tomwer 1.4.1__tar.gz → 1.4.2__tar.gz

{tomwer-1.4.1/src/tomwer.egg-info → tomwer-1.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.4.1
+Version: 1.4.2
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
@@ -28,7 +28,7 @@ Requires-Dist: silx[full]>=2.0
 Requires-Dist: tomoscan>=2.1.0a18
 Requires-Dist: nxtomo>=1.3.0dev4
 Requires-Dist: nxtomomill>=1.1.0a0
-Requires-Dist: processview>=1.4.3
+Requires-Dist: processview>=1.5.0
 Requires-Dist: ewoks>=0.1.1
 Requires-Dist: sluurp>=0.4.1
 Requires-Dist: packaging

{tomwer-1.4.1 → tomwer-1.4.2}/setup.cfg

@@ -37,7 +37,7 @@ install_requires =
 	tomoscan>=2.1.0a18
 	nxtomo>=1.3.0dev4
 	nxtomomill>=1.1.0a0
-	processview>=1.4.3
+	processview>=1.5.0
 	ewoks>=0.1.1
 	sluurp>=0.4.1
 	packaging

{tomwer-1.4.1 → tomwer-1.4.2}/src/orangecontrib/tomwer/orange/managedprocess.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import functools
+import logging
 
 from ewoksorange.bindings import OWEwoksWidgetWithTaskStack
 from ewoksorange.bindings.owwidgets import invalid_data
@@ -10,6 +11,8 @@ from processview.core.superviseprocess import SuperviseProcess
 
 from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 
+_logger = logging.getLogger(__name__)
+
 
 class _SuperviseMixIn(SuperviseProcess):
     def __init__(self, process_id=None):
@@ -18,6 +21,10 @@ class _SuperviseMixIn(SuperviseProcess):
 
     def setCaption(self, caption):
         self.name = caption
+        try:
+            ProcessManager().process_renamed(process=self)
+        except Exception as e:
+            _logger.warning(f"Fail to update process name. Error is {e}")
 
     def notify_skip(self, scan, details=None):
         ProcessManager().notify_dataset_state(

{tomwer-1.4.1 → tomwer-1.4.2}/src/orangecontrib/tomwer/widgets/edit/ImageKeyUpgraderOW.py

@@ -78,6 +78,7 @@ class ImageKeyUpgraderOW(
 
     def get_task_inputs(self):
         task_inputs = super().get_task_inputs()
+        task_inputs["serialize_output_data"] = False
         try:
             scan = task_inputs["data"]
         except Exception:
@@ -86,14 +87,14 @@ class ImageKeyUpgraderOW(
             self.notify_pending(scan=scan)
         return task_inputs
 
-    def _execute_ewoks_task(self, propagate):
+    def _execute_ewoks_task(self, propagate, log_missing_inputs=False):
         task_arguments = self._get_task_arguments()
         scan = task_arguments.get("inputs", {}).get("data", None)
         if scan is not None:
             self.notify_pending(scan=scan)
-        super()._execute_ewoks_task(  # pylint: disable=E1123
-            propagate=propagate, log_missing_inputs=False
-        )
+            super()._execute_ewoks_task(  # pylint: disable=E1123
+                propagate=propagate, log_missing_inputs=log_missing_inputs
+            )
 
     def _notify_state(self):
         try:

{tomwer-1.4.1 → tomwer-1.4.2}/src/orangecontrib/tomwer/widgets/reconstruction/DarkRefAndCopyOW.py

@@ -144,8 +144,6 @@ class DarkRefAndCopyOW(SuperviseOW, WidgetLongProcessing):
             except Exception:
                 _logger.warning("fail to load reconstruction settings")
 
-        self.setCaption(self.windowTitle())
-
     def __new__(cls, *args, **kwargs):
         # ensure backward compatibility with 'static_input'
         static_input = kwargs.get("stored_settings", {}).get("static_input", None)

{tomwer-1.4.1 → tomwer-1.4.2}/src/tomwer/core/process/reconstruction/axis/axis.py

@@ -56,7 +56,7 @@ def _absolute_pos_to_relative_with_warning(absolute_pos: float, det_width: int |
     return absolute_pos_to_relative(absolute_pos=absolute_pos, det_width=det_width)
 
 
-def adapt_tomwer_scan_to_nabu(scan: TomwerScanBase):
+def adapt_tomwer_scan_to_nabu(scan: TomwerScanBase, do_flatfield: bool):
     """simple util to convert tomwer scan to a nabu DataAnalizer and
     updating infos regarding flat and dark if needed
     """
@@ -65,7 +65,7 @@ def adapt_tomwer_scan_to_nabu(scan: TomwerScanBase):
         try:
             update_dataset_info_flats_darks(
                 dataset_infos,
-                flatfield_mode=None,
+                flatfield_mode=do_flatfield,
             )
         except ValueError as exception:
             # nabu raise an error if no darks / flats set. But this can make sense at this stage if the NXtomo has no
@@ -429,11 +429,13 @@ class AxisTask(
         else:
             has_darks = scan.reduced_darks is not None and len(scan.reduced_darks) > 0
             has_flats = scan.reduced_flats is not None and len(scan.reduced_flats) > 0
-
+            do_flatfield = has_darks and has_flats
             res = estimate_cor(
                 method=mode.value,
-                dataset_info=adapt_tomwer_scan_to_nabu(scan=scan),
-                do_flatfield=has_darks and has_flats,
+                dataset_info=adapt_tomwer_scan_to_nabu(
+                    scan=scan, do_flatfield=do_flatfield
+                ),
+                do_flatfield=do_flatfield,
                 cor_options=scan.axis_params.get_nabu_cor_options_as_dict(),
             )
             # convert back to relative

tomwer-1.4.2/src/tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_i_norm.py

@@ -0,0 +1,157 @@
+# coding: utf-8
+from __future__ import annotations
+
+import logging
+import os
+import pickle
+
+from orangecanvas.scheme.readwrite import literal_dumps
+from processview.core.manager import DatasetState, ProcessManager
+from silx.gui import qt
+
+from orangecontrib.tomwer.widgets.reconstruction.SinoNormOW import (
+    SinoNormOW as _SinoNormOW,
+)
+from tomwer.core.utils.scanutils import MockNXtomo
+from tomwer.tests.conftest import qtapp  # noqa F401
+
+logger = logging.getLogger(__name__)
+
+
+class SinoNormOW(_SinoNormOW):
+    def __init__(self, parent=None):
+        self._scans_finished = []
+        super().__init__(parent)
+
+    def processing_finished(self, scan):
+        self._scans_finished.append(scan)
+
+    def wait_processing(self, wait_time):
+        self._window._processing_stack._computationThread.wait(wait_time)
+
+    @property
+    def scans_finished(self):
+        return self._scans_finished
+
+    def compute(self):
+        self._window._processCurrentScan()
+
+    def setROI(self, start_x, end_x, start_y, end_y):
+        self._window.setROI(start_x=start_x, end_x=end_x, start_y=start_y, end_y=end_y)
+
+    def close(self):
+        self._scans_finished = {}
+        super().close()
+
+
+FRAME_DIM = 100
+
+
+def create_scan(folder_name):
+    return MockNXtomo(
+        scan_path=folder_name,
+        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=FRAME_DIM,
+    ).scan
+
+
+def test_SinoNormOW(
+    qtapp,  # noqa F811
+    tmp_path,
+):
+    source_dir = tmp_path / "source"
+    source_dir.mkdir()
+
+    # create scans
+    scan_1 = create_scan(os.path.join(source_dir, "scan_1"))
+    scan_2 = create_scan(os.path.join(source_dir, "scan_2"))
+    scan_3 = create_scan(os.path.join(source_dir, "scan_3"))
+    process_manager = ProcessManager()
+
+    widget = SinoNormOW()
+    widget.show()
+
+    # test serialization
+    pickle.dumps(widget.getConfiguration())
+
+    # test literal dumps
+    widget._updateSettings()
+    literal_dumps(widget._ewoks_default_inputs)
+
+    # test behavior when the widget is unlocked
+    """Test result when used with some interaction"""
+    widget.setLocked(False)
+
+    def process_scalar_manually():
+        widget.setCurrentMethod("division")
+        widget.setCurrentSource("manual ROI")
+
+        qt.QApplication.processEvents()
+        widget.setROI(start_x=0, end_x=10, start_y=0, end_y=10)
+        qt.QApplication.processEvents()
+        widget.compute()
+        widget.wait_processing(5000)
+        qt.QApplication.processEvents()
+
+    widget.process(scan_1)
+    process_scalar_manually()
+    assert (
+        process_manager.get_dataset_state(
+            dataset_id=scan_1.get_identifier(),
+            process=widget,
+        )
+        == DatasetState.WAIT_USER_VALIDATION
+    )
+
+    widget.process(scan_2)
+    process_scalar_manually()
+    assert len(widget.scans_finished) == 0
+    assert (
+        process_manager.get_dataset_state(
+            dataset_id=scan_1.get_identifier(),
+            process=widget,
+        )
+        == DatasetState.SKIPPED
+    )
+    assert (
+        process_manager.get_dataset_state(
+            dataset_id=scan_2.get_identifier(),
+            process=widget,
+        )
+        == DatasetState.WAIT_USER_VALIDATION
+    )
+
+    widget.process(scan_3)
+    process_scalar_manually()
+    widget.validateCurrentScan()
+    assert (
+        process_manager.get_dataset_state(
+            dataset_id=scan_3.get_identifier(),
+            process=widget,
+        )
+        == DatasetState.SUCCEED
+    )
+
+    # test behavior when the widget is locked
+
+    widget.setLocked(True)
+    for scan in (scan_1, scan_2, scan_3):
+        widget.process(scan)
+        widget.wait_processing(5000)
+        qt.QApplication.processEvents()
+
+    for scan in (scan_1, scan_2, scan_3):
+        # test status is SUCCEED
+        assert (
+            process_manager.get_dataset_state(
+                dataset_id=scan.get_identifier(),
+                process=widget,
+            )
+            == DatasetState.SUCCEED
+        )

{tomwer-1.4.1 → tomwer-1.4.2}/src/tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 4
-MICRO = 1
+MICRO = 2
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.4.1 → tomwer-1.4.2/src/tomwer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.4.1
+Version: 1.4.2
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
@@ -28,7 +28,7 @@ Requires-Dist: silx[full]>=2.0
 Requires-Dist: tomoscan>=2.1.0a18
 Requires-Dist: nxtomo>=1.3.0dev4
 Requires-Dist: nxtomomill>=1.1.0a0
-Requires-Dist: processview>=1.4.3
+Requires-Dist: processview>=1.5.0
 Requires-Dist: ewoks>=0.1.1
 Requires-Dist: sluurp>=0.4.1
 Requires-Dist: packaging

{tomwer-1.4.1 → tomwer-1.4.2}/src/tomwer.egg-info/requires.txt

@@ -5,7 +5,7 @@ silx[full]>=2.0
 tomoscan>=2.1.0a18
 nxtomo>=1.3.0dev4
 nxtomomill>=1.1.0a0
-processview>=1.4.3
+processview>=1.5.0
 ewoks>=0.1.1
 sluurp>=0.4.1
 packaging

tomwer-1.4.1/src/tomwer/tests/orangecontrib/tomwer/widgets/reconstruction/tests/test_i_norm.py

@@ -1,190 +0,0 @@
-# coding: utf-8
-from __future__ import annotations
-
-import gc
-import logging
-import os
-import pickle
-import shutil
-import tempfile
-
-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 orangecontrib.tomwer.widgets.reconstruction.SinoNormOW import (
-    SinoNormOW as _NormIOW,
-)
-from tomwer.core import settings
-from tomwer.core.utils.lbsram import mock_low_memory
-from tomwer.core.utils.scanutils import MockNXtomo
-
-logger = logging.getLogger(__name__)
-
-
-class NormIOW(_NormIOW):
-    def __init__(self, parent=None):
-        self._scans_finished = []
-        super().__init__(parent)
-
-    def processing_finished(self, scan):
-        self._scans_finished.append(scan)
-
-    def wait_processing(self, wait_time):
-        self._window._processing_stack._computationThread.wait(wait_time)
-
-    @property
-    def scans_finished(self):
-        return self._scans_finished
-
-    def compute(self):
-        self._window._processCurrentScan()
-
-    def setROI(self, start_x, end_x, start_y, end_y):
-        self._window.setROI(start_x=start_x, end_x=end_x, start_y=start_y, end_y=end_y)
-
-    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 = NormIOW()
-        self.widget.show()
-
-    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):
-        self.widget._updateSettings()
-        literal_dumps(self.widget._ewoks_default_inputs)
-
-    def testUnlocked(self):
-        """Test result when used with some interaction"""
-        self.widget.setLocked(False)
-
-        def process_scalar_manually():
-            self.widget.setCurrentMethod("division")
-            self.widget.setCurrentSource("manual ROI")
-
-            self.qapp.processEvents()
-            self.widget.setROI(start_x=0, end_x=10, start_y=0, end_y=10)
-            self.qapp.processEvents()
-            self.widget.compute()
-            self.widget.wait_processing(5000)
-            self.qapp.processEvents()
-
-        self.widget.process(self.scan_1)
-        process_scalar_manually()
-        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)
-        process_scalar_manually()
-        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)
-        process_scalar_manually()
-        self.widget.validateCurrentScan()
-        self.assertEqual(
-            self._process_manager.get_dataset_state(
-                dataset_id=self.scan_3.get_identifier(),
-                process=self.widget,
-            ),
-            DatasetState.SUCCEED,
-        )
-
-    def testTestLbsram(self):
-        """Test scan are all validated if 'low memory on lbsram' scenario is
-        activated"""
-        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 testLocked(self):
-        """Test scan are all validated if the widget is lock"""
-        self.widget.setLocked(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):
-            # test status is SUCCEED
-            with self.subTest(scan=str(scan)):
-                self.assertEqual(
-                    self._process_manager.get_dataset_state(
-                        dataset_id=scan.get_identifier(),
-                        process=self.widget,
-                    ),
-                    DatasetState.SUCCEED,
-                )