clip and slice for the plots

Author: otvam

examples/config/cfg_data_matplotlib.yaml

@@ -5,4 +5,4 @@
 
 "style": "default"         # string with a Matplotlib style
 "legend": "best"           # location of the legend box
-"font": 12                 # reference font size of the figure
+"font": 12.0               # reference font size of the figure

examples/config/cfg_data_pyvista.yaml

@@ -4,22 +4,23 @@
 # Mozilla Public License Version 2.0
 
 # options for defining cut planes
-"plot_clip":
-    "clip_plot": false                 # add (or not) a clip plane for rendering
-    "clip_invert": false               # invert (or not) the clipping direction
-    "clip_normal": "z"                 # normal of the clipping direction
-    "clip_value": 0.0                  # initial position for the clipping
+"plot_filter":
+    "slice": false                 # add (or not) a slice plane for rendering
+    "clip": false                 # add (or not) a clip plane for rendering
+    "invert": false               # invert (or not) the clipping/slicing direction
+    "normal": "x"                 # normal of the clipping/slicing direction
+    "value": 0.0                  # initial position for the clipping/slicing
 
 # theme of the figure
 "plot_theme":
     "text_color": "black"              # color of the text elements
-    "title_font": 10                   # font size of the text displayed on the window corner
-    "colorbar_font": 15                # font size of the color bar
-    "colorbar_size": 5                 # number of division for the colorbar
+    "title_font": 10.0                 # font size of the text displayed on the window corner
+    "colorbar_font": 15.0              # font size of the color bar
+    "colorbar_size": 5.0               # number of division for the colorbar
     "colorbar_plot": true              # show (or not) the colorbar
     "background_color": "gray"         # background color of the plot
     "axis_add": true                   # add (or not) the axis marker
-    "axis_size": 2                     # size of the axis marker
+    "axis_size": 2.0                  # size of the axis marker
 
 # options controlling the view rendering
 "plot_view":

examples/config/viewer.yaml

@@ -23,6 +23,8 @@
 #       - title: title located at the corner of the plot (null for hiding)
 #       - color_voxel: face color for the voxelized structure
 #       - color_reference: face color for the reference structure
+#       - width_voxel: edge thickness for the voxelized structure
+#       - width_reference: edge thickness for the reference structure
 #       - opacity_voxel: face opacity for the voxelized structure
 #       - opacity_reference: face opacity for the reference structure
 #
@@ -70,6 +72,8 @@
         "title": "Voxelization Results"
         "color_voxel": "red"
         "color_reference": "blue"
+        "width_voxel": 2.0
+        "width_reference": 2.0
         "opacity_voxel": 0.5
         "opacity_reference": 0.5
 "connected":

examples/run_plotter.py

@@ -24,12 +24,7 @@
     file_plotter = os.path.join(PATH_ROOT, FOLDER_CONFIG, "plotter.yaml")
 
     # list of plots to be shown (defined in plotter.yaml)
-    tag_plot = [
-        "V_c_norm",
-        "J_c_norm",
-        "H_p_norm",
-        "residuum",
-    ]
+    tag_plot = ["V_c_norm", "J_c_norm", "H_p_norm", "residuum"]
 
     # method used for rendering the plots
     plot_mode = "qt"

pypeec/data/schema_list_viewer.yaml

@@ -45,6 +45,8 @@
         - "title"
         - "color_voxel"
         - "color_reference"
+        - "width_voxel"
+        - "width_reference"
         - "opacity_voxel"
         - "opacity_reference"
     properties:
@@ -59,6 +61,12 @@
         "color_reference":
             "type": "string"
             "minLength": 1
+        "width_voxel":
+            "type": "number"
+            "minimum": 0
+        "width_reference":
+            "type": "number"
+            "minimum": 0
         "opacity_voxel":
             "type": "number"
             "minimum": 0

pypeec/data/schema_plot_matplotlib.yaml

@@ -11,5 +11,5 @@
         "type": "string"
         "minLength": 1
     "font":
-        "type": "integer"
+        "type": "number"
         "minimum": 0

pypeec/data/schema_plot_pyvista.yaml

@@ -1,28 +1,31 @@
 "type": "object"
 "required":
-    - "plot_clip"
+    - "plot_filter"
     - "plot_theme"
     - "plot_view"
 "properties":
-    "plot_clip":
+    "plot_filter":
         "type": "object"
         "required":
-            - "clip_plot"
-            - "clip_invert"
-            - "clip_normal"
-            - "clip_value"
+            - "clip"
+            - "slice"
+            - "invert"
+            - "normal"
+            - "value"
         "properties":
-            "plot_clip":
+            "clip":
                 "type": "boolean"
-            "clip_invert":
+            "slice":
                 "type": "boolean"
-            "clip_normal":
+            "invert":
+                "type": "boolean"
+            "normal":
                 "type": "string"
                 "enum":
                     - "x"
                     - "y"
                     - "z"
-            "clip_value":
+            "value":
                 "type": "number"
     "plot_theme":
         "type": "object"
@@ -40,13 +43,13 @@
                 "type": "string"
                 "minLength": 1
             "title_font":
-                "type": "integer"
+                "type": "number"
                 "minimum": 0
             "colorbar_font":
-                "type": "integer"
+                "type": "number"
                 "minimum": 0
             "colorbar_size":
-                "type": "integer"
+                "type": "number"
                 "minimum": 0
             "colorbar_plot":
                 "type": "boolean"
@@ -56,7 +59,7 @@
             "axis_add":
                 "type": "boolean"
             "axis_size":
-                "type": "integer"
+                "type": "number"
                 "minimum": 0
     "plot_view":
         "type": "object"

pypeec/lib_plot/manage_pyvista.py

@@ -97,26 +97,32 @@ def _get_plot_title(pl, title, plot_theme):
     )
 
 
-def _get_clip_mesh(pl, obj, arg, plot_clip):
+def _get_filter_mesh(pl, obj, arg, plot_filter):
     """
     Add an object (either full view or clipped).
     """
 
     # extract
-    clip_plot = plot_clip["clip_plot"]
-    clip_invert = plot_clip["clip_invert"]
-    clip_normal = plot_clip["clip_normal"]
-    clip_value = plot_clip["clip_value"]
+    clip = plot_filter["clip"]
+    slice = plot_filter["slice"]
+    invert = plot_filter["invert"]
+    normal = plot_filter["normal"]
+    value = plot_filter["value"]
 
     # clip the plot
-    if clip_plot:
-        obj = obj.clip(normal=clip_normal, value=clip_value, invert=clip_invert)
+    if clip:
+        obj = obj.clip(normal=normal, origin=(value, value, value), invert=invert)
+
+    # slice the plot
+    if slice:
+        obj = obj.slice(normal=normal, origin=(value, value, value))
 
     # add the full plot
-    pl.add_mesh(
-        obj,
-        **arg,
-     )
+    if obj.n_cells > 0:
+        pl.add_mesh(
+            obj,
+            **arg,
+         )
 
 
 def _get_scale_norm(obj, scale):
@@ -327,7 +333,7 @@ def _get_arrow(obj, data_plot):
     return obj_tmp
 
 
-def _plot_scalar(pl, obj, data_plot, plot_clip, plot_theme):
+def _plot_scalar(pl, obj, data_plot, plot_filter, plot_theme):
     """
     Plot a scalar variable.
     """
@@ -367,11 +373,10 @@ def _plot_scalar(pl, obj, data_plot, plot_clip, plot_theme):
         scalar_bar_args=scalar_bar_args,
         render_points_as_spheres=True,
     )
-    if obj.n_cells > 0:
-        _get_clip_mesh(pl, obj, arg, plot_clip)
+    _get_filter_mesh(pl, obj, arg, plot_filter)
 
 
-def _plot_arrow(pl, grid, obj, data_plot, plot_clip, plot_theme):
+def _plot_arrow(pl, grid, obj, data_plot, plot_filter, plot_theme):
     """
     Plot a vector variable with an arrow plot (quiver plot).
     A scalar variable is used to determine the color of the arrows.
@@ -417,10 +422,10 @@ def _plot_arrow(pl, grid, obj, data_plot, plot_clip, plot_theme):
     )
     if obj.n_cells > 0:
         glyph_tmp = obj.glyph(orient="vector", scale=False, factor=factor)
-        _get_clip_mesh(pl, glyph_tmp, arg, plot_clip)
+        _get_filter_mesh(pl, glyph_tmp, arg, plot_filter)
 
 
-def _plot_material(pl, voxel, data_plot, plot_clip, plot_theme):
+def _plot_material(pl, voxel, data_plot, plot_filter, plot_theme):
     """
     Plot the material and source description.
     """
@@ -455,11 +460,10 @@ def _plot_material(pl, voxel, data_plot, plot_clip, plot_theme):
         scalars="material_tag",
         cmap=cmap,
     )
-    if voxel_tmp.n_cells > 0:
-        _get_clip_mesh(pl, voxel_tmp, arg, plot_clip)
+    _get_filter_mesh(pl, voxel_tmp, arg, plot_filter)
 
 
-def _plot_geometry(pl, voxel, data_plot, plot_clip, plot_theme, var):
+def _plot_geometry(pl, voxel, data_plot, plot_filter, plot_theme, var):
     """
     Plot an integer variable on the voxel structure (material or connection).
     """
@@ -482,18 +486,19 @@ def _plot_geometry(pl, voxel, data_plot, plot_clip, plot_theme, var):
         cmap=colormap,
         opacity=opacity,
     )
-    if voxel_tmp.n_cells > 0:
-        _get_clip_mesh(pl, voxel_tmp, arg, plot_clip)
+    _get_filter_mesh(pl, voxel_tmp, arg, plot_filter)
 
 
-def _plot_voxelization(pl, voxel, reference, data_plot, plot_clip, plot_theme):
+def _plot_voxelization(pl, voxel, reference, data_plot, plot_filter, plot_theme):
     """
     Plot the reference and voxelized structures in order to assess the voxelization error.
     """
 
     # extract the data
     color_voxel = data_plot["color_voxel"]
     color_reference = data_plot["color_reference"]
+    width_voxel = data_plot["width_voxel"]
+    width_reference = data_plot["width_reference"]
     opacity_voxel = data_plot["opacity_voxel"]
     opacity_reference = data_plot["opacity_reference"]
     title = data_plot["title"]
@@ -510,18 +515,18 @@ def _plot_voxelization(pl, voxel, reference, data_plot, plot_clip, plot_theme):
         show_scalar_bar=False,
         color=color_voxel,
         opacity=opacity_voxel,
+        line_width=width_voxel,
     )
-    if voxel_tmp.n_cells > 0:
-        _get_clip_mesh(pl, voxel_tmp, arg, plot_clip)
+    _get_filter_mesh(pl, voxel_tmp, arg, plot_filter)
 
     # add the resulting plot to the plotter
     arg = dict(
         show_scalar_bar=False,
         color=color_reference,
         opacity=opacity_reference,
+        line_width=width_reference,
     )
-    if voxel_tmp.n_cells > 0:
-        _get_clip_mesh(pl, reference_tmp, arg, plot_clip)
+    _get_filter_mesh(pl, reference_tmp, arg, plot_filter)
 
 
 def get_plot_viewer(pl, grid, voxel, point, reference, layout, data_plot, data_options):
@@ -533,17 +538,17 @@ def get_plot_viewer(pl, grid, voxel, point, reference, layout, data_plot, data_o
     """
 
     # extract the data
-    plot_clip = data_options["plot_clip"]
+    plot_filter = data_options["plot_filter"]
     plot_view = data_options["plot_view"]
     plot_theme = data_options["plot_theme"]
 
     # plot the geometry
     if layout == "domain":
-        _plot_geometry(pl, voxel, data_plot, plot_clip, plot_theme, "domain_tag")
+        _plot_geometry(pl, voxel, data_plot, plot_filter, plot_theme, "domain_tag")
     elif layout == "component":
-        _plot_geometry(pl, voxel, data_plot, plot_clip, plot_theme, "component_tag")
+        _plot_geometry(pl, voxel, data_plot, plot_filter, plot_theme, "component_tag")
     elif layout == "voxelization":
-        _plot_voxelization(pl, voxel, reference, data_plot, plot_clip, plot_theme)
+        _plot_voxelization(pl, voxel, reference, data_plot, plot_filter, plot_theme)
     else:
         raise ValueError("invalid plot layout")
 
@@ -561,7 +566,7 @@ def get_plot_plotter(pl, grid, voxel, point, layout, data_plot, data_options):
     """
 
     # extract the data
-    plot_clip = data_options["plot_clip"]
+    plot_filter = data_options["plot_filter"]
     plot_view = data_options["plot_view"]
     plot_theme = data_options["plot_theme"]
 
@@ -577,16 +582,16 @@ def get_plot_plotter(pl, grid, voxel, point, layout, data_plot, data_options):
 
     # plot the geometry
     if layout == "material":
-        _plot_material(pl, voxel, data_plot, plot_clip, plot_theme)
+        _plot_material(pl, voxel, data_plot, plot_filter, plot_theme)
     elif layout in ["norm_voxel", "norm_point"]:
         obj = _get_norm(obj, data_plot)
-        _plot_scalar(pl, obj, data_plot, plot_clip, plot_theme)
+        _plot_scalar(pl, obj, data_plot, plot_filter, plot_theme)
     elif layout in ["phasor_voxel", "phasor_point"]:
         obj = _get_phasor(obj, data_plot)
-        _plot_scalar(pl, obj, data_plot, plot_clip, plot_theme)
+        _plot_scalar(pl, obj, data_plot, plot_filter, plot_theme)
     elif layout in ["arrow_voxel", "arrow_point"]:
         obj = _get_arrow(obj, data_plot)
-        _plot_arrow(pl, grid, obj, data_plot, plot_clip, plot_theme)
+        _plot_arrow(pl, grid, obj, data_plot, plot_filter, plot_theme)
     else:
         raise ValueError("invalid plot layout")