cubevis 0.5.11__py3-none-any.whl → 0.5.13__py3-none-any.whl

cubevis/__version__.py

@@ -1 +1 @@
-__version__ = '0.5.11'
+__version__ = '0.5.13'

cubevis/bokeh/sources/_image_pipe.py

@@ -208,15 +208,19 @@ class ImagePipe(DataPipe):
             ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
             amin = image_plane.min( )           ## array min
             amax = image_plane.max( )           ## array max
-            rg = [ amin if len(self.__quant_adjustments['bounds'][0]) == 0 else self.__quant_adjustments['bounds'][0][0],
-                   amax if len(self.__quant_adjustments['bounds'][1]) == 0 else self.__quant_adjustments['bounds'][1][0] ]
-            umin = min(rg)                      ## user specified min
-            umax = max(rg)                      ## user specified max
+
+            ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
+            ### Extract user bounds (use array bounds as fallback)
+            ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
+            umin = amin if len(self.__quant_adjustments['bounds'][0]) == 0 else self.__quant_adjustments['bounds'][0][0]
+            umax = amax if len(self.__quant_adjustments['bounds'][1]) == 0 else self.__quant_adjustments['bounds'][1][0]
+
+            ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
+            ### Handle cropping (when user bounds are narrower than data)
+            ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
             if umin > amin:
-                ## elements that are masked to the minumum color for the image
                 exclude_below = image_plane < umin
             if umax < amax:
-                ## elements that are masked to the maximum color for the image
                 exclude_above = image_plane > umax
 
             ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
@@ -240,13 +244,26 @@ class ImagePipe(DataPipe):
                 else:
                     normalize = 0 if umin > 0 else -umin
                     result = np.ma.zeros(image_plane.shape,image_plane.dtype)
-                    result[included] = self.__quant_scaling[selected_scaling]( image_plane[included]+normalize if included is not None else image_plane+normalize,
-                                                                               **self.__quant_adjustments['transfer']['args'] )
-                    if exclude_below is not None:
-                        result[exclude_below] = result[included].min( )
-                    if exclude_above is not None:
-                        result[exclude_above] = result[included].max( )
+
+                    if included is not None:
+
+                        result[included] = self.__quant_scaling[selected_scaling](
+                            image_plane[included] + normalize,
+                            **self.__quant_adjustments['transfer']['args']
+                        )
+
+                        # Set excluded regions to min/max of included values
+                        if exclude_below is not None:
+                            result[exclude_below] = result[included].min( )
+                        if exclude_above is not None:
+                            result[exclude_above] = result[included].max( )
+                    else:
+                        result = self.__quant_scaling[selected_scaling](
+                            image_plane + normalize,
+                            **self.__quant_adjustments['transfer']['args']
+                        )
             else:
+
                 result = image_plane
 
             ### --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---

cubevis/private/casatasks/__init__.py

@@ -1,6 +1,6 @@
 ########################################################################
 #
-# Copyright (C) 2024
+# Copyright (C) 2025
 # Associated Universities, Inc. Washington DC, USA.
 #
 # This script is free software; you can redistribute it and/or modify it
@@ -25,116 +25,6 @@
 #                        Charlottesville, VA 22903-2475 USA
 #
 ########################################################################
-'''casatasks provides on-the-fly creation of inp/go wrappers for tasks
-https://bayesianbrad.github.io/posts/2017_loader-finder-python.html
-'''
+'''casatask equivalent bindings'''
 
-from importlib.abc import Loader as _Loader, MetaPathFinder as _MetaPathFinder
-
-import subprocess
-import re
-import os
-import sys
-
-class CasaTasks_Loader(_Loader):
-
-    def __init__( self, java, jarpath, args, templ, xml ):
-        self.__java = java
-        self.__jarpath = jarpath
-        self.__args = args
-        self.__templ = templ
-        self.__xml = xml
-
-    def create_module(self, spec):
-        return None
-
-    def exec_module(self, module):
-        python_source = subprocess.run( [ self.__java, '-jar', self.__jarpath ] + self.__args + [self.__templ, self.__xml], stdout=subprocess.PIPE ).stdout.decode('utf-8')
-        exec( python_source, module.__dict__ )
-
-
-class CasaTasks_Finder(_MetaPathFinder):
-
-    def __init__( self ):
-        super(CasaTasks_Finder, self).__init__( )
-        self.__java = None
-        self.__source_dir = os.path.dirname(__file__)
-        self.__jarpath = None
-        self.__jarfile_name = "xml-casa-assembly-1.86.jar"
-        self.__task_xml_files = None
-
-    def __which( self, program ):
-        def is_exe(fpath):
-            return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
-
-        fpath, fname = os.path.split(program)
-        if fpath:
-            if is_exe(program):
-                return os.path.realpath(program)
-        else:
-            os.environ.get("PATH", "")
-            for path in os.environ.get("PATH", "").split(os.pathsep):
-                exe_file = os.path.join(path, program)
-                if is_exe(exe_file):
-                    return os.path.realpath(exe_file)
-        return None
-
-    def __find_parameters( self, taskname ):
-        templ = os.path.join( self.__source_dir, f'''{taskname}.mustache''' )
-        if os.path.isfile(templ):
-            ### <TASK>.mustache exists -------------------------------------------------------------------------------------------------------------
-            with open(templ) as f:
-                header = [ (m.group(1), m.group(2), m.group(0)) for m in [ re.match( "^\#+\s*TASK XML\s*>\s*(\S+)(.*)", next(f) ) for _ in range(5) ] if m ]
-                if len(header) == 1:
-                    ### <TASK>.mustache has processing specification line --------------------------------------------------------------------------
-                    task = os.path.splitext(header[0][0])[0]
-                    if task in self.__task_xml_files:
-                        ### <TASK>.mustache has processing specification line and includes valid CASA task name ------------------------------------
-                        return templ, self.__task_xml_files[task], header[0][1].split( )
-                    elif taskname in self.__task_xml_files:
-                        ### <TASK>.mustache has processing specification line and <TASK> is a valid CASA task --------------------------------------
-                        return templ, self.__task_xml_files[taskname], header[0][1].split( )
-                elif taskname in self.__task_xml_files:
-                    ### <TASK>.mustache does not have a processing specification line but <TASK> is a valid CASA task-------------------------------
-                    return templ, self.__task_xml_files[taskname], [ ]
-
-        if taskname in self.__task_xml_files:
-            ### <TASK>.mustache does not exist but <TASK> is a valid CASA task ---------------------------------------------------------------------
-            templ = os.path.join( self.__source_dir, f'''generic.mustache''' )
-            if os.path.isfile(templ):
-                ### <TASK> is a valid CASA task and generic.mustache exists ------------------------------------------------------------------------
-                with open(templ) as f:
-                    header = [ (m.group(1), m.group(2), m.group(0)) for m in [ re.match( "^\#+\s*TASK XML\s*>\s*(\S+)(.*)", next(f) ) for _ in range(5) ] if m ]
-                    if len(header) == 1:
-                        ### <TASK> is a valid CASA task, generic.mustache exists and has a processing specification line ---------------------------
-                        return templ, self.__task_xml_files[taskname], header[0][1].split( )
-                    else:
-                        ### <TASK> is a valid CASA task, generic.mustache exists but does not have a processing specification line -----------------
-                        return templ, self.__task_xml_files[taskname], [ ]
-
-        return None, None, [ ]
-
-    def find_spec(self, fullname, path, target = None):
-
-        if fullname.startswith('cubevis.private.casatasks.'):
-            if self.__java is None:
-                self.__java = self.__which( "java" )
-            if self.__jarpath is None:
-                p = os.path.join( os.path.dirname(os.path.dirname(__file__)), "__java__", self.__jarfile_name )
-                if os.path.isfile(p):
-                    self.__jarpath = p
-            if self.__task_xml_files is None:
-                try:
-                    from casatasks import xml_interface_defs
-                    self.__task_xml_files = { k:v for (k,v) in xml_interface_defs( ).items( ) if os.path.isfile(v) }
-                except: pass
-
-            module = fullname.split(sep='.')[-1]
-            templ, xml, args = self.__find_parameters( fullname.split(sep='.')[-1] )
-            if templ is not None and xml is not None:
-                from importlib.machinery import ModuleSpec
-                return ModuleSpec( fullname, CasaTasks_Loader( self.__java, self.__jarpath, args, templ, xml ) )
-
-        return None
-
-sys.meta_path.append(CasaTasks_Finder( ))
+from .iclean import iclean

{cubevis-0.5.11.dist-info → cubevis-0.5.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cubevis
-Version: 0.5.11
+Version: 0.5.13
 Summary: visualization toolkit and apps for casa
 License: LGPL
 Author-email: Darrell Schiebel <darrell@schiebel.us>,Pam Harris <pharris@nrao.edu>

{cubevis-0.5.11.dist-info → cubevis-0.5.13.dist-info}/RECORD

@@ -45,7 +45,7 @@ cubevis/bokeh/models/_tip_button.py,sha256=Dw4aO37o0J3n6EoaJ3ui1y8d04qNn3x2dbKiw
 cubevis/bokeh/sources/__init__.py,sha256=4FsudFuVU4o7VG5OG3K1tiMoxIXcJWNz_K9yzMDE8ls,1581
 cubevis/bokeh/sources/_data_pipe.py,sha256=PI4vZ_4eywHJfGEanyx-eMJvoeuMrPdMcF_ZbScYSi8,13779
 cubevis/bokeh/sources/_image_data_source.py,sha256=ezgTWHtHMpbT-jAd1F_xnq3jdcvIGbqNvN9MTbTOnNs,3537
-cubevis/bokeh/sources/_image_pipe.py,sha256=4v1-fuE-2LnL18hArkvurQeIy0TsaiX0H0_3iN-n4Xw,27770
+cubevis/bokeh/sources/_image_pipe.py,sha256=4pvoy517N199OMD_q40NkPChsGPSMaR58hw1Gb348NU,28475
 cubevis/bokeh/sources/_spectra_data_source.py,sha256=Tbq4JczbmWfW9OPTzY2OuCMPOrr9yGQ1xVB63QTHnOw,2200
 cubevis/bokeh/sources/_updatable_data_source.py,sha256=KlEUTFI26tC7FLu5KF0U36CjjyBmNhSro0-PrLSi7i8,10709
 cubevis/bokeh/state/__init__.py,sha256=pUzr7PWrFKhGa8G1ogrGqBywrT8nUJ5kh3vKr0z4Zao,1628
@@ -88,7 +88,6 @@ cubevis/plot/ms_plot/_ms_plot_selectors.py,sha256=bus0R6R8BNS6Y2dMxVngf6v54AIZTd
 cubevis/plot/ms_plot/_raster_plot.py,sha256=OtEDX5cjNZ65Wn1vB8vTxEr1JZejyXgE9nW_liUNAwc,12958
 cubevis/plot/ms_plot/_raster_plot_inputs.py,sha256=yUFob7t4JMXTwHjzNWZMEMLCvQdJ55SyWj3mZBxHgos,5173
 cubevis/plot/ms_plot/_xds_plot_axes.py,sha256=EeWvAbiKV33nEWdI8V3M0uwLTnycq4bFYBOyVWkxCu0,4429
-cubevis/private/__java__/xml-casa-assembly-1.86.jar,sha256=dBT_OxPtczAfWKRaOrHWwNZbDfEjtKkuQGuFOaKOczA,8041045
 cubevis/private/_gclean.py,sha256=ExdR6cRxSa6Xne2veGNKhbTtx-tXUIWr2htzEmEZ9Z4,41107
 cubevis/private/apps/__init__.py,sha256=-9U6o-SClwJolGDnFhlH1au4tz-w4HgRcyT4_OQ_Z7E,2510
 cubevis/private/apps/_createmask.py,sha256=bKFpME5MYhLh7HxlJZINBTwG25t0_T_d1nYrWYAWYPA,23527
@@ -101,7 +100,7 @@ cubevis/private/apps/_plotants.py,sha256=top6VWVd_sE48IVPH_sIg3_sQeDl5tadi5DL7r5
 cubevis/private/apps/_plotbandpass.py,sha256=NwOgKSRnpLw9Pt3KIdBpoV78q1OnjCvj6lWFqeyICt8,185
 cubevis/private/casashell/createmask.py,sha256=C1eSUUsttSGghjZ5aDUVhRxnjir5MlYXVyxzEYLcI3k,14457
 cubevis/private/casashell/iclean.py,sha256=FUrCMrfXuTjUHFBA0PVEctDXlHsZrMZBePwZ_otDwxI,294787
-cubevis/private/casatasks/__init__.py,sha256=yLL13GDxSxIkqjjap_sJO_aGVaBUW9gXMwlAlPli97g,6963
+cubevis/private/casatasks/__init__.py,sha256=Uzt9uNiTl0ORavzuoIDJ8gfYUhdWwAAj1D2VJ3wAvvQ,1333
 cubevis/private/casatasks/createmask.py,sha256=qtp8IvFCB1BG2pqRbyP8CmTr-RRqLMBSjMIO86mZ7WA,3770
 cubevis/private/casatasks/createregion.py,sha256=f2KIrkbbdczZk3EHd3x9ZTUaewdjSxlRge-Es8BivNk,3355
 cubevis/private/casatasks/iclean.py,sha256=YO9RRtWVD3MxizqxTB-7yPD8NkX-mvbsB2yTyRcrvT0,152997
@@ -126,8 +125,8 @@ cubevis/utils/_pkgs.py,sha256=mu2CCzndmJZYP81UkFhxveW_CisWLUvagJVolHOEVgM,2294
 cubevis/utils/_regions.py,sha256=TdAg4ZUUyhg3nFmX9_KLboqmc0LkyOdEW8M1WDR5Udk,1669
 cubevis/utils/_static.py,sha256=rN-sqXNqQ5R2M3wmPHU1GPP5OTyyWQlUPRuimCrht-g,2347
 cubevis/utils/_tiles.py,sha256=A9W1X61VOhBMTOKXVajzOIoiV2FBdO5N2SFB9SUpDOo,7336
-cubevis/__version__.py,sha256=IB1CJxlYThFf3KnjTGeCxoPXiCTJ_Y8r_YEqVfavyqQ,22
-cubevis-0.5.11.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-cubevis-0.5.11.dist-info/METADATA,sha256=aJ3zH7H6h5nmNT9NndGFo8vlt0nbxq9mbW0oa_Ikkck,2629
-cubevis-0.5.11.dist-info/licenses/LICENSE,sha256=IMF9i4xIpgCADf0U-V1cuf9HBmqWQd3qtI3FSuyW4zE,26526
-cubevis-0.5.11.dist-info/RECORD,,
+cubevis/__version__.py,sha256=OYo7Ah0wICBCFc4dNdr54AMBYTK_lp1kbfjO8-QZR9E,22
+cubevis-0.5.13.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+cubevis-0.5.13.dist-info/METADATA,sha256=M40RMt0Lxgq23-vGyqIEYLW_sdbUhzTPkf_N8pHxUpI,2629
+cubevis-0.5.13.dist-info/licenses/LICENSE,sha256=IMF9i4xIpgCADf0U-V1cuf9HBmqWQd3qtI3FSuyW4zE,26526
+cubevis-0.5.13.dist-info/RECORD,,