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

tomwer/gui/reconstruction/saaxis/corrangeselector.py

@@ -16,10 +16,6 @@ from silx.gui.plot import items
 from silx.utils.enum import Enum as _Enum
 from tomoscan.esrf.scan.utils import get_data
 
-from tomwer.core.process.reconstruction.utils.cor import (
-    absolute_pos_to_relative,
-    relative_pos_to_absolute,
-)
 from tomwer.core.process.reconstruction.saaxis.saaxis import ReconstructionMode
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui import icons
@@ -27,7 +23,6 @@ from tomwer.gui.reconstruction.saaxis.sliceselector import SliceSelector
 from tomwer.gui.utils.lineselector import QSliceSelectorDialog
 from tomwer.gui.utils.slider import LogSlider
 from tomwer.gui.visualization.sinogramviewer import SinogramViewer as _SinogramViewer
-from tomwer.gui.fonts import FONT_MEDIUM, FONT_IMPORTANT
 
 _logger = logging.getLogger(__name__)
 
@@ -498,9 +493,7 @@ class _EstimatedCorWidget(qt.QGroupBox):
                 return 0.0
             elif mode in ("abs", "absolute"):
                 if self._frameWidth is not None:
-                    return relative_pos_to_absolute(
-                        relative_pos=0.0, det_width=self._frameWidth
-                    )
+                    return (self._frameWidth - 1) / 2.0
                 else:
                     return self._MIDDLE_COR_TXT
             else:
@@ -526,9 +519,7 @@ class _EstimatedCorWidget(qt.QGroupBox):
             old = self.blockSignals(True)
             old_mcor = self._manualCORAbs.blockSignals(True)
             self._manualCORAbs.setValue(
-                relative_pos_to_absolute(
-                    relative_pos=self._manualCORRel.value(), det_width=self._frameWidth
-                )
+                self._manualCORRel.value() + (self._frameWidth - 1) / 2.0
             )
             self._manualCORAbs.blockSignals(old_mcor)
             self.blockSignals(old)
@@ -538,10 +529,7 @@ class _EstimatedCorWidget(qt.QGroupBox):
             old = self.blockSignals(True)
             old_mcor = self._manualCORRel.blockSignals(True)
             self._manualCORRel.setValue(
-                absolute_pos_to_relative(
-                    absolute_pos=self._manualCORAbs.value(),
-                    det_width=self._frameWidth,
-                )
+                self._manualCORAbs.value() - (self._frameWidth - 1) / 2.0
             )
             self._manualCORRel.blockSignals(old_mcor)
             self.blockSignals(old)
@@ -594,12 +582,15 @@ class SAAxisOptions(qt.QWidget):
     sigConfigurationChanged = qt.Signal()
     """signal emitted when the configuration change"""
 
+    _FONT_IMPORTANT = qt.QFont("Arial", 12)
+    _FONT_MEDIUM = qt.QFont("Arial", 10)
+
     def __init__(self, parent=None):
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QVBoxLayout())
         # reconstruction mode
         self._reconstructionMode = _ReconstructionModeGB(parent=self)
-        self._reconstructionMode.setFont(FONT_MEDIUM)
+        self._reconstructionMode.setFont(self._FONT_MEDIUM)
         self.layout().addWidget(self._reconstructionMode)
 
         # estimated cor
@@ -607,12 +598,12 @@ class SAAxisOptions(qt.QWidget):
             self,
             title="Estimated cor position (x axis)",
         )
-        self._estimatedCorWidget.setFont(FONT_IMPORTANT)
+        self._estimatedCorWidget.setFont(self._FONT_IMPORTANT)
         self.layout().addWidget(self._estimatedCorWidget)
 
         # detection accuracy
         self._detectionAccuracy = _DetectionAccuracyGB(parent=self)
-        self._detectionAccuracy.setFont(FONT_MEDIUM)
+        self._detectionAccuracy.setFont(self._FONT_MEDIUM)
         self.layout().addWidget(self._detectionAccuracy)
 
         # number of reconstructions eq volume size
@@ -622,7 +613,7 @@ class SAAxisOptions(qt.QWidget):
         self._nReconsSB = qt.QSpinBox(self._nReconsWidget)
         self._nReconsSB.setRange(0, 2000)
         self._nReconsSB.setValue(30)
-        self._nReconsWidget.setFont(FONT_IMPORTANT)
+        self._nReconsWidget.setFont(self._FONT_IMPORTANT)
         self._nReconsWidget.layout().addRow("Number of reconstruction", self._nReconsSB)
         self.layout().addWidget(self._nReconsWidget)
 

tomwer/gui/reconstruction/scores/scoreplot.py

@@ -14,7 +14,6 @@ from matplotlib import image as _matplotlib_image
 from silx.gui import qt
 from silx.gui.plot import PlotWidget
 
-from tomwer.core.process.reconstruction.utils.cor import relative_pos_to_absolute
 from tomwer.core.process.reconstruction.scores.params import ScoreMethod
 from tomwer.gui import icons, settings
 from tomwer.gui.reconstruction.saaxis.dimensionwidget import DimensionWidget
@@ -308,9 +307,7 @@ class CorSelection(VariableSelection):
         if relative_value is None or self._img_width is None:
             self._absoluteVarValueLE.clear()
         else:
-            absolute_value = relative_pos_to_absolute(
-                relative_pos=relative_value, det_width=self._img_width
-            )
+            absolute_value = relative_value + (self._img_width - 1) / 2.0
             self._absoluteVarValueLE.setText(f"{absolute_value:.3f}")
 
     def getWindowTitle(self):
@@ -425,7 +422,7 @@ class _VariableValueLabels(qt.QWidget):
             # paint oblique text
             with PainterRotationCM(
                 painter=painter,
-                x=var_px_pos + (self._slider_ticks_margin / 2.0),
+                x=var_px_pos + self._slider_ticks_margin / 2.0,
                 y=0,
                 angle=self.rotation_angle_degree,
             ) as l_painter:

tomwer/gui/reconstruction/tests/test_nabu.py

@@ -19,11 +19,8 @@ from tomwer.gui.reconstruction.nabu.nabuconfig.reconstruction import (
 )
 from tomwer.gui.reconstruction.nabu.nabuflow import NabuFlowControl
 from tomwer.gui.reconstruction.nabu.volume import NabuVolumeTabWidget
-from tomwer.gui.reconstruction.axis.EstimatedCORWidget import EstimatedCORWidget
 from tomwer.tests.utils import skip_gui_test
 from tomwer.core.process.output import ProcessDataOutputDirMode
-from tomwer.tests.conftest import qtapp  # noqa F401
-from tomwer.synctools.axis import QAxisRP
 
 
 class ProcessClass:
@@ -359,8 +356,3 @@ class TestNabuVolumeWidget(TestCaseQt):
             }
         )
         self.assertEqual(self.nabuWidget.getConfiguration(), conf)
-
-
-def test_EstimatedCorWidget(qtapp):  # noqa F811
-    """test of EstimatedCorWidget"""
-    EstimatedCORWidget(parent=None, axis_params=QAxisRP())

tomwer/gui/stitching/config/axisparams.py

@@ -119,8 +119,6 @@ class StitcherAxisParams(qt.QWidget):
             for option in options:
                 clean_option = option.rstrip(" ").lstrip(" ")
                 opt_name, opt_value = clean_option.split("=")
-                if opt_value == "":
-                    continue
                 if opt_name == stitching_config.KEY_IMG_REG_METHOD:
                     self.setShiftSearchMethod(opt_value)
                 elif opt_name == stitching_config.KEY_WINDOW_SIZE:

tomwer/gui/stitching/z_stitching/fineestimation.py

@@ -73,7 +73,7 @@ class Axis_N_Params(qt.QGroupBox):
 
 class AutoRefineWidget(qt.QWidget):
     """
-    widget grouping information not specific to objects (output file, stitching strategy...)
+    widget grouping information not specific to objects (output file, stithcing strategy...)
     """
 
     def __init__(self, parent=None):

tomwer/gui/tests/test_axis_gui.py

@@ -1,5 +1,4 @@
 import pytest
-import numpy
 
 from tomwer.gui.reconstruction.axis.AxisSettingsWidget import AxisSettingsTabWidget
 from tomwer.synctools.axis import QAxisRP
@@ -11,33 +10,18 @@ from tomwer.tests.conftest import qtapp  # noqa F401
 def test_get_nabu_cor_opts(qtapp):  # noqa F811
     axis_params = QAxisRP()
     widget = AxisSettingsTabWidget(recons_params=axis_params)
-    assert axis_params.get_nabu_cor_options_as_dict() == {
-        "side": "right",
-        "radio_angles": (0.0, numpy.pi),
-        "slice_idx": "middle",
-    }
-    widget._optionsWidget._corOpts.setText("low_pass=2.0")
-    widget._optionsWidget._corOpts.editingFinished.emit()
-    assert axis_params.get_nabu_cor_options_as_dict() == {
-        "side": "right",
-        "radio_angles": (0.0, numpy.pi),
-        "slice_idx": "middle",
-        "low_pass": 2.0,
-    }
-    widget._optionsWidget._corOpts.setText("low_pass=2 ; high_pass=10")
-    widget._optionsWidget._corOpts.editingFinished.emit()
-    assert axis_params.get_nabu_cor_options_as_dict() == {
-        "side": "right",
-        "radio_angles": (0.0, numpy.pi),
-        "slice_idx": "middle",
-        "low_pass": 2.0,
-        "high_pass": 10.0,
-    }
-    widget._calculationWidget.setEstimatedCorValue("left")
-    assert axis_params.get_nabu_cor_options_as_dict() == {
-        "side": "left",
-        "radio_angles": (0.0, numpy.pi),
-        "slice_idx": "middle",
-        "low_pass": 2.0,
-        "high_pass": 10.0,
-    }
+    assert axis_params.get_nabu_cor_options_as_str() == "side='right'"
+    widget._calculationWidget._corOpts.setText("low_pass=2")
+    widget._calculationWidget._corOpts.editingFinished.emit()
+    assert axis_params.get_nabu_cor_options_as_str() == "side='right' ; low_pass=2"
+    widget._calculationWidget._corOpts.setText("low_pass=2 ; high_pass=10")
+    widget._calculationWidget._corOpts.editingFinished.emit()
+    assert axis_params.get_nabu_cor_options_as_str() == (
+        "side='right' ; low_pass=2 ; high_pass=10"
+    )
+    widget._calculationWidget._sideCB.setCurrentText("left")
+    widget._calculationWidget._corOpts.editingFinished.emit()
+    assert (
+        axis_params.get_nabu_cor_options_as_str()
+        == "side='left' ; low_pass=2 ; high_pass=10"
+    )

tomwer/synctools/stacks/reconstruction/axis.py

@@ -23,7 +23,7 @@ _logger = logging.getLogger(__name__)
 
 
 class AxisProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisTask` but having a stack for treating
+    """Implementation of the `.AxisProcess` but having a stack for treating
     scans and making computation in threads"""
 
     def __init__(self, axis_params, process_id=None):
@@ -55,7 +55,7 @@ class AxisProcessStack(FIFO, qt.QObject):
             if callback is not None:
                 callback()
             self.scan_ready(scan=data)
-        elif mode is (AxisMode.manual,):
+        elif not self._axis_params.use_sinogram and mode in (AxisMode.manual,):
             # if cor is not set then set it to 0 (can be the case if no)
             # interaction has been dne
             cor = self._axis_params.relative_cor_value
@@ -84,6 +84,14 @@ class AxisProcessStack(FIFO, qt.QObject):
             # we will keep the actual one (should have been defined previously)
             self._end_computation(data=data, future_tomo_obj=None, callback=callback)
 
+        elif (
+            not self._axis_params.use_sinogram
+            and mode not in AxisTask._CALCULATIONS_METHODS
+        ):
+            _logger.warning(f"no method defined to compute {mode}")
+            if callback is not None:
+                callback()
+            self._process_next()
         else:
             _logger.processStarted(
                 f"Start cor calculation on {data} ({self._axis_params.get_simple_str()})"
@@ -105,7 +113,7 @@ class AxisProcessStack(FIFO, qt.QObject):
         """
         assert isinstance(data, TomwerScanBase)
         assert self._axis_params is not None
-        # copy result computed on scan on the AxisTask reconsparams
+        # copy result computed on scan on the AxisProcess reconsparams
         self._axis_params.set_relative_value(
             data.axis_params.relative_cor_value
         )  # noqa
@@ -159,13 +167,23 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
             },
             process_id=self.process_id,
         )
+        axis = self.apply_patch(axis=axis)
         try:
             axis.run()
         except NoAxisUrl as e:
             self.center_of_rotation = None
-            _logger.error(f"CoR calculation failed. Issue with input ({e})")
+            _logger.error(str(e))
         except Exception as e:
-            _logger.error(f"CoR calculation failed ({e})", stack_info=True)
+            _logger.error(str(e))
             self.center_of_rotation = None
         else:
             self.center_of_rotation = self._scan.axis_params.relative_cor_value
+
+    def patch_calc_method(self, mode, function):
+        self.__patch[mode] = function
+
+    def apply_patch(self, axis):
+        for mode, patch_fct in self.__patch.items():
+            if mode in AxisMode:
+                axis._CALCULATIONS_METHODS[mode] = patch_fct
+        return axis

tomwer/synctools/stacks/reconstruction/dkrefcopy.py

@@ -23,7 +23,7 @@ _logger = logging.getLogger(__name__)
 
 
 class DarkRefCopyProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisTask` but having a stack for treating
+    """Implementation of the `.AxisProcess` but having a stack for treating
     scans and making computation in threads"""
 
     sigRefSetted = qt.Signal(str)

tomwer/synctools/stacks/reconstruction/nabu.py

@@ -21,7 +21,7 @@ _logger = logging.getLogger(__name__)
 
 
 class NabuSliceProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisTask` but having a stack for treating
+    """Implementation of the `.AxisProcess` but having a stack for treating
     scans and making computation in threads"""
 
     def __init__(self, parent=None, process_id=None):
@@ -78,7 +78,7 @@ class NabuSliceProcessStack(FIFO, qt.QObject):
 
 
 class NabuVolumeProcessStack(NabuSliceProcessStack):
-    """Implementation of the `.AxisTask` but having a stack for treating
+    """Implementation of the `.AxisProcess` but having a stack for treating
     scans and making computation in threads"""
 
     def _create_processing_thread(self, process_id=None) -> qt.QThread:

tomwer/synctools/stacks/reconstruction/normalization.py

@@ -20,7 +20,7 @@ _logger = logging.getLogger(__name__)
 
 
 class INormalizationProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisTask` but having a stack for treating
+    """Implementation of the `.AxisProcess` but having a stack for treating
     scans and making computation in threads"""
 
     def __init__(self, process_id=None):

tomwer/synctools/stacks/reconstruction/saaxis.py

@@ -22,7 +22,7 @@ _logger = logging.getLogger(__name__)
 
 
 class SAAxisProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisTask` but having a stack for treating
+    """Implementation of the `.AxisProcess` but having a stack for treating
     scans and making computation in threads"""
 
     def __init__(self, saaxis_params, process_id=None):

tomwer/synctools/stacks/reconstruction/sadeltabeta.py

@@ -24,7 +24,7 @@ _logger = logging.getLogger(__name__)
 
 
 class SADeltaBetaProcessStack(FIFO, qt.QObject):
-    """Implementation of the `.AxisTask` but having a stack for treating
+    """Implementation of the `.AxisProcess` but having a stack for treating
     scans and making computation in threads"""
 
     def __init__(self, sa_delta_beta_params, process_id=None):

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

@@ -179,6 +179,22 @@ class TestAxisStack(TestCaseQt):
         self.assertEqual(self._scan2.axis_params, None)
         self.assertEqual(self._scan3.axis_params, None)
 
+    def testUnlockStack(self):
+        """Check that all axis position will be computed properly if we set a
+        stack of scan"""
+        self._mainWindow.recons_params.set_relative_value(1.0)
+        for scan in (self._scan1, self._scan2, self._scan3):
+            self._mainWindow.process(scan)
+
+        for i in range(5):
+            self.qapp.processEvents()
+            time.sleep(0.2)
+            self.qapp.processEvents()
+
+        self.assertNotEqual(self._scan1.axis_params, None)
+        self.assertNotEqual(self._scan2.axis_params, None)
+        self.assertNotEqual(self._scan3.axis_params, None)
+
     def testLockStack(self):
         """Check that axis position will be simply copy if we are in a lock
         stack"""

tomwer/tests/test_ewoks/test_single_node_execution.py

@@ -37,7 +37,7 @@ pytest.mark.skipif(condition=not has_nabu, reason="nabu not installed")
 
 classes_to_test = {
     "darkref": "tomwer.core.process.reconstruction.darkref.darkrefs.DarkRefs",
-    "axis": "tomwer.core.process.reconstruction.axis.axis.AxisTask",
+    "axis": "tomwer.core.process.reconstruction.axis.axis.AxisProcess",
     "nabu slices": "tomwer.core.process.reconstruction.nabu.nabuslices.NabuSlices",
 }
 

tomwer/tests/test_ewoks/test_workflows.py

@@ -55,7 +55,7 @@ def test_simple_workflow_nabu():
                     {
                         "id": "axis",
                         "task_type": "class",
-                        "task_identifier": "tomwer.core.process.reconstruction.axis.axis.AxisTask",
+                        "task_identifier": "tomwer.core.process.reconstruction.axis.axis.AxisProcess",
                         "default_inputs": [
                             {
                                 "name": "axis_params",

tomwer/version.py

@@ -78,7 +78,7 @@ RELEASE_LEVEL_VALUE = {
 MAJOR = 1
 MINOR = 4
 MICRO = 0
-RELEV = "final"  # <16
+RELEV = "rc"  # <16
 SERIAL = 0  # <16
 
 date = __date__

{tomwer-1.4.0.dist-info → tomwer-1.4.0rc0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.4.0
+Version: 1.4.0rc0
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone
@@ -28,9 +28,9 @@ 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>=1.3
 Requires-Dist: ewoks>=0.1.1
-Requires-Dist: sluurp>=0.4.1
+Requires-Dist: sluurp>=0.4.0
 Requires-Dist: packaging
 Requires-Dist: flufl-lock
 Requires-Dist: pyunitsystem>=2.0.0a