Opened 5 years ago

Closed 5 years ago

#791 closed enhancement (fixed)

Upload microscope images in the histology scoring wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v3.4
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

We should implement an image upload feature in the Histology scoring wizard.

  • The interface should be quick and simple. If possible a drag-and-drop solution should be used that automatically uploads an image to the currently active histology item.
  • An image preview should be displayed in a reasonable size.
  • The glass slides view should have markers indicating if an image is attached or not.
  • PNG/JPG should be accepted (maybe TIFF, but that should be converted to PNG/JPG on the fly before it is saved on the server).
  • The images should be saved in a dedicated BASE filesystem folder which should maybe divided into subfolders (similar to how it is done in the secondary analysis). The images are linked with the histology items using AnyToAny links.

Change History (8)

comment:1 Changed 5 years ago by Nicklas Nordborg

Milestone: Reggie v3.xReggie v3.4
Status: newassigned

comment:2 Changed 5 years ago by Nicklas Nordborg

(In [3367]) References #791: Upload microscope images in the histology scoring wizard

Started to implement this feature. Histology samples are checked if the have an existing image (eg. an AnyToAny link with name "image" that is leading to a FILE item).

Existing images are displayed in a preview area located to the right of the HE slides. The image can be clicked to open the full version in a popup window.

Drag-and-drop has been implemented for JPG and PNG images. The images are loaded and displayed in the preview area.

Uploading/saving to the BASE server is not yet implemented.

comment:3 Changed 5 years ago by Nicklas Nordborg

(In [3368]) References #791: Upload microscope images in the histology scoring wizard

Implemented uploading to the BASE server. The image is uploaded and saved immediately when it has been dropped. The preview is updated to load the image from the server.

The upload/preview seems to be quick enough to not require any progress bar...

The root folder for uploded images is /home/SCANB/HistologyImages. Subdirectories are created automatically using the same pattern as in the secondary analysis. For example, the image for a sample with name 1105094.1.his.he1 ends up in the file /home/SCANB/HistologyImages/11/1105/1105094.1.his.he1.jpg

comment:4 Changed 5 years ago by Nicklas Nordborg

(In [3369]) References #791: Upload microscope images in the histology scoring wizard

  • Add support for selecting image file using the regular file upload dialog (click instead of drag-and-drop).
  • Added delete icon for deleting an existing image
  • Zoom popup now tries to use the real image width/height when opening the popup
  • The original file name is saved in the description field

comment:5 Changed 5 years ago by Nicklas Nordborg

(In [3372]) References #791: Upload microscope images in the histology scoring wizard

Added support for uploading TIF images (which will automatically be converted to JPG on the server).

Added an 'Uploading...' animation. Mainly needed when converting a TIF to JPG. A short delay is deliberately introduced on the server so that it doesn't just flash by which can be annoying for the user.

comment:6 Changed 5 years ago by Nicklas Nordborg

(In [3373]) References #791: Upload microscope images in the histology scoring wizard

Added link to the histology image in the case summary wizard.

comment:7 Changed 5 years ago by Nicklas Nordborg

(In [3374]) References #770 and #791. The retraction wizard (destruction step) will now check all items for outgoing AnyToAny links. Mainly to find files that are linked to various items (eg. histology images).

Files with have set the "write protected" flag are a bit tricky since they are not possible to delete and re-setting the flag doesn't update the permissions unless DbControl.reattachItem() is called.

comment:8 Changed 5 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
Note: See TracTickets for help on using tickets.