diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b36ed0ed4d8aea5a7410f1ad31c016165cc53b34..fea2f94bf7e2b83cb587da6b86de3c7b5f2a604e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,8 +1,2 @@
-unittests:
- script: python -m unittest discover tests -v
-core doctests:
- script: python -m doctest -v AmpScan/core.py
-registration doctests:
- script: python -m doctest -v AmpScan/registration.py
-align doctests:
- script: python -m doctest -v AmpScan/align.py
\ No newline at end of file
+doctests and unitests:
+ script: pytest --doctest-modules -v --ignore=GUIs
\ No newline at end of file
diff --git a/AmpScan/align.py b/AmpScan/align.py
index 204902336e39c34dd7fb7270c0cdb97bd85f2cf6..6327e4cf3bf76458c5e1c5cbc22c66ba159af299 100644
--- a/AmpScan/align.py
+++ b/AmpScan/align.py
@@ -280,7 +280,7 @@ class align(object):
Examples
--------
- >>> import AmpScan, os
+ >>> import os, AmpScan
>>> staticfh = os.getcwd()+"\\tests\\stl_file.stl"
>>> movingfh = os.getcwd()+"\\tests\\stl_file_2.stl"
>>> static = AmpScan.AmpObject(staticfh)
diff --git a/AmpScan/core.py b/AmpScan/core.py
index 834c775e3994d2f98fd1726364abd121ccf94cde..1e2f836d6cbd6bcf297c5219494511796d43cfe1 100644
--- a/AmpScan/core.py
+++ b/AmpScan/core.py
@@ -6,12 +6,18 @@ Copyright: Joshua Steer 2018, Joshua.Steer@soton.ac.uk
"""
import numpy as np
+import os
import struct
from AmpScan.trim import trimMixin
from AmpScan.smooth import smoothMixin
from AmpScan.analyse import analyseMixin
from AmpScan.ampVis import visMixin
+
+# The file path used in doc examples
+filename = os.getcwd()+"\\tests\\stl_file.stl"
+
+
class AmpObject(trimMixin, smoothMixin, analyseMixin, visMixin):
r"""
Base class for the AmpScan project.
@@ -36,9 +42,6 @@ class AmpObject(trimMixin, smoothMixin, analyseMixin, visMixin):
Examples
-------
- >>> import AmpScan
- >>> import os
- >>> filename = os.getcwd()+"\\tests\\stl_file.stl"
>>> amp = AmpObject(filename)
"""
@@ -151,8 +154,6 @@ class AmpObject(trimMixin, smoothMixin, analyseMixin, visMixin):
Examples
--------
- >>> import os
- >>> filename = os.getcwd()+"\\tests\\stl_file.stl"
>>> amp = AmpObject(filename, unify=False)
>>> amp.vert.shape
(44832, 3)
@@ -349,8 +350,6 @@ class AmpObject(trimMixin, smoothMixin, analyseMixin, visMixin):
Examples
--------
- >>> import os
- >>> filename = os.getcwd()+"\\tests\\stl_file.stl"
>>> amp = AmpObject(filename)
>>> ang = [np.pi/2, -np.pi/4, np.pi/3]
>>> amp.rotateAng(ang, ang='rad')
diff --git a/AmpScan/ssm.py b/AmpScan/ssm.py
index 4cb054114d06f753b486c4110968915fb28a4d80..b1b685bff421635d7fb3bad950edb8287fd34d4a 100644
--- a/AmpScan/ssm.py
+++ b/AmpScan/ssm.py
@@ -19,20 +19,20 @@ class pca(object):
Examples
--------
+ >>> import os
>>> p = pca()
- >>> p.importFolder('/path/')
- >>> p.baseline('dir/baselinefh.stl')
- >>> p.register(save = '/regpath/')
+ >>> p.importFolder(os.getcwd()+"\\tests\\pca_tests")
+ >>> p.setBaseline(os.getcwd()+"\\tests\\pca_tests\\sample_stl_sphere_BIN.stl")
+ >>> p.register(save=os.getcwd()+"\\tests\\pca_tests\\")
>>> p.pca()
- >>> sfs = [0, 0.1, -0.5 ... 0]
+ >>> sfs = [1, 2]
>>> newS = p.newShape(sfs)
"""
-
+
def __init__(self):
self.shapes = []
-
-
+
def setBaseline(self, baseline):
r"""
Function to set the baseline mesh used for registration of the
@@ -45,8 +45,7 @@ class pca(object):
"""
self.baseline = AmpObject(baseline, 'limb')
-
-
+
def importFolder(self, path, unify=True):
r"""
Function to import multiple stl files from folder into the pca object
@@ -64,7 +63,7 @@ class pca(object):
self.shapes = [AmpObject(os.path.join(path, f), 'limb', unify=unify) for f in self.fnames]
for s in self.shapes:
s.lp_smooth(3, brim=True)
-
+
def sliceFiles(self, height):
r"""
Function to run a planar trim on all the training data for the PCA
@@ -78,7 +77,7 @@ class pca(object):
"""
for s in self.shapes:
s.planarTrim(height)
-
+
def register(self, scale=None, save=None, baseline=True):
r"""
Register all the AmpObject training data to the baseline AmpObject
@@ -105,8 +104,7 @@ class pca(object):
self.X = np.array([r.vert.flatten() for r in self.registered]).T
if baseline is True:
self.X = np.c_[self.X, self.baseline.vert.flatten()]
-
-
+
def pca(self):
r"""
Function to run mean centered pca using a singular value decomposition
@@ -118,8 +116,8 @@ class pca(object):
(self.pca_U, self.pca_S, self.pca_V) = np.linalg.svd(X_meanC, full_matrices=False)
self.pc_weights = np.dot(np.diag(self.pca_S), self.pca_V)
self.pc_stdevs = np.std(self.pc_weights, axis=1)
-
- def newShape(self, sfs, scale = 'eigs'):
+
+ def newShape(self, sfs, scale='eigs'):
r"""
Function to calculate a new shape based upon the eigenvalues
or stdevs
@@ -134,11 +132,14 @@ class pca(object):
to standard deviations about the mean
"""
- try: len(sfs) == len(self.pc_stdevs)
- except: ValueError('sfs must be of the same length as the number of '
- 'principal components')
+ sfs = np.array(sfs)
+ if not sfs.shape == self.pc_stdevs.shape:
+ raise ValueError('sfs must be of the same length as the number of '
+ 'principal components (expected {} but found {})'.format(self.pc_stdevs.shape, sfs.shape))
if scale == 'eigs':
sf = (self.pca_U * sfs).sum(axis=1)
elif scale == 'std':
sf = (self.pca_U * self.pc_stdevs * sfs).sum(axis=1)
+ else:
+ raise ValueError("Invalid scale (expected 'eigs' or 'std' but found{}".format(scale))
return self.pca_mean + sf
diff --git a/AmpScan/trim.py b/AmpScan/trim.py
index 7bc61a2d9343cdfae17ee53b7001e7e9ff8f858b..cc0abefc31890c80b451e483bdd026d3d2d0424c 100644
--- a/AmpScan/trim.py
+++ b/AmpScan/trim.py
@@ -6,6 +6,8 @@ Copyright: Joshua Steer 2018, Joshua.Steer@soton.ac.uk
import numpy as np
from numbers import Number
+import os
+
class trimMixin(object):
r"""
@@ -27,7 +29,10 @@ class trimMixin(object):
Examples
--------
- >>> amp = AmpObject(fh)
+
+ >>> from AmpScan import AmpObject
+ >>> filename = os.getcwd()+"\\tests\\stl_file.stl"
+ >>> amp = AmpObject(filename)
>>> amp.planarTrim(100, 2)
"""
@@ -53,4 +58,4 @@ class trimMixin(object):
self.values = self.values[~delv]
self.calcStruct()
else:
- raise TypeError("height arg must be a float")
\ No newline at end of file
+ raise TypeError("height arg must be a float")
diff --git a/tests/sample_stl_sphere_ASCII.stl b/tests/ascii_examples/sample_stl_sphere_ASCII.stl
similarity index 100%
rename from tests/sample_stl_sphere_ASCII.stl
rename to tests/ascii_examples/sample_stl_sphere_ASCII.stl
diff --git a/tests/pca_tests/sample_stl_sphere_BIN.stl b/tests/pca_tests/sample_stl_sphere_BIN.stl
new file mode 100644
index 0000000000000000000000000000000000000000..de40fb579910b12e4b6577fe1a171e6b574de3c5
--- /dev/null
+++ b/tests/pca_tests/sample_stl_sphere_BIN.stl
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1f92d690baf69fd2dc5817c90ee85c5ffb9b36dc627521dc6be136c6c7fd4de6
+size 64084
diff --git a/tests/sample_test_local.py b/tests/sample_test_local.py
deleted file mode 100644
index 7232f18a1677a11f1508d9836f9cdbe3e0c9dbac..0000000000000000000000000000000000000000
--- a/tests/sample_test_local.py
+++ /dev/null
@@ -1,53 +0,0 @@
-import unittest
-import os
-import sys
-
-class TestBasicFunction(unittest.TestCase):
-
- def SetUp(self):
- modPath = os.path.abspath(os.getcwd())
- sys.path.insert(0, modPath)
-
- def test_running(self):
- print("Running sample_test.py")
- self.assertTrue(True)
-
- def test_python_imports(self):
- import numpy, scipy, matplotlib, vtk, AmpScan.core
- s = str(type(numpy))
- self.assertEqual(s, "<class 'module'>")
- s = str(type(scipy))
- self.assertEqual(s, "<class 'module'>")
- s = str(type(matplotlib))
- self.assertEqual(s, "<class 'module'>")
- s = str(type(vtk))
- self.assertEqual(s, "<class 'module'>")
- s = str(type(AmpScan.core))
- self.assertEqual(s, "<class 'module'>", "Failed import: AmpScan.core")
-
- @unittest.expectedFailure
- def test_failure(self):
- s = str(type("string"))
- self.assertEqual(s, "<class 'module'>")
-
- def test_rotate(self):
- stlPath = os.path.abspath(os.getcwd()) + "/sample_stl_sphere_BIN.stl"
- from AmpScan.core import AmpObject
- Amp = AmpObject(stlPath)
- s = str(type(Amp))
- self.assertEqual(s, "<class 'AmpScan.core.AmpObject'>", "Not expected Object")
- with self.assertRaises(TypeError):
- Amp.rotateAng(7)
- Amp.rotateAng({})
-
- def test_trim(self):
- # a new test for the trim module
- stlPath = os.path.abspath(os.getcwd()) + "/sample_stl_sphere_BIN.stl"
- from AmpScan.core import AmpObject
- Amp = AmpObject(stlPath)
- #with self.assertRaises(TypeError):
- #Amp.planarTrim([], plane=[])
-
-
-if __name__ == '__main__':
- unittest.main()