tomwer 1.3.26__py3-none-any.whl → 1.4.0__py3-none-any.whl

tomwer/gui/stitching/axisorderedlist.py

@@ -1,27 +1,25 @@
 """widgets to perform a z-sttiching in pre processing (from projections) or post processing (from reconstructed volumes)"""
 
-__author__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "20/01/2023"
+from __future__ import annotations
+
 
 import logging
-from typing import Optional
 
 from silx.gui import qt
 from silx.gui.utils import blockSignals
 from tomoscan.scanbase import TomoScanBase
-from tomoscan.serie import Serie
+from tomoscan.series import Series
 
 from tomwer.io.utils.tomoobj import get_tomo_objs_instances
 from tomwer.core.tomwer_object import TomwerObject
 from tomwer.gui.stitching.metadataholder import QStitchingMetadata
 from tomwer.gui.utils.illustrations import _IllustrationWidget
-
+from .singleaxis import _SingleAxisMixIn
 
 _logger = logging.getLogger(__name__)
 
 
-class ZOrderedTomoObjWidget(qt.QWidget):
+class AxisOrderedTomoObjWidget(qt.QWidget, _SingleAxisMixIn):
     """
     main widget to define configuration of a z-stitching
     """
@@ -33,8 +31,11 @@ class ZOrderedTomoObjWidget(qt.QWidget):
     sigRemoveObjRequest = qt.Signal(TomwerObject)
     """request when an object should be removed by calling the 'remove button'."""
 
-    def __init__(self, parent=None):
+    def __init__(self, axis: int, parent=None):
         super().__init__(parent=parent)
+        if axis not in (0, 1, 2):
+            raise ValueError(f"axis should be in (0, 1, 2). Got {axis}")
+        self._axis = axis  # implement _SingleAxisMixIn interface
         self.setLayout(qt.QGridLayout())
 
         self._addTomoObjCallbacks = tuple()
@@ -43,14 +44,15 @@ class ZOrderedTomoObjWidget(qt.QWidget):
         # left panel with arrow
         img_flow = "flow_down"
         left_panel_width = 50
-        self._zLabel = qt.QLabel("z", parent=self)
-        self._zLabel.setToolTip("z is also know as axis 0")
-        font = self._zLabel.font()
+        axis_label = self.axis_alias(axis)
+        self._axisLabel = qt.QLabel(axis_label, parent=self)
+        self._axisLabel.setToolTip(f"{axis_label} is also know as axis {axis}")
+        font = self._axisLabel.font()
         font.setPixelSize(40)
-        self._zLabel.setFont(font)
-        self._zLabel.setAlignment(qt.Qt.AlignCenter)
-        self._zLabel.setFixedWidth(left_panel_width)
-        self.layout().addWidget(self._zLabel, 1, 0, 1, 1)
+        self._axisLabel.setFont(font)
+        self._axisLabel.setAlignment(qt.Qt.AlignCenter)
+        self._axisLabel.setFixedWidth(left_panel_width)
+        self.layout().addWidget(self._axisLabel, 1, 0, 1, 1)
 
         self._flowIllustration = _IllustrationWidget(parent=self, img=img_flow)
         self._flowIllustration.setFixedWidth(left_panel_width)
@@ -59,13 +61,13 @@ class ZOrderedTomoObjWidget(qt.QWidget):
         )
         self.layout().addWidget(self._flowIllustration, 2, 0, 1, 1)
         self._flowIllustration.setToolTip(
-            "we are first ordering tomo object from z (aka axis 0) position to apply stitching"
+            f"we are first ordering tomo object along axis {axis} (aka {self.axis_alias(axis)}) position to apply stitching"
         )
 
         # central object list
         self._tomoObjsTableView = qt.QTableView(parent=self)
         self._tomoObjsTableView.setModel(
-            AxisOrderedTomoObjsModel(parent=self._tomoObjsTableView, axis=0)
+            AxisOrderedTomoObjsModel(parent=self._tomoObjsTableView, axis=axis)
         )
         self._tomoObjsTableView.setSelectionBehavior(qt.QAbstractItemView.SelectRows)
 
@@ -83,25 +85,25 @@ class ZOrderedTomoObjWidget(qt.QWidget):
         else:
             self._tomoObjsTableView.model().addTomoObj(tomo_obj)
             # register tomo obj metadata modification to make sure we tell the z ordered list up to data
-            tomo_obj.stitching_metadata.sigChanged.connect(self._orderMightHavechanged)
+            tomo_obj.stitching_metadata.sigChanged.connect(self._orderMightHaveChanged)
             if trigger_callbacks:
                 for callback in self._addTomoObjCallbacks:
                     callback(tomo_obj)
 
     def removeTomoObj(self, tomo_obj, trigger_callbacks=False):
         self._tomoObjsTableView.model().removeTomoObj(tomo_obj)
-        tomo_obj.stitching_metadata.sigChanged.disconnect(self._orderMightHavechanged)
+        tomo_obj.stitching_metadata.sigChanged.disconnect(self._orderMightHaveChanged)
         if trigger_callbacks:
             for callback in self._removetomoObjCallbacks:
                 callback(tomo_obj)
 
-    def _orderMightHavechanged(self):
-        # when z position is updated from the GUI, make sure the z ordered list of tomo object is still
+    def _orderMightHaveChanged(self):
+        # when position over {axis} is updated from the GUI, make sure the {axis} ordered list of tomo object is still
         # ordered and selection is still the accurate one.
         # this case is not handled on this widget
-        pass
+        self._tomoObjsTableView.model().reorder_objs()
 
-    def getTomoObjsZOrdered(self) -> tuple:
+    def getTomoObjsAxisOrdered(self) -> tuple:
         return tuple(self._tomoObjsTableView.model()._axis_decreasing_ordered_objs)
 
     def clearTomoObjs(self):
@@ -111,9 +113,10 @@ class ZOrderedTomoObjWidget(qt.QWidget):
 class AxisOrderedTomoObjsModel(qt.QAbstractTableModel):
     def __init__(self, axis: int, parent=None) -> None:
         super().__init__(parent)
+        assert axis in (0, 1, 2)
         self._axis = axis
         # either we plot the tomo_obj in the list within the full identifier or with the reduce str (in this case two scans can have identical name. Identifier is unique)
-        self._objs = Serie(name="unordered tomo obj", use_identifiers=False)
+        self._objs = Series(name="unordered tomo obj", use_identifiers=False)
         self._axis_decreasing_ordered_objs = []
         self._headers = ["index", "tomo obj"]
         self._tomoObjToIndex = {}
@@ -142,7 +145,7 @@ class AxisOrderedTomoObjsModel(qt.QAbstractTableModel):
             return index
 
     def clearTomoObjs(self):
-        self._objs = Serie(name="unordered tomo obj", use_identifiers=False)
+        self._objs = Series(name="unordered tomo obj", use_identifiers=False)
         self._axis_decreasing_ordered_objs = []
         self.layoutChanged.emit()
 
@@ -154,7 +157,7 @@ class AxisOrderedTomoObjsModel(qt.QAbstractTableModel):
                 tomo_obj.stitching_metadata.get_abs_position_px(axis=self._axis) or 0.0
             )
 
-        self._axis_decreasing_ordered_objs = Serie(
+        self._axis_decreasing_ordered_objs = Series(
             "ordered tomo obj",
             sorted(self._objs[:], key=get_min_axis_or_0, reverse=True),
             use_identifiers=False,
@@ -235,15 +238,15 @@ class AxisOrderedTomoObjsModel(qt.QAbstractTableModel):
             return None
 
 
-class ZOrderedTomoObjWidgetSingleSel(ZOrderedTomoObjWidget):
+class AxisOrderedTomoObjWidgetSingleSel(AxisOrderedTomoObjWidget):
     """
-    ZOrderedTomoObjWidget with a list that can select a single line.
+    AxisOrderedTomoObjWidget with a list that can select a single line.
 
     The idea is that it can be used to select the object to be edited on another widget
     """
 
-    def __init__(self, parent=None):
-        super().__init__(parent)
+    def __init__(self, axis: int, parent=None):
+        super().__init__(axis=axis, parent=parent)
         self._tomoObjsTableView.setSelectionMode(qt.QAbstractItemView.SingleSelection)
 
     def removeTomoObj(self, tomo_obj):
@@ -260,7 +263,7 @@ class ZOrderedTomoObjWidgetSingleSel(ZOrderedTomoObjWidget):
             return self._tomoObjsTableView.model().getTomoObj(selection[0])
         return None
 
-    def setSelectedTomoObj(self, tomo_obj: Optional[TomwerObject]):
+    def setSelectedTomoObj(self, tomo_obj: TomwerObject | None):
         self._tomoObjsTableView.selectionModel().clearSelection()
         if tomo_obj is not None:
             model = self._tomoObjsTableView.model()
@@ -287,13 +290,16 @@ class ZOrderedTomoObjWidgetSingleSel(ZOrderedTomoObjWidget):
             self.setSelectedTomoObj(selectedTomoObj)
 
 
-class EditableZOrderedTomoObjWidget(ZOrderedTomoObjWidget):
+class EditableOrderedTomoObjWidget(AxisOrderedTomoObjWidget):
     """
     same as the ZOrderedTomoObjWidget but you can add and remove tomo obj to the list
     """
 
-    def __init__(self, parent=None):
-        super().__init__(parent)
+    def __init__(self, axis: int, parent=None):
+        super().__init__(axis=axis, parent=parent)
+        if axis not in (0, 1, 2):
+            raise ValueError(f"axis must be in (0, 1, 2). Got {axis}")
+        self._axis = axis
         self.setAcceptDrops(True)
 
         # allow multiple selection as we might want to remove several object at the same time
@@ -320,6 +326,10 @@ class EditableZOrderedTomoObjWidget(ZOrderedTomoObjWidget):
 
         self.layout().addWidget(self._buttons, 999, 0, 1, 2)
 
+    @property
+    def axis(self) -> int:
+        return self._axis
+
     def removeTomoObj(self, tomo_obj, trigger_callbacks=False):
         selected = set(self.getSelectedTomoObjs())
         super().removeTomoObj(tomo_obj=tomo_obj, trigger_callbacks=trigger_callbacks)

tomwer/gui/stitching/config/axisparams.py

@@ -1,5 +1,6 @@
+from __future__ import annotations
+
 import logging
-from typing import Union
 
 from nabu.stitching import config as stitching_config
 from nabu.stitching.utils import ShiftAlgorithm as StitchShiftAlgorithm
@@ -7,6 +8,9 @@ from silx.gui import qt
 
 from tomwer.gui.utils.qt_utils import block_signals
 from tomwer.gui.configuration.level import ConfigurationLevel
+from tomwer.gui.utils.scrollarea import QComboBoxIgnoreWheel as QComboBox
+from tomwer.gui.utils.scrollarea import QSpinBoxIgnoreWheel as QSpinBox
+
 
 _logger = logging.getLogger(__name__)
 
@@ -17,7 +21,7 @@ class StitcherAxisParams(qt.QWidget):
     """
 
     sigConfigChanged = qt.Signal()
-    # signal emit when the configuration is updated
+    """signal emit when the configuration is updated"""
 
     DEFAULT_WINDOW_SEARCH_SIZE = 400
     # default window size for shift search
@@ -29,15 +33,15 @@ class StitcherAxisParams(qt.QWidget):
         assert axis in (0, 1, 2)
         self._axis = axis
         self.setLayout(qt.QGridLayout())
-        self._shiftSearchMethodCB = qt.QComboBox(self)
+        self._shiftSearchMethodCB = QComboBox(parent=self)
         # shift algorithm
-        axis_0_shift_search_method = [
+        shift_search_methods = [
             StitchShiftAlgorithm.NABU_FFT,
             StitchShiftAlgorithm.SKIMAGE,
             StitchShiftAlgorithm.ITK_IMG_REG_V4,
             StitchShiftAlgorithm.NONE,
         ]
-        for method in axis_0_shift_search_method:
+        for method in shift_search_methods:
             self._shiftSearchMethodCB.addItem(method.value)
         self._methodLabel = qt.QLabel("shift search method", self)
         self.layout().addWidget(self._methodLabel, 0, 0, 1, 1)
@@ -45,10 +49,11 @@ class StitcherAxisParams(qt.QWidget):
         # stitching options
         self._windowSizeLabel = qt.QLabel("window size", self)
         self.layout().addWidget(self._windowSizeLabel, 1, 0, 1, 1)
-        self._windowSizeSB = qt.QSpinBox(self)
+        self._windowSizeSB = QSpinBox(self)
         self._windowSizeSB.setMinimum(1)
         self._windowSizeSB.setMaximum(9999999)
         self._windowSizeSB.setValue(self.DEFAULT_WINDOW_SEARCH_SIZE)
+        self._windowSizeSB.setSuffix("px")
         self.layout().addWidget(self._windowSizeSB, 1, 1, 1, 1)
         tooltip = "size of the window to try to refine shift"
         self._windowSizeLabel.setToolTip(tooltip)
@@ -77,7 +82,7 @@ class StitcherAxisParams(qt.QWidget):
     def getShiftSearchMethod(self) -> StitchShiftAlgorithm:
         return StitchShiftAlgorithm.from_value(self._shiftSearchMethodCB.currentText())
 
-    def setShiftSearchMethod(self, method: Union[StitchShiftAlgorithm, str]) -> None:
+    def setShiftSearchMethod(self, method: StitchShiftAlgorithm | str) -> None:
         method = StitchShiftAlgorithm.from_value(method)
         idx = self._shiftSearchMethodCB.findText(method.value)
         self._shiftSearchMethodCB.setCurrentIndex(idx)
@@ -114,6 +119,8 @@ 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:
@@ -141,8 +148,15 @@ class StitcherAxisParams(qt.QWidget):
         self.sigConfigChanged.emit()
 
     def setConfigurationLevel(self, level: ConfigurationLevel):
-        self._windowSizeLabel.setVisible(level >= ConfigurationLevel.OPTIONAL)
-        self._windowSizeSB.setVisible(level >= ConfigurationLevel.OPTIONAL)
+        method = self.getShiftSearchMethod()
+        self._windowSizeLabel.setVisible(
+            level >= ConfigurationLevel.OPTIONAL
+            and method is not StitchShiftAlgorithm.NONE
+        )
+        self._windowSizeSB.setVisible(
+            level >= ConfigurationLevel.OPTIONAL
+            and method is not StitchShiftAlgorithm.NONE
+        )
         self._filteringGroup.setVisible(level >= ConfigurationLevel.ADVANCED)
 
 
@@ -155,10 +169,10 @@ class _FilteringGroupBox(qt.QGroupBox):
 
         self.setLayout(qt.QFormLayout())
 
-        self._lowPassFilterSP = qt.QSpinBox(self)
+        self._lowPassFilterSP = QSpinBox(self)
         self.layout().addRow("low pass filter", self._lowPassFilterSP)
 
-        self._highPassFilterSP = qt.QSpinBox(self)
+        self._highPassFilterSP = QSpinBox(self)
         self.layout().addRow("high pass filter", self._highPassFilterSP)
 
         # connect signal / slot

tomwer/gui/stitching/config/output.py

@@ -62,6 +62,7 @@ class StitchingOutput(qt.QWidget):
     """
 
     sigChanged = qt.Signal()
+    """emit when stithcing output change"""
 
     def __init__(self, parent=None) -> None:
         super().__init__(parent)
@@ -98,7 +99,7 @@ class StitchingOutput(qt.QWidget):
         if self.__stitching_type is StitchingType.Z_POSTPROC:
             config.update(
                 {
-                    stitching_config.Z_POST_PROC_SECTION: {
+                    stitching_config.POST_PROC_SECTION: {
                         stitching_config.OUTPUT_VOLUME: self._postProcOutput.getUrl()
                     },
                 }
@@ -118,7 +119,7 @@ class StitchingOutput(qt.QWidget):
             else:
                 config.update(
                     {
-                        stitching_config.Z_PRE_PROC_SECTION: {
+                        stitching_config.PRE_PROC_SECTION: {
                             stitching_config.DATA_FILE_FIELD: scan.master_file,
                             stitching_config.DATA_PATH_FIELD: scan.entry,
                         },
@@ -135,16 +136,16 @@ class StitchingOutput(qt.QWidget):
         if stitching_type is not None:
             self._updateOutputForStitchingType(stitching_type)
 
-        output_volume = config.get(stitching_config.Z_POST_PROC_SECTION, {}).get(
+        output_volume = config.get(stitching_config.POST_PROC_SECTION, {}).get(
             stitching_config.OUTPUT_VOLUME, None
         )
         if output_volume:
             self._postProcOutput.setUrl(output_volume)
 
-        location = config.get(stitching_config.Z_PRE_PROC_SECTION, {}).get(
+        location = config.get(stitching_config.PRE_PROC_SECTION, {}).get(
             stitching_config.DATA_FILE_FIELD, None
         )
-        data_path = config.get(stitching_config.Z_PRE_PROC_SECTION, {}).get(
+        data_path = config.get(stitching_config.PRE_PROC_SECTION, {}).get(
             stitching_config.DATA_PATH_FIELD, None
         )
         if location is not None: