tomwer 1.3.26__py3-none-any.whl → 1.4.0__py3-none-any.whl

tomwer/gui/{qfolderdialog.py → dialog/QVolumeDialog.py}

@@ -1,32 +1,7 @@
-# /*##########################################################################
-# Copyright (C) 2016-2017 European Synchrotron Radiation Facility
-#
-# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
-# the ESRF by the Software group.
-#
-# 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.
-#
-#############################################################################*/
-
-__author__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "11/07/2022"
+"""contains dialogs to select a Volume (reconstruction of a scan)
+"""
+
+from __future__ import annotations
 
 import logging
 import os
@@ -52,85 +27,11 @@ from tomwer.core.volume import (
 )
 from tomwer.core.volume.volumefactory import VolumeFactory as Factory
 from tomwer.io.utils.tomoobj import DEFAULT_SCHEME_TO_VOL
-
-_logger = logging.getLogger()
+from tomwer.gui.qlefilesystem import QLFileSystem
+from .QDataDialog import QDataDialog
 
 
-class QDataDialog(qt.QFileDialog):
-    """dialog to select a scans (aka data)"""
-
-    def __init__(self, parent, multiSelection=False):
-        qt.QFileDialog.__init__(self, parent)
-        self.setNameFilters(
-            [
-                "HDF5 files (*.h5 *.hdf5 *.nx *.nxs *.nexus)",
-                "Nexus files (*.nx *.nxs *.nexus)",
-                "Any files (*)",
-            ]
-        )
-        self._selected_files = []
-        self.setFileMode(qt.QFileDialog.ExistingFiles)
-
-        # self.QDialogButtonBox
-        self.multiSelection = multiSelection
-        # check if 'TOMWER_DEFAULT_INPUT_DIR' has been set
-        if os.environ.get("TOMWER_DEFAULT_INPUT_DIR", None) and os.path.exists(
-            os.environ["TOMWER_DEFAULT_INPUT_DIR"]
-        ):
-            self.setDirectory(os.environ["TOMWER_DEFAULT_INPUT_DIR"])
-        elif self.directory() != os.getcwd() or str(self.directory()).startswith(
-            "/data"
-        ):
-            # if the directory as already been set by the user. Avoid redefining it
-            pass
-        elif os.path.isdir("/data"):
-            self.setDirectory("/data")
-
-        btns = self.findChildren(qt.QPushButton)
-        if len(btns) == 0:
-            _logger.error(
-                "Cannot retrieve open button. switch to none " "native QFileDialog"
-            )
-            self.setOption(qt.QFileDialog.DontUseNativeDialog)
-            btns = self.findChildren(qt.QPushButton)
-
-        if self.multiSelection is True:
-            # to make it possible to select multiple directories:
-            self.file_view = self.findChild(qt.QListView, "listView")
-            if self.file_view:
-                self.file_view.setSelectionMode(qt.QAbstractItemView.MultiSelection)
-                self.file_view.setSelectionMode(qt.QAbstractItemView.ExtendedSelection)
-
-            self.f_tree_view = self.findChild(qt.QTreeView)
-            if self.f_tree_view:
-                self.f_tree_view.setSelectionMode(qt.QAbstractItemView.MultiSelection)
-                self.f_tree_view.setSelectionMode(
-                    qt.QAbstractItemView.ExtendedSelection
-                )
-
-            if len(btns) > 0:
-                self.openBtn = [x for x in btns if "open" in str(x.text()).lower()][0]
-                self.openBtn.clicked.disconnect()
-                self.openBtn.hide()
-                parent = self.openBtn.parent()
-                self.openBtn = qt.QPushButton("Select", parent=parent)
-                self.openBtn.clicked.connect(self.openClicked)
-                parent.layout().insertWidget(0, self.openBtn)
-
-    def openClicked(self):
-        inds = self.f_tree_view.selectionModel().selectedIndexes()
-        for i in inds:
-            if i.column() == 0:
-                self._selected_files.append(
-                    os.path.join(str(self.directory().absolutePath()), str(i.data()))
-                )
-        self.accept()
-        self.done(1)
-
-    def files_selected(self):
-        for file_ in self.selectedFiles():
-            self._selected_files.append(file_)
-        return self._selected_files
+_logger = logging.getLogger()
 
 
 class QVolumeDialog(qt.QDialog):
@@ -178,7 +79,7 @@ class QVolumeDialog(qt.QDialog):
         self.layout().addWidget(
             qt.QLabel("file or folder path", parent=self), 1, 0, 1, 1
         )
-        self._filePathQL = qt.QLineEdit(parent=self)
+        self._filePathQL = QLFileSystem(text="", parent=self)
         self._filePathQL.setToolTip(
             "File path (for hdf5 and multi-tiff) or folder path (for edf, jp2k, tiff...)"
         )

tomwer/gui/dialog/__init__.py

@@ -0,0 +1 @@
+"""Different dialog used to select TomwerObject (like a scans - aka data or volumes)"""

tomwer/gui/edit/__init__.py

@@ -0,0 +1,2 @@
+"""Widgets related to 'control' tasks (select a scan, convert a scan with nxtomomill...)
+"""

tomwer/gui/edit/dkrfpatch.py

@@ -1,35 +1,6 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016 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__ = "30/10/2020"
-
+from __future__ import annotations
 
 import logging
-from typing import Union
 
 import h5py
 from silx.gui import qt
@@ -101,14 +72,14 @@ class _DarkOrFlatUrl(qt.QWidget):
         self.blockSignals(old)
         self.editingFinished.emit()
 
-    def setSerie(self, serie):
+    def setSeries(self, series):
         type_name = self._type.name.lower().replace("_", " ")
-        item_txt = f"{type_name} serie n°{serie}"
+        item_txt = f"{type_name} series n°{series}"
         idx = self._optionsCB.findText(item_txt)
         if idx >= 0:
             self._optionsCB.setCurrentIndex(idx)
 
-    def getSerieIndex(self):
+    def getSeriesIndex(self):
         return self._optionsCB.currentIndex()
 
     def _redirectDataPath(self, url, logger=None):
@@ -164,23 +135,23 @@ class _DarkOrFlatUrl(qt.QWidget):
         # image_key information
         image_keys = self._getImageKey(url)
         if image_keys is not None:
-            n_serie = nxtomo_utils.get_n_series(
+            n_series = nxtomo_utils.get_n_series(
                 image_key_values=image_keys, image_key_type=self._type
             )
-            if n_serie is not None:
+            if n_series is not None:
                 type_name = self._type.name.lower().replace("_", " ")
-                series_indexes = list(range(n_serie))
-                for i_serie in series_indexes:
-                    self._optionsCB.addItem(f"{type_name} serie n°{i_serie}")
+                series_indexes = list(range(n_series))
+                for i_series in series_indexes:
+                    self._optionsCB.addItem(f"{type_name} series n°{i_series}")
                 # if this is a end url then set to the last found entry
                 if self._when == "end":
                     opt_idx = self._optionsCB.findText(
-                        f"{type_name} serie n°{series_indexes[-1]}"
+                        f"{type_name} series n°{series_indexes[-1]}"
                     )
                 else:
                     # else set it to the first entry
                     opt_idx = self._optionsCB.findText(
-                        f"{type_name} serie n°{series_indexes[0]}"
+                        f"{type_name} series n°{series_indexes[0]}"
                     )
                 if opt_idx >= 0:
                     self._optionsCB.setCurrentIndex(opt_idx)
@@ -196,19 +167,19 @@ class _DarkOrFlatUrl(qt.QWidget):
                     return h5py_read_dataset(grp_parent["image_key"])
         return None
 
-    def _getSlices(self, image_key_values, serie_index):
-        n_serie = -1
+    def _getSlices(self, image_key_values, series_index):
+        n_series = -1
         start = None
-        is_in_a_serie = False
+        is_in_a_series = False
         for i_frame, frame in enumerate(image_key_values):
-            if frame == self._type.value and not is_in_a_serie:
-                n_serie += 1
-                is_in_a_serie = True
-                if n_serie == serie_index:
+            if frame == self._type.value and not is_in_a_series:
+                n_series += 1
+                is_in_a_series = True
+                if n_series == series_index:
                     start = i_frame
-            elif frame != self._type.value and is_in_a_serie:
-                is_in_a_serie = False
-                if n_serie == serie_index:
+            elif frame != self._type.value and is_in_a_series:
+                is_in_a_series = False
+                if n_series == series_index:
                     return slice(start, i_frame)
         if start is not None:
             return slice(start, len(image_key_values))
@@ -217,16 +188,16 @@ class _DarkOrFlatUrl(qt.QWidget):
     def getUrl(self):
         try:
             url_no_slices = DataUrl(path=self._qle.text())
-            serie_index = self._optionsCB.currentText()
-            if serie_index in ("", None):
+            series_index = self._optionsCB.currentText()
+            if series_index in ("", None):
                 return None
-            if serie_index == "full dataset":
+            if series_index == "full dataset":
                 slices = None
             else:
-                serie_index = int(serie_index.split("n°")[1])
+                series_index = int(series_index.split("n°")[1])
                 slices = self._getSlices(
                     image_key_values=self._getImageKey(url_no_slices),
-                    serie_index=serie_index,
+                    series_index=series_index,
                 )
             data_path = url_no_slices.data_path()
             url_slices = slices
@@ -372,11 +343,10 @@ class DarkRefPatchWidget(qt.QWidget):
             outputQLE.blockSignals(old)
             outputQLE.editingFinished.emit()
 
-    def getStartDarkUrl(self) -> Union[None, DataUrl]:
+    def getStartDarkUrl(self) -> DataUrl | None:
         """
 
         :return: url defined by the user for patching the start darks
-        :rtype:  Union[None, DataUrl]
         """
         if self._sdCB.isChecked():
             return self._sdQLE.getUrl()
@@ -384,24 +354,23 @@ class DarkRefPatchWidget(qt.QWidget):
             return None
 
     def getStartDarkIndex(self):
-        return self._sdQLE.getSerieIndex()
+        return self._sdQLE.getSeriesIndex()
 
-    def setStartDarkUrl(self, url, serie_index=None) -> None:
+    def setStartDarkUrl(self, url: DataUrl, series_index: int | None = None) -> None:
         """
 
-        :param DataUrl url:
-        :param Union[int,None] serie_index: index of the serie to set
+        :param url:
+        :param series_index: index of the series to set
         """
         self._sdCB.setChecked(True)
         self._sdQLE.setUrl(url)
-        if serie_index is not None:
-            self._sdQLE.setSerie(serie_index)
+        if series_index is not None:
+            self._sdQLE.setSeries(series_index)
 
-    def getStartFlatUrl(self) -> Union[None, DataUrl]:
+    def getStartFlatUrl(self) -> DataUrl | None:
         """
 
         :return: url defined by the user for patching the start flats
-        :rtype:  Union[None, DataUrl]
         """
         if self._sfCB.isChecked():
             return self._sfQLE.getUrl()
@@ -409,24 +378,23 @@ class DarkRefPatchWidget(qt.QWidget):
             return None
 
     def getStartFlatIndex(self):
-        return self._sfQLE.getSerieIndex()
+        return self._sfQLE.getSeriesIndex()
 
-    def setStartFlatUrl(self, url, serie_index=None) -> None:
+    def setStartFlatUrl(self, url: DataUrl, series_index: int | None = None) -> None:
         """
 
-        :param DataUrl url:
-        :param Union[int,None] serie_index: index of the serie to set
+        :param url:
+        :param series_index: index of the serie to set
         """
         self._sfCB.setChecked(True)
         self._sfQLE.setUrl(url)
-        if serie_index is not None:
-            self._sfQLE.setSerie(serie_index)
+        if series_index is not None:
+            self._sfQLE.setSeries(series_index)
 
-    def getEndDarkUrl(self) -> Union[None, DataUrl]:
+    def getEndDarkUrl(self) -> DataUrl | None:
         """
 
         :return: url defined by the user for patching the end darks
-        :rtype:  Union[None, DataUrl]
         """
         if self._edCB.isChecked():
             return self._edQLE.getUrl()
@@ -434,24 +402,22 @@ class DarkRefPatchWidget(qt.QWidget):
             return None
 
     def getEndDarkIndex(self):
-        return self._edQLE.getSerieIndex()
+        return self._edQLE.getSeriesIndex()
 
-    def setEndDarkUrl(self, url, serie_index=None) -> None:
+    def setEndDarkUrl(self, url: DataUrl, series_index: int | None = None) -> None:
         """
 
-        :param DataUrl url:
-        :param Union[int,None] serie_index: index of the serie to set
+        :param series_index: index of the serie to set
         """
         self._edCB.setChecked(True)
         self._edQLE.setUrl(url)
-        if serie_index is not None:
-            self._edQLE.setSerie(serie_index)
+        if series_index is not None:
+            self._edQLE.setSeries(series_index)
 
-    def getEndFlatUrl(self) -> Union[None, DataUrl]:
+    def getEndFlatUrl(self) -> DataUrl | None:
         """
 
         :return: url defined by the user for patching the end flats
-        :rtype:  Union[None, DataUrl]
         """
         if self._efCB.isChecked():
             return self._efQLE.getUrl()
@@ -459,18 +425,17 @@ class DarkRefPatchWidget(qt.QWidget):
             return None
 
     def getEndFlatIndex(self):
-        return self._efQLE.getSerieIndex()
+        return self._efQLE.getSeriesIndex()
 
-    def setEndFlatUrl(self, url, serie_index=None) -> None:
+    def setEndFlatUrl(self, url: DataUrl, series_index: int | None = None) -> None:
         """
 
-        :param DataUrl url:
-        :param Union[int,None] serie_index: index of the serie to set
+        :param series_index: index of the serie to set
         """
         self._efCB.setChecked(True)
         self._efQLE.setUrl(url)
-        if serie_index is not None:
-            self._efQLE.setSerie(serie_index)
+        if series_index is not None:
+            self._efQLE.setSeries(series_index)
 
     def clear(self):
         for cb in self._sdCB, self._edCB, self._efCB, self._sfCB:

tomwer/gui/edit/imagekeyeditor.py

@@ -1,38 +1,9 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016 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__ = "26/10/2020"
-
+from __future__ import annotations
 
 import functools
 import logging
 import weakref
-from collections.abc import Iterable
-from typing import Union
+from typing import Iterable
 
 from silx.gui import qt
 from nxtomo.nxobject.nxdetector import ImageKey as _ImageKey
@@ -79,21 +50,20 @@ class ImageKeyDialog(qt.QDialog):
     def _resetReleased(self, *args, **kwargs):
         self._widget.reset()
 
-    def getModifications(self):
+    def getModifications(self) -> list[int]:
         """
 
         :return: list of indexes to be modified
-        :rtype: list
         """
         return self._widget.getModifications()
 
     def setModifications(self, modifications):
         self._widget.setModifications(modifications)
 
-    def setScan(self, scan):
+    def setScan(self, scan: NXtomoScan):
         """
 
-        :param NXtomoScan scan: scan to be edited
+        :param scan: scan to be edited
         """
         self._widget.setScan(scan)
 
@@ -117,10 +87,10 @@ class ImageKeyWindow(qt.QMainWindow):
         # signal / slot connection
         self._editorControl.sigApply.connect(self._updateModifications)
 
-    def setScan(self, scan) -> None:
+    def setScan(self, scan: NXtomoScan) -> None:
         """
 
-        :param NXtomoScan scan: scan to be edited
+        :param scan: scan to be edited
         """
         self._mainWindow.setScan(scan=scan)
         self._editorControl.setScan(scan=scan)
@@ -132,11 +102,10 @@ class ImageKeyWindow(qt.QMainWindow):
             modifications=modifications, new_image_key=to_
         )
 
-    def getModifications(self):
+    def getModifications(self) -> list[int]:
         """
 
         :return: list of indexes to be modified
-        :rtype: list
         """
         return self._mainWindow.getModifications()
 
@@ -219,7 +188,6 @@ class _ImageKeyEditor(qt.QDialog):
         """
 
         :return: selected image key as literal
-        :rtype: str
         """
         return self._upgradeToCB.currentText()
 
@@ -230,11 +198,10 @@ class _ImageKeyEditor(qt.QDialog):
         """
         return self._selectionModeCB.currentText()
 
-    def getModifications(self) -> list:
+    def getModifications(self) -> list[int]:
         """
 
         :return: list of indexes to be modified
-        :rtype: list
         """
         if self.getSelectionMode() == "range":
             return self._selectionWidget.getSlice()
@@ -286,7 +253,6 @@ class _SliceSelection(qt.QWidget):
         """
 
         :return: slice defined
-        :rtype: slice
         """
         return slice(self._fromQLE.value(), self._toQLE.value(), self._stepsQLE.value())
 
@@ -330,11 +296,10 @@ class _ListSelection(qt.QWidget):
             frame_indexes = dialog.getSelectedFrameIndexes()
             return self.setList(frame_indexes)
 
-    def getList(self) -> list:
+    def getList(self) -> list[int]:
         """
 
         :return: list of indexes selected
-        :rtype: list
         """
         text = self._listQLE.text()
         text = text.replace(" ", "")
@@ -343,11 +308,10 @@ class _ListSelection(qt.QWidget):
         else:
             return [int(element) for element in text.split(",")]
 
-    def setList(self, list_: Union[str, Iterable]):
+    def setList(self, list_: str | Iterable[str]):
         """
 
-        :param Union[str,Iterable] list_:
-        :return:
+        :param list_:
         """
         if isinstance(list_, str):
             txt = list_
@@ -374,7 +338,7 @@ class _EditionSelection(qt.QWidget):
     def setSelectionMode(self, mode: str) -> None:
         """
 
-        :param str mode: define indexes selection mode. Can be 'range' or
+        :param mode: define indexes selection mode. Can be 'range' or
                          'list'
         """
         if mode == "slice":
@@ -434,7 +398,7 @@ class _ImageKeyList(qt.QTableWidget):
         """
         Define the filter mode to use and update the QTableWidget
 
-        :param str mode: filtering mode
+        :param mode: filtering mode
         """
         self._filterMode = mode
         self.updateFiltering()
@@ -447,8 +411,8 @@ class _ImageKeyList(qt.QTableWidget):
         """
         Update the QTableWidget for the provided frames
 
-        :param Iterable frames: Iterable of tomoscan.esrf.scan.NXtomoScan.Frame
-        :param dict frames_new_keys: dictionary with frame edited. key is frame
+        :param frames: Iterable of tomoscan.esrf.scan.NXtomoScan.Frame
+        :param frames_new_keys: dictionary with frame edited. key is frame
                                      index. Value is the new `image_key` value
         """
         self.clear()
@@ -553,7 +517,7 @@ class _ImageKeyList(qt.QTableWidget):
         """
         Update list of modification and emit sigKeyUpdated
 
-        :param int frame_index:
+        :param frame_index:
         """
         assert isinstance(frame_index, int), "frame index should be an int"
         frame_row = self._getFrameRowIndex(frame_index)
@@ -608,7 +572,7 @@ class _ImageKeyListFiltered(qt.QWidget):
         # connect signal / slot
         self._filterCB.currentIndexChanged.connect(self._updateFilter)
 
-    def applyModifications(self, modifications: Union[slice, list], new_image_key):
+    def applyModifications(self, modifications: slice | list, new_image_key):
         if new_image_key in IMAGE_KEYS:
             new_image_key = IMAGE_KEYS[new_image_key]
         self._imageKeyList.applyModifications(modifications, new_image_key)