Merge branch 'main' of https://github.com/mantidproject/mantidimaging …

…into 2001_Live_Viewer_brightness_adjustment

.github/actions/publish-package/action.yml

@@ -4,6 +4,10 @@ inputs:
   repository:
     description: 'Anaconda repository'
     required: true
+    default: 'mantidimaging'
+  repository-old:
+    description: 'Anaconda repository - old'
+    required: true
     default: 'mantid'
   label:
     description: 'Label'
@@ -12,6 +16,9 @@ inputs:
   token:
     description: 'Anaconda API Token'
     required: true
+  token-old:
+    description: 'Anaconda API Token - old'
+    required: true
 
 description: Build conda package
 runs:
@@ -35,8 +42,10 @@ runs:
     shell: bash -l {0}
     run: |
       conda activate build-env
-      conda config --set anaconda_upload yes
+      conda config --set anaconda_upload no
       # if the upload silently fails - check the token expiration. Conda can fail silently!
-      conda mambabuild --user ${{ inputs.repository }} --token ${{ inputs.token }} --label ${{ inputs.label }} $GITHUB_WORKSPACE/conda |& tee upload.log
+      conda mambabuild $GITHUB_WORKSPACE/conda
+      anaconda -t ${{ inputs.token }} upload --user ${{ inputs.repository }} --label ${{ inputs.label }} ${CONDA_PREFIX}/conda-bld/*/mantidimaging*.tar.bz2 |& tee upload.log
+      anaconda -t ${{ inputs.token-old }} upload --user ${{ inputs.repository-old }} --label ${{ inputs.label }} ${CONDA_PREFIX}/conda-bld/*/mantidimaging*.tar.bz2
       # Check that upload completed
       grep "Upload complete" upload.log

.github/workflows/conda.yml

@@ -140,4 +140,5 @@ jobs:
         uses: ./.github/actions/publish-package
         with:
           label: unstable
-          token: ${{ secrets.ANACONDA_API_TOKEN }}
+          token: ${{ secrets.ANACONDA_API_TOKEN_MANTIDIMAGING }}
+          token-old: ${{ secrets.ANACONDA_API_TOKEN }}

.github/workflows/windows.yml

@@ -126,4 +126,5 @@ jobs:
         uses: ./.github/actions/publish-package
         with:
           label: unstable
-          token: ${{ secrets.ANACONDA_API_TOKEN }}
+          token: ${{ secrets.ANACONDA_API_TOKEN_MANTIDIMAGING }}
+          token-old: ${{ secrets.ANACONDA_API_TOKEN }}

README.md

@@ -1,12 +1,28 @@
+<div align="center">
+  <a href="https://mantidproject.github.io/mantidimaging/">
+    <img src="images/mantid_imaging_64px.ico" alt="Logo" width="80" height="80">
+  </a>
+
+  <h1 align="center">MantidImaging</h1>
+
+  <p align="center" style="font-size: 18px">
+    <strong>A graphical toolkit for 3D reconstruction of neutron tomography data</strong>
+    <br />
+     <br />
+    <a href="https://mantidproject.github.io/mantidimaging/"><strong>Explore the docs »</strong></a>
+    <br />
+    <br />
+    <a href="https://anaconda.org/mantid/mantidimaging"><b>Anaconda Package</b></a>
+    ·
+    <a href="https://github.com/mantidproject/mantidimaging"><b>Code Repository</b></a>
+    ·
+    <a href="https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?SUBED1=MANTID-IMAGING-ANNOUNCE&A=1"><b>Release Mailing List</b></a>
+  </p>
+</div>
+
 # MantidImaging
 
 Mantid Imaging is a graphical toolkit for performing 3D reconstruction of neutron tomography data. It provides an easy-to-use graphical interface to a wide range of pre/post-processing operations, tilt correction and reconstruction algorithms, accommodating for tomography users with varying data complexity and image analysis background knowledge. It utilises a flexible plugin system that allows easy integration of external software, and has allowed us to re-use software widely known in the neutron tomography community.
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4728059.svg)](https://doi.org/10.5281/zenodo.4728059)
 [![Coverage Status](https://coveralls.io/repos/github/mantidproject/mantidimaging/badge.svg?branch=main)](https://coveralls.io/github/mantidproject/mantidimaging?branch=main)
-
-## Links
-
- - Documentation: https://mantidproject.github.io/mantidimaging/
- - Anaconda package: https://anaconda.org/mantid/mantidimaging
- - Code repository: https://github.com/mantidproject/mantidimaging

docs/index.rst

@@ -32,3 +32,5 @@ Please cite as:
 Tasev, Dimitar; Akello-Egwel, Dolica; Allen, Jack; Baust, Rachel; Gigg, Martyn; Jones, Samuel; Nixon, Daniel; Stock, Samuel; Taylor, Will; Tygier, Sam. (2023). Mantid Imaging (2.5.0), Zenodo https://doi.org/10.5281/zenodo.4728059
 
 (See `Zenodo <https://doi.org/10.5281/zenodo.4728059>`_ for citing specific versions).
+
+Sign up to our `mailing list <https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?SUBED1=MANTID-IMAGING-ANNOUNCE&A=1>`_ to receive updates on the project

docs/release_notes/next/feature-1943-RITS-transmission-error

@@ -0,0 +1,2 @@
+#1943 : RITS export transmission errors
+

docs/release_notes/next/fix-2002-default-values

@@ -0,0 +1,2 @@
+#2002 : Better default values in Remove all stripes
+

docs/support.rst

@@ -5,3 +5,8 @@ Issues can be reported on the `Github project page <https://github.com/mantidpro
 
 The developers can be contacted at
 [email protected]
+
+Release Updates
+===============
+
+Sign up to our `mailing list <https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?SUBED1=MANTID-IMAGING-ANNOUNCE&A=1>`_ to receive updates on the project

mantidimaging/core/operations/remove_all_stripe/remove_all_stripe.py

@@ -84,23 +84,23 @@ def register_gui(form, on_change, view):
 
         _, la_size = add_property_to_form('Large stripe kernel',
                                           Type.INT,
-                                          default_value=61,
+                                          default_value=21,
                                           valid_values=(1, 100),
                                           form=form,
                                           on_change=on_change,
                                           tooltip="Window size of the median filter to remove large stripes.")
 
         _, sm_size = add_property_to_form('Small stripe kernel',
                                           Type.INT,
-                                          default_value=21,
+                                          default_value=7,
                                           valid_values=(1, 100),
                                           form=form,
                                           on_change=on_change,
                                           tooltip="Window size of the median filter to remove small-to-medium stripes.")
 
         _, dim = add_property_to_form('Dimension of the window',
                                       Type.INT,
-                                      default_value=1,
+                                      default_value=2,
                                       valid_values=(1, 2),
                                       form=form,
                                       on_change=on_change,

mantidimaging/gui/ui/spectrum_viewer.ui

@@ -255,12 +255,75 @@
              </widget>
             </item>
             <item>
-             <widget class="QComboBox" name="image_output_mode">
+             <widget class="QComboBox" name="image_output_mode_combobox">
               <item>
                <property name="text">
                 <string>Single Spectrum</string>
                </property>
               </item>
+              <item>
+               <property name="text">
+                <string>2D Binned</string>
+               </property>
+              </item>
+             </widget>
+            </item>
+            <item>
+             <widget class="QLabel" name="label_2">
+              <property name="text">
+               <string>Error Mode</string>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QComboBox" name="transmission_error_mode_combobox">
+              <item>
+               <property name="text">
+                <string>Standard Deviation</string>
+               </property>
+              </item>
+              <item>
+               <property name="text">
+                <string>Propagated</string>
+               </property>
+              </item>
+             </widget>
+            </item>
+            <item>
+             <widget class="QLabel" name="bin_size_label">
+              <property name="text">
+               <string>Bin Size</string>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QSpinBox" name="bin_size_spinBox">
+              <property name="minimum">
+               <number>1</number>
+              </property>
+              <property name="maximum">
+               <number>1000</number>
+              </property>
+              <property name="value">
+               <number>10</number>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QLabel" name="bin_step_label">
+              <property name="text">
+               <string>Bin Step</string>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QSpinBox" name="bin_step_spinBox">
+              <property name="minimum">
+               <number>1</number>
+              </property>
+              <property name="maximum">
+               <number>1000</number>
+              </property>
              </widget>
             </item>
             <item>

mantidimaging/gui/windows/spectrum_viewer/model.py

@@ -31,8 +31,15 @@ class SpecType(Enum):
 
 
 class ErrorMode(Enum):
-    STANDARD_DEVIATION = 1
-    PROPAGATED = 2
+    STANDARD_DEVIATION = "Standard Deviation"
+    PROPAGATED = "Propagated"
+
+    @classmethod
+    def get_by_value(cls, value: str) -> ErrorMode:
+        for element in cls:
+            if element.value == value:
+                return element
+        raise ValueError(f"Unknown error mode: {value}")
 
 
 class SpectrumViewerWindowModel:

mantidimaging/gui/windows/spectrum_viewer/presenter.py

@@ -177,7 +177,8 @@ def handle_rits_export(self) -> None:
             return
         if path.suffix != ".dat":
             path = path.with_suffix(".dat")
-        self.model.save_rits(path, self.spectrum_mode == SpecType.SAMPLE_NORMED, ErrorMode.STANDARD_DEVIATION)
+        error_mode = ErrorMode.get_by_value(self.view.transmission_error_mode)
+        self.model.save_rits(path, self.spectrum_mode == SpecType.SAMPLE_NORMED, error_mode)
 
     def handle_enable_normalised(self, enabled: bool) -> None:
         if enabled:

mantidimaging/gui/windows/spectrum_viewer/test/model_test.py

@@ -406,3 +406,8 @@ def test_WHEN_stack_tof_THEN_tof_correct(self):
         tof_result = self.model.get_stack_time_of_flight()
         self.assertIsInstance(tof_result, np.ndarray)
         npt.assert_array_equal(tof_result, np.arange(0, 10) * 0.1)
+
+    def test_error_modes(self):
+        self.assertEqual(ErrorMode.get_by_value("Standard Deviation"), ErrorMode.STANDARD_DEVIATION)
+        self.assertEqual(ErrorMode.get_by_value("Propagated"), ErrorMode.PROPAGATED)
+        self.assertRaises(ValueError, ErrorMode.get_by_value, "")

mantidimaging/gui/windows/spectrum_viewer/test/presenter_test.py

@@ -192,6 +192,7 @@ def test_handle_export_csv(self, path_name: str, mock_save_csv: mock.Mock):
     @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.save_rits")
     def test_handle_rits_export(self, path_name: str, mock_save_rits: mock.Mock):
         self.view.get_rits_export_filename = mock.Mock(return_value=Path(path_name))
+        self.view.transmission_error_mode = "Standard Deviation"
 
         self.presenter.model.set_stack(generate_images())
 

mantidimaging/gui/windows/spectrum_viewer/view.py

@@ -6,7 +6,7 @@
 
 from PyQt5.QtGui import QPixmap
 from PyQt5.QtWidgets import QCheckBox, QVBoxLayout, QFileDialog, QPushButton, QLabel, QAbstractItemView, QHeaderView, \
-    QTabWidget
+    QTabWidget, QComboBox, QSpinBox
 
 from mantidimaging.core.utility import finder
 from mantidimaging.gui.mvp_base import BaseMainWindowView
@@ -36,6 +36,10 @@ class SpectrumViewerWindowView(BaseMainWindowView):
     normaliseErrorIcon: QLabel
     _current_dataset_id: Optional['UUID']
     normalise_error_issue: str = ""
+    image_output_mode_combobox: QComboBox
+    transmission_error_mode_combobox: QComboBox
+    bin_size_spinBox: QSpinBox
+    bin_step_spinBox: QSpinBox
 
     def __init__(self, main_window: 'MainWindowView'):
         super().__init__(None, 'gui/ui/spectrum_viewer.ui')
@@ -67,6 +71,8 @@ def __init__(self, main_window: 'MainWindowView'):
         self.normaliseCheckBox.stateChanged.connect(self.presenter.handle_button_enabled)
 
         self.exportTabs.currentChanged.connect(self.presenter.handle_export_tab_change)
+        self.image_output_mode_combobox.currentTextChanged.connect(self.set_binning_visibility)
+        self.set_binning_visibility()
 
         # ROI action buttons
         self.addBtn.clicked.connect(self.set_new_roi)
@@ -305,3 +311,26 @@ def clear_all_rois(self) -> None:
         self.spectrum.spectrum_data_dict = {}
         self.spectrum.spectrum.clearPlots()
         self.removeBtn.setEnabled(False)
+
+    @property
+    def transmission_error_mode(self) -> str:
+        return self.transmission_error_mode_combobox.currentText()
+
+    @property
+    def image_output_mode(self) -> str:
+        return self.image_output_mode_combobox.currentText()
+
+    @property
+    def bin_size(self) -> int:
+        return self.bin_size_spinbox.value()
+
+    @property
+    def bin_step(self) -> int:
+        return self.bin_step_spinbox.value()
+
+    def set_binning_visibility(self) -> None:
+        hide_binning = self.image_output_mode != "2D Binned"
+        self.bin_size_label.setHidden(hide_binning)
+        self.bin_size_spinBox.setHidden(hide_binning)
+        self.bin_step_label.setHidden(hide_binning)
+        self.bin_step_spinBox.setHidden(hide_binning)