add trasparency to screenshot and others fixes

docs/changes.md

@@ -34,13 +34,13 @@
 
 
 ## Soft-breaking Changes
-Changes that will break existing code whose fixing is trivial:
+Changes that may break existing code whose fixing is trivial:
 
-- None
+- in `file_io.screenshot()` add fourth channel representing trasparency @miek0tube
 
 
 ## Hard-breaking Changes
-Changes that will break existing code and need active thinking and work to adapt
+Changes that will break existing code and need active thinking and some work to adapt
 
 - None
 

examples/basic/cells_within_bounds.py

@@ -14,7 +14,7 @@
 ids = mesh.find_cells_in_bounds(zbounds=(z1,z2))
 
 # Print the cell IDs in green to the console
-printc('IDs of cells within bounds:\n', sorted(ids), c='g')
+printc('IDs of cells within bounds:\n', ids, c='g')
 
 # Create two Plane objects at the specified z-positions
 p1 = Plane(normal=(0,0,1), s=[2,2]).z(z1).alpha(0.5)

examples/basic/voronoi1.py

@@ -11,6 +11,7 @@
 vor.cmap('Set3', "VoronoiID", on='cells').wireframe(False)
 
 # Create a label for each cell showing its ID
+vor.compute_normals() # needed for the labels to face the camera
 labels = vor.labels("VoronoiID", on='cells', scale=0.01, justify='center')
 
 # Plot the objects and close the window to continue

tests/issues/issue_1109.py

@@ -21,6 +21,8 @@
 cc = CellCenters(zslice).shift([-spacing[0] / 2, -spacing[1] / 2, 0])
 cc.resample_data_from(zslice)
 
+zslice.compute_normals()
+
 zslice2 = zslice.clone()
 zslice2.celldata["pixel_value"] = cc.pointdata["input_scalars"]
 print(zslice2.celldata["pixel_value"])

tests/pipeline.txt

@@ -112,7 +112,7 @@ cd ~/Projects/server/welsh_embryo_stager
    python stager.py pics/E14.5_L3-03_HL2.5X.jpg
 ################
 cd ~/Projects/oocytes
-   python step3.py
+   python step5.py
 ################
 cd ~/Projects/umap_viewer3d
    python main6.py

vedo/assembly.py

@@ -1,7 +1,9 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 from weakref import ref as weak_ref_to
-from typing import List, Union, Any, Self
+from typing import List, Union, Any
+from typing_extensions import Self
+
 import numpy as np
 
 import vedo.file_io
@@ -331,8 +333,8 @@ def __str__(self):
 
         n = len(self.unpack())
         out += "n. of objects".ljust(14) + ": " + str(n) + " "
-        names = set([a.name for a in self.unpack() if a.name])
-        if names:
+        names = np.unique([a.name for a in self.unpack() if a.name])
+        if len(names):
             out += str(names).replace("'","")[:56]
         out += "\n"
 

vedo/file_io.py

@@ -1881,16 +1881,12 @@ def screenshot(filename="screenshot.png", scale=1, asarray=False) -> Union["vedo
     if asarray:
         pd = w2if.GetOutput().GetPointData()
         npdata = utils.vtk2numpy(pd.GetArray("ImageScalars"))
-        npdata = npdata[:, [0, 1, 2]]
+        # npdata = npdata[:, [0, 1, 2]]  # remove alpha channel, issue #1199
         ydim, xdim, _ = w2if.GetOutput().GetDimensions()
         npdata = npdata.reshape([xdim, ydim, -1])
         npdata = np.flip(npdata, axis=0)
         return npdata ###########################
 
-    # elif settings.default_backend == "2d" and vedo.notebook_plotter:
-    #     vedo.notebook_plotter.save(filename) # a PIL Image
-    #     return vedo.notebook_plotter  ##########
-
     if filename.lower().endswith(".png"):
         writer = vtki.new("PNGWriter")
         writer.SetFileName(filename)

vedo/mesh.py

@@ -283,7 +283,11 @@ def cell_normals(self):
         vtknormals = self.dataset.GetCellData().GetNormals()
         numpy_normals = vtk2numpy(vtknormals)
         if len(numpy_normals) == 0 and len(self.cells) != 0:
-            raise ValueError("VTK failed to return any normal vectors. You may need to call `Mesh.compute_normals()` before accessing `Mesh.cell_normals`.")
+            vedo.logger.warning(
+                "failed to return normal vectors.\n"
+                "You may need to call `Mesh.compute_normals()` before accessing 'Mesh.cell_normals'."
+            )
+            numpy_normals = np.zeros((self.ncells, 3)) + [0,0,1]
         return numpy_normals
 
     def compute_normals(self, points=True, cells=True, feature_angle=None, consistency=True) -> Self:

vedo/pyplot.py

@@ -3683,6 +3683,7 @@ def matrix(
         sbar = gr.scalarbar
     labs = None
     if scale != 0:
+        gr.compute_normals(points=False)
         labs = gr.labels(
             on="cells",
             scale=scale / max(m, n),

vedo/volume.py

@@ -190,7 +190,12 @@ def __init__(
                 self.properties.SetShade(True)
                 self.properties.SetInterpolationType(1)
                 self.cmap("RdBu_r")
-                self.alpha([0.0, 0.2, 0.4, 0.6, 0.8, 1.0])
+                # make asigmoidal transfer function by default
+                # xvalues = np.linspace(0, 1, 11)
+                # sigmoid = np.clip(1/(1+np.exp(-20*(xvalues-0.5))), 0, 1)
+                # print("Volume: setting sigmoidal transfer function", xvalues, sigmoid)
+                # self.alpha(sigmoid)
+                self.alpha([0.0, 0.001, 0.3, 0.5, 0.7, 0.8, 1.0]) # we need to revert this..
                 self.alpha_gradient(None)
                 self.properties.SetScalarOpacityUnitDistance(1.0)