Merge branch 'normalization_image_intensities' into 'master'

start adding intensity normalization

See merge request tomotools/tomwer!335

.coveragerc

@@ -16,3 +16,7 @@ omit =
     *benchmark.py
     # tomwer main
     tomwer/__main__.py
+    # utils for test
+    tomwer/test/utils/utilstest.py
+    # some files no more tested
+    orangecontrib/tomwer/widgets/control/OldDataValidatorOW.py

.gitlab-ci.yml

@@ -72,6 +72,7 @@ tomwer:
     - python -m pip install .[full_no_cuda]
     - python -m pip install PyQt5==5.11.3
     - python -m pip install pyqtgraph==0.11.0
+    - python -m pip install git+https://gitlab.esrf.fr/tomotools/tomoscan
     - python -m pip install pytest-cov
     - python -m pip install git+https://gitlab.esrf.fr/tomotools/nabu
     - python -m tomwer --help
@@ -93,6 +94,7 @@ test:test-tomwer-tutorials:
     - python -m pip install fabio --upgrade --pre
     - python -m pip install silx --upgrade --pre
     - python -m pip install .[full_no_cuda]
+    - python -m pip install git+https://gitlab.esrf.fr/tomotools/tomoscan
     - mkdir tmp_dir
     - cd tmp_dir
   script:

doc/index.rst

@@ -126,6 +126,7 @@ Reconstruction
   widgets/reconstruction/sadeltabetawidget.rst
   widgets/reconstruction/tofuwidget.rst
   widgets/reconstruction/castvolumewidget.rst
+  widgets/reconstruction/intensitynormalization.rst
 
 
 Cluster

doc/widgets/reconstruction/intensitynormalization.rst

+.. _sinogram normalization:
+
+sino normalization
+``````````````````
+
+.. image:: img/sino_normalization/main_screen.png
+
+
+Behavior
+''''''''
+
+The goal of this widget is to let the user define some normalization to be applied to sinograms.
+This normalization can be one of the following:
+
+* None: no extra normalization will be applied to the sinogram
+* chebyshev: chebyshev normalization will be applied to sinograms
+* division: a value or an array of value will divide the sinogram (during nabu preprocessing step)
+* subtraction: a value or an array of value will subtract the sinogram (during nabu preprocessing step)
+
+For **division** and **subtraction** the user can either provide:
+
+* a scalar value which will be constant
+* a roi to compute one scalar value *per projections* in order to be applied on the sinogram.
+* an URL to be provided directly to nabu. In this case the dataset can be provided locally or globally.
+  If provided locally then the path will be updated for each scan. If provided globally then it will be constant.

orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py

+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2020 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__ = "19/07/2021"
+
+
+import logging
+from silx.gui import qt
+from tomwer.core.scan.scanbase import TomwerScanBase
+from orangecontrib.tomwer.widgets.utils import WidgetLongProcessing
+from orangewidget.settings import Setting
+from orangewidget import gui
+from orangewidget.widget import Input, Output
+from ...orange.managedprocess import SuperviseOW
+from tomwer.gui.reconstruction.normalization.intensity import (
+    SinoNormWindow as _SinoNormWindow,
+)
+from tomwer.synctools.stacks.reconstruction.normalization import (
+    INormalizationProcessStack,
+)
+from processview.core.manager import ProcessManager
+from processview.core.manager import DatasetState
+from tomwer.core.process.reconstruction.normalization import (
+    SinoNormalizationTask,
+)
+from tomwer.core import settings
+from tomwer.core import utils
+from tomoscan.normalization import Method as NormMethod
+from tomwer.core.process.reconstruction.normalization.params import _ValueSource
+import functools
+
+_logger = logging.getLogger(__name__)
+
+
+class SinoNormWindow(_SinoNormWindow):
+    """
+    implementation of NormIntensityWindow for orange. Add a lock processing
+    and a processing stack
+    """
+
+    sigValidate = qt.Signal()
+
+    def __init__(self, parent, process_id=None):
+        assert isinstance(parent, SinoNormOW)
+        super().__init__(parent)
+        self._parentValidate = self.parent()._validate
+        self._processing_stack = INormalizationProcessStack(process_id=process_id)
+        # connect signal / slot
+        self._optsWidget.sigProcessingRequested.connect(self._processCurrentScan)
+
+    def _validated(self):
+        scan = self.getScan()
+        self._parentValidate(scan)
+
+    def _processCurrentScan(self):
+        scan = self.getScan()
+        if scan is None:
+            return
+        self._processScan(scan)
+
+    def _processScan(self, scan):
+        self._processing_stack.add(
+            scan=scan,
+            configuration=self.getConfiguration(),
+            callback=functools.partial(
+                self._mightUpdateResult,
+                scan,
+                self.isLocked(),
+            ),
+        )
+
+    def _mightUpdateResult(self, scan, validate):
+        extra_info = scan.intensity_normalization.get_extra_infos()
+        if "value" in extra_info:
+            self.setResult(result=extra_info["value"])
+        else:
+            self.setResult(None)
+        if validate is True:
+            self._parentValidate(scan)
+
+
+class SinoNormOW(WidgetLongProcessing, SuperviseOW):
+    """
+    A simple widget managing the copy of an incoming folder to an other one
+
+    :param parent: the parent widget
+    """
+
+    # note of this widget should be the one registered on the documentation
+    name = "sino normalization"
+    id = "orange.widgets.tomwer.reconstruction.SinoNormOW.SinoNormOW"
+    description = "Define normalization on intensity to be applied on projections"
+    icon = "icons/norm_I.svg"
+    priority = 28
+    keywords = [
+        "tomography",
+        "normalization",
+        "norm",
+        "I",
+        "intensity",
+        "projections",
+        "radios",
+    ]
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+    allows_cycle = True
+
+    _rpSetting = Setting(dict())
+
+    sigScanReady = qt.Signal(TomwerScanBase)
+    "Signal emitted when a scan is ended"
+
+    class Inputs:
+        data_in = Input(name="data", type=TomwerScanBase)
+
+    class Outputs:
+        data_out = Output(name="data", type=TomwerScanBase)
+
+    def __init__(self, parent=None):
+        """
+        Widget allowing the user to define the normalization to be applied on
+        projections. This can be a scalar or an array.
+        """
+        SuperviseOW.__init__(self, parent)
+        WidgetLongProcessing.__init__(self)
+
+        self._window = SinoNormWindow(self, process_id=self.process_id)
+
+        self._layout = gui.vBox(self.mainArea, self.name).layout()
+        self._layout.setContentsMargins(0, 0, 0, 0)
+
+        self._layout.addWidget(self._window)
+        try:
+            self.loadSettings()
+        except Exception as e:
+            _logger.warning(f"Failed to load settings: {e}")
+
+        # connect signal / slot
+        self._window.sigConfigurationChanged.connect(self._updateSettings)
+        self.destroyed.connect(self._window.stop)
+        self._window._processing_stack.sigComputationStarted.connect(
+            self._startProcessing
+        )
+        self._window._processing_stack.sigComputationEnded.connect(self._endProcessing)
+
+    def isLocked(self):
+        return self._window.isLocked()
+
+    def setLocked(self, locked):
+        self._window.setLocked(locked)
+
+    def setCurrentMethod(self, mode):
+        self._window.setCurrentMethod(mode)
+
+    def getCurrentMethod(self):
+        return self._window.getCurrentMethod()
+
+    def setCurrentSource(self, source):
+        self._window.setCurrentSource(source)
+
+    def getCurrentSource(self):
+        return self._window.getCurrentSource()
+
+    @Inputs.data_in
+    def process(self, scan: TomwerScanBase):
+        if not isinstance(scan, (TomwerScanBase, type(None))):
+            raise TypeError(
+                "scan should be None or an instance of "
+                "TomwerScanBase. Not {}".format(type(scan))
+            )
+        if scan is None:
+            return
+
+        self._skipCurrentScan(new_scan=scan)
+        if settings.isOnLbsram(scan) and utils.isLowOnMemory(
+            settings.get_lbsram_path()
+        ):
+            details = "skip {} because low memory on lbsram".format(str(scan))
+            self.notify_skip(scan=scan, details=details)
+            self.Outputs.data_out.send(scan)
+        else:
+            self._window.setScan(scan=scan)
+
+            if self.isLocked():
+                self._window._processScan(scan=scan)
+
+    def _validate(self, scan):
+        if scan is None:
+            return
+
+        # save processing result for the one with interaction. Otherwise
+        # this will be saved in the processing thread
+        extra_infos = scan.intensity_normalization.get_extra_infos()
+        tomwer_processing_res_code = extra_infos.pop(
+            "tomwer_processing_res_code", "unprocessed"
+        )
+        SinoNormalizationTask._register_process(
+            process_file=scan.process_file,
+            process=SinoNormalizationTask,
+            entry=scan.entry,
+            configuration=self.getConfiguration(),
+            results={
+                "method": scan.intensity_normalization.method.value,
+                "extra_infos": extra_infos,
+            },
+            process_index=scan.pop_process_index(),
+        )
+        if tomwer_processing_res_code is True:
+            # if defined by manual scalar we need to set the value
+            if extra_infos.get("source", None) == _ValueSource.MANUAL_SCALAR.value:
+                extra_infos["value"] = self.getCurrentlyDefinedValues()
+            self.notify_succeed(scan=scan)
+        elif tomwer_processing_res_code is False:
+            self.notify_failed(scan=scan)
+        elif tomwer_processing_res_code is None:
+            self.notify_skip(scan=scan)
+        elif tomwer_processing_res_code == "unprocessed":
+            # if validate manually we must set current method + value
+            scan.intensity_normalization = self.getCurrentMethod()
+
+            if self.getCurrentMethod() in (
+                NormMethod.NONE,
+                NormMethod.CHEBYSHEV,
+                NormMethod.LSQR_SPLINE,
+            ):
+                extra_infos = {}
+            elif self.getCurrentSource() is _ValueSource.DATASET:
+                extra_infos = {
+                    "dataset_url": self._window._optsWidget._datasetWidget.getDatasetUrl().path(),
+                }
+            else:
+                extra_infos = {
+                    "value": self.getCurrentlyDefinedValues(),
+                    "source": self.getCurrentSource(),
+                }
+            self.notify_succeed(scan=scan)
+        # clear flag
+        scan.intensity_normalization.set_extra_infos(extra_infos)
+
+        self.Outputs.data_out.send(scan)
+
+    def _skipCurrentScan(self, new_scan):
+        scan = self._window.getScan()
+        # if the same scan has been run several scan
+        if scan is None or str(scan) == str(new_scan):
+            return
+        current_scan_state = ProcessManager().get_dataset_state(
+            dataset_id=scan.get_dataset_identifier(), process=self
+        )
+        if current_scan_state in (
+            DatasetState.PENDING,
+            DatasetState.WAIT_USER_VALIDATION,
+        ):
+            details = "Was pending and has been replaced by another scan."
+            self.notify_skip(scan=scan, details=details)
+            self.Outputs.data_out.send(scan)
+
+    def getCurrentlyDefinedValues(self):
+        return self._window._crtWidget.getResult()
+
+    def validateCurrentScan(self):
+        scan = self._window.getScan()
+        self._validate(scan)
+
+    def clear(self):
+        self._window.clear()
+
+    def getConfiguration(self):
+        return self._window.getConfiguration()
+
+    def stop(self):
+        self._window.stop()
+
+    def _updateSettings(self):
+        self._rpSetting = self._window.getConfiguration()
+        self._rpSetting["__lock__"] = self.isLocked()
+
+    def loadSettings(self):
+        self._window.setConfiguration(self._rpSetting)
+        if "__lock__" in self._rpSetting:
+            self.setLocked(self._rpSetting["__lock__"])

orangecontrib/tomwer/widgets/reconstruction/icons/norm_I.svg

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orangecontrib/tomwer/widgets/reconstruction/test/test_i_norm.py

+# 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__ = "09/06/2021"
+
+from silx.gui.utils.testutils import TestCaseQt
+from silx.gui import qt
+from tomwer.core.utils.scanutils import MockHDF5
+from orangecontrib.tomwer.widgets.reconstruction.SinoNormOW import (
+    SinoNormOW as _NormIOW,
+)
+from processview.core.manager import ProcessManager, DatasetState
+from tomwer.io.utils.h5pyutils import EntryReader
+from tomwer.core.process.reconstruction.normalization import (
+    SinoNormalizationTask,
+)
+from silx.io.utils import h5py_read_dataset
+import tempfile
+import shutil
+import logging
+import os
+from tomwer.core import utils, settings
+
+logger = logging.getLogger(__name__)
+
+
+class NormIOW(_NormIOW):
+    def __init__(self, parent=None):
+        self._scans_finished = []
+        super().__init__(parent)
+
+    def processing_finished(self, scan):
+        self._scans_finished.append(scan)
+
+    def wait_processing(self, wait_time):
+        self._window._processing_stack._computationThread.wait(wait_time)
+
+    @property
+    def scans_finished(self):
+        return self._scans_finished
+
+    def compute(self):
+        self._window._processCurrentScan()
+
+    def setROI(self, start_x, end_x, start_y, end_y):
+        self._window.setROI(start_x=start_x, end_x=end_x, start_y=start_y, end_y=end_y)
+
+    def close(self):
+        self._scans_finished = {}
+        super().close()
+
+
+class TestProcessing(TestCaseQt):
+
+    DIM = 100
+
+    def setUp(self):
+        super().setUp()
+        utils.mockLowMemory(False)
+        settings.mock_lsbram(False)
+        self._source_dir = tempfile.mkdtemp()
+
+        def create_scan(folder_name):
+            _dir = os.path.join(self._source_dir, folder_name)
+            return MockHDF5(
+                scan_path=_dir,
+                n_ini_proj=20,
+                n_proj=20,
+                n_alignement_proj=2,
+                create_final_ref=False,
+                create_ini_dark=True,
+                create_ini_ref=True,
+                n_refs=1,
+                dim=self.DIM,
+            ).scan
+
+        # create scans
+        self.scan_1 = create_scan("scan_1")
+        self.scan_2 = create_scan("scan_2")
+        self.scan_3 = create_scan("scan_3")
+        self._process_manager = ProcessManager()
+
+        self.widget = NormIOW()
+        self.widget.show()
+
+    def tearDown(self):
+        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.widget.stop()
+        self.widget.close()