Export scripts

Batch Image Export

This script takes a number of images and saves individual image planes in a zip file for download.

Batch_Image_Export.compress(target, base)

Creates a ZIP recursively from a given base directory.

Parameters

  • target – Name of the zip file we want to write e.g. “folder.zip”

  • base – Name of folder that we want to zip up E.g. “folder”

Batch_Image_Export.log(text)

Adds the text to a list of logs. Compiled into text file at the end.

Batch_Image_Export.make_image_name(original_name, c_name, z_range, t, extension, folder_name)

Produces the name for the saved image. E.g. imported/myImage.dv -> myImage_DAPI_z13_t01.png

Batch_Image_Export.run_script()

The main entry point of the script, as called by the client via the scripting service, passing the required parameters.

Batch_Image_Export.save_as_ome_tiff(conn, image, folder_name=None)

Saves the image as an ome.tif in the specified folder

Batch_Image_Export.save_plane(image, format, c_name, z_range, project_z, t=0, channel=None, greyscale=False, zoom_percent=None, folder_name=None)

Renders and saves an image to disk.

Parameters

  • image – The image to render

  • format – The format to save as

  • c_name – The name to use

  • z_range – Tuple of (zIndex,) OR (zStart, zStop) for projection

  • t – T index

  • channel – Active channel index. If None, use current rendering settings

  • greyscale – If true, all visible channels will begreyscale

  • zoom_percent – Resize image by this percent if specified

  • folder_name – Indicate where to save the plane

Batch_Image_Export.save_planes_for_image(conn, image, size_c, split_cs, merged_cs, channel_names=None, z_range=None, t_range=None, greyscale=False, zoom_percent=None, project_z=False, format='PNG', folder_name=None)

Saves all the required planes for a single image, either as individual planes or projection.

Parameters

  • renderingEngine – Rendering Engine, NOT initialised.

  • queryService – OMERO query service

  • imageId – Image ID

  • zRange – Tuple: (zStart, zStop). If None, use default Zindex

  • tRange – Tuple: (tStart, tStop). If None, use default Tindex

  • greyscale – If true, all visible channels will be greyscale

  • zoomPercent – Resize image by this percent if specified.

  • projectZ – If true, project over Z range.

Batch ROI Export

This script exports ROI intensities for selected images.

Batch_ROI_Export.add_shape_coords(shape, row_data, pixel_size_x, pixel_size_y, include_points=True)

Add shape coordinates and length or area to the row_data dict.

Batch_ROI_Export.batch_roi_export(conn, script_params)

Main entry point. Get images, process them and return result.

Batch_ROI_Export.get_export_data(conn, script_params, image, units=None)

Get pixel data for shapes on image and returns list of dicts.

Link the File Annotation to each object.

Batch_ROI_Export.log(data)

Handle logging or printing in one place.

Batch_ROI_Export.run_script()

The main entry point of the script, as called by the client.

Make Movie