Introduction
Some tasks are included in the Anchor distribution, to be easily
run from the command-line with -t taskname
, and are termed predefined tasks.
Tip: See Example Usage for step-by-step guides on using these tasks. A good starting point!
Listing available predefined tasks
To list the names of all available predefined tasks, type in a shell either:
anchor -st
oranchor -t
(without an argument)
A user can extend the available predefined tasks, by adding BeanXML to the /config/tasks
subdirectory in an Anchor distribution.
How to run a predefined task
To run a task, open a shell (e.g. Command Prompt
or Powershell
in Windows), change to a directory with images, and then:
Next, consider enabling additional outputs with the -o
options or refining your
inputs with the -i
options.
Tip: In Windows, hold the shift key when right-clicking on a folder in Windows Explorer to open a Command Prompt or Powershell in that folder.
See some Quick Start - Example Commands and the following tables for guidance.
Image processing
Task Name | Input Type | Description |
---|---|---|
histogram | images | extracts histograms of the intensity values an image. |
resize | images | scales each image to fit inside fixed dimensions, preserving aspect ratio. Optionally accepts -ps. |
center | images | like resize but uses a common output size for all images, and centers within it. Optionally accepts -ps. |
Image segmentation
Task Name | Input Type | Description |
---|---|---|
segment/coco | images | instance segmentation based on 80 MSCOCO object categories. |
segment/text | images | finds text-regions in images. |
Feature extraction
Task Name | Input Type | Description |
---|---|---|
feature/hog | images | extracts a HOG feature descriptor for all images. |
feature/intensity | images | extracts statistics of pixel values. |
feature/metadata | images | extracts basic metadata as features, including dimensions. |
Clustering
Task Name | Input Type | Description |
---|---|---|
cluster/timestamp | any files | clusters files by timestamp (from (from EXIF, file attributes or naming). |
File copying / conversion
Task Name | Input Type | Description |
---|---|---|
anonymize | any files | copies files, randomizing order and hiding the original naming. |
convert | images | converts the file format** of input images. |
copy | any files | copies files, preserving naming and subdirectory structure. |
Montages
Task Name | Input Type | Description |
---|---|---|
montage | images | creates a montage that balances available space. |
montage/balance | images | identical to above. |
montage/table | images | creates a montage that imposes a table structure. |
montage/slices | images | creates a montage of all z-slices in a 3D image. |
Summarizing inputs
Task Name | Input Type | Description |
---|---|---|
count | any files | counts the number of input-files. |
list | any files | shows a line inputName -> inputPath for each input. |
list/names | any files | shows each input’s name on a separate line. |
list/paths | any files | shows each input’s path on a separate line. |
summarize | images | combines the summaries in summarizeImages and summarizePaths |
summarize/images | images | summarizes image attributes (dimensions, bit depth etc.) |
summarize/paths | any files | summarizes file attributes (size, patterns among the file-paths etc.) |
Projections across images
Task Name | Input Type | Description |
---|---|---|
project/mean | images | creates a mean-intensity projection of all inputs. |
project/meanResize | images | scales inputs to a constant size, then the mean projection. |
project/max | images | creates a maximum-intensity projection of all inputs. |
project/maxResize | images | scales inputs to constant size, then the max projection. |
project/min | images | creates a minimum-intensity projection of all inputs. |
project/minResize | images | scales inputs to constant size, then the mean projection. |
project/standardDeviation | images | creates a standard-deviation projection of all inputs. |
project/standardDeviationResize | images | scales inputs to constant size, then the above projection. |