vidavis 0.0.4__tar.gz → 0.0.6__tar.gz

{vidavis-0.0.4 → vidavis-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vidavis
-Version: 0.0.4
+Version: 0.0.6
 Summary: Radio astronomy visibility data visualization
 License: LGPL
 Author-email: Darrell Schiebel <darrell@schiebel.us>,Pam Harris <pharris@nrao.edu>
@@ -43,9 +43,6 @@ Requirements
 - Optionally `python-casacore <https://pypi.org/project/python-casacore/>`_ or
   `casatools <https://pypi.org/project/casatools/>`_ for MSv2 conversion
 
-- Optionally `Selenium <https://www.selenium.dev/documentation/en/>`_ along with
-  a web driver to export to file using ``save()``
-
 Install
 ```````
 
@@ -62,25 +59,6 @@ On macOS it is required to pre-install `python-casacore` using:
 
 - :code:`conda install -c conda-forge python-casacore`
 
-Exporting Plots
-^^^^^^^^^^^^^^^
-
-To enable exporting plots to file without showing the plot, using preferred web
-driver:
-
-**Selenium** with **geckodriver** and **Firefox** (to ensure compatible versions):
-
-- :code:`conda install -c conda-forge selenium firefox geckodriver`
-
-**Selenium** with **ChromeDriver** (Chrome), with the executable
-**chromedriver** in your PATH:
-
-- :code:`conda install -c conda-forge selenium python-chromedriver-binary`
-
-or:
-
-- :code:`pip install selenium chromedriver-binary`
-
 Simple MsRaster Usage Example
 `````````````````````````````
 

{vidavis-0.0.4 → vidavis-0.0.6}/pyproject.toml

@@ -8,13 +8,14 @@ authors = [
 ]
 dependencies = [
     "bokeh==3.6.1",
+    "matplotlib",
     "hvplot",
-    "xradio>=0.0.56",
     "graphviper",
+    "selenium",
 ]
 requires-python = ">=3.11, <3.14"
 readme = "readme.rst"
-version = "0.0.4"
+version = "0.0.6"
 
 [project.license]
 text = "LGPL"

{vidavis-0.0.4 → vidavis-0.0.6}/readme.rst

@@ -34,9 +34,6 @@ Requirements
 - Optionally `python-casacore <https://pypi.org/project/python-casacore/>`_ or
   `casatools <https://pypi.org/project/casatools/>`_ for MSv2 conversion
 
-- Optionally `Selenium <https://www.selenium.dev/documentation/en/>`_ along with
-  a web driver to export to file using ``save()``
-
 Install
 ```````
 
@@ -53,25 +50,6 @@ On macOS it is required to pre-install `python-casacore` using:
 
 - :code:`conda install -c conda-forge python-casacore`
 
-Exporting Plots
-^^^^^^^^^^^^^^^
-
-To enable exporting plots to file without showing the plot, using preferred web
-driver:
-
-**Selenium** with **geckodriver** and **Firefox** (to ensure compatible versions):
-
-- :code:`conda install -c conda-forge selenium firefox geckodriver`
-
-**Selenium** with **ChromeDriver** (Chrome), with the executable
-**chromedriver** in your PATH:
-
-- :code:`conda install -c conda-forge selenium python-chromedriver-binary`
-
-or:
-
-- :code:`pip install selenium chromedriver-binary`
-
 Simple MsRaster Usage Example
 `````````````````````````````
 

{vidavis-0.0.4 → vidavis-0.0.6}/src/vidavis/__init__.py

@@ -25,10 +25,8 @@
 #                        Charlottesville, VA 22903-2475 USA
 #
 ########################################################################
-'''vidavis provides a number of python applications to visualize
-visibility data'''
-
-import os as __os
+'''vidavis provides python applications to visualize radio astronomy visibility
+data'''
 
 try:
     from .__version__ import __version__

vidavis-0.0.6/src/vidavis/apps/__init__.py

@@ -0,0 +1,3 @@
+'''End user applications supplied by ``vidavis``.'''
+
+from ._ms_raster import MsRaster

{vidavis-0.0.4 → vidavis-0.0.6}/src/vidavis/apps/_ms_raster.py

@@ -10,7 +10,7 @@ import numpy as np
 import panel as pn
 from pandas import to_datetime
 
-from vidavis.bokeh.state._palette import available_palettes
+from vidavis.bokeh._palette import available_palettes
 from vidavis.plot.ms_plot._time_ticks import get_time_formatter
 from vidavis.plot.ms_plot._ms_plot import MsPlot
 from vidavis.plot.ms_plot._ms_plot_constants import VIS_AXIS_OPTIONS, SPECTRUM_AXIS_OPTIONS, PS_SELECTION_OPTIONS, MS_SELECTION_OPTIONS
@@ -244,10 +244,13 @@ class MsRaster(MsPlot):
         Args:
             filename (str): Name of file to save. Default '': the plot will be saved as {ms}_raster.{ext}.
                 If fmt is not set for extension, plot will be saved as .png.
-            fmt (str): Format of file to save ('png', 'html', or 'gif').
+            fmt (str): Format of file to save ('png', 'svg', or 'html').
                 Default 'auto': inferred from filename extension.
-            width (int): width of exported plot.
-            height (int): height of exported plot.
+            width (int): width of exported plot in pixels.
+            height (int): height of exported plot in pixels.
+
+        If subplots defines a grid layout, width and height describe the size of each plot in the layout.
+            The layout plot size will be (width * columns, height * rows) pixels.
 
         If iteration plots were created:
             If subplots is a grid, the layout plot will be saved to a single file.

vidavis-0.0.6/src/vidavis/bokeh/__init__.py

@@ -0,0 +1,2 @@
+'''This module contains the extensions and additions to the functionality
+provided by Bokeh'''

vidavis-0.0.6/src/vidavis/data/measurement_set/__init__.py

@@ -0,0 +1 @@
+''' Module to access MeasurementSet data using MsData class. '''

vidavis-0.0.6/src/vidavis/data/measurement_set/processing_set/__init__.py

@@ -0,0 +1,2 @@
+''' Module to access MeasurementSet data using xradio ProcessingSetXdt and
+Xarray objects. '''

{vidavis-0.0.4 → vidavis-0.0.6}/src/vidavis/data/measurement_set/processing_set/_ps_io.py

@@ -34,10 +34,10 @@ def get_processing_set(ms_path, logger):
     if ext == ".zarr":
         zarr_path = ms_path
     else:
-        if not __HAVE_CASACORE:
-            raise RuntimeError("Cannot convert MSv2 to xradio zarr file: python-casacore not installed.")
         zarr_path = basename + ".ps.zarr"
         if not os.path.exists(zarr_path):
+            if not __HAVE_CASACORE:
+                raise RuntimeError("Cannot convert MSv2 to xradio zarr file: python-casacore not installed.")
             logger.info(f"Converting input MS {ms_path} to zarr {zarr_path}")
             convert_msv2_to_processing_set(
                 in_file=ms_path,

{vidavis-0.0.4 → vidavis-0.0.6}/src/vidavis/plot/__init__.py

@@ -1 +1,2 @@
-''' Module for plotting functions.  Currently supports MeasurementSet Xarray plots only. '''
+''' Module for plotting functions.  Currently supports MeasurementSetv4 Xarray
+plots only. '''

vidavis-0.0.6/src/vidavis/plot/ms_plot/__init__.py

@@ -0,0 +1 @@
+''' This module contains classes and utilities to support MS plotting '''

{vidavis-0.0.4 → vidavis-0.0.6}/src/vidavis/plot/ms_plot/_ms_plot.py

@@ -5,11 +5,13 @@ Base class for ms plots
 import os
 import time
 
-from bokeh.plotting import show
+from bokeh.io import export_png, export_svg
+from bokeh.plotting import save, show
 import hvplot
 import holoviews as hv
 import numpy as np
 import panel as pn
+from selenium import webdriver
 
 try:
     from toolviper.utils.logger import get_logger, setup_logger
@@ -140,27 +142,21 @@ class MsPlot:
         self._plots_locked = True
 
         # Single plot or combine plots into layout using subplots (rows, columns)
-        # Not layout if subplots is single plot (default if None) or if only one plot saved
-        subplots = self._plot_inputs['subplots']
-        layout_plot, is_layout = self._layout_plots(subplots)
-
-        # Render to bokeh figure
-        if is_layout:
-            # Show plots in columns
-            plot = hv.render(layout_plot.cols(subplots[1]))
-        else:
-            # Show single plot
-            plot = hv.render(layout_plot)
+        layout_plot = self._layout_plots(self._plot_inputs['subplots'])
+
+        # Render plot as Bokeh Figure or GridPlot
+        bokeh_fig = hv.render(layout_plot)
 
         self._plots_locked = False
         if self._plot_params:
+            # Show plot and plot inputs in tabs
             column = pn.Column()
             for param in self._plot_params:
                 column.append(pn.pane.Str(param))
-            tabs = pn.Tabs(('Plot', plot), ('Plot Inputs', column))
+            tabs = pn.Tabs(('Plot', bokeh_fig), ('Plot Inputs', column))
             tabs.show(title=self._app_name, threaded=True)
         else:
-            show(plot)
+            show(bokeh_fig)
 
     def save(self, filename='ms_plot.png', fmt='auto', width=900, height=600):
         '''
@@ -175,51 +171,78 @@ class MsPlot:
 
         start_time = time.time()
 
-        # Save single plot or combine plots into layout using subplots (rows, columns).
-        # Not layout if subplots is single plot or if only one plot saved.
-        subplots = self._plot_inputs['subplots']
-        layout_plot, is_layout = self._layout_plots(subplots)
-
-        if is_layout:
-            # Save plots combined into one layout
-            hvplot.save(layout_plot.cols(subplots[1]), filename=filename, fmt=fmt)
-            self._logger.info("Saved plot to %s.", filename)
-        else:
-            # Save plots individually, with index appended if exprange='all' and multiple plots.
-            if self._plot_inputs['iter_axis'] is None:
-                hvplot.save(layout_plot.opts(width=width, height=height), filename=filename, fmt=fmt)
-                self._logger.info("Saved plot to %s.", filename)
-            else:
-                name, ext = os.path.splitext(filename)
-                iter_range = self._plot_inputs['iter_range'] # None or (start, end)
-                plot_idx = 0 if iter_range is None else iter_range[0]
+        name, ext = os.path.splitext(filename)
+        fmt = ext[1:] if fmt=='auto' else fmt
 
-                for plot in self._plots:
-                    exportname = f"{name}_{plot_idx}{ext}"
-                    hvplot.save(plot.opts(width=width, height=height), filename=exportname, fmt=fmt)
-                    self._logger.info("Saved plot to %s.", exportname)
-                    plot_idx += 1
+        # Combine plots into layout using subplots (rows, columns) if not single plot.
+        # Set fixed size for export.
+        layout_plot = self._layout_plots(self._plot_inputs['subplots'], (width, height))
 
+        if not isinstance(layout_plot, hv.Layout) and self._plot_inputs['iter_axis']:
+            # Save iterated plots individually, with index appended to filename
+            plot_idx = 0 if self._plot_inputs['iter_range'] is None else self._plot_inputs['iter_range'][0]
+            for plot in self._plots:
+                exportname = f"{name}_{plot_idx}{ext}"
+                self._save_plot(plot, exportname, fmt)
+                plot_idx += 1
+        else:
+            self._save_plot(layout_plot, filename, fmt)
         self._logger.debug("Save elapsed time: %.2fs.", time.time() - start_time)
 
-    def _layout_plots(self, subplots):
+    def _layout_plots(self, subplots, fixed_size=None):
+        ''' Combine plots in a layout, using fixed size for the layout if given '''
         subplots = (1, 1) if subplots is None else subplots
-        num_plots = len(self._plots)
-        num_layout_plots = min(num_plots, np.prod(subplots))
+        num_plots = min(len(self._plots), np.prod(subplots))
+        plot_width = fixed_size[0] if fixed_size else None
+        plot_height = fixed_size[1] if fixed_size else None
 
-        if num_layout_plots == 1:
-            return self._plots[0], False
+        if num_plots == 1:
+            # Single plot, not layout
+            plot = self._plots[0]
+            if fixed_size:
+                plot = plot.opts(responsive=False, width=plot_width, height=plot_height, clone=True)
+            return plot
 
         # Set plots in layout
-        plot_count = 0
-        layout = None
-        for i in range(num_layout_plots):
+        layout_plot = None
+        for i in range(num_plots):
             plot = self._plots[i]
-            layout = plot if layout is None else layout + plot
-            plot_count += 1
-
-        is_layout = plot_count > 1
-        return layout, is_layout
+            if fixed_size:
+                plot = plot.opts(responsive=False, width=plot_width, height=plot_height, clone=True)
+            layout_plot = plot if layout_plot is None else layout_plot + plot
+
+        # Layout in columns
+        return layout_plot.cols(subplots[1])
+
+    def _save_plot(self, plot, filename, fmt):
+        ''' Save plot using hvplot, else bokeh '''
+        # Remove toolbar unless html
+        toolbar = 'right' if fmt=='html' else None
+        plot = plot.opts(toolbar=toolbar, clone=True)
+
+        try:
+            hvplot.save(plot, filename=filename, fmt=fmt)
+        except (Exception, RuntimeError) as exc:
+            # Fails if hvplot cannot find web driver or fmt is svg.
+            # Render a Bokeh Figure or GridPlot, create webdriver, then use Bokeh to export.
+            fig = hv.render(plot)
+            if fmt=='html':
+                save(fig, filename)
+            elif fmt in ['png', 'svg']:
+                # Use Chrome web driver
+                service = webdriver.ChromeService()
+                options = webdriver.ChromeOptions()
+                options.add_argument('--headless')
+                options.add_argument('--no-sandbox')
+
+                with webdriver.Chrome(service=service, options=options) as driver:
+                    if fmt=='png':
+                        export_png(fig, filename=filename, webdriver=driver)
+                    elif fmt=='svg':
+                        export_svg(fig, filename=filename, webdriver=driver)
+            else:
+                raise ValueError(f"Invalid fmt or filename extension {fmt} for save()") from exc
+        self._logger.info("Saved plot to %s.", filename)
 
     def _set_ms(self, ms_path):
         ''' Set MsData and update ms info for input ms filepath (MSv2 or zarr), if set.

{vidavis-0.0.4 → vidavis-0.0.6}/src/vidavis/plot/ms_plot/_ms_plot_selectors.py

@@ -4,7 +4,7 @@ Create panel widgets for various functions
 
 import panel as pn
 
-from vidavis.bokeh.state._palette import available_palettes
+from vidavis.bokeh._palette import available_palettes
 from vidavis.plot.ms_plot._ms_plot_constants import VIS_AXIS_OPTIONS, AGGREGATOR_OPTIONS, PS_SELECTION_OPTIONS, MS_SELECTION_OPTIONS, DEFAULT_UNFLAGGED_CMAP, DEFAULT_FLAGGED_CMAP
 
 def file_selector(description, start_dir, callback):

{vidavis-0.0.4 → vidavis-0.0.6}/src/vidavis/toolbox/__init__.py

@@ -30,5 +30,3 @@
 from ._app_context import AppContext
 
 from ._logging import get_logger
-
-from ._static import static_vars, static_dir

vidavis-0.0.4/src/vidavis/apps/__init__.py

@@ -1,29 +0,0 @@
-########################################################################
-#
-# 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
-#
-########################################################################
-'''End user applications supplied by ``vidavis``.'''
-
-from ._ms_raster import MsRaster

vidavis-0.0.4/src/vidavis/bokeh/__init__.py

@@ -1,29 +0,0 @@
-########################################################################
-#
-# Copyright (C) 2021, 2022
-# 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
-#
-########################################################################
-'''This module contains the extensions and additions to the functionality
-provided by Bokeh'''

vidavis-0.0.4/src/vidavis/bokeh/state/__init__.py

@@ -1,31 +0,0 @@
-########################################################################
-#
-# Copyright (C) 2025
-# 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
-#
-########################################################################
-'''Bokeh state management functions (both within the Bokeh distribution
-and with the Bokeh extensions found in ``vidavis.bokeh``.'''
-
-from ._palette import available_palettes, find_palette, default_palette

vidavis-0.0.4/src/vidavis/data/measurement_set/__init__.py

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

vidavis-0.0.4/src/vidavis/data/measurement_set/processing_set/__init__.py

@@ -1,35 +0,0 @@
-'''
-    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 ._ps_select import (
-    select_ps,
-    select_ms,
-)
-
-from ._xds_data import (
-    get_axis_data,
-    get_correlated_data,
-)

vidavis-0.0.4/src/vidavis/plot/ms_plot/__init__.py

@@ -1,29 +0,0 @@
-''' This module contains classes and utilities to support MS plotting '''
-
-from ._ms_plot import MsPlot
-
-from ._ms_plot_constants import (
-    SPECTRUM_AXIS_OPTIONS,
-    UVW_AXIS_OPTIONS,
-    VIS_AXIS_OPTIONS,
-    WEIGHT_AXIS_OPTIONS,
-    PS_SELECTION_OPTIONS,
-    MS_SELECTION_OPTIONS,
-    AGGREGATOR_OPTIONS,
-    DEFAULT_UNFLAGGED_CMAP,
-    DEFAULT_FLAGGED_CMAP,
-)
-
-from ._ms_plot_selectors import (
-    file_selector,
-    title_selector,
-    style_selector,
-    axis_selector,
-    aggregation_selector,
-    iteration_selector,
-    selection_selector,
-    plot_starter,
-)
-
-from ._raster_plot_inputs import check_inputs
-from ._raster_plot import RasterPlot