fixes to file_io and mesh browser

marcomusy · Jun 20, 2023 · dba6d01 · dba6d01
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diff --git a/docs/changes.md b/docs/changes.md
@@ -1,54 +1,11 @@
 ## Main changes
 
-- Rename module `io.py` to `file_io.py` to avoid override stlib io.
-- Complete revision of cutter widgets funcionatlity
-- Integration in napari thanks to @jo-mueller
-
-
 ### Breaking changes
-- method `plotter.add()` no more accepts keyword `render=True/False`. Please use `plotter.add().render()` explicitly. Same thing for `plotter.remove()`.
-
-### Other fixes and improvements
-- added gpu acceleration for CLI volumetric visualization in #832 by @zhang-qiang-github
-- fixes for `k3d` jupyter backend
-- added `plotter.fov(value)` (field of view, the so called "fish-eye" effect)
-- fix `ploter.get_meshes()`
-- fix for `plotter.remove(unpack_assemblies=False)` method
-- fix for `io.import_window()` method
-- added `cut_with_cookiecutter()` to cut 2D contours.
-- fix `shapes.NormalLines()` class
-- added `vedo.interactor_modes` module
-- added `vedo.interactor_modes.BlenderStyle` class
-- added `base.pointdata.clear()` to remove all associated data 
-- added `volume.hide_voxels()` for visualization
-- added `Event.timerid` attribute
-- fix to `Volume.operation` by @DanKrsi
-- fix links in `pyplot` examples by @androbaza
-- fix `screenshot_scale` and remove it from settings.
-- allow initializing `ScalarBar` with a tuple range `(min, max)`
-- Update API Documentation for Changing Backend by @bhacha
-- Add `application.Browser().play()` to autoplay a slider
-- Add `pad()` to padding a Volume with zeros voxels (useful to `dilate()`)
-- Add `ProgressBarWidget()` to show a progress bar in the rendering window
-- Fix Scalarbar3D logscale and change separator symbol by @XushanLu
-- Fix `vedo/interactor_modes.mouse_left_move()` by @MiticoDan
-- Added `applications.AnimationPlayer` class by @mikaeltulldahl
-- fix convex hull in 2D by @ManuGraiph
 
 
 -------------------------
 ## New/Revised Examples
 ```
-examples/basic/sliders_range.py
-examples/basic/interaction_modes.py
-examples/advanced/timer_callback3.py
-examples/advanced/warp6.py
-examples/pyplot/histo_1d_e.py
-examples/other/tensor_grid2.py
-examples/simulations/airplane1.py
-examples/simulations/lorenz.py
-examples/simulations/gas.py
-examples/simulations/aspring2_player.py
 ```
 
 ### Broken Examples

diff --git a/examples/notebooks/align1.ipynb b/examples/notebooks/align1.ipynb
diff --git a/examples/notebooks/slider2d.ipynb b/examples/notebooks/slider2d.ipynb
@@ -9,7 +9,7 @@
  {
  "data": {
  "application/vnd.jupyter.widget-view+json": {
- "model_id": "716726825db64bcaa5bafc8cc7e1724b",
+ "model_id": "e9c49f3446564b878da7b61202e6ecaf",
  "version_major": 2,
  "version_minor": 0
  },
@@ -23,7 +23,7 @@
  {
  "data": {
  "application/vnd.jupyter.widget-view+json": {
- "model_id": "1f0d759367104490968f688f3fba6fe2",
+ "model_id": "cae768630c2547f68a5ed31f5717b44c",
  "version_major": 2,
  "version_minor": 0
  },
@@ -37,7 +37,7 @@
  {
  "data": {
  "application/vnd.jupyter.widget-view+json": {
- "model_id": "05ec1be35400418582e8e22aff3ba330",
+ "model_id": "ea344652cf2247369609f6b6ad98de33",
  "version_major": 2,
  "version_minor": 0
  },

diff --git a/vedo/applications.py b/vedo/applications.py
@@ -763,6 +763,9 @@ def __init__(
  """
  Plotter.__init__(self, axes=axes, **kwargs)
 
+ if isinstance(objects, str):
+ objects = vedo.file_io.load(objects)
+
  self += objects
 
  self.slider = None

diff --git a/vedo/base.py b/vedo/base.py
@@ -2042,6 +2042,10 @@ def color(self, col, alpha=None, vmin=None, vmax=None):
  force the max of the scalar range to be this value
  """
  # supersedes method in Points, Mesh
+
+ if col is None:
+ return self
+
  if vmin is None:
  vmin, _ = self._data.GetScalarRange()
  if vmax is None:

diff --git a/vedo/cli.py b/vedo/cli.py
@@ -118,7 +118,7 @@ def get_parser():
  pr.add_argument("-bg2", "--background-grad", help="use background color gradient", default='', metavar='')
  pr.add_argument("-z", "--zoom", type=float, help="zooming factor", default=1, metavar='')
  pr.add_argument("-n", "--multirenderer-mode", help="multi renderer mode: files go to separate renderers", action="store_true")
- pr.add_argument("-s", "--scrolling-mode", help="scrolling Mode: use slider to scroll files", action="store_true")
+ pr.add_argument("-s", "--sequence-mode",  help="sequence mode: use slider to browse files", action="store_true")
  pr.add_argument("-g", "--ray-cast-mode", help="GPU Ray-casting Mode for 3D image files", action="store_true")
  pr.add_argument("-gx", "--x-spacing", type=float, help="volume x-spacing factor [1]", default=1, metavar='')
  pr.add_argument("-gy", "--y-spacing", type=float, help="volume y-spacing factor [1]", default=1, metavar='')
@@ -683,7 +683,7 @@ def draw_scene(args):
  applications.Browser(frames).show(bg=args.background, bg2=args.background_grad)
  return ##########################################################
 
- if args.scrolling_mode:
+ if args.sequence_mode:
  args.multirenderer_mode = False
  settings.default_font = args.font
 
@@ -832,7 +832,7 @@ def draw_scene(args):
 
  ########################################################################
  # NORMAL mode for single or multiple files, or multiren mode, or numpy scene
- elif nfiles == 1 or (not args.scrolling_mode):
+ elif nfiles == 1 or (not args.sequence_mode):
  # print('DEBUG NORMAL mode for single or multiple files, or multiren mode')
 
  interactor_mode = 0
@@ -918,7 +918,7 @@ def draw_scene(args):
  return
 
  ########################################################################
- # scrolling mode -s
+ # sequence mode -s
  else:
  # print("DEBUG simple browser mode -s")
  if plt.axes == 4:

diff --git a/vedo/file_io.py b/vedo/file_io.py
@@ -209,7 +209,8 @@ def load(inputobj, unpack=True, force=False):
  elif isinstance(inputobj, str) and inputobj.startswith("https://"):
  flist = [inputobj]
  else:
- flist = sorted(glob.glob(inputobj))
+ # flist = sorted(glob.glob(inputobj))
+ flist = utils.humansort(glob.glob(inputobj))
 
  for fod in flist:
 

diff --git a/vedo/plotter.py b/vedo/plotter.py
@@ -3894,7 +3894,8 @@ def _keypress(self, iren, event):
  except:
  pass
  self.axes_instances[clickedr] = None
- addons.add_global_axes(axtype=asso[key], c=None)
+ bounds = renderer.ComputeVisiblePropBounds()
+ addons.add_global_axes(axtype=asso[key], c=None, bounds=bounds)
  self.interactor.Render()
 
  if key == "O":

diff --git a/vedo/version.py b/vedo/version.py
@@ -1 +1 @@
-_version = '2023.4.5'
+_version = '2023.4.5+dev1'
diff --git a/vedo/volume.py b/vedo/volume.py
@@ -432,7 +432,7 @@ def pad(self, voxels=10, value=0):
  
  Example:
  ```python
- from vedo import Volume, dataurl
+ from vedo import Volume, dataurl, show
  iso = Volume(dataurl+'embryo.tif').isosurface()
  vol = iso.binarize(spacing=(100, 100, 100)).pad(10)
  vol.dilate([15,15,15])