[plotter] added LIC + vector overlay overhaul

plotter.py

@@ -29,7 +29,10 @@ if os.environ.get("DISPLAY", "") == "":
 import datetime
 
 import matplotlib.pyplot as plt
+try:
     from moviepy.video.io.ImageSequenceClip import ImageSequenceClip
+except ModuleNotFoundError:
+    print("WARNING: no movie support (missing module moviepy)")
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 
 import pspec_read
@@ -39,6 +42,13 @@ from studyprocessor import StudyProcessor
 from run_selector import RunSelector
 from units import U, unit_str, convert_exp
 
+try:
+    import lic
+except ModuleNotFoundError:
+    print("WARNING: no LIC support (missing module lic)")
+
+from matplotlib.cm import ScalarMappable
+
 
 from astrophysix.simdm.experiment import (
     ParameterSetting,
@@ -57,6 +67,81 @@ def not_array_error(err):
     return str(err)[-len(epy2) :] == epy2 or str(err)[-len(epy3) :] == epy3
 
 
+
+def gethv(map_h, map_v, extent):
+    # Number of selected vectors
+    nh = map_h.shape[0]
+    nv = map_h.shape[1]
+
+    # Creates vectors position grid
+    size_h = extent[1] - extent[0]  # size of the map
+    dh = size_h / map_h.shape[0]  # size of cell
+    seph = size_h / nh  # separation between vectors
+    h = extent[0] + dh + np.arange(nh) * seph
+
+    size_v = extent[3] - extent[2]
+    dv = size_v / map_h.shape[1]
+    sepv = size_v / nv
+    v = extent[2] + dv + np.arange(nv) * sepv
+
+    return np.meshgrid(h, v)
+
+def streamplot(ax, map_h, map_v, extent, **kwargs):
+    """
+    Add an overlay :  streamlines
+    """
+    hh, vv = gethv(map_h, map_v, extent)
+    ax.streamplot(hh, vv, map_h, map_v, **kwargs)
+
+
+def quiver(ax, map_h, map_v, extent, key_v, label, **kwargs):
+
+
+    hh, vv = gethv(map_h, map_v, extent)
+
+    # plot vector field
+    vec_field = ax.quiver(hh, vv, map_h, map_v, units="width", **kwargs)
+
+    # get norm information
+    norm_v = np.sqrt(map_h ** 2 + map_v ** 2)
+    max_v = np.max(norm_v)
+    min_v = np.min(norm_v)
+    # add vector key
+    if key_v is None:
+        key_v = (max_v + min_v) / 2.0
+        ax.quiverkey(
+            vec_field,
+            0.6,
+            0.98,
+            key_v,
+            f"${key_v:g}$ {label}",
+            labelpos="E",
+            coordinates="figure",
+        )
+
+def line_integral_convolution(ax, map_h, map_v, extent, **kwargs):
+    """
+    from Adnan Ali Ahmad
+    """
+
+    lic_res = lic.lic(map_v, map_h,length=20) #compute line integral convolution
+
+    # Amplify contrast on lic
+    lim=(.1,.9)
+    lic_data_clip = np.clip(lic_res,lim[0],lim[1])
+    lic_data_rgba = ScalarMappable(norm=None, cmap="binary").to_rgba(lic_data_clip)
+    lic_data_clip_rescale = (lic_data_clip-lim[0])/(lim[1]-lim[0])
+    lic_data_rgba[...,3] = lic_data_clip_rescale * 1
+
+    args = [lic_data_rgba]
+    plot_args = {**kwargs}
+    plot_args["cmap"] = "binary"
+    plot_args["extent"] = extent
+    plot_args["origin"] = "lower"
+    ax.imshow(*args, **plot_args)
+
+
+
 class PlotRule(Rule):
     """
     The rule class, speficic to plot.
@@ -626,7 +711,6 @@ class Plotter(Aggregator, BaseProcessor):
                 pad=1,
                 color="white",
                 frameon=False,
-                size_vertical=1,
             )
             plt.gca().add_artist(scalebar)
 
@@ -858,90 +942,37 @@ class Plotter(Aggregator, BaseProcessor):
         # Scatter plot
         plt.scatter(part_h, part_v, s=mass[mask] / 5e3, **kwargs)
 
-    def _overlay_speed(
+    def _overlay_vector(
-        self, ax_los, im_extent, unit=U.km_s, unit_coeff=1.0, key_v=None, **kwargs
+            self, name, ax_los, extent, unit=U.km_s, unit_coeff=1.0, reduce_res=1, kind="quiver", **kwargs
     ):
         """
         Add an overlay : velocity vector field
         """
-        dmap_vh = self.current_processor.get_value("/maps/speed_h_{}".format(ax_los))
-        dmap_vv = self.current_processor.get_value("/maps/speed_v_{}".format(ax_los))
 
-        label, unit_old, unit = self._ax_label_unit(
+        self.current_processor.process(f"{name}_h", ax_los)
-            f"/maps/speed_h_{ax_los}", "", unit, unit_coeff
+        self.current_processor.process(f"{name}_v", ax_los)
-        )
+
+        map_h = self.current_processor.get_value("/maps/speed_h_{}".format(ax_los))
+        map_v = self.current_processor.get_value("/maps/speed_v_{}".format(ax_los))
+        label, unit_old, unit = self._ax_label_unit(f"/maps/speed_h_{ax_los}", "", unit, unit_coeff)
 
-        vel_red = self.params.plot.vel_red
 
         # take only a subset of velocities
-        map_vh_red = dmap_vh[::vel_red, ::vel_red] * unit_old.express(unit)
+        map_h = map_h[::reduce_res, ::reduce_res] * unit_old.express(unit)
-        map_vv_red = dmap_vv[::vel_red, ::vel_red] * unit_old.express(unit)
+        map_v = map_v[::reduce_res, ::reduce_res] * unit_old.express(unit)
 
-        # get norm information
+        if kind == "quiver":
-        norm_v = np.sqrt(map_vh_red ** 2 + map_vv_red ** 2)
+            quiver(plt.gca(), map_h, map_v, extent=extent, label=label, **kwargs)
-        max_v = np.max(norm_v)
+        elif kind == "streamplot":
-        min_v = np.min(norm_v)
+            streamplot(plt.gca(), map_h, map_v, extent=extent, **kwargs)
+        elif kind == "lic":
+            line_integral_convolution(plt.gca(), map_h, map_v, extent=extent, **kwargs)
 
-        # Number of selected vectors
+    def _overlay_speed(self, ax_los, **kwargs):
-        nh = map_vh_red.shape[0]
+        self._overlay_vector("speed", ax_los, **kwargs)
-        nv = map_vh_red.shape[1]
 
-        # Creates vectors position grid
+    def _overlay_B(self, ax_los, **kwargs):
-        size_h = im_extent[1] - im_extent[0]  # size of the map
+        self._overlay_vector("B", ax_los, **kwargs)
-        dh = size_h / dmap_vh.shape[0]  # size of cell
-        seph = size_h / nh  # separation between vectors
-        h = im_extent[0] + dh + np.arange(nh) * seph
-
-        size_v = im_extent[3] - im_extent[2]
-        dv = size_v / dmap_vh.shape[1]
-        sepv = size_v / nv
-        v = im_extent[2] + dv + np.arange(nv) * sepv
-
-        hh, vv = np.meshgrid(h, v)
-
-        # plot vector field
-        vec_field = plt.quiver(hh, vv, map_vh_red, map_vv_red, units="width", **kwargs)
-
-        # add vector key
-        if key_v is None:
-            key_v = (max_v + min_v) / 2.0
-        plt.quiverkey(
-            vec_field,
-            0.6,
-            0.98,
-            key_v,
-            r"${:g}$".format(key_v) + label,
-            labelpos="E",
-            coordinates="figure",
-        )
-
-    def _overlay_B(self, ax_los, im_extent, **kwargs):
-        """
-        Add an overlay : magnetic streamlines
-        """
-        dmap_Bh = self.current_processor.get_value(f"/maps/B_h_{ax_los}")
-        dmap_Bv = self.current_processor.get_value(f"/maps/B_v_{ax_los}")
-
-        # TODO : redo this with im_extent
-
-        vel_red = self.params.plot.vel_red
-        radius = self.current_processor.attribute("/maps", "radius")
-        center = self.current_processor.attribute("/maps", "center")
-        lbox = self.current_processor.lbox
-
-        map_Bh_red = dmap_Bh[::vel_red, ::vel_red]  # take only a subset of velocities
-        map_Bv_red = dmap_Bv[::vel_red, ::vel_red]
-        nh = map_Bh_red.shape[0]
-        nv = map_Bv_red.shape[1]
-        vec_h = (
-            np.arange(nh) * 2.0 / nh * radius - radius + center[0] + radius / nh
-        ) * lbox
-        vec_v = (
-            np.arange(nv) * 2.0 / nv * radius - radius + center[1] + radius / nv
-        ) * lbox
-        hh, vv = np.meshgrid(vec_h, vec_v)
-
-        plt.streamplot(hh, vv, map_Bh_red, map_Bv_red, **kwargs)
 
     def _plot_hist(
         self,