Helical: add a dedicated widget for `nabu-helical-prepare-weights-double`

orangecontrib/tomwer/widgets/reconstruction/NabuHelicalPrepareWeightsDoubleOW.py

+import logging
+
+from orangewidget import gui
+from orangewidget.settings import Setting
+from orangewidget.widget import Input, Output
+from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
+from silx.gui import qt
+from typing import Optional
+
+from tomwer.core.futureobject import FutureTomwerObject
+from tomwer.core.scan.scanbase import TomwerScanBase
+from tomwer.gui.reconstruction.nabu.helical import HelicalPrepareWeightsDouble
+from tomwer.core.process.reconstruction.nabu.helical import (
+    NabuHelicalPrepareWeightsDouble,
+)
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+
+_logger = logging.getLogger(__name__)
+
+
+class NabuHelicalPrepareWeightsDoubleOW(
+    TomwerWithStackStack,
+    ewokstaskclass=NabuHelicalPrepareWeightsDouble,
+):
+    """
+    widget used to call the `nabu-helical-prepare-weights-double` application on a dedicated thread
+
+    :param parent: the parent widget
+    """
+
+    # note of this widget should be the one registered on the documentation
+    name = "helical prepate weights double"
+    id = "orange.widgets.tomwer.reconstruction.NabuHelicalPrepareWeightsDoubleOW.NabuHelicalPrepareWeightsDoubleOW"
+    description = "compute map of weights requested for nabu helical reconstruction"
+    icon = "icons/nabu_prepare_weights_double.svg"
+    priority = 199
+    keywords = [
+        "tomography",
+        "nabu",
+        "reconstruction",
+        "nabu-helical",
+        "helical",
+        "weights",
+        "prepare",
+    ]
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+    allows_cycle = True
+
+    _ewoks_default_inputs = Setting(
+        {
+            "data": None,
+            "transition_width": 50,
+            "processes_file": "",
+        }
+    )
+
+    sigScanReady = qt.Signal(TomwerScanBase)
+    "Signal emitted when a scan is ended"
+
+    TIMEOUT = 30
+
+    class Inputs:
+        data = Input(
+            name="data",
+            type=TomwerScanBase,
+            doc="one scan to be process",
+            default=True,
+            multiple=False,
+        )
+
+    class Outputs:
+        data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
+        future_tomo_obj = Output(
+            name="future_tomo_obj",
+            type=FutureTomwerObject,
+            doc="future object (process remotely)",
+        )
+
+    LOGGER = _logger
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.__scan = None
+
+        # gui definition
+        _layout = gui.vBox(self.mainArea, self.name).layout()
+        self.widget = HelicalPrepareWeightsDouble(parent=self)
+        _layout.addWidget(self.widget)
+
+        ## connect signal / slot
+        self.widget.sigConfigChanged.connect(self._updateSettings)
+
+        self.task_output_changed_callbacks.add(self._notify_state)
+
+        ## handle settings
+        self._loadSettings()
+        self.task_executor_queue.sigComputationStarted.connect(self._newTaskStarted)
+
+    def _updateSettings(self):
+        config = self.widget.getConfiguration()
+        for key in ("transition_width", "processes_file"):
+            self._ewoks_default_inputs[key] = config[key]
+
+    @property
+    def request_input(self):
+        return self.__request_input
+
+    @request_input.setter
+    def request_input(self, request):
+        self.__request_input = request
+
+    def get_task_inputs(self):
+        assert self.__scan is not None
+        return {
+            "data": self.__scan,
+            "transition_width": self.widget.getConfiguration()["transition_width"],
+            "processes_file": self.widget.getConfiguration()["processes_file"],
+        }
+
+    def handleNewSignals(self) -> None:
+        """Invoked by the workflow signal propagation manager after all
+        signals handlers have been called.
+        """
+        # for now we want to avoid propagation any processing.
+        # task will be executed only when the user validates the dialog
+        data = super().get_task_inputs().get("data", None)
+        if data is not None:
+            if not isinstance(data, HDF5TomoScan):
+                raise TypeError(
+                    f"data is expected to be an instance of HDF5TomoScan. {type(data)} are not handled"
+                )
+            self.add(data.path)
+
+    def _loadSettings(self):
+        self.widget.setConfiguration(self._ewoks_default_inputs)
+
+    def _newTaskStarted(self):
+        try:
+            task_executor = self.sender()
+            scan = task_executor.current_task.inputs.data
+            self.notify_on_going(scan)
+        except Exception:
+            pass
+
+    def _notify_state(self):
+        try:
+            task_executor = self.sender()
+            task_suceeded = task_executor.succeeded
+            scan = task_executor.current_task.outputs.data
+            if task_suceeded:
+                self.notify_succeed(scan=scan)
+            else:
+                self.notify_failed(scan=scan)
+        except Exception as e:
+            _logger.error(f"failed to handle task finished callback. Raiseon is {e}")
+
+    @Inputs.data
+    def process_data(self, scan: Optional[TomwerScanBase]):
+        if scan is None:
+            return
+        else:
+            self.__scan = scan
+            self.notify_pending(scan=scan)
+            self.execute_ewoks_task()
+
+    def sizeHint(self) -> qt.QSize:
+        return qt.QSize(400, 60)

orangecontrib/tomwer/widgets/reconstruction/icons/nabu_prepare_weights_double.svg

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orangecontrib/tomwer/widgets/reconstruction/test/test_nabu_helical_prepare_weights_double.py

+import pickle
+
+from orangecanvas.scheme.readwrite import literal_dumps
+
+from tomwer.tests.conftest import qtapp  # noqa F401
+
+from orangecontrib.tomwer.widgets.reconstruction.NabuHelicalPrepareWeightsDoubleOW import (
+    NabuHelicalPrepareWeightsDoubleOW,
+)
+
+
+def test_NabuHelicalPrepareWeightsDoubleOW(
+    qtapp,  # noqa F811
+):
+    """simple test of the _DeltaBetaSelectorDialog"""
+    widget = NabuHelicalPrepareWeightsDoubleOW()
+    widget._loadSettings()
+    # test settings serialization
+    pickle.dumps(widget._ewoks_default_inputs)
+    literal_dumps(widget._ewoks_default_inputs)

tomwer/core/process/reconstruction/nabu/helical.py

+import logging
+
+from nabu.resources.nxflatfield import update_dataset_info_flats_darks
+from nabu.resources.dataset_analyzer import HDF5DatasetAnalyzer
+from nabu.io.reader import load_images_from_dataurl_dict
+from nabu.app.prepare_weights_double import create_heli_maps
+
+from tomwer.core.process.task import TaskWithProgress
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.utils.scanutils import format_output_location
+
+
+_logger = logging.getLogger(__name__)
+
+
+class NabuHelicalPrepareWeightsDouble(
+    TaskWithProgress,
+    input_names=(
+        "data",
+        "transition_width",
+        "processes_file",
+    ),
+    optional_input_names=("progress"),
+    output_names=("data",),
+):
+    def run(self):
+        # TODO: handle future /cluster config ???
+        scan = self.inputs.data
+        if not isinstance(scan, HDF5TomoScan):
+            raise TypeError(f"data is expected to be an instance of {HDF5TomoScan}")
+        dataset_info = HDF5DatasetAnalyzer(
+            scan.master_file,
+            extra_options={"h5_entry": scan.entry},
+        )
+        update_dataset_info_flats_darks(dataset_info, flatfield_mode=1)
+
+        mappe = 0
+        my_flats = load_images_from_dataurl_dict(dataset_info.flats)
+
+        for _, flat in my_flats.items():
+            mappe += flat
+        mappe = mappe / len(list(dataset_info.flats.keys()))
+
+        scan.helical.processes_files = format_output_location(
+            location=self.inputs.processes_file, scan=scan
+        )
+        create_heli_maps(
+            profile=mappe,
+            process_file_name=scan.helical.processes_files,
+            entry_name=scan.entry,
+            transition_width=self.inputs.transition_width,
+        )
+
+        self.outputs.data = scan

tomwer/core/process/reconstruction/nabu/utils.py

@@ -252,6 +252,7 @@ def get_recons_volume_identifier(
 class _NabuMode(_Enum):
     FULL_FIELD = "standard acquisition"
     HALF_ACQ = "half acquisition"
+    HELICAL = "helical acquisition"
 
 
 class _NabuStages(_Enum):

tomwer/core/scan/hdf5scan.py

@@ -47,6 +47,7 @@ from tomoscan.esrf.scan.hdf5scan import ImageKey
 from tomoscan.io import HDF5File
 
 from tomwer.utils import docstring
+from tomwer.core.scan.helicalmetadata import HelicalMetadata
 
 from .scanbase import TomwerScanBase
 
@@ -110,6 +111,7 @@ class HDF5TomoScan(_tsHDF5TomoScan, TomwerScanBase):
         _tsHDF5TomoScan.__init__(self, scan=scan, entry=entry, index=index)
         # register at least the 'default' working directory as a possible reconstruction path
         self.add_reconstruction_path(self.path)
+        self._helical = HelicalMetadata()
 
         self._reconstruction_urls = None
         self._projections_with_angles = None
@@ -137,6 +139,10 @@ class HDF5TomoScan(_tsHDF5TomoScan, TomwerScanBase):
         else:
             return os.path.realpath(os.path.dirname(self.master_file))
 
+    @property
+    def helical(self):
+        return self._helical
+
     @staticmethod
     def from_identifier(identifier):
         """Return the Dataset from a identifier"""

tomwer/core/scan/helicalmetadata.py

+class HelicalMetadata:
+    def __init__(self) -> None:
+        self._processes_files = (
+            "{scan_parent_dir_basename}/{scan_dir_name}/map_and_doubleff.hdf5"
+        )
+
+    @property
+    def processes_files(self) -> str:
+        return self._processes_files
+
+    @processes_files.setter
+    def processes_files(self, path: str):
+        if not isinstance(path, str):
+            raise TypeError(f"expects a str. Get {path}")
+        self._processes_files = path

tomwer/gui/qlefilesystem.py

@@ -2,6 +2,10 @@ from silx.gui import qt
 
 
 class QLFileSystem(qt.QLineEdit):
+    """
+    QLineEdit with a completer using a QDirModel
+    """
+
     def __init__(self, text, parent, filters=None, **kwargs):
         super().__init__(parent=parent, **kwargs)
         self.completer = qt.QCompleter()
@@ -10,3 +14,5 @@ class QLFileSystem(qt.QLineEdit):
             model.setFilter(filters)
         self.completer.setModel(model)
         self.setCompleter(self.completer)
+        if text is not None:
+            self.setText(text)

tomwer/gui/reconstruction/nabu/helical.py

+from silx.gui import qt
+from tomwer.gui.qlefilesystem import QLFileSystem
+
+
+class HelicalPrepareWeightsDouble(qt.QWidget):
+    sigConfigChanged = qt.Signal()
+    """emit when the configuration has changed"""
+
+    def __init__(self, parent=None, *args, **kwargs) -> None:
+        super().__init__(parent, *args, **kwargs)
+
+        self.setLayout(qt.QGridLayout())
+        # TODO: optional outptu file path. Default or set by the user
+        self._outputFilePathLabel = qt.QLabel("output file", self)
+        self.layout().addWidget(self._outputFilePathLabel, 0, 0, 1, 1)
+        self._outputFilePathQLE = QLFileSystem(
+            text="{scan_parent_dir_basename}/{scan_dir_name}/map_and_doubleff.hdf5",
+            parent=self,
+        )
+        self._outputFilePathQLE.setToolTip(
+            "location of the output file. Which will contain the weight map."
+        )
+        self.layout().addWidget(self._outputFilePathQLE, 0, 2, 1, 1)
+
+        # transition_width
+        self._transitionWidthQDSP = qt.QLabel("transition width", self)
+        self.layout().addWidget(self._transitionWidthQDSP, 1, 0, 1, 1)
+        self._transitionWidthQDSP = qt.QDoubleSpinBox(self)
+        self._transitionWidthQDSP.setRange(0.0, 99999999)
+        self._transitionWidthQDSP.setValue(50.0)
+        self._transitionWidthQDSP.setToolTip(
+            "the transition width is used to determine the vertical borders"
+        )
+        # TODO: improve tooltip of this
+        self.layout().addWidget(self._transitionWidthQDSP, 1, 1, 1, 2)
+
+        spacer = qt.QWidget(parent=self)
+        spacer.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
+        self.layout().addWidget(spacer, 100, 0, 1, 3)
+
+        # connect signal / slot
+        self._outputFilePathQLE.editingFinished.connect(self._changed)
+        self._transitionWidthQDSP.valueChanged.connect(self._changed)
+
+    def _changed(self, *args, **kwargs):
+        self.sigConfigChanged.emit()
+
+    def getConfiguration(self) -> dict:
+        return {
+            "processes_file": self._outputFilePathQLE.text(),
+            "transition_width": self._transitionWidthQDSP.value(),
+        }
+
+    def setConfiguration(self, config: dict):
+        processes_file = config.get("processes_file", None)
+        if processes_file is not None:
+            self._outputFilePathQLE.setText(processes_file)
+
+        transition_width = config.get("transition_width", None)
+        if transition_width is not None:
+            self._transitionWidthQDSP.setValue(float(transition_width))

tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py

@@ -60,13 +60,14 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QGridLayout())
 
-        # flat field
+        # default options
+        ## flat field
         self._flatFieldCB = qt.QCheckBox("flat field correction", self)
         self._flatFieldCB.setToolTip("Whether to enable flat-field " "normalization")
         self.layout().addWidget(self._flatFieldCB, 0, 0, 1, 2)
         self.registerWidget(self._flatFieldCB, "optional")
 
-        # double flat field
+        ## double flat field
         self._dffCB = qt.QCheckBox("double flat field correction", self)
         self._dffCB.setToolTip("Whether to enable double flat field " "normalization")
         self.layout().addWidget(self._dffCB, 1, 0, 1, 2)
@@ -84,7 +85,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
             self.registerWidget(self._dffSigmaQDSB, "required"),
         ]
 
-        # sino ring corrcetion
+        ## sino ring corrcetion
         self._sinoRingCorrectionCB = qt.QLabel("rings removal method", self)
         self._sinoRingCorrectionCB.setToolTip("Sinogram rings removal method")
         self.layout().addWidget(self._sinoRingCorrectionCB, 2, 0, 1, 2)
@@ -93,7 +94,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         self._sinoRingCorrectionMthd = QComboBox(parent=self, scrollArea=scrollArea)
         for method in _RingCorrectionMethod:
             self._sinoRingCorrectionMthd.addItem(method.value)
-        # force method to be None by default
+        ## force method to be None by default
         idx = self._sinoRingCorrectionMthd.findText(_RingCorrectionMethod.NONE.value)
         self._sinoRingCorrectionMthd.setCurrentIndex(idx)
 
@@ -103,13 +104,13 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         self._sinoRingsOpts = SinoRingsOptions(parent=self)
         self.layout().addWidget(self._sinoRingsOpts, 3, 1, 1, 3)
 
-        # ccd filter
+        ## ccd filter
         self._ccdFilterCB = qt.QCheckBox("CCD hot spot correction", self)
         self._ccdFilterCB.setToolTip("Whether to enable the CCD hotspots " "correction")
         self.layout().addWidget(self._ccdFilterCB, 4, 0, 1, 2)
         self.registerWidget(self._ccdFilterCB, "optional")
 
-        # ccd filter threshold
+        ## ccd filter threshold
         self._ccdHotspotLabel = qt.QLabel("threshold:", self)
         self._ccdHotspotLabel.setAlignment(qt.Qt.AlignRight)
         self.layout().addWidget(self._ccdHotspotLabel, 5, 2, 1, 1)
@@ -131,7 +132,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
             self.registerWidget(self._ccdThreshold, "optional"),
         ]
 
-        # sr current normalization
+        ## sr current normalization
         self._normalizeCurrent = qt.QCheckBox("normalize with current", self)
         self._normalizeCurrent.setToolTip(
             "Whether to normalize frames with Synchrotron Current. This can correct the effect of a beam refill not taken into account by flats."
@@ -139,12 +140,12 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
         self.layout().addWidget(self._normalizeCurrent, 6, 0, 1, 2)
         self.registerWidget(self._normalizeCurrent, "required")
 
-        # take logarithm
+        ## take logarithm
         self._takeLogarithmCB = qt.QCheckBox("take logarithm", self)
         self.layout().addWidget(self._takeLogarithmCB, 7, 0, 1, 2)
         self.registerWidget(self._takeLogarithmCB, "advanced")
 
-        # log min clip value
+        ## log min clip value
         self._clipMinLogValueLabel = qt.QLabel("log min clip value:", self)
         self._clipMinLogValueLabel.setAlignment(qt.Qt.AlignRight)
         self.layout().addWidget(self._clipMinLogValueLabel, 8, 2, 1, 1)
@@ -159,7 +160,7 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
             self.registerWidget(self._clipMinLogValue, "optional"),
         ]
 
-        # log max clip value
+        ## log max clip value
         self._clipMaxLogValueLabel = qt.QLabel("log max clip value:", self)
         self._clipMaxLogValueLabel.setAlignment(qt.Qt.AlignRight)
         self.layout().addWidget(self._clipMaxLogValueLabel, 9, 2, 1, 1)
@@ -176,11 +177,24 @@ class _NabuPreProcessingConfig(_NabuStageConfigBase, qt.QWidget):
             ]
         )
 
-        # tilt correction
+        ## tilt correction
         self._tiltCorrection = TiltCorrection("tilt correction", self)
         self.registerWidget(self._tiltCorrection, "advanced")
         self.layout().addWidget(self._tiltCorrection, 10, 0, 1, 4)
 
+        # option dedicated to Helical
+        ## process file
+        self._processFileQLE = qt.QLabel("file containing weights maps", self)
+        self._processFileQLE.setToolTip(
+            "also know as 'process_file'. If you don't have this file it can be created from the 'helical-prepare-weights' widget"
+        )
+        self.layout().addWidget(self._processFileQLE, 20, 0, 1, 1)
+        self._processFileQLE = qt.QLineEdit("", self)
+        self.registerWidget(self._processFileQLE, "advanced")
+        self.layout().addWidget(self._processFileQLE, 20, 1, 1, 3)
+
+        # style
+
         # spacer for style
         spacer = qt.QWidget(self)
         spacer.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Expanding)

tomwer/gui/reconstruction/nabu/test/test_helical.py

+from tomwer.tests.conftest import qtapp  # noqa F401
+from tomwer.gui.reconstruction.nabu.helical import HelicalPrepareWeightsDouble
+
+
+def test_DeltaBetaSelector(
+    qtapp,  # noqa F811
+):
+    """simple test of the _DeltaBetaSelectorDialog"""
+    widget = HelicalPrepareWeightsDouble()
+    assert widget.getConfiguration() == {
+        "processes_file": "{scan_dir_name}/map_and_doubleff.hdf5",
+        "transition_width": 50.0,
+    }
+    config = {
+        "processes_file": "test.hdf5",
+        "transition_width": 12.5,
+    }
+    widget.setConfiguration(config=config)
+    assert widget.getConfiguration() == config