drim2p
A dreamy 2-photon imaging processing pipeline.
Args: verbosity (int, optional): Verbosity level. Level 0 is INFO (default). Level 1 is DEBUG. quietness (int, optional): Quietness level. Level 0 suppresses INFO messages. Level 1 suppresses WARNING messages. no_colour (bool, optional): Whether to disable logging colours.
Usage:
drim2p [OPTIONS] COMMAND [ARGS]...
Options:
-v, --verbose Set verbosity level. Level 0 is INFO (default). Level 1 is
DEBUG.
-q, --quiet Suppress log output. One '--quiet' suppresses INFO messages.
Two '--quiet' and up suppresses WARNING messages.This
overrides verbosity set using '--verbose'.
--no-colour Disable logging colours.
--help Show this message and exit.
Subcommands
- convert: Converts data to HDF5/NWB.
- deltaf: Computes ΔF/F₀ for extracted signals.
- draw: Allows for drawing ROIs on HDF5 dataset.
- extract: Extracts signals.
- motion: Handles motion correction.
drim2p convert
Converts data to HDF5/NWB.
Usage:
drim2p convert [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Subcommands
- raw: Converts RAW data and metadata to HDF5.
drim2p convert raw
Converts RAW data and metadata to HDF5.
Note that SOURCE can be either a single file or a directory. If it is a directory, all the RAW files it contains will be converted.
If '--ini-path' is not provided, it will default to the same path as the source file with the extension changed to '.ini'. If '--xml-path' is not provided, it will default to the same path as the source file with the extension changed to '.xml', and the 'XYT' ending changed to 'OME'. Note the OME-XML path is optional if the INI file contains the OME-XML as an entry.
If generate_timestamps is set, a .notes.txt file with the same name as the RAW
file should also be present.
Usage:
drim2p convert raw [OPTIONS] [SOURCE]
Options:
--ini-path FILE Path to the INI file containing metadata about
SOURCE. This is ignored if SOURCE is a
directory.
--xml-path FILE Path to the OME-XML file containing metadata
about SOURCE. This is ignored if SOURCE is a
directory.
-o, --out DIRECTORY Output directory in which to put the converted
files. Default is to output in the same
directory as SOURCE.
-r, --recursive Whether to search directories recursively when
looking for RAW files.
-i, --include TEXT Include filters to apply when searching for
RAW files. This supports regular-expressions.
Include filters are applied before any exclude
filters.
-e, --exclude TEXT Exclude filters to apply when searching for
RAW files. This supports regular-expressions.
Exclude filters are applied after all include
filters.
-c, --compression [gzip|lzf] Compression algorithm to use.
--aggression INTEGER RANGE Aggression level to use for GZIP compression.
Lower means faster/worse compression, higher
means slower/better compression. Ignored if '
--compression' is not GZIP. [0<=x<=9]
--generate-timestamps Whether to generate timestamps from the notes
entries of the RAW files.
--force Whether to overwrite output files if they
exist.
--help Show this message and exit.
drim2p deltaf
Computes ΔF/F₀ for extracted signals.
Input arrays should be 1- or 2D arrays, where the first dimension is the one along which to compute f₀.
If given a rolling window width, f₀ is computed for each entry along the first dimension of the input array. For values around the edges (within half of window width), the array is padded using the provided method (default is padding with 0s). Because of this, choosing a window that is too large can produce some unexpected values far into the array.
Usage:
drim2p deltaf [OPTIONS] [SOURCE]
Options:
-m, --method [percentile|mean|median]
Computation method for f₀.
-p, --percentile INTEGER Percentile to use when computing f₀ using
the 'percentile' method. Ignored if
computing with a different method.
-w, --window-width INTEGER Rolling window width in frames to use when
computing f₀. Pass 0 to disable it
(default). If greater than 0, the window is
used to compute a running value of f₀ for
each timepoint of the input, with padding
applied according to '--padding' around the
edges. If greater than 0, the rolling window
should be less than twice the size of the
first dimension of the input minus 1.
--padding [constant|reflect|wrap|edge]
Mode to use when padding the input. Ignored
if '--window-width' is 0.
--padding-value INTEGER Constant value to use when padding using
'constant' mode. Ignored if '--padding' is
not 'constant'.
-r, --recursive Whether to search directories recursively
when looking for files.
-i, --include TEXT Include filters to apply when searching for
files. This supports regular expressions.
Include filters are applied before any
exclude filters. They should be a semi-
colon-separated string of filters (e.g.,
'foo;bar' contains two filters, 'foo' and
'bar').
-e, --exclude TEXT Exclude filters to apply when searching for
files. This supports regular expressions.
Exclude filters are applied after all
include filters. They should be a semi-
colon-separated string of filters (e.g.,
'foo;bar' contains two filters, 'foo' and
'bar').
--force Whether to overwrite output files if they
exist.
--help Show this message and exit.
drim2p draw
Allows for drawing ROIs on HDF5 dataset.
Usage:
drim2p draw [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Subcommands
- roi: Starts a napari GUI to draw ROIs on HDF5 datasets.
drim2p draw roi
Starts a napari GUI to draw ROIs on HDF5 datasets.
Note that SOURCE can be either a single file or a directory. If it is a directory, all the HDF5 files it contains will be queued for ROI drawing.
Usage:
drim2p draw roi [OPTIONS] [SOURCE]
Options:
-t, --template FILE Path to the HDF5 file to read default ROIs
from. When provided, any ROIs already
present in the file will be used as the
default ROIs for all SOURCE file. Use in
conjunction with '--force' to overwrite any
existing ROIs with the template ones.
-d, --dataset TEXT Name of the HDF5 dataset to display for ROI
drawing.
-w, --projection-window INTEGER
Window size to use for grouped Z
projections.
-r, --recursive Whether to search directories recursively
when looking for HDF5 files.
-i, --include TEXT Include filters to apply when searching for
HDF5 files. This supports regular-
expressions. Include filters are applied
before any exclude filters.
-e, --exclude TEXT Exclude filters to apply when searching for
HDF5 files. This supports regular-
expressions. Exclude filters are applied
after all include filters.
--lazy Whether to lazily load the file. This will
speed up the GUI startup time but will slow
down any slicing when it is open. This will
also disable themean intensity projection.
--force Whether to ovewrite ROIs if some are found
in SOURCE. Otherwise, ROIs are appended. Be
careful when using this option as it will
lead to all ROIs being deleted when opening
a file.
--help Show this message and exit.
drim2p extract
Extracts signals.
Usage:
drim2p extract [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Subcommands
- signal: Extracts decontaminated signals from ROIs.
drim2p extract signal
Extracts decontaminated signals from ROIs.
Note that SOURCE can be either a single file or a directory. If it is a directory, all the HDF5 files it contains will be converted.
By default, all provided files are treated as separate sessions. In order to process files together, use 'group-by-regex' to group paths together based on a regular expression. If you wish to group all files together, pass an empty string as the regular expression.
Usage:
drim2p extract signal [OPTIONS] [SOURCE]
Options:
--group-by-regex TEXT Regular expression to use when grouping
SOURCEs together. This results in the paths
being preprocessed together based on the
regex. This is ignored if SOURCE is a single
file. Note that using this can lead to a very
high memory usage depending on how many chunks
needs to be loaded. Also note that for
grouping to work, grouped files should have
the same number of ROIs.
-d, --dataset TEXT Name of the HDF5 dataset to display for ROI
drawing.
-r, --recursive Whether to search directories recursively when
looking for HDF5 files.
-i, --include TEXT Include filters to apply when searching for
HDF5 files. This supports regular-expressions.
Include filters are applied before any exclude
filters.
-e, --exclude TEXT Exclude filters to apply when searching for
HDF5 files. This supports regular-expressions.
Exclude filters are applied after all include
filters.
--dont-abort-on-skipped-file Whether to keep working on a group if one or
more of its files is skipped for any reason
(e.g., file was already preprocessed by '--
force' is not set).
--force Whether to overwrite output files if they
exist.
--help Show this message and exit.
drim2p motion
Handles motion correction.
Usage:
drim2p motion [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Subcommands
- correct: Applies motion correction on HDF5 chunks.
drim2p motion correct
Applies motion correction on HDF5 chunks.
The motion correction is configured through a TOML settings file (available from the source code in the resources directory). The file allows customising behaviour such as the strategy to use or the maximum displacement allowed.
Usage:
drim2p motion correct [OPTIONS] [SOURCE]
Options:
-s, --settings-path FILE Path to the settings file to use.
-r, --recursive Whether to search directories recursively when
looking for RAW files.
-i, --include TEXT Include filters to apply when searching for
RAW files. This supports regular-expressions.
Include filters are applied before any exclude
filters.
-e, --exclude TEXT Exclude filters to apply when searching for
RAW files. This supports regular-expressions.
Exclude filters are applied after all include
filters.
-c, --compression [gzip|lzf] Compression algorithm to use.
--aggression INTEGER RANGE Aggression level to use for GZIP compression.
Lower means faster/worse compression, higher
means slower/better compression. Ignored if '
--compression' is not GZIP. [0<=x<=9]
--force Whether to overwrite output datasets if they
exist.
--help Show this message and exit.