tomwer 1.0.3__py3-none-any.whl → 1.1.0__py3-none-any.whl

orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py

@@ -58,7 +58,6 @@ _logger = logging.getLogger(__name__)
 
 
 class SAAxisWindow(_SAAxisWindow):
-
     sigResultsToBeShow = qt.Signal()
     """signal emit when some results are ready to be display"""
 
@@ -75,7 +74,6 @@ class SAAxisWindow(_SAAxisWindow):
         self._clusterConfig = None
 
     def setClusterConfig(self, cluster_config: dict):
-
         if not isinstance(
             cluster_config, (dict, type(None), SlurmClusterConfiguration)
         ):
@@ -192,7 +190,8 @@ class SAAxisWindow(_SAAxisWindow):
         if scan is None:
             return
         assert isinstance(scan, TomwerScanBase)
-        selected_cor_value = self.getCurrentCorValue()
+        selected_cor_value = self.getCurrentCorValue() or scan.saaxis_params.autofocus
+        # if validate is done manually then pick current cor value; else we are in 'auto mode' and get it from the autofocus.
         details = ProcessManager().get_dataset_details(
             dataset_id=scan.get_identifier(), process=self._processing_stack
         )
@@ -208,6 +207,12 @@ class SAAxisWindow(_SAAxisWindow):
             )
         else:
             scan.axis_params.set_relative_value(selected_cor_value)
+            if scan.nabu_recons_params is not None:
+                if "reconstruction" not in scan.nabu_recons_params:
+                    scan.nabu_recons_params["reconstruction"] = {}
+                scan.nabu_recons_params["reconstruction"][
+                    "rotation_axis_position"
+                ] = scan.axis_params.absolute_cor_value
             infos = "cor selected for {}: relative: {}, absolute: {}".format(
                 scan,
                 scan.axis_params.relative_cor_value,
@@ -288,11 +293,7 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
     sigScanReady = qt.Signal(TomwerScanBase)
     """Signal emitted when a scan is ready"""
 
-    _rpSetting = Setting(dict())
-    # kept for compatibility
-    "SAAxisRP store as dict"
-
-    static_input = Setting({"data": None, "sa_axis_params": None})
+    _ewoks_default_inputs = Setting({"data": None, "sa_axis_params": None})
 
     class Inputs:
         data = Input(
@@ -336,10 +337,8 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
         )
         self._layout.addWidget(self._widget)
 
-        sa_axis_params = self.static_input.get("sa_axis_params", None)
-        if sa_axis_params is None:
-            sa_axis_params = self._rpSetting
-        self.setConfiguration(sa_axis_params)
+        sa_axis_params = self._ewoks_default_inputs.get("sa_axis_params", None)
+        self.setConfiguration(sa_axis_params or {})
 
         # connect signal / slot
         self._widget.sigConfigurationChanged.connect(self._updateSettings)
@@ -354,6 +353,16 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
         # expose API
         self.wait_processing = self._widget.wait_processing
 
+    def __new__(cls, *args, **kwargs):
+        # ensure backward compatibility with 'static_input'
+        static_input = kwargs.get("stored_settings", {}).get("static_input", None)
+        if static_input not in (None, {}):
+            _logger.warning(
+                "static_input has been deprecated. Will be replaced by _ewoks_default_inputs in the workflow file. Please save the workflow to apply modifications"
+            )
+            kwargs["stored_settings"]["_ewoks_default_inputs"] = static_input
+        return super().__new__(cls, *args, **kwargs)
+
     def setConfiguration(self, configuration):
         if "workflow" in configuration:
             autofocus_lock = configuration["workflow"].get("autofocus_lock", None)
@@ -365,6 +374,9 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
     def getCurrentCorValue(self):
         return self._widget.getCurrentCorValue()
 
+    def setEstimatedCorPosition(self, value):
+        self._widget.setEstimatedCorPosition(value=value)
+
     def load_sinogram(self):
         self._widget.loadSinogram()
 
@@ -437,18 +449,14 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
     def _updateSettings(self):
         config = self._widget.getConfiguration()
         config.pop("cluster_config", None)
-        self._rpSetting = config
-        self._rpSetting["workflow"] = {
-            "autofocus_lock": self._widget.isAutoFocusLock(),
-        }
 
-        self.static_input = {
+        self._ewoks_default_inputs = {
             "data": None,
             "sa_axis_params": self._widget.getConfiguration(),
         }
-        self.static_input["sa_axis_params"][
-            "autofocus_lock"
-        ] = self._widget.isAutoFocusLock()
+        self._ewoks_default_inputs["sa_axis_params"]["workflow"] = {
+            "autofocus_lock": self._widget.isAutoFocusLock(),
+        }
 
     def _raiseResults(self):
         if not self.isAutoFocusLock():

orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py

@@ -67,7 +67,6 @@ class SADeltaBetaWindow(_SADeltaBetaWindow):
         self._clusterConfig = None
 
     def setClusterConfig(self, cluster_config: dict):
-
         if not isinstance(
             cluster_config, (dict, type(None), SlurmClusterConfiguration)
         ):
@@ -126,7 +125,9 @@ class SADeltaBetaWindow(_SADeltaBetaWindow):
         if scan is None:
             return
         assert isinstance(scan, TomwerScanBase)
-        selected_db_value = self.getCurrentDeltaBetaValue()
+        selected_db_value = (
+            self.getCurrentDeltaBetaValue() or scan.sa_delta_beta_params.autofocus
+        )
         if selected_db_value is None:
             infos = "no selected delta / beta value. {} skip SADeltaBetaParams".format(
                 scan
@@ -138,6 +139,10 @@ class SADeltaBetaWindow(_SADeltaBetaWindow):
             )
         else:
             scan.sa_delta_beta_params.set_db_selected_value(selected_db_value)
+            if scan.nabu_recons_params is not None:
+                if "phase" not in scan.nabu_recons_params:
+                    scan.nabu_recons_params["phase"] = {}
+                scan.nabu_recons_params["phase"]["delta_beta"] = (selected_db_value,)
             infos = "delta / beta selected for {}: {},".format(
                 scan, scan.sa_delta_beta_params.value
             )
@@ -222,10 +227,7 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
     sigScanReady = qt.Signal(TomwerScanBase)
     """Signal emitted when a scan is ready"""
 
-    _rpSetting = Setting(dict())
-    "settings store as dict"
-
-    static_input = Setting({"data": None, "sa_delta_beta_params": None})
+    _ewoks_default_inputs = Setting({"data": None, "sa_delta_beta_params": None})
 
     class Inputs:
         data = Input(name="data", type=TomwerScanBase, default=True, multiple=False)
@@ -265,10 +267,10 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
         )
         self._layout.addWidget(self._widget)
 
-        sa_delta_beta_params = self.static_input.get("sa_delta_beta_params", None)
-        if sa_delta_beta_params is None:
-            sa_delta_beta_params = self._rpSetting
-        self.setConfiguration(sa_delta_beta_params)
+        sa_delta_beta_params = self._ewoks_default_inputs.get(
+            "sa_delta_beta_params", None
+        )
+        self.setConfiguration(sa_delta_beta_params or {})
 
         # connect signal / slot
         self._widget.sigConfigurationChanged.connect(self._updateSettings)
@@ -280,6 +282,16 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
         # expose API
         self.wait_processing = self._widget.wait_processing
 
+    def __new__(cls, *args, **kwargs):
+        # ensure backward compatibility with 'static_input'
+        static_input = kwargs.get("stored_settings", {}).get("static_input", None)
+        if static_input not in (None, {}):
+            _logger.warning(
+                "static_input has been deprecated. Will be replaced by _ewoks_default_inputs in the workflow file. Please save the workflow to apply modifications"
+            )
+            kwargs["stored_settings"]["_ewoks_default_inputs"] = static_input
+        return super().__new__(cls, *args, **kwargs)
+
     def setConfiguration(self, configuration):
         if "workflow" in configuration:
             autofocus_lock = configuration["workflow"].get("autofocus_lock", None)
@@ -363,17 +375,11 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
     def _updateSettings(self):
         config = self._widget.getConfiguration()
         config.pop("cluster_config", None)
-        self._rpSetting = config
-        self._rpSetting["workflow"] = {
-            "autofocus_lock": self._widget.isAutoFocusLock(),
-        }
-        # keep for backward compatibility
-
-        self.static_input = {
+        self._ewoks_default_inputs = {
             "data": None,
             "sa_delta_beta_params": self._widget.getConfiguration(),
         }
-        self.static_input["sa_delta_beta_params"]["workflow"] = {
+        self._ewoks_default_inputs["sa_delta_beta_params"]["workflow"] = {
             "autofocus_lock": self._widget.isAutoFocusLock(),
         }
 

orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py

@@ -133,7 +133,7 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
     compress_signal = False
     allows_cycle = True
 
-    _rpSetting = Setting(dict())
+    _ewoks_default_inputs = Setting(dict())
 
     sigScanReady = qt.Signal(TomwerScanBase)
     "Signal emitted when a scan is ended"
@@ -300,10 +300,10 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
         self._window.stop()
 
     def _updateSettings(self):
-        self._rpSetting = self._window.getConfiguration()
-        self._rpSetting["__lock__"] = self.isLocked()
+        self._ewoks_default_inputs = self._window.getConfiguration()
+        self._ewoks_default_inputs["__lock__"] = self.isLocked()
 
     def loadSettings(self):
-        self._window.setConfiguration(self._rpSetting)
-        if "__lock__" in self._rpSetting:
-            self.setLocked(self._rpSetting["__lock__"])
+        self._window.setConfiguration(self._ewoks_default_inputs)
+        if "__lock__" in self._ewoks_default_inputs:
+            self.setLocked(self._ewoks_default_inputs["__lock__"])

orangecontrib/tomwer/widgets/reconstruction/TofuOW.py

@@ -75,7 +75,7 @@ class TofuOW(WidgetLongProcessing, SuperviseOW):
     _reconsParams = settings.Setting(dict())
     """Parameters directly editabled from the TOFU interface"""
     # kept for compatibility
-    static_input = settings.Setting({"data": None, "lamino_params": None})
+    _ewoks_default_inputs = settings.Setting({"data": None, "lamino_params": None})
 
     _additionalOpts = settings.Setting(dict())
     """Parameters which can be add on the expert tab from TOFU"""
@@ -108,7 +108,9 @@ class TofuOW(WidgetLongProcessing, SuperviseOW):
         self._box.layout().addWidget(self._mainWidget)
         self._box.layout().addWidget(self._widgetControl)
 
-        lamino_params = self.static_input.get("lamino_params", None)
+        lamino_params = self._ewoks_default_inputs.get(  # pylint: disable=E1101
+            "lamino_params", None
+        )
         if lamino_params is None:
             lamino_params = self._reconsParams
         self._mainWidget.setParameters(lamino_params)

orangecontrib/tomwer/widgets/reconstruction/icons/nabu_2d.svg

@@ -14,8 +14,11 @@
    viewBox="0 0 48 48"
    version="1.1"
    id="SVGRoot"
-   inkscape:version="0.92.4 (5da689c313, 2019-01-14)"
-   sodipodi:docname="nabu.svg">
+   inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
+   sodipodi:docname="nabu_2d.svg"
+   inkscape:export-filename="/media/payno/830add5c-f5d7-4db2-875e-03be4f0a67f0/dev/tomography/tomwer/orangecontrib/tomwer/widgets/reconstruction/icons/nabu_2d.png"
+   inkscape:export-xdpi="59.900002"
+   inkscape:export-ydpi="59.900002">
   <defs
      id="defs815" />
   <sodipodi:namedview
@@ -26,14 +29,14 @@
      inkscape:pageopacity="0.0"
      inkscape:pageshadow="2"
      inkscape:zoom="5.3333333"
-     inkscape:cx="-29.508774"
-     inkscape:cy="36.425261"
+     inkscape:cx="-96.821274"
+     inkscape:cy="34.925261"
      inkscape:document-units="px"
      inkscape:current-layer="g1399"
      showgrid="false"
-     inkscape:window-width="1920"
-     inkscape:window-height="1016"
-     inkscape:window-x="0"
+     inkscape:window-width="1848"
+     inkscape:window-height="1136"
+     inkscape:window-x="72"
      inkscape:window-y="27"
      inkscape:window-maximized="1"
      inkscape:grid-bbox="true" />
@@ -45,7 +48,7 @@
         <dc:format>image/svg+xml</dc:format>
         <dc:type
            rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
-        <dc:title></dc:title>
+        <dc:title />
       </cc:Work>
     </rdf:RDF>
   </metadata>

orangecontrib/tomwer/widgets/visualization/DataViewerOW.py

@@ -70,7 +70,7 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         data = Input(name="data", type=TomwerScanBase)
 
     def __init__(self, parent=None):
-        widget.OWBaseWidget.__init__(self, parent)
+        super().__init__(parent)
         self._layout = gui.vBox(self.mainArea, self.name).layout()
         self.viewer = DataViewer(parent=self)
         self.viewer.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
@@ -115,9 +115,15 @@ class DataViewerOW(widget.OWBaseWidget, openclass=True):
         return qt.QSize(400, 500)
 
     def _updateSettings(self):
-        self._viewer_config["mode"] = self.viewer.getDisplayMode()
-        self._viewer_config["slice_opt"] = self.viewer.getSliceOption()
-        self._viewer_config["radio_opt"] = self.viewer.getRadioOption()
+        self._viewer_config[  # pylint: disable=E1137
+            "mode"
+        ] = self.viewer.getDisplayMode().value
+        self._viewer_config[  # pylint: disable=E1137
+            "slice_opt"
+        ] = self.viewer.getSliceOption().value
+        self._viewer_config[  # pylint: disable=E1137
+            "radio_opt"
+        ] = self.viewer.getRadioOption().value
 
     def _setSettings(self, settings):
         old_state = self.viewer.blockSignals(True)

orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py

@@ -74,4 +74,4 @@ class DiffViewerOW(widget.OWBaseWidget, openclass=True):
         self.viewer.addScan(scan)
 
     def sizeHint(self):
-        return qt.QSize(400, 500)
+        return qt.QSize(500, 700)

orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py

@@ -0,0 +1,69 @@
+from orangewidget import widget, gui
+from tomwer.gui.visualization.nxtomometadata import NXtomoMetadataViewer
+from orangewidget.widget import Input, Output
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.scanbase import TomwerScanBase
+from silx.gui import qt
+
+
+class NXtomoMetadataViewerOW(widget.OWBaseWidget, openclass=True):
+    """
+    Widget to siplay NXtomo metadata
+    """
+
+    name = "nxtomo-metadata-viewer"
+    id = "orange.widgets.tomwer.visualization.NXtomoMetadataViewerOW.NXtomoMetadataViewerOW"
+    description = "Interface to display some metadata of an NXtomo"
+    icon = "icons/nx_tomo_metadata_viewer.svg"
+    priority = 13
+    keywords = [
+        "hdf5",
+        "nexus",
+        "tomwer",
+        "file",
+        "visualize",
+        "visualization",
+        "display",
+        "NXTomo",
+        "editor",
+        "energy",
+        "distance",
+        "pixel size",
+    ]
+
+    class Inputs:
+        data = Input(name="data", type=TomwerScanBase)
+
+    class Outputs:
+        data = Output(name="data", type=TomwerScanBase)
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+
+    def __init__(self, parent=None, *args, **kwargs):
+        super().__init__(parent=parent, *args, **kwargs)
+
+        _layout = gui.vBox(self.mainArea, self.name).layout()
+        self.widget = NXtomoMetadataViewer(parent=self)
+        _layout.addWidget(self.widget)
+
+    def _validateScan(self, scan):
+        self.Outputs.data.send(scan)
+        super().hide()
+
+    @Inputs.data
+    def setScan(self, scan):
+        if scan is None:
+            pass
+        elif not isinstance(scan, HDF5TomoScan):
+            raise TypeError(
+                f"expect to have an instance of {HDF5TomoScan}. {type(scan)} provided."
+            )
+        else:
+            self.widget.setScan(scan)
+            self.show()
+            self.raise_()
+
+    def sizeHint(self):
+        return qt.QSize(400, 500)

orangecontrib/tomwer/widgets/visualization/SampleMovedOW.py

@@ -30,7 +30,6 @@ __date__ = "19/03/2018"
 from silx.gui import qt
 from orangewidget import widget, gui
 from orangewidget.widget import Input
-from tomwer.web.client import OWClient
 from tomwer.gui.samplemoved import SampleMovedWidget
 from tomwer.core.scan.scanbase import TomwerScanBase
 import tomwer.core.process.visualization.samplemoved
@@ -40,7 +39,7 @@ import logging
 logger = logging.getLogger(__name__)
 
 
-class SampleMovedOW(widget.OWBaseWidget, OWClient, openclass=True):
+class SampleMovedOW(widget.OWBaseWidget, openclass=True):
     """
     Simple widget exposing two images side by side to see if a sample moved
     during the acquisition.
@@ -72,8 +71,7 @@ class SampleMovedOW(widget.OWBaseWidget, OWClient, openclass=True):
         data = Input(name="data", type=TomwerScanBase)
 
     def __init__(self, parent=None):
-        widget.OWBaseWidget.__init__(self, parent)
-        OWClient.__init__(self)
+        super().__init__(parent)
 
         layout = gui.vBox(self.mainArea, self.name).layout()
 

orangecontrib/tomwer/widgets/visualization/icons/nx_tomo_metadata_viewer.svg

@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:xlink="http://www.w3.org/1999/xlink"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="48"
+   height="48"
+   viewBox="0 0 12.7 12.7"
+   version="1.1"
+   id="svg901"
+   inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
+   sodipodi:docname="nx_tomo_metadata_viewer.svg"
+   inkscape:export-filename="/media/payno/830add5c-f5d7-4db2-875e-03be4f0a67f0/dev/tomography/tomwer/orangecontrib/tomwer/widgets/visualization/icons/nx_tomo_metadata_viewer.png"
+   inkscape:export-xdpi="59.900002"
+   inkscape:export-ydpi="59.900002">
+  <defs
+     id="defs895" />
+  <sodipodi:namedview
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+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1.0"
+     inkscape:pageopacity="0.0"
+     inkscape:pageshadow="2"
+     inkscape:zoom="3.959798"
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+     inkscape:document-units="mm"
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+     inkscape:window-height="1136"
+     inkscape:window-x="72"
+     inkscape:window-y="27"
+     inkscape:window-maximized="1" />
+  <metadata
+     id="metadata898">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title></dc:title>
+      </cc:Work>
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+       id="image1813"
+       x="4.855176"
+       y="283.63773" />
+  </g>
+</svg>

tomwer/__main__.py

@@ -80,6 +80,11 @@ def main():
         module_name="tomwer.app.imagekeyeditor",
         description="Tool to modify in place frames image key parameter.",
     )
+    launcher.add_command(
+        "image-key-upgrader",
+        module_name="tomwer.app.imagekeyupgrader",
+        description="Tool to upgrade in place frames image key parameter.",
+    )
     launcher.add_command(
         "norm-intensity",
         module_name="tomwer.app.intensitynormalization",
@@ -100,16 +105,16 @@ def main():
         module_name="tomwer.app.nabuapp",
         description="Use nabu to reconstruct a given scan",
     )
+    launcher.add_command(
+        "nxtomo-editor",
+        module_name="tomwer.app.nxtomoeditor",
+        description="Use to edit an NXtomo",
+    )
     launcher.add_command(
         "ows-to-script",
         module_name="tomwer.app.ows_to_script",
         description="Convert a .ows file to python script",
     )
-    launcher.add_command(
-        "process",
-        module_name="tomwer.app.process",
-        description="Process a given scan with a defined" "workflow",
-    )
     launcher.add_command(
         "rsync",
         module_name="tomwer.app.rsync",

tomwer/app/canvas_launcher/config.py

@@ -124,12 +124,12 @@ class TomwerConfig(config.Config):
         #: Submit a bug report action in the Help menu
         "Bug Report": "https://gitlab.esrf.fr/tomotools/tomwer/-/issues",
         #: A url quick tour/getting started url
-        "Quick Start": "http://www.edna-site.org/pub/doc/tomwer/video/canvas/start_up/",
+        "Quick Start": "https://www.youtube.com/playlist?list=PLddRXwP6Z6F9KOu1V5o6H24KPH5Ikuk2f",
         #: The 'full' documentation, should be something like current /docs/
         #: but specific for 'Visual Programing' only
-        "Documentation": "http://www.edna-site.org/pub/doc/tomwer/latest/",
+        "Documentation": "https://tomotools.gitlab-pages.esrf.fr/nxtomomill/index.html",
         #: YouTube tutorials
-        "Screencasts": "http://www.edna-site.org/pub/doc/tomwer/video",
+        "Screencasts": "https://www.youtube.com/@tomotools",
     }
 
 
@@ -187,13 +187,13 @@ class TerminalTextDocument(_TerminalTextDocument):
         # remove linux reset sequence
         string = string.replace("\033[1;%dm", "")
         # remove linux reset sequence
-        string = string.replace("", "")
-        string = string.replace("", "")
-        string = string.replace("", "")
-        string = string.replace("", "")
-        string = string.replace("", "")
-        string = string.replace("", "")
-        string = string.replace("", "")
+        string = string.replace("\x1B[1m", "")
+        string = string.replace("\x1B[1;30m", "")
+        string = string.replace("\x1B[1;31m", "")
+        string = string.replace("\x1B[1;32m", "")
+        string = string.replace("\x1B[1;33m", "")
+        string = string.replace("\x1B[1;34m", "")
+        string = string.replace("\x1B[1;35m", "")
 
         color = self.get_log_level(string) or qt.Qt.red
         charformat.setForeground(color)