make_lsm_df: Make summary dataframe for lsm files and their key metadata

In jefferislab/jimpipeline: Package to wrap Jefferis lab image processing / registration pipeline

Description

Make summary dataframe for lsm files and their key metadata

Usage

make_lsm_df(lsmdir, oldlsmdf = NULL, extrafields = NULL, Verbose = TRUE)

Arguments

lsmdir	Path to directory containing lsm files
oldlsmdf	Dataframe or path to rda file containing one
extrafields	Function to parse extra fields from metadata for each image
Verbose	Logical: Show messages about progress/updating of cached data

Details

Will calculate md5 sums for all input files and then use this to update a dataframe.

If an extrafields function is supplied, it should take one parameter, the list output of parse_key_lsm_metadata, which will include as an attribute the full contents of the metadata file dumped by the loci showinf tool. The function should take care to return values for all fields that it could return each time it is called even if these are NA and to ensure that values have a consistent data type per field.

Value

dataframe

See Also

lsm_metadata, parse_key_lsm_metadata

jefferislab/jimpipeline documentation built on Sept. 14, 2020, 3:41 p.m.