flim.core package¶
Submodules¶
flim.core.analysisgraph module¶
Created on Fri Dec 4 09:25:32 2020
@author: khs3z
- class flim.core.analysisgraph.AnalysisNode(layer, config)¶
Bases:
flim.core.analysisgraph.BasicNode- apply()¶
- create_graph()¶
- get_graph()¶
- get_outputs()¶
- set_inputs(inp)¶
- class flim.core.analysisgraph.CreateColumn(layer, config)¶
Bases:
flim.core.analysisgraph.AnalysisNode- apply()¶
- class flim.core.analysisgraph.DataNode(layer, data, description)¶
- class flim.core.analysisgraph.Merge(layer, config)¶
Bases:
flim.core.analysisgraph.AnalysisNode- apply()¶
- flim.core.analysisgraph.next_nodeid()¶
flim.core.analyzer module¶
Created on Fri May 4 19:37:11 2018
@author: khs3z
- class flim.core.analyzer.dataanalyzer¶
Bases:
object- add_filters(newfilters)¶
- add_rangefilters(newfilters)¶
- apply_filter(data, dropna=True, onlyselected=True, inplace=True, dropsonly=False)¶
- categorize_data(data, col, bins=[- 1, 1], labels='1', normalizeto={}, grouping=[], dropna=True, use_minvalue=False, joinmaster=True, add_ascategory=True, category_colheader='Category')¶
- columns_available(data, args)¶
- get_analysis_function(analysis_name)¶
- get_analysis_options()¶
- get_config()¶
- get_filters()¶
- get_rangefilters()¶
- set_rangefilters(newfilters)¶
- set_seriesfilter(newseriesfilter)¶
flim.core.calculator module¶
flim.core.configuration module¶
Created on Thu Jul 5 12:45:21 2018
@author: khs3z
- class flim.core.configuration.Config¶
Bases:
object- create_default()¶
- fix()¶
- get(searchkey=None, startin=None, returnkeys=False)¶
- get_keys(startin=None)¶
- get_nodekeys()¶
- get_parent(searchkey, parameters=None, returnkeys=False)¶
- is_modified()¶
- is_not_None(searchkeys)¶
- is_valid()¶
- read_from_json(configfile, defaultonfail=True)¶
- remove(searchkey)¶
- update(parameters, parentkeys=None, addmissing=True)¶
- validate()¶
- write_to_json(configfile)¶
flim.core.filter module¶
Created on Fri May 18 07:53:29 2018
@author: khs3z
- class flim.core.filter.Filter(name, selected=False, params=None, descr='')¶
Bases:
object- apply(data)¶
- get_description()¶
- get_dropped(data)¶
- get_name()¶
- get_params()¶
- is_selected()¶
- select(sel=True)¶
- set_name(newname)¶
- set_parameter_item(key, value)¶
- set_params(params)¶
- class flim.core.filter.RangeFilter(name='', rangelow=0, rangehigh=100, allowedmin=None, allowedmax=None, selected=False, dropna=True, params=None)¶
Bases:
flim.core.filter.Filter- apply_filter(data, inplace=True)¶
- clip_range()¶
- get_dropped(data)¶
- get_params()¶
- get_range()¶
- get_rangehigh()¶
- get_rangelow()¶
- is_identical_range(rlow, rhigh)¶
- set_allowed(mina, maxa)¶
- set_params(params)¶
- set_range(low, high)¶
- set_rangehigh(high)¶
- set_rangelow(low)¶
- class flim.core.filter.SeriesFilter(*args, **kwargs)¶
Bases:
flim.core.filter.Filter
flim.core.importer module¶
Created on Fri May 4 02:53:40 2018
@author: khs3z
- class flim.core.importer.dataimporter¶
Bases:
object- add_files(files, extensions=['.txt', '.csv'], exclude=None, sort=True)¶
- get_config()¶
- get_delimiter()¶
- get_excluded_files()¶
- get_files()¶
- get_parser()¶
- get_preprocessor()¶
- get_reserved_categorycols(parser=None)¶
- import_data(delimiter=None, parser=None, preprocessor=None, nrows=None)¶
- remove_allfiles()¶
- remove_files(rfiles)¶
- set_column_combos(combolist)¶
- set_delimiter(delimiter)¶
- set_excluded_files(exclude)¶
- set_files(files, extensions=['.txt', '.csv'], exclude=None, sort=True)¶
- set_parser(parser)¶
- set_preprocessor(preprocessor)¶
flim.core.parser module¶
Created on Fri May 4 04:02:09 2018
@author: khs3z
- class flim.core.parser.celltype_compartment_fov_treatment_cell_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
- class flim.core.parser.compartment_fov_treatment_cell_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
- class flim.core.parser.compartment_treatment_fov_cell_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
- class flim.core.parser.defaultparser¶
Bases:
object- compile_patterns()¶
- get_config()¶
- get_name()¶
- get_regexpatterns()¶
- init_patterns()¶
- is_readonly()¶
- parsefilename(fname)¶
- set_regexpatterns(patterns)¶
- class flim.core.parser.fov_time_well_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
- class flim.core.parser.fov_treatment_cell_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
- flim.core.parser.get_available_parsers(pkdir='core.parser')¶
- flim.core.parser.instantiate_parser(fullname)¶
- class flim.core.parser.no_parser¶
Bases:
flim.core.parser.defaultparser- parsefilename(fname)¶
- set_regexpatterns(patterns)¶
- class flim.core.parser.treatment_fov_cell_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
- class flim.core.parser.treatment_fov_time_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
- class flim.core.parser.treatment_time_parser¶
Bases:
flim.core.parser.defaultparser- init_patterns()¶
flim.core.plots module¶
Created on Sat May 5 14:53:15 2018
@author: khs3z
- flim.core.plots.bindata(binvalues, binedges, groupnames)¶
- flim.core.plots.fix_label(label)¶
- flim.core.plots.grouped_boxplot(ax, data, column, title=None, groups=[], dropna=True, pivot_level=1, **kwargs)¶
- flim.core.plots.grouped_kdeplot(ax, data, column, title=None, groups=[], dropna=True, linestyles=None, pivot_level=1, **kwargs)¶
- flim.core.plots.grouped_meanbarplot(ax, data, column, title=None, groups=[], dropna=True, pivot_level=1, **kwargs)¶
- flim.core.plots.grouped_meanbarplot_new(ax, data, column, groups=[], dropna=True, pivot_level=1, **kwargs)¶
- flim.core.plots.grouped_scatterplot(ax, data, combination, title=None, groups=[], dropna=True, pivot_level=1, **kwargs)¶
- flim.core.plots.histogram(ax, data, column, title=None, groups=[], normalize=None, titlesuffix=None, **kwargs)¶
- flim.core.plots.normalize(value, totalcounts)¶
- flim.core.plots.stacked_histogram(ax, data, column, title=None, groups=[], minx=None, maxx=None, normalize=None, **kwargs)¶
flim.core.preprocessor module¶
Created on Fri May 4 05:16:56 2018
@author: khs3z
- class flim.core.preprocessor.defaultpreprocessor(calculator=None)¶
Bases:
object- calculate(data, inplace=True)¶
- columns_available(data, args)¶
- drop_columns(data, drops=None, func='contains', dropemptyheader=True, inplace=True, preview=False)¶
- get_config()¶
- get_replacementheaders()¶
- rename_headers(data, newheaders=None, preview=False)¶
- reorder_columns(data, first=[])¶
- set_dropcolumns(cols)¶
- set_replacementheaders(headers)¶
- flim.core.preprocessor.nadh_perc(nadph_perc)¶
- flim.core.preprocessor.nadph_perc(nadph_t2)¶
- flim.core.preprocessor.percentile(n)¶
- flim.core.preprocessor.ratio(v1, v2)¶
- flim.core.preprocessor.tm(a1perc, t1, a2perc, t2)¶
- flim.core.preprocessor.trp_Eperc_1(trp_tm, const=3100)¶
- flim.core.preprocessor.trp_Eperc_2(trp_t1, trp_t2)¶
- flim.core.preprocessor.trp_Eperc_3(trp_t1, const=3100)¶
- flim.core.preprocessor.trp_r(trp_Eperc)¶
flim.core.tools module¶
Created on Fri May 4 02:42:45 2018
@author: khs3z
- class flim.core.tools.FLIMAnalyzer(importer=<flim.core.importer.dataimporter object>, preprocessor=<flim.core.preprocessor.defaultpreprocessor object>, danalyzer=<flim.core.analyzer.dataanalyzer object>, executor=<class 'prefect.executors.local.LocalExecutor'>, execargs='', **kwargs)¶
Bases:
object- get_analyzer()¶
- get_data()¶
- get_executor()¶
- get_importer()¶
- get_preprocessor()¶
- set_analyzer(anl)¶
- set_importer(imp)¶
- set_outputgenerator(og)¶
- set_preprocessor(pp)¶
- flim.core.tools.noninteractive_test(fa, logger, args)¶
- flim.core.tools.parse_arguments()¶