Index: /issm/trunk-jpl/src/m/plot/plot_unit.py =================================================================== --- /issm/trunk-jpl/src/m/plot/plot_unit.py (revision 21426) +++ /issm/trunk-jpl/src/m/plot/plot_unit.py (revision 21427) @@ -42,4 +42,13 @@ options.addfield('colormap',cmap) # }}} + # {{{ if plotting only one of several layers reduce dataset + if options.getfieldvalue('layer',0)>=1: + plotlayer=options.getfieldvalue('layer',1) + if datatype==1: + slicesize=np.shape(elements)[0] + elif datatype in [2,3]: + slicesize=len(x) + data=data[(plotlayer-1)*slicesize:plotlayer*slicesize] + # }}} # {{{ Get the colormap limits if options.exist('clim'): @@ -86,5 +95,5 @@ else: triangles=mpl.tri.Triangulation(x,y,elements) - ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha) + tri=ax.tricontourf(triangles,data,colorlevels,cmap=cmap,norm=norm,alpha=alpha) if edgecolor != 'None': ax.triplot(x,y,elements,color=edgecolor) @@ -93,5 +102,5 @@ return # }}} - # {{{ plotting quiver (TODO) + # {{{ plotting quiver elif datatype==3: if is2d: @@ -103,12 +112,16 @@ # }}} # {{{ plotting P1 Patch (TODO) + elif datatype==4: print 'plot_unit message: P1 patch plot not implemented yet' return + # }}} # {{{ plotting P0 Patch (TODO) + elif datatype==5: print 'plot_unit message: P0 patch plot not implemented yet' return + # }}} else: Index: /issm/trunk-jpl/src/m/plot/plotdoc.py =================================================================== --- /issm/trunk-jpl/src/m/plot/plotdoc.py (revision 21426) +++ /issm/trunk-jpl/src/m/plot/plotdoc.py (revision 21427) @@ -10,40 +10,40 @@ 'elementnumbering':' numbering of elements (matlab indices)'} TODOdata={'basal_drag':' plot the basal drag on the bed (in kPa) based on the velocity in md.initialization', - 'basal_dragx or basal_dragy' :' plot a component of the basal drag on the bed (in kPa)', - 'boundaries':' this will draw all the segment boundaries to the model, including rifts.', - 'icefront':' this will show segments that are used to define the icefront of the model (Neumann boundary conditions).', - 'deviatoricstress_tensor':' plot the components of the deviatoric stress tensor (tauxx,tauyy,tauzz,tauxy,tauxz,tauyz, if computed', - 'deviatoricstress_principal':' plot the deviatoricstress tensor principal axis and principal values', - 'deviatoricstress_principalaxis1':' arrow plot the first principal axis of the deviatoricstress tensor(replace 1 by 2 or 3 if needed)', - 'driving_stress':' plot the driving stress (in kPa)', - 'elements_type':' model used for each element', - 'vertexnumbering':' numbering of vertices', - 'highlightelements':' to highlight elements to highlight the element list', - 'highlightvertices':' to highlight vertices (use highlight option to enter the vertex list', - 'referential':' stressbalance referential', - 'riftvel':' velocities along rifts', - 'riftrelvel':' relative velocities along rifts', - 'riftpenetration':' penetration levels for a fault', - 'riftfraction':' fill fractions for every node of the rifts', - 'rifts':' plot mesh with an offset so that rifts are visible', - 'strainrate_tensor':' plot the components of the strainrate tensor (exx,eyy,ezz,exy,exz,eyz) if computed', - 'strainrate_principal':' plot the strainrate tensor principal axis and principal values)', - 'strainrate_principalaxis1':' arrow plot the first principal axis of the strainrate tensor(replace 1 by 2 or 3 if needed)', - 'stress_tensor':' plot the components of stress tensor (sxx,syy,szz,sxy,sxz,syz) if computed', - 'stress_principal':' plot the stress tensor principal axis and principal values', - 'stress_principalaxis1':' arrow plot the first principal axis of the stress tensor(replace 1 by 2 or 3 if needed)', - 'transient_results':' this will printlay all the time steps of a transient run (use steps to specify the steps requested)', - 'transient_vel':' this will printlay the velocity for the time steps requested in ''steps'' of a transient run', - 'transient_vel':' vel can be by any field of the transient results (vx, vy, vz, vel, temperature, melting, pressure, bed, thickness, surface)', - 'transient_field':' dynamic plot of results. specify ''steps'' option, as fell as ''field'' (defaults are all steps, for ''Vel'' field)', - 'transient_movie':' this will printlay the time steps of a given field of a transient run', - 'transient_movie_field':' field to be printlayed when doing transient_movie data printlay', - 'transient_movie_output':' filename if output is desired for movie', - 'transient_movie_time':' time for each image (default 2 seconds)', - 'thermaltransient_results':' this will printlay all the time steps of a thermal transient run', - 'qmuhistnorm':' histogram normal distribution. needs option qmudata', - 'qmumean':' plot of mean distribution in sampling analysis with scaled response. needs option qmudata for descriptor', - 'qmustddev':' plot of stddev distribution in sampling analysis with scaled response. needs option qmudata for descriptor', - 'part_hist':' partitioning node and area histogram'} + 'basal_dragx or basal_dragy' :' plot a component of the basal drag on the bed (in kPa)', + 'boundaries':' this will draw all the segment boundaries to the model, including rifts.', + 'icefront':' this will show segments that are used to define the icefront of the model (Neumann boundary conditions).', + 'deviatoricstress_tensor':' plot the components of the deviatoric stress tensor (tauxx,tauyy,tauzz,tauxy,tauxz,tauyz, if computed', + 'deviatoricstress_principal':' plot the deviatoricstress tensor principal axis and principal values', + 'deviatoricstress_principalaxis1':' arrow plot the first principal axis of the deviatoricstress tensor(replace 1 by 2 or 3 if needed)', + 'driving_stress':' plot the driving stress (in kPa)', + 'elements_type':' model used for each element', + 'vertexnumbering':' numbering of vertices', + 'highlightelements':' to highlight elements to highlight the element list', + 'highlightvertices':' to highlight vertices (use highlight option to enter the vertex list', + 'referential':' stressbalance referential', + 'riftvel':' velocities along rifts', + 'riftrelvel':' relative velocities along rifts', + 'riftpenetration':' penetration levels for a fault', + 'riftfraction':' fill fractions for every node of the rifts', + 'rifts':' plot mesh with an offset so that rifts are visible', + 'strainrate_tensor':' plot the components of the strainrate tensor (exx,eyy,ezz,exy,exz,eyz) if computed', + 'strainrate_principal':' plot the strainrate tensor principal axis and principal values)', + 'strainrate_principalaxis1':' arrow plot the first principal axis of the strainrate tensor(replace 1 by 2 or 3 if needed)', + 'stress_tensor':' plot the components of stress tensor (sxx,syy,szz,sxy,sxz,syz) if computed', + 'stress_principal':' plot the stress tensor principal axis and principal values', + 'stress_principalaxis1':' arrow plot the first principal axis of the stress tensor(replace 1 by 2 or 3 if needed)', + 'transient_results':' this will printlay all the time steps of a transient run (use steps to specify the steps requested)', + 'transient_vel':' this will printlay the velocity for the time steps requested in ''steps'' of a transient run', + 'transient_vel':' vel can be by any field of the transient results (vx, vy, vz, vel, temperature, melting, pressure, bed, thickness, surface)', + 'transient_field':' dynamic plot of results. specify ''steps'' option, as fell as ''field'' (defaults are all steps, for ''Vel'' field)', + 'transient_movie':' this will printlay the time steps of a given field of a transient run', + 'transient_movie_field':' field to be printlayed when doing transient_movie data printlay', + 'transient_movie_output':' filename if output is desired for movie', + 'transient_movie_time':' time for each image (default 2 seconds)', + 'thermaltransient_results':' this will printlay all the time steps of a thermal transient run', + 'qmuhistnorm':' histogram normal distribution. needs option qmudata', + 'qmumean':' plot of mean distribution in sampling analysis with scaled response. needs option qmudata for descriptor', + 'qmustddev':' plot of stddev distribution in sampling analysis with scaled response. needs option qmudata for descriptor', + 'part_hist':' partitioning node and area histogram'} pyoptions={'axis':" show ('on') or hide ('off') axes", @@ -77,91 +77,88 @@ 'log':" cutoff value for log", 'backgroundcolor':" plot background color. RGB tuple or standard string", - 'expdisp':" path (or list of paths) to the exp file to be plotted ", - 'explinewidth':" linewidth ", - 'explinestyle':" matplotlib linestyle string ", - 'explinecolor':" matplotlib color string ", - 'expfill':" (True/False) fill a closed contour ", - 'expfillcolor':" Color for a filled contour, only used if expfill is True ", - 'expfillalpha':" alpha transparency for filled contour ", - 'overlay':" True/False. Overlay a georeferenced image (radar/visible) ", - 'overlay_image':" path to overlay image ", - 'overlayhist':" plot a histogram of overlay image, used for setting overlaylims ", - 'overlaylims':" normalized limits to clip and stretch contrast of overlay image (in [0,1], ex. [0.25,0.75]) ", - 'alpha':" set transparency of plotted data (in [0,1]) " - } + 'expdisp':" path (or list of paths) to the exp file to be plotted ", + 'explinewidth':" linewidth ", + 'explinestyle':" matplotlib linestyle string ", + 'explinecolor':" matplotlib color string ", + 'expfill':" (True/False) fill a closed contour ", + 'expfillcolor':" Color for a filled contour, only used if expfill is True ", + 'expfillalpha':" alpha transparency for filled contour ", + 'overlay':" True/False. Overlay a georeferenced image (radar/visible) ", + 'overlay_image':" path to overlay image ", + 'overlayhist':" plot a histogram of overlay image, used for setting overlaylims ", + 'overlaylims':" normalized limits to clip and stretch contrast of overlay image (in [0,1], ex. [0.25,0.75]) ", + 'alpha':" set transparency of plotted data (in [0,1]) ", + 'layer':"number of the layer to display for 3D runs"} TODOoptions={'basin':" zoom on a given basin ('pineislandglacier','ronneiceshelf', use isbasin to identify a basin", - 'figurebackgroundcolor':" figure background color. (default is 'none',", - 'coord':" 'xy' (default) or 'latlon'", - 'colorbarpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", - 'colorbarcornerposition':" 'West','North',etc ...", - 'colorbartitlerotation':" -90, etc ...", - 'colorbarfontsize':" specify colorbar fontsize", - 'colorbarwidth':" multiplier (default 1) to the default width colorbar", - 'colorbarheight':" multiplier (default 1) to the default height colorbar", - 'contourticks':" 'on' or 'off' to printlay the ticks of the contours", - 'contouronly':" 'on' or 'off' to printlay the contours on a white background", - 'contourcolor':" ticks and contour color", - 'density':" density of quivers (one arrow every N nodes, N integer)", - 'inset':" add an inset (zoom) of the current figure if 1 (use 'insetx', 'insety' and 'insetpos' to determine the inset position and content)", - 'insetx':" [min(x) max(x)] where min(x) and max(x) are values determining the inset content", - 'insety':" [min(y) max(y)] where min(y) and max(y) are values determining the inset content", - 'insetpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", - 'resolution':" resolution used by section value (array of type [horizontal_resolution vertical_resolution])", - 'showsection':" show section used by 'sectionvalue' (string 'on' or a number of labels)", - 'sectionvalue':" give the value of data on a profile given by an Argus file (string 'Argusfile_name.exp',", - 'profile':" give the value of data along a vertical profile ([xlocation ylocation])", - 'smooth':" smooth element data (string 'yes' or integer)", - - 'view':" same as standard matlab option (ex: 2, 3 or [90 180]", - 'zlim':" same as standard matlab option", - 'xticklabel':" specifiy xticklabel", - 'yticklabel':" specifiy yticklabel", - 'contrast':" (default 1) coefficient to add contrast to the radar amplitude image used in overlays", - 'highres':" resolution of overlayed radar amplitude image (default is 0, high resolution is 1).", - 'alpha':" transparency coefficient (the higher, the more transparent). Default is 1.5", - 'scaling':" scaling factor used by quiver plots. Default is 0.4", - 'autoscale':" set to 'off' to have all the quivers with the same size. Default is 'on'", - 'linewidth':" line width for expprint plot (use a cell of strings if more than one)", - 'border':" size of printlay border (in pixels). active only for overlay plots", - - 'nan':" value assigned to NaNs (convenient when plotting BC)", - 'partitionedges':" 'off' by default. overlay plot of partition edges", - - 'latlon':" 'on' or {latstep lonstep [resolution [color]]} where latstep,longstep and resolution are in degrees, color is a [r g b] array", - 'latlonnumbering':" 'on' or {latgap longap colornumber latangle lonangle} where latgap and longap are pixel gaps for the numbers", - 'latlonclick':" 'on' to click on latlon ticks positions colornumber is a [r g b] array and latangle and lonangle are angles to flip the numbers", - 'northarrow':" add an arrow pointing north, 'on' for default value or [x0 y0 length [ratio width fontsize]] where (x0,y0) are the coordinates of the base, ratio=headlength/length", - 'offset':" mesh offset used by 'rifts', default is 500", - 'scaleruler':" add a scale ruler, 'on' for default value or [x0 y0 length width numberofticks] where (x0,y0) are the coordinates of the lower left corner", - 'showregion':" show domain in Antarctica on an inset, use 'insetpos' properties", - 'visible':" 'off' to make figure unvisible, default is 'on'", - 'wrapping':" repeat 'n' times the colormap ('n' must be an integer)", - 'unit':" by default, in m, otherwise, 'km' is available", - 'legend_position':" by default, 'NorthEasth'", - 'qmudata':" ", - 'figposition':" position of figure: 'fullscreen', 'halfright', 'halfleft', 'portrait', 'landscape',... (hardcoded in applyoptions.m)", - 'offsetaxispos':" offset of current axis position to get more space (ex: [-0.02 0 0.04 0])", - 'axispos':" axis position to get more space", - 'hmin':" (numeric, minimum for histogram)", - 'hmax':" (numeric, maximum for histogram)", - 'hnint':" (numeric, number of intervals for histogram)", - 'ymin1':" (numeric, minimum of histogram y-axis)", - 'ymax1':" (numeric, maximum of histogram y-axis)", - 'ymin2':" (numeric, minimum of cdf y-axis)", - 'ymax2':" (numeric, maximum of cdf y-axis)", - 'cdfplt':" (char, 'off' to turn off cdf line plots)", - 'cdfleg':" (char, 'off' to turn off cdf legends)", - 'segmentnumbering':" ('off' by default)", - 'kmlgroundoverlay':" ('off' by default)", - 'kmlfilename':" ('tempfile.kml' by default)", - 'kmlroot':" ('./' by default)", - 'kmlimagename':" ('tempimage' by default)", - 'kmlimagetype':" ('png' by default)", - 'kmlresolution':" (1 by default)", - 'kmlfolder':" ('Ground Overlay' by default)", - 'kmlfolderdescription':" ('' by default)", - 'kmlgroundoverlayname':" ('' by default)", - 'kmlgroundoverlaydescription':"N/A by default')"} + 'figurebackgroundcolor':" figure background color. (default is 'none',", + 'coord':" 'xy' (default) or 'latlon'", + 'colorbarpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", + 'colorbarcornerposition':" 'West','North',etc ...", + 'colorbartitlerotation':" -90, etc ...", + 'colorbarfontsize':" specify colorbar fontsize", + 'colorbarwidth':" multiplier (default 1) to the default width colorbar", + 'colorbarheight':" multiplier (default 1) to the default height colorbar", + 'contourticks':" 'on' or 'off' to printlay the ticks of the contours", + 'contouronly':" 'on' or 'off' to printlay the contours on a white background", + 'contourcolor':" ticks and contour color", + 'density':" density of quivers (one arrow every N nodes, N integer)", + 'inset':" add an inset (zoom) of the current figure if 1 (use 'insetx', 'insety' and 'insetpos' to determine the inset position and content)", + 'insetx':" [min(x) max(x)] where min(x) and max(x) are values determining the inset content", + 'insety':" [min(y) max(y)] where min(y) and max(y) are values determining the inset content", + 'insetpos':" [x,y,dx,dy] where x,y,dx and dy are within [0 1]", + 'resolution':" resolution used by section value (array of type [horizontal_resolution vertical_resolution])", + 'showsection':" show section used by 'sectionvalue' (string 'on' or a number of labels)", + 'sectionvalue':" give the value of data on a profile given by an Argus file (string 'Argusfile_name.exp',", + 'profile':" give the value of data along a vertical profile ([xlocation ylocation])", + 'smooth':" smooth element data (string 'yes' or integer)", + 'view':" same as standard matlab option (ex: 2, 3 or [90 180]", + 'zlim':" same as standard matlab option", + 'xticklabel':" specifiy xticklabel", + 'yticklabel':" specifiy yticklabel", + 'contrast':" (default 1) coefficient to add contrast to the radar amplitude image used in overlays", + 'highres':" resolution of overlayed radar amplitude image (default is 0, high resolution is 1).", + 'alpha':" transparency coefficient (the higher, the more transparent). Default is 1.5", + 'scaling':" scaling factor used by quiver plots. Default is 0.4", + 'autoscale':" set to 'off' to have all the quivers with the same size. Default is 'on'", + 'linewidth':" line width for expprint plot (use a cell of strings if more than one)", + 'border':" size of printlay border (in pixels). active only for overlay plots", + 'nan':" value assigned to NaNs (convenient when plotting BC)", + 'partitionedges':" 'off' by default. overlay plot of partition edges", + 'latlon':" 'on' or {latstep lonstep [resolution [color]]} where latstep,longstep and resolution are in degrees, color is a [r g b] array", + 'latlonnumbering':" 'on' or {latgap longap colornumber latangle lonangle} where latgap and longap are pixel gaps for the numbers", + 'latlonclick':" 'on' to click on latlon ticks positions colornumber is a [r g b] array and latangle and lonangle are angles to flip the numbers", + 'northarrow':" add an arrow pointing north, 'on' for default value or [x0 y0 length [ratio width fontsize]] where (x0,y0) are the coordinates of the base, ratio=headlength/length", + 'offset':" mesh offset used by 'rifts', default is 500", + 'scaleruler':" add a scale ruler, 'on' for default value or [x0 y0 length width numberofticks] where (x0,y0) are the coordinates of the lower left corner", + 'showregion':" show domain in Antarctica on an inset, use 'insetpos' properties", + 'visible':" 'off' to make figure unvisible, default is 'on'", + 'wrapping':" repeat 'n' times the colormap ('n' must be an integer)", + 'unit':" by default, in m, otherwise, 'km' is available", + 'legend_position':" by default, 'NorthEasth'", + 'qmudata':" ", + 'figposition':" position of figure: 'fullscreen', 'halfright', 'halfleft', 'portrait', 'landscape',... (hardcoded in applyoptions.m)", + 'offsetaxispos':" offset of current axis position to get more space (ex: [-0.02 0 0.04 0])", + 'axispos':" axis position to get more space", + 'hmin':" (numeric, minimum for histogram)", + 'hmax':" (numeric, maximum for histogram)", + 'hnint':" (numeric, number of intervals for histogram)", + 'ymin1':" (numeric, minimum of histogram y-axis)", + 'ymax1':" (numeric, maximum of histogram y-axis)", + 'ymin2':" (numeric, minimum of cdf y-axis)", + 'ymax2':" (numeric, maximum of cdf y-axis)", + 'cdfplt':" (char, 'off' to turn off cdf line plots)", + 'cdfleg':" (char, 'off' to turn off cdf legends)", + 'segmentnumbering':" ('off' by default)", + 'kmlgroundoverlay':" ('off' by default)", + 'kmlfilename':" ('tempfile.kml' by default)", + 'kmlroot':" ('./' by default)", + 'kmlimagename':" ('tempimage' by default)", + 'kmlimagetype':" ('png' by default)", + 'kmlresolution':" (1 by default)", + 'kmlfolder':" ('Ground Overlay' by default)", + 'kmlfolderdescription':" ('' by default)", + 'kmlgroundoverlayname':" ('' by default)", + 'kmlgroundoverlaydescription':"N/A by default')"} Index: /issm/trunk-jpl/src/m/plot/processmesh.py =================================================================== --- /issm/trunk-jpl/src/m/plot/processmesh.py (revision 21426) +++ /issm/trunk-jpl/src/m/plot/processmesh.py (revision 21427) @@ -5,16 +5,16 @@ """ PROCESSMESH - process the mesh for plotting - + Usage: - x,y,z,elements,is2d=processmech(md,data,options) - + x,y,z,elements,is2d=processmech(md,data,options) + See also: PLOTMODEL, PROCESSDATA """ - + # {{{ check mesh size parameters if md.mesh.numberofvertices==0: raise ValueError('processmesh error: mesh is empty') - if md.mesh.numberofvertices==md.mesh.numberofelements: - raise ValueError('processmesh error: the number of elements is the same as the number of nodes') + if md.mesh.numberofvertices==md.mesh.numberofelements: + raise ValueError('processmesh error: the number of elements is the same as the number of nodes') # }}} # {{{ treating non data plots mesh @@ -26,5 +26,5 @@ x=md.mesh.x try: - y=md.mesh.x2d + y=md.mesh.y2d except AttributeError: y=md.mesh.y @@ -53,9 +53,6 @@ raise ValueError('processmesh error: cannot work with 3D mesh in lat-lon coords') #we modify the mesh temporarily to a 2D mesh from which the 3D mesh was extruded - #Basile: does not seem necessary as we already picked x as x2d - # x=x2d - # y=y2d - # z=zeros(size(x2d)) - # elements=elements2d + z=np.zeros(np.size(x)) + elements=elements else: #Process mesh for plotting @@ -65,5 +62,4 @@ # process polycollection here for 3D plot is2d=0 - #units if options.exist('unit'):