Merge branch 'main' into operations_improve_1

.github/ISSUE_TEMPLATE/release.md

@@ -0,0 +1,86 @@
+---
+
+name: Pre-Release Issue Template for Developers
+about: For Developers Only - Should be used when Preparing for a release to make sure no tasks are missed during the build-up for a release
+title: 'FOR DEVELOPERS: Mantid Imaging [V.V.V] Pre-Release'
+labels: 'Release 🚀'
+assignees: ''
+
+---
+
+## Description
+
+As part of preparations for the release of Mantid Imaging version [**VERSION***], the following tasks need to be completed.
+
+
+## High Priority Bugs
+<!-- Make sure any high priority bugs which are found during smoke testing are resolved -->
+- [ ] [High priority bugs](https://github.com/mantidproject/mantidimaging/issues?)
+
+
+## Create release branch  
+- [ ] Create branch from main named release-x.x.x  
+- [ ] Check that branch protection rules are being applied  
+
+
+## Version Update PR
+<!-- Update version references to version [**VERSION**] in the following locations (Update versions within `docs/release_notes/index.rst` as a separate PR updating release notes - See "Update Release Notes PR"). -->
+
+**PR:**
+- [ ] `CITATION.cff`
+    - Version: `version: "V.V.V"`
+    - Release Date: `date-released: YYYY-MM-DD`
+- [ ] `docs/_templates/versioning.html`
+    - Version: Under `<h3>{{ _('Versions') }}</h3>`
+- [ ] `docs/conf.py`
+    - Release Date:
+    - Version: `release = 'V.V.V<tag>'` (alpha/beta/rc)
+    - Version: `smv_tag_whitelist = r'^(2.3.0|2.4.0|2.5.0|2.6.0|2.7.0)$'`
+- [ ] `docs/index.rst`
+    - Year: update year within Citation if out of date
+    - Version: update version within Citation
+
+
+## Authors PR (if required)
+<!--  Make sure list of authors remains in alphabetical order by surname -->
+
+**PR:**
+- [ ] `CITATION.cff`
+- [ ] `docs/conf.py`
+- [ ] `docs/index.rst`
+
+
+## Release Notes PR
+<!-- Update release notes for new version and format "next" release notes -->
+
+**PR:**
+- [ ] Compile Release Notes using the following command `python setup.py release_notes` - Copy output and place in new file `docs/release_notes/<V.V.rst>`
+- [ ] Add newest version under "next": `docs/release_notes/index.rst`
+- [ ] Delete all release notes within: `docs/release_notes/next/`
+
+
+## Create Release
+
+- [ ] Create release from tag (See internal docs for how to do this)
+
+
+## Move IDAaas to Stable Branch
+
+- [ ] IDAaaS - move stable branch (See internal docs for how to do this)
+
+
+## Update Versions on Main
+
+- [ ] Versions on main
+    - Tag commit as alpha for next release (e.g. after releasing V.V)
+    - Once merged checkout main and run `git describe ` to check if the tag is part of the history (See internal docs for additional info)
+
+
+## Windows NSIS Installer
+ - [ ] Build Windows NSIS Installer (See internal docs for how to do this)
+
+
+### Additional Info
+<!-- Add any additional information below related to the release which may be useful t ou or the reviewer -->
+
+

CITATION.cff

@@ -1,34 +1,41 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 authors:
-  - family-names: Tasev
-    given-names: Dimitar
-    orcid: https://orcid.org/0000-0002-5435-1936
   - family-names: Akello-Egwel
     given-names: Dolica
   - family-names: Allen
     given-names: Jack
+    orcid: https://orcid.org/0009-0007-2873-3731
   - family-names: Baust
     given-names: Rachel
   - family-names: Gigg
     given-names: Martyn
   - family-names: Jones
     given-names: Samuel
     orcid: https://orcid.org/0000-0001-7217-2280
+  - family-names: Meigh
+    given-names: Ashley
+    orcid: https://orcid.org/0009-0001-6357-0516
   - family-names: Nixon
     given-names: Daniel
   - family-names: Stock
     given-names: Samuel
+  - family-names: Sullivan
+    given-names: Michael
+    orcid: https://orcid.org/0000-0003-4910-7784
+  - family-names: Tasev
+    given-names: Dimitar
+    orcid: https://orcid.org/0000-0002-5435-1936
   - family-names: Taylor
     given-names: Will
   - family-names: Tygier
     given-names: Sam
     orcid: https://orcid.org/0000-0002-7495-8655
 title: "Mantid Imaging"
 abstract: "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."
-version: "2.5.0"
+version: "2.7.0"
 doi: 10.5281/zenodo.4728059
-date-released: 2023-05-04
+date-released: 2024-02-21
 license: "GPL-3.0-or-later"
 repository-code: https://github.com/mantidproject/mantidimaging
 url: https://mantidproject.github.io/mantidimaging

docs/_templates/versioning.html

@@ -13,7 +13,7 @@ <h3>{{ _('Versions') }}</h3>
 <h3>{{ _('Versions') }}</h3>
 <ul>
   <li><a href="{{ pathto("",1)}}index.html">Latest</a></li>
-  {%- for item in ['2.3.0', '2.4.0', '2.5.0', '2.6.0'] %}
+  {%- for item in ['2.3.0', '2.4.0', '2.5.0', '2.6.0', '2.7.0'] %}
   <li><a href="{{ pathto("",1)}}{{ item }}/index.html">{{ item }}</a></li>
   {%- endfor %}
 </ul>

docs/conf.py

@@ -69,18 +69,18 @@
 
 # General information about the project.
 project = 'MantidImaging'
-copyright = '2017-2023, Mantid Project'
-author = 'Dimitar Tasev, Jack Allen, Dolica Akello-Egwel, Rachel Baust, Martyn Gigg, Samuel Jones, Dan Nixon, ' \
-         'Samuel Stock, Will Taylor, Sam Tygier'
+copyright = '2017-2024, Mantid Project'
+author = ("Dolica Akello-Egwel, Jack Allen, Rachel Baust, Martyn Gigg, Samuel Jones, Ashley Meigh, Daniel Nixon, "
+          "Samuel Stock, Michael Sullivan, Dimitar Tasev, Will Taylor, Sam Tygier")
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '2.7'
+version = '2.8'
 # The full version, including alpha/beta/rc tags.
-release = '2.7.0a1'
+release = '2.8.0a1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -174,7 +174,10 @@
 html_use_smartypants = False
 
 # sphinx-multiversion
-smv_tag_whitelist = r'^(2.3.0|2.4.0|2.5.0|2.6.0)$'
+smv_tag_whitelist = r'^(2.3.0|2.4.0|2.5.0|2.6.0|2.7.0)$'
 smv_branch_whitelist = None  # No branches
 smv_released_pattern = r''
-smv_prebuild_command = "python setup.py docs_api || python setup.py internal_docs_api"
+smv_prebuild_command = (
+    'sphinx-apidoc -f -M -e -T -d 3 mantidimaging **/test **/test_helpers **/eyes_tests -o docs/api/ || '
+    'python setup.py docs_api || '
+    'python setup.py internal_docs_api')

docs/index.rst

@@ -29,7 +29,7 @@ Mantid Imaging is a graphical toolkit for performing 3D reconstruction of neutro
 
 
 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
+Akello-Egwel, Dolica; Allen, Jack; Baust, Rachel; Gigg, Martyn; Jones, Samuel; Meigh, Ashley; Nixon, Daniel; Stock, Samuel; Sullivan, Michael; Tasev, Dimitar; Taylor, Will; Tygier, Sam. (2024). Mantid Imaging (2.7.0), Zenodo https://doi.org/10.5281/zenodo.4728059
 
 (See `Zenodo <https://doi.org/10.5281/zenodo.4728059>`_ for citing specific versions).
 

docs/release_notes/2.7.rst

@@ -0,0 +1,29 @@
+New Features
+------------
+- #1912 : Support sub-directories in Live viewer
+- #1941 : Spectrum viewer tab for exporting to RITS
+- #1943 : RITS export transmission errors
+- #1945 : Export Binned RITS Formatted Data within Spectrum Viewer.
+- #1957 : ROI support for RITS export
+- #1992 : Spectrum Viewer: Change ROI Colour Through Right Click Dialog Menu
+- #1996 : Added .fits file compatibility for Live Viewer
+- #2026: Time of flight graph in the Spectrum Viewer is now resizable
+- #2027: The Spectrum ROI details display in an adjustable table via spinboxes
+- #2048: Update spectrum documentation to reflect changes made to the Spectrum Viewer.
+
+Fixes
+-----
+- #1873 : fix typeError: qWait(ms: int): argument 1 has unexpected type 'float'
+- #1966: ExecutionTimer unit test fails intermittently for Windows GitHub Action
+- #2002 : Better default values in Remove all stripes
+- #2009 : Improve type annotation in gui.windows.recon
+- #2012 : numpy2 deprication
+- #2031 : Speed up imageview by avoiding unneeded calculation
+
+Developer Changes
+-----------------
+- #1932 : RITS Export Backend
+- #1951 : Various fixes to speedup pytest
+- #1955 : Add InstrumentLog as new log reader
+- #1960 : Update developer tools
+- #2011 : Move to a new conda repo https://anaconda.org/mantidimaging/mantidimaging

docs/release_notes/index.rst

@@ -6,6 +6,7 @@ Release Notes
    :caption: Contents:
 
    next
+   2.7
    2.6
    2.5
    2.4

docs/release_notes/next/feature-2046-ROI_Colors _table

@@ -0,0 +1 @@
+#2046 : Enhancement: Implement Click Dialog for Changing ROI Colors in Table

docs/release_notes/next/feature-2051-operations

@@ -0,0 +1 @@
+#2051: Move operations to compute_function style

docs/release_notes/next/next.rst

@@ -0,0 +1,16 @@
+Mantid Imaging next release
+===========================
+
+This contains changes for the next not yet released Mantid Imaging versions.
+
+New Features
+------------
+.. release_notes:: feature
+
+Fixes
+-----
+.. release_notes:: fix
+
+Developer Changes
+-----------------
+.. release_notes:: dev

mantidimaging/core/operations/gaussian/gaussian.py

@@ -3,20 +3,19 @@
 from __future__ import annotations
 
 from functools import partial
-from logging import getLogger
 from typing import TYPE_CHECKING
 
 import scipy.ndimage as scipy_ndimage
 
 from mantidimaging import helper as h
 from mantidimaging.core.operations.base_filter import BaseFilter
 from mantidimaging.core.parallel import shared as ps
-from mantidimaging.core.utility.progress_reporting import Progress
 from mantidimaging.gui.utility import add_property_to_form
 from mantidimaging.gui.utility.qt_helpers import Type
 
 if TYPE_CHECKING:
     from mantidimaging.core.data import ImageStack
+    import numpy as np
 
 
 class GaussianFilter(BaseFilter):
@@ -53,10 +52,20 @@ def filter_func(data: ImageStack, size=None, mode=None, order=None, progress=Non
         if not size or not size > 1:
             raise ValueError(f'Size parameter must be greater than 1, but value provided was {size}')
 
-        _execute(data, size, mode, order, progress)
+        params = {'size': size, 'mode': mode, 'order': order}
+        ps.run_compute_func(GaussianFilter.compute_function, data.data.shape[0], data.shared_array, params, progress)
+
         h.check_data_stack(data)
         return data
 
+    @staticmethod
+    def compute_function(i: int, array: np.ndarray, params):
+        scipy_ndimage.gaussian_filter(array[i],
+                                      sigma=params['size'],
+                                      mode=params['mode'],
+                                      order=params['order'],
+                                      output=array[i])
+
     @staticmethod
     def register_gui(form, on_change, view):
         _, size_field = add_property_to_form('Kernel Size',
@@ -92,20 +101,3 @@ def execute_wrapper(size_field=None, order_field=None, mode_field=None):
 
 def modes():
     return ['reflect', 'constant', 'nearest', 'mirror', 'wrap']
-
-
-def _execute(images: ImageStack, size, mode, order, progress=None):
-    log = getLogger(__name__)
-    progress = Progress.ensure_instance(progress, task_name='Gaussian filter')
-
-    f = ps.create_partial(scipy_ndimage.gaussian_filter, ps.return_to_self, sigma=size, mode=mode, order=order)
-
-    log.info("Starting PARALLEL gaussian filter, with pixel data type: {0}, "
-             "filter size/width: {1}.".format(images.dtype, size))
-
-    progress.update()
-    ps.execute(f, [images.shared_array], images.data.shape[0], progress, msg="Gaussian filter")
-
-    progress.mark_complete()
-    log.info("Finished  gaussian filter, with pixel data type: {0}, "
-             "filter size/width: {1}.".format(images.dtype, size))

mantidimaging/gui/ui/image_load_dialog.ui

@@ -116,7 +116,7 @@
      </item>
      <item>
       <property name="text">
-       <string>Sample Log</string>
+       <string>Sample / Spectra Log</string>
       </property>
       <property name="text">
        <string/>

mantidimaging/gui/windows/spectrum_viewer/presenter.py

@@ -137,8 +137,10 @@ def handle_roi_moved(self, force_new_spectrums: bool = False) -> None:
                 self.view.set_spectrum(name, self.model.get_spectrum(name, self.spectrum_mode))
 
     def handle_roi_clicked(self, roi) -> None:
-        self.view.current_roi = roi.name
-        self.view.set_roi_properties()
+        if not roi.name == ROI_RITS:
+            self.view.current_roi = roi.name
+            self.view.last_clicked_roi = roi.name
+            self.view.set_roi_properties()
 
     def redraw_spectrum(self, name: str) -> None:
         """
@@ -241,7 +243,8 @@ def change_roi_colour(self, roi_name: str, new_colour: tuple) -> None:
         """
         if roi_name in self.view.spectrum_widget.roi_dict:
             self.view.spectrum_widget.roi_dict[roi_name].colour = new_colour
-        self.view.update_roi_color_in_table(roi_name, new_colour)
+        self.view.update_roi_color(roi_name, new_colour)
+        self.view.on_visibility_change()
 
     def add_rits_roi(self) -> None:
         roi_name = ROI_RITS