Contents
38. OMERO.figure
To test in: Web
Purpose of the test is to check that the OMERO.figure as an OMERO.web application is functioning correctly.
The redeployment of the daily CI servers currently causes the external scripts to be lost. If you need to test the export script, you can reupload it as follows where servername and JOB_NAME need to be replaced:
$ ssh <servername> $ cd /home/hudson/OMERO.webapps/figure/scripts $ eval $(bash /home/hudson/ice/ice-multi-config.sh ice35) $ /home/hudson/<jobname>/bin/omero login root@<servername> -w omero $ /home/hudson/<jobname>/bin/omero script upload omero/figure_scripts/Figure_To_Pdf.py --official
See also
- Deployment servers
Table of the contributing documentation listing the servers and their corresponding deployment job.
Go to https://<servername>.openmicroscopy.org/merge/webclient/, login to the webclient then click on Figure in top toolbar to open OMERO.figure in another tab.
This first series of tests checks that saved and unsaved changes are not lost inadvertantly. Creating unsaved figure can be easily done by adding a single image to a new figure (note an image ID from the webclient). If you need to make more changes, simply copy, paste and move or edit the panel.
38.1. Saving files to OMERO
Test that saved figures are not lost
Select images in the webclient -> Open with (in tree OR right panel) -> OMERO.figure. This will open OMERO.figure in a new tab, adding the images to the figure. Try to include big images in the various testing scenarios.
Check that the ‘Save’ button becomes enabled, indicating you have an unsaved figure.
Save the figure (click ‘Save’ button or Menu: File > Save) and choose a figure name. ‘Figure1’
Check that the ‘Save’ button becomes disabled and the url updates with the figure ID.
Check that you can refresh your browser without any message popup and the figure is refreshed (not lost)
Copy the url, then navigate to the webclient and logout. Open new window and paste the url.
Check that after login, you are redirected to the saved figure.
Make another change to ‘Figure1’ and Save. Go to File > New. Add an Image (copy image URL from webclient and paste into the Add Images dialog) and Save ‘Figure2’.
Check that no popup messages asked you to save.
Check that File > Open > Figure1 shows your latest changes to Figure1 (no ‘save’ popups)
Check that hitting the back button takes you to your saved Figure2 (no ‘save’ popups)
Test that unsaved changes are not lost on existing figures
Open a saved figure, make some changes without saving. Try to refresh the browser, navigate to webclient or close browser window.
Check that you get a “Leave Page” or “Stay on Page” alert (or equivalent).
Check that choosing “Stay on page” cancels and returns to page, allowing Save.
Check that choosing “Leave Page” results in losing of unsaved changes (when you return).
Again, open saved figure and make some unsaved changes. Try to create new file: File > New.
Check that you get a “Save”, “Don’t Save” or “Cancel” dialog.
Check that “Cancel” returns you to the figure.
Check that “Don’t Save” continues with the New File without saving.
Check that “Save” continues with the New File and the unsaved changes are saved.
Check that saving the New figure creates a NEW figure and does not overwrite the previous figure.
Again, open saved figure and make some unsaved changes. Try to open figure: File > Open.
Check that you get a “Save”, “Don’t Save” or “Cancel” dialog before the ‘Open Figure’ list.
Check that these choices work as described above.
Open a saved figure, then open another saved figure and make some unsaved changes.
Now try hitting the browser ‘Back’ button.
Check that the url reverts to the first figure and you get a “Save” or “Don’t Save” dialog.
Check that “Don’t Save” results in the loss of your unsaved changes.
Check that “Save” does save the changes, when you return to the figure (using Forward button).
Test that unsaved changes on a NEW figure are not lost
Open a new figure, make some changes without saving.
Try to refresh the browser, navigate to webclient or close browser window.
Check that you get a “Leave Page” or “Stay on Page” alert (or equivalent).
Check that choosing “Stay on page” cancels and returns to page, allowing Save.
Check that choosing “Leave Page” results in losing of unsaved changes.
Again, open new figure and make some unsaved changes.
Try to create new file: File > New
Check that you get a “Save”, “Don’t Save” or “Cancel” dialog.
Check that “Cancel” returns you to the figure.
Check that “Don’t Save” continues with the New File without saving.
Check that “Save” opens a ‘Enter Figure Name’ dialog.
Check that a new figure is created with the chosen name and no changes are lost.
Again, open new figure and make some unsaved changes.
Try to open figure: File > Open
Check that you get a “Save”, “Don’t Save” or “Cancel” dialog before the new figure is started.
Check that these choices work as described above.
Open a saved figure, then open a new figure and make some unsaved changes. Now try hitting the browser ‘Back’ button.
Check that the url reverts to the first figure and you get a “Save” or “Don’t Save” dialog.
Check that “Don’t Save” results in the loss of your unsaved changes.
Check that “Save” does save the changes, when you return to the new figure (using File > Open).
Test renaming figures in the top toolbar.
Open a new figure, add a panel and edit the figure name by clicking where name usually appears.
Check that name is displayed when Enter is pressed or field loses focus.
Check that when figure is saved, suggested name is already filled in
Enter Figure Namedialog.Check that File > Open shows correct name in files list.
Check that renaming figure again and Save updates the name in the
File > Openlist
Additional tests below are for less critical features
Select
File > Delete a Figure.Check that when you try to delete couple of figures in a row, the workflow makes sense.
Select
File > Opento open an existing figure.Check that you can sort the file list by name and date.
Check that files can be filtered by name.
Check that only files you own are shown by default.
Check that you can choose to show other users’ files or ‘All files’.
Check that clicking on a Figure name opens the figure.
Check that there is a name of the Figure which is on display above the canvas.
Check that exported PDF or TIFFs are linked to images they contain. Export a PDF or TIFF of a figure. Click image urls in the PDF to open in webclient.
Check that these images are annotated with the PDF.
Check that the PDF also contains a link to the figure url itself.
Check that export to New OMERO Image creates a new image, and link appears when export is done.
38.2. Layout of image panels, paper setup
Add several images (all same width and height) to a new Figure.
Check that when you paste a non-existent ID or URL, you get a warning message
Check that added panels are laid out as a grid that fills the width of the paper and all are selected.
Check that delete key removes selected panels.
Check that delete button in top toolbar removes selected panels.
Check that delete button is only enabled when one or more panels are selected.
De-select panels by clicking on empty canvas space. Select by clicking/dragging on panels:
Check that single click on a panel selects only that panel (other de-selected).
Check that shift-click adds panel to selection (others not de-selected).
Check that dragging-selection, starting on empty space, selects all panels covered by selection.
Check that shift dragging adds selected panels to selection (others not de-selected).
Move and resize panels by dragging and keys:
Check that click -> drag on unselected panel selects it and starts drag.
Check that click -> drag on selected panel / panels moves them without changing selection.
Check that up, down, left, right keys nudge all selected panels in the correct direction.
Check that dragging on corner handles resizes all selected panels, maintaining width/height ratio.
Check that dragging on side handle stretches width or height alone.
Align selected images with toolbar buttons:
Check that alignment buttons are only enabled when more than one panel is selected.
Check that ‘align left’ aligns all selected panels to the left-most selected panel.
Check that ‘align to grid’ snaps all selected panels to grid, starting at top-left panel.
Check that ‘align top’ aligns all selected panels to the top-most selected panel.
Resize selected images with toolbar buttons:
Check that ‘align sizes’ (width, height and width and height) resize all panels to match the dimensions of top-left selected panel.
Check that ‘Align Magnification’ resizes selected panels so that the scalebars in the all the selected panels have either equal, or proportional apparent length to the scalebar in the top-left panel. For example if top-left panel displays a scalebar representing 10 microns, all the selected images with scalebars representing 10 microns should have the same apparent length as the one in top-left panel after the alignment of magnification. The scalebars representing 100 microns in the other images should appear as being 10 times longer than the top-left image scalebar and so on.
Copy and Paste duplicate panels into grid layout:
Check that copy and paste works with keyboard short-cuts.
Check that copy and paste works with Menu items: Edit -> Copy/Paste.
Check that copy and paste of a ‘column’ of panels duplicates it to the right.
Check that copy and paste of a ‘row’ of panels duplicates it to the bottom.
Test paper setup. Click File -> Paper Setup:
Check that Number of Pages, Size and Orientation are shown correctly.
Check that changing the number of pages updates the figure.
Check that changing the page size updates pages in the figure.
Check that changing Orientation switches the width and height corretly.
Check that choosing Size > crop page… crops page to fit panels and will reduce multi-page figures to single page.
Check that setting the page color works as expected.
Finally, export to PDF and TIFF - Check that layout corresponds to web UI. - Check that each page of multi-page figure has correct panels, page color, labels and scalebars.
38.3. Preview Tab - Z/T and rendering
Add image with multiple Z sections. Select panel and ‘Preview’ tab:
Check that Z slider is shown beside viewer in Preview tab.
Check that current Z / total Z numbers are shown at bottom of slider.
Check that sliding Z updates Z number while sliding.
Check that when sliding stops, Preview viewer and selected panel update.
Check that Undo/Redo toggles to the previous Z-section.
Check that clicking the ^ and v buttons increment Z by 1, but stops at 1 or sizeZ.
Copy and paste to duplicate image with multiple Z sections. Adjust Z on ONE of them, then select both:
Check that Z slider is shown and is enabled.
Check that current Z is - / total Z at bottom of slider.
Check that clicking the ^ and v buttons increment Z by 1 (Z still different between panels)
Check that sliding Z updates Z number while sliding.
Check that when sliding stops, Preview viewer and selected panel update.
Check that current Z number is now shown (both panels same Z)
Check behaviour of T-slider is same as Z-slider for all tests above.
Check that for images that have timestamp data, time in hrs:mins:secs is shown while sliding.
Select 2 images with different number of Z-sections.
Check that Z-slider is disabled.
Select 2 images with different number of T-sections.
Check that T-slider is not disabled, but T-section is restricted to smaller sizeT.
Select a panel with multiple Z, note Z-section, turn on Z-projection:
Check that Z slider has 2 handles, +/- 2 from previous Z-section.
Check that Preview viewer and selected panel show Z-projected images.
Check that current Z-range is shown: start-end / total Z at bottom of slider.
Check that clicking the ^ and v buttons increment Z-start and stop by 1.
Check that dragging each slider updates start or end of Z-range.
Check that turning Z-projection off returns to single Z-selection.
Check that single Z-selection is mid-way between Z-start and end when projection is toggled.
Check that range of Z-start to Z-end is maintained when projection is toggled.
Select a multi-channel image:
Check that the channels are shown as ‘toggle’ buttons beside Preview viewer.
Check that channels can be turned on and off by clicking toggle buttons.
Check that Preview viewer and selected panel images are updated.
Check that Channel color can be changed via drop-down button beside toggle buttons.
Check that Invert option works in the channel color drop-down.
Check that Color-picker option launches color-picker and this works OK.
Check that Lookup tables work as expected.
Check that Channel sliders behave as expected and update viewer and panel on stop.
Check that you can enter numbers into the Channel start/end fields and slider updates accordingly.
Select multiple images with the same channel count.
Check that channel ON/OFF and color changes are applied to all selected images.
Turn a channel ON in one panel and OFF in another. Select both.
Check that if toggling the channel turns it ON in all selected panels.
Change channel color in one panel and select both.
Check that a ‘null’ grey color is shown on the toggle button.
Check that picking a new color is applied to all selected panels.
Change channel sliders start/end to different values in different panels. Select both.
Check that start/end numbers are replaced by - where values are not same in all panels.
Check that changing start/end values applies to all panels and value replaces -.
Select multiple images with different channel counts.
Check that channel toggle buttons and channel sliders are not shown.
Finally, export to PDF and TIFF
Check that layout corresponds to web UI and check that rendering settings, LUTs, Invert etc. look right.
Check that each page of multi-page figure has correct panels, labels and scalebars.
38.4. Preview Tab - Zoom, pan and rotation
All behaviours below need to be tested on Big (tiled) images and small images.
Test behaviour of Zoom and Pan. Select a panel.
Check that changing Zoom slider updates viewer while sliding.
Check that stop of Zoom slider updates selected panel too.
Check that dragging the viewer image pans the viewer.
Check that when dragging ends, the selected panel updates too.
Check that Zooming back out to 100% resets the panning to zero offset.
Check that max zoom level is appropriate for images of different sizes.
Test cropping to region. Select one or more panels and click the crop button below zoom slider.
Check that a dialog opens showing image at current Z/T with the current crop region shown.
Check that a region can be drawn on the image by click and drag.
Check that the region can be manipulated by dragging corner or side handles or the whole region.
Check that clicking OK crops the selected panels to the chosen region, keeping within existing boundaries.
Check that clicking Reset button restores the shape of the panel to the shape of the image and sets Zoom at 100%.
Test crop to ROI. Choose a timelapse image that has multiple Rectangular ROIs in OMERO. Select several panels from the same Timepoint. Click crop button.
Check that the crop dialog loads and shows Rectangle ROIs from OMERO with Z and T indices.
Check that clicking ROIs shows them in the dialog viewer, updating to the correct Z/T plane.
Check that choosing a single-Rectangle ROI updates all seleced panels to the shape of the selected ROI and to the Z and T indices on which this ROI is drawn.
Check that if panels with a range of Timepoints are selected, the T value is not changed.
Test rotation of panels.
Check that rotation slider is shown when rotation icon clicked.
Check that while sliding rotation, viewer is updated.
Check that when rotation sliding stops, selected panel updates too.
Check that rotation of the image is centered on the centre of the viewer.
Zoom and drag to pan the rotated image in the viewer.
Check that the zooming and panning behaves correctly.
Check that additional rotation is centered on the new centre.
Test rotation with multiple panels selected.
Check that rotation and zoom sliders show average values.
Check that update to zoom syncronises zoom but not panning in selected panels.
Check that update to rotation syncronises rotation in selected panels.
Check that dragging on viewer image pans to same spot for all selected panels.
Finally, export to PDF and TIFF to check that it looks same
38.5. Labels Tab
Test adding a scalebar. Add an image that does NOT have pixel size metadata. Select the image and the Labels tab.
Check that pixel size is ‘NOT SET’.
Check that pixel size can be edited by clicking on it, editing and ‘Enter’.
Check that selecting an image WITH pixel size metadata, it is shown correctly.
Check that clicking ‘Show’ adds a scalebar to selected panel.
Check that editing the length, position $ color of the scalebar update scalebar on selected panel.
Test scalebar label.
Check that clicking ‘Label’ on the scalebar dialog adds a label above scalebar on the figure panel.
Check that a font-size widget appears in the scalebar form.
Check that choosing a different font-size for the label updates the label in the selected panel.
Check that unchecking / rechecking ‘Label’ checkbox hides and shows the label.
Check that moving scalebar to top left or right of panel shifts label below the scalebar.
Test units display and conversion. You need an image that has different units for pixel size. See https://docs.openmicroscopy.org/latest/omero/developers/Python.html#create-image and look for “Set the pixel size using units” for how to edit this.
Check that the unit of pixel size is shown in the scalebar dialog.
Check that the unit is also shown on scalebar labels.
Check that saving figure and refreshing the page preserves units display.
Check that ‘Align magnification’ conversion works correctly when images with different units are chosen.
Select multiple panels, with some showing, some NOT showing scalebars.
Check that clicking “Show” adds scalebar to all panels.
Select multiple panels, with scalebars of different lengths / location / color / label / font-size
Check that editing scalebar length / location / color / label / font-size applies change to all selected panels.
Check that zooming of the image (in Preview tab) updates scalebar size accoringly.
Test manual adding labels to one or more panels.
Select an image and enter some text in the ‘Add Labels’ form. Hit Enter.
Check that label is added to the selected image with default parameters.
Check that choosing different font-sizes / position are shown in new labels.
Check that color-picker works for picking label color.
Check that adding a white label outside the panel creates a Black label.
Check that multiple labels added to a single position are stacked in rows.
Check that markdown syntax works for italic and bold fonts in labels.
Test creating labels from metadata to one or more panels. Select ‘Image Name’ from the drop-down option under ‘Label’ field.
Check that new label is created with Image name.
Check that new label can also be created with ‘Dataset Name’.
Check that ‘Tags’ option creates new labels from Tags on each selected image.
Create new labels from ‘Channels’ option.
Check that labels are only created from active channels.
Check that labels are colored according to channel color.
Add a time-lapse image with time-stamp info, E.g. DV movie.
Check that ‘Time’ drop-down options are only enabled if timestamp info exists.
Check new labels created with ‘Time’ add correctly formatted time label to each panel.
Check that scrolling through time (in Prevew tab) updates timestamp labels on each panel.
Test editing existing labels on multiple panels.
Check that identical labels on multiple panels are combined under ‘Edit Labels’ (no duplicates).
Check that editing all labels update labels on selected panels.
Check that Time-stamp labels can be updated for Size, Color and Position without affecting time shown.
Finally, export to PDF and TIFF to check that all labels and scalebars looks the same as in web.
Check that the PDF includes a note about the length of scalebars in the figure.
Check that scalebar labels appear the same in the PDF as in the web figure.
38.6. ROIs
Test drawing of ROIs.
Check that ROI viewer is launched when the ‘Draw’ button is clicked.
Check that you can choose shape type with the toolbar buttons.
Check that you can draw a Rectangle, Ellipse, Line and Arrow.
Check that holding down Shift key while creating/updating shapes constrains shape to cicle, rectangle, or horizontal/vertical line.
Check that you can tweak the last-drawn shape while still adding more shapes (without switching to select mode).
Check that Select mode allows you to select single shapes with click, multiple shapes with drag.
Check that currently selected shape(s) color and line width are shown in toolbar (or defaults are chosen if not the same in all shapes).
Check that changing the color and line width updates the currently selected shapes.
Check that selected shapes can be copied, pasted and deleted using Edit menu or keyboard shortcuts.
Check that clicking OK closes the dialog and updates the figure with shapes.
Test loading ROIs from OMERO by clicking Load ROIs in ROIs dialog, using a multi-plane image with a number of different ROI shapes on it (Ellipse, Rectangle, Line, Arrow, Polyline, Polygon).
Check that Load ROIs button is disabled if image has no ROIs in OMERO.
Check that clicking button loads and displays ROIs from OMERO.
Check that hovering over each Shape shows it temporarily on the image.
Check that clicking on a Shape in the list moves the image to the corresponding Z/T index.
Check that clicking Add adds the shape to the image and selects it.
Check that added shapes can be edited (drag, resize, color, line-width) including Polyline and Polygon.
Check that saving figure and refreshing correctly reloads all shapes.
Copy and Paste ROIs.
Draw some ROIs in the ROI dialog, OK to close.
Check that the number of ROIs in selected panels is shown at top of Labels tab.
Check that you can now copy all the ROIs on the panel with the Copy button.
Check that you can paste ROIs onto another panel (or panels).
Check that you can also Delete all ROIs on selected panels with the Delete button.
Check that you can use the Colour and Line width choosers on the ROI controls on the Labels tab to apply chosen colour or line width to all shapes in selected panels.
Copy and Paste crop region.
Check that the View x, y, width height update in the Preview tab when you zoom and pan the viewport.
Check that you can copy the crop region and paste onto another panel / panels.
Check that multiple selected panels with different view regions show ‘-’ for x, y, width, height.
Check that the “Crop” button launches the crop dialog and the “Reset” button reverts to uncropped panel.
Copy ROIs Rectangle -> Crop region.
Duplicate a panel by copying and pasting the panel
Copy a single Rectangle on the first panel by opening the ROI viewer, selecting/drawing a rectangle and ‘Copy’.
Check that clicking Paste in the Preview tab crops the other panel.
Check that crop region matches the region highlighted by the rectangle in first panel.
Copy Crop region -> Rectangle.
Again, copy and paste a panel to duplicate and zoom and pan one panel to chosen viewport.
Copy the view region by clicking Copy in the View section of the Preview tab, select the other panel and click Paste under the ROI header of Labels tab.
Check that a new Rectangle ROI is created and this corresponds to the viewport region of the other panel.
Check that you can then update the colour / line width of this rectangle using the ROI color and line width controls.
Crop dialog using regions from Clipboard or ROIs on the image
Copy some ROIs (including Rectangle(s)) to the clipboard.
Open the Crop dialog (green button) on an image that has some Rectangular ROIs drawn on it.
Check that you can pick regions from the clipboard or from ROIs on the image and use these to crop the image.
Check that if you are cropping an image that has ROIs on it, you are asked if you want to remove these ROIs when you crop it.
Check that clicking Yes, No or Cancel on this dialog has the expected effect.
Finally, export to PDF and TIFF to check that ROIs look the same as in web UI.
Check that rotated images have ROIs showing in correct location on export.
Check that multi-page figures have ROIs in correct location on all pages.
38.7. Info Tab
Test Info for a single panel. Select panel and click the ‘Info’ tab.
Check that Image Name is shown at the top of Info tab.
Check that other metadata (sizes and channels) are shown and correct.
Check that clicking ‘Show in webclient’ shows image in new tab.
Check that resizing or moving panel updates x, y, width, height while dragging.
Check that DPI value is updated while resizing.
Test Info for a multiple panels.
Check that number of panels selected is shown in place of Name.
Check that clicking ‘Show in webclient’ shows images in new tab.
Check that metadata is shown only if it is same in all panels.
Check that x, y, width, height are shown only if same in all panels.
Check that DPI is shown only if same in all panels.
Test Open-with with one or more images selected.
Check that single image can be opened in webclient and Image viewer (and iviewer if installed).
Check that multiple selected images can be opened in Webclient (both selected if in same Dataset) and iviewer.
Test Editing the ID for multiple panels. Copy and paste panels to create multiple panels from the same Image.
Check that ‘Edit ID’ button is only enabled if all selected panels have the same Image ID.
Pick another similar image in webclient. Note ID. Select multiple panels with same ID and click ‘Edit ID’. Enter new image ID.
Check that ‘Preview’ is only enabled when valid ID is entered.
Check that clicking ‘Preview’ displays new image thumbnail and other metadata.
Check that Green/Red flags are shown where x, y, z, c, t matches.
Check that warning are shown below in Red if new image has fewer timepoints / channels than selected panels.
Check that other mismatches are shown as Green messages.
Click ‘Update’ to replace selected panels with new image.
Check that Timepoints and Channels are preserved but Z-indecies are not.
Test setting the panel x, y, width and height on a multi-page figure.
Check that x and y coordinates apply to the page that the panel is on.
Check that setting x and y for muliple panels on different pages works as expected.
Check that setting width and height of panels works.
Check that the aspect ratio can be preserved by clicking to link width and height.
Test the display and update of panel resolution (dpi).
Check that the ‘dpi’ is displayed for each panel and updates when zoomed or resized.
Check that the “Set dpi” button allows you to choose a min and max dpi for export in the pop-up.
Check that you can change the max dpi (a valid number is required) but setting min dpi is optional.
Check that if the export dpi is shown in the Info tab if different from the default dpi.
Check that you can remove the minimum export dpi with the X button.
Check that if the export dpi is expected to be > 300 that the image appears interpolated, not pixelated.
Finally, export to PDF and TIFF to check that it looks the same as the web UI.
Check that dpi is as expected in exported PDFs using Adobe Illustrator and https://web.archive.org/web/20200223222335/http://swainhart.org/how-to-check-the-dpi-of-an-image-in-adobe-illustrator-cs5/.
Check that export ‘with images’ includes extra folders with images that have been interpolated (this will be all images for TIFF export).
38.8. Export Options
There are 4 export options: PDF, PDF with Images, TIFF and TIFF with images. Choose each in turn and export:
Check that the TIFFs or PDF figures look the same as they do in the web.
Check that when ‘with Images’ option is chosen, the export should produce a zip containing 3 directories of images (original, pre-resampled and final). Images named the same in each directory should show progression of processing.
Check that single page figures produce a single TIFF image download when ‘TIFF’ (no images) is chosen.
Check that multi-page figures produce a zip of TIFFs (one per page) with a PDF ‘info’ page.