import os from core.modules.basic_modules import File, Directory, new_constant from core.modules.module_registry import get_module_registry from core.modules.vistrails_module import Module, ModuleError, ModuleConnector reg = get_module_registry() RSource = \ reg.get_descriptor_by_name('edu.utah.sci.vistrails.rpy', 'RSource').module RFigure = reg.get_descriptor_by_name('edu.utah.sci.vistrails.rpy', 'RFigure', 'Figures').module def create_file_module(fname, f=None): if f is None: f = File() f.name = fname f.upToDate = True return f def create_dir_module(dname, d=None): if d is None: d = Directory() d.name = dname d.upToDate = True return d def get_path(fname=''): return os.path.join(os.path.dirname(__file__), fname) def build_params(input_ports, remap={}): def get_name(port): if port in remap: return remap[port] return port params = ",\n".join(["%s=%s" % (get_name(port[0]), get_name(port[0])) for port in input_ports if port[0] not in remap.keys() or (port[0] in remap.keys() and remap[port[0]] is not None)]) return params def processActivePortData(inputPorts, object): portData = [] if object.hasInputFromPort('stem.globals'): stemGlobals = object.getInputFromPort('stem.globals') else : stemGlobals = None for port in inputPorts: if port[0] != 'stem.globals' and object.hasInputFromPort(port[0]) and object.getInputFromPort(port[0]) is not None: portData.append((port[0], port[0])) if port[1] == '(edu.utah.sci.vistrails.basic:Directory)' or port[1] == '(edu.utah.sci.vistrails.basic:File)': object.set_variable(port[0], object.getInputFromPort(port[0]).name) else: object.set_variable(port[0], object.getInputFromPort(port[0])) elif stemGlobals: if stemGlobals.global_vars.has_key(port[0]) and stemGlobals.global_vars[port[0]] is not None: portData.append((port[0], port[0])) return portData class STEMConfiguration(RSource): _input_ports = [] _output_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')] def compute(self): self.chdir(get_path()) self.run_file(get_path('STEM_Configuration.R'), excluded_outputs=set(['config'])) self.setResult('config', self) class RunModels(RSource): _input_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)'), ('spp.name', '(edu.utah.sci.vistrails.basic:String)'), ('spp.common', '(edu.utah.sci.vistrails.basic:String)')] _output_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')] def compute(self): self.chdir(get_path()) self.set_variable('spp.dir.name', self.getInputFromPort('spp.name')) self.run_file(get_path('STEM_ModelingEngine.R'), excluded_inputs=set(['source', 'config']), excluded_outputs=set(['config'])) self.setResult('config', self.getInputFromPort('config')) class BuildVisualizations(RSource): _input_ports = [('config', '(edu.cornell.birds.stem:STEMConfiguration)')] _output_ports = [('results.dir', '(edu.utah.sci.vistrails.basic:Directory)')] def compute(self): self.chdir(get_path()) self.run_file(get_path('STEM.nfold.pp.comp_2.12.10.R'), excluded_inputs=set(['source', 'config']), excluded_outputs=set(['results.dir'])) dname = list(self.get_variable('results.dir'))[0] self.setResult('results.dir', create_dir_module(dname)) class STEMFigure(RFigure): """Write only the R figure code. You do not need the png or pdf graphics setup code or the dev.off calls""" _input_ports = [('results.dir', '(edu.utah.sci.vistrails.basic:Directory)', ), ('pp.metric', '(edu.utah.sci.vistrails.basic:String)')] def compute(self): self.chdir(get_path()) self.set_variable('results.dir', self.getInputFromPort('results.dir').name) self.run_figure_file(get_path('STEM_Figure.R'), 'png', 800, 600, excluded_inputs=set(['source', 'results.dir'])) # class STEMCreateData(Module): # """Data preparation""" # def compute(self): # self.run_file(get_path('STEM.erd.data.creation.R')) class STEMGlobals(RSource): _input_ports = [('debugOutput', '(edu.utah.sci.vistrails.basic:Boolean)'), ('platform', '(edu.utah.sci.vistrails.basic:String)'), ('parent.dir', '(edu.utah.sci.vistrails.basic:Directory)'), ('code.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('species.name', '(edu.utah.sci.vistrails.basic:String)'), ('common.name', '(edu.utah.sci.vistrails.basic:String)'), ('erd.data.file', '(edu.utah.sci.vistrails.basic:File)'), ('srd.pred.design.file', '(edu.utah.sci.vistrails.basic:File)')] _output_ports = [('self', '(edu.cornell.birds.stem:STEMGlobals)')] def compute(self): # run the requires and the loading of STEM libs parent_dir = self.getInputFromPort('parent.dir') self.chdir(self.getInputFromPort('code.directory').name) self.set_variable('parent.dir', parent_dir.name) # FIXME code.directory defaults to parent.dir if not self.hasInputFromPort('code.directory'): self.set_variable('code.directory', parent_dir.name) else: self.set_variable('code.directory', self.getInputFromPort('code.directory').name) self.set_variable('erd.data.filename', ''.join([parent_dir.name, "Data/", self.getInputFromPort('erd.data.file').name])) self.set_variable('srd.pred.design.filename', ''.join([parent_dir.name, "Data/", self.getInputFromPort('srd.pred.design.file').name])) species_name = self.getInputFromPort('species.name') stem_directory = create_dir_module(os.path.join(parent_dir.name, species_name)) self.set_variable('stem.directory', stem_directory.name) self.set_variable('species.name', species_name) self.set_variable('common.name', self.getInputFromPort('common.name')) # FIXME add erd.data.filename and srd.pred.design.filename # No tags needed, then self.run_code(''.join(["source(\"", "STEM_Globals.R", "\")"]), excluded_inputs=set(['source', 'parent.dir', 'code.directory', 'erd.data.file', 'srd.pred.design.file'])) # FIXME need to actually use and output the globals global_var_list = ['debugOutput', 'platform', 'parent.dir', 'code.directory', 'species.name', 'common.name', 'erd.data.filename', 'srd.pred.design.filename', 'stem.directory', 'spatial.extent.list', 'temporal.extent.list', 'predictor.names', 'response.family', 'cv.folds', 'cv.folds.par.list', 'cv.list', 'stem.init.par.list', 'base.model.par.list', 'srd.max.sample.size', 'split.par.list', 'st.matrix.name', 'jdate.seq', 'year.seq', 'conditioning.vars', 'st.matrix.ave.maps', 'begin.seq', 'end.seq', 'pred.grid.size', 'map.plot.width', 'spatial.extent.list', 'z.max', 'z.min', 'map.tag', 'date.bar', 'print.date', 'county.map', 'county.map.lwd', 'state.map', 'state.map.lwd'] self.global_vars = dict((name, self.get_variable(name)) for name in global_var_list) class InitERDMapAnalysis(RSource): _input_ports = [('project.directory', '(edu.utah.sci.vistrails.basic:String)'), ('species.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'), ('map.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'), ('map.file.nametag', '(edu.utah.sci.vistrails.basic:String)'), ('map.rows', '(edu.utah.sci.vistrails.basic:Integer)'), ('z.max', '(edu.utah.sci.vistrails.basic:Float)'), ('z.min', '(edu.utah.sci.vistrails.basic:Float)'), ('map.number', '(edu.utah.sci.vistrails.basic:Integer)'), ('lat.max', '(edu.utah.sci.vistrails.basic:Float)'), ('lat.min', '(edu.utah.sci.vistrails.basic:Float)'), ('lon.max', '(edu.utah.sci.vistrails.basic:Float)'), ('lon.min', '(edu.utah.sci.vistrails.basic:Float)')] _output_ports = [('self', '(edu.cornell.birds.stem:InitERDMapAnalysis)')] def compute(self): # run the requires and the loading of STEM libs self.chdir(self.getInputFromPort('project.directory')) self.set_variable('project.directory', self.getInputFromPort('project.directory')) self.set_variable('species.directory.nametag', self.getInputFromPort('species.directory.nametag')) self.set_variable('map.directory.nametag', self.getInputFromPort('map.directory.nametag')) self.set_variable('map.file.nametag', self.getInputFromPort('map.file.nametag')) self.set_variable('map.rows', self.getInputFromPort('map.rows')) self.set_variable('z.max', self.getInputFromPort('z.max')) self.set_variable('z.min', self.getInputFromPort('z.min')) self.set_variable('map.number', self.getInputFromPort('map.number')) latMax = self.getInputFromPort('lat.max') if latMax: self.set_variable('lat.max', latMax) else: ## self.set_variable('lat.max', "as.null(lat.max)") self.run_code("lat.max <- NULL") latMin = self.getInputFromPort('lat.min') if latMin: self.set_variable('lat.min', latMin) else : self.run_code("lat.min <- NULL") lonMax = self.getInputFromPort('lon.max') if lonMax: self.set_variable('lon.max', lonMax) else: self.run_code("lon.max <- NULL") lonMin = self.getInputFromPort('lon.min') if lonMin: self.set_variable('lon.min', lonMin) else: self.run_code("lon.min <- NULL") self.run_code(''.join(["source(\"", self.getInputFromPort('project.directory'), '/code/stem.vt.erd.map.function.R', "\")"])) global_var_list = ['project.directory', 'species.directory.nametag', 'map.directory.nametag', 'map.file.nametag', 'map.rows', 'z.max', 'z.min', 'map.number', 'lat.max', 'lat.min', 'lon.max', 'lon.min'] self.global_vars = dict((name, self.get_variable(name)) for name in global_var_list if name is not None) class PlotERDMaps(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:InitERDMapAnalysis)'), ('project.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('species.directory.nametag', '(edu.utah.sci.vistrails.basic:String)'), ('map.directory.nametag', '(edu.utah.sci.vistrails.basic:Directory)'), ('map.file.nametag', '(edu.utah.sci.vistrails.basic:File)'), ('map.rows', '(edu.utah.sci.vistrails.basic:Integer)'), ('z.max', '(edu.utah.sci.vistrails.basic:Float)'), ('z.min', '(edu.utah.sci.vistrails.basic:Float)'), ('map.number', '(edu.utah.sci.vistrails.basic:Integer)'), ('lat.max', '(edu.utah.sci.vistrails.basic:Float)'), ('lat.min', '(edu.utah.sci.vistrails.basic:Float)'), ('lon.max', '(edu.utah.sci.vistrails.basic:Float)'), ('lon.min', '(edu.utah.sci.vistrails.basic:Float)')] _output_ports = [('map_file', '(edu.utah.sci.vistrails.basic:File)')] def compute(self): ## stem_globals = self.getInputFromPort('stem.globals') ## for k, v in stem_globals.global_vars.iteritems(): ## self.set_variable(k,v) activePorts = processActivePortData(PlotERDMaps._input_ports, self) remap = {'stem.globals': None} params = build_params(activePorts, remap) code_str = "mapFile <-stem.erd.maps(%s)" % params self.run_code(code_str) self.setResult('map_file', create_file_module(str(list(self.get_variable('mapFile'))[0]))) class ERDDataCreation(RSource): _input_ports = [('protocol.tag', '(edu.utah.sci.vistrails.basic:String)'), ('max.effort.hours', '(edu.utah.sci.vistrails.basic:Float)'), ('max.effort.distance.fm', '(edu.utah.sci.vistrails.basic:Float)'), ('min.obs.time', '(edu.utah.sci.vistrails.basic:Float)'), ('max.obs.time', '(edu.utah.sci.vistrails.basic:Float)'), ('response.type', '(edu.utah.sci.vistrails.basic:String)'), ('ebird.data.dir', '(edu.utah.sci.vistrails.basic:Directory)'), ('erd.data.tag', '(edu.utah.sci.vistrails.basic:String)'), ('spatial.erd.tag', '(edu.utah.sci.vistrails.basic:String)'), ('checklist.covariate.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('core.covariate.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('NLCD.class.neighborhood.size', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('NLCD.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('class.level.fragstats', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('landscape.fragstat.tags', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('landscape.neighborhood.size', '(edu.utah.sci.vistrails.rpy:RVector:Types)')] _output_ports = [('srd.pred.design.file', '(edu.utah.sci.vistrails.basic:File)'), ('erd.design.file', '(edu.utah.sci.vistrails.basic:File)')] def compute(self): self.chdir(get_path()) self.set_variable('ebird.data.dir', self.getInputFromPort('ebird.data.dir').name) self.run_file(get_path('STEM_Globals.R'), excluded_inputs=set(['source', 'ebird.data.dir'])) srd_fname = list(self.get_variable('srd.pred.design.filename'))[0] erd_fname = list(self.get_variable('erd.design.filename'))[0] self.setResult('srd.pred.design.file', create_file_module(srd_fname)) self.setResult('erd.design.file', create_file_module(erd_fname)) class ERDDataSubsetting(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('erd.data.filename', '(edu.utah.sci.vistrails.basic:File)'), ('srd.pred.design.filename', '(edu.utah.sci.vistrails.basic:File)'), ('spatial.extent.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('temporal.extent.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('species.name', '(edu.utah.sci.vistrails.basic:String)'), ('predictor.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('response.family', '(edu.utah.sci.vistrails.basic:String)'), ('srd.max.sample.size', '(edu.utah.sci.vistrails.basic:Integer)'), ('split.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)')] _output_ports = [('train.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('test.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('stem.predictor.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)')] # Get train.data, test.data, srd.data from eBird.data and expose # these three as the output ports def compute(self): ## stem_globals = self.getInputFromPort('stem.globals') ## for k, v in stem_globals.global_vars.iteritems(): ## self.set_variable(k,v) activePorts = processActivePortData(ERDDataSubsetting._input_ports, self) remap = {'srd.pred.design.file': 'srd.pred.design.filename', 'stem.globals': None} params = build_params(activePorts, remap) code_str = "eBird.data <- erd.srd.data.subsetting(%s)" % params self.run_code(code_str, excluded_inputs=set(['source', 'srd.pred.design.file']), excluded_outputs=set(['eBird.data'])) train = self.get_variable('eBird.data$train.data') test = self.get_variable('eBird.data$test.data') srd = self.get_variable('eBird.data$srd.data') self.run_code("stem.predictor.names <- names(eBird.data$train.data$X)") stem_predictor_names = self.get_variable('stem.predictor.names') self.setResult('train.data', train) self.setResult('test.data', test) self.setResult('pred.data', srd) self.setResult('stem.predictor.names', stem_predictor_names) class FitSTEM(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('train.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('response.family', '(edu.utah.sci.vistrails.basic:String)'), ('cv.folds', '(edu.utah.sci.vistrails.basic:Integer)'), ('cv.folds.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('stem.init.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('base.model.par.list', '(edu.utah.sci.vistrails.rpy:RList:Types)')] _output_ports = [('models.directory', '(edu.utah.sci.vistrails.basic:Directory)')] def compute(self): # use a single models dir with a variable number of # subdirectories depending on the cv.folds value # same for results, now -- models/stem.models.[1-10] ## stem_globals = self.getInputFromPort('stem.globals') ## for k, v in stem_globals.global_vars.iteritems(): ## self.set_variable(k,v) activePorts = processActivePortData(FitSTEM._input_ports, self) remap = {'stem.globals': None} params = build_params(activePorts, remap) code_str = "stem(%s)" % params self.run_code(code_str) class ERDPredictivePerformance(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('test.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('pp.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('n.mc', '(edu.utah.sci.vistrails.basic:Integer)'), ('grid.cell.min.lat', '(edu.utah.sci.vistrails.basic:Float)'), ('grid.cell.min.lon', '(edu.utah.sci.vistrails.basic:Float)'), ('min.val.cell.locs', '(edu.utah.sci.vistrails.basic:Integer)'), ('threshold', '(edu.utah.sci.vistrails.basic:Float)'), ('min.testset.sample.size', '(edu.utah.sci.vistrails.basic:Integer)'), ('plot.it', '(edu.utah.sci.vistrails.basic:Boolean)')] # pp.directory specifies where, but we can move this, i think _output_ports = [('pp.directory', '(edu.utah.sci.vistrails.basic:Directory)')] def compute(self): self.set_variable('stem.directory', self.getInputFromPort('stem.directory').name) pp_directory = self.getInputFromPort('pp.directory') self.set_variable('pp.directory', pp_directory.name) self.run_file('') self.setResult('pp.directory', pp_directory) class PredictSTEM(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('st.pred.tag', '(edu.utah.sci.vistrails.basic:String)'), ('st.prediction.filename', '(edu.utah.sci.vistrails.basic:File)')] _output_ports = [('st.pred', '(edu.utah.sci.vistrails.rpy:RList:Types)')] def compute(self): pas class ERDPredictSTMatrix(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('pred.data', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('stem.predictor.names', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('st.matrix.name', '(edu.utah.sci.vistrails.basic:String)'), ('jdate.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('year.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('conditioning.vars', '(edu.utah.sci.vistrails.rpy:RList:Types)')] _output_ports = [('st.matrix.directory', '(edu.utah.sci.vistrails.basic:Directory)')] def compute(self): stem_globals = self.getInputFromPort('stem.globals') ## for k, v in stem_globals.global_vars.iteritems(): ## self.set_variable(k,v) activePorts = processActivePortData(ERDPredictSTMatrix._input_ports, self) remap = {'stem.globals': None} params = build_params(activePorts, remap) code_str = "predict.erd.st.matrix(%s)" % params self.run_code(code_str) if self.hasInputFromPort('stem.directory'): if self.hasInputFromPort('st.matrix.name'): self.setResult('st.matrix.directory', create_dir_module(os.path.join(self.getInputFromPort('stem.directory').name, self.getInputFromPort('st.matrix.name')))) else: self.setResult('st.matrix.directory', create_dir_module(os.path.join(self.getInputFromPort('stem.directory').name, str(list(stem_globals.global_vars['st.matrix.name'])[0])))) else: if self.hasInputFromPort('st.matrix.name'): self.setResult('st.matrix.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]), self.getInputFromPort('st.matrix.name')))) else: self.setResult('st.matrix.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]), str(list(stem_globals.global_vars['st.matrix.name'])[0])))) class STMatrixCVAvg(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('st.matrix.input.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('jdate.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('year.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('st.matrix.output.directory', '(edu.utah.sci.vistrails.basic:Directory)')] _output_ports = [('st.matrix.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('map.directory', '(edu.utah.sci.vistrails.basic:Directory)')] def compute(self): self.set_variable('st.matrix.input.directory', self.getInputFromPort('st.matrix.input.directory').name) st_matrix_output_directory = self.getInputFromPort('st.matrix.input.directory') self.set_variable('st.matrix.output.directory', st_matrix_output_directory.name) stem_globals = self.getInputFromPort('stem.globals') ## for k, v in stem_globals.global_vars.iteritems(): ## self.set_variable(k,v) activePorts = processActivePortData(STMatrixCVAvg._input_ports, self) remap = {'stem.globals': None} params = build_params(activePorts, remap) code_str = "st.matrix.cv.average(%s)" % params self.run_code(code_str) self.setResult('st.matrix.directory', st_matrix_output_directory) self.setResult('map.directory', create_dir_module(os.path.join(str(list(stem_globals.global_vars['stem.directory'])[0]), str(list(stem_globals.global_vars['st.matrix.ave.maps'])[0])))) class STMatrixMaps(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('st.matrix.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('map.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('jdate.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('year.seq', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('begin.seq', '(edu.utah.sci.vistrails.basic:Integer)'), ('end.seq', '(edu.utah.sci.vistrails.basic:Integer)'), ('pred.grid.size', '(edu.utah.sci.vistrails.basic:Integer)'), ('map.plot.width', '(edu.utah.sci.vistrails.basic:Integer)'), ('spatial.extent.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('z.max', '(edu.utah.sci.vistrails.basic:Float)'), ('z.min', '(edu.utah.sci.vistrails.basic:Float)'), ('map.tag', '(edu.utah.sci.vistrails.basic:String)'), ('date.bar', '(edu.utah.sci.vistrails.basic:Boolean)'), ('print.date', '(edu.utah.sci.vistrails.basic:Boolean)'), ('county.map', '(edu.utah.sci.vistrails.basic:Boolean)'), ('county.map.lwd', '(edu.utah.sci.vistrails.basic:Float)'), ('state.map', '(edu.utah.sci.vistrails.basic:Boolean)'), ('state.map.lwd', '(edu.utah.sci.vistrails.basic:Float)')] _output_ports = [('map.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('map_file_1', '(edu.utah.sci.vistrails.basic:File)')] def compute(self): self.set_variable('st.matrix.directory', ''.join([self.getInputFromPort('st.matrix.directory').name])) map_directory = self.getInputFromPort('map.directory') self.set_variable('map.directory', map_directory.name) ## stem_globals = self.getInputFromPort('stem.globals') ## for k, v in stem_globals.global_vars.iteritems(): ## self.set_variable(k,v) activePorts = processActivePortData(STMatrixMaps._input_ports, self) remap = {'stem.globals': None} params = build_params(activePorts, remap) code_str = "st.matrix.maps(%s)" % params self.run_code(code_str) self.setResult('map.directory', map_directory) class ERD_CV_Avg_Maps(RSource): _input_ports = [('stem.globals', '(edu.cornell.birds.stem:STEMGlobals)'), ('stem.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('st.matrix.file.tag', '(edu.utah.sci.vistrails.basic:String)'), ('cv.list', '(edu.utah.sci.vistrails.rpy:RVector:Types)'), ('maps.directory', '(edu.utah.sci.vistrails.basic:Directory)'), ('map.file.tag', '(edu.utah.sci.vistrails.basic:String)'), ('ns.rows', '(edu.utah.sci.vistrails.basic:Integer)'), ('map.plot.pixel.width', '(edu.utah.sci.vistrails.basic:Integer)'), ('mapping.spatial.extent', '(edu.utah.sci.vistrails.rpy:RList:Types)'), ('z.max', '(edu.utah.sci.vistrails.basic:Float)')] _output_ports = [('erd.cv.avg.maps.directory', '(edu.utah.sci.vistrails.basic:Directory)')] def compute(self): pass # _modules = [STEMConfiguration, # RunModels, # BuildVisualizations, # STEMFigure] _modules = [ERDDataCreation, ERDDataSubsetting, FitSTEM, ERDPredictivePerformance, PredictSTEM, ERDPredictSTMatrix, STMatrixCVAvg, STMatrixMaps, # ERD_CV_Avg_Maps, STEMGlobals, InitERDMapAnalysis, PlotERDMaps ]