tomwer 1.3.27__py3-none-any.whl → 1.4.0rc0__py3-none-any.whl

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

@@ -0,0 +1,194 @@
+# coding: utf-8
+from __future__ import annotations
+
+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,
+            )

tomwer/tests/orangecontrib/tomwer/widgets/stitching/tests/test_zstitching.py

@@ -0,0 +1,313 @@
+import os
+import pickle
+import shutil
+import tempfile
+
+import numpy
+
+from orangecanvas.scheme.readwrite import literal_dumps
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from orangecontrib.tomwer.widgets.stitching.ZStitchingConfigOW import ZStitchingConfigOW
+from tomwer.core.utils.scanutils import MockNXtomo
+from tomwer.core.volume.hdf5volume import HDF5Volume
+
+
+class TestScansZStitchingConfigOW(TestCaseQt):
+    """
+    Test stitching with scans
+    """
+
+    def setUp(self):
+        super().setUp()
+        self._widget = ZStitchingConfigOW()
+        self._tmp_dir = tempfile.mkdtemp()
+        self._scans = []
+        for i_scan in range(3):
+            scan = MockNXtomo(
+                scan_path=os.path.join(self._tmp_dir, f"scan_{i_scan}.nx"),
+                n_ini_proj=20,
+                n_proj=20,
+                n_alignement_proj=2,
+                dim=10,
+            ).scan
+            self._scans.append(scan)
+        self._widget.setConfiguration(
+            {
+                "inputs": {
+                    "input_datasets": [
+                        scan.get_identifier().to_str() for scan in self._scans
+                    ],
+                },
+                "stitching": {
+                    "type": "z-preproc",
+                    "stitching_strategy": "closest",
+                    "alignment_axis_1": "center",
+                    "alignment_axis_2": "center",
+                    "pad_mode": "constant",
+                },
+                "preproc": {
+                    "data_path": "myentry",
+                    "location": "/path/to/mynexusfile.nx",
+                },
+            }
+        )
+        self.qapp.processEvents()
+
+    def test_get_configuration(self):
+        """Make sure the set configuration will be the get configuration"""
+        config = self._widget.getConfiguration()
+        assert config == {
+            "inputs": {
+                "input_datasets": list(
+                    [scan.get_identifier().to_str() for scan in self._scans]
+                ),
+                "slices": "",
+            },
+            "stitching": {
+                "stitching_strategy": "cosinus weights",
+                "type": "z-preproc",
+                "axis_0_pos_px": [0] * len(self._scans),
+                "axis_0_params": "overlap_size=;img_reg_method=nabu-fft;window_size=400",
+                "axis_1_pos_px": [0] * len(self._scans),
+                "axis_1_params": "img_reg_method=None;window_size=400",
+                "flipud": False,
+                "fliplr": False,
+                "avoid_data_duplication": False,
+                "rescale_frames": False,
+                "rescale_params": "rescale_min_percentile=0;rescale_max_percentile=100",
+                "alignment_axis_1": "center",
+                "alignment_axis_2": "center",
+                "pad_mode": "constant",
+            },
+            "preproc": {
+                "data_path": "myentry",
+                "location": "/path/to/mynexusfile.nx",
+            },
+            "output": {
+                "overwrite_results": True,
+            },
+            "normalization_by_sample": {
+                "active": False,
+                "margin": 0,
+                "method": "median",
+                "side": "left",
+                "width": 30,
+            },
+        }
+        # test setting some metadata for stitching
+        for i_scan, scan in enumerate(
+            self._widget.widget._widget._mainWidget.getTomoObjs()
+        ):
+            scan.stitching_metadata.setPxPos(-i_scan, axis=0)
+            scan.stitching_metadata.setPxPos(-i_scan * 10, axis=1)
+        self.qapp.processEvents()
+        config = self._widget.getConfiguration()
+        assert config == {
+            "inputs": {
+                "input_datasets": list(
+                    [scan.get_identifier().to_str() for scan in self._scans]
+                ),
+                "slices": "",
+            },
+            "stitching": {
+                "type": "z-preproc",
+                "stitching_strategy": "cosinus weights",
+                "axis_0_pos_px": [0, -1, -2],
+                "axis_0_params": "overlap_size=;img_reg_method=nabu-fft;window_size=400",
+                "axis_1_pos_px": [0, -10, -20],
+                "axis_1_params": "img_reg_method=None;window_size=400",
+                "flipud": False,
+                "fliplr": False,
+                "avoid_data_duplication": False,
+                "rescale_frames": False,
+                "rescale_params": "rescale_min_percentile=0;rescale_max_percentile=100",
+                "alignment_axis_1": "center",
+                "alignment_axis_2": "center",
+                "pad_mode": "constant",
+            },
+            "preproc": {
+                "data_path": "myentry",
+                "location": "/path/to/mynexusfile.nx",
+            },
+            "output": {
+                "overwrite_results": True,
+            },
+            "normalization_by_sample": {
+                "active": False,
+                "margin": 0,
+                "method": "median",
+                "side": "left",
+                "width": 30,
+            },
+        }
+        config["stitching"]["axis_1_pos_px"] = [0, -1, -2]
+        config["output"]["overwrite_results"] = False
+        self._widget.setConfiguration(config)
+        assert self._widget.getConfiguration() == config
+
+    def tearDown(self):
+        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self._widget.close()
+        self._widget = None
+        shutil.rmtree(self._tmp_dir)
+
+    def test_serializing(self):
+        pickle.dumps(self._widget.getConfiguration())
+
+    def test_literal_dumps(self):
+        literal_dumps(self._widget.getConfiguration())
+
+
+class TestVolumesZStitchingConfigOW(TestCaseQt):
+    """
+    Test ZStitchingConfigOW with volumes
+    """
+
+    def setUp(self):
+        super().setUp()
+        self._widget = ZStitchingConfigOW()
+        self._tmp_dir = tempfile.mkdtemp()
+        self._volumes = []
+        for i_volumes in range(4):
+            volume = HDF5Volume(
+                file_path=os.path.join(self._tmp_dir, f"volume_{i_volumes}.hdf5"),
+                data_path="entry0000",
+                data=numpy.ones(shape=(10, 20, 30)),
+                metadata={},
+            )
+            volume.save()
+            self._volumes.append(volume)
+
+        self.output_volume = HDF5Volume(
+            file_path=os.path.join(self._tmp_dir, "result.hdf5"),
+            data_path="stitched",
+        )
+        self._widget.setConfiguration(
+            {
+                "inputs": {
+                    "input_datasets": [
+                        volume.get_identifier().to_str() for volume in self._volumes
+                    ],
+                },
+                "stitching": {
+                    "type": "z-postproc",
+                    "stitching_strategy": "closest",
+                    "alignment_axis_1": "center",
+                    "alignment_axis_2": "center",
+                    "pad_mode": "constant",
+                },
+                "postproc": {
+                    "output_volume": self.output_volume.get_identifier().to_str(),
+                },
+            }
+        )
+        self.qapp.processEvents()
+
+    def test_get_configuration(self):
+        """Make sure the set configuration will be the get configuration"""
+        config = self._widget.getConfiguration()
+        assert config == {
+            "inputs": {
+                "input_datasets": list(
+                    [scan.get_identifier().to_str() for scan in self._volumes]
+                ),
+                "slices": "",
+            },
+            "stitching": {
+                "stitching_strategy": "cosinus weights",
+                "type": "z-postproc",
+                "axis_0_pos_px": [0] * len(self._volumes),
+                "axis_0_params": "overlap_size=;img_reg_method=nabu-fft;window_size=400",
+                "axis_1_pos_px": [0] * len(self._volumes),
+                "axis_1_params": "img_reg_method=None;window_size=400",
+                "flipud": False,
+                "fliplr": False,
+                "avoid_data_duplication": False,
+                "rescale_frames": False,
+                "rescale_params": "rescale_min_percentile=0;rescale_max_percentile=100",
+                "alignment_axis_1": "center",
+                "alignment_axis_2": "center",
+                "pad_mode": "constant",
+            },
+            "postproc": {
+                "output_volume": self.output_volume.get_identifier().to_str(),
+            },
+            "output": {
+                "overwrite_results": True,
+            },
+            "normalization_by_sample": {
+                "active": False,
+                "margin": 0,
+                "method": "median",
+                "side": "left",
+                "width": 30,
+            },
+        }
+        # test setting some metadata for stitching
+        for i_scan, scan in enumerate(
+            self._widget.widget._widget._mainWidget.getTomoObjs()
+        ):
+            scan.stitching_metadata.setPxPos(-i_scan, axis=0)
+            scan.stitching_metadata.setPxPos(-i_scan * 10, axis=1)
+        self.qapp.processEvents()
+        config = self._widget.getConfiguration()
+        assert config == {
+            "inputs": {
+                "input_datasets": list(
+                    [scan.get_identifier().to_str() for scan in self._volumes]
+                ),
+                "slices": "",
+            },
+            "stitching": {
+                "stitching_strategy": "cosinus weights",
+                "type": "z-postproc",
+                "axis_0_pos_px": [0, -1, -2, -3],
+                "axis_0_params": "overlap_size=;img_reg_method=nabu-fft;window_size=400",
+                "axis_1_pos_px": [0, -10, -20, -30],
+                "axis_1_params": "img_reg_method=None;window_size=400",
+                "flipud": False,
+                "fliplr": False,
+                "avoid_data_duplication": False,
+                "rescale_frames": False,
+                "rescale_params": "rescale_min_percentile=0;rescale_max_percentile=100",
+                "alignment_axis_1": "center",
+                "alignment_axis_2": "center",
+                "pad_mode": "constant",
+            },
+            "postproc": {
+                "output_volume": self.output_volume.get_identifier().to_str(),
+            },
+            "output": {
+                "overwrite_results": True,
+            },
+            "normalization_by_sample": {
+                "active": False,
+                "margin": 0,
+                "method": "median",
+                "side": "left",
+                "width": 30,
+            },
+        }
+        # update some field to enhance test
+        config["stitching"]["axis_1_pos_px"] = [0, -100, -200, -300]
+        config["stitching"]["rescale_frames"] = True
+        config["stitching"][
+            "rescale_params"
+        ] = "rescale_min_percentile=10;rescale_max_percentile=35"
+        config["output"]["overwrite_results"] = False
+        self._widget.setConfiguration(config)
+        assert self._widget.getConfiguration() == config
+
+    def tearDown(self):
+        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self._widget.close()
+        self._widget = None
+        shutil.rmtree(self._tmp_dir)
+
+    def test_serializing(self):
+        pickle.dumps(self._widget.getConfiguration())
+
+    def test_literal_dumps(self):
+        literal_dumps(self._widget.getConfiguration())

tomwer/tests/orangecontrib/tomwer/widgets/tests/test_conditions.py

@@ -0,0 +1,85 @@
+# coding: utf-8
+from __future__ import annotations
+
+import gc
+import logging
+import os
+import shutil
+import tempfile
+
+from silx.gui import qt
+from silx.gui.utils.testutils import SignalListener, TestCaseQt
+
+from orangecontrib.tomwer.widgets.control.FilterOW import NameFilterOW
+from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.utils.scanutils import MockEDF, MockNXtomo
+
+logging.disable(logging.INFO)
+
+
+class NameFilterOWCI(NameFilterOW):
+    sigScanReady = qt.Signal(str)
+    """signal emitted when a scan is ready; Parameter is folder path of the
+    scan"""
+
+    def _signalScanReady(self, scan):
+        self.sigScanReady.emit(scan.path)
+
+
+class TestFilterWidget(TestCaseQt):
+    """class testing the DarkRefWidget"""
+
+    def setUp(self):
+        TestCaseQt.setUp(self)
+        self.widget = NameFilterOWCI(parent=None)
+
+        self.tmpdir = tempfile.mkdtemp()
+        # create hdf5 dataset
+        self._hdf5with_mytotodir = MockNXtomo(
+            scan_path=os.path.join(self.tmpdir, "mytotodir120"), n_proj=10
+        ).scan
+        self._hdf5without_mytotodir = MockNXtomo(
+            scan_path=os.path.join(self.tmpdir, "totodir120"), n_proj=10
+        ).scan
+        # create edf dataset
+        mockEDF1 = MockEDF(
+            scan_path=os.path.join(self.tmpdir, "mytotodir20"), n_radio=10
+        )
+        self.edfwith_mytotodir = EDFTomoScan(scan=mockEDF1.scan_path)
+
+        mockEDF2 = MockEDF(scan_path=os.path.join(self.tmpdir, "dir120"), n_radio=10)
+        self.edfwithout_mytotodir = EDFTomoScan(scan=mockEDF2.scan_path)
+
+        # add a signal listener
+        self.signalListener = SignalListener()
+        self.widget.sigScanReady.connect(self.signalListener)
+
+        # define the unix file pattern
+        self.widget.setPattern("*mytotodir*")
+
+    def tearDown(self):
+        shutil.rmtree(self.tmpdir)
+        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.widget.close()
+        self.widget = None
+        gc.collect()
+
+    def testEDF(self):
+        """Make sure filtering works with EDF"""
+        self.assertEqual(self.signalListener.callCount(), 0)
+        self.widget.applyfilter(self.edfwith_mytotodir)
+        self.qapp.processEvents()
+        self.assertEqual(self.signalListener.callCount(), 1)
+        self.widget.applyfilter(self.edfwithout_mytotodir)
+        self.qapp.processEvents()
+        self.assertEqual(self.signalListener.callCount(), 1)
+
+    def testHDF5(self):
+        """Make sure filtering works with HDF5"""
+        self.assertEqual(self.signalListener.callCount(), 0)
+        self.widget.applyfilter(self._hdf5without_mytotodir)
+        self.qapp.processEvents()
+        self.assertEqual(self.signalListener.callCount(), 0)
+        self.widget.applyfilter(self._hdf5with_mytotodir)
+        self.qapp.processEvents()
+        self.assertEqual(self.signalListener.callCount(), 1)