tomwer 1.3.0.dev2__py3-none-any.whl → 1.3.0rc10__py3-none-any.whl

tomwer/core/process/test/test_lamino.py

@@ -1,76 +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__ = "05/04/2019"
-
-
-import shutil
-import tempfile
-import unittest
-
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.utils.scanutils import MockEDF
-
-from ..reconstruction.lamino import LaminoReconstructionTask
-
-
-class TestLaminoIO(unittest.TestCase):
-    """Test inputs and outputs types of the handler functions"""
-
-    def setUp(self):
-        self.scan_folder = tempfile.mkdtemp()
-
-        self.scan = MockEDF.mockScan(
-            scanID=self.scan_folder, nRadio=10, nRecons=1, nPagRecons=4, dim=10
-        )
-
-    def tearDown(self):
-        shutil.rmtree(self.scan_folder)
-
-    def testInputOutput(self):
-        for input_type in (dict, TomwerScanBase):
-            for serialize_output_data in (True, False):
-                with self.subTest(
-                    serialize_output_data=serialize_output_data,
-                    input_type=input_type,
-                ):
-                    input_obj = self.scan
-                    if input_obj is dict:
-                        input_obj = input_obj.to_dict()
-                    lamino_process = LaminoReconstructionTask(
-                        inputs={
-                            "dry_run": True,
-                            "data": input_obj,
-                            "serialize_output_data": serialize_output_data,
-                        }
-                    )
-                    lamino_process.run()
-                    out = lamino_process.outputs.data
-                    if serialize_output_data:
-                        self.assertTrue(isinstance(out, dict))
-                    else:
-                        self.assertTrue(isinstance(out, TomwerScanBase))

tomwer/core/test/test_lamino.py

@@ -1,92 +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__ = "19/07/2018"
-
-import shutil
-import tempfile
-import unittest
-
-from tomwer.core.process.reconstruction.lamino import tofu
-from tomwer.core.scan.edfscan import EDFTomoScan
-
-
-class TestTofuReconstruction(unittest.TestCase):
-    """Simple test of the Lamino reconstruction API"""
-
-    def tearDown(self):
-        shutil.rmtree(self._scan_path)
-
-    def setUp(self):
-        self._scan_path = tempfile.mkdtemp()
-        self.scan = EDFTomoScan(self._scan_path)
-        self.reconstruction = tofu.LaminoReconstructionTask(
-            inputs={
-                "dry_run": True,
-                "data": self.scan,
-                "lamino_params": {
-                    "center-position-x": 5.0,
-                    "projections": "tata-yoyo",
-                    "output": "output_dir",
-                },
-                "serialize_output_data": False,
-            }
-        )
-
-    def testProcessAPI(self):
-        self.reconstruction.run()
-
-    def testPreProcessAPI(self):
-        self.assertFalse(
-            self.reconstruction.is_ffc_has_been_preprocessed(
-                scan=self.scan, x_center=5.0, method=None, darks=None, ff=[None, None]
-            )
-        )
-        self.reconstruction.preprocess_ff(self.scan)
-        self.assertTrue(
-            self.reconstruction.is_ffc_has_been_preprocessed(
-                scan=self.scan, x_center=5.0, method=None, darks=None, ff=[None, None]
-            )
-        )
-        self.reconstruction.run()
-        self.assertTrue(
-            self.reconstruction.is_ffc_has_been_preprocessed(
-                scan=self.scan, x_center=5.0, method=None, darks=None, ff=[None, None]
-            )
-        )
-        self.reconstruction.reconstruction_parameters["center-position-x"] = 2.0
-        self.assertFalse(
-            self.reconstruction.is_ffc_has_been_preprocessed(
-                scan=self.scan, x_center=2.0, method=None, darks=None, ff=[None, None]
-            )
-        )
-        self.reconstruction.preprocess_ff(self.scan)
-        self.assertTrue(
-            self.reconstruction.is_ffc_has_been_preprocessed(
-                scan=self.scan, x_center=2.0, method=None, darks=None, ff=[None, None]
-            )
-        )

tomwer/gui/reconstruction/lamino/__init__.py

@@ -1,31 +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.
-#
-# ###########################################################################*/
-"""This package contains all the widget which are not inheriting from
-WidgetOW (orange widgets)
-"""
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "01/06/2018"

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

@@ -1,107 +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"
-
-
-from collections import namedtuple
-
-_getterSetter = namedtuple("_getterSetter", ["getter", "setter"])
-
-
-class _TofuOptionLoader(object):
-    """Simple class used to register the options managed by a TofuXWidget"""
-
-    def __init__(self, options, childs=None):
-        self._options = options
-        self._childs = childs or []
-        # expose API
-        self._addChild = self._childs.append
-
-    def _hasOption(self, option):
-        return option in self._options
-
-    def _setOption(self, option, value):
-        assert option in self._options
-        if value == "":
-            self._options[option].setter()
-        else:
-            self._options[option].setter(value)
-
-    def getParameters(self):
-        """Add the value of the detain options + some extra parameters to be
-        passed as 'free string'
-
-        :return:
-        :rtype: tuple (dict, list)
-        """
-        _ddict, extraParams = self._getNodeParameters()
-        for child in self._childs:
-            _childDict = child.getParameters()
-            _ddict.update(_childDict)
-        return _ddict
-
-    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, []
-
-    def setParameters(self, _ddict):
-        """
-
-        :param _ddict:
-        :return: initial dictionary less the parameters managed by this option
-                 loader
-         :rtype dict:
-        """
-        _lddict = _ddict.copy()
-        for child in self._childs:
-            _lddict = child.setParameters(_lddict)
-        _lddict = self._setNodeParameters(_lddict)
-        return _lddict
-
-    def _setNodeParameters(self, _ddict):
-        """
-
-        :param _ddict:
-        :return: initial dictionary less the parameters managed by this option
-                 loader
-         :rtype dict:
-        """
-        updatedDict = _ddict.copy()
-        for param, value in _ddict.items():
-            if param in self._options:
-                self._options[param].setter(value)
-                del updatedDict[param]
-        return updatedDict

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

@@ -1 +0,0 @@
-from .tofu import TofuWidget, TofuWindow  # noqa F401

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

@@ -1,148 +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
-
-from silx.gui import qt
-
-from tomwer.gui import icons
-from tomwer.gui.utils.buttons import PadlockButton
-
-_logger = logging.getLogger()
-
-
-class _AngleWidget(qt.QWidget):
-    """Simple widget used to defined an angle"""
-
-    def __init__(self, parent, name, defaultVal=0, lockable=False, information=None):
-        """
-
-        :param parent:
-        :param name:
-        :param defaultVal:
-        :param lockable: if True then add a push button to lock / unlock the
-                         variable
-        :param information: callabak to display some information. If not None
-                            then add a QPushButton calling this callback
-        """
-        assert type(defaultVal) in (int, float)
-        self._lockable = lockable
-        qt.QWidget.__init__(self, parent=parent)
-        self.setLayout(qt.QHBoxLayout())
-        self.layout().setContentsMargins(0, 0, 0, 0)
-        self.layout().addWidget(qt.QLabel(name + ":", parent=self))
-        self._angleLE = qt.QLineEdit(str(defaultVal), parent=self)
-        validator = qt.QDoubleValidator(self._angleLE)
-        self._angleLE.setValidator(validator)
-        self.layout().addWidget(self._angleLE)
-
-        self._infoCallback = information
-        if self._infoCallback is not None:
-            icon = icons.getQIcon("information")
-            self._infoPB = qt.QPushButton(parent=self, icon=icon)
-            self._infoPB.pressed.connect(self._infoCallback)
-            self._infoPB.setCheckable(False)
-            self.layout().addWidget(self._infoPB)
-
-        self._lockButton = PadlockButton(parent=self)
-        self.layout().addWidget(self._lockButton)
-        self._lockButton.setVisible(self.isLockable())
-
-        self.sigEdited = self._angleLE.textEdited
-        """Signal emitted when the angle is edited"""
-
-    def getAngle(self):
-        return float(self._angleLE.text())
-
-    def setAngle(self, val):
-        if not type(val) is str:
-            assert type(val) in (float, int)
-        self._angleLE.setText(str(val))
-
-    def isLockable(self):
-        return self._lockable
-
-    def isLocked(self):
-        return self._lockable and self._lockButton.isLocked()
-
-    def lock(self):
-        if self._lockable is False:
-            _logger.warning(
-                "unable to lock the _AngleWidget cause not defined " "as lockable"
-            )
-        self._lockButton.setChecked(True)
-
-
-class _RegionLE(qt.QWidget):
-    """Widget used to defined a region as (start, end, step)"""
-
-    def __init__(self, parent, name):
-        super().__init__(parent)
-        self.setLayout(qt.QHBoxLayout())
-        self.layout().setContentsMargins(0, 0, 0, 0)
-        self.layout().addWidget(qt.QLabel(name, parent=self))
-        self._regionLE = qt.QLineEdit(parent=self)
-        self.layout().addWidget(self._regionLE)
-        self.setToolTip("region should be defined as: start, end, step")
-
-    def getRegion(self):
-        """
-
-        :return: start voxel, end voxel, step voxel
-        :rtype: tuple of int
-        """
-
-        def _getParam(regions, index, default):
-            try:
-                # if len(regions) > index and regions[index].isdigit():
-                # try to avoid failure if regions[index] is a negative
-                return int(regions[index])
-            except Exception:
-                return default
-
-        if self._regionLE.text() == "":
-            return None
-        regions = self._regionLE.text().replace(" ", "").split(",")
-        sv = _getParam(regions, 0, 0)
-        se = _getParam(regions, 1, -1)
-        ss = _getParam(regions, 2, 1)
-        return (sv, se, ss)
-
-    def setRegion(self, startVox, endVox, stepVox):
-        self.setRegionFromStr(",".join([str(startVox), str(endVox), str(stepVox)]))
-
-    def setRegionFromStr(self, _str):
-        if _str is None:
-            self._regionLE.clear()
-        else:
-            assert type(_str) is str
-            _str = _str.lstrip("(")
-            _str = _str.rstrip(")")
-            self._regionLE.setText(_str)