tomwer 1.2.9__py3-none-any.whl → 1.3.0a0__py3-none-any.whl

orangecontrib/tomwer/widgets/reconstruction/NabuVolumeOW.py

@@ -45,6 +45,11 @@ from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 from tomwer.core import settings
 from tomwer.core.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
+from tomwer.core.process.icat.gallery import (
+    IcatScreenshots,
+    deduce_dataset_gallery_location,
+    select_screenshot_from_volume,
+)
 from tomwer.core.process.reconstruction.nabu import utils as nabu_utils
 from tomwer.core.process.reconstruction.nabu.nabuvolume import NabuVolumeTask
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -123,6 +128,11 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
         volume_urls = Output(
             name="volume urls", type=tuple, doc="url of the volume(s) reconstructed"
         )
+        screenshots = Output(
+            name="screenshots",
+            type=IcatScreenshots,
+            doc="screenshots that can be saved",
+        )
 
     class DialogCM(AbstractContextManager):
         """Simple context manager to hida / show button dialogs"""
@@ -172,7 +182,7 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
 
         if nabu_volume_params not in (dict(), None):
             try:
-                self._nabuWidget.setConfiguration(nabu_volume_params)
+                self.setConfiguration(nabu_volume_params)
             except Exception:
                 _logger.warning("fail to load reconstruction settings")
 
@@ -213,14 +223,19 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
         config = scan.nabu_recons_params
         # update output format if requested
         if self._nabuWidget._mainWidget.redefineNabuFileFormat():
-            config.get("output")[
+            config["output"][
                 "file_format"
             ] = self._nabuWidget._mainWidget.getNabuFileFormat()
         # update output location if requested
         if self._nabuWidget._mainWidget.redefineOutputLocation():
-            config.get("output")["location"] = format_output_location(
-                location=self._nabuWidget._mainWidget.getNabuOutputLocation(),
-                scan=scan,
+            location = self._nabuWidget._mainWidget.getNabuOutputLocation()
+            if location is not None:
+                location = format_output_location(location=location, scan=scan)
+            config["output"]["location"] = location
+            config["output"][
+                "output_dir_mode"
+            ] = (
+                self._nabuWidget._mainWidget._outputLocationWidget.getOutputDirMode().value
             )
 
         if "phase" in config and "delta_beta" in config["phase"]:
@@ -314,7 +329,26 @@ class NabuVolumeOW(WidgetLongProcessing, SuperviseOW):
                 assert isinstance(volume_id, VolumeIdentifier)
                 volume_urls.extend(VolumeFactory.from_identifier_to_vol_urls(volume_id))
             if len(volume_urls) > 0:
+                # send list of reconcstructed volume
                 self.Outputs.volume_urls.send(tuple(volume_urls))
+                # send list of screenshots
+                screenshots = {}
+                [
+                    screenshots.update(
+                        select_screenshot_from_volume(
+                            VolumeFactory.create_tomo_object_from_identifier(volume_id)
+                        )
+                    )
+                    for volume_id in scan.latest_vol_reconstructions
+                ]
+                self.Outputs.screenshots.send(
+                    IcatScreenshots(
+                        data_dir=deduce_dataset_gallery_location(scan),
+                        screenshots=screenshots,
+                        scan=scan,
+                    ),
+                )
+
             # send volume identifier(s)  # only one expected
             n_rec_volumes = len(scan.latest_vol_reconstructions)
             if n_rec_volumes > 0:

orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py

@@ -43,9 +43,9 @@ from silx.gui import qt
 import tomwer.core.process.reconstruction.saaxis.saaxis
 from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
 from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
-from tomwer.core import settings, utils
+from tomwer.core import settings
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.cluster import SlurmClusterConfiguration
-from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.process.reconstruction.axis import AxisTask
 from tomwer.core.process.reconstruction.saaxis.saaxis import SAAxisTask
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
@@ -270,12 +270,14 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
     Details about :ref:`saaxis score calculation`
     """
 
-    name = "semi-automated center of rotation"
+    name = "multi-cor (sa-axis)"
     id = "orange.widgets.tomwer.sa_axis"
-    description = "use to compute the center of rotation semi automatic way"
+    description = "Reconstruct a slice with different center of rotation (cor) values"
     icon = "icons/saaxis.png"
     priority = 21
     keywords = [
+        "multi",
+        "multi-cor",
         "tomography",
         "semi automatic",
         "half automatic",
@@ -322,12 +324,6 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
     class Outputs:
         data = Output(name="data", type=TomwerScanBase, doc="one scan to be process")
 
-        future_out = Output(
-            name="future_tomo_obj",
-            type=FutureTomwerObject,
-            doc="data with some remote processing",
-        )
-
     def __init__(self, parent=None):
         """
 
@@ -404,9 +400,7 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
             scan.saaxis_params = QSAAxisParams()
         self._skipCurrentScan(new_scan=scan)
 
-        if settings.isOnLbsram(scan) and utils.isLowOnMemory(
-            settings.get_lbsram_path()
-        ):
+        if settings.isOnLbsram(scan) and is_low_on_memory(settings.get_lbsram_path()):
             self.notify_skip(
                 scan=scan,
                 details=f"saaxis has been skiped for {scan} because of low space in lbsram",

orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py

@@ -41,9 +41,9 @@ from silx.gui import qt
 import tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta
 from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
 from orangecontrib.tomwer.orange.settings import CallbackSettingsHandler
-from tomwer.core import settings, utils
+from tomwer.core import settings
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.cluster import SlurmClusterConfiguration
-from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.process.reconstruction.sadeltabeta import SADeltaBetaTask
 from tomwer.core.scan.scanbase import TomwerScanBase, _TomwerBaseDock
 from tomwer.gui.reconstruction.sadeltabeta import (
@@ -198,16 +198,14 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
     Details about :ref:`sadeltabeta score calculation`
     """
 
-    name = "semi automatic delta/beta calculation"
+    name = "multi-pag (sa-delta/beta calculation)"
     id = "orange.widgets.tomwer.sa_delta_beta"
-    description = (
-        "compute several delta / beta value to get the optimal "
-        "delta / beta value (before reconstructing a volume for "
-        "example."
-    )
+    description = "Reconstruct a slice with several delta / beta values."
     icon = "icons/delta_beta_range.png"
     priority = 22
     keywords = [
+        "multi",
+        "multi-pag",
         "tomography",
         "semi automatic",
         "half automatic",
@@ -257,12 +255,6 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
     class Outputs:
         data = Output(name="data", type=TomwerScanBase)
 
-        future_out = Output(
-            name="future_tomo_obj",
-            type=FutureTomwerObject,
-            doc="data with some remote processing",
-        )
-
     def __init__(self, parent=None):
         """
 
@@ -336,9 +328,7 @@ class SADeltaBetaOW(SuperviseOW, WidgetLongProcessing):
             scan.sa_delta_beta_params = QSADeltaBetaParams()
         self._skipCurrentScan(new_scan=scan)
 
-        if settings.isOnLbsram(scan) and utils.isLowOnMemory(
-            settings.get_lbsram_path()
-        ):
+        if settings.isOnLbsram(scan) and is_low_on_memory(settings.get_lbsram_path()):
             self.notify_skip(
                 scan=scan,
                 details=f"sa-delta-beta has been skiped for {scan} because of low space in lbsram",

orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py

@@ -42,7 +42,8 @@ from tomoscan.normalization import Method as NormMethod
 
 from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
 
-from tomwer.core import settings, utils
+from tomwer.core import settings
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.process.reconstruction.normalization import SinoNormalizationTask
 from tomwer.core.process.reconstruction.normalization.params import _ValueSource
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -197,9 +198,7 @@ class SinoNormOW(WidgetLongProcessing, SuperviseOW):
             return
 
         self._skipCurrentScan(new_scan=scan)
-        if settings.isOnLbsram(scan) and utils.isLowOnMemory(
-            settings.get_lbsram_path()
-        ):
+        if settings.isOnLbsram(scan) and is_low_on_memory(settings.get_lbsram_path()):
             details = f"skip {scan} because low memory on lbsram"
             self.notify_skip(scan=scan, details=details)
             self.Outputs.data_out.send(scan)

orangecontrib/tomwer/widgets/visualization/LivesliceOW.py

@@ -32,7 +32,7 @@ from orangewidget.widget import Input
 
 import tomwer.core.process.visualization.liveslice
 from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.utils import getFirstProjFile
+from tomwer.core.utils.spec import getFirstProjFile
 
 try:
     from liveslice.gui.liveslice_gui import ReconstructionApp

orangecontrib/tomwer/widgets/visualization/NXtomoMetadataViewerOW.py

@@ -2,7 +2,7 @@ from orangewidget import gui, widget
 from orangewidget.widget import Input, Output
 from silx.gui import qt
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.visualization.nxtomometadata import NXtomoMetadataViewer
 
@@ -56,9 +56,9 @@ class NXtomoMetadataViewerOW(widget.OWBaseWidget, openclass=True):
     def setScan(self, scan):
         if scan is None:
             pass
-        elif not isinstance(scan, HDF5TomoScan):
+        elif not isinstance(scan, NXtomoScan):
             raise TypeError(
-                f"expect to have an instance of {HDF5TomoScan}. {type(scan)} provided."
+                f"expect to have an instance of {NXtomoScan}. {type(scan)} provided."
             )
         else:
             self.widget.setScan(scan)

orangecontrib/tomwer/widgets/visualization/VolumeViewerOW.py

@@ -1,32 +1,3 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "21/07/2020"
-
 import pytest
 from orangewidget import gui, widget
 from orangewidget.widget import Input
@@ -79,6 +50,9 @@ class VolumeViewerOW(widget.OWBaseWidget, openclass=True):
         self.viewer.setScan(scan)
 
     @Inputs.volume
+    def _volumeReceived(self, volume, *args, **kwargs):
+        self.addVolume(volume)
+
     def addVolume(self, volume):
         if volume is None:
             return

tomwer/__main__.py

@@ -36,21 +36,16 @@ __date__ = "10/11/2020"
 
 
 import sys
-import logging
-import traceback
 from collections import namedtuple
 import tomwer.version
 from tomwer.utils import Launcher as _Launcher
-
+from tomwer.core.utils.deprecation import deprecated_warning
 
 DeprecationWarning = namedtuple(
     "DeprecationWarning", ["since", "reason", "replacement"]
 )
 
 
-depreclog = logging.getLogger("nxtomomill.DEPRECATION")
-
-
 class Launcher(_Launcher):
     """
     Manage launch of module.
@@ -115,48 +110,6 @@ class Launcher(_Launcher):
         super().execute(argv=argv)
 
 
-def deprecated_warning(
-    type_,
-    name,
-    reason=None,
-    replacement=None,
-    since_version=None,
-    skip_backtrace_count=0,
-):
-    """
-    Function to log a deprecation warning
-
-    :param str type_: Nature of the object to be deprecated:
-        "Module", "Function", "Class" ...
-    :param name: Object name.
-    :param str reason: Reason for deprecating this function
-        (e.g. "feature no longer provided",
-    :param str replacement: Name of replacement function (if the reason for
-        deprecating was to rename the function)
-    :param str since_version: First *silx* version for which the function was
-        deprecated (e.g. "0.5.0").
-    :param int skip_backtrace_count: Amount of last backtrace to ignore when
-        logging the backtrace
-    """
-    if not depreclog.isEnabledFor(logging.WARNING):
-        # Avoid computation when it is not logged
-        return
-
-    msg = "%s %s is deprecated"
-    if since_version is not None:
-        msg += " since silx version %s" % since_version
-    msg += "."
-    if reason is not None:
-        msg += " Reason: %s." % reason
-    if replacement is not None:
-        msg += " Use '%s' instead." % replacement
-    msg += "\n%s"
-    limit = 2 + skip_backtrace_count
-    backtrace = "".join(traceback.format_stack(limit=limit)[0])
-    backtrace = backtrace.rstrip()
-    depreclog.warning(msg, type_, name, backtrace)
-
-
 def main():
     """Main function of the launcher
 
@@ -225,6 +178,16 @@ def main():
         module_name="tomwer.app.liveslice",
         description="Run liveslice application",
     )
+    launcher.add_command(
+        "multi-cor",
+        module_name="tomwer.app.multicor",
+        description="Compute a slice with different values of cor",
+    )
+    launcher.add_command(
+        "multi-pag",
+        module_name="tomwer.app.multipag",
+        description="compute a slice with different values of delta / beta values",
+    )
     launcher.add_command(
         "nabu",
         module_name="tomwer.app.nabuapp",
@@ -273,16 +236,6 @@ def main():
         module_name="tomwer.app.sinogramviewer",
         description="Allows to compute on the fly sinogram " "and display them",
     )
-    launcher.add_command(
-        "sa-axis",
-        module_name="tomwer.app.saaxis",
-        description="Semi-automatic center of rotation research",
-    )
-    launcher.add_command(
-        "sa-delta-beta",
-        module_name="tomwer.app.sadeltabeta",
-        description="Semi-automatic delta/beta Paganin parameter research",
-    )
     launcher.add_command(
         "scan-viewer",
         module_name="tomwer.app.scanviewer",

tomwer/app/canvas.py

@@ -23,11 +23,19 @@ except ImportError:
     has_nabu = False
 else:
     has_nabu = True
+try:
+    import nxtomo.version
+except ImportError:
+    has_nxtomo = False
+else:
+    has_nxtomo = True
 
 
 def print_versions():
     print(f"tomwer version is {tomwer.version.version}")
     print(f"tomoscan version is {tomoscan.version.version}")
+    if has_nxtomo:
+        print(f"nxtomo version is {nxtomo.version.version}")
     if has_nxtomomill:
         print(f"nxtomomill version is {nxtomomill.version.version}")
     if has_nabu:

tomwer/app/canvas_launcher/config.py

@@ -185,17 +185,19 @@ class TerminalTextDocument(_TerminalTextDocument):
     def writeWithFormat(self, string: str, charformat) -> None:
         assert qt.QThread.currentThread() is self.thread()
         # remove linux reset sequence
-        string = string.replace("\033[0m", "")
-        # remove linux reset sequence
-        string = string.replace("\033[1;%dm", "")
-        # remove linux reset sequence
-        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", "")
+        from tomwer.core.log import logger as tomwer_logger
+
+        for sequence in (
+            tomwer_logger._RESET_SEQ,
+            tomwer_logger._BOLD_SEQ,
+            tomwer_logger._BLACK,
+            tomwer_logger._RED,
+            tomwer_logger._GREEN,
+            tomwer_logger._YELLOW,
+            tomwer_logger._BLUE,
+            tomwer_logger._MAGENTA,
+        ):
+            string = string.replace(sequence, "")
 
         color = self.get_log_level(string) or qt.Qt.red
         charformat.setForeground(color)

tomwer/app/darkref.py

@@ -1,4 +1,4 @@
-from silx.utils.deprecation import deprecated_warning
+from tomwer.core.utils.deprecation import deprecated_warning
 
 deprecated_warning(
     "module",

tomwer/app/darkrefpatch.py

@@ -1,4 +1,4 @@
-from silx.utils.deprecation import deprecated_warning
+from tomwer.core.utils.deprecation import deprecated_warning
 
 deprecated_warning(
     "module",

tomwer/app/imagekeyeditor.py

@@ -8,7 +8,7 @@ import sys
 
 from silx.gui import qt
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.core.process.edit.imagekeyeditor import ImageKeyEditorTask
 from tomwer.gui import icons
@@ -25,8 +25,8 @@ class ImageKeyDialog(_ImageKeyDialog):
         self._scan = None
 
     def setScan(self, scan):
-        if not isinstance(scan, HDF5TomoScan):
-            raise TypeError("This only manage HDF5TomoScan")
+        if not isinstance(scan, NXtomoScan):
+            raise TypeError("This only manage NXtomoScan")
         self._scan = scan
         _ImageKeyDialog.setScan(self, scan)
 
@@ -65,8 +65,8 @@ def main(argv):
     parser.add_argument("entry", default=None, help="Entry to treat")
     options = parser.parse_args(argv[1:])
 
-    # image key can only handle HDF5Tomoscan for now
-    scan = HDF5TomoScan(scan=options.scan_path, entry=options.entry)
+    # image key can only handle NXtomoScan for now
+    scan = NXtomoScan(scan=options.scan_path, entry=options.entry)
     increase_max_number_file()
 
     app = qt.QApplication.instance() or qt.QApplication(["tomwer"])

tomwer/app/imagekeyupgrader.py

@@ -9,7 +9,7 @@ import sys
 from silx.gui import qt
 
 from tomwer.core.process.edit.imagekeyeditor import ImageKeyUpgraderTask
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
 from tomwer.gui.edit.imagekeyeditor import (
@@ -40,8 +40,8 @@ class ImageKeyUpgraderDialog(qt.QDialog):
         self._buttons.button(qt.QDialogButtonBox.Cancel).released.connect(self.close)
 
     def setScan(self, scan):
-        if not isinstance(scan, HDF5TomoScan):
-            raise TypeError("This only manage HDF5TomoScan")
+        if not isinstance(scan, NXtomoScan):
+            raise TypeError("This only manage NXtomoScan")
         self._scan = scan
 
     def validate(self):
@@ -74,8 +74,8 @@ def main(argv):
     parser.add_argument("entry", default=None, help="Entry to treat")
     options = parser.parse_args(argv[1:])
 
-    # image key can only handle HDF5Tomoscan for now
-    scan = HDF5TomoScan(scan=options.scan_path, entry=options.entry)
+    # image key can only handle NXtomoScan for now
+    scan = NXtomoScan(scan=options.scan_path, entry=options.entry)
     increase_max_number_file()
 
     app = qt.QApplication.instance() or qt.QApplication(["tomwer"])

tomwer/app/intensitynormalization.py

@@ -10,7 +10,7 @@ import sys
 from silx.gui import qt
 
 from tomwer.core.process.reconstruction.normalization import SinoNormalizationTask
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
 from tomwer.gui import icons
@@ -175,7 +175,7 @@ def main(argv):
                 )
             if options.entry is None:
                 raise ValueError("entry in the master file should be specify")
-            scan = HDF5TomoScan(scan=options.scan_path, entry=options.entry)
+            scan = NXtomoScan(scan=options.scan_path, entry=options.entry)
     else:
         scan = ScanFactory.mock_scan()
     # define the process_index is any tomwer_processes_existing

tomwer/app/radiostack.py

@@ -9,7 +9,7 @@ import sys
 
 from silx.gui import qt
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.utils.resource import increase_max_number_file
 from tomwer.gui import icons
 from tomwer.gui.stacks import RadioStack
@@ -29,7 +29,7 @@ def addFolderAndSubFolder(stack, path):
         _path = os.path.join(path, f)
         if os.path.isdir(_path) is True:
             addFolderAndSubFolder(stack, _path)
-        elif os.path.isfile(_path) and HDF5TomoScan.is_nexus_nxtomo_file(_path):
+        elif os.path.isfile(_path) and NXtomoScan.is_nexus_nxtomo_file(_path):
             stack.addLeafScan(_path)