attempt to move coverage from unittest to pytest

.coveragerc

@@ -19,10 +19,11 @@ omit =
      */_*
      */plotting/*
      *optionsParser.py
-     *viewer*
-     *Viewer*
+     */visual/*
 
-source = spam
+source =
+     spam
+#concurrency = multiprocessing
 
 [html]
 directory = coverage

.gitlab-ci.yml

@@ -38,7 +38,7 @@ pages:
     - python setup.py build_sphinx
     - mkdir public
     - mv build/sphinx/html/* public
-    - coverage run setup.py test
+    - coverage run -m pytest
     - coverage report
     - coverage html
     - mv coverage public

setup.py

@@ -10,10 +10,9 @@ TTK_modules. C/C++ code must be in the src directory of the package.
 
 *swig*
 If you use swig numpy.i, please symlink it from tools/swig directory.
-
 """
 
-from setuptools import setup
+from setuptools import setup, Command
 from distutils.extension import Extension
 import os
 import sys
@@ -79,6 +78,22 @@ class get_pybind_include(object):
         import pybind11
         return pybind11.get_include(self.user)
 
+# This is what is suggested in https://docs.pytest.org/en/2.7.3/goodpractises.html
+class PyTest(Command):
+    user_options = []
+    def initialize_options(self):
+        pass
+
+    def finalize_options(self):
+        pass
+
+    def run(self):
+        import subprocess
+        import sys
+        errno = subprocess.call(['pytest'])
+        raise SystemExit(errno)
+
+
 
 name = 'spam'
 description = 'Software for the Practical Analysis of Materials'
@@ -195,6 +210,7 @@ class Build_ext(_build_ext):
 
 cmdclass = {'install': Install,
             'build_ext': Build_ext,
+            'test': PyTest,
             }
 
 try:
@@ -261,7 +277,7 @@ metadata = dict(
                         'version': ('setup.py', version),
                         'release': ('setup.py', version),
                         'copyright': ('setup.py', copyright)}},
-                test_suite="tests",
+                #test_suite="tests",
                 data_files=[('share/img', ['docs/source/images/icon.png', 'docs/source/images/logo.png'])]
                 )
 

tools/label/label.py

@@ -381,37 +381,6 @@ def makeLabelsSequential(lab):
     return lab
 
 
-def _checkSlice(topOfSlice, botOfSlice, topLimit, botLimit):
-    # Do we have any negative positions? Set all negative numbers to zero and see if there was any difference
-    topOfSliceLimited = topOfSlice.copy()
-    if topOfSliceLimited[0] < topLimit[0]:
-       topOfSliceLimited[0] = topLimit[0]
-    if topOfSliceLimited[1] < topLimit[1]:
-       topOfSliceLimited[1] = topLimit[1]
-    if topOfSliceLimited[2] < topLimit[2]:
-       topOfSliceLimited[2] = topLimit[2]
-    topOfSliceOffset = topOfSliceLimited - topOfSlice
-
-    botOfSliceLimited = botOfSlice.copy()
-    if botOfSliceLimited[0] > botLimit[0]:
-       botOfSliceLimited[0] = botLimit[0]
-    if botOfSliceLimited[1] > botLimit[1]:
-       botOfSliceLimited[1] = botLimit[1]
-    if botOfSliceLimited[2] > botLimit[2]:
-       botOfSliceLimited[2] = botLimit[2]
-    botOfSliceOffset = botOfSliceLimited - botOfSlice
-
-    returnSliceLimited = (slice(int(topOfSliceLimited[0]), int(botOfSliceLimited[0])),
-                          slice(int(topOfSliceLimited[1]), int(botOfSliceLimited[1])),
-                          slice(int(topOfSliceLimited[2]), int(botOfSliceLimited[2])))
-
-    returnSliceOffset = (slice(int(topOfSliceOffset[0]), int(topOfSliceOffset[0] + botOfSliceLimited[0] - topOfSliceLimited[0])),
-                         slice(int(topOfSliceOffset[1]), int(topOfSliceOffset[1] + botOfSliceLimited[1] - topOfSliceLimited[1])),
-                         slice(int(topOfSliceOffset[2]), int(topOfSliceOffset[2] + botOfSliceLimited[2] - topOfSliceLimited[2])))
-
-    return returnSliceLimited, returnSliceOffset
-
-
 def getLabel(labelledVolume, label, boundingBoxes=None, centresOfMass=None, margin=0, extractCube=False, extractCubeSize=None, maskOtherLabels=True, labelDilate=0, labelDilateMaskOtherLabels=False):
     """
     Helper function to extract labels from a labelled image/volume.

tools/tests/test_ITKwatershed.py

+# -*- coding: utf-8 -*-
+
+import unittest
+import os
+import tifffile
+import numpy
+
+import spam.label
+import spam.kalisphera
+
+VERBOSE = True
+
+
+
+
+class TestFunctionITKWatershed(unittest.TestCase):
+
+    # def tearDown(self):
+    #     try:
+    #         pass
+    #     except OSError:
+    #         pass
+
+    def test_ITKwatershed(self):
+        # First try without markers
+        im = numpy.zeros([50, 50, 50], dtype='<f8')
+
+        # Generate and binarise two touching balls on the z-plane
+        centres = [[25, 25, 15], [25, 25, 35]]
+        radii = [10, 10]
+        spam.kalisphera.makeSphere(im, centres, radii)
+        # Threshold at 0.5
+        im[im > 0.5]  = 1.0
+        im[im <= 0.5] = 0.0
+        # Watershed
+        lab = spam.label.watershed(im)
+        self.assertEqual(lab.max(), 2)
+        equivRadii = spam.label.equivalentRadii(lab)
+        self.assertAlmostEqual(equivRadii[1], radii[0], places=1)
+        self.assertAlmostEqual(equivRadii[2], radii[1], places=1)
+
+        # Let's compute markers
+        m1 = numpy.zeros([50, 50, 50], dtype='<f8')
+        m2 = numpy.zeros([50, 50, 50], dtype='<f8')
+
+        # Generate and binarise two small internal balls
+        spam.kalisphera.makeSphere(m1, [25, 25, 15], 3)
+        spam.kalisphera.makeSphere(m2, [25, 25, 35], 3)
+        # Threshold at 0.5
+        m1[m1 > 0.5]  = 1.0
+        m1[m1 <= 0.5] = 0.0
+        m2[m2 > 0.5]  = 2.0
+        m2[m2 <= 0.5] = 0.0
+        markers = m1 + m2
+
+        # Watershed with markers
+        lab = spam.label.watershed(im, markers=markers)
+        self.assertEqual(lab.max(), 2)
+        equivRadii = spam.label.equivalentRadii(lab)
+        self.assertAlmostEqual(equivRadii[1], radii[0], places=1)
+        self.assertAlmostEqual(equivRadii[2], radii[1], places=1)
+
+if __name__ == '__main__':
+    unittest.main()

tests/test_label.py → tools/tests/test_label.py

@@ -501,53 +501,53 @@ class TestFunctionLabel(unittest.TestCase):
         res = spam.label.label.Spheroid(10, 20, dim = 3).digitize()
         self.assertIsNotNone(res)
 
-    #def test_FixUnderSegmentation(self):
-        #Generate two prolate grains (rice-like)
-        #grain1 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
-        #grain2 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
-        #Create the bigger  labelled image
-        #grainIm = numpy.concatenate((grain1,grain2))
-        #grainIm = numpy.zeros(grainIm.shape)
-        #Add the grains to the bigger image
-        #grainIm[:grain1.shape[0]-1,:,:] = grain1[:grain1.shape[0]-1,:,:]
-        #grainIm[grain2.shape[0]-5:-5,:,:] =  grainIm[grain2.shape[0]-5:-5,:,:] + grain1[:,:,:]
-        #Set all the labels to 1
-        #grainIm = numpy.where(grainIm >= 1, 3, grainIm)
-        #Pad a border
-        #grainIm = numpy.pad(grainIm, pad_width=10, mode='constant', constant_values = 0)
-        #Create the 'greyScale' image
-        #greyIm = numpy.where(grainIm == 3, 30000, 10000)
-
-        #Check that the greyscale image is normalized
-        #res1 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.5, 20*0.5)
-        #self.assertEqual(res1, None)
-        #Check that a or c is valid
-        #res2 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], numpy.nan, numpy.nan)
-        #self.assertEqual(res2, None)
-        #Check that a or c are positive
-        #res3 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], -1, 10)
-        #self.assertEqual(res3, None)
-
-        #Run fixUnderSegmentation
-        #greyIm = numpy.where(grainIm == 3, 0.75, 0.25)
-        #res4 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
-        #Check that there are two grains
-        #self.assertEqual(numpy.max(numpy.unique(res4)), 2)
-        #Check that it runs even if the label does not exist
-        #res5 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
-        #self.assertIsNotNone(res5)
-        #Check for a vect that is not a list
-        #res6 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = (0,1,0))
-        #self.assertIsNone(res6)
-        #Check that it works without the input vect
-        #res7 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1)
-        #self.assertIsNotNone(res7)
-        #Check that it works with verbose = True
-        #res8 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1, verbose = True)
-        #self.assertIsNotNone(res8)
-        #Check that it works even for a non-existing label
-        #res9 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [5], 10*0.8, 20*0.8, numVect = 1)
-        #self.assertIsNotNone(res9)
+    def _test_FixUnderSegmentation(self):
+        # Generate two prolate grains (rice-like)
+        grain1 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
+        grain2 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
+        # Create the bigger  labelled image
+        grainIm = numpy.concatenate((grain1,grain2))
+        grainIm = numpy.zeros(grainIm.shape)
+        # Add the grains to the bigger image
+        grainIm[:grain1.shape[0]-1,:,:] = grain1[:grain1.shape[0]-1,:,:]
+        grainIm[grain2.shape[0]-5:-5,:,:] =  grainIm[grain2.shape[0]-5:-5,:,:] + grain1[:,:,:]
+        # Set all the labels to 1
+        grainIm = numpy.where(grainIm >= 1, 3, grainIm)
+        # Pad a border
+        grainIm = numpy.pad(grainIm, pad_width=10, mode='constant', constant_values = 0)
+        # Create the 'greyScale' image
+        greyIm = numpy.where(grainIm == 3, 30000, 10000)
+
+        # Check that the greyscale image is normalized
+        res1 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.5, 20*0.5)
+        self.assertEqual(res1, None)
+        # Check that a or c is valid
+        res2 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], numpy.nan, numpy.nan)
+        self.assertEqual(res2, None)
+        # Check that a or c are positive
+        res3 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], -1, 10)
+        self.assertEqual(res3, None)
+
+        # Run fixUnderSegmentation
+        greyIm = numpy.where(grainIm == 3, 0.75, 0.25)
+        res4 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
+        # Check that there are two grains
+        self.assertEqual(numpy.max(numpy.unique(res4)), 2)
+        # Check that it runs even if the label does not exist
+        res5 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
+        self.assertIsNotNone(res5)
+        # Check for a vect that is not a list
+        res6 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = (0,1,0))
+        self.assertIsNone(res6)
+        # Check that it works without the input vect
+        res7 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1)
+        self.assertIsNotNone(res7)
+        # Check that it works with verbose = True
+        res8 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1, verbose = True)
+        self.assertIsNotNone(res8)
+        # Check that it works even for a non-existing label
+        res9 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [5], 10*0.8, 20*0.8, numVect = 1)
+        self.assertIsNotNone(res9)
         
 
     def test_contactOrientations(self):
@@ -709,32 +709,6 @@ class TestFunctionLabel(unittest.TestCase):
         imLab2 = spam.label.moveLabels(imLab, PhiField, boundingBoxes = boundingBoxes, centresOfMass = centresOfMass)
         self.assertIsNotNone(imLab2)
         
-        # Test 7 -> Check that it runs for more than one grain....
-        # Create two grains
-        grain1 = spam.label.label.Spheroid(15, 15, numpy.asarray([0,1,0])).digitize()
-        grain1 = numpy.pad(grain1, (5), 'constant', constant_values=(0))
-        grain1 = numpy.where(grain1, 1, 0)
-        grain2 = spam.label.label.Spheroid(15, 15, numpy.asarray([0,1,0])).digitize()
-        grain2 = numpy.pad(grain2, (5), 'constant', constant_values=(0))
-        grain2 = numpy.where(grain2, 2, 0)
-        grainIm = numpy.concatenate((grain1,grain2))
-        grainIm = numpy.zeros(grainIm.shape)
-        grainIm[:grain1.shape[0]-1,:,:] = grain1[:grain1.shape[0]-1,:,:]
-        grainIm[grain2.shape[0]-5:-5,:,:] =  grainIm[grain2.shape[0]-5:-5,:,:] + grain2[:,:,:]
-        grainIm = grainIm.astype(int)
-        # Create empty PhiField
-        PhiField = numpy.zeros((3, 4, 4))
-        # Compute initial volume & COM
-        COM = spam.label.centresOfMass(grainIm)
-        iniVol = spam.label.volumes(grainIm)
-        # Apply a displacement
-        transformation = {'t': [1, 1, 1]}
-        PhiField[1] = spam.deformation.computePhi(transformation)
-        transformation = {'t': [-1, -1, -1]}
-        PhiField[2] = spam.deformation.computePhi(transformation)
-        imLab2 = spam.label.moveLabels(grainIm, PhiField)
-        self.assertIsNotNone(imLab2)
-        
     def test_erodeLabels(self):
         # Create the sphere
         imLab = skimage.morphology.ball(20)