New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Export to omero #210

Merged

jburel merged 12 commits into ome:master from will-moore:export_to_omero

Jun 13, 2017

Member

will-moore commented Apr 27, 2017 •

edited

Loading

Allows export of a figure as new OMERO Images (one per page).

This is a preliminary part of https://trello.com/c/qqpED5kE/129-export-as-movie

To test:

Choose "New OMERO Image" from the export options drop-down menu
Export the figure... when done, should see a link to the new Image.
Image will be named according to figure name and have the figure legend as it's description (if legend exists).
Multi-page figures should create an Image per page, named ..._page_01 etc.

NB: I'll need to upload the figure export script before this is tested...

will-moore added 5 commits

April 26, 2017 12:34


          Initial support for export-to-OMERO in script and UI

3998c01


          Export script returns new OMERO image

6d07fc8


          New OMERO Image link displayed on script finished in UI

197fe4b


          Export image into Dataset in correct group

fcf28a0

Also handle multiple page figures


          flake8 fixes

7cce2d4

Member

jburel commented Apr 28, 2017

omero_api_IScript_ice.py", line 909, in runScript
    return _M_omero.api.IScript._op_runScript.invoke(self, ((scriptID, inputs, waitSecs), _ctx))
ValidationException: exception ::omero::ValidationException
{
    serverStackTrace = 
    serverExceptionClass = 
    message = Invalid parameters:
VALUE LIST for "Export_Option": OMERO not in ['PDF', 'PDF_IMAGES', 'TIFF', 'TIFF_IMAGES']

Member Author

will-moore commented Apr 28, 2017

Ah, yes, I needed to update the script on eel.... Done now, and seems to be working.

snoopycrimecop mentioned this pull request

Page colour #211

Merged

Member

jburel commented May 1, 2017

Did some initial tests the creation works fine
I have not tested yet the multi-pages situations,
Image from plate will always be orphaned, we should probably rethink that section

Member Author

will-moore commented May 2, 2017

@jburel If none of the images from the figure are in a Dataset then new image will simply be an orphan. I'm not sure there's a better way to handle that, but an orphaned image is not a major problem. I mostly assume people aren't using HCS images to make figures, and also the 'export to OMERO' is mostly meant for showing your figure alongside the images in a Dataset, so HCS users can't do that anyway.

will-moore added 3 commits

May 2, 2017 16:00


          Use try/except to import numpy

2309f90

Since we only use numpy for OMERO export, this means the script can
still be used for other export if we happen to be missing numpy


          Export script handles missing images (image is None)

bf9b3be


          Provide more info and url in new image description

3660fba

Member Author

will-moore commented May 2, 2017

Improved new image description. If the figure is saved, description will have a link to the figure, so you can find the figure from the image.


          flake8 fix

33ec09b

jburel reviewed

View reviewed changes

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py Outdated

		@@ -60,6 +60,11 @@
		logger.error("Reportlab not installed. See"

Member

jburel May 3, 2017

The message should be reviewed since we no longer recommend to install from pypi

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py Outdated

@@ @@ -60,6 +60,11 @@ @@
                   logger.error("Reportlab not installed. See"
                                " https://pypi.python.org/pypi/reportlab/")
+              try:

Member

jburel May 3, 2017

unlike since it is a dependency we already have for omero

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py Outdated

                       self.save_figure()
                       # PDF will get created in this group
                       if group_id is None:
                           group_id = self.conn.getEventContext().groupId
                       self.conn.SERVICE_OPTS.setOmeroGroup(group_id)
+                      file_ann = self.create_file_annotation(image_ids)

Member

jburel May 3, 2017

no real to assign file_ann can do return self.create_file_annotation(image_ids)

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py Outdated

+                  def save_page(self, page=None):
+                      """
+                      Save the current PIL image page as a new OMERO images and start a new

Member

jburel May 3, 2017

new OMERO image no s

omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py

@@ @@ -1616,7 +1697,8 @@ def run_script(): @@
                   """
                   export_options = [rstring('PDF'), rstring('PDF_IMAGES'),
-                                    rstring('TIFF'), rstring('TIFF_IMAGES')]
+                                    rstring('TIFF'), rstring('TIFF_IMAGES'),
+                                    rstring('OMERO')]

Member

jburel May 3, 2017

better to be explicit in the option i.e. OMERO_IMAGES

Member Author

will-moore May 3, 2017

For the others PDF_IMAGES/ TIFF_IMAGES means create a zip file with the Figure as a PDF/TIFF and include all the rendered images in the figure as TIFFs (so you have a record of how the figure was created on export and you can use them to tweak the figure later). We don't need to support the equivalent option for export to OMERO.

Member

jburel May 3, 2017

it was just to be more explicit

omero_figure/templates/figure/index.html Outdated

@@ @@ -758,6 +759,11 @@ <h4 class="modal-title">Open</h4> @@
                                               <span class="glyphicon glyphicon-ok" style="color:#333; visibility:hidden"></span>
                                               TIFF with images</a>
                                           </li>
+                                          <li><a href="#" data-export-option="to OMERO"
+                                                  title="Export as an Image in OMERO">

Member

jburel May 3, 2017

Image(s)

Member

jburel commented May 3, 2017

Export of figure with multiple pages generates as expected the corresponding number of images in OMERO

The color of the button during the generation is modified, but having a spinner will be clearer in general since the generation could take some time

will-moore added 2 commits

May 3, 2017 12:05


          Revert "Use try/except to import numpy"

8835b05

This reverts commit 2309f90.


          Fixed suggestions from PR 210

a47f0db

Member Author

will-moore commented May 3, 2017

@jburel Addressed those suggestions.

Member Author

will-moore commented May 3, 2017

I can look into showing a spinner during export, but I wouldn't want it to hold up this PR since it's not related to this PR and this PR is conflicting with #211

Member

jburel commented May 3, 2017

I will not do that in that PR. I will add a card on the priorities board


          Show spinner for 'Exporting Figure'

e32835b

Member Author

will-moore commented May 3, 2017

Ah, I just pushed a commit for that:

Member

jburel commented May 3, 2017

looks better thanks

Member Author

will-moore commented May 9, 2017

@jburel - If this can be merged I can fix and re-open #211, thanks.

jburel merged commit cb9299f into ome:master

jburel added this to the 3.1.0 milestone

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet