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

tomwer/gui/stitching/tests/test_z_stitching.py

@@ -1,67 +0,0 @@
-import os
-import tempfile
-
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-from tomoscan.serie import Serie
-
-from tomwer.gui.stitching.stitching import ZStitchingWindow
-from tomwer.gui.stitching.tests.utils import create_scans_z_serie
-
-
-class TestAxis_N_Params(TestCaseQt):
-    """
-    Test definition of an axis shift research parameters
-    """
-
-    def setUp(self):
-        super().setUp()
-        self._window = ZStitchingWindow()
-
-        self._tmp_path = tempfile.mkdtemp()
-        self.axis_0_positions = (90, 0.0, -90.0)
-        self.axis_2_positions = (0.0, 0.0, 0.0)
-        pixel_size = 1.0
-
-        self.output_file_path = os.path.join(self._tmp_path, "output", "stitched.nx")
-        self._input_dir = os.path.join(self._tmp_path, "input")
-
-        self._scans = create_scans_z_serie(
-            output_dir=self._input_dir,
-            z_positions_m=self.axis_0_positions,
-            x_positions_m=self.axis_2_positions,
-            shifts=((0.0, 0.0), (-90.0, 0.0), (-180.0, 0.0)),
-            pixel_size=pixel_size,
-            raw_frame_width=280,
-            final_frame_width=100,
-        )
-        self._serie = Serie("z-serie", self._scans)
-
-    def tearDown(self):
-        self._window.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._window.close()
-        self._window = None
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-
-    def test(self):
-        self._window.show()
-        for scan in self._scans:
-            self._window.addTomoObj(scan)
-        self._window.clean()
-        self._window.setSerie(self._serie)
-
-        # test dumping and loading configuration to a file
-        with tempfile.TemporaryDirectory() as dump_dir:
-            config_file = os.path.join(dump_dir, "configuration.cfg")
-            self._window._saveSettings(file_path=config_file)
-            assert os.path.exists(config_file)
-            self._window._loadSettings(config_file)
-            # remove configuration
-            self._window.clean()
-            assert len(self._window._widget._mainWidget.getTomoObjs()) == 0
-            # reload it
-            self._window._loadSettings(file_path=config_file)
-            assert len(self._window._widget._mainWidget.getTomoObjs()) == len(
-                self._serie
-            )

tomwer/gui/stitching/tests/utils.py

@@ -1,79 +0,0 @@
-import os
-
-import numpy
-from nxtomo.application.nxtomo import NXtomo
-from scipy.ndimage import shift as shift_scipy
-from silx.image.phantomgenerator import PhantomGenerator
-from nxtomo.nxobject.nxdetector import ImageKey
-
-from tomwer.core.scan.nxtomoscan import NXtomoScan
-
-
-def create_scans_z_serie(
-    output_dir,
-    z_positions_m,
-    x_positions_m=None,
-    pixel_size=10e-6,
-    n_proj=20,
-    raw_frame_width=100,
-    final_frame_width=100,
-    shifts=None,
-    z_rois=None,
-):
-    """
-    :param Optioanl tuple: shift to be applied on the 2D frame
-    """
-    if not os.path.exists(output_dir):
-        os.makedirs(output_dir)
-    frame = (
-        PhantomGenerator.get2DPhantomSheppLogan(n=raw_frame_width).astype(numpy.float32)
-        * 256.0
-    )
-    if x_positions_m is None:
-        x_positions_m = [None] * len(z_positions_m)
-    if shifts is None:
-        shifts = [None] * len(z_positions_m)
-    if z_rois is None:
-        z_rois = [None] * len(z_positions_m)
-    scans = []
-    for i_frame, (z_pos, x_pos, z_roi, shift) in enumerate(
-        zip(z_positions_m, x_positions_m, z_rois, shifts)
-    ):
-        nx_tomo = NXtomo()
-        if z_pos is not None:
-            nx_tomo.sample.z_translation = [z_pos] * n_proj
-        if x_pos is not None:
-            nx_tomo.sample.x_translation = [x_pos] * n_proj
-        nx_tomo.sample.rotation_angle = numpy.linspace(
-            0, 180, num=n_proj, endpoint=False
-        )
-        nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION] * n_proj
-        if pixel_size is not None:
-            if isinstance(pixel_size, (tuple, list)):
-                y_pix_size, x_pix_size = pixel_size
-            else:
-                y_pix_size, x_pix_size = pixel_size, pixel_size
-            nx_tomo.instrument.detector.x_pixel_size = x_pix_size
-            nx_tomo.instrument.detector.y_pixel_size = y_pix_size
-        nx_tomo.instrument.detector.distance = 2.3
-        nx_tomo.energy = 19.2
-
-        if shift is not None:
-            sub_frame = shift_scipy(
-                input=frame.copy(), shift=shift, order=1, mode="constant"
-            )[:final_frame_width]
-        else:
-            sub_frame = frame
-        if z_roi is not None:
-            roi_start, roi_end = z_roi
-            sub_frame = sub_frame[roi_start:roi_end]
-        else:
-            sub_frame = sub_frame
-        nx_tomo.instrument.detector.data = numpy.asarray([sub_frame] * n_proj)
-
-        file_path = os.path.join(output_dir, f"nxtomo_{i_frame}.nx")
-        entry = f"entry000{i_frame}"
-        nx_tomo.save(file_path=file_path, data_path=entry)
-        scans.append(NXtomoScan(scan=file_path, entry=entry))
-
-    return scans

tomwer/gui/stitching/z_stitching/tests/test_fine_estimation.py

@@ -1,35 +0,0 @@
-from nabu.stitching.utils import ShiftAlgorithm as _NabuShiftAlgorithm
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-
-from tomwer.gui.stitching.z_stitching.fineestimation import Axis_N_Params
-
-
-class TestAxis_N_Params(TestCaseQt):
-    """
-    Test definition of an axis shift research parameters
-    """
-
-    def setUp(self):
-        super().setUp()
-        self._widget = Axis_N_Params("axis n", None)
-
-    def tearDown(self):
-        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._widget.close()
-        self._widget = None
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-
-    def test(self):
-        self._widget.show()
-        assert self._widget.getCurrentMethod() == _NabuShiftAlgorithm.NONE
-        opts1 = self._widget.getOptsLine()
-        assert opts1 == "img_reg_method=None"
-        self._widget.setCurrentMethod(_NabuShiftAlgorithm.NABU_FFT)
-        opts2 = self._widget.getOptsLine()
-        assert opts2 == "img_reg_method=nabu-fft"
-        self._widget.setOptsLine(opts1)
-        assert self._widget.getOptsLine() == opts1
-        self._widget.setOptsLine(opts2)
-        assert self._widget.getOptsLine() == opts2

tomwer/gui/stitching/z_stitching/tests/test_raw_estimation.py

@@ -1,215 +0,0 @@
-import os
-import shutil
-import tempfile
-
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-
-from tomwer.core.process.stitching.metadataholder import StitchingMetadata
-from tomwer.gui.stitching.metadataholder import QStitchingMetadata
-from tomwer.gui.stitching.tests.utils import create_scans_z_serie
-from tomwer.gui.stitching.config.tomoobjdetails import TomoObjectPositionInfos
-from tomwer.gui.stitching.axisorderedlist import AxisOrderedTomoObjsModel
-
-
-class TestTomoObjectPositionInfos(TestCaseQt):
-    """
-    Test edition of the tomo object position information
-    """
-
-    def setUp(self):
-        super().setUp()
-        self._tmp_path = tempfile.mkdtemp()
-        self._y_pixel_size = 0.002
-        self._x_pixel_size = 0.001
-        self.scans = create_scans_z_serie(
-            self._tmp_path,
-            z_positions_m=(0.200, 0.205, 0.210),
-            x_positions_m=(0.0, 0.0, None),
-            pixel_size=(self._y_pixel_size, self._x_pixel_size),
-            raw_frame_width=100,
-        )
-        self.scan_0_metadata = QStitchingMetadata(tomo_obj=self.scans[0])
-        assert self.scan_0_metadata.get_raw_position_m(axis=0) == 0.20
-        assert self.scan_0_metadata.get_raw_position_m(axis=2) == 0.0
-        self.scan_2_metadata = QStitchingMetadata(tomo_obj=self.scans[2])
-        assert self.scan_2_metadata.get_raw_position_m(axis=0) == 0.21
-        self._widget = TomoObjectPositionInfos()
-
-    def tearDown(self):
-        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._widget.close()
-        self._widget = None
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-        shutil.rmtree(self._tmp_path)
-
-    def testEdition(self):
-        # test QStitchingMetadata are correctly read
-        self._widget.show()
-        self._widget.setStitchingMetadata(self.scan_0_metadata)
-        self.qapp.processEvents()
-        assert self._widget._axis_0_pos.get_final_px_position() == int(0.20 / 0.002)
-        assert self._widget._axis_2_pos.get_final_px_position() == 0
-        self._widget.setStitchingMetadata(self.scan_2_metadata)
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-        assert self._widget._axis_0_pos.get_final_px_position() == int(0.21 / 0.002)
-        assert self._widget._axis_2_pos.get_final_px_position() is None
-        # test editing some parameters from the GUI. Make sure GUI is updated as the underlying metadata object
-        self._widget._axis_0_pos._overrideMetricPositionCB.setChecked(True)
-        self._widget._axis_0_pos.setRawMetricPosition(
-            position_m=0.4, displayed_unit="nm"
-        )
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-        assert self._widget._axis_0_pos.get_final_px_position() == int(
-            0.4 * 10e-6 / 0.002
-        )
-        self._widget._axis_0_pos._overridePixelPositionCB.setChecked(True)
-        self._widget._axis_0_pos.setOverrridePxPosition(position_px=120)
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-        assert self._widget._axis_0_pos.get_final_px_position() == int(120)
-        assert self.scan_2_metadata.get_abs_position_px(axis=0) == int(120)
-
-
-class TestAxisOrderedTomoObjsModel(TestCaseQt):
-    """
-    test the behavior of the z ordered model used for stitching
-    """
-
-    def setUp(self):
-        super().setUp()
-        self._tmp_path = tempfile.mkdtemp()
-        self.scans_with_pos_and_pixel_size = create_scans_z_serie(
-            os.path.join(self._tmp_path, "case1"),
-            z_positions_m=(0.200, 0.205, 0.210),
-            pixel_size=0.001,
-            raw_frame_width=100,
-        )
-        self.scans_with_pixel_size = create_scans_z_serie(
-            os.path.join(self._tmp_path, "case2"),
-            z_positions_m=(None, None, None),
-            pixel_size=0.001,
-            raw_frame_width=100,
-        )
-        self.scans_without_metadata = create_scans_z_serie(
-            os.path.join(self._tmp_path, "case3"),
-            z_positions_m=(None, None, None),
-            pixel_size=None,
-            raw_frame_width=100,
-        )
-        self._widget = qt.QTableView()
-        self._widget.setModel(AxisOrderedTomoObjsModel(parent=self._widget, axis=0))
-
-    def tearDown(self):
-        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._widget.close()
-        self._widget = None
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-        shutil.rmtree(self._tmp_path)
-
-    def testWithMetadata(self):
-        """
-        make sure z ordering works in the best case scenario
-        """
-        first_expected_scan = (
-            self.scans_with_pos_and_pixel_size[2].get_identifier().short_description()
-        )
-        # try giving it ordered
-        for scan in self.scans_with_pos_and_pixel_size[::-1]:
-            self._widget.model().addTomoObj(scan)
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(0, 1), qt.Qt.DisplayRole
-            )
-            == first_expected_scan
-        )
-        self._widget.model().clearTomoObjs()
-        # try giving it ordered (but inverted)
-        for scan in self.scans_with_pos_and_pixel_size:
-            self._widget.model().addTomoObj(scan)
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(0, 1), qt.Qt.DisplayRole
-            )
-            == first_expected_scan
-        )
-
-    def testWithPixelSizeOnly(self):
-        """
-        make sure z ordering works when we are only aware about pixel size
-        """
-        for scan in self.scans_with_pixel_size[::-1]:
-            self._widget.model().addTomoObj(scan)
-
-        # try adding some metadata to object
-        scans = self._widget.model()._objs
-        scans = self._widget.model()._objs
-        scans[0].stitching_metadata = StitchingMetadata(tomo_obj=scans[0])
-        scans[1].stitching_metadata = QStitchingMetadata(tomo_obj=scans[1])
-
-        scans[0].stitching_metadata._pos_as_m = (0.1, 1, 2)
-        scans[1].stitching_metadata._pos_as_m = (-0.03, 1, 2)
-        scans[2].stitching_metadata._pos_as_m = (0.23, 1, 2)
-
-        self._widget.model().reorder_objs()
-        self._widget.model().layoutChanged.emit()
-
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(0, 1), qt.Qt.DisplayRole
-            )
-            == scans[2].get_identifier().short_description()
-        )
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(1, 1), qt.Qt.DisplayRole
-            )
-            == scans[0].get_identifier().short_description()
-        )
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(2, 1), qt.Qt.DisplayRole
-            )
-            == scans[1].get_identifier().short_description()
-        )
-
-    def testWithoutMetadata(self):
-        """
-        make sure tomo obj are still displayed even if there is no metadata at all
-        """
-        for scan in self.scans_without_metadata[::-1]:
-            self._widget.model().addTomoObj(scan)
-        # try adding some metadata to object
-        scans = self._widget.model()._objs
-        scans[0].stitching_metadata = StitchingMetadata(tomo_obj=scans[0])
-        scans[1].stitching_metadata = QStitchingMetadata(tomo_obj=scans[1])
-
-        scans[0].stitching_metadata._pos_as_px = (12, None, 2)
-        scans[1].stitching_metadata._pos_as_px = (-12, None, None)
-        scans[2].stitching_metadata._pos_as_px = (9999, None, None)
-
-        self._widget.model().reorder_objs()
-        self._widget.model().layoutChanged.emit()
-
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(0, 1), qt.Qt.DisplayRole
-            )
-            == scans[2].get_identifier().short_description()
-        )
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(1, 1), qt.Qt.DisplayRole
-            )
-            == scans[0].get_identifier().short_description()
-        )
-        assert (
-            self._widget.model().data(
-                self._widget.model().index(2, 1), qt.Qt.DisplayRole
-            )
-            == scans[1].get_identifier().short_description()
-        )

tomwer/gui/stitching/z_stitching/tests/test_stitching_window.py

@@ -1,51 +0,0 @@
-import os
-import shutil
-import tempfile
-
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-
-from tomwer.gui.stitching.tests.utils import create_scans_z_serie
-from tomwer.gui.stitching.stitching import ZStitchingWindow
-
-
-class TestZStichingWindow(TestCaseQt):
-    """
-    Test high level z stitching definition
-    """
-
-    def setUp(self):
-        super().setUp()
-        self._tmp_path = tempfile.mkdtemp()
-        self.scans = create_scans_z_serie(
-            os.path.join(self._tmp_path, "case1"),
-            z_positions_m=(0.200, 0.205, 0.210),
-            pixel_size=0.001,
-            raw_frame_width=100,
-        )
-
-        self._widget = ZStitchingWindow()
-
-    def tearDown(self):
-        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._widget.close()
-        self._widget = None
-        while self.qapp.hasPendingEvents():
-            self.qapp.processEvents()
-        shutil.rmtree(self._tmp_path)
-
-    @staticmethod
-    def checkNbReceivers(scan, nb_receivers):
-        return (
-            scan.stitching_metadata.receivers(scan.stitching_metadata.sigChanged)
-            == nb_receivers
-        )
-
-    def test(self):
-        self._widget.show()
-        # fill the widget with scans
-
-        scan_0, scan_1, scan_2 = self.scans
-        for scan in self.scans:
-            self._widget.addTomoObj(scan)
-            # note: add the sigChanged to the z oredred list 'update z' slot

tomwer/gui/utils/test/test_completer.py

@@ -1,67 +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.
-#
-# ###########################################################################*/
-
-"""module defining dedicated completer"""
-
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "23/03/2022"
-
-
-import pytest
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-
-from tomwer.gui.utils.completer import UrlCompleterDialog
-from tomwer.tests.utils import skip_gui_test
-
-
-@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
-class TestUrlCompleterDialog(TestCaseQt):
-    def setUp(self):
-        super().setUp()
-        self._urls = (
-            "test",
-            "test1",
-            "test2",
-        )
-        self._dialog = UrlCompleterDialog(
-            urls=self._urls,
-            current_url="test",
-        )
-
-    def tearDown(self):
-        self._dialog.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._dialog.close()
-        self._dialog = None
-        super().tearDown()
-
-    def test(self):
-        """simple test on the dialog behavior"""
-        assert self._dialog._buttons.button(qt.QDialogButtonBox.Ok).isEnabled()
-        self._dialog._completerWidget.setText("toto")
-        self.qapp.processEvents()
-        assert not self._dialog._buttons.button(qt.QDialogButtonBox.Ok).isEnabled()

tomwer/gui/utils/test/test_line_selector.py

@@ -1,21 +0,0 @@
-import numpy
-
-from tomwer.gui.utils.lineselector.lineselector import QSliceSelectorDialog
-from tomwer.tests.conftest import qtapp  # noqa F401
-
-
-def test_line_selector(
-    qtapp,  # noqa F811
-):
-    dialog = QSliceSelectorDialog(parent=None)
-    dialog.setData(
-        numpy.ones((100, 100)),
-    )
-    dialog.mainWidget.addSlice(2)
-    dialog.mainWidget.addSlice(12)
-    assert dialog.getSelection() == (2, 12)
-    dialog.mainWidget.removeSlice(12)
-    assert dialog.getSelection() == (2,)
-    dialog.setSelection((12, 23))
-    assert dialog.getSelection() == (12, 23)
-    assert dialog.mainWidget.nSelected() == 2

tomwer/gui/utils/test/test_splashscreen.py

@@ -1,8 +0,0 @@
-from silx.gui import qt
-
-from tomwer.gui.utils.splashscreen import getMainSplashScreen
-from tomwer.tests.conftest import qtapp  # noqa F401
-
-
-def test_get_splash_screen(qtapp):  # noqa F401
-    assert isinstance(getMainSplashScreen(), qt.QSplashScreen)

tomwer/gui/utils/test/test_vignettes.py

@@ -1,68 +0,0 @@
-"""
-test vignettes
-"""
-
-import time
-import numpy
-import pytest
-from silx.gui import qt
-from silx.gui.utils.testutils import TestCaseQt
-
-from tomwer.core.process.reconstruction.scores.scores import ComputedScore, ScoreMethod
-from tomwer.gui.utils.vignettes import VignettesQDialog
-from tomwer.tests.utils import skip_gui_test
-
-
-@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
-class TestVignettes(TestCaseQt):
-    def setUp(self):
-        super().setUp()
-        self._window = VignettesQDialog(
-            value_name="cor",
-            score_name="score",
-        )
-
-    def tearDown(self):
-        self._window.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._window.close()
-        self._window = None
-        super().tearDown()
-
-    def test(self):
-        self._window.setScores(
-            scores={
-                "3": (numpy.ones((100, 100)), ComputedScore(tv=2.0, std=3.2)),
-                "7": (numpy.zeros((100, 100)), ComputedScore(tv=25, std=0.6)),
-            },
-            score_method="standard deviation",
-        )
-        self._window.show()
-        self.qWaitForWindowExposed(self._window)
-
-        def assert_scores_are_equal(scores_1, scores_2):
-            assert scores_1.keys() == scores_2.keys()
-            for key, (data_1, computed_score_1) in scores_1.items():
-                data_2, computed_score_2 = scores_2[key]
-                numpy.testing.assert_array_almost_equal(data_1, data_2)
-                assert computed_score_1 == computed_score_2
-
-        scores, score_method = self._window._vignettesWidget.getScores()
-        assert_scores_are_equal(
-            scores_1=scores,
-            scores_2={
-                "3": (numpy.ones((100, 100)), ComputedScore(std=3.2, tv=None)),
-                "7": (numpy.zeros((100, 100)), ComputedScore(std=0.6, tv=None)),
-            },
-        )
-        assert score_method is ScoreMethod.STD
-
-        self._window.setNbColumn(4)
-        self._window.setNbColumn(2)
-        with pytest.raises(ValueError):
-            self._window.setNbColumn(20)
-        self._window.setNbColumn("auto")
-
-        self._window.resize(qt.QSize(400, 400))
-        self.qapp.processEvents()
-        time.sleep(VignettesQDialog.RESIZE_MAX_TIME * 2 / 1000)
-        self.qapp.processEvents()

tomwer/io/utils/test/test_raw_and_processed_data.py

@@ -1,10 +0,0 @@
-from tomwer.io.utils.raw_and_processed_data import file_is_on_processed_data
-
-
-def test_file_is_on_processed_data():
-    """test file_is_on_processed_data function"""
-    assert file_is_on_processed_data("/path/to/file") == False
-    assert file_is_on_processed_data("/path/to/PROCESSED_DATA/file") == True
-    assert file_is_on_processed_data("/path/to/RAW_DATA/file") == False
-    assert file_is_on_processed_data("/path/to/RAW_DATA/PROCESSED_DATA/file") == True
-    assert file_is_on_processed_data("/path/to/PROCESSED_DATA/RAW_DATA/file") == False