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Output

Utilities for handling spatial and structured simulation output.

SpatialOutput

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from idmtools_calibra.output.spatial_output import SpatialOutput

Helper class for reading and processing spatially-structured output files produced by simulations (e.g. spatial binary files from EMOD such as SpatialReport_*.bin).

Class methods

from_file(filename) (classmethod)

Load a spatial binary output file.

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spatial = SpatialOutput.from_file('output/SpatialReport_Prevalence.bin')
Parameter Type Description
filename str Path to the spatial binary output file

Returns a SpatialOutput instance.

Instance methods

to_dataframe()

Convert the spatial output to a pandas.DataFrame indexed by node and time.

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df = spatial.to_dataframe()
# Returns DataFrame with columns: node_id, time, value

Usage example

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from idmtools_calibra.output.spatial_output import SpatialOutput

# Load EMOD spatial prevalence report
spatial = SpatialOutput.from_file('output/SpatialReport_Prevalence.bin')

# Convert to DataFrame for analysis
df = spatial.to_dataframe()
print(df.head())
# node_id  time  value
#       0     0  0.002
#       0     1  0.004
#       ...

# Use in an analyzer
class SpatialAnalyzer(BaseCalibrationAnalyzer):
    def map(self, data, item):
        spatial = SpatialOutput.from_file(data['output/SpatialReport_Prevalence.bin'])
        return spatial.to_dataframe()