Startup

config/variables.properties

@@ -1,2 +1,2 @@
-#Tue Dec 10 12:46:16 CET 2019
-FileSequentialNumber=232
+#Wed Dec 11 15:53:53 CET 2019
+FileSequentialNumber=235

script/scitest/external_test.py

@@ -0,0 +1,184 @@
+###
+# Copyright 2013 Diamond Light Source Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+###
+
+"""
+Test random class
+import unittest
+unittest.TestProgram(argv=["external_test"])
+"""
+import unittest
+
+from scisoftpy.external import save_args, load_args, pyenv
+import scisoftpy as dnp
+
+import shutil
+
+
+class Test(unittest.TestCase):
+    from os import path
+
+    epath_list = [path.dirname(__file__)]
+
+    def checkArgs(self, arg):
+        d = save_args(arg)
+        a = load_args(d)
+        shutil.rmtree(d)
+        self.assertTrue(self.equals(arg, a), "%s != %s" % (arg, a))
+
+    def equals(self, a, b):
+        if type(a) != type(b):
+            return False
+        if isinstance(a, dict):
+            if a.keys() != b.keys():
+                return False
+            for k in a:
+                if not self.equals(a[k], b[k]):
+                    return False
+        elif isinstance(a, (list, tuple)):
+            if len(a) != len(b):
+                return False
+            for ia, ib in zip(a, b):
+                if not self.equals(ia, ib):
+                    return False
+        elif isinstance(a, dnp.ndarray):
+            return dnp.all(a == b)
+        else:
+            return a == b
+        return True
+
+    def testSaveArgs(self):
+        self.checkArgs(None)
+        self.checkArgs(([None, None], [None]))
+        self.checkArgs(([None, 1, 1.5], [None]))
+        self.checkArgs(([None, 1, 1.5], (None,)))
+        self.checkArgs(([None, 1, 1.5], dnp.arange(12)))
+        self.checkArgs(([None, 1, 1.5], {"blah": dnp.arange(12), "foo": dnp.ones((3, 4)), "boo": -2.345}))
+
+    def testSubprocess(self):
+        import subprocess as sub
+
+        pyexe, pypath, _pyldpath = pyenv()
+        import os
+
+        env = dict(os.environ)
+        env["PYTHONPATH"] = ":".join(pypath)
+        from pprint import pprint
+
+        pprint(pypath)
+        #        p = sub.Popen('echo $PYTHONPATH', shell=True, env=_env, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
+        #        print p.communicate()
+        p = sub.Popen([pyexe], env=env, shell=False, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
+        p.stdin.write('print "Hello World"\n')
+        p.stdin.write('print "Hello World2"\n')
+        p.stdin.close()
+        l = p.stdout.read()
+        print l
+
+    def testDLSmodule(self):
+        print dnp.external.get_dls_module()
+
+    def testPythonInstallation(self):
+        print dnp.external.get_python()
+
+    def testExternal(self):
+        from external_functions import fun, funadd, fundec  # , funexception
+
+        a = fun()
+        efun = dnp.external.create_function(fun, dls_module=True)
+        print a, self.equals(efun(), a)
+        efun = dnp.external.create_function("fun", "external_functions", dls_module=True)
+        print a, self.equals(efun(), a)
+
+        a = funadd(dnp.arange(3.0), 1.5)
+        efun = dnp.external.create_function(funadd, dls_module=True)
+        print a, self.equals(efun(dnp.arange(3.0), 1.5), a)
+        efun = dnp.external.create_function("funadd", "external_functions", dls_module=True)
+        print a, self.equals(efun(dnp.arange(3.0), 1.5), a)
+
+        a = fundec(dnp.arange(3.0))
+        efun = dnp.external.create_function(fundec, dls_module=True)
+        print a, self.equals(efun(dnp.arange(3.0)), a)
+        efun = dnp.external.create_function("fundec", "external_functions", dls_module=True)
+        print a, self.equals(efun(dnp.arange(3.0)), a)
+
+        a = fundec(dnp.arange(3.0), b=2.5)
+        efun = dnp.external.create_function(fundec, dls_module=True)
+        print a, self.equals(efun(dnp.arange(3.0), b=2.5), a)
+        efun = dnp.external.create_function("fundec", "external_functions", dls_module=True)
+        print a, self.equals(efun(dnp.arange(3.0), b=2.5), a)
+
+    def testException(self):
+        #        from external_functions import funexception
+        #        funexception()
+        efunexception = dnp.external.create_function(
+            "funexception", "external_functions", extra_path=Test.epath_list, dls_module=True
+        )
+        self.assertRaises(ValueError, efunexception)
+
+    #        efunexception()
+
+    def testSciPy(self):
+        efun = dnp.external.create_function(
+            "funscipy", "external_functions", extra_path=Test.epath_list, dls_module="scipy/0.10.0"
+        )
+        print "0.10.0",
+        self.assertEquals(efun(), "0.10.0")
+        print "passed"
+
+    def testArrayScalar(self):
+        efun = dnp.external.create_function(
+            "funarrayscalar", "external_functions", extra_path=Test.epath_list, dls_module=True
+        )
+        a = 2 + 3j, 1.0, 123, True
+        print a,
+        self.assertEquals(efun(), a)
+        print "passed"
+
+    def testSpeed(self):
+        efun = dnp.external.create_function(
+            "fun", "external_functions", extra_path=Test.epath_list, dls_module=True, keep=False
+        )
+        import time
+
+        t = time.clock()
+        for _i in xrange(10):
+            efun()
+        print time.clock() - t
+        efun = dnp.external.create_function(
+            "fun", "external_functions", extra_path=Test.epath_list, dls_module=True, keep=True
+        )
+        t = time.clock()
+        for _i in xrange(10):
+            efun()
+        print time.clock() - t
+
+    def testHello(self):
+        py = dnp.external.PythonSubProcess("python", None)
+        print py.communicate('print "Hello World!"\n')
+        print py.communicate('print "Hello World2!"\n')
+        print py.communicate("for i in range(4): print i\n")
+        py.stop()
+
+
+def suite():
+    suite = unittest.TestSuite()
+    suite.addTest(unittest.TestLoader().loadTestsFromTestCase(Test))
+    return suite
+
+
+if __name__ == "__main__":
+    __import__("__main__").Test = Test
+    unittest.TextTestRunner(verbosity=2).run(suite())

script/scitest/io_test.py

@@ -0,0 +1,176 @@
+###
+# Copyright 2011 Diamond Light Source Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+###
+
+"""
+Test random class
+import unittest
+unittest.TestProgram(argv=["io_test"])
+"""
+import unittest
+
+import scisoftpy as dnp
+
+TestFolder = "../../../uk.ac.diamond.scisoft.analysis/testfiles/images/"
+IOTestFolder = TestFolder + "../gda/analysis/io/"
+OutTestFolder = TestFolder + "../../test-scratch/"
+
+import os
+
+isjava = os.name == "java"
+
+
+class Test(unittest.TestCase):
+    def load(self, name, testfolder=TestFolder):
+        path = testfolder + name
+        im = dnp.io.load(path)
+        print type(im[0]), im[0].shape
+        return im
+
+    def colourload(self, name, testfolder=TestFolder):
+        path = testfolder + name
+        im = dnp.io.load(path, ascolour=True)
+        print type(im[0]), im[0].shape
+        return im[0]
+
+    def testLoading(self):
+        import os
+
+        print os.getcwd()
+        self.load("test.png")
+        self.load("testrgb.png")
+
+        self.colourload("test.png")
+        im = self.colourload("testrgb.png")
+        print "slicing RGB: ", type(im[:5, 2])
+
+        self.load("test.jpg")
+        self.load("testlossy85.jpg")
+        self.load("testrgb.jpg")
+        self.load("testrgblossy85.jpg")
+
+        self.colourload("test.jpg")
+        self.colourload("testrgb.jpg")
+        self.colourload("testrgblossy85.jpg")
+
+        self.load("test.tiff")
+        self.load("test-df.tiff")
+        self.load("test-pb.tiff")
+        self.load("testrgb.tiff")
+        self.load("testrgb-df.tiff")
+        self.load("testrgb-lzw.tiff")
+        self.load("testrgb-pb.tiff")
+        try:
+            self.load("test-trunc.tiff")
+        except IOError, e:
+            print "Expected IO error caught:", e
+        except:
+            import sys
+
+            print "Unexpected exception caught", sys.exc_info()
+
+        self.colourload("testrgb.tiff")
+        self.colourload("testrgb-df.tiff")
+        self.colourload("testrgb-lzw.tiff")
+        self.colourload("testrgb-pb.tiff")
+        return True
+
+    def testLoadingSRS(self):
+        dh = self.load("96356.dat", IOTestFolder + "SRSLoaderTest/")
+        print dh.eta
+
+    def testLoadingNXS(self):
+        if isjava:
+            f = IOTestFolder + "NexusLoaderTest/"
+            nm = dnp.io.loadnexus(f + "FeKedge_1_15.nxs")
+            print 'There are %d datasets called "Energy"' % len(nm["Energy"])
+
+    def testLoadingHDF(self):
+        f = IOTestFolder + "NexusLoaderTest/"
+        t = dnp.io.load(f + "FeKedge_1_15.nxs", formats=["hdf5"])
+        self.checkTree(t)
+        t = dnp.io.load(f + "FeKedge_1_15.nxs")
+        self.checkTree(t)
+
+    def checkTree(self, t):
+        print t
+        g = t["entry1/instrument/FFI0"]
+        h = g["/entry1/instrument/FFI0"]
+        self.assertEquals(g, h, "relative and absolute do not match!")
+        ga = g[".."]
+        assert ga is t["entry1/instrument"], "parent is wrong!"
+        assert g["."] is g, "self is wrong!"
+        print t["entry1/instrument/FFI0/../../"]
+        print t["entry1/counterTimer01"].keys()
+        l = t.getnodes("Energy")
+        print "List of energy datasets is:", len(l)
+        assert len(l) is 1, "Number of energy datasets should be 1"
+        d = l[0]
+        print type(d)
+        assert d.shape == (489,), "Wrong shape"
+        dd = d[...]
+        assert dd.shape == (489,), "Wrong shape"
+        print type(d), type(dd)
+
+    def save(self, name, data, testfolder=OutTestFolder):
+        path = testfolder + name
+        dnp.io.save(path, data)
+
+    def testSaving(self):
+        d = dnp.arange(100).reshape(10, 10) % 3
+        self.save("chequered.png", d)
+        im = self.load("chequered.png", testfolder=OutTestFolder)
+        im = self.load("test.png")
+        self.save("grey.png", im)
+        im2 = self.load("grey.png", testfolder=OutTestFolder)
+
+    def testSavingOthers(self):
+        im = self.colourload("testrgb.png")
+        self.save("colour.png", im)
+        im2 = self.colourload("colour.png", testfolder=OutTestFolder)
+
+    def testSavingBits(self):
+        d = dnp.arange(12 * 32).reshape((12, 32))
+        b = dnp.abs(dnp.array(d, dnp.int8))
+        b[b < 0] = 0
+        print b.min(), b.max()
+        dnp.io.save(OutTestFolder + "uint.tiff", d, bits=32, signed=False)
+        dnp.io.save(OutTestFolder + "ushort.tiff", d, bits=16, signed=False)
+        dnp.io.save(OutTestFolder + "ubyte.tiff", b, bits=8, signed=False)
+        dnp.io.save(OutTestFolder + "int.tiff", d, bits=32)
+        dnp.io.save(OutTestFolder + "short.tiff", d, bits=16)
+        dnp.io.save(OutTestFolder + "byte.tiff", dnp.array(d, dnp.int8), bits=8)
+        dnp.io.save(OutTestFolder + "double.tiff", d, bits=33)
+        dnp.io.save(OutTestFolder + "float.tiff", d, bits=33)
+        dnp.io.save(OutTestFolder + "short.png", d, bits=16)
+        dnp.io.save(OutTestFolder + "byte.png", b, bits=8)
+
+    def testB16data(self):
+        d = dnp.io.load(IOTestFolder + "SRSLoaderTest/34146.dat", formats=["srs"])
+        print d.keys()
+        print d.metadata.keys()
+        print d.metadata.values()
+
+    def testNulldata(self):
+        try:
+            d = self.load("null.dat")
+        except Exception, e:
+            print "Expected exception caught:", e
+
+
+if __name__ == "__main__":
+    # import sys;sys.argv = ['', 'Test.testName']
+    __import__("__main__").Test = Test
+    unittest.main()