tomwer 1.2.1__py3-none-any.whl → 1.3.12__py3-none-any.whl

tomwer/gui/reconstruction/lamino/tofu/tofuexpert.py

@@ -1,567 +0,0 @@
-# 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__ = "01/06/2018"
-
-
-import logging
-import subprocess
-
-from silx.gui import qt
-
-import tomwer.core.utils.gpu
-from tomwer.core.process.reconstruction.lamino.tofu import has_tofu
-
-from .TofuOptionLoader import _getterSetter, _TofuOptionLoader
-
-_logger = logging.getLogger(__name__)
-
-
-class ExpertTofuWidget(_TofuOptionLoader, qt.QWidget):
-    """
-    Widget used to define the parameters for the tofu script
-    """
-
-    def __init__(self, parent):
-        qt.QWidget.__init__(self, parent=parent)
-        self.setLayout(qt.QVBoxLayout())
-
-        self._verbose = qt.QCheckBox("verbose", parent=self)
-        self._verbose.setChecked(True)
-        self.layout().addWidget(self._verbose)
-
-        # retries group
-        self._retriesGB = qt.QGroupBox("retries parameters", parent=self)
-        self._retriesGB.setLayout(qt.QGridLayout())
-        self._retriesGB.layout().addWidget(
-            qt.QLabel("n retries:", parent=self._retriesGB), 0, 0
-        )
-        self._retriesSP = qt.QSpinBox(parent=self._retriesGB)
-        self._retriesSP.setMinimum(0)
-        self._retriesGB.layout().addWidget(self._retriesSP, 0, 1)
-        self._retriesGB.layout().addWidget(
-            qt.QLabel("timeout:", parent=self._retriesGB), 1, 0
-        )
-        self._timeoutLE = qt.QLineEdit("0", parent=self._retriesGB)
-        validator = qt.QDoubleValidator(parent=self._timeoutLE)
-        validator.setBottom(0.0)
-        self._timeoutLE.setValidator(validator)
-        self._retriesGB.layout().addWidget(self._timeoutLE, 1, 1)
-        self.layout().addWidget(self._retriesGB)
-
-        # GPU group
-        self._gpuGrp = GpuGroupBox(parent=self)
-        self.layout().addWidget(self._gpuGrp)
-
-        # options text edit
-        self._qteOptions = OptionEdit(parent=self)
-        self.layout().addWidget(self._qteOptions)
-
-        # expose API
-        self.getAdditionalRecoOptions = self._qteOptions.getAdditionalRecoOptions
-        self.addAdditionalRecoOption = self._qteOptions.addAdditionalRecoOption
-        self.setAdditionalRecoOptions = self._qteOptions.setAdditionalRecoOptions
-        self.getAdditionalPreprocessOptions = (
-            self._qteOptions.getAdditionalPreprocessOptions
-        )
-        self.addAdditionalPreprocessOption = (
-            self._qteOptions.addAdditionalPreprocessOption
-        )
-        self.setAdditionalPreprocessOptions = (
-            self._qteOptions.setAdditionalPreprocessOptions
-        )
-        self.getHighLimit = self._gpuGrp.getHighLimit
-
-        options = {
-            "verbose": _getterSetter(
-                getter=self.requireVerbose, setter=self.setVerbose
-            ),
-            "retries": _getterSetter(getter=self.getNRetries, setter=self.setNRetries),
-            "retry-timeout": _getterSetter(
-                getter=self.getNRetries, setter=self.setRetriesTimeout
-            ),
-            "slices-per-device": _getterSetter(
-                getter=self.getSlicePerDevice, setter=self.setSlicePerDevice
-            ),
-            "slice-memory-coeff": _getterSetter(
-                getter=self.getSliceMemoryCoeff, setter=self.setSliceMemoryCoeff
-            ),
-        }
-        _TofuOptionLoader.__init__(self, options=options)
-
-    def getNRetries(self):
-        """
-
-        :return: return number of retry before avoiding the reconstruction
-        """
-        return self._retriesSP.value()
-
-    def setNRetries(self, value):
-        """ """
-        try:
-            self._retriesSP.setValue(int(value))
-        except Exception as error:
-            _logger.warning(f"Fails to set N tries, error is {error}")
-
-    def getRetriesTimeout(self):
-        """
-
-        :return: return time (in second) of the time out for the tofu
-                 reconstruction
-        """
-        return float(self._timeoutLE.text())
-
-    def setRetriesTimeout(self, value):
-        """ """
-        if value is None:
-            return
-        try:
-            self._timeoutLE.setText(str(value))
-        except Exception as error:
-            _logger.warning(f"Fails to set N tries, error is {error}")
-
-    def getSliceMemoryCoeff(self):
-        """
-
-        :return: None if want default, otherwise value between 0.01 and 0.9
-        """
-        return self._gpuGrp.getSliceMemoryCoeff()
-
-    def getSlicePerDevice(self):
-        """
-
-        :return: None if we don't want to activate this option. Otherwise int
-                 from 1 to inf
-        """
-        return self._gpuGrp.getSlicePerDevice()
-
-    def setSlicePerDevice(self, nslice):
-        if nslice is not None:
-            self._gpuGrp.setSlicePerDevice(nslice)
-
-    def setSliceMemoryCoeff(self, value):
-        if value is not None:
-            self._gpuGrp.setSliceMemoryCoeff(value)
-
-    def requireVerbose(self):
-        """
-
-        :return: True if the user require verbose for reconstruction
-        """
-        return self._verbose.isChecked()
-
-    def setVerbose(self, value=True):
-        _value = value
-        if _value == "":
-            _value = True
-        self._verbose.setChecked(_value)
-
-    def loadFromScan(self, scanID):
-        # nothing to be done here
-        pass
-
-    def resetAdditionalRecoOptions(self):
-        self._qteOptions.resetAdditionalRecoOptions()
-
-    def resetAdditionalPreprocessOptions(self):
-        self._qteOptions.resetAdditionalPreprocessOptions()
-
-
-class OptionEdit(qt.QWidget):
-    def __init__(self, parent):
-        qt.QWidget.__init__(self, parent)
-        self.setLayout(qt.QVBoxLayout())
-        self.layout().addWidget(qt.QLabel("options:"))
-        self._tabWidget = qt.QTabWidget(parent=self)
-
-        # recons opt
-        self._qteAddReconsOptions = qt.QTextEdit(parent=self._tabWidget)
-        self._addAdditionalReconsOptions()
-        self._tabWidget.addTab(self._qteAddReconsOptions, "Additional reco options")
-        self._addAdditionalReconsOptions()
-        # ffc options
-        self._qteAddPreprocessOptions = qt.QTextEdit(parent=self._tabWidget)
-        self._addAdditionalReconsOptions()
-        self._tabWidget.addTab(
-            self._qteAddPreprocessOptions, "Additional preprocess options"
-        )
-        self._addAdditionalPreprocessOptions()
-        # fixed options
-        self._qteFixedOptions = qt.QTextEdit(parent=self._tabWidget)
-        self._qteFixedOptions.setDisabled(True)
-        self._addFixedOptions()
-        self._tabWidget.addTab(self._qteFixedOptions, "Options managed by the GUI")
-        self.layout().addWidget(self._tabWidget)
-        # reco help
-        self._recoHelpScrollArea = qt.QScrollArea(parent=self)
-        self._qteTofuRecoHelp = qt.QLabel("", parent=self._recoHelpScrollArea)
-        self._addTofuRecoHelp()
-        self._recoHelpScrollArea.setWidget(self._qteTofuRecoHelp)
-        self._tabWidget.addTab(self._recoHelpScrollArea, "See tofu reco help")
-        # ffc help
-        self._preprocessHelpScrollArea = qt.QScrollArea(parent=self)
-        self._qteTofuPreprocessHelp = qt.QLabel(
-            "", parent=self._preprocessHelpScrollArea
-        )
-        self._addTofuPreprocessHelp()
-        self._preprocessHelpScrollArea.setWidget(self._qteTofuPreprocessHelp)
-        self._tabWidget.addTab(
-            self._preprocessHelpScrollArea, "See tofu preprocess help"
-        )
-
-        # add some tooltip
-        self._qteAddReconsOptions.setToolTip(
-            "If you want some options to be "
-            "passed to tofu reco which are not "
-            "present in 'options managed' "
-            "then add the option and value if "
-            "necessary in the list"
-        )
-        self._qteAddPreprocessOptions.setToolTip(
-            "If you want some options to be "
-            "passed to tofu preprocess which are not "
-            "present in 'options managed' "
-            "then add the option and value if "
-            "necessary in the list"
-        )
-        self._qteFixedOptions.setToolTip(
-            "This list all the options "
-            "that are generated automatically "
-            "with there values (if necessary) "
-            "by the interface"
-        )
-        self._qteTofuRecoHelp.setToolTip("See help from the used tofu version")
-
-    def _addFixedOptions(self):
-        """
-        Add information about the fixed option (the one always generated
-        in the tofu reco call)
-        :return:
-        """
-        options = [
-            "z-parameter []",
-            "retry-timeout []",
-            "retries []",
-            "verbose",
-            "slices-per-device []",
-            "slice-memory-coeff []",
-            "projections []",
-            "darks []",
-            "flats []",
-            "flats2 []",
-            "fix-nan-and-inf",
-            "number []",
-            "pixel-size []",
-            "volume-angle-x []",
-            "volume-angle-y []",
-            "volume-angle-z []",
-            "region []",
-            "output []",
-            "dry-run (activated if no output specify)",
-            "center-position-x []",
-            "center-position-z []",
-            "overall-angle []",
-            "axis-angle-x []",
-            "axis-angle-y []",
-            "x-region []",
-            "y-region []",
-            "regularization-rate",
-            "absorptivity",
-            "thresholding-rate",
-            "retrieval-method",
-            "energy",
-            "propagation-distance",
-        ]
-        self._qteFixedOptions.setText(" --".join(options))
-
-    def _addAdditionalReconsOptions(self):
-        self._qteAddReconsOptions.setText(
-            " ".join(
-                (
-                    "--resize 0",
-                    "--projection-padding-mode clamp_to_edge",
-                    "--genreco-padding-mode clamp_to_edge",
-                )
-            )
-        )
-
-    def _addAdditionalPreprocessOptions(self):
-        self._qteAddPreprocessOptions.setText(
-            " ".join(
-                (
-                    "--resize 0",
-                    "--projection-padding-mode clamp_to_edge",
-                    "--fix-nan-and-inf",
-                    "--projection-filter none",
-                )
-            )
-        )
-
-    def addAdditionalRecoOption(self, option, value):
-        self._qteAddReconsOptions.setText(
-            " ".join(
-                (
-                    self._qteAddReconsOptions.toPlainText(),
-                    "--" + option + " " + str(value),
-                )
-            )
-        )
-
-    def addAdditionalPreprocessOption(self, option, value):
-        self._qteAddPreprocessOptions.setText(
-            " ".join(
-                (
-                    self._qteAddPreprocessOptions.toPlainText(),
-                    "--" + option + " " + str(value),
-                )
-            )
-        )
-
-    def setAdditionalRecoOptions(self, text):
-        self._qteAddReconsOptions.setText(text)
-
-    def setAdditionalPreprocessOptions(self, text):
-        self._qteAddPreprocessOptions.setText(text)
-
-    def getAdditionalRecoOptions(self):
-        return self._qteAddReconsOptions.toPlainText().replace("\n", " ")
-
-    def getAdditionalPreprocessOptions(self):
-        return self._qteAddPreprocessOptions.toPlainText().replace("\n", " ")
-
-    def resetAdditionalRecoOptions(self):
-        self._qteAddReconsOptions.clear()
-
-    def resetAdditionalPreprocessOptions(self):
-        self._qteAddPreprocessOptions.clear()
-
-    def _getNodeParameters(self):
-        """Add the value of the detain options + some extra parameters to be
-        passed as 'free string'
-
-        :return:
-        :rtype: tuple (dict, list)
-        """
-        _ddict = {}
-        for option in self._options:
-            _ddict[option] = self._options[option].getter()
-        return _ddict, self.getAdditionalRecoOptions()
-
-    def _addTofuRecoHelp(self):
-        if has_tofu() is True:
-            try:
-                process = subprocess.Popen(
-                    ["tofu", "reco", "--help"],
-                    stdout=subprocess.PIPE,
-                    stderr=subprocess.PIPE,
-                )
-                stdout, stderr = process.communicate()
-                if (len(stdout.decode("utf-8"))) > 0:
-                    self._qteTofuRecoHelp.setText(stdout.decode("utf-8"))
-                else:
-                    self._qteTofuRecoHelp.setText(stderr.decode("utf-8"))
-            except Exception:
-                try:
-                    process.kill()
-                    process.wait()
-                except Exception:
-                    self._qteTofuRecoHelp.setText("Tofu reco help not found")
-        else:
-            self._qteTofuRecoHelp.setText("Tofu not found")
-        self._qteTofuRecoHelp.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
-        self._qteTofuRecoHelp.setAlignment(qt.Qt.AlignTop)
-
-    def _addTofuPreprocessHelp(self):
-        if has_tofu() is True:
-            try:
-                process = subprocess.Popen(
-                    ["tofu", "preprocess", "--help"],
-                    stdout=subprocess.PIPE,
-                    stderr=subprocess.PIPE,
-                )
-                stdout, stderr = process.communicate()
-                if (len(stdout.decode("utf-8"))) > 0:
-                    self._qteTofuPreprocessHelp.setText(stdout.decode("utf-8"))
-                else:
-                    self._qteTofuPreprocessHelp.setText(stderr.decode("utf-8"))
-            except Exception:
-                try:
-                    process.kill()
-                    process.wait()
-                except Exception:
-                    self._qteTofuPreprocessHelp.setText(
-                        "Tofu preprocess help not found"
-                    )
-        else:
-            self._qteTofuPreprocessHelp.setText("Tofu not found")
-        self._qteTofuPreprocessHelp.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
-        self._qteTofuPreprocessHelp.setAlignment(qt.Qt.AlignTop)
-
-
-class GpuGroupBox(qt.QGroupBox):
-    """
-    Class grouping all the options relative to GPU
-    """
-
-    gpuOptionChanged = qt.Signal()
-    """Signal emitted when the option of the gpu are modified"""
-
-    class SlicePerDeviceWidget(qt.QWidget):
-        def __init__(self, parent):
-            qt.QWidget.__init__(self, parent)
-            self.setLayout(qt.QVBoxLayout())
-            self.layout().setContentsMargins(0, 0, 0, 0)
-            self._noneLabel = qt.QLabel("None", parent=self)
-            self.layout().addWidget(self._noneLabel)
-            self._slicePerDevice = qt.QSpinBox(parent=self)
-            self._slicePerDevice.setMinimum(1)
-            self._slicePerDevice.setMaximum(1000000)
-            self.layout().addWidget(self._slicePerDevice)
-            self._slicePerDevice.setVisible(False)
-
-        def setValue(self, value):
-            self._slicePerDevice.setVisible(value is not None)
-            self._noneLabel.setVisible(value is None)
-
-            if value is not None:
-                self._slicePerDevice.setValue(value)
-
-        def getValue(self):
-            if self._noneLabel.isVisible():
-                return None
-            else:
-                return self._slicePerDevice.value()
-
-        def activeValueMode(self, b):
-            self._slicePerDevice.setVisible(b is True)
-            self._slicePerDevice.setEnabled(b is True)
-            self._noneLabel.setVisible(b is False)
-            self.setVisible(True)
-
-    def __init__(self, parent):
-        qt.QGroupBox.__init__(self, "GPU optional parameters", parent)
-        self.setLayout(qt.QGridLayout())
-
-        self._sliceMemoryCoeffRB = qt.QRadioButton("slice memory coeff", parent=self)
-
-        self.layout().addWidget(self._sliceMemoryCoeffRB, 0, 0)
-
-        self._sliceMemoryCoeff = qt.QLineEdit("0.8", parent=self)
-        validator = qt.QDoubleValidator(parent=self._sliceMemoryCoeff)
-        validator.setBottom(0.01)
-        validator.setTop(0.9)
-        self._sliceMemoryCoeff.setValidator(validator)
-
-        self.layout().addWidget(self._sliceMemoryCoeff, 0, 2)
-        self._sliceMemoryCoeffRB.toggled.connect(self._mvToMemoCoeff)
-
-        self._slicePerDeviceRB = qt.QRadioButton("slices per device", parent=self)
-        self.layout().addWidget(self._slicePerDeviceRB, 1, 0)
-
-        self._slicePerDevice = self.SlicePerDeviceWidget(parent=self)
-        self.layout().addWidget(self._slicePerDevice, 1, 2)
-        self._slicePerDevice.setSizePolicy(
-            qt.QSizePolicy.Expanding, qt.QSizePolicy.Minimum
-        )
-
-        self._slicePerDeviceRB.toggled.connect(self._mvToSlicePerDevice)
-
-        self._autoRB = qt.QRadioButton("auto", parent=self)
-        self.layout().addWidget(self._autoRB, 2, 0)
-        self._autoRB.toggled.connect(self._mvToAuto)
-        self._autoRB.setChecked(True)
-
-        for _radioButton in (
-            self._slicePerDeviceRB,
-            self._sliceMemoryCoeffRB,
-            self._autoRB,
-        ):
-            _radioButton.toggled.connect(self.__gpuOptionChange)
-        self._slicePerDevice._slicePerDevice.valueChanged.connect(
-            self.__gpuOptionChange
-        )
-        self._sliceMemoryCoeff.textChanged.connect(self.__gpuOptionChange)
-
-    def _mvToAuto(self):
-        """Move to auto mode"""
-        self._sliceMemoryCoeff.setText("0.8")
-        self._sliceMemoryCoeff.setVisible(True)
-        self._sliceMemoryCoeff.setEnabled(False)
-        self._slicePerDevice.setValue(None)
-        self._slicePerDevice.setVisible(True)
-        self._slicePerDevice.setEnabled(False)
-
-    def _mvToMemoCoeff(self):
-        self._slicePerDevice.setEnabled(False)
-        self._sliceMemoryCoeff.setVisible(True)
-        self._sliceMemoryCoeff.setEnabled(True)
-        self._slicePerDevice.setValue(None)
-        self._slicePerDevice.setVisible(False)
-
-    def _mvToSlicePerDevice(self):
-        self._slicePerDevice.setEnabled(True)
-        self._sliceMemoryCoeff.setVisible(False)
-        self._sliceMemoryCoeff.setEnabled(False)
-        self._slicePerDevice.activeValueMode(True)
-
-    def getSliceMemoryCoeff(self):
-        if self._sliceMemoryCoeff.isVisible():
-            return float(self._sliceMemoryCoeff.text())
-        else:
-            return None
-
-    def getSlicePerDevice(self):
-        if self._slicePerDevice.isVisible():
-            return self._slicePerDevice.getValue()
-        else:
-            return None
-
-    def setSlicePerDevice(self, value):
-        self._slicePerDevice.setEnabled(True)
-        self._slicePerDevice.setVisible(True)
-        try:
-            self._slicePerDevice.setValue(int(value))
-        except Exception as error:
-            _logger.warning(f"Fails to set slice per device, error is {error}")
-
-    def setSliceMemoryCoeff(self, value):
-        self._sliceMemoryCoeff.setVisible(True)
-        self._sliceMemoryCoeff.setEnabled(True)
-        try:
-            self._sliceMemoryCoeff.setText(value)
-        except Exception as error:
-            _logger.warning(f"Fails to set memory coefficient, error is {error}")
-
-    def getHighLimit(self):
-        if self._slicePerDeviceRB.isChecked():
-            n_gpu = tomwer.core.utils.gpu.getNumberOfDevice() or 1
-            return self._slicePerDevice._slicePerDevice.value() * n_gpu
-        else:
-            return None
-
-    def __gpuOptionChange(self, *args, **kwargs):
-        self.gpuOptionChanged.emit()