cubevis 1.0.0__py3-none-any.whl → 1.0.4__py3-none-any.whl

cubevis/private/casatasks/iclean.py

@@ -1828,4 +1828,8 @@ class _iclean:
             task_result = _end_log( _logging_state_, 'iclean', task_result )
         return task_result
 
+    def notebook( self, *args, **kwargs ):
+        from .iclean_notebook import iclean_notebook
+        return iclean_notebook( *args, **kwargs )
+
 iclean = _iclean( )

cubevis/toolbox/_app_context.py

@@ -1,6 +1,6 @@
 ########################################################################
 #
-# Copyright (C) 2024
+# Copyright (C) 2024,2025
 # Associated Universities, Inc. Washington DC, USA.
 #
 # This script is free software; you can redistribute it and/or modify it
@@ -25,13 +25,14 @@
 #                        Charlottesville, VA 22903-2475 USA
 #
 ########################################################################
-from cubevis.bokeh.state import initialize_bokeh
 from tempfile import TemporaryDirectory
 from bokeh.io import output_file
 from os.path import join
 import unicodedata
 import re
 
+from ..utils import is_interactive_jupyter
+
 class AppContext:
 
     def _slugify(self, value, allow_unicode=False):
@@ -53,18 +54,13 @@ class AppContext:
 
     def __init__( self, title, prefix=None, init_bokeh=True ):
 
-        ###
-        ### Setup up Bokeh paths, inject cubevis libraries into Bokeh HTML output
-        ###
-        if init_bokeh:
-            initialize_bokeh( )
-
         if prefix is None:
             ## create a prefix from the title
             prefix = self._slugify(title)[:10]
         self.__workdir = TemporaryDirectory(prefix=prefix)
         self.__htmlpath = join( self.__workdir.name, f'''{self._slugify(title)}.html''' )
-        output_file( self.__htmlpath, title=title )
+        if not is_interactive_jupyter( ):
+            output_file( self.__htmlpath, title=title )
 
     def __del__( self ):
         ### remove work directory and its contents

cubevis/toolbox/_cube.py

@@ -100,7 +100,7 @@ class CubeMask:
         self.COUNT = 1
         self.CCOUNT = 1
 
-        self._is_notebook = is_interactive_jupyter()
+        ##self._is_notebook = is_interactive_jupyter()
         #self._color = '#00FF00'                               # anti-green user feedback (issue #40 2024-05-02 13:08:32)
         self._region_style=dict( fill_alpha=0, hover_fill_alpha=0.3,
                                  fill_color='white', hover_fill_color='white',
@@ -1505,7 +1505,11 @@ class CubeMask:
                                                                           function done_close_window( msg ) {
                                                                               if ( msg.result === 'stopped' ) {""" +
                                                                             # Don't close tab if running in a jupyter notebook
-                                                                            ("""console.log("Running in jupyter notebook. Not closing window.")""" if self._is_notebook else
+                                                                            ##("""console.log("Running in jupyter notebook. Not closing window.")""" if self._is_notebook else
+                                                                            ##     """console.log("Running from script/terminal. Closing window.")
+                                                                            ##        window.close()"""
+                                                                            ##) +
+                                                                            ("""console.log("Running in jupyter notebook. Not closing window.")""" if is_interactive_jupyter( ) else
                                                                                  """console.log("Running from script/terminal. Closing window.")
                                                                                     window.close()"""
                                                                             ) +

cubevis/toolbox/_interactive_clean_ui.mustache

@@ -29,15 +29,6 @@
 '''implementation of the ``InteractiveCleanUI`` application for interactive control
 of tclean'''
 
-###
-### Useful for debugging
-###
-###from cubevis.bokeh.state import initialize_bokeh
-###initialize_bokeh( bokehjs_subst=".../bokeh-3.2.2.js" )
-###
-
-from pprint import pprint
-
 import os
 import sys
 import copy
@@ -137,8 +128,8 @@ class InteractiveCleanUI:
             ports.append( imdetails['gui']['cube']._pipe['control'].address[1] )
 
         # Also forward http port if serving webpage
-        if not self._is_notebook:
-            ports.append(self._http_port)
+        #if not self._is_notebook:
+        #    ports.append(self._http_port)
 
         cmd = 'ssh'
         for port in ports:
@@ -187,7 +178,7 @@ class InteractiveCleanUI:
         ###
         ### whether or not the session is being run from a jupyter notebook or script
         ###
-        self._is_notebook = is_interactive_jupyter()
+        #self._is_notebook = is_interactive_jupyter()
 
         ##
         ## the http port for serving GUI in webpage if not running in script
@@ -520,7 +511,7 @@ class InteractiveCleanUI:
             'flux_axis': flux_axis
         }
 
-    def _launch_gui( self ):
+    def _build_bokeh( self ):
         '''create and show GUI
         '''
         ###
@@ -625,7 +616,7 @@ class InteractiveCleanUI:
         icw = SharedWidgets( )
         toolbars = [ ]
         for imid, imdetails in self._clean_targets.items( ):
-            imdetails['gui']['stats'] = imdetails['gui']['cube'].statistics( )
+            imdetails['gui']['stats'] = imdetails['gui']['cube'].statistics( name=f"{imid} stats" )
             imdetails['image-channels'] = imdetails['gui']['cube'].shape( )[3]
 
             status_line = imdetails['gui']['stopcode'] = imdetails['gui']['cube'].status_text( "<p>initial residual image</p>" if imdetails['image-channels'] > 1 else "<p>initial <b>single-channel</b> residual image</p>", width=230, reuse=status_line )
@@ -969,15 +960,15 @@ class InteractiveCleanUI:
                                                              itergroups[document._casa_image_name].active = document._casa_last_control_tab''' ) )
 
         # Change display type depending on runtime environment
-        if self._is_notebook:
-            output_notebook()
-        else:
-            ### Directory is created when an HTTP server is running
-            ### (MAX)
-###         output_file(self._imagename+'_webpage/index.html')
-            pass
+        #if self._is_notebook:
+        #    output_notebook()
+        #else:
+        #    ### Directory is created when an HTTP server is running
+        #    ### (MAX)
+###     #    output_file(self._imagename+'_webpage/index.html')
+        #    pass
 
-        show(self._fig['layout'])
+        return self._fig['layout']
 
     def _create_colormap_adjust( self, imdetails ):
         palette = imdetails['gui']['cube'].palette( reuse=self._cube_palette )
@@ -1015,7 +1006,7 @@ class InteractiveCleanUI:
                                       title='Colormap' ),
                             TabPanel( child=column( *imdetails['gui']['stats'] ),
                                       title='Statistics' ) ] + imdetails['gui']['auto-masking-panel'],
-                     width=500, sizing_mode='stretch_height', tabs_location='below' )
+                     sizing_mode='stretch_height', tabs_location='below' )
 
         if not hasattr(self,'_image_control_tab_groups'):
             self._image_control_tab_groups = { }
@@ -1046,7 +1037,7 @@ class InteractiveCleanUI:
                                             height_policy='max', width_policy='max' ),
                                        height_policy='max', width_policy='max' ), title=imid )
 
-    def __call__( self, setting, exec_context, id=None ):
+    def __call__( self, exec_context, task_id=None ):
         '''Display GUI and process events until the user stops the application.
 
         Example:
@@ -1075,13 +1066,12 @@ class InteractiveCleanUI:
 
         ###
         ### cubevis.exe subpkg supports adding a stop condition to allow for interrupt,
-        ### but it is not needed for synchronous execution
+        ### but it is not needed for synchronous execution, e.g.
+        ### self._exec['stop-condition'], self._exec['id'] = exec_context.create_stop_condition(task_id)
         ###
         self._exec = { 'stop-condition': None }
-        #self._exec['stop-condition'], self._exec['id'] = exec_context.create_stop_condition(id)
 
-        return exe.Task( self._task_server )
-                         # , stop_condition=self._exec['stop-condition'] )
+        return self._build_bokeh( ), exe.Task( self._task_server )
 
     async def _task_server( self ):
         """Wrapper for your serve() context manager"""
@@ -1131,8 +1121,6 @@ class InteractiveCleanUI:
 
                     httpd.serve_forever()
 
-            self._launch_gui( )
-
             async with CMC( *( [ ctx for img in self._clean_targets.keys( ) for ctx in
                                  [
                                      self._clean_targets[img]['gui']['cube'].serve(self.__stop),
@@ -1296,6 +1284,7 @@ class InteractiveCleanUI:
                      ### -- document is used storing state                                                        --
                      ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
                      'initialize':      '''if ( ! document._casa_initialized ) {
+                                               console.log(`casalib version: ${casalib.version}`)
                                                document._casa_image_name = initial_image
                                                document._casa_initialized = true
                                                document._casa_window_closed = false
@@ -1303,7 +1292,7 @@ class InteractiveCleanUI:
                                                                         function (e) {
                                                                             // if the window is already closed this message is never
                                                                             // delivered (unless interactive clean is called again then
-                                                                            // the event shows up in the newly created control pipe
+                                                                            // the event shows up in the newly created control pipe)
                                                                             if ( document._casa_window_closed == false ) {
                                                                                 ctrl_pipe.send( ids['stop'],
                                                                                                 { action: 'stop', value: { } },

cubevis/toolbox/_interactive_clean_ui.py

@@ -28,15 +28,6 @@
 '''implementation of the ``InteractiveCleanUI`` application for interactive control
 of tclean'''
 
-###
-### Useful for debugging
-###
-###from cubevis.bokeh.state import initialize_bokeh
-###initialize_bokeh( bokehjs_subst=".../bokeh-3.2.2.js" )
-###
-
-from pprint import pprint
-
 import os
 import sys
 import copy
@@ -136,8 +127,8 @@ class InteractiveCleanUI:
             ports.append( imdetails['gui']['cube']._pipe['control'].address[1] )
 
         # Also forward http port if serving webpage
-        if not self._is_notebook:
-            ports.append(self._http_port)
+        #if not self._is_notebook:
+        #    ports.append(self._http_port)
 
         cmd = 'ssh'
         for port in ports:
@@ -186,7 +177,7 @@ class InteractiveCleanUI:
         ###
         ### whether or not the session is being run from a jupyter notebook or script
         ###
-        self._is_notebook = is_interactive_jupyter()
+        #self._is_notebook = is_interactive_jupyter()
 
         ##
         ## the http port for serving GUI in webpage if not running in script
@@ -519,7 +510,7 @@ class InteractiveCleanUI:
             'flux_axis': flux_axis
         }
 
-    def _launch_gui( self ):
+    def _build_bokeh( self ):
         '''create and show GUI
         '''
         ###
@@ -624,7 +615,7 @@ class InteractiveCleanUI:
         icw = SharedWidgets( )
         toolbars = [ ]
         for imid, imdetails in self._clean_targets.items( ):
-            imdetails['gui']['stats'] = imdetails['gui']['cube'].statistics( )
+            imdetails['gui']['stats'] = imdetails['gui']['cube'].statistics( name=f"{imid} stats" )
             imdetails['image-channels'] = imdetails['gui']['cube'].shape( )[3]
 
             status_line = imdetails['gui']['stopcode'] = imdetails['gui']['cube'].status_text( "<p>initial residual image</p>" if imdetails['image-channels'] > 1 else "<p>initial <b>single-channel</b> residual image</p>", width=230, reuse=status_line )
@@ -968,15 +959,15 @@ class InteractiveCleanUI:
                                                              itergroups[document._casa_image_name].active = document._casa_last_control_tab''' ) )
 
         # Change display type depending on runtime environment
-        if self._is_notebook:
-            output_notebook()
-        else:
-            ### Directory is created when an HTTP server is running
-            ### (MAX)
-###         output_file(self._imagename+'_webpage/index.html')
-            pass
+        #if self._is_notebook:
+        #    output_notebook()
+        #else:
+        #    ### Directory is created when an HTTP server is running
+        #    ### (MAX)
+###     #    output_file(self._imagename+'_webpage/index.html')
+        #    pass
 
-        show(self._fig['layout'])
+        return self._fig['layout']
 
     def _create_colormap_adjust( self, imdetails ):
         palette = imdetails['gui']['cube'].palette( reuse=self._cube_palette )
@@ -1014,7 +1005,7 @@ class InteractiveCleanUI:
                                       title='Colormap' ),
                             TabPanel( child=column( *imdetails['gui']['stats'] ),
                                       title='Statistics' ) ] + imdetails['gui']['auto-masking-panel'],
-                     width=500, sizing_mode='stretch_height', tabs_location='below' )
+                     sizing_mode='stretch_height', tabs_location='below' )
 
         if not hasattr(self,'_image_control_tab_groups'):
             self._image_control_tab_groups = { }
@@ -1045,7 +1036,7 @@ class InteractiveCleanUI:
                                             height_policy='max', width_policy='max' ),
                                        height_policy='max', width_policy='max' ), title=imid )
 
-    def __call__( self, setting, exec_context, id=None ):
+    def __call__( self, exec_context, task_id=None ):
         '''Display GUI and process events until the user stops the application.
 
         Example:
@@ -1074,13 +1065,12 @@ class InteractiveCleanUI:
 
         ###
         ### cubevis.exe subpkg supports adding a stop condition to allow for interrupt,
-        ### but it is not needed for synchronous execution
+        ### but it is not needed for synchronous execution, e.g.
+        ### self._exec['stop-condition'], self._exec['id'] = exec_context.create_stop_condition(task_id)
         ###
         self._exec = { 'stop-condition': None }
-        #self._exec['stop-condition'], self._exec['id'] = exec_context.create_stop_condition(id)
 
-        return exe.Task( self._task_server )
-                         # , stop_condition=self._exec['stop-condition'] )
+        return self._build_bokeh( ), exe.Task( self._task_server )
 
     async def _task_server( self ):
         """Wrapper for your serve() context manager"""
@@ -1130,8 +1120,6 @@ class InteractiveCleanUI:
 
                     httpd.serve_forever()
 
-            self._launch_gui( )
-
             async with CMC( *( [ ctx for img in self._clean_targets.keys( ) for ctx in
                                  [
                                      self._clean_targets[img]['gui']['cube'].serve(self.__stop),
@@ -1295,6 +1283,7 @@ class InteractiveCleanUI:
                      ### -- document is used storing state                                                        --
                      ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
                      'initialize':      '''if ( ! document._casa_initialized ) {
+                                               console.log(`casalib version: ${casalib.version}`)
                                                document._casa_image_name = initial_image
                                                document._casa_initialized = true
                                                document._casa_window_closed = false
@@ -1302,7 +1291,7 @@ class InteractiveCleanUI:
                                                                         function (e) {
                                                                             // if the window is already closed this message is never
                                                                             // delivered (unless interactive clean is called again then
-                                                                            // the event shows up in the newly created control pipe
+                                                                            // the event shows up in the newly created control pipe)
                                                                             if ( document._casa_window_closed == false ) {
                                                                                 ctrl_pipe.send( ids['stop'],
                                                                                                 { action: 'stop', value: { } },

cubevis/utils/__init__.py

@@ -45,6 +45,7 @@ from ._copydoc import copydoc
 from ._pkgs import find_pkg, load_pkg
 from ._jupyter import is_interactive_jupyter
 from ._browser import have_firefox
+from ._git import max_git_version
 
 from astropy import units
 from regions import PixCoord
@@ -103,29 +104,69 @@ def path_to_url(path):
         else:
             return path
 
-
-def find_ws_address(address='127.0.0.1'):
-    '''Find free port on ``address`` network and return a tuple with ``address`` and port number
-
-    This function uses the low level socket function to find a free port and return
-    a tuple representing the address plus port number.
-
-    Parameters
-    ----------
-    address: str
-        network to be probed for an available port
-
-    Returns
-    -------
-    tuple of str and int
-        network address (`str`) and port number (`int`)
-    '''
-    sock = socket()
-    sock.bind((address, 0))
-    result = sock.getsockname()
-    sock.close()
-    return result
-
+_DEBUG_NOTEBOOK_REUSE_ = False
+if _DEBUG_NOTEBOOK_REUSE_:
+    def find_ws_address(address='127.0.0.1'):
+        '''Find free port on ``address`` network and return a tuple with ``address`` and port number
+
+        This function uses the low level socket function to find a free port and return
+        a tuple representing the address plus port number.
+
+        Parameters
+        ----------
+        address: str
+            network to be probed for an available port
+
+        Returns
+        -------
+        tuple of str and int
+            network address (`str`) and port number (`int`)
+        '''
+        sock = socket()
+        sock.bind((address, 0))
+        result = sock.getsockname()
+        sock.close()
+        return result
+else:
+
+    _returned_ports = set()
+
+    def find_ws_address(address='127.0.0.1'):
+        '''Find free port on ``address`` network and return a tuple with ``address`` and port number
+
+        This function finds a free port that hasn't been returned before in this session.
+        It keeps sockets open during the search to guarantee uniqueness, then closes them
+        before returning.
+
+        Parameters
+        ----------
+        address: str
+            network to be probed for an available port
+
+        Returns
+        -------
+        tuple of str and int
+            network address (`str`) and port number (`int`)
+        '''
+        opened_sockets = []
+        try:
+            max_attempts = 2500
+            for _ in range(max_attempts):
+                sock = socket()
+                sock.bind((address, 0))
+                opened_sockets.append(sock)
+                result = sock.getsockname()
+                port = result[1]
+
+                if port not in _returned_ports:
+                    _returned_ports.add(port)
+                    return result
+
+            raise RuntimeError(f"Could not find unused port after {max_attempts} attempts")
+        finally:
+            # Always close all opened sockets
+            for sock in opened_sockets:
+                sock.close()
 
 def partition(pred, iterable):
     '''Split ``iterable`` into two lists based on ``pred`` predicate.
@@ -167,28 +208,129 @@ def warn_import(package):
         error_msg("warning, %s" % warn_import.msgs[package].format(package=package))
 
 
-@static_vars(url='http://clients3.google.com/generate_204')
+@static_vars(url='http://clients3.google.com/generate_204',
+             cached_result=None,
+             cache_timeout=30)  # Cache result for 30 seconds
 def have_network():
-    '''check to see if an active network with general internet connectivity
-    is available. returns ``True`` if we have internet connectivity and
+    '''Check to see if an active network with general internet connectivity
+    is available. Returns ``True`` if we have internet connectivity and
     ``False`` if we do not.
+
+    Uses Google's connectivity check endpoint and caches the result briefly
+    to avoid repeated network calls.
     '''
-    ###
-    ### see: https://stackoverflow.com/questions/50558000/test-internet-connection-for-python3
-    ###
-    try:
-        with urllib.request.urlopen(have_network.url) as response:
-            return response.status == 204
-    except urllib.error.HTTPError:
-        ### http error
-        return False
-    except urllib.error.ContentTooShortError:
-        return False
-    except urllib.error.URLError:
-        return False
-    except Exception:
-        return False
+    import time
+
+    # Check cache first
+    current_time = time.time()
+    if (hasattr(have_network, 'last_check_time') and
+        have_network.cached_result is not None and
+        current_time - have_network.last_check_time < have_network.cache_timeout):
+        return have_network.cached_result
+
+    def check_connectivity():
+        try:
+            # Set a reasonable timeout to avoid hanging
+            request = urllib.request.Request(
+                have_network.url,
+                headers={'User-Agent': 'Mozilla/5.0 (compatible; connectivity-check)'}
+            )
+
+            with urllib.request.urlopen(request, timeout=5) as response:
+                return response.status == 204
+
+        except urllib.error.HTTPError as e:
+            # Some proxies might return different status codes but still have connectivity
+            if e.code in [200, 301, 302]:
+                return True
+            return False
+        except (urllib.error.ContentTooShortError,
+                urllib.error.URLError,
+                socket.timeout,
+                socket.gaierror,  # DNS resolution errors
+                OSError) as e:
+            return False
+        except Exception:
+            # Catch any other unexpected errors
+            return False
+
+    # Perform the check
+    result = check_connectivity()
+
+    # Cache the result
+    have_network.cached_result = result
+    have_network.last_check_time = current_time
 
+    return result
+
+# Alternative version with fallback URLs
+@static_vars(urls=['http://clients3.google.com/generate_204',
+                   'http://detectportal.firefox.com/success.txt',
+                   'http://www.msftconnecttest.com/connecttest.txt'],
+             cached_result=None,
+             cache_timeout=30)
+def have_network_with_fallback():
+    '''Check network connectivity using multiple fallback endpoints.
+
+    Tries multiple well-known connectivity check endpoints to increase
+    reliability in different network environments.
+    '''
+    import time
+
+    # Check cache first
+    current_time = time.time()
+    if (hasattr(have_network_with_fallback, 'last_check_time') and
+        have_network_with_fallback.cached_result is not None and
+        current_time - have_network_with_fallback.last_check_time < have_network_with_fallback.cache_timeout):
+        return have_network_with_fallback.cached_result
+
+    def try_url(url, expected_status=None, expected_content=None):
+        try:
+            request = urllib.request.Request(
+                url,
+                headers={'User-Agent': 'Mozilla/5.0 (compatible; connectivity-check)'}
+            )
+
+            with urllib.request.urlopen(request, timeout=5) as response:
+                if expected_status and response.status != expected_status:
+                    return False
+
+                if expected_content:
+                    content = response.read().decode('utf-8').strip()
+                    return content == expected_content
+
+                # For Google's endpoint, expect 204 No Content
+                if 'generate_204' in url:
+                    return response.status == 204
+
+                # For other endpoints, any successful response is good
+                return 200 <= response.status < 400
+
+        except Exception:
+            return False
+
+    # Try each URL until one succeeds
+    for url in have_network_with_fallback.urls:
+        if url == 'http://detectportal.firefox.com/success.txt':
+            if try_url(url, expected_content='success'):
+                result = True
+                break
+        elif url == 'http://www.msftconnecttest.com/connecttest.txt':
+            if try_url(url, expected_content='Microsoft Connect Test'):
+                result = True
+                break
+        else:  # Google's endpoint
+            if try_url(url):
+                result = True
+                break
+    else:
+        result = False
+
+    # Cache the result
+    have_network_with_fallback.cached_result = result
+    have_network_with_fallback.last_check_time = current_time
+
+    return result
 
 def ranges(iterable, order=sorted, key=lambda x: x):
     '''collect elements of ``iterable`` into tuple ranges where each tuple represents

cubevis/utils/_git.py

@@ -0,0 +1,36 @@
+import subprocess
+from os import path
+from typing import Optional
+from packaging import version
+
+_VERSION = None
+def max_git_version() -> Optional[str]:
+    """Get maximum version from all git tags"""
+    global _VERSION
+    package_parent = path.dirname(path.dirname(path.dirname(path.realpath(__file__))))
+    if _VERSION is None and path.basename( package_parent ) == 'cubevis' and \
+       path.isdir(path.join( package_parent, '.git' )):
+        result = subprocess.run(
+            ['git', 'tag'],
+            cwd=package_parent,
+            capture_output=True,
+            text=True,
+            check=True
+        )
+    
+        # Filter tags matching version pattern v#.#.#
+        tags = [
+            tag[1:] for tag in result.stdout.strip().split('\n')
+                if tag.startswith('v') and all(part.isdigit() for part in tag[1:].split('.'))
+        ]
+
+        if not tags:
+            return None
+    
+        # Sort by version number and get maximum
+        try:
+            max_tag = max(tags, key=lambda v: version.parse(v))
+            _VERSION = max_tag
+        except: pass
+
+    return _VERSION