improvements to applications.MorphPlotter

docs/changes.md

@@ -9,15 +9,16 @@
 - add `utils.circle_from_3points()` function.
 - add example `examples/other/iminuit2.py`
 - add `rotation=..` to `Arrow2D()` class
+- improvements to `applications.MorphPlotter`
 
 
-## Soft Breaking Changes
+## Soft-breaking Changes
 Changes that will break existing code whose fixing is trivial:
 
 - None
 
 
-## Hard Breaking Changes
+## Hard-breaking Changes
 Changes that will break existing code and need active thinking and work to adapt
 
 - None
@@ -27,6 +28,7 @@ Changes that will break existing code and need active thinking and work to adapt
 ```
 examples/other/magic-class1.py
 examples/other/iminuit2.py
+examples/advanced/warp4b.py
 ```
 
 ### Broken Examples

docs/examples_db.js

@@ -1903,6 +1903,14 @@ vedo_example_db =
         long  : 'Visualize a vedo mesh in the '+insertLink('napari','napari.org/')+' image viewer. Check out also the '+insertLink('napari-vedo plugin','github.com/jo-mueller/napari-vedo-bridge')+'for napari.',
         imgsrc: 'images/other/napari1.png',
     },
+    {
+        pyname: 'magic-class1',
+        kbd   : '',
+        categ : 'other',
+        short : 'magic-class library',
+        long  : 'Visualize objects using the '+insertLink('magic-class','github.com/hanjinliu/magic-class')+' library.',
+        imgsrc: 'images/other/magic-class1.png',
+    },
     {
         pyname: 'dolfin/elasticity2',
         kbd   : '',

examples/advanced/warp4b.py

@@ -34,7 +34,7 @@
 #         self.at(0).add(source, self.msg0, self.instructions).reset_camera()
 #         self.at(1).add(f"Reference {target.filename}", self.msg1, target)
 #         cam1 = self.camera  # save camera at 1
-#         self.at(2).add("Morphing Output", target, Axes(target)).background("k9")
+#         self.at(2).add("Morphing Output", target).background("k9")
 #         self.camera = cam1  # use the same camera of renderer1
 #
 #         self.callid1 = self.add_callback("on key press", self.on_keypress)
@@ -99,13 +99,15 @@
 ################################################################################
 
 settings.default_font = "Calco"
-settings.enable_default_mouse_callbacks = False
 
 source = Mesh(dataurl+"limb_surface.vtk").color("k5")
 source.rotate_y(90).rotate_z(-60).rotate_x(40)
-target = Mesh(dataurl+"290.vtk").cut_with_plane(origin=(1,0,0)).color("yellow5")
 
-plt = MorphPlotter(source, target, size=(2490, 850))
+target = Mesh(dataurl+"290.vtk").color("yellow5")
+target.rotate_y(-40)
+
+plt = MorphPlotter(source, target, size=(2490, 850), axes=14)
+plt.cmap_name = "RdYlBu_r"
 plt.show()
 plt.close()
 

vedo/addons.py

@@ -3687,7 +3687,7 @@ def Axes(
             if xlabel_backface_color is None:
                 bfc = 1 - np.array(get_color(xlabel_color))
                 xlab.backcolor(bfc)
-            xlab.name = f"xNumericLabel{i}"
+            xlab.name = f"xNumericLabel {i}"
             labels.append(xlab)
 
     if ylabel_size and ytitle:
@@ -3740,7 +3740,7 @@ def Axes(
             if ylabel_backface_color is None:
                 bfc = 1 - np.array(get_color(ylabel_color))
                 ylab.backcolor(bfc)
-            ylab.name = f"yNumericLabel{i}"
+            ylab.name = f"yNumericLabel {i}"
             labels.append(ylab)
 
     if zlabel_size and ztitle:
@@ -3792,7 +3792,7 @@ def Axes(
             if zlabel_backface_color is None:
                 bfc = 1 - np.array(get_color(zlabel_color))
                 zlab.backcolor(bfc)
-            zlab.name = f"zNumericLabel{i}"
+            zlab.name = f"zNumericLabel {i}"
             labels.append(zlab)
 
     ################################################ axes titles
@@ -3857,7 +3857,7 @@ def Axes(
         xt.use_bounds(x_use_bounds)
         if xtitle == " ":
             xt.use_bounds(False)
-        xt.name = f"xtitle {xtitle}"
+        xt.name = "xtitle"
         titles.append(xt)
         if xtitle_box:
             titles.append(xt.box(scale=1.1).use_bounds(x_use_bounds))
@@ -3923,7 +3923,7 @@ def Axes(
         yt.use_bounds(y_use_bounds)
         if ytitle == " ":
             yt.use_bounds(False)
-        yt.name = f"ytitle {ytitle}"
+        yt.name = "ytitle"
         titles.append(yt)
         if ytitle_box:
             titles.append(yt.box(scale=1.1).use_bounds(y_use_bounds))
@@ -3985,7 +3985,7 @@ def Axes(
         zt.use_bounds(z_use_bounds)
         if ztitle == " ":
             zt.use_bounds(False)
-        zt.name = f"ztitle {ztitle}"
+        zt.name = "ztitle"
         titles.append(zt)
 
     ################################################### header title
@@ -4009,7 +4009,7 @@ def Axes(
         htit.rotate_x(htitle_rotation)
         wpos = [htitle_offset[0]*dx, (1 + htitle_offset[1])*dy, htitle_offset[2]*dz]
         htit.shift(np.array(wpos) + [0, 0, xyshift*dz])
-        htit.name = f"htitle {htitle}"
+        htit.name = "htitle"
         titles.append(htit)
 
     ######

vedo/applications.py

@@ -483,7 +483,11 @@ class MorphPlotter(Plotter):
 
     def __init__(self, source, target, **kwargs):
 
-        kwargs.update(dict(N=3, sharecam=0))
+        vedo.settings.enable_default_keyboard_callbacks = False
+        vedo.settings.enable_default_mouse_callbacks = False
+
+        kwargs.update({"N": 3})
+        kwargs.update({"sharecam": 0})
         super().__init__(**kwargs)
 
         self.source = source.pickable(True)
@@ -492,29 +496,34 @@ def __init__(self, source, target, **kwargs):
         self.sources = []
         self.targets = []
         self.warped = None
+        self.source_labels = None
+        self.target_labels = None
+        self.automatic_picking_distance = 0.075
         self.cmap_name = "coolwarm"
+        self.nbins = 25
         self.msg0 = Text2D("Pick a point on the surface",
                            pos="bottom-center", c='white', bg="blue4", alpha=1, font="Calco")
         self.msg1 = Text2D(pos="bottom-center", c='white', bg="blue4", alpha=1, font="Calco")
-        instructions = (
-            "Morphological alignment of 3D surfaces.\n"
+        self.instructions = Text2D(s=0.7, bg="blue4", alpha=0.1, font="Calco")
+        self.instructions.text(
+            "  Morphological alignment of 3D surfaces\n\n"
             "Pick a point on the source surface, then\n"
-            "pick the corresponding point on the target\n"
+            "pick the corresponding point on the target \n"
             "Pick at least 4 point pairs. Press:\n"
             "- c to clear all landmarks\n"
-            "- d to delete the last pair\n"
+            "- d to delete the last landmark pair\n"
+            "- a to auto-pick additional landmarks\n"
             "- z to compute and show the residuals\n"
             "- q to quit and proceed"
         )
-        self.instructions = Text2D(instructions, s=0.7, bg="blue4", alpha=0.1, font="Calco")
-        self.at(0).add_renderer_frame().add(source, self.msg0, self.instructions).reset_camera()
+        self.at(0).add_renderer_frame()
+        self.add(source, self.msg0, self.instructions).reset_camera()
         self.at(1).add_renderer_frame()
         self.add(Text2D(f"Target: {target.filename[-35:]}", bg="blue4", alpha=0.1, font="Calco"))
         self.add(self.msg1, target)
         cam1 = self.camera  # save camera at 1
         self.at(2).background("k9")
-        self.add(Text2D("Morphing Output", font="Calco"))
-        self.add(target, vedo.Axes(target))
+        self.add(target, Text2D("Morphing Output", font="Calco"))
         self.camera = cam1  # use the same camera of renderer1
 
         self.add_renderer_frame()
@@ -529,12 +538,12 @@ def update(self):
         target_pts = Points(self.targets).color("purple5").ps(12)
         source_pts.name = "source_pts"
         target_pts.name = "target_pts"
-        slabels = source_pts.labels2d("id", c="purple3")
-        tlabels = target_pts.labels2d("id", c="purple3")
-        slabels.name = "source_pts"
-        tlabels.name = "target_pts"
-        self.at(0).remove("source_pts").add(source_pts, slabels)
-        self.at(1).remove("target_pts").add(target_pts, tlabels)
+        self.source_labels = source_pts.labels2d("id", c="purple3")
+        self.target_labels = target_pts.labels2d("id", c="purple3")
+        self.source_labels.name = "source_pts"
+        self.target_labels.name = "target_pts"
+        self.at(0).remove("source_pts").add(source_pts, self.source_labels)
+        self.at(1).remove("target_pts").add(target_pts, self.target_labels)
         self.render()
 
         if len(self.sources) == len(self.targets) and len(self.sources) > 3:
@@ -571,7 +580,11 @@ def on_keypress(self, evt):
             self.source.pickable(True)
             self.target.pickable(False)
             self.update()
-        elif evt.keypress == "d":
+        if evt.keypress == "w":
+            rep = (self.warped.properties.GetRepresentation() == 1)
+            self.warped.wireframe(not rep)
+            self.render()
+        if evt.keypress == "d":
             n = min(len(self.sources), len(self.targets))
             self.sources = self.sources[:n-1]
             self.targets = self.targets[:n-1]
@@ -580,25 +593,69 @@ def on_keypress(self, evt):
             self.source.pickable(True)
             self.target.pickable(False)
             self.update()
-        elif evt.keypress == "z":
+        if evt.keypress == "a":
+            # auto-pick points on the target surface
+            if not self.warped:
+                vedo.printc("At least 4 points are needed.", c="r")
+                return
+            pts = self.target.clone().subsample(self.automatic_picking_distance)
+            if len(self.sources) > len(self.targets):
+                self.sources.pop()
+            d = self.target.diagonal_size()
+            r = d * self.automatic_picking_distance
+            TI = self.warped.transform.compute_inverse()
+            for p in pts.coordinates:
+                pp = vedo.utils.closest(p, self.targets)[1]
+                if vedo.mag(pp - p) < r:
+                    continue
+                q = self.warped.closest_point(p)
+                self.sources.append(TI(q))
+                self.targets.append(p)
+            self.source.pickable(True)
+            self.target.pickable(False)
+            self.update()            
+        if evt.keypress == "z" or evt.keypress == "a":
+            self.nbins = 25
             dists = self.warped.distance_to(self.target, signed=True)
-            mind, maxd = np.min(dists), np.max(dists)
-            v = min(abs(mind), abs(maxd))
+            v = np.std(dists) * 2
             self.warped.cmap(self.cmap_name, dists, vmin=-v, vmax=+v)
+
             h = vedo.pyplot.histogram(
                 dists, 
-                bins=25,
-                title="Residuals",
+                bins=self.nbins,
+                title=" ",
+                xtitle=f"STD = {v/2:.2f}",
+                ytitle="",
                 c=self.cmap_name, 
                 xlim=(-v, v),
                 aspect=16/9,
-                axes=dict(text_scale=1.9),
+                axes=dict(
+                    number_of_divisions=5,
+                    text_scale=2,
+                    xtitle_offset=0.075,
+                    xlabel_justify="top-center"),
             )
-            h = h.clone2d(pos="bottom-left", size=0.55)
+
+            # try to fit a gaussian to the histogram
+            def gauss(x, A, B, sigma):
+                return A + B * np.exp(-x**2 / (2 * sigma**2))
+            try:
+                from scipy.optimize import curve_fit
+                inits = [0, len(dists)/self.nbins*2.5, v/2]
+                popt, _ = curve_fit(gauss, xdata=h.centers, ydata=h.frequencies, p0=inits)
+                print(inits, popt)
+                x = np.linspace(-v, v, 300)
+                h += vedo.pyplot.plot(x, gauss(x, *popt), like=h, lw=1, lc="k2")
+                h["Axes"]["xtitle"].text(f":sigma = {abs(popt[2]):.3f}", font="VictorMono")
+            except:
+                pass
+
+            h = h.clone2d(pos="bottom-left", size=0.575)
             h.name = "warped"
             self.at(2).add(h)
             self.render()
-        elif evt.keypress == "q":
+
+        if evt.keypress == "q":
             self.break_interaction()
 
 

vedo/shapes.py

@@ -4103,6 +4103,7 @@ def __init__(
         self.init_scale = s
         self.name = "Text3D"
         self.txt = txt
+        self.justify = justify
 
     def text(
         self,
@@ -4113,7 +4114,7 @@ def text(
         vspacing=2.15,
         depth=0,
         italic=False,
-        justify="bottom-left",
+        justify="",
         literal=False,
     ) -> "Text3D":
         """
@@ -4123,6 +4124,8 @@ def text(
         """
         if txt is None:
             return self.txt
+        if not justify:
+            justify = self.justify
 
         poly = self._get_text3d_poly(
             txt, self.init_scale * s, font, hspacing, vspacing,

vedo/version.py

@@ -1 +1 @@
-_version = '2024.5.1+dev05'
+_version = '2024.5.1+dev06'