tomwer 1.1.0rc6__tar.gz → 1.1.1__tar.gz

{tomwer-1.1.0rc6/tomwer.egg-info → tomwer-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.1.0rc6
+Version: 1.1.1
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

{tomwer-1.1.0rc6 → tomwer-1.1.1}/orangecontrib/tomwer/widgets/cluster/__init__.py

@@ -22,7 +22,7 @@
 #
 #############################################################################
 
-NAME = "cluster"
+NAME = "compute cluster"
 
 ID = "orangecontrib.tomwer.widgets.cluster"
 

{tomwer-1.1.0rc6 → tomwer-1.1.1}/orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py

@@ -115,7 +115,6 @@ class EDF2NXOW(
         self._loadSettings()
 
     def _updateSettings(self):
-        super()._updateSettings()
         self._ewoks_default_inputs[  # pylint: disable=E1137
             "convert_auto_edfscan_channel"
         ] = self.convertAutoEDFScanReceivedFromChannel()

{tomwer-1.1.0rc6 → tomwer-1.1.1}/orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py

@@ -190,7 +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
         )
@@ -453,9 +454,9 @@ class SAAxisOW(SuperviseOW, WidgetLongProcessing):
             "data": None,
             "sa_axis_params": self._widget.getConfiguration(),
         }
-        self._ewoks_default_inputs["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():

{tomwer-1.1.0rc6 → tomwer-1.1.1}/orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py

@@ -125,7 +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

{tomwer-1.1.0rc6 → tomwer-1.1.1}/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)

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/app/canvas_launcher/mainwindow.py

@@ -16,6 +16,7 @@ from orangecanvas.application.outputview import (
     ExceptHook,
     TerminalTextDocument,
 )
+from xml.sax.saxutils import escape
 import logging
 import os
 import shutil
@@ -26,6 +27,19 @@ from .config import TomwerConfig, TomwerSplashScreen
 import tomwer.version
 from urllib.request import urlopen
 
+try:
+    import nabu
+except ImportError:
+    has_nabu = False
+else:
+    has_nabu = True
+try:
+    import nxtomomill.version
+except ImportError:
+    has_nxtomomill = False
+else:
+    has_nxtomomill = True
+
 _logger = logging.getLogger(__file__)
 
 MAX_LOG_FILE = 10
@@ -68,6 +82,13 @@ class MainWindow(_MainWindow):
         super().setup_menu()
         self.view_menu.addAction(self.show_processes_manager_action)
 
+    def open_about(self):
+        # type: () -> None
+        """Open the about dialog."""
+        dlg = AboutDialog(self)
+        dlg.setAttribute(qt.Qt.WA_DeleteOnClose)
+        dlg.exec()
+
 
 log = logging.getLogger(__name__)
 
@@ -175,6 +196,47 @@ def widget_settings_dir():
     return os.path.join(data_dir(), "widgets")
 
 
+ABOUT_TEMPLATE = """\
+<center>
+<h4>{name}</h4>
+<p>tomwer version: {tomwer_version}</p>
+<p>nabu version: {nabu_version}</p>
+<p>nxtomomill version: {nxtomomill_version}</p>
+</center>
+"""
+
+
+class AboutDialog(qt.QDialog):
+    def __init__(self, parent=None, **kwargs) -> None:
+        super().__init__(parent, **kwargs)
+        layout = qt.QVBoxLayout()
+        label = qt.QLabel(self)
+
+        pixmap, _ = TomwerConfig.splash_screen()
+        pixmap = pixmap.scaled(150, 150)
+
+        label.setPixmap(pixmap)
+
+        layout.addWidget(label, qt.Qt.AlignCenter)
+
+        text = ABOUT_TEMPLATE.format(
+            name=escape("tomwer"),
+            tomwer_version=escape(tomwer.version.version),
+            nabu_version=escape(nabu.version if has_nabu else "not installed"),
+            nxtomomill_version=escape(
+                nxtomomill.version.version if has_nxtomomill else "not installed"
+            ),
+        )
+        text_label = qt.QLabel(text)
+        layout.addWidget(text_label, qt.Qt.AlignCenter)
+
+        buttons = qt.QDialogButtonBox(qt.QDialogButtonBox.Close, qt.Qt.Horizontal, self)
+        layout.addWidget(buttons)
+        buttons.rejected.connect(self.accept)
+        layout.setSizeConstraint(qt.QVBoxLayout.SetFixedSize)
+        self.setLayout(layout)
+
+
 class OMain(_OMain):
     config: TomwerConfig
     DefaultConfig = "tomwer.app.canvas_launcher.config.TomwerConfig"

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/process/reconstruction/nabu/nabucommon.py

@@ -453,13 +453,18 @@ class _NabuBaseReconstructor:
         """
         # handle phase
         pag = False
+        ctf = False
         db = None
         if "phase" in config:
-            if (
+            pag = (
                 "method" in config["phase"]
                 and config["phase"]["method"] == _NabuPhaseMethod.PAGANIN.value
-            ):
-                pag = True
+            )
+            ctf = (
+                "method" in config["phase"]
+                and config["phase"]["method"] == _NabuPhaseMethod.CTF.value
+            )
+            if pag or ctf:
                 if "delta_beta" in config["phase"]:
                     if not numpy.isscalar(config["phase"]["delta_beta"]):
                         if len(config["phase"]["delta_beta"]) > 1:
@@ -473,7 +478,7 @@ class _NabuBaseReconstructor:
                     db = round(float(config["phase"]["delta_beta"]))
         # handle output
         if "output" in config:
-            _file_name = self._get_file_basename_reconstruction(pag=pag, db=db)
+            _file_name = self._get_file_basename_reconstruction(pag=pag, db=db, ctf=ctf)
             config["output"]["file_prefix"] = _file_name
             location = config["output"].get("location", None)
             if location not in ("", None):
@@ -565,7 +570,7 @@ class _NabuBaseReconstructor:
 
         return config
 
-    def _get_file_basename_reconstruction(self, pag, db):
+    def _get_file_basename_reconstruction(self, pag, db, ctf):
         """return created file base name"""
         raise NotImplementedError("Base class")
 

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/process/reconstruction/nabu/nabuscores.py

@@ -235,18 +235,24 @@ class _Reconstructor(_NabuBaseReconstructor):
         - create the output directory if does not exist
         """
         pag = False
+        ctf = False
         db = None
         if "phase" in _config:
-            if "method" in _config["phase"] and _config["phase"]["method"] not in (
-                "",
-                utils._NabuPhaseMethod.NONE.value,
-            ):
+            phase_method = _config["phase"].get("method", "").lower()
+            if phase_method in ("pag", "paganin"):
                 pag = True
-                if "delta_beta" in _config["phase"]:
-                    db = round(float(_config["phase"]["delta_beta"]))
+            elif phase_method in ("ctf",):
+                ctf = True
+
+            if "delta_beta" in _config["phase"]:
+                db = round(float(_config["phase"]["delta_beta"]))
         if "output" in _config:
             _file_name = SingleSliceRunner.get_file_basename_reconstruction(
-                scan=self.scan, slice_index=self.slice_index, pag=pag, db=db
+                scan=self.scan,
+                slice_index=self.slice_index,
+                pag=pag,
+                db=db,
+                ctf=ctf,
             )
             _config["output"]["file_prefix"] = "cor_{}_{}".format(_file_name, cor)
             if _config["output"]["location"] not in ("", None):

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/process/reconstruction/nabu/nabuslices.py

@@ -643,7 +643,9 @@ class SingleSliceRunner(_NabuBaseReconstructor):
             return super()._get_futures_slurm_callback(config_to_dump)
 
     @staticmethod
-    def get_file_basename_reconstruction(scan, pag, db, slice_index: Union[str, int]):
+    def get_file_basename_reconstruction(
+        scan, pag, ctf, db, slice_index: Union[str, int]
+    ):
         if pag:
             assert db is not None, "if paganin defined, db should not be None"
         if slice_index == "middle":
@@ -657,6 +659,8 @@ class SingleSliceRunner(_NabuBaseReconstructor):
         if slice_index is None:
             if pag:
                 return "_".join((basename + "pag", "db" + str(db).zfill(4)))
+            elif ctf:
+                return "_".join((basename + "ctf", "db" + str(db).zfill(4)))
             else:
                 return basename
         else:
@@ -668,11 +672,19 @@ class SingleSliceRunner(_NabuBaseReconstructor):
                         "db" + str(db).zfill(4),
                     )
                 )
+            elif ctf:
+                return "_".join(
+                    (
+                        basename + "slice_ctf",
+                        str(slice_index).zfill(4),
+                        "db" + str(db).zfill(4),
+                    )
+                )
             else:
                 return "_".join((basename + "slice", str(slice_index).zfill(4)))
 
     @docstring(_NabuBaseReconstructor)
-    def _get_file_basename_reconstruction(self, pag, db):
+    def _get_file_basename_reconstruction(self, pag, db, ctf):
         """
 
         :param TomwerScanBase scan: scan reconstructed
@@ -684,7 +696,7 @@ class SingleSliceRunner(_NabuBaseReconstructor):
         :return: basename of the file reconstructed (without any extension)
         """
         return self.get_file_basename_reconstruction(
-            scan=self.scan, db=db, pag=pag, slice_index=self.slice_index
+            scan=self.scan, db=db, pag=pag, slice_index=self.slice_index, ctf=ctf
         )
 
 

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/process/reconstruction/nabu/nabuvolume.py

@@ -340,7 +340,7 @@ class VolumeRunner(_NabuBaseReconstructor):
         return config_s, extra_opts
 
     @docstring(_NabuBaseReconstructor)
-    def _get_file_basename_reconstruction(self, pag, db):
+    def _get_file_basename_reconstruction(self, pag, db, ctf):
         """
 
         :param TomwerScanBase scan: scan reconstructed
@@ -352,6 +352,7 @@ class VolumeRunner(_NabuBaseReconstructor):
         :return: basename of the file reconstructed (without any extension)
         """
         assert type(db) in (int, type(None))
+        assert not pag == ctf == True, "cannot ask for both pag and ctf active"
         if isinstance(self.scan, HDF5TomoScan):
             basename, _ = os.path.splitext(self.scan.master_file)
             basename = os.path.basename(basename)
@@ -359,6 +360,8 @@ class VolumeRunner(_NabuBaseReconstructor):
             basename = os.path.basename(self.scan.path)
         if pag:
             return "_".join((basename + "pag", "db" + str(db).zfill(4), "vol"))
+        elif ctf:
+            return "_".join((basename + "ctf", "db" + str(db).zfill(4), "vol"))
         else:
             return "_".join((basename, "vol"))
 

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/process/reconstruction/nabu/utils.py

@@ -413,6 +413,7 @@ def nabu_std_err_has_error(errs: typing.Optional[bytes]):
         return (
             "warning" in line
             or "Warning" in line
+            or "deprecated" in line
             or line.replace(" ", "") == ""
             or "unable to load" in line
         )

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/process/reconstruction/saaxis/saaxis.py

@@ -149,12 +149,16 @@ def one_slice_several_cor(
         output_dir = os.path.join(scan.path, DEFAULT_RECONS_FOLDER)
 
     db = None
-    pag = None
+    pag = False
+    ctf = False
     if "phase" in nabu_config:
-        if "method" in nabu_config["phase"] and nabu_config["phase"]["method"] != "":
-            if "delta_beta" in nabu_config["phase"]:
-                pag = True
-                db = round(float(nabu_config["phase"]["delta_beta"]))
+        phase_method = nabu_config["phase"].get("method", "").lower()
+        if phase_method in ("pag", "paganin"):
+            pag = True
+        elif phase_method in ("ctf",):
+            ctf = True
+        if "delta_beta" in nabu_config["phase"]:
+            db = round(float(nabu_config["phase"]["delta_beta"]))
 
     for cor, future_tomo_obj in future_tomo_objs.items():
         future_tomo_obj.results()
@@ -163,7 +167,11 @@ def one_slice_several_cor(
             continue
         else:
             _file_name = SingleSliceRunner.get_file_basename_reconstruction(
-                scan=scan, slice_index=slice_index, pag=pag, db=db
+                scan=scan,
+                slice_index=slice_index,
+                pag=pag,
+                db=db,
+                ctf=ctf,
             )
             file_prefix = "cor_{}_{}".format(_file_name, cor)
 

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py

@@ -192,9 +192,13 @@ def one_slice_several_db(
             advancement.increaseAdvancement(1)
 
     pag = False
+    ctf = False
     if "phase" in config:
-        if "method" in config["phase"] and config["phase"]["method"] != "":
+        phase_method = config["phase"].get("method", "").lower()
+        if phase_method in ("pag", "paganin"):
             pag = True
+        elif phase_method in ("ctf",):
+            ctf = True
 
     # treat future.
     for db, future_tomo_obj_list in future_tomo_objs.items():
@@ -210,6 +214,7 @@ def one_slice_several_db(
             slice_index=slice_index,
             pag=pag,
             db=int(db) if db is not None else None,
+            ctf=ctf,
         )
         # retrieve url
         volume_identifier = nabu_utils.get_recons_volume_identifier(

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/scan/edfscan.py

@@ -256,6 +256,10 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
                                 indexStr = local_str.split("slice_pag_")[-1].split("_")[
                                     0
                                 ]
+                            elif "slice_ctf_" in local_str:
+                                indexStr = local_str.split("slice_ctf_")[-1].split("_")[
+                                    0
+                                ]
                             else:
                                 indexStr = local_str.split("slice_")[-1].split("_")[0]
                             if containsDigits(indexStr):

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/scan/test/test_scan.py

@@ -90,38 +90,40 @@ class TestScanValidatorFindNabuFiles(unittest.TestCase):
 
     def test(self) -> None:
         for slice_index in (None, 1, 15):
-            for pag_db in (None, 100, 500):
-                file_name = (
-                    nabuslices.SingleSliceRunner.get_file_basename_reconstruction(
-                        slice_index=slice_index,
-                        scan=self.scan,
-                        pag=pag_db is not None,
-                        db=pag_db,
-                    )
-                )
-                for file_extension in ("npy", "npz", "hdf5"):
-                    with self.subTest(
-                        slice_index=slice_index,
-                        pag_db=pag_db,
-                        file_extension=file_extension,
-                    ):
-                        file_path = os.path.join(
-                            self.scan.path, file_name + "." + file_extension
+            for delta_beta in (None, 100, 500):
+                for pag in (True, False):
+                    for ctf in (True, False):
+                        file_name = nabuslices.SingleSliceRunner.get_file_basename_reconstruction(
+                            slice_index=slice_index,
+                            scan=self.scan,
+                            pag=pag if delta_beta is not None else False,
+                            ctf=ctf if delta_beta is not None else False,
+                            db=delta_beta,
                         )
-
-                        # simple context Manager which create the file
-                        # and remove it when leave
-                        with TestScanValidatorFindNabuFiles.FileCreator(file_path):
-                            n_to_discover = 1
-                            if slice_index is None:
-                                n_to_discover = 0
-                            self.assertEqual(
-                                len(
-                                    self.scan.get_reconstructions_paths(self.scan.path)
-                                ),
-                                n_to_discover,
+                        print("file_name is", file_name)
+                        with self.subTest(
+                            slice_index=slice_index,
+                            pag_db=delta_beta,
+                        ):
+                            file_path = os.path.join(
+                                self.scan.path, file_name + ".hdf5"
                             )
 
+                            # simple context Manager which create the file
+                            # and remove it when leave
+                            with TestScanValidatorFindNabuFiles.FileCreator(file_path):
+                                n_to_discover = 1
+                                if slice_index is None:
+                                    n_to_discover = 0
+                                self.assertEqual(
+                                    len(
+                                        self.scan.get_reconstructions_paths(
+                                            self.scan.path
+                                        )
+                                    ),
+                                    n_to_discover,
+                                )
+
 
 class TestScanValidatorFindPyHSTFiles(unittest.TestCase):
     """Function testing the getReconstructionsPaths function is correctly

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/core/utils/char.py

@@ -39,3 +39,5 @@ DELTA_CHAR = (b"\xce\xb4").decode("utf-8")
 PSI_CHAR = (b"\xcf\x88").decode("utf-8")
 
 THETA_CHAR = (b"\xce\xb8").decode("utf-8")
+
+MU_CHAR = (b"\xce\xbc").decode("utf-8")

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/gui/edit/imagekeyeditor.py

@@ -171,7 +171,7 @@ class _ImageKeyEditor(qt.QDialog):
         # mode selection
         self.layout().addWidget(qt.QLabel("selection mode"), 1, 0, 1, 1)
         self._selectionModeCB = qt.QComboBox(self)
-        for mode in ("slice", "list"):
+        for mode in ("range", "list"):
             self._selectionModeCB.addItem(mode)
         self._selectionModeCB.setCurrentIndex(self._selectionModeCB.findText("list"))
         self.layout().addWidget(self._selectionModeCB, 1, 1, 1, 1)
@@ -224,7 +224,7 @@ class _ImageKeyEditor(qt.QDialog):
     def getSelectionMode(self) -> str:
         """
 
-        :return: frame indexes selection mode. Can be 'slice' or 'list'
+        :return: frame indexes selection mode. Can be 'range' or 'list'
         """
         return self._selectionModeCB.currentText()
 
@@ -234,7 +234,7 @@ class _ImageKeyEditor(qt.QDialog):
         :return: list of indexes to be modified
         :rtype: list
         """
-        if self.getSelectionMode() == "slice":
+        if self.getSelectionMode() == "range":
             return self._selectionWidget.getSlice()
         elif self.getSelectionMode() == "list":
             return self._selectionWidget.getList()
@@ -321,7 +321,7 @@ class _ListSelection(qt.QWidget):
     def _selectFrames(self):
         if self._scan is None or self._scan() is None:
             _logger.warning(
-                "No scan set or has been moved. Unable to select " "slices from it."
+                "No scan set or has been moved. Unable to select slices from it."
             )
             return
         scan = self._scan()
@@ -375,11 +375,14 @@ class _EditionSelection(qt.QWidget):
     def setSelectionMode(self, mode: str) -> None:
         """
 
-        :param str mode: define indexes selection mode. Can be 'slice' or
+        :param str mode: define indexes selection mode. Can be 'range' or
                          'list'
         """
-        assert mode in ("slice", "list")
-        self._sliceSelection.setVisible(mode == "slice")
+        if mode == "slice":
+            # for backward compatibility (user can have .ows with old name)
+            mode = "range"
+        assert mode in ("range", "list")
+        self._sliceSelection.setVisible(mode == "range")
         self._listSelection.setVisible(mode == "list")
 
     def getList(self) -> list:

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/gui/edit/nxtomoeditor.py

@@ -225,8 +225,10 @@ class NXtomoEditor(qt.QWidget):
             self._fieldOfViewCB.setCurrentIndex(idx)
 
     def _updateFlipped(self, scan):
-        self._xFlippedCB.setChecked(scan.x_flipped)
-        self._yFlippedCB.setChecked(scan.y_flipped)
+        if scan.x_flipped is not None:
+            self._xFlippedCB.setChecked(scan.x_flipped)
+        if scan.y_flipped is not None:
+            self._yFlippedCB.setChecked(scan.y_flipped)
 
     def _updateDistance(self, scan):
         self._distanceMetricEntry.setValue(scan.distance)

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/gui/reconstruction/nabu/castvolume.py

@@ -66,30 +66,17 @@ class CastVolumeWidget(qt.QWidget):
         self.layout().addWidget(self._outputFileformatLabel, 1, 0, 1, 1)
         self._outputFileformatCB = QNabuFileFormatComboBox(self)
         self.layout().addWidget(self._outputFileformatCB, 1, 1, 1, 3)
-        # rescale percentiles
-        self._percentilesLabel = qt.QLabel("rescale percentiles")
-        self.layout().addWidget(self._percentilesLabel, 2, 0, 1, 1)
-        self._lowPercentileQSB = qt.QSpinBox(self)
-        self._lowPercentileQSB.setRange(0, 100)
-        self._lowPercentileQSB.setPrefix("min:")
-        self._lowPercentileQSB.setSuffix("%")
-        self._lowPercentileQSB.setValue(RESCALE_MIN_PERCENTILE)
-        self.layout().addWidget(self._lowPercentileQSB, 2, 1, 1, 1)
-        self._highPercentileQSB = qt.QSpinBox(self)
-        self._highPercentileQSB.setRange(0, 100)
-        self._highPercentileQSB.setPrefix("max:")
-        self._highPercentileQSB.setSuffix("%")
-        self._highPercentileQSB.setValue(RESCALE_MAX_PERCENTILE)
-        self.layout().addWidget(self._highPercentileQSB, 2, 2, 1, 1)
+
         # let the user provide min and max manually
         self._minMaxLabel = qt.QLabel("min max values")
-        self.layout().addWidget(self._minMaxLabel, 3, 0, 1, 1)
-        self._minMaxAuto = qt.QCheckBox("auto")
+        self.layout().addWidget(self._minMaxLabel, 2, 0, 1, 1)
+        self._minMaxAuto = qt.QCheckBox("auto with rescale from percentiles")
         self._minMaxAuto.setChecked(True)
         self._minMaxAuto.setToolTip(
             "If set to auto will try to get min/max pixel values from nabu histogram else will compute it. Otherwise will values provided by the user"
         )
-        self.layout().addWidget(self._minMaxAuto, 3, 1, 1, 1)
+        self.layout().addWidget(self._minMaxAuto, 2, 1, 1, 1)
+
         self._minPixValue = qt.QLineEdit("", self)
         self._minPixValue.setPlaceholderText("min")
         self._maxPixValue = qt.QLineEdit("", self)
@@ -98,14 +85,28 @@ class CastVolumeWidget(qt.QWidget):
         validator.setNotation(qt.QDoubleValidator.ScientificNotation)
         self._minPixValue.setValidator(validator)
         self._maxPixValue.setValidator(validator)
-        self.layout().addWidget(self._minPixValue, 3, 2, 1, 1)
-        self.layout().addWidget(self._maxPixValue, 3, 3, 1, 1)
+        self.layout().addWidget(self._minPixValue, 4, 2, 1, 1)
+        self.layout().addWidget(self._maxPixValue, 4, 3, 1, 1)
         self._minPixValue.setVisible(False)
         self._maxPixValue.setVisible(False)
-
+        # or from percentiles
+        self._percentilesLabel = qt.QLabel("rescale percentiles")
+        self.layout().addWidget(self._percentilesLabel, 3, 1, 1, 1)
+        self._lowPercentileQSB = qt.QSpinBox(self)
+        self._lowPercentileQSB.setRange(0, 100)
+        self._lowPercentileQSB.setPrefix("min:")
+        self._lowPercentileQSB.setSuffix("%")
+        self._lowPercentileQSB.setValue(RESCALE_MIN_PERCENTILE)
+        self.layout().addWidget(self._lowPercentileQSB, 3, 2, 1, 1)
+        self._highPercentileQSB = qt.QSpinBox(self)
+        self._highPercentileQSB.setRange(0, 100)
+        self._highPercentileQSB.setPrefix("max:")
+        self._highPercentileQSB.setSuffix("%")
+        self._highPercentileQSB.setValue(RESCALE_MAX_PERCENTILE)
+        self.layout().addWidget(self._highPercentileQSB, 3, 3, 1, 1)
         # save dir
         self._saveDirLabel = qt.QLabel("output directory", self)
-        self.layout().addWidget(self._saveDirLabel, 4, 0, 1, 1)
+        self.layout().addWidget(self._saveDirLabel, 5, 0, 1, 1)
         self._useDefaultSaveDirQCB = qt.QCheckBox("default", self)
         self._useDefaultSaveDirQCB.setToolTip(
             f"Default directory is: {DEFAULT_OUTPUT_DIR}"
@@ -114,7 +115,7 @@ class CastVolumeWidget(qt.QWidget):
             qt.QSizePolicy.Minimum, qt.QSizePolicy.Minimum
         )
         self._useDefaultSaveDirQCB.setChecked(True)
-        self.layout().addWidget(self._useDefaultSaveDirQCB, 4, 1, 1, 1)
+        self.layout().addWidget(self._useDefaultSaveDirQCB, 5, 1, 1, 1)
         self._saveDirQLE = QLFileSystem(text=DEFAULT_OUTPUT_DIR, parent=self)
         # force text because this is not a valid path
         self._saveDirQLE.setText(DEFAULT_OUTPUT_DIR)
@@ -125,11 +126,11 @@ class CastVolumeWidget(qt.QWidget):
             """
         )
         self._saveDirQLE.setVisible(False)
-        self.layout().addWidget(self._saveDirQLE, 4, 2, 1, 2)
+        self.layout().addWidget(self._saveDirQLE, 5, 2, 1, 2)
         # overwrite
         self._overwriteCB = qt.QCheckBox("overwrite", self)
         self._overwriteCB.setChecked(True)
-        self.layout().addWidget(self._overwriteCB, 5, 0, 1, 1)
+        self.layout().addWidget(self._overwriteCB, 6, 0, 1, 1)
         # spacer
         self._spacer = qt.QWidget(self)
         self._spacer.setSizePolicy(
@@ -275,3 +276,6 @@ class CastVolumeWidget(qt.QWidget):
     def _updatePixMinMaxVis(self, *args, **kwargs):
         self._minPixValue.setVisible(not self._minMaxAuto.isChecked())
         self._maxPixValue.setVisible(not self._minMaxAuto.isChecked())
+        self._percentilesLabel.setVisible(self._minMaxAuto.isChecked())
+        self._lowPercentileQSB.setVisible(self._minMaxAuto.isChecked())
+        self._highPercentileQSB.setVisible(self._minMaxAuto.isChecked())

{tomwer-1.1.0rc6 → tomwer-1.1.1}/tomwer/gui/reconstruction/nabu/nabuconfig/phase.py

@@ -147,7 +147,7 @@ class _NabuPhaseConfig(qt.QWidget, base._NabuStageConfigBase):
     @docstring(base._NabuStageConfigBase)
     def getConfiguration(self) -> dict:
         configuration = {"method": self.getMethod().value}
-        if self.getMethod() is _NabuPhaseMethod.PAGANIN:
+        if self.getMethod() in (_NabuPhaseMethod.PAGANIN, _NabuPhaseMethod.CTF):
             configuration.update(self._paganinOpts.getConfiguration())
         configuration.update(self._unsharpOpts.getConfiguration())
         configuration.update(self._ctfOpts.getConfiguration())