tomwer 0.5.2b3__tar.gz → 0.5.2b4__tar.gz

home/payno/.local/share/virtualenvs/tomwer_venv/bin/tomwer

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+#!/home/payno/.local/share/virtualenvs/tomwer_venv/bin/python
+# EASY-INSTALL-ENTRY-SCRIPT: 'tomwer==0.5.2b4','console_scripts','tomwer'
+__requires__ = 'tomwer==0.5.2b4'
+import re
+import sys
+from pkg_resources import load_entry_point
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
+    sys.exit(
+        load_entry_point('tomwer==0.5.2b4', 'console_scripts', 'tomwer')()
+    )

home/payno/.local/share/virtualenvs/tomwer_venv/lib/python3.7/site-packages/tomwer/app/test/test_process.py

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+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "31/07/2020"
+
+
+import unittest
+from tomwer.test.utils import UtilsTest
+import h5py
+import shutil
+import tempfile
+from tomwer.core.utils.scanutils import MockBlissAcquisition
+from tomwer.core.scan.blissscan import BlissScan
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from pypushflow.representation.scheme.ows_parser import OwsParser
+from tomwer.core.process.reconstruction.nabu import settings as nabu_settings
+from ..process import _exec
+from glob import glob
+import os
+
+
+class TestNxTomoDarkRef(unittest.TestCase):
+    """
+    Test the execution of the following workflow:
+    nxtomomill -> dark and flat field
+    uses:
+
+    - 'nxtomomill_darkref.ows': where dark is not computed and ref is average
+    - 'nxtomomill_darkref_2.ows': where dark is average and ref is median
+    """
+    TIMEOUT = 120
+
+    def setUp(self) -> None:
+        unittest.TestCase.setUp(self)
+        self._data_dir = tempfile.mkdtemp()
+        self._bliss_mock = MockBlissAcquisition(n_sample=1, n_sequence=1,
+                                                n_darks=10, n_flats=10,
+                                                n_scan_per_sequence=2,
+                                                output_dir=self._data_dir)
+        self.master_file = self._bliss_mock.samples[0].sample_file
+        assert os.path.exists(self.master_file)
+        self.bliss_scan = BlissScan(master_file=self.master_file,
+                                    entry='/1.1', proposal_file=None)
+        self.tomwer_file = os.path.join(self._bliss_mock.samples[0].path,
+                                        'tomwer_processes.h5')
+
+    @staticmethod
+    def get_scheme(file_path):
+        return OwsParser.scheme_load(file_path, load_handlers=True)
+
+    def tearDown(self) -> None:
+        if os.path.isdir(self._data_dir):
+            shutil.rmtree(self._data_dir)
+
+    def testProcessing_1(self):
+        self.assertFalse(os.path.exists(self.tomwer_file))
+        scheme_file = UtilsTest.getOrangeExecTestFile('nxtomomill_darkref.ows')
+        self.scheme = self.get_scheme(scheme_file)
+        _exec(scheme=self.scheme, scan=self.bliss_scan, timeout=self.TIMEOUT)
+        self.assertTrue(os.path.exists(self.tomwer_file))
+        with h5py.File(self.tomwer_file, 'r') as h5s:
+            self.assertTrue('entry0000' in h5s)
+            self.assertTrue('entry0000/tomwer_process_0/results/flats' in h5s)
+            self.assertTrue(h5s['entry0000/tomwer_process_0/results/flats/100'].shape, (2560, 2160))
+            self.assertFalse('entry0000/tomwer_process_0/results/darks' in h5s)
+
+    def testProcessing_2(self):
+        self.assertFalse(os.path.exists(self.tomwer_file))
+        scheme_file = UtilsTest.getOrangeExecTestFile('nxtomomill_darkref_2.ows')
+        self.scheme = self.get_scheme(scheme_file)
+        _exec(scheme=self.scheme, scan=self.bliss_scan, timeout=self.TIMEOUT)
+        self.assertTrue(os.path.exists(self.tomwer_file))
+        with h5py.File(self.tomwer_file, 'r') as h5s:
+            self.assertTrue('entry0000' in h5s)
+            self.assertTrue('entry0000/tomwer_process_0/results/flats' in h5s)
+            self.assertTrue(h5s['entry0000/tomwer_process_0/results/flats/100'].shape, (2560, 2160))
+            self.assertTrue('entry0000/tomwer_process_0/results/darks' in h5s)
+            self.assertTrue(h5s['entry0000/tomwer_process_0/results/darks/0'].shape, (2560, 2160))
+
+
+class TestDarkRefAxisNabu(unittest.TestCase):
+    """
+    Test the execution of the following workflow:
+    dark and flat field -> center of rotation -> nabu reconstruction
+    uses:
+
+    - 'darkref_axis_nabu.ows'
+        - dark: average, ref: median
+        - cor: manual at 70
+        - nabu: reconstruct slice 20
+    - 'darkref_axis_nabu_2.ows'
+        - dark: average, ref: median
+        - cor: use accurate (value should be ~79)
+        - nabu: reconstruct middle slice (1080)
+    """
+    TIMEOUT = 120
+
+    def setUp(self) -> None:
+        unittest.TestCase.setUp(self)
+        self._data_dir = tempfile.mkdtemp()
+        self.master_file = os.path.join(self._data_dir,
+                                        'frm_edftomomill_twoentries.nx')
+        self.tomwer_file = os.path.join(self._data_dir,
+                                        'tomwer_processes.h5')
+
+        shutil.copyfile(
+            UtilsTest.getH5Dataset(folderID='frm_edftomomill_twoentries.nx'),
+            self.master_file)
+        self.scan = HDF5TomoScan(scan=self.master_file, entry='entry0000')
+        self._nabu_cfg_folder = os.path.join(self.scan.path, nabu_settings.NABU_CFG_FILE_FOLDER)
+
+    @staticmethod
+    def get_scheme(file_path):
+        return OwsParser.scheme_load(file_path, load_handlers=True)
+
+    def tearDown(self) -> None:
+        if os.path.isdir(self._data_dir):
+            shutil.rmtree(self._data_dir)
+
+    def testProcessing_1(self):
+        self.assertFalse(os.path.exists(self.tomwer_file))
+        self.assertEqual(len(glob(self._nabu_cfg_folder + os.sep + '*.cfg')), 0)
+        scheme_file = UtilsTest.getOrangeExecTestFile('darkref_axis_nabu.ows')
+        self.scheme = self.get_scheme(scheme_file)
+        # monkey patch parameters to use nabu in dry tun mode
+        self.scheme.nodes[2].properties['_rpSetting']['dry_run'] = True
+        _exec(scheme=self.scheme, scan=self.scan, timeout=self.TIMEOUT)
+        self.assertTrue(os.path.exists(self.tomwer_file))
+        with h5py.File(self.tomwer_file, 'r') as h5s:
+            # check darks
+            self.assertTrue('entry0000' in h5s)
+            self.assertTrue('entry0000/tomwer_process_0/results/flats' in h5s)
+            self.assertTrue(
+                h5s['entry0000/tomwer_process_0/results/flats/1'].shape,
+                (2560, 2160))
+            self.assertTrue('entry0000/tomwer_process_0/results/darks' in h5s)
+            self.assertTrue(
+                h5s['entry0000/tomwer_process_0/results/darks/0'].shape,
+                (2560, 2160))
+            # check axis
+            self.assertEqual(h5s['entry0000/tomwer_process_1/program'][()],
+                             'tomwer_axis')
+            self.assertAlmostEqual(
+                h5s['entry0000/tomwer_process_1/results/center_of_rotation'][
+                    ()], 70.0, places=4)
+
+            # check nabu
+            self.assertEqual(h5s['entry0000/tomwer_process_2/program'][()], 'nabu-slices')
+            axp = h5s[ 'entry0000/tomwer_process_2/configuration/reconstruction/rotation_axis_position'][()]
+            self.assertAlmostEqual(float(axp), (10. + 70.0), places=4)
+            # +10: moved to nabu system (half width
+        # check nabu files
+        self.assertEqual(len(glob(self._nabu_cfg_folder + os.sep + '*.cfg')), 2)
+
+    def testProcessing_2(self):
+        self.assertFalse(os.path.exists(self.tomwer_file))
+        self.assertEqual(len(glob(self._nabu_cfg_folder + os.sep + '*.cfg')), 0)
+
+        scheme_file = UtilsTest.getOrangeExecTestFile('darkref_axis_nabu_2.ows')
+        self.scheme = self.get_scheme(scheme_file)
+        # monkey patch parameters to use nabu in dry tun mode
+        self.scheme.nodes[2].properties['_rpSetting']['dry_run'] = True
+
+        _exec(scheme=self.scheme, scan=self.scan, timeout=self.TIMEOUT)
+        self.assertTrue(os.path.exists(self.tomwer_file))
+        with h5py.File(self.tomwer_file, 'r') as h5s:
+            # check darks
+            self.assertTrue('entry0000' in h5s)
+            self.assertTrue('entry0000/tomwer_process_0/results/flats' in h5s)
+            self.assertTrue(
+                h5s['entry0000/tomwer_process_0/results/flats/1'].shape,
+                (2560, 2160))
+            self.assertTrue('entry0000/tomwer_process_0/results/darks' in h5s)
+            self.assertTrue(
+                h5s['entry0000/tomwer_process_0/results/darks/0'].shape,
+                (2560, 2160))
+            # check axis
+            self.assertEqual(h5s['entry0000/tomwer_process_1/program'][()], 'tomwer_axis')
+            axis_cor = h5s['entry0000/tomwer_process_1/results/center_of_rotation'][()]
+
+            # check nabu
+            self.assertEqual(h5s['entry0000/tomwer_process_2/program'][()], 'nabu-slices')
+            axp = h5s['entry0000/tomwer_process_2/configuration/reconstruction/rotation_axis_position'][()]
+            self.assertAlmostEqual(float(axp), (10. + axis_cor), places=4)
+            # +10: moved to nabu system (half width
+        # check nabu files
+        self.assertEqual(len(glob(self._nabu_cfg_folder + os.sep + '*.cfg')), 2)
+
+
+class TestPythonScript(unittest.TestCase):
+    """
+    Test the execution of the following workflow:
+    Data list -> Python script test -> Python script test 2
+
+    Data list will be ignored
+    The first scripts create a 'test.txt' file at the root level
+    The second scripts create a 'test2.txt' file at the root level
+
+    Make sure the code is correctly executed and that it.
+    """
+    TIMEOUT = 120
+
+    def setUp(self) -> None:
+        unittest.TestCase.setUp(self)
+        self._data_dir = tempfile.mkdtemp()
+        self.master_file = os.path.join(self._data_dir,
+                                        'frm_edftomomill_twoentries.nx')
+        self.tomwer_file = os.path.join(self._data_dir,
+                                        'tomwer_processes.h5')
+
+        shutil.copyfile(
+            UtilsTest.getH5Dataset(folderID='frm_edftomomill_twoentries.nx'),
+            self.master_file)
+        self.scan = HDF5TomoScan(scan=self.master_file, entry='entry0000')
+
+    @staticmethod
+    def get_scheme(file_path):
+        return OwsParser.scheme_load(file_path, load_handlers=True)
+
+    def tearDown(self) -> None:
+        if os.path.isdir(self._data_dir):
+            shutil.rmtree(self._data_dir)
+
+    def testProcessing(self):
+        self.assertEqual(len(glob(self.scan.path + os.sep + 'test*.txt')), 0)
+        scheme_file = UtilsTest.getOrangeExecTestFile('test_tomwer_python_scripts.ows')
+        self.scheme = self.get_scheme(scheme_file)
+        _exec(scheme=self.scheme, scan=self.scan, timeout=self.TIMEOUT)
+        self.assertEqual(len(glob(self.scan.path + os.sep + 'test*.txt')), 2)
+
+
+def suite():
+    test_suite = unittest.TestSuite()
+    for ui in (TestNxTomoDarkRef, TestDarkRefAxisNabu, TestPythonScript, ):
+        test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
+    return test_suite
+
+
+if __name__ == '__main__':
+    unittest.main(defaultTest="suite")