Skip to content

Latest commit

 

History

History
243 lines (199 loc) · 7.04 KB

TODO-BDV.md

File metadata and controls

243 lines (199 loc) · 7.04 KB
Raw

BDV processing-options-class TODO

/!\ WARNING /!\

When the auto-loader is used, view enumeration in BigStitcher is based on metadata, for example the first channel in a ligthsheet dataset might then be called Channel 488 instead of Channel 1 or Channel 0.

-> It's actually very difficult to forsee this properly, upfront image metadata inspection would be required to do this!

In case the manual loader is used, view enumeration follows the file naming pattern, e.g. the file name for the first tile and first channel would read myimage_tile0_channel1.

-> In that case, tile enumeration starts at zero while channel enumeration starts at one!

Options

First options block: "what to process"

The first options block is selecting which parts of the h5/xml dataset will be processed.

This block is relevant for most of our BDV functions:

  • resave_as_h5
  • flip_axes
  • phase_correlation_pairwise_shifts_calculation
  • filter_pairwise_shifts
  • optimize_and_apply_shifts
  • detect_interest_points
  • interest_points_registration
  • duplicate_transformations
  • fuse_dataset

Valid choices are:

  • [All Xs]
  • [Single X (Select from List)]
  • [Multiple Xs (Select from List)]
  • [Range of Xs (Specify by Name)]

With X being one of angle, channel, illumination, tile, timepoint.

Second options block: details for "what to process"

The second options block is required for each component having selected anything other than All Xs in the in the first options block.

  • For Single X (Select from List) the required option is processing_X=[X n], e.g. processing_channel=[channel 1] for [Single channel (Select from List)].
  • For Multiple Xs (Select from List) the required options are X_n X_m, e.g. channel_1 channel_3 for [Multiple channels (Select from List)].
  • For Range of Xs (Specify by Name) the required option is process_following_X=n-m, e.g. process_following_channels=1-3 for [Range of channels (Specify by Name)].

Third options block: "how to treat"

The third options block selects how the components will be processed.

This options block is relevant for some of our BDV functions, for example:

  • phase_correlation_pairwise_shifts_calculation
  • optimize_and_apply_shifts

Valid choices are:

  • [treat individually]
  • group
  • compare

Fourth options block: details for "how to treat"

The fourth option block is required for each component that has group as their setting in the third options block. Exceptions are when e.g. the dataset only has a single illumination (then nothing illumination-related needs to be put into the fourth block, even if group was selected in the third block), or if the first block already restricted the used data to a single item (for example Single channel (Select from List) was selected in block 1, then nothing channel-related is required in block 4).

Valid choices are:

  • Average Ys
  • Use Y n

With Y being one of Angle, Channel, Illumination, Tile, Timepoint. Note the difference in uppercase / lowercase compared to the X from blocks 1 and 2!

Examples

Example 1

Selected options:

  • First block:
    • Process angle: all angles
    • Process channel: all channels
    • Process illumination: all illuminations
    • Process tile: all tiles
    • Process timepoint: all Timepoints
  • Second block:
    • (N/A)
  • Third block:
    • How to treat Angles: treat individually
    • How to treat Channels: group
    • How to treat Illuminations: group
    • How to treat Tiles: compare
    • How to treat Timepoints: treat individually
  • Fourth block:
    • [use Channel 1]

Resulting macro parameters:

process_angle=[All angles]
process_channel=[All channels]
process_illumination=[All illuminations]
process_tile=[All tiles]
process_timepoint=[All Timepoints]
method=[Phase Correlation]
show_expert_grouping_options
how_to_treat_angles=[treat individually]
how_to_treat_channels=group
how_to_treat_illuminations=group
how_to_treat_tiles=compare
how_to_treat_timepoints=[treat individually]
channels=[use Channel 1]

Example 2

Selected options:

  • First block:
    • Process angle: All angles
    • Process channel: Single channel (Select from List)
    • Process illumination: all illuminations
    • Process tile: all tiles
    • Process timepoint: all Timepoints
  • Second block:
    • Processing channel: channel 1
  • Third block:
    • How to treat Timepoints: treat individually
    • How to treat Channels: group
    • How to treat Illuminations: group
    • How to treat Angles: treat individually
    • How to treat Tiles: group
  • Fourth block:
    • [use Tile 3]
process_angle=[All angles]
process_channel=[Single channel (Select from List)]
process_illumination=[All illuminations]
process_tile=[All tiles]
process_timepoint=[All Timepoints]
processing_channel=[channel 1]
method=[Phase Correlation]
show_expert_grouping_options
how_to_treat_timepoints=[treat individually]
how_to_treat_channels=group
how_to_treat_illuminations=group
how_to_treat_angles=[treat individually]
how_to_treat_tiles=group
tiles=[use Tile 3]

Example 3

Selected options:

  • First block:
    • Process angle: All angles
    • Process channel: Multiple channels (Select from List)
    • Process illumination: all illuminations
    • Process tile: all tiles
    • Process timepoint: all Timepoints
  • Second block:
    • Processing channel: channel_n channel_m etc
  • Third block:
    • How to treat Timepoints: treat individually
    • How to treat Channels: group
    • How to treat Illuminations: group
    • How to treat Angles: treat individually
    • How to treat Tiles: compare
  • Fourth block:
    • Average Channels
process_angle=[All angles]
process_channel=[Multiple channels (Select from List)]
process_illumination=[All illuminations]
process_tile=[All tiles]
process_timepoint=[All Timepoints]
channel_1
channel_2
method=[Phase Correlation]
show_expert_grouping_options
how_to_treat_timepoints=[treat individually]
how_to_treat_channels=group
how_to_treat_illuminations=group
how_to_treat_angles=[treat individually]
how_to_treat_tiles=compare
channels=[Average Channels]

Example 4

  • First block:
    • Process angle: All angles
    • Process channel: Range of channels (Specify by Name)
    • Process illumination: all illuminations
    • Process tile: all tiles
    • Process timepoint: all Timepoints
  • Second block:
    • Processing following channels: n-m, e.g. 1-3
  • Third block:
    • How to treat Timepoints: treat individually
    • How to treat Channels: group
    • How to treat Illuminations: group
    • How to treat Angles: treat individually
    • How to treat Tiles: compare
  • Fourth block:
    • Average Channels
process_angle=[All angles]
process_channel=[Range of channels (Specify by Name)]
process_illumination=[All illuminations]
process_tile=[All tiles]
process_timepoint=[All Timepoints]
process_following_channels=1-3
method=[Phase Correlation]
show_expert_grouping_options
how_to_treat_timepoints=[treat individually]
how_to_treat_channels=group
how_to_treat_illuminations=group
how_to_treat_angles=[treat individually]
how_to_treat_tiles=compare
channels=[Average Channels]