8.78,10,8.5,10h-5C3.22,10,3,10.22,3,10.5
+			C3,10.78,3.22,11,3.5,11z M19,1H1C0.45,1,0,1.45,0,2v16c0,0.55,0.45,1,1,1h18c0.55,0,1-0.45,1-1V2C20,1.45,19.55,1,19,1z M18,17H2
+			V6h16V17z M3.5,13h7c0.28,0,0.5-0.22,0.5-0.5c0-0.28-0.22-0.5-0.5-0.5h-7C3.22,12,3,12.22,3,12.5C3,12.78,3.22,13,3.5,13z"/>
+	</g>
+</g>
+</svg>''',
+                         'bp-application-sm': '''<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 viewBox="0 0 16 16" enable-background="new 0 0 16 16" xml:space="preserve">
+<g id="application_1_">
+	<g>
+		<path fill-rule="evenodd" clip-rule="evenodd" d="M3.5,7h7C10.78,7,11,6.78,11,6.5C11,6.22,10.78,6,10.5,6h-7C3.22,6,3,6.22,3,6.5
+			C3,6.78,3.22,7,3.5,7z M15,1H1C0.45,1,0,1.45,0,2v12c0,0.55,0.45,1,1,1h14c0.55,0,1-0.45,1-1V2C16,1.45,15.55,1,15,1z M14,13H2V5
+			h12V13z M3.5,9h4C7.78,9,8,8.78,8,8.5C8,8.22,7.78,8,7.5,8h-4C3.22,8,3,8.22,3,8.5C3,8.78,3.22,9,3.5,9z M3.5,11h5
+			C8.78,11,9,10.78,9,10.5C9,10.22,8.78,10,8.5,10h-5C3.22,10,3,10.22,3,10.5C3,10.78,3.22,11,3.5,11z"/>
+	</g>
+</g>
+</svg>'''
+
+} )
+def svg_icon( icon_name, **kwargs ):
+    if type(icon_name) == str and icon_name in svg_icon.values:
+        return SVGIcon( **kwargs, svg=svg_icon.values[icon_name] )
+
+    elif type(icon_name) == str or type(icon_name) == list and len(icon_name) > 0:
+        if type(icon_name) == str: _icon_name = [ icon_name ]
+        else: _icon_name = icon_name
+        if type(_icon_name) == list:
+            icon_dir = join( dirname(dirname(dirname(__file__))),'__icons__', *_icon_name[:-1] )
+            icons = [f for f in listdir(icon_dir) if isfile(join(icon_dir, f)) and f.startswith(_icon_name[-1]) and f.endswith('.svg')]
+            if len(icons) > 1:
+                raise RuntimeError( f'''multiple icon files {icons} found in {icon_dir}''' )
+            elif len(icons) > 0:
+                path = join( icon_dir, icons[0] )
+                if isfile(path):
+                    if getsize(path) > 2 * 1024 * 1024:
+                        raise RuntimeError( f'''{path} seems too large to be an SVG file...''' )
+                    with open( path, "r" ) as f:
+                        svg_string = f.read( )
+                    return SVGIcon( **kwargs, svg=svg_string )
+
+    raise RuntimeError( f'''icon_name={icon_name} is not a known icon''' )

cubevis/data/__init__.py

@@ -0,0 +1 @@
+""" Module for interface to CASA image utilities and MeasurementSet data """

cubevis/data/casaimage/__init__.py

@@ -0,0 +1,114 @@
+########################################################################
+#
+# Copyright (C) 2023, 2024
+# Associated Universities, Inc. Washington DC, USA.
+#
+# This script is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Library General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or (at your
+# option) any later version.
+#
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Library General Public
+# License for more details.
+#
+# You should have received a copy of the GNU Library General Public License
+# along with this library; if not, write to the Free Software Foundation,
+# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
+#
+# Correspondence concerning AIPS++ should be adressed as follows:
+#        Internet email: casa-feedback@nrao.edu.
+#        Postal address: AIPS++ Project Office
+#                        National Radio Astronomy Observatory
+#                        520 Edgemont Road
+#                        Charlottesville, VA 22903-2475 USA
+#
+########################################################################
+'''image utilities'''
+
+from os.path import isfile, exists
+from io import BytesIO
+from pathlib import Path
+import PIL.Image
+import base64
+
+try:
+    import casatools as ct
+    from casatools import image as imagetool
+except:
+    ct = None
+    from cubevis.utils import warn_import
+    warn_import('casatools')
+
+def as_mime( path ):
+
+    value = path
+    if isinstance( value, str ) and isfile(value):
+        value = Path(value)
+
+    if isinstance( value, Path ):
+        value = PIL.Image.open(value)
+
+    if isinstance( value, PIL.Image.Image ):
+        out = BytesIO()
+        fmt = value.format or "PNG"
+        value.save(out, fmt)
+        encoded = base64.b64encode( out.getvalue() ).decode( 'ascii' )
+        return f"data:image/{fmt.lower()};base64,{encoded}"
+
+    raise RuntimeError( f'''could not load {path}''' )
+
+def new( pattern, path, overwrite=False ):
+    '''Create a new image using ``pattern`` as a pattern. ``pattern`` supplies the
+    shape for the new image as well as the coordinate system for the new image.
+
+    Parameters
+    ----------
+    path: str
+        path to the image to be created
+
+    pattern: str
+        path to the image on which the new image should be based
+
+    overwrite: bool
+        overwrite any existing image, directory or file
+    '''
+    if ct is None:
+        raise RuntimeError( 'casaimage.new: casatools is not available' )
+    if exists(path) and not overwrite:
+        raise RuntimeError( '''casaimage.new: image already exists (and 'overwrite=False')''' )
+    if not exists(pattern):
+        raise RuntimeError( 'casaimage.new: an original image is required' )
+    im = imagetool( )
+    im.open(pattern)
+    print(repr(im.coordsys( )))
+    newim = im.newimagefromshape( path, shape=im.shape( ), csys=im.coordsys( ).torecord( ), overwrite=overwrite )
+    im.close( )
+    im.done( )
+    result = newim.name( )
+    newim.close( )
+    newim.done( )
+    return result
+
+def shape( path ):
+    '''Return the shape of an image.
+
+    Parameters
+    ----------
+    path: str
+        path to the image
+
+    Returns
+    -------
+    list of int
+        shape of image
+    '''
+    if not exists(path):
+        raise RuntimeError( '''casaimage.shape: image does not exist''' )
+    im = imagetool( )
+    im.open(path)
+    result = im.shape( )
+    im.close( )
+    im.done( )
+    return result

cubevis/data/measurement_set/__init__.py

@@ -0,0 +1,7 @@
+'''
+    Module to access MeasurementSet data using MsData class.
+'''
+
+from ._ms_data import (
+    MsData
+)

cubevis/data/measurement_set/_ms_data.py

@@ -0,0 +1,178 @@
+'''
+    Class for accessing and selecting MeasurementSet data using a data backend.
+'''
+
+from cubevis.data.measurement_set.processing_set._ps_data import PsData
+
+class MsData:
+    '''
+    Access and select MeasurementSet data.
+    Current backend implementation is PsData using xradio Processing Set.
+    '''
+
+    def __init__(self, ms_path, logger):
+        self._ms_path = ms_path
+        self._logger = logger
+        self._data = None
+        self._data_initialized = False
+        self._init_data(ms_path)
+
+    def is_valid(self):
+        ''' Returns whether MS path has been set so data can be accessed. '''
+        return self._data_initialized
+
+    def is_ms_path(self, path):
+        ''' Check if input path matches input ms path or zarr path '''
+        return path == self.get_path() or path == self._ms_path
+
+    def get_path(self):
+        ''' Returns path of MS/zarr file or None if not set. '''
+        if self._data_initialized:
+            return self._data.get_path() # path to zarr file
+        if self._ms_path:
+            return self._ms_path # path to ms v2
+        return None
+
+    def summary(self, data_group='base', columns=None):
+        ''' Print summary of Processing Set data.
+                columns (None, str, list): type of metadata to list.
+                    None:      Print all summary columns in ProcessingSet.
+                    'by_msv4': Print formatted summary metadata by MSv4.
+                    str, list: Print a subset of summary columns in ProcessingSet.
+                        Options: 'name', 'intents', 'shape', 'polarization', 'scan_number', 'spw_name',
+                                 'field_name, 'source_name', 'field_coords', 'start_frequency', 'end_frequency'
+        '''
+        # ProcessingSet function
+        if self._data_initialized:
+            self._data.summary(data_group, columns)
+        else:
+            self._log_no_ms()
+
+    def get_ps_summary(self):
+        ''' Return Pandas DataFrame summary of ProcessingSet '''
+        if self._data_initialized:
+            return self._data.get_summary()
+        self._log_no_ms()
+        return None
+
+    def data_groups(self):
+        ''' Returns set of data group names in Processing Set data. '''
+        # ProcessingSet function
+        if self._data_initialized:
+            return self._data.get_data_groups()
+        self._log_no_ms()
+        return None
+
+    def get_antennas(self, plot_positions=False, label_antennas=False):
+        ''' Returns list of antenna names in data.
+                plot_positions (bool): show plot of antenna positions.
+                label_antennas (bool): label positions with antenna names.
+        '''
+        # Antenna positions plot is ProcessingSet function
+        if self._data_initialized:
+            return self._data.get_antennas(plot_positions, label_antennas)
+        self._log_no_ms()
+        return None
+
+    def plot_phase_centers(self, data_group='base', label_all_fields=False):
+        ''' Plot the phase center locations of all fields in the Processing Set (original or selected) and label central field.
+                label_all_fields (bool); label all fields on the plot
+                data_group (str); data group to use for processing.
+        '''
+        # ProcessingSet function
+        if self._data_initialized:
+            self._data.plot_phase_centers(label_all_fields, data_group)
+        else:
+            self._log_no_ms()
+
+    def get_num_ms(self):
+        ''' Returns number of MeasurementSets in data. '''
+        if self._data_initialized:
+            return self._data.get_ps_len()
+        self._log_no_ms()
+        return None
+
+    def get_max_data_dims(self):
+        ''' Returns maximum length of dimensions in data. '''
+        if self._data_initialized:
+            return self._data.get_max_dims()
+        self._log_no_ms()
+        return None
+
+    def get_data_dimensions(self):
+        ''' Returns names of data dimensions. '''
+        if self._data_initialized:
+            return self._data.get_data_dimensions()
+        self._log_no_ms()
+        return None
+
+    def get_dimension_values(self, dim):
+        ''' Return values for dimension in current data.
+                dim (str): dimension name
+        '''
+        if self._data_initialized:
+            return self._data.get_dimension_values(dim)
+        self._log_no_ms()
+        return None
+
+    def get_dimension_attrs(self, dim):
+        ''' Return dict of data attributes for dimension.
+                dim (str): dimension name
+        '''
+        if self._data_initialized:
+            return self._data.get_dimension_attrs(dim)
+        self._log_no_ms()
+        return None
+
+    def get_first_spw(self):
+        ''' Returns name of first spw by id. '''
+        if self._data_initialized:
+            return self._data.get_first_spw()
+        self._log_no_ms()
+        return None
+
+    def select_data(self, selection):
+        ''' Apply selection in data.
+                selection (dict): fields and values to select
+        '''
+        if self._data_initialized:
+            self._data.select_data(selection)
+        else:
+            self._log_no_ms()
+
+    def clear_selection(self):
+        ''' Clears selection dict and selected data. '''
+        if self._data_initialized:
+            self._data.clear_selection()
+
+    def get_vis_stats(self, selection, vis_axis):
+        ''' Returns statistics (min, max, mean, std) for data selected by selection.
+                selection (dict): fields and values to select
+        '''
+        if self._data_initialized:
+            return self._data.get_vis_stats(selection, vis_axis)
+        self._log_no_ms()
+        return None
+
+    def get_correlated_data(self, data_group):
+        ''' Returns name of correlated data variable in Processing Set data group '''
+        if self._data_initialized:
+            return self._data.get_correlated_data(data_group)
+        self._log_no_ms()
+        return None
+
+    def get_raster_data(self, plot_inputs):
+        ''' Returns xarray Dataset after applying plot inputs and raster plane selection '''
+        if self._data_initialized:
+            return self._data.get_raster_data(plot_inputs)
+        self._log_no_ms()
+        return None
+
+    def _log_no_ms(self):
+        self._logger.info("No MS path set, cannot access data")
+
+    def _init_data(self, ms_path):
+        ''' Data backend for MeasurementSet; currently xradio ProcessingSet '''
+        if ms_path:
+            self._data = PsData(ms_path, self._logger)
+            self._data_initialized = True

cubevis/data/measurement_set/processing_set/__init__.py

@@ -0,0 +1,30 @@
+'''
+    Module to access MeasurementSet data using xradio ProcessingSetXdt and Xarray objects.
+'''
+
+from ._ps_concat import (
+    concat_ps_xdt,
+)
+
+from ._ps_coords import (
+    set_coordinates,
+    set_datetime_coordinate,
+    set_index_coordinates,
+)
+
+from ._ps_data import (
+    PsData,
+)
+
+from ._ps_io import (
+    get_processing_set,
+)
+
+from ._ps_raster_data import (
+    raster_data,
+)
+
+from ._xds_data import (
+    get_axis_data,
+    get_correlated_data,
+)

cubevis/data/measurement_set/processing_set/_ps_concat.py

@@ -0,0 +1,98 @@
+'''
+Concat ProcessingSet xarray DataSets into single xds by time dimension (in order)
+'''
+
+import xarray as xr
+
+from cubevis.data.measurement_set.processing_set._ps_coords import set_coordinates
+
+def concat_ps_xdt(ps_xdt, logger):
+    ''' Concatenate xarray Datasets in ProcessingSet by time dimension.
+        Return concat xds. '''
+    if len(ps_xdt) == 0:
+        raise RuntimeError("Processing set empty after selection.")
+
+    ps = {}
+    for name, ms_xdt in ps_xdt.items():
+        # Set units to str not list and set baseline coordinate.  Returns xarray.Dataset
+        ps[name] = set_coordinates(ms_xdt)
+
+    if len(ps) == 1:
+        logger.debug("Processing set contains one dataset, nothing to concat.")
+        return list(ps.values())[0]
+
+    # Split xds by time gaps
+    sorted_times = _get_sorted_times(ps)
+    xds_list = []
+    time_list = []
+    for xds in ps.values():
+        xdss, times = _split_xds_by_time_gap(xds, sorted_times)
+        xds_list.extend(xdss)
+        time_list.extend(times)
+
+    if len(xds_list) > len(ps_xdt):
+        logger.debug(f"Split {len(ps_xdt)} datasets by time gap into {len(xds_list)} datasets.")
+
+    # Create sorted xds list using sorted times
+    time_list.sort()
+    sorted_xds = [None] * len(time_list)
+
+    for xds in xds_list:
+        try:
+            first_xds_time = xds.time.values[0]
+        except IndexError: # only one value
+            first_xds_time = xds.time.values
+
+        for idx, value in enumerate(time_list):
+            if value == first_xds_time and sorted_xds[idx] is None:
+                if "baseline" in xds.coords:
+                    # Cannot concat with non-dim string coord
+                    xds = xds.drop("baseline_antenna1_name")
+                    xds = xds.drop("baseline_antenna2_name")
+                # Convert MeasurementSetXds to xr Dataset for concat
+                # (TypeError: MeasurementSetXds.__init__() got an unexpected keyword argument 'coords')
+                sorted_xds[idx] = xr.Dataset(xds.data_vars, xds.coords, xds.attrs)
+                break
+    return xr.concat(sorted_xds, dim='time')
+
+def _get_sorted_times(ps):
+    values = []
+    for key in ps:
+        time_values = ps[key].time.values
+        if time_values.size > 1:
+            values.extend(time_values.tolist())
+        else:
+            values.append(time_values)
+    return sorted(values)
+
+def _split_xds_by_time_gap(xds, sorted_times):
+    ''' Split xds where there is a gap in sorted times.
+        Return list of xds and first time in each one. '''
+    times = xds.time.values.ravel()
+    xds_list = []
+    first_times = [times[0]]
+
+    if len(times) == 1:
+        xds_list.append(xds)
+    else:
+        sorted_time_idx = sorted_times.index(times[0])
+        idx = xds_start_idx = 0 # start for iselection
+
+        for idx, time in enumerate(times):
+            if time == sorted_times[sorted_time_idx]:
+                # No time gap, go to next time
+                sorted_time_idx += 1
+                continue
+
+            # Found time gap, select xds
+            xds_list.append(xds.isel(time=slice(xds_start_idx, idx)))
+
+            # start next xds with new first time, find idx in sorted times (skip ahead)
+            xds_start_idx = idx
+            first_times.append(times[idx])
+            sorted_time_idx = sorted_times.index(time) + 1 # for next time
+
+        # add last time range xds
+        xds_list.append(xds.isel(time=slice(xds_start_idx, idx + 1)))
+
+    return xds_list, first_times