tomwer 1.3.7__py3-none-any.whl → 1.3.9__py3-none-any.whl

orangecontrib/tomwer/widgets/reconstruction/test/test_nabu_helical_prepare_weights_double.py

@@ -1,20 +0,0 @@
-import pickle
-
-from orangecanvas.scheme.readwrite import literal_dumps
-
-from tomwer.tests.conftest import qtapp  # noqa F401
-
-from orangecontrib.tomwer.widgets.reconstruction.NabuHelicalPrepareWeightsDoubleOW import (
-    NabuHelicalPrepareWeightsDoubleOW,
-)
-
-
-def test_NabuHelicalPrepareWeightsDoubleOW(
-    qtapp,  # noqa F811
-):
-    """simple test of the _DeltaBetaSelectorDialog"""
-    widget = NabuHelicalPrepareWeightsDoubleOW()
-    widget._loadSettings()
-    # test settings serialization
-    pickle.dumps(widget._ewoks_default_inputs)
-    literal_dumps(widget._ewoks_default_inputs)

orangecontrib/tomwer/widgets/reconstruction/test/test_nabu_volume.py

@@ -1,100 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2017-2021 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__ = "21/06/2021"
-
-
-import gc
-import os
-import pickle
-import shutil
-import tempfile
-from time import sleep
-
-from nabu.pipeline.config import get_default_nabu_config
-from nabu.pipeline.fullfield.nabu_config import (
-    nabu_config as nabu_fullfield_default_config,
-)
-from orangecanvas.scheme.readwrite import literal_dumps
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-
-from orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW import NabuVolumeOW
-from tomwer.core.utils.scanutils import MockNXtomo
-
-
-class TestNabuVolumeOW(TestCaseQt):
-    def setUp(self):
-        super().setUp()
-        self.tmp_dir = tempfile.mkdtemp()
-        self.scan = MockNXtomo(
-            scan_path=os.path.join(self.tmp_dir, "myscan"),
-            n_proj=20,
-            n_ini_proj=20,
-            dim=10,
-        ).scan
-        self.widget = NabuVolumeOW()
-        self.widget._processingStack.setDryRun(True)
-
-    def tearDown(self):
-        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self.widget.close()
-        self.widget = None
-        shutil.rmtree(self.tmp_dir)
-        self.qapp.processEvents()
-        gc.collect()
-
-    def test_serializing(self):
-        pickle.dumps(self.widget.getConfiguration())
-
-    def test_literal_dumps(self):
-        literal_dumps(self.widget.getConfiguration())
-
-    def test_scan_as_None(self):
-        "test if scan is None"
-        self.widget.process(None)
-
-    def test_scan_un_preprocessed(self):
-        "test when scan is unconfigured (No nabu_recons_params defined)"
-        assert self.scan.nabu_recons_params is None
-        self.widget.process(self.scan)
-
-    def test_scan_ready_to_be_processed(self):
-        "test if scan has valid reconstruction parameters to be runned"
-        self.scan.nabu_recons_params = get_default_nabu_config(
-            nabu_fullfield_default_config
-        )
-        self.widget.process(self.scan)
-        timeout = 3
-        loop_sleep_time = 0.05
-        while not self.widget._processingStack.can_process_next():
-            self.qapp.processEvents()
-            timeout -= loop_sleep_time
-            if timeout <= 0.0:
-                raise TimeoutError("volume not process within expected time")
-            else:
-                sleep(loop_sleep_time)

orangecontrib/tomwer/widgets/reconstruction/test/test_nabu_widget.py

@@ -1,107 +0,0 @@
-import gc
-import logging
-import os
-import pickle
-import shutil
-import tempfile
-import time
-from glob import glob
-
-import h5py
-from orangecanvas.scheme.readwrite import literal_dumps
-from silx.gui import qt
-from silx.gui.utils.testutils import SignalListener, TestCaseQt
-from nxtomo.nxobject.nxdetector import FOV
-
-from orangecontrib.tomwer.widgets.reconstruction.NabuOW import NabuOW
-from tomwer.core.process.reconstruction.nabu.utils import _NabuMode
-from tomwer.core.scan.nxtomoscan import NXtomoScan
-from tomwer.core.settings import mock_lsbram
-from tomwer.core.utils.lbsram import mock_low_memory
-from tomwer.synctools.darkref import QDKRFRP
-from tomwer.tests.datasets import TomwerCIDatasets
-
-logging.disable(logging.INFO)
-
-
-class TestNabuWidget(TestCaseQt):
-    """class testing the NabuOW"""
-
-    def setUp(self):
-        TestCaseQt.setUp(self)
-        self._recons_params = QDKRFRP()
-        self.widget = NabuOW(parent=None)
-        self.scan_dir = tempfile.mkdtemp()
-        # create dataset
-        self.master_file = os.path.join(self.scan_dir, "frm_edftomomill_twoentries.nx")
-        shutil.copyfile(
-            TomwerCIDatasets.get_dataset(
-                "h5_datasets/frm_edftomomill_twoentries.nx",
-            ),
-            self.master_file,
-        )
-        self.scan = NXtomoScan(scan=self.master_file, entry="entry0000")
-        # create listener for the nabu widget
-        self.signal_listener = SignalListener()
-
-        # connect signal / slot
-        self.widget.sigScanReady.connect(self.signal_listener)
-
-        # set up
-        mock_low_memory(True)
-        mock_lsbram(True)
-        self.widget.setDryRun(dry_run=True)
-
-    def tearDown(self):
-        mock_low_memory(False)
-        mock_lsbram(False)
-        self.widget.sigScanReady.disconnect(self.signal_listener)
-        self._recons_params = None
-        self.scan = None
-        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self.widget.close()
-        self.widget = None
-        gc.collect()
-
-    def test_serializing(self):
-        pickle.dumps(self.widget.getConfiguration())
-
-    def test_literal_dumps(self):
-        literal_dumps(self.widget.getConfiguration())
-
-    def testLowMemory(self):
-        """Make sure no reconstruction is started if we are low in memory in
-        lbsram"""
-        self.assertEqual(len(glob(os.path.join(self.scan_dir, "*.cfg"))), 0)
-        self.widget.process(self.scan)
-        self.wait_processing()
-        self.assertEqual(len(glob(os.path.join(self.scan_dir, "*.cfg"))), 0)
-
-    def wait_processing(self):
-        timeout = 10
-        while timeout >= 0 and self.signal_listener.callCount() == 0:
-            timeout -= 0.1
-            time.sleep(0.1)
-        if timeout <= 0.0:
-            raise TimeoutError("nabu widget never end processing")
-
-    def patch_fov(self, value: str):
-        with h5py.File(self.scan.master_file, mode="a") as h5s:
-            for entry in ("entry0000", "entry0001"):
-                entry_node = h5s[entry]
-                if "instrument/detector/field_of_view" in entry_node:
-                    del entry_node["instrument/detector/field_of_view"]
-                entry_node["instrument/detector/field_of_view"] = value
-
-    def testSetConfiguration(self):
-        """Make sure the configuration evolve from scan information"""
-        self.assertEqual(self.widget.getMode(), _NabuMode.FULL_FIELD)
-        self.patch_fov(value=FOV.HALF.value)
-        self.widget.process(self.scan)
-        self.wait_processing()
-        self.assertEqual(self.widget.getMode(), _NabuMode.HALF_ACQ)
-        self.patch_fov(value=FOV.FULL.value)
-        self.scan.clear_caches()
-        self.widget.process(self.scan)
-        self.wait_processing()
-        self.assertEqual(self.widget.getMode(), _NabuMode.FULL_FIELD)

orangecontrib/tomwer/widgets/reconstruction/test/test_sa_delta_beta.py

@@ -1,194 +0,0 @@
-import gc
-import logging
-import os
-import pickle
-import shutil
-import tempfile
-import uuid
-
-import h5py
-import numpy
-from orangecanvas.scheme.readwrite import literal_dumps
-from processview.core.manager import DatasetState, ProcessManager
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-from silx.io.url import DataUrl
-
-from orangecontrib.tomwer.widgets.reconstruction.SADeltaBetaOW import (
-    SADeltaBetaOW as _SADeltaBetaOW,
-)
-from tomwer.core import settings
-from tomwer.core.utils.lbsram import mock_low_memory
-from tomwer.core.process.reconstruction.scores import ComputedScore
-from tomwer.core.utils.scanutils import MockNXtomo
-
-logger = logging.getLogger(__name__)
-
-
-class SADeltaBetaOW(_SADeltaBetaOW):
-    def __init__(self, parent=None):
-        self._scans_finished = []
-        super().__init__(parent)
-
-    def processing_finished(self, scan):
-        # TODO: add message processing finished
-        self._scans_finished.append(scan)
-
-    @property
-    def scans_finished(self):
-        return self._scans_finished
-
-    def close(self):
-        self._scans_finished = {}
-        super().close()
-
-
-class TestProcessing(TestCaseQt):
-    DIM = 100
-
-    def setUp(self):
-        super().setUp()
-        self._source_dir = tempfile.mkdtemp()
-
-        def create_scan(folder_name):
-            _dir = os.path.join(self._source_dir, folder_name)
-            return MockNXtomo(
-                scan_path=_dir,
-                n_ini_proj=20,
-                n_proj=20,
-                n_alignement_proj=2,
-                create_final_flat=False,
-                create_ini_dark=True,
-                create_ini_flat=True,
-                n_refs=1,
-                dim=self.DIM,
-            ).scan
-
-        # create scans
-        self.scan_1 = create_scan("scan_1")
-        self.scan_2 = create_scan("scan_2")
-        self.scan_3 = create_scan("scan_3")
-        self._process_manager = ProcessManager()
-
-        self.widget = SADeltaBetaOW()
-        self.widget.show()
-
-        def patch_score(cor):
-            data = numpy.random.random(TestProcessing.DIM * TestProcessing.DIM)
-            data = data.reshape(TestProcessing.DIM, TestProcessing.DIM)
-            slice_file_path = os.path.join(
-                self._source_dir, str(uuid.uuid1()) + ".hdf5"
-            )
-            data_url = DataUrl(
-                file_path=slice_file_path, data_path="data", scheme="silx"
-            )
-            with h5py.File(slice_file_path, mode="a") as h5f:
-                h5f["data"] = data
-            return data_url, ComputedScore(
-                tv=numpy.random.random(),
-                std=numpy.random.random(),
-            )
-
-        self.widget._widget._processing_stack.patch_processing(patch_score)
-
-    def tearDown(self):
-        mock_low_memory(False)
-        settings.mock_lsbram(False)
-        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self.widget.close()
-        self.widget = None
-        self.qapp.processEvents()
-        shutil.rmtree(self._source_dir)
-        gc.collect()
-
-    def test_serializing(self):
-        pickle.dumps(self.widget.getConfiguration())
-
-    def test_literal_dumps(self):
-        literal_dumps(self.widget.getConfiguration())
-
-    def testAutoFocusUnlock(self):
-        self.widget.lockAutofocus(False)
-
-        def manual_processing():
-            self.widget.compute()
-            self.qapp.processEvents()
-            self.widget.wait_processing(5000)
-            self.qapp.processEvents()
-
-        self.widget.process(self.scan_1)
-        manual_processing()
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_1.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.WAIT_USER_VALIDATION,
-        )
-
-        self.widget.process(self.scan_2)
-        manual_processing()
-        self.assertEqual(len(self.widget.scans_finished), 0)
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_1.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.SKIPPED,
-        )
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_2.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.WAIT_USER_VALIDATION,
-        )
-        self.widget.process(self.scan_3)
-        manual_processing()
-        self.widget.validateCurrentScan()
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_3.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.SUCCEED,
-        )
-        # insure a cor has been registered
-        self.assertNotEqual(
-            self.scan_3.sa_delta_beta_params.selected_delta_beta_value, None
-        )
-
-    def testTestLbsram(self):
-        mock_low_memory(True)
-        settings.mock_lsbram(True)
-        for scan in (self.scan_1, self.scan_2, self.scan_3):
-            self.widget.process(scan)
-            self.widget.wait_processing(5000)
-            self.qapp.processEvents()
-
-        for scan in (self.scan_1, self.scan_2, self.scan_3):
-            with self.subTest(scan=str(scan)):
-                self.assertEqual(
-                    self._process_manager.get_dataset_state(
-                        dataset_id=scan.get_identifier(),
-                        process=self.widget,
-                    ),
-                    DatasetState.SKIPPED,
-                )
-
-    def testAutoFocusLock(self):
-        self.widget.lockAutofocus(True)
-        for scan in (self.scan_1, self.scan_2, self.scan_3):
-            self.widget.process(scan)
-            self.widget.wait_processing(5000)
-            self.qapp.processEvents()
-
-        for scan in (self.scan_1, self.scan_2, self.scan_3):
-            with self.subTest(scan=str(scan)):
-                self.assertEqual(
-                    self._process_manager.get_dataset_state(
-                        dataset_id=scan.get_identifier(),
-                        process=self.widget,
-                    ),
-                    DatasetState.SUCCEED,
-                )

orangecontrib/tomwer/widgets/reconstruction/test/test_saaxis.py

@@ -1,220 +0,0 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 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__ = "12/04/2021"
-
-import gc
-import logging
-import os
-import pickle
-import shutil
-import tempfile
-import time
-import uuid
-
-import h5py
-import numpy
-from orangecanvas.scheme.readwrite import literal_dumps
-from processview.core.manager import DatasetState, ProcessManager
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-from silx.io.url import DataUrl
-
-from orangecontrib.tomwer.widgets.reconstruction.SAAxisOW import SAAxisOW as _SAAxisOW
-from tomwer.core import settings
-from tomwer.core.utils.lbsram import mock_low_memory
-from tomwer.core.process.reconstruction.scores import ComputedScore
-from tomwer.core.utils.scanutils import MockNXtomo
-
-logger = logging.getLogger(__name__)
-
-
-class SAAxisOW(_SAAxisOW):
-    def __init__(self, parent=None):
-        self._scans_finished = []
-        super().__init__(parent)
-
-    def processing_finished(self, scan):
-        # TODO: add message processing finished
-        self._scans_finished.append(scan)
-
-    @property
-    def scans_finished(self):
-        return self._scans_finished
-
-    def close(self):
-        self._scans_finished = {}
-        super().close()
-
-
-class TestProcessing(TestCaseQt):
-    DIM = 100
-
-    def setUp(self):
-        super().setUp()
-        self._source_dir = tempfile.mkdtemp()
-
-        def create_scan(folder_name):
-            _dir = os.path.join(self._source_dir, folder_name)
-            return MockNXtomo(
-                scan_path=_dir,
-                n_ini_proj=20,
-                n_proj=20,
-                n_alignement_proj=2,
-                create_final_flat=False,
-                create_ini_dark=True,
-                create_ini_flat=True,
-                n_refs=1,
-                dim=self.DIM,
-            ).scan
-
-        # create scans
-        self.scan_1 = create_scan("scan_1")
-        self.scan_2 = create_scan("scan_2")
-        self.scan_3 = create_scan("scan_3")
-        self._process_manager = ProcessManager()
-
-        self.widget = SAAxisOW()
-        self.widget.show()
-
-        def patch_score(*args, **kwargs):
-            data = numpy.random.random(TestProcessing.DIM * TestProcessing.DIM)
-            data = data.reshape(TestProcessing.DIM, TestProcessing.DIM)
-            slice_file_path = os.path.join(
-                self._source_dir, str(uuid.uuid1()) + ".hdf5"
-            )
-            data_url = DataUrl(
-                file_path=slice_file_path, data_path="data", scheme="silx"
-            )
-            with h5py.File(slice_file_path, mode="a") as h5f:
-                h5f["data"] = data
-            return data_url, ComputedScore(
-                tv=numpy.random.random(),
-                std=numpy.random.random(),
-            )
-
-        self.widget._widget._processing_stack.patch_processing(patch_score)
-
-    def tearDown(self):
-        mock_low_memory(False)
-        settings.mock_lsbram(False)
-        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self.widget.close()
-        self.widget = None
-        self.qapp.processEvents()
-        shutil.rmtree(self._source_dir)
-        gc.collect()
-
-    def test_serializing(self):
-        pickle.dumps(self.widget.getConfiguration())
-
-    def test_literal_dumps(self):
-        literal_dumps(self.widget.getConfiguration())
-
-    def testAutoFocusUnlock(self):
-        self.widget.lockAutofocus(False)
-
-        def manual_processing():
-            self.widget.load_sinogram()
-            self.widget.compute()
-            self.qapp.processEvents()
-            self.widget.wait_processing(5000)
-            self.qapp.processEvents()
-
-        self.widget.process(self.scan_1)
-        manual_processing()
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_1.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.WAIT_USER_VALIDATION,
-        )
-
-        self.widget.process(self.scan_2)
-        manual_processing()
-        self.assertEqual(len(self.widget.scans_finished), 0)
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_1.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.SKIPPED,
-        )
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_2.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.WAIT_USER_VALIDATION,
-        )
-        self.widget.process(self.scan_3)
-        manual_processing()
-        self.widget.validateCurrentScan()
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_3.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.SUCCEED,
-        )
-        # insure a cor has been registered
-        self.assertNotEqual(self.scan_3.axis_params.relative_cor_value, None)
-
-    def testTestLbsram(self):
-        mock_low_memory(True)
-        settings.mock_lsbram(True)
-        for scan in (self.scan_1, self.scan_2, self.scan_3):
-            self.widget.process(scan)
-            self.widget.wait_processing(5000)
-            self.qapp.processEvents()
-
-        for scan in (self.scan_1, self.scan_2, self.scan_3):
-            with self.subTest(scan=str(scan)):
-                self.assertEqual(
-                    self._process_manager.get_dataset_state(
-                        dataset_id=scan.get_identifier(),
-                        process=self.widget,
-                    ),
-                    DatasetState.SKIPPED,
-                )
-
-    def testAutoFocusLock(self):
-        self.widget.lockAutofocus(True)
-        for scan in (self.scan_1, self.scan_2, self.scan_3):
-            self.widget.process(scan)
-            self.widget.wait_processing(10000)
-            self.qapp.processEvents()
-            time.sleep(0.1)
-            self.qapp.processEvents()
-            self.assertEqual(
-                self._process_manager.get_dataset_state(
-                    dataset_id=scan.get_identifier(),
-                    process=self.widget,
-                ),
-                DatasetState.SUCCEED,
-            )