jackeallen / newprojectboardsdemo

Repo for containing issues as part of new project boards demo

NewProjectBoardsDemo

Repo for containing issues as part of new project boards demo

newprojectboardsdemo's Issues

Formula for wavelength conversion

Lock Sidebar for Spectrum Viewer Window

Desired Behaviour

Lock spectrum viewer window sidebar in position.

Current Behaviour

Sidebar is not locked in place which means it's easy for the user to minimise and potentially struggle to understand how to get back again.

Acceptance Criteria

What is the acceptance criteria?

• Sidebar is locked and can't be minimised

Extra Information

Why it is needed?

• Feature requested by user
• Project requirement

Where required files/links are

• GUI
  • Workflow > Spectrum Viewer (Beta) - gui/ui/spectrum_viewer.ui
• Repo gui/windows/spectrum_viewer/
  • model.py
  • presenter.py
  • view.py

Current Behaviour

Open	Closed

How to Test

verbose instructions for the reviewer to test changes

• Open GUI
• Open Spectrum Viewer window
• Try to drag the sidebar to the left to minimise (if not possible, desired functionality is achieved)

Spectrum export button enable/disable

As a User: I would like the export spectrum button to be disabled if there is not a currently active stack in the spectrum viewer window as currently this causes a ValueError.

The export spectrum button should be disabled if there is not a currently active stack in the spectrum viewer window.

Acceptance Criteria

What is the acceptance criteria?

• Export spectrum button is disabled if there not active stack in the spectrum viewer window.
• Export spectrum button enabled if there is an active stack in the spectrum viewer window.
• Export spectrum button when clicked does not trigger a ValueError when there is no active stack in the spectrum viewer window.

Extra Information

Why it is needed?

• Feature requested by user
• Project requirement

Where required files/links are

• GUI
  • Workflow > Spectrum Viewer (Beta) - gui/ui/spectrum_viewer.ui
• Repo gui/windows/spectrum_viewer/
  • model.py
  • presenter.py
  • view.py
  • spectrum_widget.py

How to Test

verbose instructions for the reviewer to test changes

• Open up GUI and Load Dataset File > Load dataset > Sample
• Open Spectrum Viewer `Workflow > Spectrum Viewer (Beta)
• Click the Export button and export a spectrum
• While keeping Spectrum Viewer window open, in the main window, delete the active stack by right clicking and selecting delete
• Go back to Spectrum Viewer window and validate export button is disabled
• While keeping Spectrum Viewer window open, in the main window, repeat steps one to three to validate that export button is enabled again and has expected behaviour.

Create "Add ROI" button to Spectrum Viewer Window

Desired Behaviour

Create "Add ROI" button to spectrum viewer window which can create multiple ROIs.

Current Behaviour

No functionality exists for this feature yet.

Acceptance Criteria

What is the acceptance criteria?

• "Add ROI" button exists in spectrum viewer window
• "Add ROI" button can add a new ROI.
• Each ROI added is a different colour

Extra Information

Why it is needed?

• Feature requested by user
• Project requirement
• Created as part of an umbrella ticket to implement Multiple ROIs in spectrum viewer window

Where required files/links are

• GUI
  • Workflow > Spectrum Viewer (Beta) - gui/ui/spectrum_viewer.ui
• Repo gui/windows/spectrum_viewer/
  • model.py
  • presenter.py
  • view.py
  • spectrum_widget.py

How to Test

verbose instructions for the reviewer to test changes

• Open GUI
• Open Spectrum Viewer window
• Click "Add ROI" button
• Confirm that a new ROI is added each time button is pressed
• Confirm that each new ROI added is a different colour

Normalise drop-down is enabled when the spectrum window first opens

Normalise drop-down is enabled when the window first opens even though the checkbox is unticked by default. Toggling the checkbox after that has the correct enable/disable behaviour, though.

Spectrum view - show range values under spectrum plot

Under the spectrum plot add a text status line that shows the min and max values of the current range. Similar to the line profile values in the recon window.

ToF range: 100 - 800

Add a spectrum viewer dialog

I've pushed everything I've prepared on this to branch 1498-add-spectrum-viewer, so you should be able to pick the branch up to start looking at the ROI side when you're ready. The things I've put in place are:

1. Adding "Spectrum Viewer" to the "Workflows" menu in the main window. Clicking this option opens the spectrum viewer in a new window (this is why I wasn't keen to put it into PR at this stage, although if this was temporarily removed the rest could probably go in if needed).

2. The layout for the new window has a splitter, the same as the recon and operations windows use, to separate the section for input fields and the section for the image. The layout is likely to need resizing/settings tweaks as you continue to work on it, particularly around what happens when you re-size.

3. I've setup the two dropdowns to populate with stacks from the main window using the DatasetSelectorWidget. The second dropdown can be enabled and disabled with a checkbox. For now I've left it so that the checkbox simply enables and disables the dropdown, I figured we could decide further down the line if there was a need for it to do anything with the contents of the dropdown when the state changes.

4. The second dropdown will automatically try to select a flat for the selected sample dataset, if one is available. I've noticed that if you keep the window open, delete all the datasets in the main window and then (with the window still open) reload a dataset it doesn't correctly select the flat. This seemed a very minor, niche issue and so I didn't want to delay handing this over to fix it. I can continue to investigate and comment here with anything I find about how to resolve it, though.

Runtime error if delete all but a single image stack while spectrum viewer window is opened

Runtime error if delete all but a single image stack while spectrum viewer window is opened - to reproduce, load a dataset and then load an image to the tree view. Open spectrum viewer window. Delete the dataset so that only the image stack is in the tree view. A runtime error should occur.

Default name for csv file

SpectrumViewerWindowView methods for updating image and spectrum

SpectrumViewerWindowPresenter currently has things like self.view.spectrum.spectrum.clearPlots() and self.view.spectrum.image.setImage(). Add methods to the view to hide the details from the presenter.

Draggable ROIs

Desired Behaviour

Allow all ROIs added to spectrum viewer window to be draggable.

Current Behaviour

Can create ROIs, but unable to move/drag them implemented as part of #1620

Acceptance Criteria

What is the acceptance criteria?

• ROI's can be dragged around the view

Extra Information

Why it is needed?

• Feature requested by user
• Project requirement
• Created as part of an umbrella ticket to implement Multiple ROIs in spectrum viewer window

Where required files/links are

• GUI
  • Workflow > Spectrum Viewer (Beta) - gui/ui/spectrum_viewer.ui
• Repo gui/windows/spectrum_viewer/
  • model.py
  • presenter.py
  • view.py
  • spectrum_widget.py

How to Test

verbose instructions for the reviewer to test changes

• Open GUI
• Open Spectrum Viewer window
• Confirm that ROIs added can be moved around using the mouse

Spectrum viewer open beam normalisation

Allow normalising to an open beam, by enabling a checkbox.

Spectrum should show sample / open. (with divide by zero handled safely)

Spectrum Viewer: Table of ROIs

Desired Behaviour

Allow all ROIs added to be viewed within a table in the spectrum viewer window sidebar using the reconstruction windows COR table for design inspiration (See umbrella issue for image of COR table).

The table should display the name (ID) for each ROI added and a key to describe the colour each ROI is set too using squares e.g. 🟦 🟥 🟩

ROI	Colour
roi_id_1	🟩

Current Behaviour

Can create ROIs, but unable to see them in a table in the sidebar.

Acceptance Criteria

What is the acceptance criteria?

• ROIs added can be seen in a table within the sidebar of the spectrum viewer window
• The name / ID for the ROIs exists in column
• The colour set for the ROIs can be seen in a second column

Extra Information

Why it is needed?

• Feature requested by user
• Project requirement
• Created as part of an umbrella ticket to implement Multiple ROIs in spectrum viewer window

Where required files/links are

• GUI
  • Workflow > Spectrum Viewer (Beta) - gui/ui/spectrum_viewer.ui
• Repo gui/windows/spectrum_viewer/
  • model.py
  • presenter.py
  • view.py
  • spectrum_widget.py

How to Test

verbose instructions for the reviewer to test changes

• Open GUI
• Open Spectrum Viewer window
• Add ROIs using "Add ROI" button
• Confirm that ROIs details are added to table
• Ensure table correctly display ROI name and colour key

Spectrum viewer CSV export

Implement CSV export in the spectrum viewer window

Spectrum viewer handle switching stacks

A bit more needs to be done when switching stacks.

Auto Zoom if sized changed

Auto levels?

Handle switching to None

Handle selected stack being closed in main window.

Show first stack when spectrum window first opened

When the spectrum window is first opened no stack is shown. The first sample stack should be shown.

Current work around is to select a different stack and then reselect the one that you want to see.

Spectrum CSV output index as int

Validate Available Flat Stacks are Selected by Default in Open Beam Dropdown on Window Open

Double check that available flat stacks are selected by default in the open beam dropdown, including when the window first opens, even if "flat" doesn't appear in the file name.

Spectrum viewer ROI

Add a Region of Interest rectangle to the image view in the spectrum window.

The spectrum should show the values for the RoI area.

Limit Export to Selected ToF Range

screenshot test

Encapsulate deep calls made from the view through to the SpectrumWidget

Encapsulate deep calls made from the view through to the SpectrumWidget, i.e. self.spectrum.image.setImage in the view would become self.spectrum.set_image() and self.spectrum.spectrum.plot becomes self.spectrum.plot(), etc.

CSV output of normalised spectrum

CSV should have sample, open and normalised values.

Append to CSV file

Spectrum viewer range control

Add a range control to the spectrum.

Update the main view with the selected subset

Multiple ROIs (Umbrella Ticket)

As an instrument Scientist, I want to create multiple ROIs within the spectrum viewer window.
Acceptance Criteria

• #11
• #12
• #13
  • ROI Name
  • ROI line colour using squares e.g. 🟦 🟥 🟩
• ROI names can be changed
• A line is displayed for each ROI in a different colour in the line plot
• ROIs can be removed
• ROIs can be exported to a CSV file
• Documentation exists to describe usage of new functionality added to spectrum viewer window

Current Behaviour

• ROI is not yet a feature

Extra Information

why it is needed?

• Feature requested by user
• Project requirement

Where required files/links are

• GUI
  • Workflow > Spectrum Viewer (Beta) - gui/ui/spectrum_viewer.ui
• Repo gui/windows/spectrum_viewer/
  • model.py
  • presenter.py
  • view.py
  • spectrum_widget.py

Reconstruction Window COR Table:

How to Test

Verbose instructions for the reviewer to test changes
(To be filled out on completion of ticket)

Add image and spectrum views

Add an image view and spectrum viewer to the spectrum viewer dialog.