tomwer 2.0.0.dev3__tar.gz → 2.0.0.dev5__tar.gz

{tomwer-2.0.0.dev3/src/tomwer.egg-info → tomwer-2.0.0.dev5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tomwer
-Version: 2.0.0.dev3
+Version: 2.0.0.dev5
 Summary: Tomography workflow tools
 Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
 License: MIT

tomwer-2.0.0.dev5/src/orangecontrib/tomwer/tutorials/darks and flats copy - method 2.ows

@@ -0,0 +1,42 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="darks and flats copy - method 2" description="">
+	<nodes>
+		<node id="0" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector" position="(-519.0, -209.0)" />
+		<node id="1" name="image-key-upgrader" qualified_name="orangecontrib.tomwer.widgets.edit.ImageKeyUpgraderOW.ImageKeyUpgraderOW" project_name="tomwer" version="" title="image-key-upgrader" position="(-293.0, -209.0)" />
+		<node id="2" name="scan selector" qualified_name="orangecontrib.tomwer.widgets.control.DataSelectorOW.DataSelectorOW" project_name="tomwer" version="" title="scan selector (1)" position="(291.0, -211.0)" />
+		<node id="3" name="copy reduced darks and flats" qualified_name="orangecontrib.tomwer.widgets.reconstruction.CopyReducedDarkAndFlatOW.CopyReducedDarkAndFlatOW" project_name="tomwer" version="" title="copy reduced darks and flats" position="(61.0, -213.0)" />
+	</nodes>
+	<links>
+		<link id="0" source_node_id="0" sink_node_id="1" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="1" source_node_id="1" sink_node_id="3" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+		<link id="2" source_node_id="3" sink_node_id="2" source_channel="data" sink_channel="data" enabled="true" source_channel_id="data" sink_channel_id="data" />
+	</links>
+	<annotations>
+		<text id="0" type="text/plain" rect="(-597.0, -79.0, 150.0, 126.0)" font-family="Sans" font-size="16">step2: provide scans for which we need to copy reduced darks and flats</text>
+		<arrow id="1" start="(-522.0, -87.0)" end="(-523.0, -151.0)" fill="#C1272D" />
+		<text id="2" type="text/plain" rect="(-379.0, -87.0, 236.0, 111.0)" font-family="Sans" font-size="16">invalid any existing darks or flats frames (else reduced darks and flats will use them instead of making the copy)</text>
+		<arrow id="3" start="(-293.0, -97.0)" end="(-290.0, -158.0)" fill="#C1272D" />
+		<text id="4" type="text/plain" rect="(-70.0, -81.0, 270.0, 80.0)" font-family="Sans" font-size="16">will copy reduced darks / flats to `dataset_{darks|flats}.hdf5` to be used for reconstruction</text>
+		<arrow id="5" start="(61.99999999999998, -91.0)" end="(61.99999999999998, -142.0)" fill="#C1272D" />
+		<text id="6" type="text/plain" rect="(-141.0, -427.0, 464.0, 85.0)" font-family="Sans" font-size="16">step1: provide reduced darks and flats from the 'copy' tab,
+unselecting auto and setting them through `select darks url` and `select flats url`</text>
+		<arrow id="7" start="(57.0, -334.0)" end="(58.99999999999997, -259.00000000000006)" fill="#C1272D" />
+		<text id="8" type="text/plain" rect="(241.0, -94.0, 150.0, 88.0)" font-family="Sans" font-size="16">result: scans with copied reduced darks / flats</text>
+		<text id="9" type="text/plain" rect="(-601.0, -590.0, 932.0, 68.0)" font-family="Sans" font-size="16">Context: on this workflow we want to copy reduced flats / darks from a dataset to others.
+This one of the various way to do this.
+</text>
+		<text id="10" type="text/plain" rect="(-593.0, 94.0, 919.0, 84.0)" font-family="Sans" font-size="16">Note: reduced darks / flats can be saved to disk from another python script using the `silx.io.dictdump` dicttoh5 function.
+Reduced darks and flats are dictionary with index in the sequence as key (so index==0 if the dark / flat serie is done at the beginning) and the reduced darks / flats as value (2D numpy array) </text>
+		<arrow id="11" start="(291.0, -109.0)" end="(290.0, -158.0)" fill="#C1272D" />
+	</annotations>
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="1" format="literal">{'_ewoks_default_inputs': {'operations': {}}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="2" format="literal">{'_scanIDs': [], 'controlAreaVisible': True, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+		<properties node_id="3" format="literal">{'_auto_mode': True, '_ewoks_default_inputs': {}, '_ewoks_execinfo': {}, '_ewoks_task_options': {}, '_ewoks_varinfo': {}, 'controlAreaVisible': True, 'default_inputs': {}, 'savedWidgetGeometry': None, '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

tomwer-2.0.0.dev5/src/orangecontrib/tomwer/tutorials/untitled.ows

@@ -0,0 +1,15 @@
+<?xml version='1.0' encoding='utf-8'?>
+<scheme version="2.0" title="" description="">
+	<nodes>
+		<node id="0" name="nabu volume reconstruction" qualified_name="orangecontrib.tomwer.widgets.reconstruction.NabuVolumeOW.NabuVolumeOW" project_name="tomwer" version="" title="nabu volume reconstruction" position="(440.0, 214.0)" />
+	</nodes>
+	<links />
+	<annotations />
+	<thumbnail />
+	<node_properties>
+		<properties node_id="0" format="literal">{'_ewoks_default_inputs': {'data': None, 'nabu_volume_params': None, 'nabu_params': None}, 'controlAreaVisible': True, 'savedWidgetGeometry': b'\x01\xd9\xd0\xcb\x00\x03\x00\x00\x00\x00\x03\x08\x00\x00\x01o\x00\x00\x04\xd1\x00\x00\x03\xe5\x00\x00\x03\x08\x00\x00\x01\x94\x00\x00\x04\xd1\x00\x00\x03\xe5\x00\x00\x00\x00\x00\x00\x00\x00\x07\x80\x00\x00\x03\x08\x00\x00\x01\x94\x00\x00\x04\xd1\x00\x00\x03\xe5', '__version__': 1}</properties>
+	</node_properties>
+	<session_state>
+		<window_groups />
+	</session_state>
+</scheme>

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/orangecontrib/tomwer/widgets/cluster/MonitorOW.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import time
+import weakref
 
 from orangewidget import gui
 
@@ -13,7 +14,6 @@ from ewokscore.missing_data import MISSING_DATA
 from ewoksorange.gui.orange_utils.signals import Input
 
 from processview.core.manager import DatasetState, ProcessManager
-from processview.core.superviseprocess import SuperviseProcess
 from silx.gui import qt
 from silx.gui.utils.concurrent import submitToQtMainThread
 
@@ -67,9 +67,11 @@ class MonitorOW(
         # gui
         layout = gui.vBox(self.mainArea, self.name).layout()
         self._widget = FutureTomwerObjectObserverWidget(
-            parent=self, name=self.windowTitle()
+            parent=self,
+            name=self.windowTitle(),
+            process=self,
         )
-        self.set_dynamic_input("process_id", self._widget.process_id)
+        self.set_dynamic_input("process_id", self.process_id)
         layout.addWidget(self._widget)
 
     def handleNewSignals(self) -> None:
@@ -102,17 +104,19 @@ class MonitorOW(
         return super()._output_changed()
 
 
-class FutureTomwerObjectObserverWidget(
-    _FutureTomwerScanObserverWidget, SuperviseProcess
-):
+class FutureTomwerObjectObserverWidget(_FutureTomwerScanObserverWidget):
     """add dataset state notification (ProcessManager) to the original FutureTomwerScanObserverWidget"""
 
     REFRESH_FREQUENCE = 10
     """time between call to updateView"""
 
-    def __init__(self, name, parent=None):
+    def __init__(self, name, process, parent=None):
+        """
+        :param process: Process that 'controls' the futures
+        """
         super().__init__(parent=parent)
         self.name = name
+        self.__master_process = weakref.ref(process)
         self._updateThread = _RefreshThread(
             callback=self.updateView, refresh_frequence=self.REFRESH_FREQUENCE
         )
@@ -168,12 +172,13 @@ class FutureTomwerObjectObserverWidget(
             raise ValueError(
                 f"future scan status '{future_tomo_obj.status}' is not managed, {type(future_tomo_obj.status)}"
             )
-        ProcessManager().notify_dataset_state(
-            dataset=future_tomo_obj.tomo_obj,
-            process=self,
-            state=state,
-            details=details,
-        )
+        if self.__master_process():
+            ProcessManager().notify_dataset_state(
+                dataset=future_tomo_obj.tomo_obj,
+                process=self.__master_process(),
+                state=state,
+                details=details,
+            )
 
     def _updateStatus(self, future_tomo_obj):
         self._updateTomoObjSupervisor(future_tomo_obj)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/orangecontrib/tomwer/widgets/control/TomoObjSeriesOW.py

@@ -22,7 +22,7 @@ class TomoObjSeriesOW(OWBaseWidget, openclass=True):
     priority = 55
     keywords = ["tomography", "selection", "tomwer", "series", "group"]
 
-    ewokstaskclass = tomwer.tasks.control.tomoobjseries._TomoobjseriesPlaceHolder
+    ewokstaskclass = tomwer.tasks.control.tomoobjseries._TomoObjSeriesPlaceHolder
 
     want_main_area = True
     want_control_area = False

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/orangecontrib/tomwer/widgets/visualization/DataViewerOW.py

@@ -51,6 +51,7 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         self._imagejThreads = []
         # threads used to open frames with image j
         self._layout = gui.vBox(self.mainArea, self.name).layout()
+        self._layout.setContentsMargins(2, 2, 2, 2)
         self.viewer = DataViewer(parent=self)
         self.viewer.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
         self._layout.addWidget(self.viewer)
@@ -61,9 +62,14 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         self._buttons = qt.QDialogButtonBox(self)
         self._buttons.setStandardButtons(types)
         self._buttonOpenImageJ = self._buttons.button(qt.QDialogButtonBox.Apply)
-        self._buttonOpenImageJ.setText("open with ImageJ")
+        self._buttonOpenImageJ.setText("ImageJ")
+        self._buttonOpenImageJ.setToolTip(
+            "Open image(s) using ImageJ. Warning: you might need to do a 'module load fiji' first"
+        )
         self._buttonOpenImageJ.setIcon(icons.getQIcon("Imagej_icon"))
-        self.layout().addWidget(self._buttons)
+        self.viewer.getPlotWidget().getPositionInfoWidget().layout().insertWidget(
+            0, self._buttonOpenImageJ
+        )
 
         # connect signal / slot
         self.viewer.sigConfigChanged.connect(self._updateSettings)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/core/reconstruction/common/NabuBaseReconstructor.py

@@ -41,6 +41,11 @@ from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.utils.slurm import get_slurm_script_name, is_slurm_available
 from tomwer.core.volume.hdf5volume import HDF5VolumeIdentifier
+from tomwer.core.reconstruction.output import (
+    PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+    PROCESS_FOLDER_RECONSTRUCTED_VOLUMES,
+)
+from tomwer.core.reconstruction.common.settings import NABU_CFG_FILE_FOLDER
 
 from . import settings
 
@@ -218,12 +223,16 @@ class NabuBaseReconstructor:
         assert os.path.exists(
             conf_file
         ), "configuration file doesn't exists. Cannot execute it."
+        log_file = self.deduce_log_file_from_config_file(conf_file)
+        os.makedirs(os.path.dirname(log_file), exist_ok=True)
 
         command = (
             sys.executable,
             "-m",
             settings.NABU_FULL_FIELD_APP_PATH,
             f"{shlex.quote(conf_file)}",  # adding ' around file name allows to handle config file with spaces
+            "--logfile",
+            f"{shlex.quote(log_file)}",
             "--gpu_mem_fraction",
             str(gpu_mem_fraction),
             "--cpu_mem_fraction",
@@ -308,13 +317,16 @@ class NabuBaseReconstructor:
         # submit job
         script_name = get_slurm_script_name(prefix="nabu")
         conf_file = filter_esrf_mounting_points(conf_file)
+        log_file = self.deduce_log_file_from_config_file(conf_file)
+        os.makedirs(os.path.dirname(log_file), exist_ok=True)
+
         # for now force job name
         cluster_config["job_name"] = f"tomwer-nabu {conf_file}"
         act_as_a_login_shell = cluster_config.pop("act_as_login_shell", False)
         job = SBatchScriptJob(
             slurm_config=cluster_config,
             script=(
-                f"python3 -m {settings.NABU_FULL_FIELD_APP_PATH} '{conf_file}' --gpu_mem_fraction={gpu_mem_fraction} --cpu_mem_fraction={cpu_mem_fraction}",
+                f"python3 -m {settings.NABU_FULL_FIELD_APP_PATH} '{conf_file}' --logfile='{log_file}' --gpu_mem_fraction={gpu_mem_fraction} --cpu_mem_fraction={cpu_mem_fraction}",
             ),
             script_path=filter_esrf_mounting_points(
                 os.path.join(self.scan.resolved_path, "slurm_scripts", script_name)
@@ -448,6 +460,18 @@ class NabuBaseReconstructor:
             finally:
                 self._process = None
 
+    @staticmethod
+    def deduce_log_file_from_config_file(conf_file: str) -> str:
+        dirname = os.path.dirname(conf_file)
+        while os.path.basename(dirname) in (
+            PROCESS_FOLDER_RECONSTRUCTED_VOLUMES,
+            PROCESS_FOLDER_RECONSTRUCTED_SLICES,
+            NABU_CFG_FILE_FOLDER,
+        ):
+            dirname = os.path.dirname(dirname)
+        file_name, _ = os.path.splitext(os.path.basename(conf_file))
+        return os.path.join(dirname, "logs", file_name + "_nabu.log")
+
 
 def dump_normalization_array_for_nabu(
     scan: TomwerScanBase, output_file: str, array: numpy.ndarray | float | int

tomwer-2.0.0.dev5/src/tomwer/core/reconstruction/common/test/test_NabuBaseReconstructor.py

@@ -0,0 +1,16 @@
+from tomwer.core.reconstruction.common.NabuBaseReconstructor import (
+    NabuBaseReconstructor,
+)
+
+
+def test_deduce_log_file_from_config_file():
+    assert NabuBaseReconstructor.deduce_log_file_from_config_file(
+        "/data/dataset/reconstructed_slices/nabu_cfg_files/config.cfg"
+    ) == ("/data/dataset/logs/config_nabu.log")
+    assert NabuBaseReconstructor.deduce_log_file_from_config_file(
+        "/data/dataset/config.cfg"
+    ) == ("/data/dataset/logs/config_nabu.log")
+    assert (
+        NabuBaseReconstructor.deduce_log_file_from_config_file("config.cfg")
+        == "logs/config_nabu.log"
+    )

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/cor/ControlWidget.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 import logging
 import numpy
+import qtawesome
 
 from silx.gui import qt
 
@@ -127,6 +128,8 @@ class _PositionInfoWidget(qt.QWidget):
         self._defaultBackgroundColor = None
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QGridLayout())
+
+        # relative CoR
         centerLabel = qt.QLabel("center", parent=self)
         centerLabel.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum)
         font = centerLabel.font()
@@ -144,7 +147,12 @@ class _PositionInfoWidget(qt.QWidget):
         )
         self._relativePositionQLE.setStyleSheet("color: red")
         self.layout().addWidget(self._relativePositionQLE, 0, 2, 1, 1)
+        self._copyRelativeCoRButton = qt.QPushButton(
+            icon=qtawesome.icon("mdi6.content-copy")
+        )
+        self.layout().addWidget(self._copyRelativeCoRButton, 0, 3, 1, 1)
 
+        # relative CoR
         centerLabel = qt.QLabel("center", parent=self)
         centerLabel.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum)
         font = centerLabel.font()
@@ -160,6 +168,10 @@ class _PositionInfoWidget(qt.QWidget):
         )
         self._absolutePositionQLE.setStyleSheet("color: #ff8c00")
         self.layout().addWidget(self._absolutePositionQLE, 1, 2, 1, 1)
+        self._copyAbsoluteCoRButton = qt.QPushButton(
+            icon=qtawesome.icon("mdi6.content-copy")
+        )
+        self.layout().addWidget(self._copyAbsoluteCoRButton, 1, 3, 1, 1)
 
         if axis:
             self.setAxisParams(axis)
@@ -174,10 +186,11 @@ class _PositionInfoWidget(qt.QWidget):
         self._absolutePositionQLE.textEdited.connect(
             self._userStartEditingAbsolutePosition
         )
-
         self._absolutePositionQLE.editingFinished.connect(
             self._userUpdatedAbsolutePosition
         )
+        self._copyAbsoluteCoRButton.clicked.connect(self._copyAbsoluteCoRToClipBoard)
+        self._copyRelativeCoRButton.clicked.connect(self._copyRelativeCoRToClipBoard)
 
     def _getDefaultBackgroundColor(self):
         if self._defaultBackgroundColor is None:
@@ -284,3 +297,9 @@ class _PositionInfoWidget(qt.QWidget):
                     absolute_pos=abs_value, det_width=width
                 )
                 self._relativePositionQLE.setText(str(rel_value))
+
+    def _copyAbsoluteCoRToClipBoard(self):
+        qt.QApplication.clipboard().setText(self._absolutePositionQLE.text())
+
+    def _copyRelativeCoRToClipBoard(self):
+        qt.QApplication.clipboard().setText(self._relativePositionQLE.text())

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/nabu/nabuconfig/NabuSettingsWidget.py

@@ -8,7 +8,6 @@ from tomwer.gui.reconstruction.nabu.nabuflow import NabuFlowArea
 from tomwer.gui.configuration.level import ConfigurationLevel
 from tomwer.gui.utils.flow import FlowDirection
 from tomwer.gui.reconstruction.nabu.nabuconfig.nabuconfig import NabuConfiguration
-from tomwer.gui import icons as tomwer_icons
 
 
 class NabuSettingsWidget(qt.QWidget):
@@ -36,7 +35,7 @@ class NabuSettingsWidget(qt.QWidget):
         for mode in NabuMode:
             self._nabuModeCB.addItem(mode.value)
         self._widget_recons.layout().addWidget(self._nabuModeCB)
-        self.layout().addWidget(self._widget_recons, 0, 1, 1, 2)
+        self.layout().addWidget(self._widget_recons, 0, 2, 1, 2)
 
         # spacer
         spacer = qt.QWidget(self)
@@ -53,9 +52,6 @@ class NabuSettingsWidget(qt.QWidget):
         self._configurationScrollArea.setWidgetResizable(True)
         self._configuration = NabuConfiguration(parent=self)
         self._configurationScrollArea.setWidget(self._configuration)
-        self._configurationScrollArea.setHorizontalScrollBarPolicy(
-            qt.Qt.ScrollBarAlwaysOff
-        )
         self.layout().addWidget(self._configurationScrollArea, 1, 2, 5, 1)
         self._configuration.setSizePolicy(
             qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum
@@ -75,22 +71,16 @@ class NabuSettingsWidget(qt.QWidget):
 
         # set up
         pre_processing = ("pre processing",)
-        roman_one_icon = tomwer_icons.getQIcon("roman_one")
-        self.setPreProcessing(pre_processing, icons=(roman_one_icon,))
+        self.setPreProcessing(pre_processing, icons=(None,))
         phase_processing = ("phase",)
-        roman_two_icon = tomwer_icons.getQIcon("roman_two")
-        phase_icons = (roman_two_icon,)
-        self.setPhaseProcessing(phase_processing, icons=phase_icons)
+        self.setPhaseProcessing(phase_processing, icons=(None,))
         processing = ("reconstruction",)
-        processing_icons = (tomwer_icons.getQIcon("roman_three"),)
-        self.setProcessing(processes=processing, icons=processing_icons)
+        self.setProcessing(processes=processing, icons=(None,))
         post_processing = ("save",)
-        post_processing_icons = (tomwer_icons.getQIcon("roman_four"),)
-        self.setPostProcessing(post_processing, icons=post_processing_icons)
+        self.setPostProcessing(post_processing, icons=(None,))
         index_mode = self._nabuModeCB.findText(NabuMode.AUTO.value)
         assert index_mode >= 0, "full filed should be registered in the widget"
         self._nabuModeCB.setCurrentIndex(index_mode)
-        self._flow.setMaximumWidth(240)
 
         # signal / slot connections
         self._flow.sigConfigurationChanged.connect(self._processSelectionChanged)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 from silx.gui import qt
 
 from tomwer.core.reconstruction.common.stages import NabuStages
-from tomwer.gui.reconstruction.nabu.nabuconfig.output import _NabuOutputConfig
+from tomwer.gui.reconstruction.nabu.nabuconfig.output import _NabuOutputFileFormat
 from tomwer.gui.reconstruction.nabu.nabuconfig.phase import _NabuPhaseConfig
 from tomwer.gui.reconstruction.nabu.nabuconfig.preprocessing import (
     _NabuPreProcessingConfig,
@@ -60,7 +60,7 @@ class NabuConfiguration(qt.QWidget):
         self._outputGB = qt.QGroupBox("output", self)
         self._outputGB.setLayout(qt.QVBoxLayout())
 
-        self._outputWidget = _NabuOutputConfig(parent=self)
+        self._outputWidget = _NabuOutputFileFormat(parent=self)
         self._outputGB.layout().addWidget(self._outputWidget)
         self.layout().addWidget(self._outputGB)
 
@@ -185,7 +185,7 @@ class NabuConfigurationTab(qt.QTabWidget):
         self.addTab(self._reconstructionWidget, "reconstruction")
 
         # output information
-        self._outputWidget = _NabuOutputConfig(parent=self)
+        self._outputWidget = _NabuOutputFileFormat(parent=self)
         self.addTab(self._outputWidget, "output")
 
         # connect signal / slot

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/nabu/nabuconfig/output.py

@@ -61,7 +61,7 @@ class QNabuFileFormatComboBoxIgnoreWheel(QNabuFileFormatComboBox):
         pass
 
 
-class _NabuOutputConfig(_NabuStageConfigBase, qt.QWidget):
+class _NabuOutputFileFormat(_NabuStageConfigBase, qt.QWidget):
     """
     Widget to define the output configuration of nabu
     """
@@ -71,13 +71,13 @@ class _NabuOutputConfig(_NabuStageConfigBase, qt.QWidget):
     modified
     """
 
-    def __init__(self, parent):
+    def __init__(self, parent, title: str = "output file format:"):
         _NabuStageConfigBase.__init__(self, stage=NabuStages.POST)
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QGridLayout())
 
         # file format
-        self._outputFileFormatLabel = qt.QLabel("output file format:", self)
+        self._outputFileFormatLabel = qt.QLabel(title, self)
         self.layout().addWidget(self._outputFileFormatLabel, 1, 0, 1, 1)
         self._fileFormatCB = QNabuFileFormatComboBoxIgnoreWheel(self)
         self.layout().addWidget(self._fileFormatCB, 1, 2, 1, 2)
@@ -90,7 +90,7 @@ class _NabuOutputConfig(_NabuStageConfigBase, qt.QWidget):
         self.layout().addWidget(spacer, 200, 0, 1, 1)
 
         # set up
-        self.setFileformat("hdf5")
+        self.setFileFormat("hdf5")
 
         # connect signal / slot
         self._fileFormatCB.currentTextChanged.connect(self._fileFormatChanged)
@@ -101,7 +101,7 @@ class _NabuOutputConfig(_NabuStageConfigBase, qt.QWidget):
     def getFileFormat(self) -> NabuOutputFileFormat:
         return NabuOutputFileFormat(self._fileFormatCB.currentText())
 
-    def setFileformat(self, file_format):
+    def setFileFormat(self, file_format):
         file_format = NabuOutputFileFormat(file_format)
         index = self._fileFormatCB.findText(file_format.value)
         self._fileFormatCB.setCurrentIndex(index)
@@ -113,4 +113,4 @@ class _NabuOutputConfig(_NabuStageConfigBase, qt.QWidget):
 
     def setConfiguration(self, config):
         if "file_format" in config:
-            self.setFileformat(config["file_format"])
+            self.setFileFormat(config["file_format"])

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/nabu/nabuflow.py

@@ -352,6 +352,7 @@ class NabuFlowArea(qt.QWidget):
             self.layout().addWidget(self._addRmWidget)
 
         # set up
+        self.setMaximumWidth(180)
         # for now hide the add and remove option
         self._addRmWidget.setVisible(False)
 

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/nabu/test/test_cast_volume.py

@@ -11,7 +11,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": None,
         "data_min": None,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "tiff",
         "overwrite": True,
         "rescale_max_percentile": 99.9,
@@ -25,7 +25,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 0.0,
         "data_min": 0.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "tiff",
         "overwrite": True,
         "rescale_max_percentile": None,
@@ -41,7 +41,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "tiff",
         "overwrite": True,
         "rescale_max_percentile": None,
@@ -54,7 +54,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": True,
         "rescale_max_percentile": None,
@@ -67,7 +67,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "uint16",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": False,
         "rescale_max_percentile": None,
@@ -80,7 +80,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "float32",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": False,
         "rescale_max_percentile": None,
@@ -93,7 +93,7 @@ def test_CastVolumeWidget(qtapp):  # noqa F811
         "data_max": 10.0,
         "data_min": 1.0,
         "output_data_type": "float32",
-        "output_dir": "{volume_data_parent_folder}" f"{os.sep}..{os.sep}cast_volumes",
+        "output_dir": "{volume_data_parent_folder}" f"{os.sep}cast_volume",
         "output_file_format": "edf",
         "overwrite": False,
         "rescale_max_percentile": None,

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/nabu/test/test_volume.py

@@ -46,6 +46,7 @@ def test_NabuVolumeWindow(qtapp):  # noqa F811
         },
         "output": {
             "location": "/new/folder",
+            "file_format": "hdf5",
         },
     }
     widget.setConfiguration(new_config)

{tomwer-2.0.0.dev3 → tomwer-2.0.0.dev5}/src/tomwer/gui/reconstruction/nabu/volume/NabuVolumeWidget.py

@@ -3,10 +3,10 @@ from __future__ import annotations
 from silx.gui import qt
 
 from tomwer.core.reconstruction.common.stages import NabuStages
-from tomwer.gui import icons
 from tomwer.gui.reconstruction.nabu.nabuconfig.base import _NabuStageConfigBase
 from tomwer.gui.utils._outputdir import OutputDirWidget as _OutputDirWidget
 from tomwer.models.reconstruction.nabu_volume import InputModel
+from tomwer.gui.reconstruction.nabu.nabuconfig.output import _NabuOutputFileFormat
 
 from .SliceSelector import SliceSelector
 
@@ -24,31 +24,6 @@ class NabuVolumeWidget(_NabuStageConfigBase, qt.QWidget):
         _NabuStageConfigBase.__init__(self, stage=NabuStages.VOLUME)
         self.setLayout(qt.QGridLayout())
 
-        # warning about requires parameters from a nabu slice reconstruction
-        self._warning_widget = qt.QWidget(parent=self)
-        self._warning_widget.setLayout(qt.QHBoxLayout())
-        self._warningIconL = qt.QLabel("", parent=self)
-        self._warningIconL.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum)
-        self._warningIconL.setAlignment(qt.Qt.AlignRight | qt.Qt.AlignVCenter)
-        self._warningIconR = qt.QLabel("", parent=self)
-        self._warningIconR.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum)
-        self._warningIconR.setAlignment(qt.Qt.AlignLeft | qt.Qt.AlignVCenter)
-        warning_icon = icons.getQIcon("warning")
-        self._warningIconL.setPixmap(warning_icon.pixmap(20, 20))
-        self._warningIconR.setPixmap(warning_icon.pixmap(20, 20))
-        self._warning_widget.layout().addWidget(self._warningIconL)
-
-        self._labelWarning = qt.QLabel(
-            "Requires parameters from nabu slice reconstruction.", parent=self
-        )
-        self._labelWarning.setToolTip(
-            'This mean that a "nabu slice '
-            'reconstruction" widget should exist upstream'
-        )
-        self._warning_widget.layout().addWidget(self._labelWarning)
-        self._warning_widget.layout().addWidget(self._warningIconR)
-        self.layout().addWidget(self._warning_widget, 0, 0, 1, 2)
-
         # volume from and to option
         self._groupBox = qt.QGroupBox("volume to reconstruct", parent=self)
         self._groupBox.setLayout(qt.QGridLayout())
@@ -75,9 +50,21 @@ class NabuVolumeWidget(_NabuStageConfigBase, qt.QWidget):
         )
         self._groupBox.layout().addWidget(self._toSlice)
 
+        # file output format
+        self._outputFormatGB = qt.QGroupBox("Overwrite output file format", self)
+        self._outputFormatGB.setCheckable(True)
+        self._outputFormatGB.setChecked(False)
+        self._outputFormatGB.setLayout(qt.QVBoxLayout())
+
+        self._outputFormat = _NabuOutputFileFormat(
+            self, title="Volume output file format"
+        )
+        self._outputFormatGB.layout().addWidget(self._outputFormat)
+        self.layout().addWidget(self._outputFormatGB, 3, 0, 1, 2)
+
         # option to compute histogram
         self._histogramCB = qt.QCheckBox("compute volume histogram of values", self)
-        self.layout().addWidget(self._histogramCB, 3, 0, 1, 2)
+        self.layout().addWidget(self._histogramCB, 4, 0, 1, 2)
         self.registerWidget(self._histogramCB, "required")
 
         # output location
@@ -92,7 +79,7 @@ class NabuVolumeWidget(_NabuStageConfigBase, qt.QWidget):
             + "\n - 'scan_file_name': for NXtomo scans only. Return the name of the file containing the NXtomo"
             + "\n - 'scan_entry': for NXtomo scans only. Return the name of the entry containing the NXtomo"
         )
-        self.layout().addWidget(self._outputDir, 4, 0, 1, 2)
+        self.layout().addWidget(self._outputDir, 5, 0, 1, 2)
         self.registerWidget(self._outputDir, "required")
 
         # spacer for style
@@ -108,6 +95,7 @@ class NabuVolumeWidget(_NabuStageConfigBase, qt.QWidget):
         self._toSlice.valueChanged.connect(self._triggerSigConfChanged)
         self._histogramCB.stateChanged.connect(self._triggerSigConfChanged)
         self._outputDir.sigOutputChanged.connect(self._triggerSigConfChanged)
+        self._outputFormat.sigConfChanged.connect(self._triggerSigConfChanged)
 
     def _triggerSigConfChanged(self, *args, **kwargs):
         self.sigConfigChanged.emit()
@@ -137,7 +125,7 @@ class NabuVolumeWidget(_NabuStageConfigBase, qt.QWidget):
         self._histogramCB.setChecked(requested)
 
     def getConfiguration(self):
-        return {
+        config = {
             "reconstruction": {
                 "start_z": self.getStartZ(),
                 "end_z": self.getEndZ(),
@@ -149,6 +137,9 @@ class NabuVolumeWidget(_NabuStageConfigBase, qt.QWidget):
                 "location": self._outputDir.getOutputDir() or "",
             },
         }
+        if self.getFileFormat() is not None:
+            config["output"]["file_format"] = self.getFileFormat().value
+        return config
 
     def setConfiguration(self, config: dict):
         if not isinstance(config, dict):
@@ -167,3 +158,14 @@ class NabuVolumeWidget(_NabuStageConfigBase, qt.QWidget):
     def setOutputConfiguration(self, config):
         if "location" in config:
             self._outputDir.setOutputDir(config["location"])
+        self.setFileFormat(config.get("file_format", None))
+
+    def getFileFormat(self) -> None | _NabuOutputFileFormat:
+        if not self._outputFormatGB.isChecked():
+            return None
+        return self._outputFormat.getFileFormat()
+
+    def setFileFormat(self, file_format: _NabuOutputFileFormat) -> None:
+        self._outputFormatGB.setChecked(file_format is not None)
+        if file_format is not None:
+            self._outputFormat.setFileFormat(file_format=file_format)