Add possibility to Import Links

[stefanhahmann]

User Story

The importer currently lets users import spots from a simple and commonly used csv file into Mastodon. This way, users can use Mastodon’s visualization and analysis tools.

The figure shows where to find the CSV importer

Currently, users can select a .csv file from the file system. The importer displays the first line (aka header) of the file and lets users choose the correct order for the columns (like x, y, z, frame, label) without having to modify the csv file.

However, the “CSV Importer” can only import spots. It can’t handle links or cell divisions, which makes it very difficult to import anything that has been tracked outside of Mastodon. It may be be beneficial, if the functionality of importing links would be implemented into the CSV importer.

The figure shows the CSV importer in action and the result (unlinked spots)

Tasks:

• [x] Decide
  • [ ] ~Whether the initial import dialog as extended with a second file (for the links) ~
  • [ ] ~Whether there will be a separate import dialog that is just for links~
  • [x] Whether the links can be contained in a "parent" column
• [x] Add a new dialog section, where a selection of link source (i.e. parent) can be specified, similar to the existing column choices for spots

[tinevez]

A CSV file is not suitable for links. I would recommend relying on the GraphML format instead.

[stefanhahmann]

A CSV file is not suitable for links. I would recommend relying on the GraphML format instead.

But this is how I imported these data sets into Mastodon: https://github.com/mastodon-sc/mastodon-example-data/tree/master/astec

• 1 CSV file with Spots
• 1 CSV file for links (cf. https://github.com/mastodon-sc/mastodon-deep-lineage/blob/master/src/test/java/org/mastodon/mamut/astec/AstecReader.java)

GraphML is also a good idea, but it is more difficult to communicate, which attributes, we expect to be set in the GraphML file.

[tinevez]

Ok this is convincing. A good test would be to see whether we can reimport fully the CSV files generated with the CSV export of the table views.

[stefanhahmann]

A good test would be to see whether we can reimport fully the CSV files generated with the CSV export of the table views.

Exactly. Johannes, who was asking for this feature, and I had the same idea.

[tinevez]

Would you have a smallish couple of CSV files I could play with?

[stefanhahmann]

Yes. This Zip-File contains a spot.csv and a matching links.csv

Pm01.zip

If imported correctly, the result should be close to https://github.com/mastodon-sc/mastodon-example-data/blob/master/astec/Pm01.mastodon

I did the import using https://github.com/mastodon-sc/mastodon-deep-lineage/blob/master/src/test/java/org/mastodon/mamut/astec/AstecReader.java

[stefanhahmann]

Here is a 2nd example: Pm02.zip

After import, it should be similar to https://github.com/mastodon-sc/mastodon-example-data/blob/master/astec/Pm02.mastodon

[stefanhahmann]

However, these file have not been created with the Mastodon CSV export.

[stefanhahmann]

A good test would be to see whether we can reimport fully the CSV files generated with the CSV export of the table views.

Exactly. Johannes, who was asking for this feature, and I had the same idea.

Re-importing the CSV files produced with the Mastodon CSV Export function, is actually a bit harder, since these files have 3 header lines instead of only 1.

[stefanhahmann]

Resolved via #16