Added in extra modules from Craig

cwsl/init.py

@@ -54,6 +54,10 @@
 from cwsl.vt_modules.mv_output import MoveOutput
 from cwsl.vt_modules.dataset_summary import DatasetSummary
 from cwsl.vt_modules.open_dataset import OpenDataSet
+from cwsl.vt_modules.vt_plot_gridded_seas import PlotGriddedSeas
+from cwsl.vt_modules.vt_cdo_histogram import Histogram
+from cwsl.vt_modules.vt_cdo_calc_pdf import PDF
+from cwsl.vt_modules.vt_cdo_clim_statistics import ClimStatistics
 
 
 def initialize(*args, **keywords):
@@ -107,12 +111,19 @@ def initialize(*args, **keywords):
                    namespace='Statistics')
     reg.add_module(TemporalCorrelation, name='Temporal Correlation',
                    namespace='Statistics')
+    reg.add_module(ClimStatistics, name='Clim Statistics',
+                   namespace='Statistics')
+    reg.add_module(Histogram, name='Histogram',
+                   namespace='Statistics')
+    reg.add_module(PDF, name='PDF',
+                   namespace='Statistics')
 
     #Indices
     reg.add_module(IndicesNino34, name='Nino3.4', namespace='Indices')
 
     #Visualisation
     reg.add_module(PlotTimeSeries, name='Plot Timeseries', namespace='Visualisation')
+    reg.add_module(PlotGriddedSeas, name='Plot Gridded', namespace='Visualisation')
     #ImageViewerPanel depends on the Spreadsheet package
     reg.add_module(ImageViewerPanel, name='Image Viewer', namespace='Visualisation')
     reg.add_input_port(ImageViewerPanel, 'in_dataset', 'csiro.au.cwsl:VtDataSet')

cwsl/vt_modules/vt_cdo_calc_pdf.py

@@ -0,0 +1,97 @@
+"""
+Authors:  Craig Heady ([email protected])
+
+Copyright 2015 CSIRO
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+This module wraps a shell script that performs time aggregation: 
+cwsl-ctools/aggregation/cdo_calc_pdf.sh
+
+Part of the CWSLab Model Analysis Service VisTrails plugin.
+
+"""
+
+from vistrails.core.modules import vistrails_module, basic_modules
+
+from cwsl.configuration import configuration
+from cwsl.core.constraint import Constraint
+from cwsl.core.process_unit import ProcessUnit
+from cwsl.core.pattern_generator import PatternGenerator
+
+
+class PDF(vistrails_module.Module):
+    """Calc PDF.
+
+    Wraps the cwsl-ctools/statistics/cdo_calc_pdf.sh script.
+
+    Inputs:
+      in_dataset: Can consist of netCDF files
+      
+      bin_list: Comma seperated list of bin values.
+        eg temperature   -inf,-40,-30,-20,-10,0,10,20,30,40,inf"
+        eg precipitation 0,20,40,60,80,100,150,200,300,400,inf"
+    
+    Outputs:
+      out_dataset: Consists of netCDF files
+    
+    """
+
+    _input_ports = [('in_dataset', 'csiro.au.cwsl:VtDataSet', 
+                     {'labels': str(['Input dataset'])}),
+                    ('bin_list', basic_modules.String, 
+                     {'labels': str(['Bins'])}),
+                   ]
+
+    _output_ports = [('out_dataset', 'csiro.au.cwsl:VtDataSet')]
+
+    _execution_options = {'required_modules': ['cdo', 'python/2.7.5', 'python-cdat-lite/6.0rc2-py2.7.5']}
+
+    command = '${CWSL_CTOOLS}/statistics/cdo_calc_pdf.sh'
+
+    def __init__(self):
+
+        super(PDF, self).__init__()
+        self.out_pattern = PatternGenerator('user', 'default').pattern
+
+    def compute(self):
+
+        in_dataset = self.getInputFromPort('in_dataset')
+
+        bin_list = self.getInputFromPort('bin_list')
+
+
+        self.positional_args = [('%s' %bin_list, 0, 'raw'), ]
+        self.keyword_args = {}
+
+        agg_constraint = 'pdf'
+
+        new_constraints_for_output = set([Constraint('timeagg_info', [agg_constraint]),
+                                          Constraint('suffix', ['nc']),
+                                          ])
+
+        this_process = ProcessUnit([in_dataset],
+                                   self.out_pattern,
+                                   self.command,
+                                   new_constraints_for_output,
+                                   execution_options=self._execution_options,
+                                   positional_args=self.positional_args,
+                                   cons_keywords=self.keyword_args)
+
+        try:
+            this_process.execute(simulate=configuration.simulate_execution)
+        except Exception as e:
+            raise vistrails_module.ModuleError(self, repr(e))
+
+        process_output = this_process.file_creator
+
+        self.setResult('out_dataset', process_output)
+

cwsl/vt_modules/vt_cdo_clim_statistics.py

@@ -0,0 +1,114 @@
+"""
+Authors:  Craig Heady ([email protected])
+
+Copyright 2015 CSIRO
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+This module wraps a shell script that performs time aggregation: 
+cwsl-ctools/statistics/cdo_clim_statistics.sh
+
+Part of the CWSLab Model Analysis Service VisTrails plugin.
+
+"""
+
+from vistrails.core.modules import vistrails_module, basic_modules
+
+from cwsl.configuration import configuration
+from cwsl.core.constraint import Constraint
+from cwsl.core.process_unit import ProcessUnit
+from cwsl.core.pattern_generator import PatternGenerator
+
+
+class ClimStatistics(vistrails_module.Module):
+    """ClimStatistics.
+
+    Wraps the cwsl-ctools/statistics/cdo_clim_statistics.sh script.
+
+    Inputs:
+      in_dataset: Can consist of netCDF files
+      
+      method: Statistical anlaysis method.min, max, sum, mean,avg,var,std.
+        - min  (min: monthly, seasonal and annual Minimum)
+        - max  (sum: monthly, seasonal and annual Maximum)
+        - sum  (sum: monthly, seasonal and annual Sum)
+        - mean (mean:monthly, seasonal and annual Mean)
+        - avg  (avg: monthly, seasonal and annual Average)
+        - var  (var: monthly, seasonal and annual Variance)
+        - std  (std: monthly, seasonal and annual Standard Deviation)
+    
+    Outputs:
+      out_dataset_mon: Consists of netCDF files
+      out_dataset_seas:Consists of netCDF files
+      out_dataset_ann: Consists of netCDF files   
+    """
+
+    _input_ports = [('in_dataset', 'csiro.au.cwsl:VtDataSet', 
+                     {'labels': str(['Input dataset'])}),
+                    ('method', basic_modules.String, 
+                     {'labels': str(['Statistic'])}),
+                   ]
+
+    _output_ports = [('out_dataset_mon', 'csiro.au.cwsl:VtDataSet'),
+                     ('out_dataset_seas', 'csiro.au.cwsl:VtDataSet'),
+                     ('out_dataset_ann', 'csiro.au.cwsl:VtDataSet'),]
+
+    _execution_options = {'required_modules': ['cdo/1.6.4', 'python/2.7.5', 'python-cdat-lite/6.0rc2-py2.7.5']}
+
+    command = '${CWSL_CTOOLS}/aggregation/cdo_time_agg.sh'
+
+
+
+    #output_data = {'mon':'','seas':'','ann':''}
+
+    def __init__(self):
+
+        super(ClimStatistics, self).__init__()
+        self.out_pattern = PatternGenerator('user', 'default').pattern
+
+    def compute(self):
+
+        in_dataset = self.getInputFromPort('in_dataset')
+        method = self.getInputFromPort('method')
+
+        seas_list = {'mon':'ymon','seas':'yseas','ann':'tim'}
+
+        ### loop over seas_list to generate all 3 season files ###
+        for seas in seas_list.keys():
+            self.positional_args = [('%s%s' %(seas_list[seas],method), 0, 'raw'), ]
+            self.keyword_args = {}
+
+            if len(method.split(',')) > 1:
+                agg_constraint = "".join(method.split(','))
+            else:
+                agg_constraint = method
+
+            new_constraints_for_output = set([Constraint('timeagg_info', ['%s%s'%(seas_list[seas],method)],),
+                                          Constraint('suffix', ['nc']),
+                                          ])
+
+            this_process = ProcessUnit([in_dataset],
+                                       self.out_pattern,
+                                       self.command,
+                                       new_constraints_for_output,
+                                       execution_options=self._execution_options,
+                                       positional_args=self.positional_args,
+                                       cons_keywords=self.keyword_args)
+
+            try:
+                this_process.execute(simulate=configuration.simulate_execution)
+            except Exception as e:
+                raise vistrails_module.ModuleError(self, repr(e))
+
+            process_output = this_process.file_creator
+
+            self.setResult('out_dataset_%s' %seas, process_output)
+

cwsl/vt_modules/vt_cdo_histogram.py

@@ -0,0 +1,109 @@
+"""
+Authors:  Craig Heady ([email protected])
+
+Copyright 2015 CSIRO
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+This module wraps a shell script that performs time aggregation: 
+cwsl-ctools/aggregation/cdo_histogram.sh
+
+Part of the CWSLab Model Analysis Service VisTrails plugin.
+
+"""
+
+from vistrails.core.modules import vistrails_module, basic_modules
+
+from cwsl.configuration import configuration
+from cwsl.core.constraint import Constraint
+from cwsl.core.process_unit import ProcessUnit
+from cwsl.core.pattern_generator import PatternGenerator
+
+
+class Histogram(vistrails_module.Module):
+    """Histogram.
+
+    Wraps the cwsl-ctools/statistics/cdo_histogram.sh script.
+
+    Inputs:
+      in_dataset: Can consist of netCDF files
+      
+      method: Histogram method.
+        - histcount (Histogram count: Number of elements in the bin range)
+        - histsum   (Histogram sum: Sum of elements in the bin range)
+        - histmean  (Histogram mean: Mean of elements in the bin range)
+        - histfreq  (Histogram frequency: Relative frequency of elements in the bin range)
+      
+      bin_list: Comma seperated list of bin values.
+        eg temperature   -inf,-40,-30,-20,-10,0,10,20,30,40,inf"
+        eg precipitation 0,20,40,60,80,100,150,200,300,400,inf"
+    
+    Outputs:
+      out_dataset: Consists of netCDF files
+    
+    """
+
+    _input_ports = [('in_dataset', 'csiro.au.cwsl:VtDataSet', 
+                     {'labels': str(['Input dataset'])}),
+                    ('method', basic_modules.String, 
+                     {'labels': str(['Hist Method'])}),
+                    ('bin_list', basic_modules.String, 
+                     {'labels': str(['Hist Bins'])}),
+                   ]
+
+    _output_ports = [('out_dataset', 'csiro.au.cwsl:VtDataSet')]
+
+    _execution_options = {'required_modules': ['cdo', 'python/2.7.5', 'python-cdat-lite/6.0rc2-py2.7.5']}
+
+    command = '${CWSL_CTOOLS}/statistics/cdo_histogram.sh'
+
+    def __init__(self):
+
+        super(Histogram, self).__init__()
+        self.out_pattern = PatternGenerator('user', 'default').pattern
+
+    def compute(self):
+
+        in_dataset = self.getInputFromPort('in_dataset')
+        method = self.getInputFromPort('method')
+        bin_list = self.getInputFromPort('bin_list')
+
+
+        self.positional_args = [('%s,%s' %(method,bin_list), 0, 'raw'), ]
+        self.keyword_args = {}
+
+        if len(method.split(',')) > 1:
+            agg_constraint = "".join(method.split(','))
+        else:
+            agg_constraint = method
+
+
+        new_constraints_for_output = set([Constraint('timeagg_info', [agg_constraint]),
+                                          Constraint('suffix', ['nc']),
+                                          ])
+
+        this_process = ProcessUnit([in_dataset],
+                                   self.out_pattern,
+                                   self.command,
+                                   new_constraints_for_output,
+                                   execution_options=self._execution_options,
+                                   positional_args=self.positional_args,
+                                   cons_keywords=self.keyword_args)
+
+        try:
+            this_process.execute(simulate=configuration.simulate_execution)
+        except Exception as e:
+            raise vistrails_module.ModuleError(self, repr(e))
+
+        process_output = this_process.file_creator
+
+        self.setResult('out_dataset', process_output)
+