Job creation and action scheduling

Create a job, then schedule the desired actions in a job, then run the job.

Quick start example:

from shinestacker import *

job = StackJob("job", "E:/focus_stacking/project_directory/", input_path="tiff_images")
job.add_action(CombinedActions("align", actions=[AlignFrames(), BalanceFrames()]))
job.add_action(FocusStackBunch("batches", PyramidStack(), frames=12, overlap=2))
job.add_action(FocusStack("stack", PyramidStack(), prefix='pyram_'))
job.add_action(FocusStack("stack", DepthMapStack(), prefix='dmap_'))
job.run()

job = StackJob(name, working_path [, input_path])

Arguments are:

  • working_path: the directory that contains input and output images, organized in subdirectories as specified by each action

  • name: the name of the job, used for printout

  • input_path (optional): the subdirectory within working_path that contains input images for subsequent action. If not specified, at least the first action must specify an input_path.

  • callbacks (optional, default: None): dictionary of callback functions for internal use. If equal to 'tqdm', a progress bar is shown in either text mode or jupyter notebook.

  • enabled (optional, default: True): allows to switch on and off all actions within a job.

Schedule multiple actions based on a reference image: align and/or balance images

The class CombinedActions runs multiple actions on each of the frames appearing in a path.

job.add_action(CombinedActions(name, [...], *options))

Arguments for the constructor of CombinedActions are for the :

  • name: the name of the action, used for printout, and possibly for output path.

  • actions: array of action object to be applied in cascade.

  • input_path (optional): the subdirectory within working_path that contains input images to be processed. If not specified, the last output path is used, or, if this is the first action, the input_path specified with the StackJob construction is used. If the StackJob specifies no input_path, at least the first action must specify an input_path.

  • output_path (optional): the subdirectory within working_path where aligned images are written. If not specified, it is equal to name.

  • working_path (optional): the directory that contains input and output image subdirectories. If not specified, it is the same as job.working_path.

  • plot_path (optional, default: plots): the directory within working_path that contains plots produced by the different actions.

  • resample (optional, default: 1): take every nth frame in the selected directory. Default: take all frames.

  • reference_index (optional, default: 0): the index of the image used as reference. Images are numbered starting from one to N. -1 is interpreted as the last image, 0 as the median index.

  • step_process (optional): if equal to True (default), each image is processed with respect to the previous or next image, depending if its file is placed in alphabetic order after or befor the reference image.

  • enabled (optional, default: True): allows to switch on and off this module.

  • scratch_output_dir (optional, default: True): scratch output directory before processing. This avoids that existing files pollute the output.

  • delete_output_at_end (optional, default: False): delete output after processing. This cleans disk space in case of processing an intermediate step that is not part of the final output.

  • max_threads (optional, default: 2): number of parallel processes allowed. The number of actual threads will not be greater than the number of available CPU cores.

  • chunk_submit (optional, default: True): submit at most max_threads parallel processes. If chunk_submit is greater than max_threads a moderate performance gain is achieved at the cost of a possibly large memory occupancy.