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Print functions list, as requested in #11
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,148 @@ | ||
| To gain access to more advanced features of OMERO | ||
| from within a macro, put the following line at the | ||
| beginning of your macro: | ||
| ``` | ||
| run("OMERO Extensions"); | ||
| ``` | ||
| This will enable the following macro functions: | ||
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| ### Handles connection (should be used first/last) ### | ||
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| Ext.connectToOMERO(host, port, username, password) | ||
| > Connects to the given OMERO `host` (and `port`) | ||
| > using the provided `username` and `password`. | ||
| Ext.disconnect() | ||
| > Disconnects from the server. | ||
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| ### Changes the context for other commands ### | ||
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| Ext.switchGroup(groupId) | ||
| > Switches to the given group on OMERO. | ||
| Ext.listForUser(username) | ||
| > Filters listings to only include data from the given user. | ||
| Ext.sudo(username) | ||
| > Runs subsequent commands as the specified user, | ||
| > if the logged-in user has sudo rights. | ||
| Ext.endSudo() | ||
| > Switches back to the logged-in user. | ||
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| ### Retrieves data from OMERO ### | ||
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| Ext.list(type) | ||
| > Gets the IDs for objects of the given `type`, | ||
| > separated by commas. | ||
| Ext.list(type, name); | ||
| > Gets the IDs for objects with the given `type` and `name`, | ||
| > separated by commas. | ||
| Ext.list(type, parentType, parentId) | ||
| > Gets the IDs for objects of the given `type` | ||
| > inside a parent container with type `parentType` and ID `parentId`, | ||
| > separated by commas. | ||
| Ext.getName(type, id) | ||
| > Gets the name of the specified object, given its `type` and `id`. | ||
| Ext.getImage(id) | ||
| > Opens the image with the given `id`. | ||
| > Returns the image ID in ImageJ. | ||
| Ext.getROIs(imageId, toOverlay, property) | ||
| > Retrieves the ROIs for the image with the given `imageId`. | ||
| > These are added to the ROI manager by default. | ||
| > | ||
| > If `toOverlay` (optional) is true, | ||
| > they are added to the overlay instead. | ||
| > | ||
| > Moreover, shapes from 3D/4D ROIs will share the same values | ||
| > in the "ROI" and "ROI_ID" properties. | ||
| > The properties names can be optionally changed: | ||
| > `property` will store local indices, | ||
| > while `property + "_ID"` will store OMERO IDs. | ||
| > | ||
| > Returns the number of ROIs in ImageJ. | ||
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| ### Saves data ### | ||
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| Ext.createTag(name, description) | ||
| > Creates a new tag with the given `name` and `description`. | ||
| > Returns the new tag ID. | ||
| Ext.createProject(name, description) | ||
| > Creates a new project with the given `name` and `description`. | ||
| > Returns the new project ID. | ||
| Ext.createDataset(name, description, projectId) | ||
| > Creates a new dataset with the given `name` and `description`, | ||
| > inside the project with the specified `projectId`. | ||
| > Returns the new dataset ID. | ||
| Ext.importImage(datasetId) | ||
| > Saves the current image to the dataset with the given `datasetId`. | ||
| > Returns the new image ID. | ||
| Ext.saveROIs(imageId, property) | ||
| > Saves ImageJ ROIs to the image with the given `imageId` on OMERO. | ||
| > The (optional) `property` is used to group ImageJ shapes | ||
| > into a single 3D/4D ROI in OMERO. | ||
| > The default value for this (if empty or absent) is "ROI". | ||
| > | ||
| > Returns the number of 3D/4D ROIs saved to OMERO. | ||
| Ext.addFile(type, id, path) | ||
| > Attach a file on the given `path` | ||
| > to the object with the given `type` and `id` on OMERO. | ||
| > Returns the new file ID. | ||
| Ext.link(type1, id1, type2, id2) | ||
| > Links two objects together, using their types and IDs. | ||
| > The order does not matter. | ||
| > Possible types are: | ||
| > * Project and Dataset | ||
| > * Dataset and Image | ||
| > * Tag and Project, Dataset or Image | ||
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| ### Removes data on OMERO ### | ||
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| Ext.unlink(type1, id1, type2, id2) | ||
| > Unlinks two objects, using their types and IDs (see `link`). | ||
| Ext.delete(type, id) | ||
| > Deletes the object with the given `type` and `id` from OMERO. | ||
| Ext.deleteFile(id) | ||
| > Delete the attached file with the given `id` on OMERO. | ||
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| ### Table functions ### | ||
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| Ext.addToTable(tableName, resultsName, imageId, roiProperty) | ||
| > Creates or updates a local table using ImageJ results, where: | ||
| > * `tableName` is the name of the table | ||
| > * `resultsName` (optional) is the IJ results name | ||
| > * `imageId` (optional) is the image ID on OMERO | ||
| > * `roiProperty` (optional) is the ROI property used | ||
| > for grouping 2D shapes in 3D/4D ROIs. | ||
| > | ||
| > If ROIs that were saved to OMERO are in the ROI Manager | ||
| > and if their name appears in the labels | ||
| > or is in a column named "ROI", they will be added too. | ||
| Ext.saveTable(tableName, type, id) | ||
| > Saves the table with the name `tableName` to OMERO, | ||
| > and attaches it to the object with the given `type` and `id`. | ||
| Ext.saveTableAsFile(tableName, path, delimiter) | ||
| > Saves the table to a delimited text file locally (`path`). | ||
| > The default separator is ',' but can be changed with | ||
| > the optional `delimiter`. |
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