| Title: | Pre-Process and Extract Flowcam Data |
|---|---|
| Description: | More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description. |
| Authors: | Rainer M. Krug [aut, cre], SNF Project 310030_188431 [fnd] |
| Maintainer: | Rainer M. Krug <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.8.31 |
| Built: | 2024-11-11 05:45:29 UTC |
| Source: | https://github.com/LEEF-UZH/LEEF.measurement.flowcam |
Check if data in input folder is OK and move to raw data folder
add_new_data(input, output)add_new_data(input, output)
input |
The folder, where a folder |
output |
A folder, which contains a subfolder called |
a list which contains the individual reseults for each file.
TRUE if moved, FALSE if an error occured. Details of the eror
re in the error files in the input/flowcam directory.
algae_traits nad calculates densitiesClassify algae_traits nad calculates densities
classify( algae_traits, classifiers_constant, classifiers_increasing, composition, exp_design, species_tracked, timestamp )classify( algae_traits, classifiers_constant, classifiers_increasing, composition, exp_design, species_tracked, timestamp )
algae_traits |
algae_traits |
classifiers_constant |
constant temperature classifier |
classifiers_increasing |
increasing temperature classifier |
composition |
composition |
exp_design |
experimental design |
species_tracked |
species tracked |
timestamp |
timestamp to be used to stamp the classified data |
list containing two objects:
algae_traits including species
algae_densities densities of the differenc particles identifieds
extract data from all *_classes_*_data.csv files
extractor_flowcam(input, output)extractor_flowcam(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
extract data from all *_classes_*_data.csv files
extractor_flowcam_classify(input, output)extractor_flowcam_classify(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
extract data from all *_classes_*_data.csv files
extractor_flowcam_filter(input, output)extractor_flowcam_filter(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
extract data from all *_classes_*_data.csv files
extractor_flowcam_prepare(input, output)extractor_flowcam_prepare(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
file
Load parameter from file
load_parameter(file = "parameter.yaml")load_parameter(file = "parameter.yaml")
file |
name of parameter file |
invisibly TRUE
Name of classifier file for constant temperature treatment
par_classifier_constant(value)par_classifier_constant(value)
Name of classifier file for increasing temperature treatment
par_classifier_increasing(value)par_classifier_increasing(value)
Species tracked
par_species_tracked(value)par_species_tracked(value)
assign the function to a new cvariable and the name of the function woll be used for the parameter name. e.g:
fps <- par_template
par_template(value)par_template(value)
value |
if missing, the value of the parameter will be returned, |
the (new) value of the argument
Convert all .tif files in flowcam folder to zip compressed TIFF.
pre_processor_flowcam(input, output)pre_processor_flowcam(input, output)
input |
directory from which to read the data |
output |
directory to which to write the data |
invisibly TRUE when completed successful
Print the flowcam parameter
print_parameter(print_as_yaml = TRUE, echo = TRUE)print_parameter(print_as_yaml = TRUE, echo = TRUE)
print_as_yaml |
Print in yaml formated text; |
echo |
if the results should be shown on the screen or only the cache returned as a list. |
invisible returns list of parameter for further processing
Check if data in raw data folder is OK
raw_data_ok(input)raw_data_ok(input)
input |
raw data folder containing flowcam data, i.e usually is |
TRUE if ok, FALSE or list of problems if not
## Not run: raw_data_ok() ## End(Not run)## Not run: raw_data_ok() ## End(Not run)
Register the processing of flowcam data in the LEEF package
register()register()
invisibly TRUE when completed successful
.yaml fileSave parameter into .yaml file
save_parameter(file = "parameter.yaml")save_parameter(file = "parameter.yaml")
file |
name of parameter file |
invisibly TRUE