Conditional 3D Display, useful to get around buggy Mayavi install

pytissueoptics/__main__.py

@@ -5,7 +5,7 @@
 from pytissueoptics import __version__
 from pytissueoptics.examples import loadExamples
 
-ap = argparse.ArgumentParser(prog="python -m pytissueoptics", description="Run PyTissueOptics examples. ")
+ap = argparse.ArgumentParser(prog=f"{sys.executable} -m pytissueoptics", description="Run PyTissueOptics examples. ")
 ap.add_argument("-v", "--version", action="version", version=f"PyTissueOptics {__version__}")
 ap.add_argument("-e", "--examples", required=False, default="all",
                 help="Run specific examples by number, e.g. -e 1,2,3. ")
@@ -26,7 +26,7 @@
 
 if runTests:
     moduleDir = os.path.dirname(__file__)
-    err = os.system(f"python -m unittest discover -s {moduleDir} -p 'test*.py'")
+    err = os.system(f"{sys.executable} -m unittest discover -s {moduleDir} -p 'test*.py'")
     sys.exit(err)
 
 if runExamples == "all":

pytissueoptics/rayscattering/display/utils/__init__.py

@@ -1,2 +1,4 @@
 from .direction import Direction, DEFAULT_X_VIEW_DIRECTIONS, DEFAULT_Y_VIEW_DIRECTIONS, DEFAULT_Z_VIEW_DIRECTIONS
-from .volumeSlicer import VolumeSlicer
+# from .volumeSlicer import VolumeSlicer
+
+__all__ = ["Direction"]

pytissueoptics/rayscattering/display/viewer.py

@@ -2,6 +2,7 @@
 from typing import List, Tuple, Union
 
 import numpy as np
+import os
 
 from pytissueoptics.rayscattering import utils
 from pytissueoptics.rayscattering.energyLogging import EnergyLogger
@@ -93,7 +94,7 @@ def listViews(self):
     def show3D(self, visibility=Visibility.AUTO, viewsVisibility: Union[ViewGroup, List[int]] = ViewGroup.SCENE,
                pointCloudStyle=PointCloudStyle(), viewsSolidLabels: List[str] = None, viewsSurfaceLabels: List[str] = None,
                viewsLogScale: bool = True, viewsColormap: str = "viridis"):
-        if not MAYAVI_AVAILABLE:
+        if not MAYAVI_AVAILABLE or os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '1':
             utils.warn("Package 'mayavi' is not available. Please install it to use 3D visualizations.")
             return
 

pytissueoptics/rayscattering/display/views/view2D.py

@@ -184,7 +184,7 @@ def getImageDataWithDefaultAlignment(self, logScale: bool = True) -> np.ndarray:
         return image
 
     def show(self, logScale: bool = True, colormap: str = 'viridis'):
-        cmap = copy.copy(matplotlib.cm.get_cmap(colormap))
+        cmap = copy.copy(matplotlib.colormaps.get_cmap(colormap))
         cmap.set_bad(cmap.colors[0])
 
         image = self.getImageData(logScale=logScale)

pytissueoptics/rayscattering/scatteringScene.py

@@ -1,13 +1,14 @@
 from typing import List
 
 import numpy as np
+import os
 
 from pytissueoptics import Vector
 from pytissueoptics.rayscattering.materials import ScatteringMaterial
-from pytissueoptics.scene import MayaviViewer, Scene
+from pytissueoptics.scene import Scene
 from pytissueoptics.scene.solids import Solid
 from pytissueoptics.scene.viewer.displayable import Displayable
-
+from pytissueoptics.scene import MayaviViewer, MAYAVI_AVAILABLE
 
 class ScatteringScene(Scene):
     def __init__(self, solids: List[Solid], worldMaterial=ScatteringMaterial(), ignoreIntersections: bool = False):
@@ -21,11 +22,14 @@ def add(self, solid: Solid, position: Vector = None):
         super().add(solid, position)
 
     def show(self, source: Displayable = None, opacity=0.8, colormap="cool", **kwargs):
-        viewer = MayaviViewer()
-        self.addToViewer(viewer, opacity=opacity, colormap=colormap, **kwargs)
-        if source:
-            source.addToViewer(viewer)
-        viewer.show()
+        if MAYAVI_AVAILABLE:
+            viewer = MayaviViewer()
+            self.addToViewer(viewer, opacity=opacity, colormap=colormap, **kwargs)
+            if source:
+                source.addToViewer(viewer)
+            viewer.show()
+        else:
+            print("3D viewer unavailable")
 
     def getEstimatedIPP(self, weightThreshold: float) -> float:
         """

pytissueoptics/rayscattering/tests/display/testProfile1D.py

@@ -7,7 +7,7 @@
 import numpy as np
 from matplotlib import pyplot as plt
 
-from pytissueoptics import Direction
+from pytissueoptics.rayscattering.display.utils import Direction
 from pytissueoptics.rayscattering.display.profiles import Profile1D
 from pytissueoptics.rayscattering.tests import SHOW_VISUAL_TESTS
 from pytissueoptics.scene.tests import compareVisuals

pytissueoptics/rayscattering/tests/display/testViewer.py

@@ -1,28 +1,31 @@
 import sys
+import os
 import unittest
 from unittest.mock import patch
 
 import numpy as np
 from mockito import mock, when, verify, ANY
 
-from pytissueoptics import Direction, View2DProjectionX, ViewGroup
-from pytissueoptics.scene.logger import Logger
-from pytissueoptics.scene.geometry import BoundingBox
-from pytissueoptics.rayscattering.energyLogging import EnergyLogger
-from pytissueoptics.rayscattering.scatteringScene import ScatteringScene
-from pytissueoptics.rayscattering.source import Source
-from pytissueoptics.rayscattering.display.viewer import Viewer, Visibility, PointCloudStyle
-from pytissueoptics.rayscattering.display.profiles import ProfileFactory, Profile1D
-from pytissueoptics.rayscattering.display.views import View2D
-from pytissueoptics.rayscattering.energyLogging import PointCloudFactory, PointCloud
+
+if os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '0':
+    from pytissueoptics import Direction, View2DProjectionX, ViewGroup
+    from pytissueoptics.scene.logger import Logger
+    from pytissueoptics.scene.geometry import BoundingBox
+    from pytissueoptics.rayscattering.energyLogging import EnergyLogger
+    from pytissueoptics.rayscattering.scatteringScene import ScatteringScene
+    from pytissueoptics.rayscattering.source import Source
+    from pytissueoptics.rayscattering.display.viewer import Viewer, Visibility, PointCloudStyle
+    from pytissueoptics.rayscattering.display.profiles import ProfileFactory, Profile1D
+    from pytissueoptics.rayscattering.display.views import View2D
+    from pytissueoptics.rayscattering.energyLogging import PointCloudFactory, PointCloud
 
 
 def patchMayaviRender(func):
     for module in ['show', 'gcf', 'figure', 'clf', 'triangular_mesh', 'points3d']:
         func = patch('mayavi.mlab.' + module)(func)
     return func
 
-
+@unittest.skipIf(os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '1','No display available')
 class TestViewer(unittest.TestCase):
     def setUp(self):
         self.scene = mock(ScatteringScene)

pytissueoptics/rayscattering/tests/opencl/src/testCLFresnel.py

@@ -146,7 +146,7 @@ def _getReflectionCoefficient(self, rayDirection: Vector) -> float:
         self.program.launchKernel("getReflectionCoefficientKernel", N=N,
                                   arguments=[np.float32(self.n1), np.float32(self.n2),
                                              np.float32(thetaIn), coefficientBuffer])
-        return float(self.program.getData(coefficientBuffer)[0])
+        return float(self.program.getData(coefficientBuffer)[0][0])
 
     def _getFresnelResult(self, fresnelBuffer) -> FresnelResult:
         fresnelIntersection = self.program.getData(fresnelBuffer)[0]

pytissueoptics/rayscattering/tests/opencl/src/testCLProgram.py

@@ -67,9 +67,6 @@ def test_call_random_value_with_same_seeds_buffer_should_give_same_results(self)
         program.launchKernel(kernelName='fillRandomFloatBuffer', N=nWorkUnits, arguments = [seeds2, valueBuffer2])
 
         # We need to sort because values are not necessarily in order
-        print(sorted(valueBuffer1.hostBuffer))
-        print(sorted(valueBuffer2.hostBuffer))
-
         for value1, value2 in zip(sorted(valueBuffer1.hostBuffer), sorted(valueBuffer2.hostBuffer)) :
             self.assertEqual(value1, value2)
 

pytissueoptics/rayscattering/tests/opencl/src/testGeneralOpenCL.py

@@ -200,7 +200,7 @@ def test001ScalarMultiplicationOfOpenCLArrays(self):
         startTime = time.time()        
         b = a+a
         calcTime = (time.time()-startTime)*1000
-        print("\nOpenCL 1 scalar: {0:.1f} ms ".format(calcTime))
+        # print("\nOpenCL 1 scalar: {0:.1f} ms ".format(calcTime))
 
         a = np.array(object=[0]*(2<<14), dtype=pycl.cltypes.float)
         for i in range(a.size):
@@ -209,7 +209,7 @@ def test001ScalarMultiplicationOfOpenCLArrays(self):
         startTime = time.time()        
         b = a+a
         calcTime = (time.time()-startTime)*1000
-        print("\nnumpy: {0:.1f} ms ".format(calcTime))
+        # print("\nnumpy: {0:.1f} ms ".format(calcTime))
 
         a = clArray(cq=queue, shape=(2<<14,), dtype=pycl.cltypes.float)
         for i in range(a.size):
@@ -218,7 +218,7 @@ def test001ScalarMultiplicationOfOpenCLArrays(self):
         startTime = time.time()        
         b = a+a
         calcTime = (time.time()-startTime)*1000
-        print("\nOpenCL 2 scalar: {0:.1f} ms ".format(calcTime))
+        # print("\nOpenCL 2 scalar: {0:.1f} ms ".format(calcTime))
 
     @unittest.skip("Skipping for now")
     def test002ArraysWithAllocator(self):
@@ -267,7 +267,7 @@ def test002ArraysWithAllocator(self):
         calcTimeOpenCL2 = (time.time()-startTime)*1000
 
         self.assertTrue(calcTimeOpenCL2 < calcTimeNumpy,msg="\nNumpy is faster than OpenCL: CL1 {0:.1f} ms NP {1:.1f} ms CL2 {2:.1f} ms".format(calcTimeOpenCL1, calcTimeNumpy, calcTimeOpenCL2))
-        print("\nCL1 {0:.1f} ms NP {1:.1f} ms".format(calcTimeOpenCL2, calcTimeNumpy))
+        # print("\nCL1 {0:.1f} ms NP {1:.1f} ms".format(calcTimeOpenCL2, calcTimeNumpy))
 
     @unittest.skip("Skipping graphic tests")
     def test003PerformanceVsSize(self):
@@ -382,7 +382,7 @@ def test004_2x2Matrix_and_Vectors(self):
 
         knl(queue, (N,), None, matrix.data, M, vector.data, result.data)
 
-        print("\n{0:0.1f} ms".format((time.time()-startTime)*1000))
+        # print("\n{0:0.1f} ms".format((time.time()-startTime)*1000))
 
 
 class TestOpenCLIds(unittest.TestCase):

pytissueoptics/rayscattering/tests/testScatteringScene.py

@@ -1,13 +1,13 @@
 import math
 import unittest
+import os
 from unittest.mock import patch
 
 from mockito import mock, verify, when
 
 from pytissueoptics.rayscattering.scatteringScene import ScatteringScene
 from pytissueoptics.rayscattering.materials import ScatteringMaterial
 from pytissueoptics.scene.solids import Cuboid
-from pytissueoptics.scene.viewer import MayaviViewer
 
 
 def patchMayaviShow(func):
@@ -27,7 +27,10 @@ def testWhenAddingASolidWithNoScatteringMaterialDefined_shouldRaiseException(sel
         with self.assertRaises(Exception):
             ScatteringScene([Cuboid(1, 1, 1, material="Not a scattering material")])
 
+    @unittest.skipIf(os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '1','No display available')
     def testWhenAddToViewer_shouldAddAllSolidsToViewer(self):
+        from pytissueoptics.scene.viewer import MayaviViewer
+
         scene = ScatteringScene([Cuboid(1, 1, 1, material=ScatteringMaterial())])
         viewer = mock(MayaviViewer)
         when(viewer).add(...).thenReturn()
@@ -36,6 +39,7 @@ def testWhenAddToViewer_shouldAddAllSolidsToViewer(self):
 
         verify(viewer).add(*scene.solids, ...)
 
+    @unittest.skipIf(os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '1','No display available')
     @patchMayaviShow
     def testWhenShow_shouldShowInsideMayaviViewer(self, mockShow, *args):
         scene = ScatteringScene([Cuboid(1, 1, 1, material=ScatteringMaterial())])

pytissueoptics/scene/tests/viewer/testMayaviViewer.py

@@ -5,13 +5,14 @@
 
 import numpy as np
 from matplotlib import pyplot as plt
-
 from pytissueoptics import Logger
 from pytissueoptics.scene.solids import Cuboid, Sphere, Ellipsoid
 from pytissueoptics.scene.scene import Scene
 from pytissueoptics.scene.geometry import Vector
-from pytissueoptics.scene.viewer.mayavi import MayaviViewer, ViewPointStyle
-from pytissueoptics.scene.tests import SHOW_VISUAL_TESTS, compareVisuals
+
+if os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '0':
+    from pytissueoptics.scene.viewer.mayavi import MayaviViewer, ViewPointStyle
+    from pytissueoptics.scene.tests import SHOW_VISUAL_TESTS, compareVisuals
 
 TEST_IMAGES_DIR = os.path.join(os.path.dirname(__file__), 'testImages')
 
@@ -23,7 +24,7 @@ def patchMayaviShow(func):
         func = patch('mayavi.mlab.' + module)(func)
     return func
 
-
+@unittest.skipIf(os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '1','No display available')
 class TestMayaviViewer(unittest.TestCase):
     def setUp(self):
         self.viewer = MayaviViewer()

pytissueoptics/scene/viewer/mayavi/MayaviViewer.py

@@ -1,15 +1,21 @@
 import numpy as np
-
+import os
 from pytissueoptics.scene.geometry import BoundingBox
 from pytissueoptics.scene.logger import Logger
 from pytissueoptics.scene.viewer.mayavi.viewPoint import ViewPointStyle, ViewPointFactory
 
 
 try:
-    from mayavi import mlab
-    MAYAVI_AVAILABLE = True
+    if os.environ.get('PYTISSUE_NO3DDISPLAY','0') == '1':
+        MAYAVI_AVAILABLE = False
+        mlab = None
+    else:
+        from mayavi import mlab
+        MAYAVI_AVAILABLE = True
+
 except ImportError:
     MAYAVI_AVAILABLE = False
+    mlab = None
 
 from pytissueoptics.scene.viewer.mayavi import MayaviSolid
 from pytissueoptics.scene.solids import Solid