setup fixing

marcomusy · Oct 12, 2020 · 8ffdbe6 · 8ffdbe6
1 parent 1447aab
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diff --git a/examples/pyplot/whiskers.py b/examples/pyplot/whiskers.py
@@ -0,0 +1,31 @@
+"""Whisker plot with quantiles indication
+(horizontal line shows the mean value)"""
+from vedo.pyplot import whisker
+from vedo import show, buildAxes
+import numpy as np
+
+# create 5 whisker bars with some random data
+ws = []
+for i in range(5):
+    xval = i*2
+    data = np.random.randn(25) + i/2
+    w = whisker(data, bc=i, s=0.5).x(xval)
+    ws.append(w)
+
+# build custom axes
+ax = buildAxes(xrange=[-1,9],
+               yrange=[-3,5],
+               htitle='\beta_c -expression: change in time',
+               xtitle=' ',
+               ytitle='Level of \beta_c  protein in \muM/l',
+               xValuesAndLabels=[(0,'experiment^A\nat t=1h'),
+                                 (4,'experiment^B\nat t=2h'),
+                                 (8,'experiment^C\nat t=4h'),
+                                ],
+               xLabelSize=0.02,
+               )
+
+show(ws, ax, __doc__)
+# print('whisker0:', ws[0].info)
+
+
diff --git a/setup.py b/setup.py
@@ -11,8 +11,38 @@
 setup(
     name="vedo",
     version=verstr,
-    packages=["vedo", "vedo.examples"],
-    scripts=["bin/vedo", "bin/vedo-convert"],
+    packages=[
+               "vedo",
+               "vedo.examples",
+               "vedo.examples.basic",
+               "vedo.examples.advanced",
+               "vedo.examples.pyplot",
+               "vedo.examples.simulations",
+               "vedo.examples.tetmesh",
+               "vedo.examples.volumetric",
+               "vedo.examples.other.dolfin",
+               "vedo.examples.other.trimesh",
+    ],
+    package_dir={
+                  'vedo': 'vedo',
+                  'vedo.examples': 'examples',
+                  'vedo.examples.basic': 'examples/basic',
+                  'vedo.examples.advanced': 'examples/advanced',
+                  'vedo.examples.pyplot': 'examples/pyplot',
+                  'vedo.examples.simulations': 'examples/simulations',
+                  'vedo.examples.tetmesh': 'examples/tetmesh',
+                  'vedo.examples.volumetric': 'examples/volumetric',
+                  'vedo.examples.other.dolfin': 'examples/other/dolfin',
+                  'vedo.examples.other.trimesh': 'examples/other/trimesh',
+    },
+    scripts=["bin/vedo",
+             "bin/vedo-convert",
+             ],
+    #entry_points={
+    #    'console_scripts': [
+    #        "vedo = bin/vedo:main"
+    #    ]
+    #},
     install_requires=["vtk<9.0.0", "numpy"],
     description="A python module for scientific analysis and visualization of 3D objects and point clouds based on VTK.",
     long_description="A python module for scientific visualization, analysis of 3D objects and point clouds based on VTK. Check out https://vedo.embl.es for documentation.",

diff --git a/vedo/addons.py b/vedo/addons.py
@@ -1189,6 +1189,15 @@ def buildAxes(obj=None,
               axesLineWidth=1,
               gridLineWidth=1,
               reorientShortTitle=True,
+              htitle="",
+              hTitleSize=0.03,
+              hTitleFont=None,
+              hTitleItalic=True,
+              hTitleColor=None,
+              hTitleJustify='bottom-center',
+              hTitleHorizontalOffset=0,
+              hTitleVerticalOffset=0.01,
+              hTitleZOffset=0,
               titleDepth=0,
               titleFont="", # grab settings.defaultFont
               textScale=1.0,
@@ -1252,6 +1261,15 @@ def buildAxes(obj=None,
     - `titleFont`,              [''], font for axes titles
     - `labelFont`,              [''], font for numeric labels
     - `textScale`,             [1.0], global scaling factor for text elements (titles, labels)
+    - `htitle`,                 [''], header title
+    - `hTitleSize`,           [0.03], header title size
+    - `hTitleFont`,           [None], header font (defaults to `titleFont`)
+    - `hTitleItalic`,         [True], header font is italic
+    - `hTitleColor`,          [None], header title color (defaults to `xTitleColor`)
+    - `hTitleJustify`, ['bottom-center'], origin of the title justification
+    - `hTitleHorizontalOffset`,  [0], control vertical positioning of header title
+    - `hTitleVerticalOffset`, [0.01], control horizontal positioning of header title
+    - `hTitleZOffset`,           [0], control positioning of header title along z-axis
     - `xTitlePosition`,       [0.32], title fractional positions along axis
     - `xTitleOffset`,         [0.05], title fractional offset distance from axis line
     - `xTitleJustify`, ["top-right"], title justification
@@ -1319,7 +1337,9 @@ def buildAxes(obj=None,
         else:
             vbb = np.zeros(6)
             ss = np.zeros(3)
-            if xrange is None or yrange is None or zrange is None:
+            if zrange is None:
+                zrange=(0,0)
+            if xrange is None or yrange is None:
                 printc("ERROR in buildAxes(): no mesh given, so must specify ranges.", c='r')
                 raise RuntimeError()
 
@@ -1817,7 +1837,24 @@ def buildAxes(obj=None,
         zt.UseBoundsOff()
         zt.name = "ztitle "+str(ztitle)
         titles.append(zt)
-    ###################################################
+
+    ################################################### header title
+    if htitle:
+        if hTitleFont is None:
+            hTitleFont = titleFont
+        if hTitleColor is None:
+            hTitleColor = xTitleColor
+        htit = shapes.Text(htitle, s=hTitleSize, font=hTitleFont,
+                           c=hTitleColor, justify=hTitleJustify, depth=titleDepth,
+                           italic=hTitleItalic,
+                           )
+        wpos = [0.5+hTitleHorizontalOffset, 1+hTitleVerticalOffset, hTitleZOffset]
+        htit.SetScale(x_aspect_ratios)
+        htit.pos(wpos)
+        # htit.UseBoundsOff()
+        htit.name = "htitle "+str(htitle)
+        titles.append(htit)
+
 
     acts = titles + lines + labels + grids + grids2 + highlights
     acts += framelines + majorticks + minorticks + cones

diff --git a/vedo/base.py b/vedo/base.py
@@ -12,7 +12,8 @@
     + vedo.docs._defs
 )
 
-__all__ = ['Base3DProp',
+__all__ = [
+           'Base3DProp',
            'BaseActor',
            'BaseGrid',
            "probePoints",
@@ -840,6 +841,14 @@ def selectCellArray(self, name):
         self._mapper.SetScalarModeToUseCellData()
         return self
 
+    def removePointArray(self, name):
+        """Reomve point array from object."""
+        self.inputdata().GetPointData().RemoveArray(name)
+
+    def removeCellArray(self, name):
+        """Reomve cell array from object."""
+        self.inputdata().GetCellData().RemoveArray(name)
+
     def addPointArray(self, input_array, name):
         """
         Add point array and assign it a name.

diff --git a/vedo/docs.py b/vedo/docs.py
@@ -1340,5 +1340,24 @@ def tips():
 #     :width: 350 px
 #     :target: flag_labels.py_
 #     :alt: flag_labels.py
+
+# .. |whiskers.py| replace:: whiskers.py
+# .. _whiskers.py: https://github.com/marcomusy/vedo/tree/master/examples/pyplot/.whiskerspy
+# .. |whiskers| image:: https://user-images.githubusercontent.com/32848391/95772479-170cd000-0cbd-11eb-98c4-20c5ca342cb8.png
+#     :width: 350 px
+#     :target: whiskers.py_
+#     :alt: whiskers.py
+
 # """
 
+######################################################################## template
+# .. |.py| replace:: .py
+# .. _.py: https://github.com/marcomusy/vedo/tree/master/examples/pyplot/.py
+# .. || image::
+#     :width: 350 px
+#     :target: .py_
+#     :alt: .py
+########################################################################
+
+
+
diff --git a/vedo/examples b/vedo/examples
diff --git a/vedo/io.py b/vedo/io.py
@@ -1580,7 +1580,7 @@ def screenshot(filename="screenshot.png", scale=None, returnNumpy=False):
     """
     if not settings.plotter_instance or not settings.plotter_instance.window:
         colors.printc('\bomb screenshot(): Rendering window is not present, skip.', c='r')
-        return
+        return settings.plotter_instance
 
     if filename.endswith('.pdf'):
         writer = vtk.vtkGL2PSExporter()
@@ -1591,7 +1591,7 @@ def screenshot(filename="screenshot.png", scale=None, returnNumpy=False):
         writer.SetFileFormatToPDF()
         writer.SetFilePrefix(filename.replace('.pdf',''))
         writer.Write()
-        return filename ##########
+        return settings.plotter_instance ##########
     elif filename.endswith('.svg'):
         writer = vtk.vtkGL2PSExporter()
         writer.SetRenderWindow(settings.plotter_instance.window)
@@ -1601,7 +1601,7 @@ def screenshot(filename="screenshot.png", scale=None, returnNumpy=False):
         writer.SetFileFormatToSVG()
         writer.SetFilePrefix(filename.replace('.svg',''))
         writer.Write()
-        return filename ##########
+        return settings.plotter_instance ##########
     elif filename.endswith('.eps'):
         writer = vtk.vtkGL2PSExporter()
         writer.SetRenderWindow(settings.plotter_instance.window)
@@ -1611,7 +1611,7 @@ def screenshot(filename="screenshot.png", scale=None, returnNumpy=False):
         writer.SetFileFormatToEPS()
         writer.SetFilePrefix(filename.replace('.eps',''))
         writer.Write()
-        return filename ##########
+        return settings.plotter_instance ##########
 
     if scale is None:
         scale = settings.screeshotScale
@@ -1654,7 +1654,7 @@ def screenshot(filename="screenshot.png", scale=None, returnNumpy=False):
         writer.SetFileName(filename+'.png')
         writer.SetInputData(w2if.GetOutput())
         writer.Write()
-    return filename
+    return settings.plotter_instance
 
 
 class Video:

diff --git a/vedo/plotter.py b/vedo/plotter.py
@@ -2024,10 +2024,14 @@ def close(self):
         # settings.collectable_actors = []
         settings.plotter_instance = None
 
-    def screenshot(self, filename='screenshot.png'):
-        """Take a screenshot of the Plotter window."""
-        vedo.io.screenshot(filename)
-        return self
+    def screenshot(self, filename='screenshot.png', scale=None, returnNumpy=False):
+        """Take a screenshot of the Plotter window.
+
+        :param int scale: set image magnification
+        :param bool returnNumpy: return a numpy array of the image
+        """
+        retval = vedo.io.screenshot(filename, scale, returnNumpy)
+        return retval
 
     def export(self, filename='scene.npz'):
         """Export scene to file to HTML, X3D or Numpy file."""

diff --git a/vedo/pyplot.py b/vedo/pyplot.py
@@ -2068,6 +2068,63 @@ def violin(
     return asse
 
 
+def whisker(data,
+            s=0.25,
+            c='k',
+            lw=2,
+            bc='blue',
+            alpha=0.25,
+            r=3,
+            jitter=True,
+            horizontal=False,
+):
+    """
+    Generate a "whisker" bar from a 1-dimensional dataset.
+
+    :param float s: size of the box
+    :param c: color of the lines
+    :param float lw: line width
+    :param bc: color of the box
+    :param float alpha: transparency of the box
+    :param float r: point radius in pixels (use value 0 to disable)
+    :param bool jitter: add some randomness to points to avoid overlap
+    :param bool horizontal: set horizontal layout
+
+    |whiskers| |whiskers.py|_
+    """
+    xvals = np.zeros_like(data)
+    if jitter:
+        xjit = np.random.randn(len(xvals))*s/9
+        xjit = np.clip(xjit, -s/2.1, s/2.1)
+        xvals += xjit
+
+    dmean = np.mean(data)
+    dq05 = np.quantile(data, 0.05)
+    dq25 = np.quantile(data, 0.25)
+    dq75 = np.quantile(data, 0.75)
+    dq95 = np.quantile(data, 0.95)
+
+    pts = None
+    if r: pts = shapes.Points([xvals, data], c=c, r=r)
+
+    rec = shapes.Rectangle([-s/2, dq25],[s/2, dq75], c=bc, alpha=alpha)
+    rl = shapes.Line([[-s/2, dq25],[s/2, dq25],[s/2, dq75],[-s/2, dq75]], closed=True)
+    l1 = shapes.Line([0,dq05,0], [0,dq25,0], c=c, lw=lw)
+    l2 = shapes.Line([0,dq75,0], [0,dq95,0], c=c, lw=lw)
+    lm = shapes.Line([-s/2, dmean], [s/2, dmean])
+    lns = merge(l1,l2,lm,rl)
+    asse = Assembly([lns, rec, pts])
+    if horizontal:
+        asse.rotateZ(-90)
+    asse.name = "Whisker"
+    asse.info['mean'] = dmean
+    asse.info['quantile_05'] = dq05
+    asse.info['quantile_25'] = dq25
+    asse.info['quantile_75'] = dq75
+    asse.info['quantile_95'] = dq95
+    return asse
+
+
 def streamplot(X, Y, U, V, direction="both",
                maxPropagation=None, mode=1, lw=0.001, c=None, probes=()):
     """